One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/11/26/peak-motifs.2025-11-26.204716_2025-11-26.204716_g9CRAo/results/discovered_motifs/peak-motifs_motifs_discovered.tf -format2 tf -file2 $RSAT/public_html/motif_databases/FlyFactorSurvey/PWM_FlyFactorSurvey_2016.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2025/11/26/peak-motifs.2025-11-26.204716_2025-11-26.204716_g9CRAo/results/discovered_vs_db/peak-motifs_motifs_vs_db_FlyFactorSurvey.tab

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m7_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m7_shift0 (oligos_6nt_mkv4_m7)
; oligos_6nt_mkv4_m7; m=0 (reference); ncol1=10; shift=0; ncol=10; mmACTGCAcm ; Alignment reference a 280 224 857 0 0 11 0 847 189 254 c 248 345 0 857 0 7 838 3 344 244 g 195 114 0 0 0 838 12 0 175 170 t 134 174 0 0 857 1 7 7 149 189

lola-PW_SOLEXA_FBgn0005630_rc_shift0 (lola-PW_SOLEXA_FBgn0005630_rc)
; oligos_6nt_mkv4_m7 versus lola-PW_SOLEXA_FBgn0005630_rc; m=1/2; ncol2=10; w=0; offset=0; strand=R; shift=0; score=0.803184; yskCTGCAmr ; cor=; Ncor= a 76 44 22 0 0 0 0 389 204 224 c 137 102 59 392 0 0 364 0 125 31 g 75 154 103 0 0 392 0 2 18 116 t 103 90 204 0 392 0 27 0 43 19

lola-PW_SANGER_5_FBgn0005630_shift1 (lola-PW_SANGER_5_FBgn0005630)
; oligos_6nt_mkv4_m7 versus lola-PW_SANGER_5_FBgn0005630; m=2/2; ncol2=7; w=0; offset=1; strand=D; shift=1; score=0.508896; -STCTGCA-- ; cor=; Ncor= a 0 0 0 0 0 0 0 11 0 0 c 0 3 0 10 0 0 11 0 0 0 g 0 9 2 0 0 12 0 0 0 0 t 0 0 10 2 12 0 1 1 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m2_shift3 ; 19 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m2_shift3 (oligos_7nt_mkv5_m2)
; oligos_7nt_mkv5_m2; m=0 (reference); ncol1=11; shift=3; ncol=14; ---hhCCACACCmm ; Alignment reference a 0 0 0 610 665 56 47 1899 120 1884 31 37 665 597 c 0 0 0 779 651 2175 2075 185 2039 272 2139 2175 670 740 g 0 0 0 352 414 33 72 129 81 56 70 39 560 463 t 0 0 0 597 608 74 144 125 98 126 98 87 443 538

CG9895_SOLEXA_5_FBgn0034810_rc_shift3 (CG9895_SOLEXA_5_FBgn0034810_rc)
; oligos_7nt_mkv5_m2 versus CG9895_SOLEXA_5_FBgn0034810_rc; m=1/18; ncol2=11; w=0; offset=0; strand=R; shift=3; score=0.793245; ---rrCCACrCCCa ; cor=; Ncor= a 0 0 0 274 376 101 86 760 27 327 31 31 24 494 c 0 0 0 126 29 781 818 212 961 0 959 957 921 200 g 0 0 0 425 503 45 18 15 0 644 0 0 0 52 t 0 0 0 109 73 63 68 3 2 19 0 2 44 239

CG12029_SANGER_10_FBgn0035454_rc_shift4 (CG12029_SANGER_10_FBgn0035454_rc)
; oligos_7nt_mkv5_m2 versus CG12029_SANGER_10_FBgn0035454_rc; m=2/18; ncol2=11; w=0; offset=1; strand=R; shift=4; score=0.707066; ----RCCACACCCa ; cor=; Ncor= a 0 0 0 0 5 4 0 16 0 17 0 0 0 13 c 0 0 0 0 0 14 20 2 20 0 20 20 20 3 g 0 0 0 0 15 2 0 2 0 2 0 0 0 0 t 0 0 0 0 0 0 0 0 0 1 0 0 0 4

CG12029_SOLEXA_5_FBgn0035454_rc_shift1 (CG12029_SOLEXA_5_FBgn0035454_rc)
; oligos_7nt_mkv5_m2 versus CG12029_SOLEXA_5_FBgn0035454_rc; m=3/18; ncol2=15; w=-2; offset=-2; strand=R; shift=1; score=0.635932; -mvrRCCACACCCa ; cor=; Ncor= a 0 311 274 360 291 135 12 912 9 742 4 33 34 595 c 0 334 331 174 0 911 1052 109 1058 0 1062 1031 980 203 g 0 170 278 328 767 21 0 44 0 237 0 3 2 19 t 0 175 164 214 18 9 12 11 9 97 10 9 60 259

CG9895_SANGER_10_FBgn0034810_rc_shift4 (CG9895_SANGER_10_FBgn0034810_rc)
; oligos_7nt_mkv5_m2 versus CG9895_SANGER_10_FBgn0034810_rc; m=4/18; ncol2=12; w=0; offset=1; strand=R; shift=4; score=0.627766; ----rCCACrCCCw ; cor=; Ncor= a 0 0 0 0 11 3 2 20 1 10 1 0 0 14 c 0 0 0 0 0 20 21 4 23 0 22 22 22 2 g 0 0 0 0 13 1 0 0 0 14 0 2 0 2 t 0 0 0 0 0 0 1 0 0 0 1 0 2 6

CG3065_F1-3_SANGER_2.5_FBgn0034946_rc_shift4 (CG3065_F1-3_SANGER_2.5_FBgn0034946_rc)
; oligos_7nt_mkv5_m2 versus CG3065_F1-3_SANGER_2.5_FBgn0034946_rc; m=5/18; ncol2=11; w=0; offset=1; strand=R; shift=4; score=0.608842; ----rCCACGCCCm ; cor=; Ncor= a 0 0 0 0 7 2 0 20 0 0 0 0 0 12 c 0 0 0 0 0 18 21 1 21 0 21 21 20 6 g 0 0 0 0 13 1 0 0 0 21 0 0 0 1 t 0 0 0 0 0 0 0 0 0 0 0 0 1 2

CG3065_F1-5_SOLEXA_2.5_FBgn0034946_rc_shift2 (CG3065_F1-5_SOLEXA_2.5_FBgn0034946_rc)
; oligos_7nt_mkv5_m2 versus CG3065_F1-5_SOLEXA_2.5_FBgn0034946_rc; m=6/18; ncol2=14; w=-1; offset=-1; strand=R; shift=2; score=0.582618; --crrCCACGCCCm ; cor=; Ncor= a 0 0 308 363 440 154 25 1086 19 54 53 32 24 593 c 0 0 435 296 39 1022 1265 199 1290 9 1263 1276 1125 610 g 0 0 291 384 766 62 0 27 0 1205 0 0 1 20 t 0 0 218 276 74 81 29 7 10 51 3 11 169 96

luna_SOLEXA_5_FBgn0040765_rc_shift3 (luna_SOLEXA_5_FBgn0040765_rc)
; oligos_7nt_mkv5_m2 versus luna_SOLEXA_5_FBgn0040765_rc; m=7/18; ncol2=14; w=0; offset=0; strand=R; shift=3; score=0.579885; ---grCCACGCCCw ; cor=; Ncor= a 0 0 0 132 155 85 73 434 5 126 18 29 18 276 c 0 0 0 68 26 463 462 149 607 1 588 579 558 120 g 0 0 0 283 396 27 18 24 0 468 5 0 0 36 t 0 0 0 84 35 37 59 5 0 17 1 4 36 180

CG3065_F1-3_SOLEXA_2.5_FBgn0034946_rc_shift2 (CG3065_F1-3_SOLEXA_2.5_FBgn0034946_rc)
; oligos_7nt_mkv5_m2 versus CG3065_F1-3_SOLEXA_2.5_FBgn0034946_rc; m=8/18; ncol2=15; w=-1; offset=-1; strand=R; shift=2; score=0.531519; --carCCACGCCCm ; cor=; Ncor= a 0 0 47 105 85 40 1 234 11 4 9 10 13 171 c 0 0 110 52 7 211 260 29 249 0 253 253 217 77 g 0 0 53 59 166 8 0 0 0 255 0 0 0 1 t 0 0 47 44 5 4 2 0 3 4 1 0 33 14

klu_SOLEXA_5_FBgn0013469_rc_shift3 (klu_SOLEXA_5_FBgn0013469_rc)
; oligos_7nt_mkv5_m2 versus klu_SOLEXA_5_FBgn0013469_rc; m=9/18; ncol2=15; w=0; offset=0; strand=R; shift=3; score=0.523494; ---mmmmmCACCCm ; cor=; Ncor= a 0 0 0 132 156 135 134 155 9 378 3 3 5 315 c 0 0 0 152 168 188 204 298 491 6 491 485 472 168 g 0 0 0 82 90 85 64 24 0 48 0 5 0 6 t 0 0 0 91 79 95 101 26 3 71 9 10 26 14

Opa_SANGER_5_FBgn0003002_shift0 (Opa_SANGER_5_FBgn0003002)
; oligos_7nt_mkv5_m2 versus Opa_SANGER_5_FBgn0003002; m=10/18; ncol2=13; w=-3; offset=-3; strand=D; shift=0; score=0.501186; mkmmMCCCCmCyR- ; cor=; Ncor= a 7 2 4 4 3 1 0 0 0 8 0 0 3 0 c 3 0 5 7 9 9 12 11 12 3 11 8 0 0 g 1 5 2 1 0 2 0 1 0 1 1 0 9 0 t 1 5 1 0 0 0 0 0 0 0 0 4 0 0

lola-PL_SANGER_2.5_FBgn0005630_rc_shift1 (lola-PL_SANGER_2.5_FBgn0005630_rc)
; oligos_7nt_mkv5_m2 versus lola-PL_SANGER_2.5_FBgn0005630_rc; m=11/18; ncol2=9; w=-2; offset=-2; strand=R; shift=1; score=0.48165; -TGmcCCACm---- ; cor=; Ncor= a 0 2 0 4 2 0 0 11 0 4 0 0 0 0 c 0 0 0 7 5 11 11 0 11 6 0 0 0 0 g 0 0 9 0 2 0 0 0 0 0 0 0 0 0 t 0 8 2 0 2 0 0 0 0 1 0 0 0 0

CG31782-F9-11_SOLEXA_FBgn0051782_rc_shift6 (CG31782-F9-11_SOLEXA_FBgn0051782_rc)
; oligos_7nt_mkv5_m2 versus CG31782-F9-11_SOLEXA_FBgn0051782_rc; m=12/18; ncol2=11; w=0; offset=3; strand=R; shift=6; score=0.464156; ------ctCACCac ; cor=; Ncor= a 0 0 0 0 0 0 269 617 42 2023 0 0 1676 407 c 0 0 0 0 0 0 1324 287 1979 143 2554 2552 582 1464 g 0 0 0 0 0 0 584 195 25 0 0 0 27 305 t 0 0 0 0 0 0 375 1453 506 386 0 1 269 377

ac_da_SANGER_5_FBgn0000022_shift7 (ac_da_SANGER_5_FBgn0000022)
; oligos_7nt_mkv5_m2 versus ac_da_SANGER_5_FBgn0000022; m=13/18; ncol2=8; w=0; offset=4; strand=D; shift=7; score=0.436854; -------rCACCTG ; cor=; Ncor= a 0 0 0 0 0 0 0 10 0 19 0 0 0 0 c 0 0 0 0 0 0 0 1 19 0 18 19 0 0 g 0 0 0 0 0 0 0 7 0 0 1 0 0 19 t 0 0 0 0 0 0 0 1 0 0 0 0 19 0

ac_da_SANGER_5_FBgn0000413_shift7 (ac_da_SANGER_5_FBgn0000413)
; oligos_7nt_mkv5_m2 versus ac_da_SANGER_5_FBgn0000413; m=14/18; ncol2=8; w=0; offset=4; strand=D; shift=7; score=0.436854; -------rCACCTG ; cor=; Ncor= a 0 0 0 0 0 0 0 10 0 19 0 0 0 0 c 0 0 0 0 0 0 0 1 19 0 18 19 0 0 g 0 0 0 0 0 0 0 7 0 0 1 0 0 19 t 0 0 0 0 0 0 0 1 0 0 0 0 19 0

sc_da_SANGER_10_FBgn0004170_shift7 (sc_da_SANGER_10_FBgn0004170)
; oligos_7nt_mkv5_m2 versus sc_da_SANGER_10_FBgn0004170; m=15/18; ncol2=8; w=0; offset=4; strand=D; shift=7; score=0.428959; -------rCACCTG ; cor=; Ncor= a 0 0 0 0 0 0 0 11 0 24 0 0 0 0 c 0 0 0 0 0 0 0 5 23 0 21 24 0 0 g 0 0 0 0 0 0 0 7 0 0 1 0 0 24 t 0 0 0 0 0 0 0 0 0 0 2 0 24 0

sc_da_SANGER_10_FBgn0000413_shift7 (sc_da_SANGER_10_FBgn0000413)
; oligos_7nt_mkv5_m2 versus sc_da_SANGER_10_FBgn0000413; m=16/18; ncol2=8; w=0; offset=4; strand=D; shift=7; score=0.428959; -------rCACCTG ; cor=; Ncor= a 0 0 0 0 0 0 0 11 0 24 0 0 0 0 c 0 0 0 0 0 0 0 5 23 0 21 24 0 0 g 0 0 0 0 0 0 0 7 0 0 1 0 0 24 t 0 0 0 0 0 0 0 0 0 0 2 0 24 0

HLH54F_da_SANGER_5_FBgn0022740_shift6 (HLH54F_da_SANGER_5_FBgn0022740)
; oligos_7nt_mkv5_m2 versus HLH54F_da_SANGER_5_FBgn0022740; m=17/18; ncol2=11; w=0; offset=3; strand=D; shift=6; score=0.409233; ------mmCACCTG ; cor=; Ncor= a 0 0 0 0 0 0 12 12 0 24 0 0 0 0 c 0 0 0 0 0 0 10 10 23 0 24 23 1 0 g 0 0 0 0 0 0 1 2 0 0 0 0 2 24 t 0 0 0 0 0 0 1 0 1 0 0 1 21 0

HLH54F_da_SANGER_5_FBgn0000413_shift6 (HLH54F_da_SANGER_5_FBgn0000413)
; oligos_7nt_mkv5_m2 versus HLH54F_da_SANGER_5_FBgn0000413; m=18/18; ncol2=11; w=0; offset=3; strand=D; shift=6; score=0.409233; ------mmCACCTG ; cor=; Ncor= a 0 0 0 0 0 0 12 12 0 24 0 0 0 0 c 0 0 0 0 0 0 10 10 23 0 24 23 1 0 g 0 0 0 0 0 0 1 2 0 0 0 0 2 24 t 0 0 0 0 0 0 1 0 1 0 0 1 21 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m4_shift4 ; 32 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m4_shift4 (oligos_6nt_mkv4_m4)
; oligos_6nt_mkv4_m4; m=0 (reference); ncol1=11; shift=4; ncol=15; ----ammAACACCmc ; Alignment reference a 0 0 0 0 603 434 886 1461 1470 34 1378 0 0 542 381 c 0 0 0 0 379 473 435 6 49 1453 126 1550 1575 416 540 g 0 0 0 0 284 341 132 31 32 32 22 11 3 328 294 t 0 0 0 0 322 340 135 90 37 69 62 27 10 302 373

lola-PQ_SANGER_5_FBgn0005630_shift4 (lola-PQ_SANGER_5_FBgn0005630)
; oligos_6nt_mkv4_m4 versus lola-PQ_SANGER_5_FBgn0005630; m=1/31; ncol2=9; w=0; offset=0; strand=D; shift=4; score=0.70071; ----AvrAWCAmC-- ; cor=; Ncor= a 0 0 0 0 8 3 6 10 8 0 11 6 0 0 0 c 0 0 0 0 2 3 1 0 0 11 0 5 9 0 0 g 0 0 0 0 0 4 4 0 0 0 0 0 0 0 0 t 0 0 0 0 1 1 0 1 3 0 0 0 2 0 0

lola-PQ_SOLEXA_FBgn0005630_rc_shift2 (lola-PQ_SOLEXA_FBgn0005630_rc)
; oligos_6nt_mkv4_m4 versus lola-PQ_SOLEXA_FBgn0005630_rc; m=2/31; ncol2=15; w=-2; offset=-2; strand=R; shift=2; score=0.597186; --mmamrAWCAmCsc ; cor=; Ncor= a 0 0 158 198 244 157 162 446 376 0 501 322 0 111 110 c 0 0 154 160 111 222 44 0 0 504 2 180 441 158 268 g 0 0 97 86 115 81 275 38 0 0 0 0 8 181 69 t 0 0 93 57 32 41 23 18 126 0 0 0 54 52 55

Side_SANGER_5_FBgn0032741_shift5 (Side_SANGER_5_FBgn0032741)
; oligos_6nt_mkv4_m4 versus Side_SANGER_5_FBgn0032741; m=3/31; ncol2=11; w=0; offset=1; strand=D; shift=5; score=0.593552; -----rAAMCAsCTG ; cor=; Ncor= a 0 0 0 0 0 12 17 21 16 0 23 0 5 1 0 c 0 0 0 0 0 0 3 2 6 23 0 10 18 1 0 g 0 0 0 0 0 6 3 0 1 0 0 9 0 0 23 t 0 0 0 0 0 5 0 0 0 0 0 4 0 21 0

sage_da_SANGER_5_FBgn0000413_shift5 (sage_da_SANGER_5_FBgn0000413)
; oligos_6nt_mkv4_m4 versus sage_da_SANGER_5_FBgn0000413; m=4/31; ncol2=11; w=0; offset=1; strand=D; shift=5; score=0.593552; -----rAAMCAsCTG ; cor=; Ncor= a 0 0 0 0 0 12 17 21 16 0 23 0 5 1 0 c 0 0 0 0 0 0 3 2 6 23 0 10 18 1 0 g 0 0 0 0 0 6 3 0 1 0 0 9 0 0 23 t 0 0 0 0 0 5 0 0 0 0 0 4 0 21 0

sage_da_SANGER_5_FBgn0037672_shift5 (sage_da_SANGER_5_FBgn0037672)
; oligos_6nt_mkv4_m4 versus sage_da_SANGER_5_FBgn0037672; m=5/31; ncol2=11; w=0; offset=1; strand=D; shift=5; score=0.593552; -----rAAMCAsCTG ; cor=; Ncor= a 0 0 0 0 0 12 17 21 16 0 23 0 5 1 0 c 0 0 0 0 0 0 3 2 6 23 0 10 18 1 0 g 0 0 0 0 0 6 3 0 1 0 0 9 0 0 23 t 0 0 0 0 0 5 0 0 0 0 0 4 0 21 0

lola-PF_SANGER_5_FBgn0005630_shift6 (lola-PF_SANGER_5_FBgn0005630)
; oligos_6nt_mkv4_m4 versus lola-PF_SANGER_5_FBgn0005630; m=6/31; ncol2=10; w=0; offset=2; strand=D; shift=6; score=0.572099; ------mAACTCCay ; cor=; Ncor= a 0 0 0 0 0 0 5 11 12 0 0 0 0 8 0 c 0 0 0 0 0 0 5 0 0 12 0 11 12 1 6 g 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 t 0 0 0 0 0 0 2 1 0 0 12 1 0 2 6

CG5953_SANGER_5_FBgn0032587_shift4 (CG5953_SANGER_5_FBgn0032587)
; oligos_6nt_mkv4_m4 versus CG5953_SANGER_5_FBgn0032587; m=7/31; ncol2=8; w=0; offset=0; strand=D; shift=4; score=0.570579; ----aCAAACAy--- ; cor=; Ncor= a 0 0 0 0 10 0 16 16 16 0 16 1 0 0 0 c 0 0 0 0 3 16 0 0 0 16 0 5 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 3 0 0 0 0 0 0 10 0 0 0

lola-PF_SOLEXA_FBgn0005630_rc_shift4 (lola-PF_SOLEXA_FBgn0005630_rc)
; oligos_6nt_mkv4_m4 versus lola-PF_SOLEXA_FBgn0005630_rc; m=8/31; ncol2=15; w=0; offset=0; strand=R; shift=4; score=0.560189; ----cmmAACTCCAy ; cor=; Ncor= a 0 0 0 0 651 875 871 2434 2609 14 1 11 26 1831 393 c 0 0 0 0 962 1008 1111 10 4 2605 10 2506 2581 110 1367 g 0 0 0 0 367 547 123 151 5 0 2 0 1 476 145 t 0 0 0 0 638 189 513 23 0 0 2603 101 10 201 713

bin_SANGER_5_FBgn0045759_shift4 (bin_SANGER_5_FBgn0045759)
; oligos_6nt_mkv4_m4 versus bin_SANGER_5_FBgn0045759; m=9/31; ncol2=7; w=0; offset=0; strand=D; shift=4; score=0.540854; ----rTAAACA---- ; cor=; Ncor= a 0 0 0 0 9 0 20 20 20 0 19 0 0 0 0 c 0 0 0 0 0 0 0 0 0 20 0 0 0 0 0 g 0 0 0 0 10 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 1 20 0 0 0 0 1 0 0 0 0

Mirr_Cell_FBgn0014343_shift3 (Mirr_Cell_FBgn0014343)
; oligos_6nt_mkv4_m4 versus Mirr_Cell_FBgn0014343; m=10/31; ncol2=8; w=-1; offset=-1; strand=D; shift=3; score=0.535628; ---waawAACA---- ; cor=; Ncor= a 0 0 0 18 18 22 20 29 41 0 41 0 0 0 0 c 0 0 0 6 4 7 1 0 0 41 0 0 0 0 0 g 0 0 0 6 10 6 1 2 0 0 0 0 0 0 0 t 0 0 0 11 9 6 19 10 0 0 0 0 0 0 0

fd64A_SANGER_5_FBgn0004895_shift3 (fd64A_SANGER_5_FBgn0004895)
; oligos_6nt_mkv4_m4 versus fd64A_SANGER_5_FBgn0004895; m=11/31; ncol2=8; w=-1; offset=-1; strand=D; shift=3; score=0.533538; ---tvtAAACA---- ; cor=; Ncor= a 0 0 0 3 7 4 20 19 20 0 20 0 0 0 0 c 0 0 0 0 5 3 0 1 0 17 0 0 0 0 0 g 0 0 0 4 6 0 0 0 0 0 0 0 0 0 0 t 0 0 0 13 2 13 0 0 0 3 0 0 0 0 0

slp2_SANGER_5_FBgn0004567_shift4 (slp2_SANGER_5_FBgn0004567)
; oligos_6nt_mkv4_m4 versus slp2_SANGER_5_FBgn0004567; m=12/31; ncol2=8; w=0; offset=0; strand=D; shift=4; score=0.518635; ----rTAAACAa--- ; cor=; Ncor= a 0 0 0 0 6 0 18 18 18 0 18 11 0 0 0 c 0 0 0 0 0 1 0 0 0 18 0 3 0 0 0 g 0 0 0 0 12 0 0 0 0 0 0 3 0 0 0 t 0 0 0 0 0 17 0 0 0 0 0 1 0 0 0

HLH4C_da_SANGER_5_FBgn0000413_shift4 (HLH4C_da_SANGER_5_FBgn0000413)
; oligos_6nt_mkv4_m4 versus HLH4C_da_SANGER_5_FBgn0000413; m=13/31; ncol2=15; w=0; offset=0; strand=D; shift=4; score=0.51672; ----mammvCACCTG ; cor=; Ncor= a 0 0 0 0 9 12 11 11 10 0 23 0 1 0 0 c 0 0 0 0 9 3 6 6 6 23 0 21 22 0 1 g 0 0 0 0 5 5 2 1 7 0 0 1 0 0 22 t 0 0 0 0 0 3 4 5 0 0 0 1 0 23 0

HLH4C_da_SANGER_5_FBgn0011277_shift4 (HLH4C_da_SANGER_5_FBgn0011277)
; oligos_6nt_mkv4_m4 versus HLH4C_da_SANGER_5_FBgn0011277; m=14/31; ncol2=15; w=0; offset=0; strand=D; shift=4; score=0.51672; ----mammvCACCTG ; cor=; Ncor= a 0 0 0 0 9 12 11 11 10 0 23 0 1 0 0 c 0 0 0 0 9 3 6 6 6 23 0 21 22 0 1 g 0 0 0 0 5 5 2 1 7 0 0 1 0 0 22 t 0 0 0 0 0 3 4 5 0 0 0 1 0 23 0

Ara_Cell_FBgn0015904_shift3 (Ara_Cell_FBgn0015904)
; oligos_6nt_mkv4_m4 versus Ara_Cell_FBgn0015904; m=15/31; ncol2=8; w=-1; offset=-1; strand=D; shift=3; score=0.511889; ---raAwwACA---- ; cor=; Ncor= a 0 0 0 12 16 24 14 23 34 0 34 0 0 0 0 c 0 0 0 5 7 1 0 0 0 34 0 0 0 0 0 g 0 0 0 10 6 1 5 0 0 0 0 0 0 0 0 t 0 0 0 7 5 8 15 11 0 0 0 0 0 0 0

Caup_Cell_FBgn0015919_shift3 (Caup_Cell_FBgn0015919)
; oligos_6nt_mkv4_m4 versus Caup_Cell_FBgn0015919; m=16/31; ncol2=8; w=-1; offset=-1; strand=D; shift=3; score=0.502113; ---cwwtAACA---- ; cor=; Ncor= a 0 0 0 4 9 8 4 14 19 0 19 0 0 0 0 c 0 0 0 9 0 0 1 0 0 19 0 0 0 0 0 g 0 0 0 2 3 4 2 2 0 0 0 0 0 0 0 t 0 0 0 4 7 7 12 3 0 0 0 0 0 0 0

Mirr_SOLEXA_FBgn0014343_shift5 (Mirr_SOLEXA_FBgn0014343)
; oligos_6nt_mkv4_m4 versus Mirr_SOLEXA_FBgn0014343; m=17/31; ncol2=6; w=0; offset=1; strand=D; shift=5; score=0.483969; -----wwwACA---- ; cor=; Ncor= a 0 0 0 0 0 550 410 782 1415 0 1415 0 0 0 0 c 0 0 0 0 0 158 93 0 0 1415 0 0 0 0 0 g 0 0 0 0 0 327 282 204 0 0 0 0 0 0 0 t 0 0 0 0 0 380 630 429 0 0 0 0 0 0 0

Ara_SOLEXA_FBgn0015904_shift5 (Ara_SOLEXA_FBgn0015904)
; oligos_6nt_mkv4_m4 versus Ara_SOLEXA_FBgn0015904; m=18/31; ncol2=6; w=0; offset=1; strand=D; shift=5; score=0.479754; -----awwACA---- ; cor=; Ncor= a 0 0 0 0 0 155 97 193 313 0 313 0 0 0 0 c 0 0 0 0 0 36 0 0 0 313 0 0 0 0 0 g 0 0 0 0 0 44 45 38 0 0 0 0 0 0 0 t 0 0 0 0 0 78 171 82 0 0 0 0 0 0 0

foxo_SANGER_10_FBgn0038197_rc_shift2 (foxo_SANGER_10_FBgn0038197_rc)
; oligos_6nt_mkv4_m4 versus foxo_SANGER_10_FBgn0038197_rc; m=19/31; ncol2=9; w=-2; offset=-2; strand=R; shift=2; score=0.477287; --ycrwAAACA---- ; cor=; Ncor= a 0 0 0 3 8 8 16 16 20 0 20 0 0 0 0 c 0 0 6 12 0 0 1 4 0 18 0 0 0 0 0 g 0 0 3 3 11 0 0 0 0 0 0 0 0 0 0 t 0 0 11 2 1 12 3 0 0 2 0 0 0 0 0

slp1_NAR_FBgn0003430_rc_shift1 (slp1_NAR_FBgn0003430_rc)
; oligos_6nt_mkv4_m4 versus slp1_NAR_FBgn0003430_rc; m=20/31; ncol2=11; w=-3; offset=-3; strand=R; shift=1; score=0.468501; -wryrtAAACAm--- ; cor=; Ncor= a 0 19 21 1 11 10 39 40 41 0 41 16 0 0 0 c 0 4 3 15 7 4 2 1 0 38 0 14 0 0 0 g 0 3 13 8 22 0 0 0 0 0 0 3 0 0 0 t 0 15 4 17 1 27 0 0 0 3 0 8 0 0 0

CG16899_SANGER_5_FBgn0037735_shift3 (CG16899_SANGER_5_FBgn0037735)
; oligos_6nt_mkv4_m4 versus CG16899_SANGER_5_FBgn0037735; m=21/31; ncol2=9; w=-1; offset=-1; strand=D; shift=3; score=0.468017; ---vrTAAACAA--- ; cor=; Ncor= a 0 0 0 6 10 1 21 20 21 0 21 15 0 0 0 c 0 0 0 5 2 2 0 0 0 18 0 2 0 0 0 g 0 0 0 8 8 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 18 0 1 0 3 0 4 0 0 0

Caup_SOLEXA_FBgn0015919_shift5 (Caup_SOLEXA_FBgn0015919)
; oligos_6nt_mkv4_m4 versus Caup_SOLEXA_FBgn0015919; m=22/31; ncol2=6; w=0; offset=1; strand=D; shift=5; score=0.464906; -----wtwACA---- ; cor=; Ncor= a 0 0 0 0 0 999 577 1415 2904 2 2904 0 0 0 0 c 0 0 0 0 0 460 201 0 0 2902 0 0 0 0 0 g 0 0 0 0 0 626 639 511 0 0 0 0 0 0 0 t 0 0 0 0 0 819 1487 978 0 0 0 0 0 0 0

CG11617_SOLEXA_FBgn0031232_shift3 (CG11617_SOLEXA_FBgn0031232)
; oligos_6nt_mkv4_m4 versus CG11617_SOLEXA_FBgn0031232; m=23/31; ncol2=8; w=-1; offset=-1; strand=D; shift=3; score=0.454991; ---wtwTwACA---- ; cor=; Ncor= a 0 0 0 370 281 352 133 483 1159 7 1148 0 0 0 0 c 0 0 0 201 262 176 167 0 0 1152 2 0 0 0 0 g 0 0 0 211 257 176 20 283 0 0 9 0 0 0 0 t 0 0 0 377 359 455 839 393 0 0 0 0 0 0 0

ac_da_SANGER_5_FBgn0000413_shift8 (ac_da_SANGER_5_FBgn0000413)
; oligos_6nt_mkv4_m4 versus ac_da_SANGER_5_FBgn0000413; m=24/31; ncol2=8; w=0; offset=4; strand=D; shift=8; score=0.432417; --------rCACCTG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 10 0 19 0 0 0 0 c 0 0 0 0 0 0 0 0 1 19 0 18 19 0 0 g 0 0 0 0 0 0 0 0 7 0 0 1 0 0 19 t 0 0 0 0 0 0 0 0 1 0 0 0 0 19 0

ac_da_SANGER_5_FBgn0000022_shift8 (ac_da_SANGER_5_FBgn0000022)
; oligos_6nt_mkv4_m4 versus ac_da_SANGER_5_FBgn0000022; m=25/31; ncol2=8; w=0; offset=4; strand=D; shift=8; score=0.432417; --------rCACCTG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 10 0 19 0 0 0 0 c 0 0 0 0 0 0 0 0 1 19 0 18 19 0 0 g 0 0 0 0 0 0 0 0 7 0 0 1 0 0 19 t 0 0 0 0 0 0 0 0 1 0 0 0 0 19 0

sc_da_SANGER_10_FBgn0000413_shift8 (sc_da_SANGER_10_FBgn0000413)
; oligos_6nt_mkv4_m4 versus sc_da_SANGER_10_FBgn0000413; m=26/31; ncol2=8; w=0; offset=4; strand=D; shift=8; score= 0.4236; --------rCACCTG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 11 0 24 0 0 0 0 c 0 0 0 0 0 0 0 0 5 23 0 21 24 0 0 g 0 0 0 0 0 0 0 0 7 0 0 1 0 0 24 t 0 0 0 0 0 0 0 0 0 0 0 2 0 24 0

sc_da_SANGER_10_FBgn0004170_shift8 (sc_da_SANGER_10_FBgn0004170)
; oligos_6nt_mkv4_m4 versus sc_da_SANGER_10_FBgn0004170; m=27/31; ncol2=8; w=0; offset=4; strand=D; shift=8; score= 0.4236; --------rCACCTG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 11 0 24 0 0 0 0 c 0 0 0 0 0 0 0 0 5 23 0 21 24 0 0 g 0 0 0 0 0 0 0 0 7 0 0 1 0 0 24 t 0 0 0 0 0 0 0 0 0 0 0 2 0 24 0

fkh_NAR_FBgn0000659_rc_shift0 (fkh_NAR_FBgn0000659_rc)
; oligos_6nt_mkv4_m4 versus fkh_NAR_FBgn0000659_rc; m=28/31; ncol2=11; w=-4; offset=-4; strand=R; shift=0; score=0.421441; tTrrryAAACA---- ; cor=; Ncor= a 4 3 14 11 8 0 26 27 27 0 24 0 0 0 0 c 4 1 2 3 2 14 1 0 0 22 0 0 0 0 0 g 4 0 11 7 13 0 0 0 0 0 0 0 0 0 0 t 15 23 0 6 4 13 0 0 0 5 3 0 0 0 0

HLH54F_da_SANGER_5_FBgn0022740_shift7 (HLH54F_da_SANGER_5_FBgn0022740)
; oligos_6nt_mkv4_m4 versus HLH54F_da_SANGER_5_FBgn0022740; m=29/31; ncol2=11; w=0; offset=3; strand=D; shift=7; score=0.416631; -------mmCACCTG ; cor=; Ncor= a 0 0 0 0 0 0 0 12 12 0 24 0 0 0 0 c 0 0 0 0 0 0 0 10 10 23 0 24 23 1 0 g 0 0 0 0 0 0 0 1 2 0 0 0 0 2 24 t 0 0 0 0 0 0 0 1 0 1 0 0 1 21 0

HLH54F_da_SANGER_5_FBgn0000413_shift7 (HLH54F_da_SANGER_5_FBgn0000413)
; oligos_6nt_mkv4_m4 versus HLH54F_da_SANGER_5_FBgn0000413; m=30/31; ncol2=11; w=0; offset=3; strand=D; shift=7; score=0.416631; -------mmCACCTG ; cor=; Ncor= a 0 0 0 0 0 0 0 12 12 0 24 0 0 0 0 c 0 0 0 0 0 0 0 10 10 23 0 24 23 1 0 g 0 0 0 0 0 0 0 1 2 0 0 0 0 2 24 t 0 0 0 0 0 0 0 1 0 1 0 0 1 21 0

CG31782-F9-11_SOLEXA_FBgn0051782_rc_shift7 (CG31782-F9-11_SOLEXA_FBgn0051782_rc)
; oligos_6nt_mkv4_m4 versus CG31782-F9-11_SOLEXA_FBgn0051782_rc; m=31/31; ncol2=11; w=0; offset=3; strand=R; shift=7; score=0.400872; -------ctCACCac ; cor=; Ncor= a 0 0 0 0 0 0 0 269 617 42 2023 0 0 1676 407 c 0 0 0 0 0 0 0 1324 287 1979 143 2554 2552 582 1464 g 0 0 0 0 0 0 0 584 195 25 0 0 0 27 305 t 0 0 0 0 0 0 0 375 1453 506 386 0 1 269 377

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m3_shift3 ; 30 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m3_shift3 (oligos_6nt_mkv4_m3)
; oligos_6nt_mkv4_m3; m=0 (reference); ncol1=12; shift=3; ncol=15; ---mrCTGTCAaamg ; Alignment reference a 0 0 0 526 362 41 28 74 16 39 1314 942 891 393 301 c 0 0 0 353 229 1319 34 50 45 1321 36 139 210 434 341 g 0 0 0 252 522 20 27 1237 28 21 34 168 140 278 427 t 0 0 0 281 299 32 1323 51 1323 31 28 163 171 307 343

Her_SANGER_5_FBgn0030899_shift6 (Her_SANGER_5_FBgn0030899)
; oligos_6nt_mkv4_m3 versus Her_SANGER_5_FBgn0030899; m=1/29; ncol2=9; w=0; offset=3; strand=D; shift=6; score=0.674088; ------wGTCAAvmv ; cor=; Ncor= a 0 0 0 0 0 0 5 0 0 1 18 18 5 5 5 c 0 0 0 0 0 0 0 0 0 18 1 0 6 11 8 g 0 0 0 0 0 0 2 17 1 0 0 1 7 0 6 t 0 0 0 0 0 0 12 2 18 0 0 0 1 3 0

hth_SOLEXA_2_FBgn0001235_rc_shift5 (hth_SOLEXA_2_FBgn0001235_rc)
; oligos_6nt_mkv4_m3 versus hth_SOLEXA_2_FBgn0001235_rc; m=2/29; ncol2=8; w=0; offset=2; strand=R; shift=5; score=0.628894; -----cTGTCAaa-- ; cor=; Ncor= a 0 0 0 0 0 322 13 22 0 48 2585 1115 951 0 0 c 0 0 0 0 0 783 291 0 33 2681 25 527 589 0 0 g 0 0 0 0 0 172 40 2621 0 0 69 459 586 0 0 t 0 0 0 0 0 216 2358 86 2696 0 50 618 572 0 0

Exd_Cell_FBgn0000611_rc_shift6 (Exd_Cell_FBgn0000611_rc)
; oligos_6nt_mkv4_m3 versus Exd_Cell_FBgn0000611_rc; m=3/29; ncol2=8; w=0; offset=3; strand=R; shift=6; score=0.623867; ------yRTCAAAa- ; cor=; Ncor= a 0 0 0 0 0 0 0 5 0 0 17 17 14 5 0 c 0 0 0 0 0 0 6 0 0 17 0 0 2 4 0 g 0 0 0 0 0 0 0 12 0 0 0 0 0 4 0 t 0 0 0 0 0 0 11 0 17 0 0 0 1 4 0

Exd_SOLEXA_FBgn0000611_rc_shift6 (Exd_SOLEXA_FBgn0000611_rc)
; oligos_6nt_mkv4_m3 versus Exd_SOLEXA_FBgn0000611_rc; m=4/29; ncol2=8; w=0; offset=3; strand=R; shift=6; score=0.618812; ------yrTCAaaw- ; cor=; Ncor= a 0 0 0 0 0 0 77 323 0 0 883 541 408 266 0 c 0 0 0 0 0 0 259 0 0 883 0 168 143 207 0 g 0 0 0 0 0 0 26 505 0 0 0 40 172 152 0 t 0 0 0 0 0 0 521 55 883 0 0 134 160 258 0

Achi_Cell_FBgn0033749_rc_shift6 (Achi_Cell_FBgn0033749_rc)
; oligos_6nt_mkv4_m3 versus Achi_Cell_FBgn0033749_rc; m=5/29; ncol2=7; w=0; offset=3; strand=R; shift=6; score=0.577495; ------TGTCAwa-- ; cor=; Ncor= a 0 0 0 0 0 0 0 1 0 0 23 12 15 0 0 c 0 0 0 0 0 0 0 0 0 23 0 1 1 0 0 g 0 0 0 0 0 0 0 22 0 0 0 4 3 0 0 t 0 0 0 0 0 0 23 0 23 0 0 6 4 0 0

disco_SOLEXA_5_FBgn0000459_shift1 (disco_SOLEXA_5_FBgn0000459)
; oligos_6nt_mkv4_m3 versus disco_SOLEXA_5_FBgn0000459; m=6/29; ncol2=13; w=-2; offset=-2; strand=D; shift=1; score=0.570721; -aawwkTGTCACCy- ; cor=; Ncor= a 0 140 161 275 258 127 0 0 0 6 566 119 137 126 0 c 0 82 84 61 32 48 2 0 11 563 0 455 422 180 0 g 0 60 92 82 129 185 2 552 0 0 11 0 10 63 0 t 0 51 98 163 162 221 577 29 570 12 4 7 12 212 0

CG3407_SANGER_2.5_FBgn0031573_shift5 (CG3407_SANGER_2.5_FBgn0031573)
; oligos_6nt_mkv4_m3 versus CG3407_SANGER_2.5_FBgn0031573; m=7/29; ncol2=9; w=0; offset=2; strand=D; shift=5; score=0.568315; -----awGTCAAsm- ; cor=; Ncor= a 0 0 0 0 0 11 7 0 0 0 17 16 2 6 0 c 0 0 0 0 0 4 3 1 0 17 0 0 8 9 0 g 0 0 0 0 0 0 0 16 0 0 0 1 6 0 0 t 0 0 0 0 0 2 7 0 17 0 0 0 1 2 0

disco-r-F1-2_SOLEXA_FBgn0042650_rc_shift2 (disco-r-F1-2_SOLEXA_FBgn0042650_rc)
; oligos_6nt_mkv4_m3 versus disco-r-F1-2_SOLEXA_FBgn0042650_rc; m=8/29; ncol2=15; w=-1; offset=-1; strand=R; shift=2; score=0.565092; --aaadTGTCACCmr ; cor=; Ncor= a 0 0 931 1344 1271 809 0 1 8 1 2464 461 468 825 814 c 0 0 555 328 179 229 8 0 4 2584 41 2085 2015 848 635 g 0 0 582 446 563 782 272 2584 139 0 78 0 61 346 692 t 0 0 515 467 571 764 2305 0 2434 0 1 40 38 564 444

CG11617_Cell_FBgn0031232_rc_shift6 (CG11617_Cell_FBgn0031232_rc)
; oligos_6nt_mkv4_m3 versus CG11617_Cell_FBgn0031232_rc; m=9/29; ncol2=8; w=0; offset=3; strand=R; shift=6; score=0.564713; ------TGTtAAAw- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 4 17 16 14 7 0 c 0 0 0 0 0 0 0 0 0 3 0 0 1 3 0 g 0 0 0 0 0 0 0 17 0 0 0 0 0 0 0 t 0 0 0 0 0 0 17 0 17 10 0 1 2 7 0

CG11617_SOLEXA_FBgn0031232_rc_shift6 (CG11617_SOLEXA_FBgn0031232_rc)
; oligos_6nt_mkv4_m3 versus CG11617_SOLEXA_FBgn0031232_rc; m=10/29; ncol2=8; w=0; offset=3; strand=R; shift=6; score=0.550904; ------TGTwAwaw- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 393 839 455 359 377 0 c 0 0 0 0 0 0 9 0 0 283 20 176 257 211 0 g 0 0 0 0 0 0 2 1152 0 0 167 176 262 201 0 t 0 0 0 0 0 0 1148 7 1159 483 133 352 281 370 0

Six4_SOLEXA_FBgn0027364_rc_shift6 (Six4_SOLEXA_FBgn0027364_rc)
; oligos_6nt_mkv4_m3 versus Six4_SOLEXA_FBgn0027364_rc; m=11/29; ncol2=8; w=0; offset=3; strand=R; shift=6; score=0.53967; ------TaTCAhww- ; cor=; Ncor= a 0 0 0 0 0 0 0 383 0 38 599 194 203 181 0 c 0 0 0 0 0 0 0 126 0 556 0 167 83 116 0 g 0 0 0 0 0 0 40 128 0 0 38 84 91 93 0 t 0 0 0 0 0 0 597 0 637 43 0 192 260 247 0

exd_SOLEXA_2_FBgn0000611_rc_shift5 (exd_SOLEXA_2_FBgn0000611_rc)
; oligos_6nt_mkv4_m3 versus exd_SOLEXA_2_FBgn0000611_rc; m=12/29; ncol2=8; w=0; offset=2; strand=R; shift=5; score=0.509125; -----wyrTCAaa-- ; cor=; Ncor= a 0 0 0 0 0 483 259 1228 0 0 2672 1314 1025 0 0 c 0 0 0 0 0 145 914 86 0 2672 0 598 458 0 0 g 0 0 0 0 0 91 14 1169 0 0 0 204 568 0 0 t 0 0 0 0 0 474 1470 189 2672 0 0 539 587 0 0

Fer3_da_SANGER_5_FBgn0000413_shift2 (Fer3_da_SANGER_5_FBgn0000413)
; oligos_6nt_mkv4_m3 versus Fer3_da_SANGER_5_FBgn0000413; m=13/29; ncol2=10; w=-1; offset=-1; strand=D; shift=2; score=0.499373; --CAbCTGTyaC--- ; cor=; Ncor= a 0 0 2 18 1 3 0 0 3 0 11 3 0 0 0 c 0 0 17 0 5 15 1 0 2 7 4 15 0 0 0 g 0 0 0 1 8 1 0 19 0 4 2 0 0 0 0 t 0 0 0 0 5 0 18 0 14 8 2 1 0 0 0

Fer3_da_SANGER_5_FBgn0037937_shift2 (Fer3_da_SANGER_5_FBgn0037937)
; oligos_6nt_mkv4_m3 versus Fer3_da_SANGER_5_FBgn0037937; m=14/29; ncol2=10; w=-1; offset=-1; strand=D; shift=2; score=0.499373; --CAbCTGTyaC--- ; cor=; Ncor= a 0 0 2 18 1 3 0 0 3 0 11 3 0 0 0 c 0 0 17 0 5 15 1 0 2 7 4 15 0 0 0 g 0 0 0 1 8 1 0 19 0 4 2 0 0 0 0 t 0 0 0 0 5 0 18 0 14 8 2 1 0 0 0

Vis_SOLEXA_FBgn0033748_rc_shift6 (Vis_SOLEXA_FBgn0033748_rc)
; oligos_6nt_mkv4_m3 versus Vis_SOLEXA_FBgn0033748_rc; m=15/29; ncol2=6; w=0; offset=3; strand=R; shift=6; score=0.496352; ------TGTCAa--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 13 354 199 0 0 0 c 0 0 0 0 0 0 36 0 0 341 0 34 0 0 0 g 0 0 0 0 0 0 0 354 0 0 0 53 0 0 0 t 0 0 0 0 0 0 318 0 354 0 0 68 0 0 0

Achi_SOLEXA_FBgn0033749_rc_shift6 (Achi_SOLEXA_FBgn0033749_rc)
; oligos_6nt_mkv4_m3 versus Achi_SOLEXA_FBgn0033749_rc; m=16/29; ncol2=6; w=0; offset=3; strand=R; shift=6; score=0.494328; ------TGTCAa--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 368 181 0 0 0 c 0 0 0 0 0 0 29 0 0 344 0 39 0 0 0 g 0 0 0 0 0 0 0 368 0 0 0 74 0 0 0 t 0 0 0 0 0 0 339 0 368 24 0 74 0 0 0

ems_FlyReg_FBgn0000576_rc_shift6 (ems_FlyReg_FBgn0000576_rc)
; oligos_6nt_mkv4_m3 versus ems_FlyReg_FBgn0000576_rc; m=17/29; ncol2=8; w=0; offset=3; strand=R; shift=6; score=0.490415; ------TsTmAThm- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 1 3 0 1 2 0 c 0 0 0 0 0 0 0 1 0 2 0 0 1 1 0 g 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 t 0 0 0 0 0 0 3 0 3 0 0 3 1 0 0

Hth_SOLEXA_FBgn0001235_rc_shift6 (Hth_SOLEXA_FBgn0001235_rc)
; oligos_6nt_mkv4_m3 versus Hth_SOLEXA_FBgn0001235_rc; m=18/29; ncol2=6; w=0; offset=3; strand=R; shift=6; score=0.480716; ------TGTCAm--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 388 148 0 0 0 c 0 0 0 0 0 0 40 0 0 444 56 120 0 0 0 g 0 0 0 0 0 0 60 444 41 0 0 87 0 0 0 t 0 0 0 0 0 0 344 0 403 0 0 89 0 0 0

Caup_Cell_FBgn0015919_rc_shift6 (Caup_Cell_FBgn0015919_rc)
; oligos_6nt_mkv4_m3 versus Caup_Cell_FBgn0015919_rc; m=19/29; ncol2=8; w=0; offset=3; strand=R; shift=6; score=0.472683; ------TGTTawwg- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 3 12 7 7 4 0 c 0 0 0 0 0 0 0 0 0 2 2 4 3 2 0 g 0 0 0 0 0 0 0 19 0 0 1 0 0 9 0 t 0 0 0 0 0 0 19 0 19 14 4 8 9 4 0

So_SOLEXA_FBgn0003460_rc_shift6 (So_SOLEXA_FBgn0003460_rc)
; oligos_6nt_mkv4_m3 versus So_SOLEXA_FBgn0003460_rc; m=20/29; ncol2=8; w=0; offset=3; strand=R; shift=6; score=0.471011; ------TATCAyww- ; cor=; Ncor= a 0 0 0 0 0 0 0 509 0 0 467 122 165 166 0 c 0 0 0 0 0 0 0 14 0 519 4 151 117 95 0 g 0 0 0 0 0 0 0 8 0 0 58 87 92 102 0 t 0 0 0 0 0 0 531 0 531 12 2 171 157 168 0

HLHmgamma_SANGER_5_2_FBgn0002735_shift6 (HLHmgamma_SANGER_5_2_FBgn0002735)
; oligos_6nt_mkv4_m3 versus HLHmgamma_SANGER_5_2_FBgn0002735; m=21/29; ncol2=7; w=0; offset=3; strand=D; shift=6; score=0.466095; ------wGTCAAG-- ; cor=; Ncor= a 0 0 0 0 0 0 3 0 0 0 7 7 0 0 0 c 0 0 0 0 0 0 0 0 0 7 0 0 0 0 0 g 0 0 0 0 0 0 0 7 0 0 0 0 7 0 0 t 0 0 0 0 0 0 4 0 7 0 0 0 0 0 0

tap_da_SANGER_5_2_FBgn0015550_shift1 (tap_da_SANGER_5_2_FBgn0015550)
; oligos_6nt_mkv4_m3 versus tap_da_SANGER_5_2_FBgn0015550; m=22/29; ncol2=10; w=-2; offset=-2; strand=D; shift=1; score=0.441631; -SCAkATGTCA---- ; cor=; Ncor= a 0 0 0 13 1 11 0 0 0 0 10 0 0 0 0 c 0 9 12 0 3 3 0 0 0 11 0 0 0 0 0 g 0 3 0 1 5 0 0 14 1 1 3 0 0 0 0 t 0 0 0 0 5 0 14 0 13 2 1 0 0 0 0

tap_da_SANGER_5_2_FBgn0000413_shift1 (tap_da_SANGER_5_2_FBgn0000413)
; oligos_6nt_mkv4_m3 versus tap_da_SANGER_5_2_FBgn0000413; m=23/29; ncol2=10; w=-2; offset=-2; strand=D; shift=1; score=0.441631; -SCAkATGTCA---- ; cor=; Ncor= a 0 0 0 13 1 11 0 0 0 0 10 0 0 0 0 c 0 9 12 0 3 3 0 0 0 11 0 0 0 0 0 g 0 3 0 1 5 0 0 14 1 1 3 0 0 0 0 t 0 0 0 0 5 0 14 0 13 2 1 0 0 0 0

Vis_Cell_FBgn0033748_rc_shift6 (Vis_Cell_FBgn0033748_rc)
; oligos_6nt_mkv4_m3 versus Vis_Cell_FBgn0033748_rc; m=24/29; ncol2=5; w=0; offset=3; strand=R; shift=6; score=0.416374; ------TGTCA---- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 22 0 0 0 0 c 0 0 0 0 0 0 0 0 0 22 0 0 0 0 0 g 0 0 0 0 0 0 0 22 0 0 0 0 0 0 0 t 0 0 0 0 0 0 22 0 22 0 0 0 0 0 0

Hth_Cell_FBgn0001235_rc_shift6 (Hth_Cell_FBgn0001235_rc)
; oligos_6nt_mkv4_m3 versus Hth_Cell_FBgn0001235_rc; m=25/29; ncol2=5; w=0; offset=3; strand=R; shift=6; score=0.412766; ------TGTCA---- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 17 0 0 0 0 c 0 0 0 0 0 0 3 0 0 17 0 0 0 0 0 g 0 0 0 0 0 0 0 17 0 0 0 0 0 0 0 t 0 0 0 0 0 0 14 0 17 0 0 0 0 0 0

Fer1_da_SANGER_10_FBgn0037475_shift0 (Fer1_da_SANGER_10_FBgn0037475)
; oligos_6nt_mkv4_m3 versus Fer1_da_SANGER_10_FBgn0037475; m=26/29; ncol2=11; w=-3; offset=-3; strand=D; shift=0; score=0.407324; mvCAsmTGwCa---- ; cor=; Ncor= a 11 11 0 23 0 6 0 0 8 0 14 0 0 0 0 c 6 6 23 0 15 14 0 0 3 17 4 0 0 0 0 g 1 6 0 0 8 3 0 23 2 3 4 0 0 0 0 t 5 0 0 0 0 0 23 0 10 3 1 0 0 0 0

Fer1_da_SANGER_10_FBgn0000413_shift0 (Fer1_da_SANGER_10_FBgn0000413)
; oligos_6nt_mkv4_m3 versus Fer1_da_SANGER_10_FBgn0000413; m=27/29; ncol2=11; w=-3; offset=-3; strand=D; shift=0; score=0.407324; mvCAsmTGwCa---- ; cor=; Ncor= a 11 11 0 23 0 6 0 0 8 0 14 0 0 0 0 c 6 6 23 0 15 14 0 0 3 17 4 0 0 0 0 g 1 6 0 0 8 3 0 23 2 3 4 0 0 0 0 t 5 0 0 0 0 0 23 0 10 3 1 0 0 0 0

nau_da_SANGER_5_FBgn0002922_shift2 (nau_da_SANGER_5_FBgn0002922)
; oligos_6nt_mkv4_m3 versus nau_da_SANGER_5_FBgn0002922; m=28/29; ncol2=8; w=-1; offset=-1; strand=D; shift=2; score=0.402198; --CACCTGyy----- ; cor=; Ncor= a 0 0 0 22 0 0 0 0 0 1 0 0 0 0 0 c 0 0 16 0 22 22 0 0 9 14 0 0 0 0 0 g 0 0 1 0 0 0 0 22 0 1 0 0 0 0 0 t 0 0 0 0 0 0 22 0 13 6 0 0 0 0 0

nau_da_SANGER_5_FBgn0000413_shift2 (nau_da_SANGER_5_FBgn0000413)
; oligos_6nt_mkv4_m3 versus nau_da_SANGER_5_FBgn0000413; m=29/29; ncol2=8; w=-1; offset=-1; strand=D; shift=2; score=0.402198; --CACCTGyy----- ; cor=; Ncor= a 0 0 0 22 0 0 0 0 0 1 0 0 0 0 0 c 0 0 16 0 22 22 0 0 9 14 0 0 0 0 0 g 0 0 1 0 0 0 0 22 0 1 0 0 0 0 0 t 0 0 0 0 0 0 22 0 13 6 0 0 0 0 0

One-to-n matrix alignment; reference matrix: dyads_m5_shift3 ; 8 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m5_shift3 (dyads_m5)
; dyads_m5; m=0 (reference); ncol1=11; shift=3; ncol=14; ---ccACCACCAcc ; Alignment reference a 0 0 0 849 627 3918 50 30 4141 38 14 3899 676 705 c 0 0 0 2252 2408 191 4112 4096 103 4058 4126 239 2169 2498 g 0 0 0 690 543 129 102 115 126 110 85 188 692 474 t 0 0 0 681 894 234 208 231 102 266 247 146 935 795

CG31782-F9-11_SOLEXA_FBgn0051782_rc_shift2 (CG31782-F9-11_SOLEXA_FBgn0051782_rc)
; dyads_m5 versus CG31782-F9-11_SOLEXA_FBgn0051782_rc; m=1/7; ncol2=11; w=-1; offset=-1; strand=R; shift=2; score=0.662333; --ctCACCacyaa- ; cor=; Ncor= a 0 0 269 617 42 2023 0 0 1676 407 471 1282 1413 0 c 0 0 1324 287 1979 143 2554 2552 582 1464 954 350 486 0 g 0 0 584 195 25 0 0 0 27 305 289 438 420 0 t 0 0 375 1453 506 386 0 1 269 377 838 482 234 0

lola-PL_SOLEXA_FBgn0005630_shift2 (lola-PL_SOLEXA_FBgn0005630)
; dyads_m5 versus lola-PL_SOLEXA_FBgn0005630; m=2/7; ncol2=14; w=-1; offset=-1; strand=D; shift=2; score=0.576007; --kgmmCCACcgkg ; cor=; Ncor= a 0 0 357 215 944 808 0 0 2061 0 361 407 457 281 c 0 0 322 163 968 793 2061 2061 0 2061 1099 481 334 387 g 0 0 600 1232 0 137 0 0 0 0 123 834 690 939 t 0 0 780 447 148 322 0 0 0 0 476 337 576 452

CG31782_F9-11_SANGER_5_FBgn0051782_shift0 (CG31782_F9-11_SANGER_5_FBgn0051782)
; dyads_m5 versus CG31782_F9-11_SANGER_5_FBgn0051782; m=3/7; ncol2=14; w=-3; offset=-3; strand=D; shift=0; score=0.569271; AssTCWCCAMYAAA ; cor=; Ncor= a 5 0 0 1 0 5 0 0 7 2 0 6 6 5 c 0 2 2 0 7 0 7 7 0 5 5 0 0 0 g 1 4 4 0 0 0 0 0 0 0 0 0 1 0 t 1 1 1 6 0 2 0 0 0 0 2 1 0 1

lola-PL_SANGER_2.5_FBgn0005630_rc_shift2 (lola-PL_SANGER_2.5_FBgn0005630_rc)
; dyads_m5 versus lola-PL_SANGER_2.5_FBgn0005630_rc; m=4/7; ncol2=9; w=-1; offset=-1; strand=R; shift=2; score=0.506519; --TGmcCCACm--- ; cor=; Ncor= a 0 0 2 0 4 2 0 0 11 0 4 0 0 0 c 0 0 0 0 7 5 11 11 0 11 6 0 0 0 g 0 0 0 9 0 2 0 0 0 0 0 0 0 0 t 0 0 8 2 0 2 0 0 0 0 1 0 0 0

Lag1_Cell_FBgn0040918_shift6 (Lag1_Cell_FBgn0040918)
; dyads_m5 versus Lag1_Cell_FBgn0040918; m=5/7; ncol2=10; w=0; offset=3; strand=D; shift=6; score=0.49346; ------CyACyAaa ; cor=; Ncor= a 0 0 0 0 0 0 0 0 17 1 0 18 12 10 c 0 0 0 0 0 0 19 9 2 18 12 0 0 3 g 0 0 0 0 0 0 0 0 0 0 0 1 4 4 t 0 0 0 0 0 0 0 10 0 0 7 0 3 2

Lag1_SOLEXA_FBgn0040918_shift6 (Lag1_SOLEXA_FBgn0040918)
; dyads_m5 versus Lag1_SOLEXA_FBgn0040918; m=6/7; ncol2=10; w=0; offset=3; strand=D; shift=6; score=0.468916; ------CyACyAaw ; cor=; Ncor= a 0 0 0 0 0 0 1 3 186 2 19 206 128 108 c 0 0 0 0 0 0 221 72 32 197 124 0 16 31 g 0 0 0 0 0 0 0 0 5 0 9 9 38 12 t 0 0 0 0 0 0 1 148 0 24 71 8 41 72

klu_SANGER_10_FBgn0013469_rc_shift6 (klu_SANGER_10_FBgn0013469_rc)
; dyads_m5 versus klu_SANGER_10_FBgn0013469_rc; m=7/7; ncol2=11; w=0; offset=3; strand=R; shift=6; score=0.40692; ------mCACCCmC ; cor=; Ncor= a 0 0 0 0 0 0 7 0 18 0 0 0 13 0 c 0 0 0 0 0 0 11 20 0 20 20 19 7 20 g 0 0 0 0 0 0 2 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 2 0 0 1 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m6_shift1 ; 14 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m6_shift1 (oligos_6nt_mkv4_m6)
; oligos_6nt_mkv4_m6; m=0 (reference); ncol1=12; shift=1; ncol=13; -yyCTTATCagym ; Alignment reference a 0 258 185 81 30 34 1157 9 27 667 140 266 331 c 0 411 359 1020 64 33 44 19 1173 127 207 383 328 g 0 231 277 65 39 16 8 37 9 266 679 226 283 t 0 339 418 73 1106 1156 30 1174 30 179 213 364 297

srp_SANGER_5_FBgn0003507_shift2 (srp_SANGER_5_FBgn0003507)
; oligos_6nt_mkv4_m6 versus srp_SANGER_5_FBgn0003507; m=1/13; ncol2=8; w=0; offset=1; strand=D; shift=2; score=0.654325; --yCTTATCw--- ; cor=; Ncor= a 0 0 0 0 0 0 17 0 0 9 0 0 0 c 0 0 7 14 0 0 0 0 17 0 0 0 0 g 0 0 3 2 0 0 0 0 0 1 0 0 0 t 0 0 6 0 17 17 0 17 0 7 0 0 0

GATAd_SANGER_5_FBgn0032223_shift2 (GATAd_SANGER_5_FBgn0032223)
; oligos_6nt_mkv4_m6 versus GATAd_SANGER_5_FBgn0032223; m=2/13; ncol2=8; w=0; offset=1; strand=D; shift=2; score=0.633004; --csTTATCA--- ; cor=; Ncor= a 0 0 1 1 1 0 23 0 0 22 0 0 0 c 0 0 12 14 0 0 0 1 23 0 0 0 0 g 0 0 5 6 0 0 0 0 0 1 0 0 0 t 0 0 3 1 22 23 0 22 0 0 0 0 0

So_SOLEXA_FBgn0003460_rc_shift5 (So_SOLEXA_FBgn0003460_rc)
; oligos_6nt_mkv4_m6 versus So_SOLEXA_FBgn0003460_rc; m=3/13; ncol2=8; w=0; offset=4; strand=R; shift=5; score=0.627456; -----TATCAyww ; cor=; Ncor= a 0 0 0 0 0 0 509 0 0 467 122 165 166 c 0 0 0 0 0 0 14 0 519 4 151 117 95 g 0 0 0 0 0 0 8 0 0 58 87 92 102 t 0 0 0 0 0 531 0 531 12 2 171 157 168

Optix_SOLEXA_FBgn0025360_rc_shift5 (Optix_SOLEXA_FBgn0025360_rc)
; oligos_6nt_mkv4_m6 versus Optix_SOLEXA_FBgn0025360_rc; m=4/13; ncol2=8; w=0; offset=4; strand=R; shift=5; score=0.624418; -----TATCAcww ; cor=; Ncor= a 0 0 0 0 0 0 564 0 0 497 116 151 143 c 0 0 0 0 0 17 0 0 564 0 216 119 126 g 0 0 0 0 0 43 0 0 0 67 93 111 91 t 0 0 0 0 0 504 0 564 0 0 139 183 204

Optix_Cell_FBgn0025360_rc_shift5 (Optix_Cell_FBgn0025360_rc)
; oligos_6nt_mkv4_m6 versus Optix_Cell_FBgn0025360_rc; m=5/13; ncol2=8; w=0; offset=4; strand=R; shift=5; score=0.607714; -----TATCAcww ; cor=; Ncor= a 0 0 0 0 0 0 27 0 0 22 3 7 9 c 0 0 0 0 0 1 0 0 27 0 16 3 2 g 0 0 0 0 0 0 0 0 0 5 4 4 4 t 0 0 0 0 0 26 0 27 0 0 4 13 12

Six4_SOLEXA_FBgn0027364_rc_shift5 (Six4_SOLEXA_FBgn0027364_rc)
; oligos_6nt_mkv4_m6 versus Six4_SOLEXA_FBgn0027364_rc; m=6/13; ncol2=8; w=0; offset=4; strand=R; shift=5; score=0.579365; -----TaTCAhww ; cor=; Ncor= a 0 0 0 0 0 0 383 0 38 599 194 203 181 c 0 0 0 0 0 0 126 0 556 0 167 83 116 g 0 0 0 0 0 40 128 0 0 38 84 91 93 t 0 0 0 0 0 597 0 637 43 0 192 260 247

GATAe_SANGER_5_FBgn0038391_rc_shift3 (GATAe_SANGER_5_FBgn0038391_rc)
; oligos_6nt_mkv4_m6 versus GATAe_SANGER_5_FBgn0038391_rc; m=7/13; ncol2=7; w=0; offset=2; strand=R; shift=3; score=0.572773; ---CTTATCw--- ; cor=; Ncor= a 0 0 0 0 0 0 19 0 0 9 0 0 0 c 0 0 0 15 0 0 0 0 19 0 0 0 0 g 0 0 0 4 0 0 0 0 0 2 0 0 0 t 0 0 0 0 19 19 0 19 0 8 0 0 0

pnr_SANGER_5_FBgn0003117_rc_shift4 (pnr_SANGER_5_FBgn0003117_rc)
; oligos_6nt_mkv4_m6 versus pnr_SANGER_5_FBgn0003117_rc; m=8/13; ncol2=7; w=0; offset=3; strand=R; shift=4; score=0.561174; ----TTATCwg-- ; cor=; Ncor= a 0 0 0 0 0 0 16 0 0 7 3 0 0 c 0 0 0 0 0 0 0 0 17 0 3 0 0 g 0 0 0 0 0 0 0 0 0 0 9 0 0 t 0 0 0 0 16 17 1 17 0 10 2 0 0

br_SOLEXA_10_FBgn0000210_rc_shift0 (br_SOLEXA_10_FBgn0000210_rc)
; oligos_6nt_mkv4_m6 versus br_SOLEXA_10_FBgn0000210_rc; m=9/13; ncol2=11; w=-1; offset=-1; strand=R; shift=0; score=0.541536; ytTCTAATCab-- ; cor=; Ncor= a 47 73 2 0 0 359 353 37 8 147 44 0 0 c 125 21 37 362 0 0 1 0 344 41 118 0 0 g 32 54 1 0 0 0 4 21 1 78 87 0 0 t 156 212 322 0 362 3 4 304 9 86 89 0 0

So_Cell_FBgn0003460_rc_shift5 (So_Cell_FBgn0003460_rc)
; oligos_6nt_mkv4_m6 versus So_Cell_FBgn0003460_rc; m=10/13; ncol2=7; w=0; offset=4; strand=R; shift=5; score=0.527048; -----TATCAyt- ; cor=; Ncor= a 0 0 0 0 0 0 26 0 0 26 3 6 0 c 0 0 0 0 0 0 1 0 27 1 10 5 0 g 0 0 0 0 0 0 0 0 0 0 1 4 0 t 0 0 0 0 0 27 0 27 0 0 13 12 0

exd_SOLEXA_2_FBgn0000611_rc_shift4 (exd_SOLEXA_2_FBgn0000611_rc)
; oligos_6nt_mkv4_m6 versus exd_SOLEXA_2_FBgn0000611_rc; m=11/13; ncol2=8; w=0; offset=3; strand=R; shift=4; score=0.474868; ----wyrTCAaa- ; cor=; Ncor= a 0 0 0 0 483 259 1228 0 0 2672 1314 1025 0 c 0 0 0 0 145 914 86 0 2672 0 598 458 0 g 0 0 0 0 91 14 1169 0 0 0 204 568 0 t 0 0 0 0 474 1470 189 2672 0 0 539 587 0

Six4_SOLEXA_2_FBgn0027364_rc_shift3 (Six4_SOLEXA_2_FBgn0027364_rc)
; oligos_6nt_mkv4_m6 versus Six4_SOLEXA_2_FBgn0027364_rc; m=12/13; ncol2=8; w=0; offset=2; strand=R; shift=3; score=0.474572; ---sgTaTCAy-- ; cor=; Ncor= a 0 0 0 136 239 0 1624 0 143 2272 633 0 0 c 0 0 0 210 58 0 644 0 2488 74 695 0 0 g 0 0 0 377 1021 89 257 0 0 204 413 0 0 t 0 0 0 83 209 2542 106 2631 0 52 824 0 0

br_SANGER_10_FBgn0000210_rc_shift2 (br_SANGER_10_FBgn0000210_rc)
; oligos_6nt_mkv4_m6 versus br_SANGER_10_FBgn0000210_rc; m=13/13; ncol2=7; w=0; offset=1; strand=R; shift=2; score=0.420056; --TCTAATC---- ; cor=; Ncor= a 0 0 0 0 0 12 12 0 0 0 0 0 0 c 0 0 0 11 0 0 0 0 11 0 0 0 0 g 0 0 0 1 0 0 0 0 0 0 0 0 0 t 0 0 12 0 12 0 0 12 1 0 0 0 0

One-to-n matrix alignment; reference matrix: dyads_m7_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m7_shift1 (dyads_m7)
; dyads_m7; m=0 (reference); ncol1=15; shift=1; ncol=16; -camACACACACrCac ; Alignment reference a 0 746 2162 2054 3563 103 3664 76 3641 88 3518 93 1154 127 2089 496 c 0 2128 728 1297 97 3543 51 3629 30 3616 79 3585 176 3437 446 2402 g 0 453 495 139 100 64 94 52 113 38 139 81 2268 151 757 435 t 0 523 465 360 90 140 41 93 66 108 114 91 252 135 558 517

klu_SOLEXA_5_FBgn0013469_rc_shift0 (klu_SOLEXA_5_FBgn0013469_rc)
; dyads_m7 versus klu_SOLEXA_5_FBgn0013469_rc; m=1/3; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.630841; mmmmmCACCCmCrCm- ; cor=; Ncor= a 132 156 135 134 155 9 378 3 3 5 315 2 226 54 156 0 c 152 168 188 204 298 491 6 491 485 472 168 493 10 360 138 0 g 82 90 85 64 24 0 48 0 5 0 6 1 230 5 54 0 t 91 79 95 101 26 3 71 9 10 26 14 7 37 33 75 0

klu_SANGER_10_FBgn0013469_rc_shift4 (klu_SANGER_10_FBgn0013469_rc)
; dyads_m7 versus klu_SANGER_10_FBgn0013469_rc; m=2/3; ncol2=11; w=0; offset=3; strand=R; shift=4; score=0.55567; ----mCACCCmCrCa- ; cor=; Ncor= a 0 0 0 0 7 0 18 0 0 0 13 0 9 0 12 0 c 0 0 0 0 11 20 0 20 20 19 7 20 0 16 2 0 g 0 0 0 0 2 0 0 0 0 0 0 0 10 0 2 0 t 0 0 0 0 0 0 2 0 0 1 0 0 1 3 2 0

CG16778_SANGER_5_FBgn0003715_shift5 (CG16778_SANGER_5_FBgn0003715)
; dyads_m7 versus CG16778_SANGER_5_FBgn0003715; m=3/3; ncol2=8; w=0; offset=4; strand=D; shift=5; score=0.436799; -----CACAyAYG--- ; cor=; Ncor= a 0 0 0 0 0 0 18 0 20 0 17 0 0 0 0 0 c 0 0 0 0 0 15 1 20 0 9 0 6 1 0 0 0 g 0 0 0 0 0 2 0 0 0 0 3 0 18 0 0 0 t 0 0 0 0 0 1 0 0 0 11 0 14 1 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m4_shift3 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m4_shift3 (oligos_7nt_mkv5_m4)
; oligos_7nt_mkv5_m4; m=0 (reference); ncol1=13; shift=3; ncol=16; ---caCACAcACACac ; Alignment reference a 0 0 0 1616 5949 121 8874 84 8611 2218 8784 54 8849 112 5929 1185 c 0 0 0 5506 794 8776 44 8848 265 5812 99 8906 48 8808 804 5541 g 0 0 0 663 1558 47 67 42 67 257 96 17 101 57 1381 1022 t 0 0 0 1242 726 83 42 53 84 740 48 50 29 50 913 1279

klu_SANGER_10_FBgn0013469_rc_shift4 (klu_SANGER_10_FBgn0013469_rc)
; oligos_7nt_mkv5_m4 versus klu_SANGER_10_FBgn0013469_rc; m=1/6; ncol2=11; w=0; offset=1; strand=R; shift=4; score=0.624937; ----mCACCCmCrCa- ; cor=; Ncor= a 0 0 0 0 7 0 18 0 0 0 13 0 9 0 12 0 c 0 0 0 0 11 20 0 20 20 19 7 20 0 16 2 0 g 0 0 0 0 2 0 0 0 0 0 0 0 10 0 2 0 t 0 0 0 0 0 0 2 0 0 1 0 0 1 3 2 0

klu_SOLEXA_5_FBgn0013469_rc_shift0 (klu_SOLEXA_5_FBgn0013469_rc)
; oligos_7nt_mkv5_m4 versus klu_SOLEXA_5_FBgn0013469_rc; m=2/6; ncol2=15; w=-3; offset=-3; strand=R; shift=0; score=0.534019; mmmmmCACCCmCrCm- ; cor=; Ncor= a 132 156 135 134 155 9 378 3 3 5 315 2 226 54 156 0 c 152 168 188 204 298 491 6 491 485 472 168 493 10 360 138 0 g 82 90 85 64 24 0 48 0 5 0 6 1 230 5 54 0 t 91 79 95 101 26 3 71 9 10 26 14 7 37 33 75 0

CG5953_SANGER_5_FBgn0032587_shift6 (CG5953_SANGER_5_FBgn0032587)
; oligos_7nt_mkv5_m4 versus CG5953_SANGER_5_FBgn0032587; m=3/6; ncol2=8; w=0; offset=3; strand=D; shift=6; score=0.492643; ------aCAAACAy-- ; cor=; Ncor= a 0 0 0 0 0 0 10 0 16 16 16 0 16 1 0 0 c 0 0 0 0 0 0 3 16 0 0 0 16 0 5 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 3 0 0 0 0 0 0 10 0 0

Ci_SANGER_5_FBgn0004859_shift1 (Ci_SANGER_5_FBgn0004859)
; oligos_7nt_mkv5_m4 versus Ci_SANGER_5_FBgn0004859; m=4/6; ncol2=11; w=-2; offset=-2; strand=D; shift=1; score=0.433596; -rGMCCACMCAC---- ; cor=; Ncor= a 0 6 0 8 2 1 8 0 3 0 10 0 0 0 0 0 c 0 0 0 3 9 10 2 10 8 11 0 9 0 0 0 0 g 0 4 11 0 0 0 0 0 0 0 1 2 0 0 0 0 t 0 1 0 0 0 0 1 1 0 0 0 0 0 0 0 0

CG12029_SANGER_10_FBgn0035454_rc_shift1 (CG12029_SANGER_10_FBgn0035454_rc)
; oligos_7nt_mkv5_m4 versus CG12029_SANGER_10_FBgn0035454_rc; m=5/6; ncol2=11; w=-2; offset=-2; strand=R; shift=1; score=0.43286; -RCCACACCCac---- ; cor=; Ncor= a 0 5 4 0 16 0 17 0 0 0 13 4 0 0 0 0 c 0 0 14 20 2 20 0 20 20 20 3 11 0 0 0 0 g 0 15 2 0 2 0 2 0 0 0 0 1 0 0 0 0 t 0 0 0 0 0 0 1 0 0 0 4 4 0 0 0 0

CG16778_SANGER_5_FBgn0003715_shift9 (CG16778_SANGER_5_FBgn0003715)
; oligos_7nt_mkv5_m4 versus CG16778_SANGER_5_FBgn0003715; m=6/6; ncol2=8; w=0; offset=6; strand=D; shift=9; score=0.418046; ---------CACAyAY ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 18 0 20 0 17 0 c 0 0 0 0 0 0 0 0 0 15 1 20 0 9 0 6 g 0 0 0 0 0 0 0 0 0 2 0 0 0 0 3 0 t 0 0 0 0 0 0 0 0 0 1 0 0 0 11 0 14

One-to-n matrix alignment; reference matrix: dyads_m4_shift2 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m4_shift2 (dyads_m4)
; dyads_m4; m=0 (reference); ncol1=13; shift=2; ncol=15; --camACACACrCaC ; Alignment reference a 0 0 692 1932 1963 3124 46 3190 60 3155 31 986 38 2067 370 c 0 0 1862 667 1096 52 3156 14 3160 33 3190 50 3147 251 2240 g 0 0 346 403 68 60 25 53 18 45 21 2134 51 608 304 t 0 0 369 267 142 33 42 12 31 36 27 99 33 343 355

klu_SANGER_10_FBgn0013469_rc_shift3 (klu_SANGER_10_FBgn0013469_rc)
; dyads_m4 versus klu_SANGER_10_FBgn0013469_rc; m=1/5; ncol2=11; w=0; offset=1; strand=R; shift=3; score=0.601875; ---mCACCCmCrCa- ; cor=; Ncor= a 0 0 0 7 0 18 0 0 0 13 0 9 0 12 0 c 0 0 0 11 20 0 20 20 19 7 20 0 16 2 0 g 0 0 0 2 0 0 0 0 0 0 0 10 0 2 0 t 0 0 0 0 0 2 0 0 1 0 0 1 3 2 0

CG16778_SANGER_5_FBgn0003715_shift4 (CG16778_SANGER_5_FBgn0003715)
; dyads_m4 versus CG16778_SANGER_5_FBgn0003715; m=2/5; ncol2=8; w=0; offset=2; strand=D; shift=4; score=0.455999; ----CACAyAYG--- ; cor=; Ncor= a 0 0 0 0 0 18 0 20 0 17 0 0 0 0 0 c 0 0 0 0 15 1 20 0 9 0 6 1 0 0 0 g 0 0 0 0 2 0 0 0 0 3 0 18 0 0 0 t 0 0 0 0 1 0 0 0 11 0 14 1 0 0 0

Ci_SANGER_5_FBgn0004859_shift0 (Ci_SANGER_5_FBgn0004859)
; dyads_m4 versus Ci_SANGER_5_FBgn0004859; m=3/5; ncol2=11; w=-2; offset=-2; strand=D; shift=0; score=0.420771; rGMCCACMCAC---- ; cor=; Ncor= a 6 0 8 2 1 8 0 3 0 10 0 0 0 0 0 c 0 0 3 9 10 2 10 8 11 0 9 0 0 0 0 g 4 11 0 0 0 0 0 0 0 1 2 0 0 0 0 t 1 0 0 0 0 1 1 0 0 0 0 0 0 0 0

foxo_SANGER_10_FBgn0038197_rc_shift1 (foxo_SANGER_10_FBgn0038197_rc)
; dyads_m4 versus foxo_SANGER_10_FBgn0038197_rc; m=4/5; ncol2=9; w=-1; offset=-1; strand=R; shift=1; score=0.420181; -ycrwAAACA----- ; cor=; Ncor= a 0 0 3 8 8 16 16 20 0 20 0 0 0 0 0 c 0 6 12 0 0 1 4 0 18 0 0 0 0 0 0 g 0 3 3 11 0 0 0 0 0 0 0 0 0 0 0 t 0 11 2 1 12 3 0 0 2 0 0 0 0 0 0

CG5953_SANGER_5_FBgn0032587_shift1 (CG5953_SANGER_5_FBgn0032587)
; dyads_m4 versus CG5953_SANGER_5_FBgn0032587; m=5/5; ncol2=8; w=-1; offset=-1; strand=D; shift=1; score=0.408791; -aCAAACAy------ ; cor=; Ncor= a 0 10 0 16 16 16 0 16 1 0 0 0 0 0 0 c 0 3 16 0 0 0 16 0 5 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 3 0 0 0 0 0 0 10 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m3_shift5 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m3_shift5 (oligos_7nt_mkv5_m3)
; oligos_7nt_mkv5_m3; m=0 (reference); ncol1=12; shift=5; ncol=17; -----caCCAmCACCac ; Alignment reference a 0 0 0 0 0 537 1591 66 86 2670 1679 63 2659 69 354 1474 675 c 0 0 0 0 0 1526 481 2678 2677 71 919 2713 103 2669 2209 633 1190 g 0 0 0 0 0 300 368 59 42 43 104 15 52 63 104 430 431 t 0 0 0 0 0 489 412 49 47 68 150 61 38 51 185 315 556

CG10267_SANGER_5_FBgn0037446_shift6 (CG10267_SANGER_5_FBgn0037446)
; oligos_7nt_mkv5_m3 versus CG10267_SANGER_5_FBgn0037446; m=1/4; ncol2=10; w=0; offset=1; strand=D; shift=6; score=0.601382; ------whyAACACTR- ; cor=; Ncor= a 0 0 0 0 0 0 8 6 1 16 16 1 16 0 0 11 0 c 0 0 0 0 0 0 0 6 10 0 0 14 0 16 0 0 0 g 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 5 0 t 0 0 0 0 0 0 7 4 5 0 0 1 0 0 16 0 0

Aef1_FlyReg_FBgn0005694_shift8 (Aef1_FlyReg_FBgn0005694)
; oligos_7nt_mkv5_m3 versus Aef1_FlyReg_FBgn0005694; m=2/4; ncol2=8; w=0; offset=3; strand=D; shift=8; score=0.48462; --------CAACwACw- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 3 3 0 2 3 0 2 0 c 0 0 0 0 0 0 0 0 3 0 0 3 0 0 3 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0

CG31782-F9-11_SOLEXA_FBgn0051782_rc_shift3 (CG31782-F9-11_SOLEXA_FBgn0051782_rc)
; oligos_7nt_mkv5_m3 versus CG31782-F9-11_SOLEXA_FBgn0051782_rc; m=3/4; ncol2=11; w=-2; offset=-2; strand=R; shift=3; score=0.457205; ---ctCACCacyaa--- ; cor=; Ncor= a 0 0 0 269 617 42 2023 0 0 1676 407 471 1282 1413 0 0 0 c 0 0 0 1324 287 1979 143 2554 2552 582 1464 954 350 486 0 0 0 g 0 0 0 584 195 25 0 0 0 27 305 289 438 420 0 0 0 t 0 0 0 375 1453 506 386 0 1 269 377 838 482 234 0 0 0

klu_SOLEXA_5_FBgn0013469_rc_shift0 (klu_SOLEXA_5_FBgn0013469_rc)
; oligos_7nt_mkv5_m3 versus klu_SOLEXA_5_FBgn0013469_rc; m=4/4; ncol2=15; w=-5; offset=-5; strand=R; shift=0; score=0.412172; mmmmmCACCCmCrCm-- ; cor=; Ncor= a 132 156 135 134 155 9 378 3 3 5 315 2 226 54 156 0 0 c 152 168 188 204 298 491 6 491 485 472 168 493 10 360 138 0 0 g 82 90 85 64 24 0 48 0 5 0 6 1 230 5 54 0 0 t 91 79 95 101 26 3 71 9 10 26 14 7 37 33 75 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m9_shift5 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m9_shift5 (oligos_6nt_mkv4_m9)
; oligos_6nt_mkv4_m9; m=0 (reference); ncol1=11; shift=5; ncol=16; -----mycCCACAGcv ; Alignment reference a 0 0 0 0 0 351 293 194 0 22 1229 47 1193 25 335 370 c 0 0 0 0 0 446 514 929 1366 1252 59 1259 95 36 476 370 g 0 0 0 0 0 285 244 167 14 74 64 49 67 1298 267 380 t 0 0 0 0 0 320 351 112 22 54 50 47 47 43 324 282

lola-PL_SOLEXA_FBgn0005630_shift4 (lola-PL_SOLEXA_FBgn0005630)
; oligos_6nt_mkv4_m9 versus lola-PL_SOLEXA_FBgn0005630; m=1/5; ncol2=14; w=-1; offset=-1; strand=D; shift=4; score=0.598127; ----kgmmCCACcgkg ; cor=; Ncor= a 0 0 0 0 357 215 944 808 0 0 2061 0 361 407 457 281 c 0 0 0 0 322 163 968 793 2061 2061 0 2061 1099 481 334 387 g 0 0 0 0 600 1232 0 137 0 0 0 0 123 834 690 939 t 0 0 0 0 780 447 148 322 0 0 0 0 476 337 576 452

lola-PL_SANGER_2.5_FBgn0005630_rc_shift4 (lola-PL_SANGER_2.5_FBgn0005630_rc)
; oligos_6nt_mkv4_m9 versus lola-PL_SANGER_2.5_FBgn0005630_rc; m=2/5; ncol2=9; w=-1; offset=-1; strand=R; shift=4; score=0.546944; ----TGmcCCACm--- ; cor=; Ncor= a 0 0 0 0 2 0 4 2 0 0 11 0 4 0 0 0 c 0 0 0 0 0 0 7 5 11 11 0 11 6 0 0 0 g 0 0 0 0 0 9 0 2 0 0 0 0 0 0 0 0 t 0 0 0 0 8 2 0 2 0 0 0 0 1 0 0 0

lmd_SOLEXA_5_FBgn0039039_rc_shift0 (lmd_SOLEXA_5_FBgn0039039_rc)
; oligos_6nt_mkv4_m9 versus lmd_SOLEXA_5_FBgn0039039_rc; m=3/5; ncol2=15; w=-5; offset=-5; strand=R; shift=0; score=0.453161; mmgmCCCCCcrCrga- ; cor=; Ncor= a 181 206 90 318 20 45 33 3 14 77 284 3 199 113 143 0 c 196 192 128 182 516 522 516 574 550 384 30 421 130 30 72 0 g 97 85 242 70 0 0 0 0 0 0 249 134 162 339 46 0 t 78 80 117 7 41 10 28 0 13 116 14 19 86 72 56 0

Opa_SANGER_5_FBgn0003002_shift1 (Opa_SANGER_5_FBgn0003002)
; oligos_6nt_mkv4_m9 versus Opa_SANGER_5_FBgn0003002; m=4/5; ncol2=13; w=-4; offset=-4; strand=D; shift=1; score=0.44943; -mkmmMCCCCmCyR-- ; cor=; Ncor= a 0 7 2 4 4 3 1 0 0 0 8 0 0 3 0 0 c 0 3 0 5 7 9 9 12 11 12 3 11 8 0 0 0 g 0 1 5 2 1 0 2 0 1 0 1 1 0 9 0 0 t 0 1 5 1 0 0 0 0 0 0 0 0 4 0 0 0

lmd_SANGER_5_FBgn0039039_rc_shift0 (lmd_SANGER_5_FBgn0039039_rc)
; oligos_6nt_mkv4_m9 versus lmd_SANGER_5_FBgn0039039_rc; m=5/5; ncol2=14; w=-5; offset=-5; strand=R; shift=0; score=0.419373; mmkaCCCCCCrCmG-- ; cor=; Ncor= a 10 8 1 13 0 0 0 0 0 1 11 0 9 3 0 0 c 8 9 3 5 20 22 22 22 22 16 1 18 7 1 0 0 g 2 3 11 4 0 0 0 0 0 0 10 4 3 15 0 0 t 1 2 7 0 2 0 0 0 0 5 0 0 3 2 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m5_shift3 ; 8 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m5_shift3 (oligos_7nt_mkv5_m5)
; oligos_7nt_mkv5_m5; m=0 (reference); ncol1=14; shift=3; ncol=17; ---caCACGCACACmca ; Alignment reference a 0 0 0 460 1509 205 2555 45 520 37 2687 35 2652 46 968 624 1177 c 0 0 0 1722 359 2317 95 2713 96 2718 45 2733 70 2700 1562 1283 628 g 0 0 0 280 595 123 87 48 2153 40 64 21 60 67 155 526 545 t 0 0 0 389 388 206 114 45 82 56 55 62 69 38 166 418 501

klu_SANGER_10_FBgn0013469_rc_shift4 (klu_SANGER_10_FBgn0013469_rc)
; oligos_7nt_mkv5_m5 versus klu_SANGER_10_FBgn0013469_rc; m=1/7; ncol2=11; w=0; offset=1; strand=R; shift=4; score=0.585532; ----mCACCCmCrCa-- ; cor=; Ncor= a 0 0 0 0 7 0 18 0 0 0 13 0 9 0 12 0 0 c 0 0 0 0 11 20 0 20 20 19 7 20 0 16 2 0 0 g 0 0 0 0 2 0 0 0 0 0 0 0 10 0 2 0 0 t 0 0 0 0 0 0 2 0 0 1 0 0 1 3 2 0 0

klu_SOLEXA_5_FBgn0013469_rc_shift0 (klu_SOLEXA_5_FBgn0013469_rc)
; oligos_7nt_mkv5_m5 versus klu_SOLEXA_5_FBgn0013469_rc; m=2/7; ncol2=15; w=-3; offset=-3; strand=R; shift=0; score=0.532574; mmmmmCACCCmCrCm-- ; cor=; Ncor= a 132 156 135 134 155 9 378 3 3 5 315 2 226 54 156 0 0 c 152 168 188 204 298 491 6 491 485 472 168 493 10 360 138 0 0 g 82 90 85 64 24 0 48 0 5 0 6 1 230 5 54 0 0 t 91 79 95 101 26 3 71 9 10 26 14 7 37 33 75 0 0

tgo_ss_SANGER_5_FBgn0003513_rc_shift3 (tgo_ss_SANGER_5_FBgn0003513_rc)
; oligos_7nt_mkv5_m5 versus tgo_ss_SANGER_5_FBgn0003513_rc; m=3/7; ncol2=8; w=0; offset=0; strand=R; shift=3; score=0.44245; ---GTCACGCA------ ; cor=; Ncor= a 0 0 0 2 0 0 10 0 1 0 9 0 0 0 0 0 0 c 0 0 0 0 0 10 0 9 0 10 0 0 0 0 0 0 0 g 0 0 0 8 0 0 0 1 9 0 1 0 0 0 0 0 0 t 0 0 0 0 10 0 0 0 0 0 0 0 0 0 0 0 0

tgo_ss_SANGER_5_FBgn0015014_rc_shift3 (tgo_ss_SANGER_5_FBgn0015014_rc)
; oligos_7nt_mkv5_m5 versus tgo_ss_SANGER_5_FBgn0015014_rc; m=4/7; ncol2=8; w=0; offset=0; strand=R; shift=3; score=0.44245; ---GTCACGCA------ ; cor=; Ncor= a 0 0 0 2 0 0 10 0 1 0 9 0 0 0 0 0 0 c 0 0 0 0 0 10 0 9 0 10 0 0 0 0 0 0 0 g 0 0 0 8 0 0 0 1 9 0 1 0 0 0 0 0 0 t 0 0 0 0 10 0 0 0 0 0 0 0 0 0 0 0 0

CG12029_SANGER_10_FBgn0035454_rc_shift1 (CG12029_SANGER_10_FBgn0035454_rc)
; oligos_7nt_mkv5_m5 versus CG12029_SANGER_10_FBgn0035454_rc; m=5/7; ncol2=11; w=-2; offset=-2; strand=R; shift=1; score=0.424923; -RCCACACCCac----- ; cor=; Ncor= a 0 5 4 0 16 0 17 0 0 0 13 4 0 0 0 0 0 c 0 0 14 20 2 20 0 20 20 20 3 11 0 0 0 0 0 g 0 15 2 0 2 0 2 0 0 0 0 1 0 0 0 0 0 t 0 0 0 0 0 0 1 0 0 0 4 4 0 0 0 0 0

Ci_SANGER_5_FBgn0004859_shift1 (Ci_SANGER_5_FBgn0004859)
; oligos_7nt_mkv5_m5 versus Ci_SANGER_5_FBgn0004859; m=6/7; ncol2=11; w=-2; offset=-2; strand=D; shift=1; score=0.412168; -rGMCCACMCAC----- ; cor=; Ncor= a 0 6 0 8 2 1 8 0 3 0 10 0 0 0 0 0 0 c 0 0 0 3 9 10 2 10 8 11 0 9 0 0 0 0 0 g 0 4 11 0 0 0 0 0 0 0 1 2 0 0 0 0 0 t 0 1 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0

CG16778_SANGER_5_FBgn0003715_shift9 (CG16778_SANGER_5_FBgn0003715)
; oligos_7nt_mkv5_m5 versus CG16778_SANGER_5_FBgn0003715; m=7/7; ncol2=8; w=0; offset=6; strand=D; shift=9; score=0.405763; ---------CACAyAYG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 18 0 20 0 17 0 0 c 0 0 0 0 0 0 0 0 0 15 1 20 0 9 0 6 1 g 0 0 0 0 0 0 0 0 0 2 0 0 0 0 3 0 18 t 0 0 0 0 0 0 0 0 0 1 0 0 0 11 0 14 1

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m10_shift4 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m10_shift4 (oligos_7nt_mkv5_m10)
; oligos_7nt_mkv5_m10; m=0 (reference); ncol1=11; shift=4; ncol=15; ----rrCAGAGACrg ; Alignment reference a 0 0 0 0 510 713 119 1668 35 1626 74 1599 123 732 432 c 0 0 0 0 439 367 1422 60 33 93 37 80 1348 348 434 g 0 0 0 0 525 496 207 55 1666 59 1613 85 267 487 665 t 0 0 0 0 329 227 55 20 69 25 79 39 65 236 272

Adf1_SANGER_5_FBgn0000054_shift0 (Adf1_SANGER_5_FBgn0000054)
; oligos_7nt_mkv5_m10 versus Adf1_SANGER_5_FBgn0000054; m=1/3; ncol2=15; w=-4; offset=-4; strand=D; shift=0; score=0.582795; ymcmRGCAGAGmhrm ; cor=; Ncor= a 1 7 2 4 3 0 0 11 0 8 0 7 4 5 7 c 5 3 6 7 0 0 11 0 1 1 0 3 4 2 4 g 0 1 2 0 8 10 0 0 10 2 11 1 0 3 0 t 5 0 1 0 0 1 0 0 0 0 0 0 3 1 0

CG13897_SANGER_5_FBgn0035160_shift2 (CG13897_SANGER_5_FBgn0035160)
; oligos_7nt_mkv5_m10 versus CG13897_SANGER_5_FBgn0035160; m=2/3; ncol2=11; w=-2; offset=-2; strand=D; shift=2; score=0.514126; --wsrrCAGACAs-- ; cor=; Ncor= a 0 0 5 2 8 9 0 17 0 17 0 17 4 0 0 c 0 0 4 8 0 0 13 0 0 0 17 0 8 0 0 g 0 0 0 7 8 7 4 0 17 0 0 0 5 0 0 t 0 0 8 0 1 1 0 0 0 0 0 0 0 0 0

bin_FlyReg_FBgn0045759_shift2 (bin_FlyReg_FBgn0045759)
; oligos_7nt_mkv5_m10 versus bin_FlyReg_FBgn0045759; m=3/3; ncol2=10; w=-2; offset=-2; strand=D; shift=2; score=0.463785; --TAAACArmGA--- ; cor=; Ncor= a 0 0 0 4 4 4 0 5 3 2 0 4 0 0 0 c 0 0 0 0 0 1 5 0 0 2 0 0 0 0 0 g 0 0 0 0 0 0 0 0 2 1 5 1 0 0 0 t 0 0 5 1 1 0 0 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m7_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m7_shift0 (oligos_7nt_mkv5_m7)
; oligos_7nt_mkv5_m7; m=0 (reference); ncol1=14; shift=0; ncol=14; ctCTCTyTCTCTCt ; Alignment reference a 503 585 161 215 120 150 166 109 121 141 154 241 435 595 c 4268 736 5741 282 5809 301 4049 266 5870 243 5779 444 4387 960 g 471 820 143 252 136 244 156 293 76 286 147 332 524 719 t 1206 4307 403 5699 383 5753 2077 5780 381 5778 368 5431 1102 4174

Trl_FlyReg_FBgn0013263_shift3 (Trl_FlyReg_FBgn0013263)
; oligos_7nt_mkv5_m7 versus Trl_FlyReg_FBgn0013263; m=1/2; ncol2=10; w=0; offset=3; strand=D; shift=3; score=0.582354; ---yykCTCTCty- ; cor=; Ncor= a 0 0 0 4 6 12 0 3 1 13 5 7 9 0 c 0 0 0 22 23 6 64 0 70 0 54 13 33 0 g 0 0 0 9 11 30 3 14 0 2 7 11 10 0 t 0 0 0 36 31 23 4 54 0 56 5 40 19 0

ken_SANGER_10_FBgn0011236_rc_shift3 (ken_SANGER_10_FBgn0011236_rc)
; oligos_7nt_mkv5_m7 versus ken_SANGER_10_FBgn0011236_rc; m=2/2; ncol2=9; w=0; offset=3; strand=R; shift=3; score=0.450205; ---ACTTTCwCy-- ; cor=; Ncor= a 0 0 0 17 0 0 0 1 0 8 0 0 0 0 c 0 0 0 3 24 0 0 0 24 1 22 14 0 0 g 0 0 0 4 0 0 0 0 0 2 0 1 0 0 t 0 0 0 0 0 24 24 23 0 13 2 9 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m8_shift3 ; 12 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m8_shift3 (oligos_6nt_mkv4_m8)
; oligos_6nt_mkv4_m8; m=0 (reference); ncol1=10; shift=3; ncol=13; ---mrCAAAACam ; Alignment reference a 0 0 0 588 575 0 1505 1527 1517 1531 0 700 535 c 0 0 0 401 285 1520 0 0 0 0 1533 288 428 g 0 0 0 275 408 0 3 0 1 0 0 317 327 t 0 0 0 269 265 13 25 6 15 2 0 228 243

Ara_Cell_FBgn0015904_shift4 (Ara_Cell_FBgn0015904)
; oligos_6nt_mkv4_m8 versus Ara_Cell_FBgn0015904; m=1/11; ncol2=8; w=0; offset=1; strand=D; shift=4; score=0.582067; ----raAwwACA- ; cor=; Ncor= a 0 0 0 0 12 16 24 14 23 34 0 34 0 c 0 0 0 0 5 7 1 0 0 0 34 0 0 g 0 0 0 0 10 6 1 5 0 0 0 0 0 t 0 0 0 0 7 5 8 15 11 0 0 0 0

grh_FlyReg_FBgn0259211_rc_shift4 (grh_FlyReg_FBgn0259211_rc)
; oligos_6nt_mkv4_m8 versus grh_FlyReg_FBgn0259211_rc; m=2/11; ncol2=10; w=0; offset=1; strand=R; shift=4; score=0.580747; ----rbwrAACMA ; cor=; Ncor= a 0 0 0 0 4 0 4 4 8 7 1 2 7 c 0 0 0 0 0 3 1 1 0 0 6 6 0 g 0 0 0 0 3 2 1 3 0 1 0 0 1 t 0 0 0 0 1 3 2 0 0 0 1 0 0

pan_FlyReg_FBgn0085432_rc_shift2 (pan_FlyReg_FBgn0085432_rc)
; oligos_6nt_mkv4_m8 versus pan_FlyReg_FBgn0085432_rc; m=3/11; ncol2=8; w=-1; offset=-1; strand=R; shift=2; score=0.502901; --kWTCAAAr--- ; cor=; Ncor= a 0 0 4 17 3 3 23 22 20 8 0 0 0 c 0 0 3 0 5 20 0 1 0 3 0 0 0 g 0 0 11 0 0 2 0 0 3 10 0 0 0 t 0 0 7 8 17 0 2 2 2 4 0 0 0

jim_F1-9_SOLEXA_2.5_FBgn0027339_shift1 (jim_F1-9_SOLEXA_2.5_FBgn0027339)
; oligos_6nt_mkv4_m8 versus jim_F1-9_SOLEXA_2.5_FBgn0027339; m=4/11; ncol2=15; w=-2; offset=-2; strand=D; shift=1; score=0.489351; -rmAAaAAAAmma ; cor=; Ncor= a 0 202 124 372 414 259 411 369 349 412 159 154 240 c 0 60 190 26 6 104 1 52 5 0 222 122 55 g 0 102 43 6 0 0 4 2 64 11 40 74 74 t 0 25 50 19 3 60 7 0 5 0 2 73 54

Exd_Cell_FBgn0000611_rc_shift2 (Exd_Cell_FBgn0000611_rc)
; oligos_6nt_mkv4_m8 versus Exd_Cell_FBgn0000611_rc; m=5/11; ncol2=8; w=-1; offset=-1; strand=R; shift=2; score=0.464969; --yRTCAAAa--- ; cor=; Ncor= a 0 0 0 5 0 0 17 17 14 5 0 0 0 c 0 0 6 0 0 17 0 0 2 4 0 0 0 g 0 0 0 12 0 0 0 0 0 4 0 0 0 t 0 0 11 0 17 0 0 0 1 4 0 0 0

Ara_SOLEXA_FBgn0015904_shift6 (Ara_SOLEXA_FBgn0015904)
; oligos_6nt_mkv4_m8 versus Ara_SOLEXA_FBgn0015904; m=6/11; ncol2=6; w=0; offset=3; strand=D; shift=6; score=0.445715; ------awwACA- ; cor=; Ncor= a 0 0 0 0 0 0 155 97 193 313 0 313 0 c 0 0 0 0 0 0 36 0 0 0 313 0 0 g 0 0 0 0 0 0 44 45 38 0 0 0 0 t 0 0 0 0 0 0 78 171 82 0 0 0 0

exd_FlyReg_FBgn0000611_rc_shift0 (exd_FlyReg_FBgn0000611_rc)
; oligos_6nt_mkv4_m8 versus exd_FlyReg_FBgn0000611_rc; m=7/11; ncol2=10; w=-3; offset=-3; strand=R; shift=0; score=0.433853; twrawyrAAA--- ; cor=; Ncor= a 1 4 3 3 3 1 2 6 5 5 0 0 0 c 1 0 1 1 0 3 1 0 0 1 0 0 0 g 1 0 2 1 0 0 2 0 0 0 0 0 0 t 3 2 0 1 3 2 1 0 1 0 0 0 0

Mirr_SOLEXA_FBgn0014343_shift6 (Mirr_SOLEXA_FBgn0014343)
; oligos_6nt_mkv4_m8 versus Mirr_SOLEXA_FBgn0014343; m=8/11; ncol2=6; w=0; offset=3; strand=D; shift=6; score=0.425234; ------wwwACA- ; cor=; Ncor= a 0 0 0 0 0 0 550 410 782 1415 0 1415 0 c 0 0 0 0 0 0 158 93 0 0 1415 0 0 g 0 0 0 0 0 0 327 282 204 0 0 0 0 t 0 0 0 0 0 0 380 630 429 0 0 0 0

sage_da_SANGER_5_FBgn0037672_shift6 (sage_da_SANGER_5_FBgn0037672)
; oligos_6nt_mkv4_m8 versus sage_da_SANGER_5_FBgn0037672; m=9/11; ncol2=11; w=0; offset=3; strand=D; shift=6; score=0.416231; ------rAAMCAs ; cor=; Ncor= a 0 0 0 0 0 0 12 17 21 16 0 23 0 c 0 0 0 0 0 0 0 3 2 6 23 0 10 g 0 0 0 0 0 0 6 3 0 1 0 0 9 t 0 0 0 0 0 0 5 0 0 0 0 0 4

Side_SANGER_5_FBgn0032741_shift6 (Side_SANGER_5_FBgn0032741)
; oligos_6nt_mkv4_m8 versus Side_SANGER_5_FBgn0032741; m=10/11; ncol2=11; w=0; offset=3; strand=D; shift=6; score=0.416231; ------rAAMCAs ; cor=; Ncor= a 0 0 0 0 0 0 12 17 21 16 0 23 0 c 0 0 0 0 0 0 0 3 2 6 23 0 10 g 0 0 0 0 0 0 6 3 0 1 0 0 9 t 0 0 0 0 0 0 5 0 0 0 0 0 4

sage_da_SANGER_5_FBgn0000413_shift6 (sage_da_SANGER_5_FBgn0000413)
; oligos_6nt_mkv4_m8 versus sage_da_SANGER_5_FBgn0000413; m=11/11; ncol2=11; w=0; offset=3; strand=D; shift=6; score=0.416231; ------rAAMCAs ; cor=; Ncor= a 0 0 0 0 0 0 12 17 21 16 0 23 0 c 0 0 0 0 0 0 0 3 2 6 23 0 10 g 0 0 0 0 0 0 6 3 0 1 0 0 9 t 0 0 0 0 0 0 5 0 0 0 0 0 4

One-to-n matrix alignment; reference matrix: dyads_m3_shift0 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m3_shift0 (dyads_m3)
; dyads_m3; m=0 (reference); ncol1=14; shift=0; ncol=14; agCAGCAGCAGCag ; Alignment reference a 3023 732 205 4256 205 120 4427 196 120 4310 275 188 3102 833 c 572 721 4047 152 229 4354 108 164 4365 138 232 4152 534 744 g 704 2845 257 245 4149 96 157 4245 93 192 4045 171 729 2643 t 468 469 258 114 184 197 75 162 189 127 215 256 402 547

odd_NAR_FBgn0002985_shift0 (odd_NAR_FBgn0002985)
; dyads_m3 versus odd_NAR_FBgn0002985; m=1/5; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.570072; mmCAGTAGCAv--- ; cor=; Ncor= a 7 10 0 12 0 0 15 0 0 11 5 0 0 0 c 5 5 14 0 0 0 0 0 15 3 4 0 0 0 g 0 0 1 3 15 0 0 15 0 1 6 0 0 0 t 3 0 0 0 0 15 0 0 0 0 0 0 0 0

odd_NBT_5_FBgn0002985_rc_shift0 (odd_NBT_5_FBgn0002985_rc)
; dyads_m3 versus odd_NBT_5_FBgn0002985_rc; m=2/5; ncol2=9; w=0; offset=0; strand=R; shift=0; score=0.46271; wMCAGTAGC----- ; cor=; Ncor= a 9 16 0 18 0 0 23 0 0 0 0 0 0 0 c 5 6 23 0 0 0 0 0 23 0 0 0 0 0 g 0 0 0 5 23 0 0 23 0 0 0 0 0 0 t 9 1 0 0 0 23 0 0 0 0 0 0 0 0

odd_NBT_1.5_FBgn0002985_rc_shift0 (odd_NBT_1.5_FBgn0002985_rc)
; dyads_m3 versus odd_NBT_1.5_FBgn0002985_rc; m=3/5; ncol2=9; w=0; offset=0; strand=R; shift=0; score=0.461044; wmCrGWAGC----- ; cor=; Ncor= a 8 6 1 12 0 6 20 0 0 0 0 0 0 0 c 2 11 21 0 0 0 0 2 19 0 0 0 0 0 g 2 2 0 10 22 0 0 20 1 0 0 0 0 0 t 10 3 0 0 0 16 2 0 2 0 0 0 0 0

CG11504_SANGER_5_FBgn0039733_shift5 (CG11504_SANGER_5_FBgn0039733)
; dyads_m3 versus CG11504_SANGER_5_FBgn0039733; m=4/5; ncol2=9; w=0; offset=5; strand=D; shift=5; score=0.453636; -----YmGCAACAT ; cor=; Ncor= a 0 0 0 0 0 0 11 0 1 20 19 1 20 2 c 0 0 0 0 0 14 5 1 19 0 0 19 0 4 g 0 0 0 0 0 0 1 19 0 0 0 0 0 0 t 0 0 0 0 0 6 3 0 0 0 1 0 0 14

bowl_SANGER_5_FBgn0004893_shift1 (bowl_SANGER_5_FBgn0004893)
; dyads_m3 versus bowl_SANGER_5_FBgn0004893; m=5/5; ncol2=8; w=0; offset=1; strand=D; shift=1; score=0.416262; -mCrGwAGY----- ; cor=; Ncor= a 0 4 0 7 0 5 12 0 0 0 0 0 0 0 c 0 7 12 1 0 0 0 0 8 0 0 0 0 0 g 0 0 0 4 12 1 0 12 0 0 0 0 0 0 t 0 0 0 0 0 6 0 0 3 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m1_shift3 ; 16 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m1_shift3 (oligos_7nt_mkv5_m1)
; oligos_7nt_mkv5_m1; m=0 (reference); ncol1=11; shift=3; ncol=14; ---maAACACAAmm ; Alignment reference a 0 0 0 623 573 1802 1747 96 1720 81 1680 1767 555 640 c 0 0 0 544 437 1 22 1609 67 1586 57 20 518 599 g 0 0 0 384 449 28 54 61 58 114 51 39 350 326 t 0 0 0 329 421 49 57 114 35 99 92 54 457 315

CG10267_SANGER_5_FBgn0037446_shift2 (CG10267_SANGER_5_FBgn0037446)
; oligos_7nt_mkv5_m1 versus CG10267_SANGER_5_FBgn0037446; m=1/15; ncol2=10; w=-1; offset=-1; strand=D; shift=2; score=0.565316; --whyAACACTR-- ; cor=; Ncor= a 0 0 8 6 1 16 16 1 16 0 0 11 0 0 c 0 0 0 6 10 0 0 14 0 16 0 0 0 0 g 0 0 1 0 0 0 0 0 0 0 0 5 0 0 t 0 0 7 4 5 0 0 1 0 0 16 0 0 0

lola-PJ_SOLEXA_FBgn0005630_rc_shift0 (lola-PJ_SOLEXA_FBgn0005630_rc)
; oligos_7nt_mkv5_m1 versus lola-PJ_SOLEXA_FBgn0005630_rc; m=2/15; ncol2=15; w=-3; offset=-3; strand=R; shift=0; score=0.542897; mamvcArCATAAma ; cor=; Ncor= a 949 1076 776 839 556 2611 1471 0 2787 0 2752 2331 1167 928 c 872 696 1136 870 1665 49 0 2787 0 0 2 147 860 656 g 518 608 521 771 335 7 1227 0 0 2 9 254 494 560 t 446 405 352 305 229 117 87 0 0 2784 22 53 264 640

jim_F1-9_SOLEXA_2.5_FBgn0027339_shift3 (jim_F1-9_SOLEXA_2.5_FBgn0027339)
; oligos_7nt_mkv5_m1 versus jim_F1-9_SOLEXA_2.5_FBgn0027339; m=3/15; ncol2=15; w=0; offset=0; strand=D; shift=3; score=0.535592; ---rmAAaAAAAmm ; cor=; Ncor= a 0 0 0 202 124 372 414 259 411 369 349 412 159 154 c 0 0 0 60 190 26 6 104 1 52 5 0 222 122 g 0 0 0 102 43 6 0 0 4 2 64 11 40 74 t 0 0 0 25 50 19 3 60 7 0 5 0 2 73

Sox15_SANGER_5_FBgn0005613_shift6 (Sox15_SANGER_5_FBgn0005613)
; oligos_7nt_mkv5_m1 versus Sox15_SANGER_5_FBgn0005613; m=4/15; ncol2=8; w=0; offset=3; strand=D; shift=6; score= 0.532; ------aaACAATr ; cor=; Ncor= a 0 0 0 0 0 0 12 13 21 0 21 21 3 6 c 0 0 0 0 0 0 1 2 0 21 0 0 0 0 g 0 0 0 0 0 0 5 2 0 0 0 0 0 14 t 0 0 0 0 0 0 3 4 0 0 0 0 18 1

Ara_Cell_FBgn0015904_shift3 (Ara_Cell_FBgn0015904)
; oligos_7nt_mkv5_m1 versus Ara_Cell_FBgn0015904; m=5/15; ncol2=8; w=0; offset=0; strand=D; shift=3; score=0.51772; ---raAwwACA--- ; cor=; Ncor= a 0 0 0 12 16 24 14 23 34 0 34 0 0 0 c 0 0 0 5 7 1 0 0 0 34 0 0 0 0 g 0 0 0 10 6 1 5 0 0 0 0 0 0 0 t 0 0 0 7 5 8 15 11 0 0 0 0 0 0

Mirr_SOLEXA_FBgn0014343_shift3 (Mirr_SOLEXA_FBgn0014343)
; oligos_7nt_mkv5_m1 versus Mirr_SOLEXA_FBgn0014343; m=6/15; ncol2=6; w=0; offset=0; strand=D; shift=3; score=0.498442; ---wwwACA----- ; cor=; Ncor= a 0 0 0 550 410 782 1415 0 1415 0 0 0 0 0 c 0 0 0 158 93 0 0 1415 0 0 0 0 0 0 g 0 0 0 327 282 204 0 0 0 0 0 0 0 0 t 0 0 0 380 630 429 0 0 0 0 0 0 0 0

Ara_SOLEXA_FBgn0015904_shift3 (Ara_SOLEXA_FBgn0015904)
; oligos_7nt_mkv5_m1 versus Ara_SOLEXA_FBgn0015904; m=7/15; ncol2=6; w=0; offset=0; strand=D; shift=3; score=0.49709; ---awwACA----- ; cor=; Ncor= a 0 0 0 155 97 193 313 0 313 0 0 0 0 0 c 0 0 0 36 0 0 0 313 0 0 0 0 0 0 g 0 0 0 44 45 38 0 0 0 0 0 0 0 0 t 0 0 0 78 171 82 0 0 0 0 0 0 0 0

Caup_SOLEXA_FBgn0015919_shift3 (Caup_SOLEXA_FBgn0015919)
; oligos_7nt_mkv5_m1 versus Caup_SOLEXA_FBgn0015919; m=8/15; ncol2=6; w=0; offset=0; strand=D; shift=3; score=0.485439; ---wtwACA----- ; cor=; Ncor= a 0 0 0 999 577 1415 2904 2 2904 0 0 0 0 0 c 0 0 0 460 201 0 0 2902 0 0 0 0 0 0 g 0 0 0 626 639 511 0 0 0 0 0 0 0 0 t 0 0 0 819 1487 978 0 0 0 0 0 0 0 0

foxo_SANGER_10_FBgn0038197_rc_shift2 (foxo_SANGER_10_FBgn0038197_rc)
; oligos_7nt_mkv5_m1 versus foxo_SANGER_10_FBgn0038197_rc; m=9/15; ncol2=9; w=-1; offset=-1; strand=R; shift=2; score=0.472208; --ycrwAAACA--- ; cor=; Ncor= a 0 0 0 3 8 8 16 16 20 0 20 0 0 0 c 0 0 6 12 0 0 1 4 0 18 0 0 0 0 g 0 0 3 3 11 0 0 0 0 0 0 0 0 0 t 0 0 11 2 1 12 3 0 0 2 0 0 0 0

lola-PJ_SANGER_5_FBgn0005630_shift5 (lola-PJ_SANGER_5_FBgn0005630)
; oligos_7nt_mkv5_m1 versus lola-PJ_SANGER_5_FBgn0005630; m=10/15; ncol2=7; w=0; offset=2; strand=D; shift=5; score=0.471638; -----ArCATAA-- ; cor=; Ncor= a 0 0 0 0 0 11 5 0 12 0 12 12 0 0 c 0 0 0 0 0 0 0 12 0 0 0 0 0 0 g 0 0 0 0 0 0 7 0 0 0 0 0 0 0 t 0 0 0 0 0 1 0 0 0 12 0 0 0 0

CG5953_SANGER_5_FBgn0032587_shift2 (CG5953_SANGER_5_FBgn0032587)
; oligos_7nt_mkv5_m1 versus CG5953_SANGER_5_FBgn0032587; m=11/15; ncol2=8; w=-1; offset=-1; strand=D; shift=2; score=0.44424; --aCAAACAy---- ; cor=; Ncor= a 0 0 10 0 16 16 16 0 16 1 0 0 0 0 c 0 0 3 16 0 0 0 16 0 5 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 3 0 0 0 0 0 0 10 0 0 0 0

Mirr_Cell_FBgn0014343_shift1 (Mirr_Cell_FBgn0014343)
; oligos_7nt_mkv5_m1 versus Mirr_Cell_FBgn0014343; m=12/15; ncol2=8; w=-2; offset=-2; strand=D; shift=1; score=0.428582; -waawAACA----- ; cor=; Ncor= a 0 18 18 22 20 29 41 0 41 0 0 0 0 0 c 0 6 4 7 1 0 0 41 0 0 0 0 0 0 g 0 6 10 6 1 2 0 0 0 0 0 0 0 0 t 0 11 9 6 19 10 0 0 0 0 0 0 0 0

Caup_Cell_FBgn0015919_shift1 (Caup_Cell_FBgn0015919)
; oligos_7nt_mkv5_m1 versus Caup_Cell_FBgn0015919; m=13/15; ncol2=8; w=-2; offset=-2; strand=D; shift=1; score=0.422059; -cwwtAACA----- ; cor=; Ncor= a 0 4 9 8 4 14 19 0 19 0 0 0 0 0 c 0 9 0 0 1 0 0 19 0 0 0 0 0 0 g 0 2 3 4 2 2 0 0 0 0 0 0 0 0 t 0 4 7 7 12 3 0 0 0 0 0 0 0 0

slp2_SANGER_5_FBgn0004567_shift2 (slp2_SANGER_5_FBgn0004567)
; oligos_7nt_mkv5_m1 versus slp2_SANGER_5_FBgn0004567; m=14/15; ncol2=8; w=-1; offset=-1; strand=D; shift=2; score=0.415498; --rTAAACAa---- ; cor=; Ncor= a 0 0 6 0 18 18 18 0 18 11 0 0 0 0 c 0 0 0 1 0 0 0 18 0 3 0 0 0 0 g 0 0 12 0 0 0 0 0 0 3 0 0 0 0 t 0 0 0 17 0 0 0 0 0 1 0 0 0 0

bin_SANGER_5_FBgn0045759_shift2 (bin_SANGER_5_FBgn0045759)
; oligos_7nt_mkv5_m1 versus bin_SANGER_5_FBgn0045759; m=15/15; ncol2=7; w=-1; offset=-1; strand=D; shift=2; score=0.400116; --rTAAACA----- ; cor=; Ncor= a 0 0 9 0 20 20 20 0 19 0 0 0 0 0 c 0 0 0 0 0 0 0 20 0 0 0 0 0 0 g 0 0 10 0 0 0 0 0 0 0 0 0 0 0 t 0 0 1 20 0 0 0 0 1 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m1_shift6 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m1_shift6 (oligos_6nt_mkv4_m1)
; oligos_6nt_mkv4_m1; m=0 (reference); ncol1=11; shift=6; ncol=17; ------cycCCACAAmm ; Alignment reference a 0 0 0 0 0 0 354 335 306 0 2 1250 50 1267 1364 427 379 c 0 0 0 0 0 0 516 530 804 1437 1382 94 1304 72 17 444 541 g 0 0 0 0 0 0 254 207 179 0 16 42 44 36 33 264 277 t 0 0 0 0 0 0 320 372 155 7 44 58 46 69 30 309 247

lola-PL_SOLEXA_FBgn0005630_shift5 (lola-PL_SOLEXA_FBgn0005630)
; oligos_6nt_mkv4_m1 versus lola-PL_SOLEXA_FBgn0005630; m=1/4; ncol2=14; w=-1; offset=-1; strand=D; shift=5; score=0.555117; -----kgmmCCACcgkg ; cor=; Ncor= a 0 0 0 0 0 357 215 944 808 0 0 2061 0 361 407 457 281 c 0 0 0 0 0 322 163 968 793 2061 2061 0 2061 1099 481 334 387 g 0 0 0 0 0 600 1232 0 137 0 0 0 0 123 834 690 939 t 0 0 0 0 0 780 447 148 322 0 0 0 0 476 337 576 452

lola-PL_SANGER_2.5_FBgn0005630_rc_shift5 (lola-PL_SANGER_2.5_FBgn0005630_rc)
; oligos_6nt_mkv4_m1 versus lola-PL_SANGER_2.5_FBgn0005630_rc; m=2/4; ncol2=9; w=-1; offset=-1; strand=R; shift=5; score=0.544368; -----TGmcCCACm--- ; cor=; Ncor= a 0 0 0 0 0 2 0 4 2 0 0 11 0 4 0 0 0 c 0 0 0 0 0 0 0 7 5 11 11 0 11 6 0 0 0 g 0 0 0 0 0 0 9 0 2 0 0 0 0 0 0 0 0 t 0 0 0 0 0 8 2 0 2 0 0 0 0 1 0 0 0

Lag1_Cell_FBgn0040918_shift9 (Lag1_Cell_FBgn0040918)
; oligos_6nt_mkv4_m1 versus Lag1_Cell_FBgn0040918; m=3/4; ncol2=10; w=0; offset=3; strand=D; shift=9; score=0.440737; ---------CyACyAaa ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 17 1 0 18 12 10 c 0 0 0 0 0 0 0 0 0 19 9 2 18 12 0 0 3 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 4 4 t 0 0 0 0 0 0 0 0 0 0 10 0 0 7 0 3 2

CG7368_SOLEXA_2.5_FBgn0036179_rc_shift0 (CG7368_SOLEXA_2.5_FBgn0036179_rc)
; oligos_6nt_mkv4_m1 versus CG7368_SOLEXA_2.5_FBgn0036179_rc; m=4/4; ncol2=15; w=-6; offset=-6; strand=R; shift=0; score=0.400001; yyCCCCChCCCmChm-- ; cor=; Ncor= a 38 51 27 3 8 1 34 90 44 3 8 97 14 64 95 0 0 c 111 95 203 230 227 235 200 84 170 230 224 133 199 66 65 0 0 g 16 22 1 0 0 0 0 0 1 0 0 0 0 19 13 0 0 t 67 68 5 3 1 0 2 62 21 3 4 6 23 81 26 0 0

One-to-n matrix alignment; reference matrix: positions_6nt_m1_shift2 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m1_shift2 (positions_6nt_m1)
; positions_6nt_m1; m=0 (reference); ncol1=15; shift=2; ncol=17; --acACACrCACACrca ; Alignment reference a 0 0 2460 417 3456 98 3539 72 1434 73 3511 79 3438 73 998 561 1745 c 0 0 435 2532 54 3524 54 3551 73 3555 25 3556 91 3576 237 2074 601 g 0 0 560 284 179 63 121 74 2125 61 193 54 179 89 2345 565 858 t 0 0 350 572 116 120 91 108 173 116 76 116 97 67 225 605 601

klu_SOLEXA_5_FBgn0013469_rc_shift0 (klu_SOLEXA_5_FBgn0013469_rc)
; positions_6nt_m1 versus klu_SOLEXA_5_FBgn0013469_rc; m=1/3; ncol2=15; w=-2; offset=-2; strand=R; shift=0; score=0.541754; mmmmmCACCCmCrCm-- ; cor=; Ncor= a 132 156 135 134 155 9 378 3 3 5 315 2 226 54 156 0 0 c 152 168 188 204 298 491 6 491 485 472 168 493 10 360 138 0 0 g 82 90 85 64 24 0 48 0 5 0 6 1 230 5 54 0 0 t 91 79 95 101 26 3 71 9 10 26 14 7 37 33 75 0 0

klu_SANGER_10_FBgn0013469_rc_shift4 (klu_SANGER_10_FBgn0013469_rc)
; positions_6nt_m1 versus klu_SANGER_10_FBgn0013469_rc; m=2/3; ncol2=11; w=0; offset=2; strand=R; shift=4; score=0.535556; ----mCACCCmCrCa-- ; cor=; Ncor= a 0 0 0 0 7 0 18 0 0 0 13 0 9 0 12 0 0 c 0 0 0 0 11 20 0 20 20 19 7 20 0 16 2 0 0 g 0 0 0 0 2 0 0 0 0 0 0 0 10 0 2 0 0 t 0 0 0 0 0 0 2 0 0 1 0 0 1 3 2 0 0

CG12029_SANGER_10_FBgn0035454_rc_shift1 (CG12029_SANGER_10_FBgn0035454_rc)
; positions_6nt_m1 versus CG12029_SANGER_10_FBgn0035454_rc; m=3/3; ncol2=11; w=-1; offset=-1; strand=R; shift=1; score=0.471629; -RCCACACCCac----- ; cor=; Ncor= a 0 5 4 0 16 0 17 0 0 0 13 4 0 0 0 0 0 c 0 0 14 20 2 20 0 20 20 20 3 11 0 0 0 0 0 g 0 15 2 0 2 0 2 0 0 0 0 1 0 0 0 0 0 t 0 0 0 0 0 0 1 0 0 0 4 4 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m10_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m10_shift0 (oligos_6nt_mkv4_m10)
; oligos_6nt_mkv4_m10; m=0 (reference); ncol1=12; shift=0; ncol=12; rrAAGCAAcgvr ; Alignment reference a 589 587 1758 1825 53 108 1816 1760 386 322 537 607 c 425 404 74 41 44 1659 28 38 1074 268 486 435 g 571 645 48 40 1811 132 55 87 288 1155 600 504 t 354 303 59 33 31 40 40 54 191 194 316 393

CG3838_SANGER_5_FBgn0032130_shift2 (CG3838_SANGER_5_FBgn0032130)
; oligos_6nt_mkv4_m10 versus CG3838_SANGER_5_FBgn0032130; m=1/2; ncol2=9; w=0; offset=2; strand=D; shift=2; score=0.529153; --AwrCRACAW- ; cor=; Ncor= a 0 0 18 8 5 3 15 20 0 19 5 0 c 0 0 0 4 2 17 0 0 20 0 1 0 g 0 0 2 1 13 0 5 0 0 0 0 0 t 0 0 0 7 0 0 0 0 0 1 14 0

onecut_Cell_FBgn0028996_rc_shift1 (onecut_Cell_FBgn0028996_rc)
; oligos_6nt_mkv4_m10 versus onecut_Cell_FBgn0028996_rc; m=2/2; ncol2=7; w=0; offset=1; strand=R; shift=1; score=0.430483; -hAATCAA---- ; cor=; Ncor= a 0 6 15 15 0 0 15 12 0 0 0 0 c 0 4 0 0 0 15 0 0 0 0 0 0 g 0 0 0 0 0 0 0 2 0 0 0 0 t 0 5 0 0 15 0 0 1 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m9_shift2 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m9_shift2 (oligos_7nt_mkv5_m9)
; oligos_7nt_mkv5_m9; m=0 (reference); ncol1=13; shift=2; ncol=15; --caCAsACACAAam ; Alignment reference a 0 0 440 976 136 1526 103 1791 52 1809 40 1764 1473 795 494 c 0 0 845 301 1425 176 472 44 1715 23 1761 36 298 432 796 g 0 0 315 389 183 111 1213 34 68 39 57 49 71 334 324 t 0 0 284 218 140 71 96 15 49 13 26 35 42 323 270

CG13897_SANGER_5_FBgn0035160_shift0 (CG13897_SANGER_5_FBgn0035160)
; oligos_7nt_mkv5_m9 versus CG13897_SANGER_5_FBgn0035160; m=1/2; ncol2=11; w=-2; offset=-2; strand=D; shift=0; score=0.527934; wsrrCAGACAs---- ; cor=; Ncor= a 5 2 8 9 0 17 0 17 0 17 4 0 0 0 0 c 4 8 0 0 13 0 0 0 17 0 8 0 0 0 0 g 0 7 8 7 4 0 17 0 0 0 5 0 0 0 0 t 8 0 1 1 0 0 0 0 0 0 0 0 0 0 0

CG5953_SANGER_5_FBgn0032587_shift3 (CG5953_SANGER_5_FBgn0032587)
; oligos_7nt_mkv5_m9 versus CG5953_SANGER_5_FBgn0032587; m=2/2; ncol2=8; w=0; offset=1; strand=D; shift=3; score=0.452834; ---aCAAACAy---- ; cor=; Ncor= a 0 0 0 10 0 16 16 16 0 16 1 0 0 0 0 c 0 0 0 3 16 0 0 0 16 0 5 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 3 0 0 0 0 0 0 10 0 0 0 0

One-to-n matrix alignment; reference matrix: dyads_m2_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m2_shift0 (dyads_m2)
; dyads_m2; m=0 (reference); ncol1=17; shift=0; ncol=17; GaGAGAGAGAGAGAGaG ; Alignment reference a 1146 5072 674 6098 581 6400 516 6520 527 6554 534 6417 568 6169 757 5112 1251 c 601 904 326 610 226 569 166 521 148 520 134 571 200 633 274 1020 526 g 5388 771 6362 387 6628 275 6791 285 6812 285 6823 311 6662 380 6323 751 5329 t 505 893 278 545 205 396 167 314 153 281 149 341 210 458 286 757 534

Trl_FlyReg_FBgn0013263_rc_shift6 (Trl_FlyReg_FBgn0013263_rc)
; dyads_m2 versus Trl_FlyReg_FBgn0013263_rc; m=1/1; ncol2=10; w=0; offset=6; strand=R; shift=6; score=0.504203; ------raGAGAGmrr- ; cor=; Ncor= a 0 0 0 0 0 0 19 40 5 56 0 54 4 23 31 36 0 c 0 0 0 0 0 0 10 11 7 2 0 14 3 30 11 9 0 g 0 0 0 0 0 0 33 13 54 0 70 0 64 6 23 22 0 t 0 0 0 0 0 0 9 7 5 13 1 3 0 12 6 4 0

One-to-n matrix alignment; reference matrix: dyads_m6_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m6_shift1 (dyads_m6)
; dyads_m6; m=0 (reference); ncol1=13; shift=1; ncol=14; -camACACACAyac ; Alignment reference a 0 641 1787 1910 2920 40 2982 31 2973 30 2915 148 1847 393 c 0 1706 619 936 41 2945 17 2942 28 2937 41 987 432 1939 g 0 346 362 48 33 15 30 21 19 24 30 98 415 351 t 0 345 270 144 44 38 9 44 18 47 52 1805 344 355

CG16778_SANGER_5_FBgn0003715_shift5 (CG16778_SANGER_5_FBgn0003715)
; dyads_m6 versus CG16778_SANGER_5_FBgn0003715; m=1/3; ncol2=8; w=0; offset=4; strand=D; shift=5; score=0.503517; -----CACAyAYG- ; cor=; Ncor= a 0 0 0 0 0 0 18 0 20 0 17 0 0 0 c 0 0 0 0 0 15 1 20 0 9 0 6 1 0 g 0 0 0 0 0 2 0 0 0 0 3 0 18 0 t 0 0 0 0 0 1 0 0 0 11 0 14 1 0

CG5953_SANGER_5_FBgn0032587_shift4 (CG5953_SANGER_5_FBgn0032587)
; dyads_m6 versus CG5953_SANGER_5_FBgn0032587; m=2/3; ncol2=8; w=0; offset=3; strand=D; shift=4; score=0.486142; ----aCAAACAy-- ; cor=; Ncor= a 0 0 0 0 10 0 16 16 16 0 16 1 0 0 c 0 0 0 0 3 16 0 0 0 16 0 5 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 3 0 0 0 0 0 0 10 0 0

foxo_SANGER_10_FBgn0038197_rc_shift0 (foxo_SANGER_10_FBgn0038197_rc)
; dyads_m6 versus foxo_SANGER_10_FBgn0038197_rc; m=3/3; ncol2=9; w=-1; offset=-1; strand=R; shift=0; score=0.421793; ycrwAAACA----- ; cor=; Ncor= a 0 3 8 8 16 16 20 0 20 0 0 0 0 0 c 6 12 0 0 1 4 0 18 0 0 0 0 0 0 g 3 3 11 0 0 0 0 0 0 0 0 0 0 0 t 11 2 1 12 3 0 0 2 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m8_shift1 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m8_shift1 (oligos_7nt_mkv5_m8)
; oligos_7nt_mkv5_m8; m=0 (reference); ncol1=16; shift=1; ncol=17; -ACACACACACACACAC ; Alignment reference a 0 8417 950 10951 81 10965 77 11008 365 10967 66 10969 97 10629 540 7871 1079 c 0 930 9006 72 10941 81 10953 55 8641 61 10901 68 10841 199 8182 1031 7805 g 0 1252 434 157 68 126 82 127 261 144 98 141 131 216 1684 1414 1137 t 0 646 855 65 155 73 133 55 1978 73 180 67 176 201 839 929 1224

klu_SANGER_10_FBgn0013469_rc_shift1 (klu_SANGER_10_FBgn0013469_rc)
; oligos_7nt_mkv5_m8 versus klu_SANGER_10_FBgn0013469_rc; m=1/2; ncol2=11; w=0; offset=0; strand=R; shift=1; score=0.500964; -mCACCCmCrCa----- ; cor=; Ncor= a 0 7 0 18 0 0 0 13 0 9 0 12 0 0 0 0 0 c 0 11 20 0 20 20 19 7 20 0 16 2 0 0 0 0 0 g 0 2 0 0 0 0 0 0 0 10 0 2 0 0 0 0 0 t 0 0 0 2 0 0 1 0 0 1 3 2 0 0 0 0 0

CG12029_SANGER_10_FBgn0035454_rc_shift0 (CG12029_SANGER_10_FBgn0035454_rc)
; oligos_7nt_mkv5_m8 versus CG12029_SANGER_10_FBgn0035454_rc; m=2/2; ncol2=11; w=-1; offset=-1; strand=R; shift=0; score=0.419445; RCCACACCCac------ ; cor=; Ncor= a 5 4 0 16 0 17 0 0 0 13 4 0 0 0 0 0 0 c 0 14 20 2 20 0 20 20 20 3 11 0 0 0 0 0 0 g 15 2 0 2 0 2 0 0 0 0 1 0 0 0 0 0 0 t 0 0 0 0 0 1 0 0 0 4 4 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m5_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m5_shift0 (oligos_6nt_mkv4_m5)
; oligos_6nt_mkv4_m5; m=0 (reference); ncol1=16; shift=0; ncol=16; gtsTGTGyGTGTsTgt ; Alignment reference a 214 180 62 30 40 21 22 21 20 16 41 12 98 13 202 129 c 294 260 792 62 50 39 43 1077 48 32 62 38 611 57 217 297 g 895 280 760 38 1580 14 1604 24 1593 23 1556 28 898 67 1041 211 t 294 977 83 1567 27 1623 28 575 36 1626 38 1619 90 1560 237 1060

klu_SANGER_10_FBgn0013469_shift5 (klu_SANGER_10_FBgn0013469)
; oligos_6nt_mkv4_m5 versus klu_SANGER_10_FBgn0013469; m=1/1; ncol2=11; w=0; offset=5; strand=D; shift=5; score=0.491536; -----tGyGkGGGTGk ; cor=; Ncor= a 0 0 0 0 0 2 3 1 0 0 1 0 0 2 0 0 c 0 0 0 0 0 2 0 10 0 0 0 0 0 0 0 2 g 0 0 0 0 0 2 16 0 20 7 19 20 20 0 20 11 t 0 0 0 0 0 12 0 9 0 13 0 0 0 18 0 7

One-to-n matrix alignment; reference matrix: dyads_m10_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m10_shift0 (dyads_m10)
; dyads_m10; m=0 (reference); ncol1=18; shift=0; ncol=18; ACACACACACACACrCAC ; Alignment reference a 7238 1045 9369 539 9735 122 9879 128 9866 92 9777 133 9544 141 6688 222 6989 910 c 1135 7513 282 7314 129 9753 75 9760 58 9807 42 9764 113 9671 320 9327 744 7303 g 1101 600 342 286 208 86 171 64 179 69 269 87 355 180 2725 284 1578 877 t 739 1055 220 2074 141 252 88 261 110 245 125 229 201 221 480 380 902 1123

klu_SANGER_10_FBgn0013469_rc_shift6 (klu_SANGER_10_FBgn0013469_rc)
; dyads_m10 versus klu_SANGER_10_FBgn0013469_rc; m=1/1; ncol2=11; w=0; offset=6; strand=R; shift=6; score=0.463069; ------mCACCCmCrCa- ; cor=; Ncor= a 0 0 0 0 0 0 7 0 18 0 0 0 13 0 9 0 12 0 c 0 0 0 0 0 0 11 20 0 20 20 19 7 20 0 16 2 0 g 0 0 0 0 0 0 2 0 0 0 0 0 0 0 10 0 2 0 t 0 0 0 0 0 0 0 0 2 0 0 1 0 0 1 3 2 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m6_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m6_shift0 (oligos_7nt_mkv5_m6)
; oligos_7nt_mkv5_m6; m=0 (reference); ncol1=17; shift=0; ncol=17; tgsTGCTGyTGCTGytg ; Alignment reference a 167 226 113 47 59 58 27 40 40 30 21 38 39 45 109 190 250 c 335 230 1115 82 31 1919 38 44 1312 37 40 1972 68 82 1155 261 291 g 355 1425 770 45 2066 113 50 2073 102 35 2098 89 51 2015 200 279 1342 t 1343 319 202 2026 44 110 2085 43 746 2098 41 101 2042 58 736 1470 317

odd_NAR_FBgn0002985_rc_shift5 (odd_NAR_FBgn0002985_rc)
; oligos_7nt_mkv5_m6 versus odd_NAR_FBgn0002985_rc; m=1/3; ncol2=11; w=0; offset=5; strand=R; shift=5; score=0.459648; -----bTGCTACTGkk- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 15 0 0 0 0 3 0 c 0 0 0 0 0 6 1 0 15 0 0 15 3 1 0 0 0 g 0 0 0 0 0 4 3 15 0 0 0 0 0 14 5 5 0 t 0 0 0 0 0 5 11 0 0 15 0 0 12 0 10 7 0

Aef1_SANGER_5_FBgn0005694_rc_shift1 (Aef1_SANGER_5_FBgn0005694_rc)
; oligos_7nt_mkv5_m6 versus Aef1_SANGER_5_FBgn0005694_rc; m=2/3; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.453241; -GKTGTTGTTGy----- ; cor=; Ncor= a 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 g 0 9 3 0 12 0 0 12 0 0 12 2 0 0 0 0 0 t 0 2 9 12 0 12 12 0 12 12 0 6 0 0 0 0 0

CG11504_SANGER_5_FBgn0039733_rc_shift5 (CG11504_SANGER_5_FBgn0039733_rc)
; oligos_7nt_mkv5_m6 versus CG11504_SANGER_5_FBgn0039733_rc; m=3/3; ncol2=9; w=0; offset=5; strand=R; shift=5; score=0.406288; -----ATGTTGCkR--- ; cor=; Ncor= a 0 0 0 0 0 14 0 0 1 0 0 0 3 6 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 19 1 0 0 0 0 g 0 0 0 0 0 4 0 19 0 0 19 1 5 14 0 0 0 t 0 0 0 0 0 2 20 1 19 20 1 0 11 0 0 0 0

One-to-n matrix alignment; reference matrix: positions_6nt_m3_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m3_shift0 (positions_6nt_m3)
; positions_6nt_m3; m=0 (reference); ncol1=24; shift=0; ncol=24; gtGtGTGTGTGyGTGTGtkkkkkk ; Alignment reference a 706 680 497 902 143 113 101 66 117 72 126 244 108 119 146 143 227 472 711 663 797 820 1016 1069 c 591 913 397 618 94 134 36 175 33 117 58 1474 68 153 60 282 133 842 437 698 669 700 902 953 g 3680 646 4351 350 5253 63 5414 32 5399 30 5324 123 5316 75 5255 126 4915 1228 2606 1991 2070 2228 2242 1569 t 625 3363 357 3732 112 5292 51 5329 53 5383 94 3761 110 5255 141 5051 327 3060 1848 2250 2066 1854 1442 2011

klu_SOLEXA_5_FBgn0013469_shift7 (klu_SOLEXA_5_FBgn0013469)
; positions_6nt_m3 versus klu_SOLEXA_5_FBgn0013469; m=1/1; ncol2=15; w=0; offset=7; strand=D; shift=7; score=0.449315; -------kGyGkGGGTGkkkkk-- ; cor=; Ncor= a 0 0 0 0 0 0 0 75 33 37 7 14 26 10 9 71 3 26 101 95 79 91 0 0 c 0 0 0 0 0 0 0 54 5 230 1 6 0 5 0 48 0 24 64 85 90 82 0 0 g 0 0 0 0 0 0 0 138 360 10 493 168 472 485 491 6 491 298 204 188 168 152 0 0 t 0 0 0 0 0 0 0 156 54 226 2 315 5 3 3 378 9 155 134 135 156 132 0 0

One-to-n matrix alignment; reference matrix: positions_6nt_m9_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m9_shift0 (positions_6nt_m9)
; positions_6nt_m9; m=0 (reference); ncol1=24; shift=0; ncol=24; acaCacACACACACACACACACac ; Alignment reference a 5382 1628 6496 1163 6198 1950 6965 341 9355 152 9447 127 9572 127 7544 82 9553 64 9347 116 7140 653 6251 1014 c 1768 5987 1310 7182 1877 6536 1286 9166 169 9522 71 9641 64 9499 131 9623 49 9636 85 9519 511 7825 1066 6677 g 1480 953 1117 718 1014 540 1076 151 256 61 300 49 195 105 1952 60 217 54 337 129 1051 660 1499 1023 t 1328 1390 1035 895 869 932 631 300 178 223 140 141 127 227 331 193 139 204 189 194 1256 820 1142 1244

klu_SOLEXA_5_FBgn0013469_rc_shift2 (klu_SOLEXA_5_FBgn0013469_rc)
; positions_6nt_m9 versus klu_SOLEXA_5_FBgn0013469_rc; m=1/1; ncol2=15; w=0; offset=2; strand=R; shift=2; score=0.443304; --mmmmmCACCCmCrCm------- ; cor=; Ncor= a 0 0 132 156 135 134 155 9 378 3 3 5 315 2 226 54 156 0 0 0 0 0 0 0 c 0 0 152 168 188 204 298 491 6 491 485 472 168 493 10 360 138 0 0 0 0 0 0 0 g 0 0 82 90 85 64 24 0 48 0 5 0 6 1 230 5 54 0 0 0 0 0 0 0 t 0 0 91 79 95 101 26 3 71 9 10 26 14 7 37 33 75 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: dyads_m9_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m9_shift0 (dyads_m9)
; dyads_m9; m=0 (reference); ncol1=14; shift=0; ncol=14; caAACACACACmca ; Alignment reference a 665 1337 1976 2446 92 2530 67 2498 59 2477 62 891 527 1266 c 1305 637 478 94 2450 56 2487 87 2538 99 2482 1505 1329 555 g 367 345 63 67 43 57 48 47 32 30 70 152 464 441 t 356 374 176 86 108 50 91 61 64 87 79 145 373 431

CG5953_SANGER_5_FBgn0032587_shift3 (CG5953_SANGER_5_FBgn0032587)
; dyads_m9 versus CG5953_SANGER_5_FBgn0032587; m=1/3; ncol2=8; w=0; offset=3; strand=D; shift=3; score=0.414153; ---aCAAACAy--- ; cor=; Ncor= a 0 0 0 10 0 16 16 16 0 16 1 0 0 0 c 0 0 0 3 16 0 0 0 16 0 5 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 3 0 0 0 0 0 0 10 0 0 0

CG16778_SANGER_5_FBgn0003715_shift4 (CG16778_SANGER_5_FBgn0003715)
; dyads_m9 versus CG16778_SANGER_5_FBgn0003715; m=2/3; ncol2=8; w=0; offset=4; strand=D; shift=4; score=0.407586; ----CACAyAYG-- ; cor=; Ncor= a 0 0 0 0 0 18 0 20 0 17 0 0 0 0 c 0 0 0 0 15 1 20 0 9 0 6 1 0 0 g 0 0 0 0 2 0 0 0 0 3 0 18 0 0 t 0 0 0 0 1 0 0 0 11 0 14 1 0 0

Ara_Cell_FBgn0015904_shift0 (Ara_Cell_FBgn0015904)
; dyads_m9 versus Ara_Cell_FBgn0015904; m=3/3; ncol2=8; w=0; offset=0; strand=D; shift=0; score=0.40058; raAwwACA------ ; cor=; Ncor= a 12 16 24 14 23 34 0 34 0 0 0 0 0 0 c 5 7 1 0 0 0 34 0 0 0 0 0 0 0 g 10 6 1 5 0 0 0 0 0 0 0 0 0 0 t 7 5 8 15 11 0 0 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv5_m2_shift3 (oligos_7nt_mkv5_m2)				; oligos_7nt_mkv5_m2; m=0 (reference); ncol1=11; shift=3; ncol=14; ---hhCCACACCmm ; Alignment reference a 0 0 0 610 665 56 47 1899 120 1884 31 37 665 597 c 0 0 0 779 651 2175 2075 185 2039 272 2139 2175 670 740 g 0 0 0 352 414 33 72 129 81 56 70 39 560 463 t 0 0 0 597 608 74 144 125 98 126 98 87 443 538
CG9895_SOLEXA_5_FBgn0034810_rc_shift3 (CG9895_SOLEXA_5_FBgn0034810_rc)				; oligos_7nt_mkv5_m2 versus CG9895_SOLEXA_5_FBgn0034810_rc; m=1/18; ncol2=11; w=0; offset=0; strand=R; shift=3; score=0.793245; ---rrCCACrCCCa ; cor=; Ncor= a 0 0 0 274 376 101 86 760 27 327 31 31 24 494 c 0 0 0 126 29 781 818 212 961 0 959 957 921 200 g 0 0 0 425 503 45 18 15 0 644 0 0 0 52 t 0 0 0 109 73 63 68 3 2 19 0 2 44 239
CG12029_SANGER_10_FBgn0035454_rc_shift4 (CG12029_SANGER_10_FBgn0035454_rc)				; oligos_7nt_mkv5_m2 versus CG12029_SANGER_10_FBgn0035454_rc; m=2/18; ncol2=11; w=0; offset=1; strand=R; shift=4; score=0.707066; ----RCCACACCCa ; cor=; Ncor= a 0 0 0 0 5 4 0 16 0 17 0 0 0 13 c 0 0 0 0 0 14 20 2 20 0 20 20 20 3 g 0 0 0 0 15 2 0 2 0 2 0 0 0 0 t 0 0 0 0 0 0 0 0 0 1 0 0 0 4
CG12029_SOLEXA_5_FBgn0035454_rc_shift1 (CG12029_SOLEXA_5_FBgn0035454_rc)				; oligos_7nt_mkv5_m2 versus CG12029_SOLEXA_5_FBgn0035454_rc; m=3/18; ncol2=15; w=-2; offset=-2; strand=R; shift=1; score=0.635932; -mvrRCCACACCCa ; cor=; Ncor= a 0 311 274 360 291 135 12 912 9 742 4 33 34 595 c 0 334 331 174 0 911 1052 109 1058 0 1062 1031 980 203 g 0 170 278 328 767 21 0 44 0 237 0 3 2 19 t 0 175 164 214 18 9 12 11 9 97 10 9 60 259
CG9895_SANGER_10_FBgn0034810_rc_shift4 (CG9895_SANGER_10_FBgn0034810_rc)				; oligos_7nt_mkv5_m2 versus CG9895_SANGER_10_FBgn0034810_rc; m=4/18; ncol2=12; w=0; offset=1; strand=R; shift=4; score=0.627766; ----rCCACrCCCw ; cor=; Ncor= a 0 0 0 0 11 3 2 20 1 10 1 0 0 14 c 0 0 0 0 0 20 21 4 23 0 22 22 22 2 g 0 0 0 0 13 1 0 0 0 14 0 2 0 2 t 0 0 0 0 0 0 1 0 0 0 1 0 2 6
CG3065_F1-3_SANGER_2.5_FBgn0034946_rc_shift4 (CG3065_F1-3_SANGER_2.5_FBgn0034946_rc)				; oligos_7nt_mkv5_m2 versus CG3065_F1-3_SANGER_2.5_FBgn0034946_rc; m=5/18; ncol2=11; w=0; offset=1; strand=R; shift=4; score=0.608842; ----rCCACGCCCm ; cor=; Ncor= a 0 0 0 0 7 2 0 20 0 0 0 0 0 12 c 0 0 0 0 0 18 21 1 21 0 21 21 20 6 g 0 0 0 0 13 1 0 0 0 21 0 0 0 1 t 0 0 0 0 0 0 0 0 0 0 0 0 1 2
CG3065_F1-5_SOLEXA_2.5_FBgn0034946_rc_shift2 (CG3065_F1-5_SOLEXA_2.5_FBgn0034946_rc)				; oligos_7nt_mkv5_m2 versus CG3065_F1-5_SOLEXA_2.5_FBgn0034946_rc; m=6/18; ncol2=14; w=-1; offset=-1; strand=R; shift=2; score=0.582618; --crrCCACGCCCm ; cor=; Ncor= a 0 0 308 363 440 154 25 1086 19 54 53 32 24 593 c 0 0 435 296 39 1022 1265 199 1290 9 1263 1276 1125 610 g 0 0 291 384 766 62 0 27 0 1205 0 0 1 20 t 0 0 218 276 74 81 29 7 10 51 3 11 169 96
luna_SOLEXA_5_FBgn0040765_rc_shift3 (luna_SOLEXA_5_FBgn0040765_rc)				; oligos_7nt_mkv5_m2 versus luna_SOLEXA_5_FBgn0040765_rc; m=7/18; ncol2=14; w=0; offset=0; strand=R; shift=3; score=0.579885; ---grCCACGCCCw ; cor=; Ncor= a 0 0 0 132 155 85 73 434 5 126 18 29 18 276 c 0 0 0 68 26 463 462 149 607 1 588 579 558 120 g 0 0 0 283 396 27 18 24 0 468 5 0 0 36 t 0 0 0 84 35 37 59 5 0 17 1 4 36 180
CG3065_F1-3_SOLEXA_2.5_FBgn0034946_rc_shift2 (CG3065_F1-3_SOLEXA_2.5_FBgn0034946_rc)				; oligos_7nt_mkv5_m2 versus CG3065_F1-3_SOLEXA_2.5_FBgn0034946_rc; m=8/18; ncol2=15; w=-1; offset=-1; strand=R; shift=2; score=0.531519; --carCCACGCCCm ; cor=; Ncor= a 0 0 47 105 85 40 1 234 11 4 9 10 13 171 c 0 0 110 52 7 211 260 29 249 0 253 253 217 77 g 0 0 53 59 166 8 0 0 0 255 0 0 0 1 t 0 0 47 44 5 4 2 0 3 4 1 0 33 14
klu_SOLEXA_5_FBgn0013469_rc_shift3 (klu_SOLEXA_5_FBgn0013469_rc)				; oligos_7nt_mkv5_m2 versus klu_SOLEXA_5_FBgn0013469_rc; m=9/18; ncol2=15; w=0; offset=0; strand=R; shift=3; score=0.523494; ---mmmmmCACCCm ; cor=; Ncor= a 0 0 0 132 156 135 134 155 9 378 3 3 5 315 c 0 0 0 152 168 188 204 298 491 6 491 485 472 168 g 0 0 0 82 90 85 64 24 0 48 0 5 0 6 t 0 0 0 91 79 95 101 26 3 71 9 10 26 14
Opa_SANGER_5_FBgn0003002_shift0 (Opa_SANGER_5_FBgn0003002)				; oligos_7nt_mkv5_m2 versus Opa_SANGER_5_FBgn0003002; m=10/18; ncol2=13; w=-3; offset=-3; strand=D; shift=0; score=0.501186; mkmmMCCCCmCyR- ; cor=; Ncor= a 7 2 4 4 3 1 0 0 0 8 0 0 3 0 c 3 0 5 7 9 9 12 11 12 3 11 8 0 0 g 1 5 2 1 0 2 0 1 0 1 1 0 9 0 t 1 5 1 0 0 0 0 0 0 0 0 4 0 0
lola-PL_SANGER_2.5_FBgn0005630_rc_shift1 (lola-PL_SANGER_2.5_FBgn0005630_rc)				; oligos_7nt_mkv5_m2 versus lola-PL_SANGER_2.5_FBgn0005630_rc; m=11/18; ncol2=9; w=-2; offset=-2; strand=R; shift=1; score=0.48165; -TGmcCCACm---- ; cor=; Ncor= a 0 2 0 4 2 0 0 11 0 4 0 0 0 0 c 0 0 0 7 5 11 11 0 11 6 0 0 0 0 g 0 0 9 0 2 0 0 0 0 0 0 0 0 0 t 0 8 2 0 2 0 0 0 0 1 0 0 0 0
CG31782-F9-11_SOLEXA_FBgn0051782_rc_shift6 (CG31782-F9-11_SOLEXA_FBgn0051782_rc)				; oligos_7nt_mkv5_m2 versus CG31782-F9-11_SOLEXA_FBgn0051782_rc; m=12/18; ncol2=11; w=0; offset=3; strand=R; shift=6; score=0.464156; ------ctCACCac ; cor=; Ncor= a 0 0 0 0 0 0 269 617 42 2023 0 0 1676 407 c 0 0 0 0 0 0 1324 287 1979 143 2554 2552 582 1464 g 0 0 0 0 0 0 584 195 25 0 0 0 27 305 t 0 0 0 0 0 0 375 1453 506 386 0 1 269 377
ac_da_SANGER_5_FBgn0000022_shift7 (ac_da_SANGER_5_FBgn0000022)				; oligos_7nt_mkv5_m2 versus ac_da_SANGER_5_FBgn0000022; m=13/18; ncol2=8; w=0; offset=4; strand=D; shift=7; score=0.436854; -------rCACCTG ; cor=; Ncor= a 0 0 0 0 0 0 0 10 0 19 0 0 0 0 c 0 0 0 0 0 0 0 1 19 0 18 19 0 0 g 0 0 0 0 0 0 0 7 0 0 1 0 0 19 t 0 0 0 0 0 0 0 1 0 0 0 0 19 0
ac_da_SANGER_5_FBgn0000413_shift7 (ac_da_SANGER_5_FBgn0000413)				; oligos_7nt_mkv5_m2 versus ac_da_SANGER_5_FBgn0000413; m=14/18; ncol2=8; w=0; offset=4; strand=D; shift=7; score=0.436854; -------rCACCTG ; cor=; Ncor= a 0 0 0 0 0 0 0 10 0 19 0 0 0 0 c 0 0 0 0 0 0 0 1 19 0 18 19 0 0 g 0 0 0 0 0 0 0 7 0 0 1 0 0 19 t 0 0 0 0 0 0 0 1 0 0 0 0 19 0
sc_da_SANGER_10_FBgn0004170_shift7 (sc_da_SANGER_10_FBgn0004170)				; oligos_7nt_mkv5_m2 versus sc_da_SANGER_10_FBgn0004170; m=15/18; ncol2=8; w=0; offset=4; strand=D; shift=7; score=0.428959; -------rCACCTG ; cor=; Ncor= a 0 0 0 0 0 0 0 11 0 24 0 0 0 0 c 0 0 0 0 0 0 0 5 23 0 21 24 0 0 g 0 0 0 0 0 0 0 7 0 0 1 0 0 24 t 0 0 0 0 0 0 0 0 0 0 2 0 24 0
sc_da_SANGER_10_FBgn0000413_shift7 (sc_da_SANGER_10_FBgn0000413)				; oligos_7nt_mkv5_m2 versus sc_da_SANGER_10_FBgn0000413; m=16/18; ncol2=8; w=0; offset=4; strand=D; shift=7; score=0.428959; -------rCACCTG ; cor=; Ncor= a 0 0 0 0 0 0 0 11 0 24 0 0 0 0 c 0 0 0 0 0 0 0 5 23 0 21 24 0 0 g 0 0 0 0 0 0 0 7 0 0 1 0 0 24 t 0 0 0 0 0 0 0 0 0 0 2 0 24 0
HLH54F_da_SANGER_5_FBgn0022740_shift6 (HLH54F_da_SANGER_5_FBgn0022740)				; oligos_7nt_mkv5_m2 versus HLH54F_da_SANGER_5_FBgn0022740; m=17/18; ncol2=11; w=0; offset=3; strand=D; shift=6; score=0.409233; ------mmCACCTG ; cor=; Ncor= a 0 0 0 0 0 0 12 12 0 24 0 0 0 0 c 0 0 0 0 0 0 10 10 23 0 24 23 1 0 g 0 0 0 0 0 0 1 2 0 0 0 0 2 24 t 0 0 0 0 0 0 1 0 1 0 0 1 21 0
HLH54F_da_SANGER_5_FBgn0000413_shift6 (HLH54F_da_SANGER_5_FBgn0000413)				; oligos_7nt_mkv5_m2 versus HLH54F_da_SANGER_5_FBgn0000413; m=18/18; ncol2=11; w=0; offset=3; strand=D; shift=6; score=0.409233; ------mmCACCTG ; cor=; Ncor= a 0 0 0 0 0 0 12 12 0 24 0 0 0 0 c 0 0 0 0 0 0 10 10 23 0 24 23 1 0 g 0 0 0 0 0 0 1 2 0 0 0 0 2 24 t 0 0 0 0 0 0 1 0 1 0 0 1 21 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv4_m4_shift4 (oligos_6nt_mkv4_m4)				; oligos_6nt_mkv4_m4; m=0 (reference); ncol1=11; shift=4; ncol=15; ----ammAACACCmc ; Alignment reference a 0 0 0 0 603 434 886 1461 1470 34 1378 0 0 542 381 c 0 0 0 0 379 473 435 6 49 1453 126 1550 1575 416 540 g 0 0 0 0 284 341 132 31 32 32 22 11 3 328 294 t 0 0 0 0 322 340 135 90 37 69 62 27 10 302 373
lola-PQ_SANGER_5_FBgn0005630_shift4 (lola-PQ_SANGER_5_FBgn0005630)				; oligos_6nt_mkv4_m4 versus lola-PQ_SANGER_5_FBgn0005630; m=1/31; ncol2=9; w=0; offset=0; strand=D; shift=4; score=0.70071; ----AvrAWCAmC-- ; cor=; Ncor= a 0 0 0 0 8 3 6 10 8 0 11 6 0 0 0 c 0 0 0 0 2 3 1 0 0 11 0 5 9 0 0 g 0 0 0 0 0 4 4 0 0 0 0 0 0 0 0 t 0 0 0 0 1 1 0 1 3 0 0 0 2 0 0
lola-PQ_SOLEXA_FBgn0005630_rc_shift2 (lola-PQ_SOLEXA_FBgn0005630_rc)				; oligos_6nt_mkv4_m4 versus lola-PQ_SOLEXA_FBgn0005630_rc; m=2/31; ncol2=15; w=-2; offset=-2; strand=R; shift=2; score=0.597186; --mmamrAWCAmCsc ; cor=; Ncor= a 0 0 158 198 244 157 162 446 376 0 501 322 0 111 110 c 0 0 154 160 111 222 44 0 0 504 2 180 441 158 268 g 0 0 97 86 115 81 275 38 0 0 0 0 8 181 69 t 0 0 93 57 32 41 23 18 126 0 0 0 54 52 55
Side_SANGER_5_FBgn0032741_shift5 (Side_SANGER_5_FBgn0032741)				; oligos_6nt_mkv4_m4 versus Side_SANGER_5_FBgn0032741; m=3/31; ncol2=11; w=0; offset=1; strand=D; shift=5; score=0.593552; -----rAAMCAsCTG ; cor=; Ncor= a 0 0 0 0 0 12 17 21 16 0 23 0 5 1 0 c 0 0 0 0 0 0 3 2 6 23 0 10 18 1 0 g 0 0 0 0 0 6 3 0 1 0 0 9 0 0 23 t 0 0 0 0 0 5 0 0 0 0 0 4 0 21 0
sage_da_SANGER_5_FBgn0000413_shift5 (sage_da_SANGER_5_FBgn0000413)				; oligos_6nt_mkv4_m4 versus sage_da_SANGER_5_FBgn0000413; m=4/31; ncol2=11; w=0; offset=1; strand=D; shift=5; score=0.593552; -----rAAMCAsCTG ; cor=; Ncor= a 0 0 0 0 0 12 17 21 16 0 23 0 5 1 0 c 0 0 0 0 0 0 3 2 6 23 0 10 18 1 0 g 0 0 0 0 0 6 3 0 1 0 0 9 0 0 23 t 0 0 0 0 0 5 0 0 0 0 0 4 0 21 0
sage_da_SANGER_5_FBgn0037672_shift5 (sage_da_SANGER_5_FBgn0037672)				; oligos_6nt_mkv4_m4 versus sage_da_SANGER_5_FBgn0037672; m=5/31; ncol2=11; w=0; offset=1; strand=D; shift=5; score=0.593552; -----rAAMCAsCTG ; cor=; Ncor= a 0 0 0 0 0 12 17 21 16 0 23 0 5 1 0 c 0 0 0 0 0 0 3 2 6 23 0 10 18 1 0 g 0 0 0 0 0 6 3 0 1 0 0 9 0 0 23 t 0 0 0 0 0 5 0 0 0 0 0 4 0 21 0
lola-PF_SANGER_5_FBgn0005630_shift6 (lola-PF_SANGER_5_FBgn0005630)				; oligos_6nt_mkv4_m4 versus lola-PF_SANGER_5_FBgn0005630; m=6/31; ncol2=10; w=0; offset=2; strand=D; shift=6; score=0.572099; ------mAACTCCay ; cor=; Ncor= a 0 0 0 0 0 0 5 11 12 0 0 0 0 8 0 c 0 0 0 0 0 0 5 0 0 12 0 11 12 1 6 g 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 t 0 0 0 0 0 0 2 1 0 0 12 1 0 2 6
CG5953_SANGER_5_FBgn0032587_shift4 (CG5953_SANGER_5_FBgn0032587)				; oligos_6nt_mkv4_m4 versus CG5953_SANGER_5_FBgn0032587; m=7/31; ncol2=8; w=0; offset=0; strand=D; shift=4; score=0.570579; ----aCAAACAy--- ; cor=; Ncor= a 0 0 0 0 10 0 16 16 16 0 16 1 0 0 0 c 0 0 0 0 3 16 0 0 0 16 0 5 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 3 0 0 0 0 0 0 10 0 0 0
lola-PF_SOLEXA_FBgn0005630_rc_shift4 (lola-PF_SOLEXA_FBgn0005630_rc)				; oligos_6nt_mkv4_m4 versus lola-PF_SOLEXA_FBgn0005630_rc; m=8/31; ncol2=15; w=0; offset=0; strand=R; shift=4; score=0.560189; ----cmmAACTCCAy ; cor=; Ncor= a 0 0 0 0 651 875 871 2434 2609 14 1 11 26 1831 393 c 0 0 0 0 962 1008 1111 10 4 2605 10 2506 2581 110 1367 g 0 0 0 0 367 547 123 151 5 0 2 0 1 476 145 t 0 0 0 0 638 189 513 23 0 0 2603 101 10 201 713
bin_SANGER_5_FBgn0045759_shift4 (bin_SANGER_5_FBgn0045759)				; oligos_6nt_mkv4_m4 versus bin_SANGER_5_FBgn0045759; m=9/31; ncol2=7; w=0; offset=0; strand=D; shift=4; score=0.540854; ----rTAAACA---- ; cor=; Ncor= a 0 0 0 0 9 0 20 20 20 0 19 0 0 0 0 c 0 0 0 0 0 0 0 0 0 20 0 0 0 0 0 g 0 0 0 0 10 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 1 20 0 0 0 0 1 0 0 0 0
Mirr_Cell_FBgn0014343_shift3 (Mirr_Cell_FBgn0014343)				; oligos_6nt_mkv4_m4 versus Mirr_Cell_FBgn0014343; m=10/31; ncol2=8; w=-1; offset=-1; strand=D; shift=3; score=0.535628; ---waawAACA---- ; cor=; Ncor= a 0 0 0 18 18 22 20 29 41 0 41 0 0 0 0 c 0 0 0 6 4 7 1 0 0 41 0 0 0 0 0 g 0 0 0 6 10 6 1 2 0 0 0 0 0 0 0 t 0 0 0 11 9 6 19 10 0 0 0 0 0 0 0
fd64A_SANGER_5_FBgn0004895_shift3 (fd64A_SANGER_5_FBgn0004895)				; oligos_6nt_mkv4_m4 versus fd64A_SANGER_5_FBgn0004895; m=11/31; ncol2=8; w=-1; offset=-1; strand=D; shift=3; score=0.533538; ---tvtAAACA---- ; cor=; Ncor= a 0 0 0 3 7 4 20 19 20 0 20 0 0 0 0 c 0 0 0 0 5 3 0 1 0 17 0 0 0 0 0 g 0 0 0 4 6 0 0 0 0 0 0 0 0 0 0 t 0 0 0 13 2 13 0 0 0 3 0 0 0 0 0
slp2_SANGER_5_FBgn0004567_shift4 (slp2_SANGER_5_FBgn0004567)				; oligos_6nt_mkv4_m4 versus slp2_SANGER_5_FBgn0004567; m=12/31; ncol2=8; w=0; offset=0; strand=D; shift=4; score=0.518635; ----rTAAACAa--- ; cor=; Ncor= a 0 0 0 0 6 0 18 18 18 0 18 11 0 0 0 c 0 0 0 0 0 1 0 0 0 18 0 3 0 0 0 g 0 0 0 0 12 0 0 0 0 0 0 3 0 0 0 t 0 0 0 0 0 17 0 0 0 0 0 1 0 0 0
HLH4C_da_SANGER_5_FBgn0000413_shift4 (HLH4C_da_SANGER_5_FBgn0000413)				; oligos_6nt_mkv4_m4 versus HLH4C_da_SANGER_5_FBgn0000413; m=13/31; ncol2=15; w=0; offset=0; strand=D; shift=4; score=0.51672; ----mammvCACCTG ; cor=; Ncor= a 0 0 0 0 9 12 11 11 10 0 23 0 1 0 0 c 0 0 0 0 9 3 6 6 6 23 0 21 22 0 1 g 0 0 0 0 5 5 2 1 7 0 0 1 0 0 22 t 0 0 0 0 0 3 4 5 0 0 0 1 0 23 0
HLH4C_da_SANGER_5_FBgn0011277_shift4 (HLH4C_da_SANGER_5_FBgn0011277)				; oligos_6nt_mkv4_m4 versus HLH4C_da_SANGER_5_FBgn0011277; m=14/31; ncol2=15; w=0; offset=0; strand=D; shift=4; score=0.51672; ----mammvCACCTG ; cor=; Ncor= a 0 0 0 0 9 12 11 11 10 0 23 0 1 0 0 c 0 0 0 0 9 3 6 6 6 23 0 21 22 0 1 g 0 0 0 0 5 5 2 1 7 0 0 1 0 0 22 t 0 0 0 0 0 3 4 5 0 0 0 1 0 23 0
Ara_Cell_FBgn0015904_shift3 (Ara_Cell_FBgn0015904)				; oligos_6nt_mkv4_m4 versus Ara_Cell_FBgn0015904; m=15/31; ncol2=8; w=-1; offset=-1; strand=D; shift=3; score=0.511889; ---raAwwACA---- ; cor=; Ncor= a 0 0 0 12 16 24 14 23 34 0 34 0 0 0 0 c 0 0 0 5 7 1 0 0 0 34 0 0 0 0 0 g 0 0 0 10 6 1 5 0 0 0 0 0 0 0 0 t 0 0 0 7 5 8 15 11 0 0 0 0 0 0 0
Caup_Cell_FBgn0015919_shift3 (Caup_Cell_FBgn0015919)				; oligos_6nt_mkv4_m4 versus Caup_Cell_FBgn0015919; m=16/31; ncol2=8; w=-1; offset=-1; strand=D; shift=3; score=0.502113; ---cwwtAACA---- ; cor=; Ncor= a 0 0 0 4 9 8 4 14 19 0 19 0 0 0 0 c 0 0 0 9 0 0 1 0 0 19 0 0 0 0 0 g 0 0 0 2 3 4 2 2 0 0 0 0 0 0 0 t 0 0 0 4 7 7 12 3 0 0 0 0 0 0 0
Mirr_SOLEXA_FBgn0014343_shift5 (Mirr_SOLEXA_FBgn0014343)				; oligos_6nt_mkv4_m4 versus Mirr_SOLEXA_FBgn0014343; m=17/31; ncol2=6; w=0; offset=1; strand=D; shift=5; score=0.483969; -----wwwACA---- ; cor=; Ncor= a 0 0 0 0 0 550 410 782 1415 0 1415 0 0 0 0 c 0 0 0 0 0 158 93 0 0 1415 0 0 0 0 0 g 0 0 0 0 0 327 282 204 0 0 0 0 0 0 0 t 0 0 0 0 0 380 630 429 0 0 0 0 0 0 0
Ara_SOLEXA_FBgn0015904_shift5 (Ara_SOLEXA_FBgn0015904)				; oligos_6nt_mkv4_m4 versus Ara_SOLEXA_FBgn0015904; m=18/31; ncol2=6; w=0; offset=1; strand=D; shift=5; score=0.479754; -----awwACA---- ; cor=; Ncor= a 0 0 0 0 0 155 97 193 313 0 313 0 0 0 0 c 0 0 0 0 0 36 0 0 0 313 0 0 0 0 0 g 0 0 0 0 0 44 45 38 0 0 0 0 0 0 0 t 0 0 0 0 0 78 171 82 0 0 0 0 0 0 0
foxo_SANGER_10_FBgn0038197_rc_shift2 (foxo_SANGER_10_FBgn0038197_rc)				; oligos_6nt_mkv4_m4 versus foxo_SANGER_10_FBgn0038197_rc; m=19/31; ncol2=9; w=-2; offset=-2; strand=R; shift=2; score=0.477287; --ycrwAAACA---- ; cor=; Ncor= a 0 0 0 3 8 8 16 16 20 0 20 0 0 0 0 c 0 0 6 12 0 0 1 4 0 18 0 0 0 0 0 g 0 0 3 3 11 0 0 0 0 0 0 0 0 0 0 t 0 0 11 2 1 12 3 0 0 2 0 0 0 0 0
slp1_NAR_FBgn0003430_rc_shift1 (slp1_NAR_FBgn0003430_rc)				; oligos_6nt_mkv4_m4 versus slp1_NAR_FBgn0003430_rc; m=20/31; ncol2=11; w=-3; offset=-3; strand=R; shift=1; score=0.468501; -wryrtAAACAm--- ; cor=; Ncor= a 0 19 21 1 11 10 39 40 41 0 41 16 0 0 0 c 0 4 3 15 7 4 2 1 0 38 0 14 0 0 0 g 0 3 13 8 22 0 0 0 0 0 0 3 0 0 0 t 0 15 4 17 1 27 0 0 0 3 0 8 0 0 0
CG16899_SANGER_5_FBgn0037735_shift3 (CG16899_SANGER_5_FBgn0037735)				; oligos_6nt_mkv4_m4 versus CG16899_SANGER_5_FBgn0037735; m=21/31; ncol2=9; w=-1; offset=-1; strand=D; shift=3; score=0.468017; ---vrTAAACAA--- ; cor=; Ncor= a 0 0 0 6 10 1 21 20 21 0 21 15 0 0 0 c 0 0 0 5 2 2 0 0 0 18 0 2 0 0 0 g 0 0 0 8 8 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 18 0 1 0 3 0 4 0 0 0
Caup_SOLEXA_FBgn0015919_shift5 (Caup_SOLEXA_FBgn0015919)				; oligos_6nt_mkv4_m4 versus Caup_SOLEXA_FBgn0015919; m=22/31; ncol2=6; w=0; offset=1; strand=D; shift=5; score=0.464906; -----wtwACA---- ; cor=; Ncor= a 0 0 0 0 0 999 577 1415 2904 2 2904 0 0 0 0 c 0 0 0 0 0 460 201 0 0 2902 0 0 0 0 0 g 0 0 0 0 0 626 639 511 0 0 0 0 0 0 0 t 0 0 0 0 0 819 1487 978 0 0 0 0 0 0 0
CG11617_SOLEXA_FBgn0031232_shift3 (CG11617_SOLEXA_FBgn0031232)				; oligos_6nt_mkv4_m4 versus CG11617_SOLEXA_FBgn0031232; m=23/31; ncol2=8; w=-1; offset=-1; strand=D; shift=3; score=0.454991; ---wtwTwACA---- ; cor=; Ncor= a 0 0 0 370 281 352 133 483 1159 7 1148 0 0 0 0 c 0 0 0 201 262 176 167 0 0 1152 2 0 0 0 0 g 0 0 0 211 257 176 20 283 0 0 9 0 0 0 0 t 0 0 0 377 359 455 839 393 0 0 0 0 0 0 0
ac_da_SANGER_5_FBgn0000413_shift8 (ac_da_SANGER_5_FBgn0000413)				; oligos_6nt_mkv4_m4 versus ac_da_SANGER_5_FBgn0000413; m=24/31; ncol2=8; w=0; offset=4; strand=D; shift=8; score=0.432417; --------rCACCTG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 10 0 19 0 0 0 0 c 0 0 0 0 0 0 0 0 1 19 0 18 19 0 0 g 0 0 0 0 0 0 0 0 7 0 0 1 0 0 19 t 0 0 0 0 0 0 0 0 1 0 0 0 0 19 0
ac_da_SANGER_5_FBgn0000022_shift8 (ac_da_SANGER_5_FBgn0000022)				; oligos_6nt_mkv4_m4 versus ac_da_SANGER_5_FBgn0000022; m=25/31; ncol2=8; w=0; offset=4; strand=D; shift=8; score=0.432417; --------rCACCTG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 10 0 19 0 0 0 0 c 0 0 0 0 0 0 0 0 1 19 0 18 19 0 0 g 0 0 0 0 0 0 0 0 7 0 0 1 0 0 19 t 0 0 0 0 0 0 0 0 1 0 0 0 0 19 0
sc_da_SANGER_10_FBgn0000413_shift8 (sc_da_SANGER_10_FBgn0000413)				; oligos_6nt_mkv4_m4 versus sc_da_SANGER_10_FBgn0000413; m=26/31; ncol2=8; w=0; offset=4; strand=D; shift=8; score= 0.4236; --------rCACCTG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 11 0 24 0 0 0 0 c 0 0 0 0 0 0 0 0 5 23 0 21 24 0 0 g 0 0 0 0 0 0 0 0 7 0 0 1 0 0 24 t 0 0 0 0 0 0 0 0 0 0 0 2 0 24 0
sc_da_SANGER_10_FBgn0004170_shift8 (sc_da_SANGER_10_FBgn0004170)				; oligos_6nt_mkv4_m4 versus sc_da_SANGER_10_FBgn0004170; m=27/31; ncol2=8; w=0; offset=4; strand=D; shift=8; score= 0.4236; --------rCACCTG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 11 0 24 0 0 0 0 c 0 0 0 0 0 0 0 0 5 23 0 21 24 0 0 g 0 0 0 0 0 0 0 0 7 0 0 1 0 0 24 t 0 0 0 0 0 0 0 0 0 0 0 2 0 24 0
fkh_NAR_FBgn0000659_rc_shift0 (fkh_NAR_FBgn0000659_rc)				; oligos_6nt_mkv4_m4 versus fkh_NAR_FBgn0000659_rc; m=28/31; ncol2=11; w=-4; offset=-4; strand=R; shift=0; score=0.421441; tTrrryAAACA---- ; cor=; Ncor= a 4 3 14 11 8 0 26 27 27 0 24 0 0 0 0 c 4 1 2 3 2 14 1 0 0 22 0 0 0 0 0 g 4 0 11 7 13 0 0 0 0 0 0 0 0 0 0 t 15 23 0 6 4 13 0 0 0 5 3 0 0 0 0
HLH54F_da_SANGER_5_FBgn0022740_shift7 (HLH54F_da_SANGER_5_FBgn0022740)				; oligos_6nt_mkv4_m4 versus HLH54F_da_SANGER_5_FBgn0022740; m=29/31; ncol2=11; w=0; offset=3; strand=D; shift=7; score=0.416631; -------mmCACCTG ; cor=; Ncor= a 0 0 0 0 0 0 0 12 12 0 24 0 0 0 0 c 0 0 0 0 0 0 0 10 10 23 0 24 23 1 0 g 0 0 0 0 0 0 0 1 2 0 0 0 0 2 24 t 0 0 0 0 0 0 0 1 0 1 0 0 1 21 0
HLH54F_da_SANGER_5_FBgn0000413_shift7 (HLH54F_da_SANGER_5_FBgn0000413)				; oligos_6nt_mkv4_m4 versus HLH54F_da_SANGER_5_FBgn0000413; m=30/31; ncol2=11; w=0; offset=3; strand=D; shift=7; score=0.416631; -------mmCACCTG ; cor=; Ncor= a 0 0 0 0 0 0 0 12 12 0 24 0 0 0 0 c 0 0 0 0 0 0 0 10 10 23 0 24 23 1 0 g 0 0 0 0 0 0 0 1 2 0 0 0 0 2 24 t 0 0 0 0 0 0 0 1 0 1 0 0 1 21 0
CG31782-F9-11_SOLEXA_FBgn0051782_rc_shift7 (CG31782-F9-11_SOLEXA_FBgn0051782_rc)				; oligos_6nt_mkv4_m4 versus CG31782-F9-11_SOLEXA_FBgn0051782_rc; m=31/31; ncol2=11; w=0; offset=3; strand=R; shift=7; score=0.400872; -------ctCACCac ; cor=; Ncor= a 0 0 0 0 0 0 0 269 617 42 2023 0 0 1676 407 c 0 0 0 0 0 0 0 1324 287 1979 143 2554 2552 582 1464 g 0 0 0 0 0 0 0 584 195 25 0 0 0 27 305 t 0 0 0 0 0 0 0 375 1453 506 386 0 1 269 377

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv4_m3_shift3 (oligos_6nt_mkv4_m3)				; oligos_6nt_mkv4_m3; m=0 (reference); ncol1=12; shift=3; ncol=15; ---mrCTGTCAaamg ; Alignment reference a 0 0 0 526 362 41 28 74 16 39 1314 942 891 393 301 c 0 0 0 353 229 1319 34 50 45 1321 36 139 210 434 341 g 0 0 0 252 522 20 27 1237 28 21 34 168 140 278 427 t 0 0 0 281 299 32 1323 51 1323 31 28 163 171 307 343
Her_SANGER_5_FBgn0030899_shift6 (Her_SANGER_5_FBgn0030899)				; oligos_6nt_mkv4_m3 versus Her_SANGER_5_FBgn0030899; m=1/29; ncol2=9; w=0; offset=3; strand=D; shift=6; score=0.674088; ------wGTCAAvmv ; cor=; Ncor= a 0 0 0 0 0 0 5 0 0 1 18 18 5 5 5 c 0 0 0 0 0 0 0 0 0 18 1 0 6 11 8 g 0 0 0 0 0 0 2 17 1 0 0 1 7 0 6 t 0 0 0 0 0 0 12 2 18 0 0 0 1 3 0
hth_SOLEXA_2_FBgn0001235_rc_shift5 (hth_SOLEXA_2_FBgn0001235_rc)				; oligos_6nt_mkv4_m3 versus hth_SOLEXA_2_FBgn0001235_rc; m=2/29; ncol2=8; w=0; offset=2; strand=R; shift=5; score=0.628894; -----cTGTCAaa-- ; cor=; Ncor= a 0 0 0 0 0 322 13 22 0 48 2585 1115 951 0 0 c 0 0 0 0 0 783 291 0 33 2681 25 527 589 0 0 g 0 0 0 0 0 172 40 2621 0 0 69 459 586 0 0 t 0 0 0 0 0 216 2358 86 2696 0 50 618 572 0 0
Exd_Cell_FBgn0000611_rc_shift6 (Exd_Cell_FBgn0000611_rc)				; oligos_6nt_mkv4_m3 versus Exd_Cell_FBgn0000611_rc; m=3/29; ncol2=8; w=0; offset=3; strand=R; shift=6; score=0.623867; ------yRTCAAAa- ; cor=; Ncor= a 0 0 0 0 0 0 0 5 0 0 17 17 14 5 0 c 0 0 0 0 0 0 6 0 0 17 0 0 2 4 0 g 0 0 0 0 0 0 0 12 0 0 0 0 0 4 0 t 0 0 0 0 0 0 11 0 17 0 0 0 1 4 0
Exd_SOLEXA_FBgn0000611_rc_shift6 (Exd_SOLEXA_FBgn0000611_rc)				; oligos_6nt_mkv4_m3 versus Exd_SOLEXA_FBgn0000611_rc; m=4/29; ncol2=8; w=0; offset=3; strand=R; shift=6; score=0.618812; ------yrTCAaaw- ; cor=; Ncor= a 0 0 0 0 0 0 77 323 0 0 883 541 408 266 0 c 0 0 0 0 0 0 259 0 0 883 0 168 143 207 0 g 0 0 0 0 0 0 26 505 0 0 0 40 172 152 0 t 0 0 0 0 0 0 521 55 883 0 0 134 160 258 0
Achi_Cell_FBgn0033749_rc_shift6 (Achi_Cell_FBgn0033749_rc)				; oligos_6nt_mkv4_m3 versus Achi_Cell_FBgn0033749_rc; m=5/29; ncol2=7; w=0; offset=3; strand=R; shift=6; score=0.577495; ------TGTCAwa-- ; cor=; Ncor= a 0 0 0 0 0 0 0 1 0 0 23 12 15 0 0 c 0 0 0 0 0 0 0 0 0 23 0 1 1 0 0 g 0 0 0 0 0 0 0 22 0 0 0 4 3 0 0 t 0 0 0 0 0 0 23 0 23 0 0 6 4 0 0
disco_SOLEXA_5_FBgn0000459_shift1 (disco_SOLEXA_5_FBgn0000459)				; oligos_6nt_mkv4_m3 versus disco_SOLEXA_5_FBgn0000459; m=6/29; ncol2=13; w=-2; offset=-2; strand=D; shift=1; score=0.570721; -aawwkTGTCACCy- ; cor=; Ncor= a 0 140 161 275 258 127 0 0 0 6 566 119 137 126 0 c 0 82 84 61 32 48 2 0 11 563 0 455 422 180 0 g 0 60 92 82 129 185 2 552 0 0 11 0 10 63 0 t 0 51 98 163 162 221 577 29 570 12 4 7 12 212 0
CG3407_SANGER_2.5_FBgn0031573_shift5 (CG3407_SANGER_2.5_FBgn0031573)				; oligos_6nt_mkv4_m3 versus CG3407_SANGER_2.5_FBgn0031573; m=7/29; ncol2=9; w=0; offset=2; strand=D; shift=5; score=0.568315; -----awGTCAAsm- ; cor=; Ncor= a 0 0 0 0 0 11 7 0 0 0 17 16 2 6 0 c 0 0 0 0 0 4 3 1 0 17 0 0 8 9 0 g 0 0 0 0 0 0 0 16 0 0 0 1 6 0 0 t 0 0 0 0 0 2 7 0 17 0 0 0 1 2 0
disco-r-F1-2_SOLEXA_FBgn0042650_rc_shift2 (disco-r-F1-2_SOLEXA_FBgn0042650_rc)				; oligos_6nt_mkv4_m3 versus disco-r-F1-2_SOLEXA_FBgn0042650_rc; m=8/29; ncol2=15; w=-1; offset=-1; strand=R; shift=2; score=0.565092; --aaadTGTCACCmr ; cor=; Ncor= a 0 0 931 1344 1271 809 0 1 8 1 2464 461 468 825 814 c 0 0 555 328 179 229 8 0 4 2584 41 2085 2015 848 635 g 0 0 582 446 563 782 272 2584 139 0 78 0 61 346 692 t 0 0 515 467 571 764 2305 0 2434 0 1 40 38 564 444
CG11617_Cell_FBgn0031232_rc_shift6 (CG11617_Cell_FBgn0031232_rc)				; oligos_6nt_mkv4_m3 versus CG11617_Cell_FBgn0031232_rc; m=9/29; ncol2=8; w=0; offset=3; strand=R; shift=6; score=0.564713; ------TGTtAAAw- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 4 17 16 14 7 0 c 0 0 0 0 0 0 0 0 0 3 0 0 1 3 0 g 0 0 0 0 0 0 0 17 0 0 0 0 0 0 0 t 0 0 0 0 0 0 17 0 17 10 0 1 2 7 0
CG11617_SOLEXA_FBgn0031232_rc_shift6 (CG11617_SOLEXA_FBgn0031232_rc)				; oligos_6nt_mkv4_m3 versus CG11617_SOLEXA_FBgn0031232_rc; m=10/29; ncol2=8; w=0; offset=3; strand=R; shift=6; score=0.550904; ------TGTwAwaw- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 393 839 455 359 377 0 c 0 0 0 0 0 0 9 0 0 283 20 176 257 211 0 g 0 0 0 0 0 0 2 1152 0 0 167 176 262 201 0 t 0 0 0 0 0 0 1148 7 1159 483 133 352 281 370 0
Six4_SOLEXA_FBgn0027364_rc_shift6 (Six4_SOLEXA_FBgn0027364_rc)				; oligos_6nt_mkv4_m3 versus Six4_SOLEXA_FBgn0027364_rc; m=11/29; ncol2=8; w=0; offset=3; strand=R; shift=6; score=0.53967; ------TaTCAhww- ; cor=; Ncor= a 0 0 0 0 0 0 0 383 0 38 599 194 203 181 0 c 0 0 0 0 0 0 0 126 0 556 0 167 83 116 0 g 0 0 0 0 0 0 40 128 0 0 38 84 91 93 0 t 0 0 0 0 0 0 597 0 637 43 0 192 260 247 0
exd_SOLEXA_2_FBgn0000611_rc_shift5 (exd_SOLEXA_2_FBgn0000611_rc)				; oligos_6nt_mkv4_m3 versus exd_SOLEXA_2_FBgn0000611_rc; m=12/29; ncol2=8; w=0; offset=2; strand=R; shift=5; score=0.509125; -----wyrTCAaa-- ; cor=; Ncor= a 0 0 0 0 0 483 259 1228 0 0 2672 1314 1025 0 0 c 0 0 0 0 0 145 914 86 0 2672 0 598 458 0 0 g 0 0 0 0 0 91 14 1169 0 0 0 204 568 0 0 t 0 0 0 0 0 474 1470 189 2672 0 0 539 587 0 0
Fer3_da_SANGER_5_FBgn0000413_shift2 (Fer3_da_SANGER_5_FBgn0000413)				; oligos_6nt_mkv4_m3 versus Fer3_da_SANGER_5_FBgn0000413; m=13/29; ncol2=10; w=-1; offset=-1; strand=D; shift=2; score=0.499373; --CAbCTGTyaC--- ; cor=; Ncor= a 0 0 2 18 1 3 0 0 3 0 11 3 0 0 0 c 0 0 17 0 5 15 1 0 2 7 4 15 0 0 0 g 0 0 0 1 8 1 0 19 0 4 2 0 0 0 0 t 0 0 0 0 5 0 18 0 14 8 2 1 0 0 0
Fer3_da_SANGER_5_FBgn0037937_shift2 (Fer3_da_SANGER_5_FBgn0037937)				; oligos_6nt_mkv4_m3 versus Fer3_da_SANGER_5_FBgn0037937; m=14/29; ncol2=10; w=-1; offset=-1; strand=D; shift=2; score=0.499373; --CAbCTGTyaC--- ; cor=; Ncor= a 0 0 2 18 1 3 0 0 3 0 11 3 0 0 0 c 0 0 17 0 5 15 1 0 2 7 4 15 0 0 0 g 0 0 0 1 8 1 0 19 0 4 2 0 0 0 0 t 0 0 0 0 5 0 18 0 14 8 2 1 0 0 0
Vis_SOLEXA_FBgn0033748_rc_shift6 (Vis_SOLEXA_FBgn0033748_rc)				; oligos_6nt_mkv4_m3 versus Vis_SOLEXA_FBgn0033748_rc; m=15/29; ncol2=6; w=0; offset=3; strand=R; shift=6; score=0.496352; ------TGTCAa--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 13 354 199 0 0 0 c 0 0 0 0 0 0 36 0 0 341 0 34 0 0 0 g 0 0 0 0 0 0 0 354 0 0 0 53 0 0 0 t 0 0 0 0 0 0 318 0 354 0 0 68 0 0 0
Achi_SOLEXA_FBgn0033749_rc_shift6 (Achi_SOLEXA_FBgn0033749_rc)				; oligos_6nt_mkv4_m3 versus Achi_SOLEXA_FBgn0033749_rc; m=16/29; ncol2=6; w=0; offset=3; strand=R; shift=6; score=0.494328; ------TGTCAa--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 368 181 0 0 0 c 0 0 0 0 0 0 29 0 0 344 0 39 0 0 0 g 0 0 0 0 0 0 0 368 0 0 0 74 0 0 0 t 0 0 0 0 0 0 339 0 368 24 0 74 0 0 0
ems_FlyReg_FBgn0000576_rc_shift6 (ems_FlyReg_FBgn0000576_rc)				; oligos_6nt_mkv4_m3 versus ems_FlyReg_FBgn0000576_rc; m=17/29; ncol2=8; w=0; offset=3; strand=R; shift=6; score=0.490415; ------TsTmAThm- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 1 3 0 1 2 0 c 0 0 0 0 0 0 0 1 0 2 0 0 1 1 0 g 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 t 0 0 0 0 0 0 3 0 3 0 0 3 1 0 0
Hth_SOLEXA_FBgn0001235_rc_shift6 (Hth_SOLEXA_FBgn0001235_rc)				; oligos_6nt_mkv4_m3 versus Hth_SOLEXA_FBgn0001235_rc; m=18/29; ncol2=6; w=0; offset=3; strand=R; shift=6; score=0.480716; ------TGTCAm--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 388 148 0 0 0 c 0 0 0 0 0 0 40 0 0 444 56 120 0 0 0 g 0 0 0 0 0 0 60 444 41 0 0 87 0 0 0 t 0 0 0 0 0 0 344 0 403 0 0 89 0 0 0
Caup_Cell_FBgn0015919_rc_shift6 (Caup_Cell_FBgn0015919_rc)				; oligos_6nt_mkv4_m3 versus Caup_Cell_FBgn0015919_rc; m=19/29; ncol2=8; w=0; offset=3; strand=R; shift=6; score=0.472683; ------TGTTawwg- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 3 12 7 7 4 0 c 0 0 0 0 0 0 0 0 0 2 2 4 3 2 0 g 0 0 0 0 0 0 0 19 0 0 1 0 0 9 0 t 0 0 0 0 0 0 19 0 19 14 4 8 9 4 0
So_SOLEXA_FBgn0003460_rc_shift6 (So_SOLEXA_FBgn0003460_rc)				; oligos_6nt_mkv4_m3 versus So_SOLEXA_FBgn0003460_rc; m=20/29; ncol2=8; w=0; offset=3; strand=R; shift=6; score=0.471011; ------TATCAyww- ; cor=; Ncor= a 0 0 0 0 0 0 0 509 0 0 467 122 165 166 0 c 0 0 0 0 0 0 0 14 0 519 4 151 117 95 0 g 0 0 0 0 0 0 0 8 0 0 58 87 92 102 0 t 0 0 0 0 0 0 531 0 531 12 2 171 157 168 0
HLHmgamma_SANGER_5_2_FBgn0002735_shift6 (HLHmgamma_SANGER_5_2_FBgn0002735)				; oligos_6nt_mkv4_m3 versus HLHmgamma_SANGER_5_2_FBgn0002735; m=21/29; ncol2=7; w=0; offset=3; strand=D; shift=6; score=0.466095; ------wGTCAAG-- ; cor=; Ncor= a 0 0 0 0 0 0 3 0 0 0 7 7 0 0 0 c 0 0 0 0 0 0 0 0 0 7 0 0 0 0 0 g 0 0 0 0 0 0 0 7 0 0 0 0 7 0 0 t 0 0 0 0 0 0 4 0 7 0 0 0 0 0 0
tap_da_SANGER_5_2_FBgn0015550_shift1 (tap_da_SANGER_5_2_FBgn0015550)				; oligos_6nt_mkv4_m3 versus tap_da_SANGER_5_2_FBgn0015550; m=22/29; ncol2=10; w=-2; offset=-2; strand=D; shift=1; score=0.441631; -SCAkATGTCA---- ; cor=; Ncor= a 0 0 0 13 1 11 0 0 0 0 10 0 0 0 0 c 0 9 12 0 3 3 0 0 0 11 0 0 0 0 0 g 0 3 0 1 5 0 0 14 1 1 3 0 0 0 0 t 0 0 0 0 5 0 14 0 13 2 1 0 0 0 0
tap_da_SANGER_5_2_FBgn0000413_shift1 (tap_da_SANGER_5_2_FBgn0000413)				; oligos_6nt_mkv4_m3 versus tap_da_SANGER_5_2_FBgn0000413; m=23/29; ncol2=10; w=-2; offset=-2; strand=D; shift=1; score=0.441631; -SCAkATGTCA---- ; cor=; Ncor= a 0 0 0 13 1 11 0 0 0 0 10 0 0 0 0 c 0 9 12 0 3 3 0 0 0 11 0 0 0 0 0 g 0 3 0 1 5 0 0 14 1 1 3 0 0 0 0 t 0 0 0 0 5 0 14 0 13 2 1 0 0 0 0
Vis_Cell_FBgn0033748_rc_shift6 (Vis_Cell_FBgn0033748_rc)				; oligos_6nt_mkv4_m3 versus Vis_Cell_FBgn0033748_rc; m=24/29; ncol2=5; w=0; offset=3; strand=R; shift=6; score=0.416374; ------TGTCA---- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 22 0 0 0 0 c 0 0 0 0 0 0 0 0 0 22 0 0 0 0 0 g 0 0 0 0 0 0 0 22 0 0 0 0 0 0 0 t 0 0 0 0 0 0 22 0 22 0 0 0 0 0 0
Hth_Cell_FBgn0001235_rc_shift6 (Hth_Cell_FBgn0001235_rc)				; oligos_6nt_mkv4_m3 versus Hth_Cell_FBgn0001235_rc; m=25/29; ncol2=5; w=0; offset=3; strand=R; shift=6; score=0.412766; ------TGTCA---- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 17 0 0 0 0 c 0 0 0 0 0 0 3 0 0 17 0 0 0 0 0 g 0 0 0 0 0 0 0 17 0 0 0 0 0 0 0 t 0 0 0 0 0 0 14 0 17 0 0 0 0 0 0
Fer1_da_SANGER_10_FBgn0037475_shift0 (Fer1_da_SANGER_10_FBgn0037475)				; oligos_6nt_mkv4_m3 versus Fer1_da_SANGER_10_FBgn0037475; m=26/29; ncol2=11; w=-3; offset=-3; strand=D; shift=0; score=0.407324; mvCAsmTGwCa---- ; cor=; Ncor= a 11 11 0 23 0 6 0 0 8 0 14 0 0 0 0 c 6 6 23 0 15 14 0 0 3 17 4 0 0 0 0 g 1 6 0 0 8 3 0 23 2 3 4 0 0 0 0 t 5 0 0 0 0 0 23 0 10 3 1 0 0 0 0
Fer1_da_SANGER_10_FBgn0000413_shift0 (Fer1_da_SANGER_10_FBgn0000413)				; oligos_6nt_mkv4_m3 versus Fer1_da_SANGER_10_FBgn0000413; m=27/29; ncol2=11; w=-3; offset=-3; strand=D; shift=0; score=0.407324; mvCAsmTGwCa---- ; cor=; Ncor= a 11 11 0 23 0 6 0 0 8 0 14 0 0 0 0 c 6 6 23 0 15 14 0 0 3 17 4 0 0 0 0 g 1 6 0 0 8 3 0 23 2 3 4 0 0 0 0 t 5 0 0 0 0 0 23 0 10 3 1 0 0 0 0
nau_da_SANGER_5_FBgn0002922_shift2 (nau_da_SANGER_5_FBgn0002922)				; oligos_6nt_mkv4_m3 versus nau_da_SANGER_5_FBgn0002922; m=28/29; ncol2=8; w=-1; offset=-1; strand=D; shift=2; score=0.402198; --CACCTGyy----- ; cor=; Ncor= a 0 0 0 22 0 0 0 0 0 1 0 0 0 0 0 c 0 0 16 0 22 22 0 0 9 14 0 0 0 0 0 g 0 0 1 0 0 0 0 22 0 1 0 0 0 0 0 t 0 0 0 0 0 0 22 0 13 6 0 0 0 0 0
nau_da_SANGER_5_FBgn0000413_shift2 (nau_da_SANGER_5_FBgn0000413)				; oligos_6nt_mkv4_m3 versus nau_da_SANGER_5_FBgn0000413; m=29/29; ncol2=8; w=-1; offset=-1; strand=D; shift=2; score=0.402198; --CACCTGyy----- ; cor=; Ncor= a 0 0 0 22 0 0 0 0 0 1 0 0 0 0 0 c 0 0 16 0 22 22 0 0 9 14 0 0 0 0 0 g 0 0 1 0 0 0 0 22 0 1 0 0 0 0 0 t 0 0 0 0 0 0 22 0 13 6 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m5_shift3 (dyads_m5)				; dyads_m5; m=0 (reference); ncol1=11; shift=3; ncol=14; ---ccACCACCAcc ; Alignment reference a 0 0 0 849 627 3918 50 30 4141 38 14 3899 676 705 c 0 0 0 2252 2408 191 4112 4096 103 4058 4126 239 2169 2498 g 0 0 0 690 543 129 102 115 126 110 85 188 692 474 t 0 0 0 681 894 234 208 231 102 266 247 146 935 795
CG31782-F9-11_SOLEXA_FBgn0051782_rc_shift2 (CG31782-F9-11_SOLEXA_FBgn0051782_rc)				; dyads_m5 versus CG31782-F9-11_SOLEXA_FBgn0051782_rc; m=1/7; ncol2=11; w=-1; offset=-1; strand=R; shift=2; score=0.662333; --ctCACCacyaa- ; cor=; Ncor= a 0 0 269 617 42 2023 0 0 1676 407 471 1282 1413 0 c 0 0 1324 287 1979 143 2554 2552 582 1464 954 350 486 0 g 0 0 584 195 25 0 0 0 27 305 289 438 420 0 t 0 0 375 1453 506 386 0 1 269 377 838 482 234 0
lola-PL_SOLEXA_FBgn0005630_shift2 (lola-PL_SOLEXA_FBgn0005630)				; dyads_m5 versus lola-PL_SOLEXA_FBgn0005630; m=2/7; ncol2=14; w=-1; offset=-1; strand=D; shift=2; score=0.576007; --kgmmCCACcgkg ; cor=; Ncor= a 0 0 357 215 944 808 0 0 2061 0 361 407 457 281 c 0 0 322 163 968 793 2061 2061 0 2061 1099 481 334 387 g 0 0 600 1232 0 137 0 0 0 0 123 834 690 939 t 0 0 780 447 148 322 0 0 0 0 476 337 576 452
CG31782_F9-11_SANGER_5_FBgn0051782_shift0 (CG31782_F9-11_SANGER_5_FBgn0051782)				; dyads_m5 versus CG31782_F9-11_SANGER_5_FBgn0051782; m=3/7; ncol2=14; w=-3; offset=-3; strand=D; shift=0; score=0.569271; AssTCWCCAMYAAA ; cor=; Ncor= a 5 0 0 1 0 5 0 0 7 2 0 6 6 5 c 0 2 2 0 7 0 7 7 0 5 5 0 0 0 g 1 4 4 0 0 0 0 0 0 0 0 0 1 0 t 1 1 1 6 0 2 0 0 0 0 2 1 0 1
lola-PL_SANGER_2.5_FBgn0005630_rc_shift2 (lola-PL_SANGER_2.5_FBgn0005630_rc)				; dyads_m5 versus lola-PL_SANGER_2.5_FBgn0005630_rc; m=4/7; ncol2=9; w=-1; offset=-1; strand=R; shift=2; score=0.506519; --TGmcCCACm--- ; cor=; Ncor= a 0 0 2 0 4 2 0 0 11 0 4 0 0 0 c 0 0 0 0 7 5 11 11 0 11 6 0 0 0 g 0 0 0 9 0 2 0 0 0 0 0 0 0 0 t 0 0 8 2 0 2 0 0 0 0 1 0 0 0
Lag1_Cell_FBgn0040918_shift6 (Lag1_Cell_FBgn0040918)				; dyads_m5 versus Lag1_Cell_FBgn0040918; m=5/7; ncol2=10; w=0; offset=3; strand=D; shift=6; score=0.49346; ------CyACyAaa ; cor=; Ncor= a 0 0 0 0 0 0 0 0 17 1 0 18 12 10 c 0 0 0 0 0 0 19 9 2 18 12 0 0 3 g 0 0 0 0 0 0 0 0 0 0 0 1 4 4 t 0 0 0 0 0 0 0 10 0 0 7 0 3 2
Lag1_SOLEXA_FBgn0040918_shift6 (Lag1_SOLEXA_FBgn0040918)				; dyads_m5 versus Lag1_SOLEXA_FBgn0040918; m=6/7; ncol2=10; w=0; offset=3; strand=D; shift=6; score=0.468916; ------CyACyAaw ; cor=; Ncor= a 0 0 0 0 0 0 1 3 186 2 19 206 128 108 c 0 0 0 0 0 0 221 72 32 197 124 0 16 31 g 0 0 0 0 0 0 0 0 5 0 9 9 38 12 t 0 0 0 0 0 0 1 148 0 24 71 8 41 72
klu_SANGER_10_FBgn0013469_rc_shift6 (klu_SANGER_10_FBgn0013469_rc)				; dyads_m5 versus klu_SANGER_10_FBgn0013469_rc; m=7/7; ncol2=11; w=0; offset=3; strand=R; shift=6; score=0.40692; ------mCACCCmC ; cor=; Ncor= a 0 0 0 0 0 0 7 0 18 0 0 0 13 0 c 0 0 0 0 0 0 11 20 0 20 20 19 7 20 g 0 0 0 0 0 0 2 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 2 0 0 1 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv4_m6_shift1 (oligos_6nt_mkv4_m6)				; oligos_6nt_mkv4_m6; m=0 (reference); ncol1=12; shift=1; ncol=13; -yyCTTATCagym ; Alignment reference a 0 258 185 81 30 34 1157 9 27 667 140 266 331 c 0 411 359 1020 64 33 44 19 1173 127 207 383 328 g 0 231 277 65 39 16 8 37 9 266 679 226 283 t 0 339 418 73 1106 1156 30 1174 30 179 213 364 297
srp_SANGER_5_FBgn0003507_shift2 (srp_SANGER_5_FBgn0003507)				; oligos_6nt_mkv4_m6 versus srp_SANGER_5_FBgn0003507; m=1/13; ncol2=8; w=0; offset=1; strand=D; shift=2; score=0.654325; --yCTTATCw--- ; cor=; Ncor= a 0 0 0 0 0 0 17 0 0 9 0 0 0 c 0 0 7 14 0 0 0 0 17 0 0 0 0 g 0 0 3 2 0 0 0 0 0 1 0 0 0 t 0 0 6 0 17 17 0 17 0 7 0 0 0
GATAd_SANGER_5_FBgn0032223_shift2 (GATAd_SANGER_5_FBgn0032223)				; oligos_6nt_mkv4_m6 versus GATAd_SANGER_5_FBgn0032223; m=2/13; ncol2=8; w=0; offset=1; strand=D; shift=2; score=0.633004; --csTTATCA--- ; cor=; Ncor= a 0 0 1 1 1 0 23 0 0 22 0 0 0 c 0 0 12 14 0 0 0 1 23 0 0 0 0 g 0 0 5 6 0 0 0 0 0 1 0 0 0 t 0 0 3 1 22 23 0 22 0 0 0 0 0
So_SOLEXA_FBgn0003460_rc_shift5 (So_SOLEXA_FBgn0003460_rc)				; oligos_6nt_mkv4_m6 versus So_SOLEXA_FBgn0003460_rc; m=3/13; ncol2=8; w=0; offset=4; strand=R; shift=5; score=0.627456; -----TATCAyww ; cor=; Ncor= a 0 0 0 0 0 0 509 0 0 467 122 165 166 c 0 0 0 0 0 0 14 0 519 4 151 117 95 g 0 0 0 0 0 0 8 0 0 58 87 92 102 t 0 0 0 0 0 531 0 531 12 2 171 157 168
Optix_SOLEXA_FBgn0025360_rc_shift5 (Optix_SOLEXA_FBgn0025360_rc)				; oligos_6nt_mkv4_m6 versus Optix_SOLEXA_FBgn0025360_rc; m=4/13; ncol2=8; w=0; offset=4; strand=R; shift=5; score=0.624418; -----TATCAcww ; cor=; Ncor= a 0 0 0 0 0 0 564 0 0 497 116 151 143 c 0 0 0 0 0 17 0 0 564 0 216 119 126 g 0 0 0 0 0 43 0 0 0 67 93 111 91 t 0 0 0 0 0 504 0 564 0 0 139 183 204
Optix_Cell_FBgn0025360_rc_shift5 (Optix_Cell_FBgn0025360_rc)				; oligos_6nt_mkv4_m6 versus Optix_Cell_FBgn0025360_rc; m=5/13; ncol2=8; w=0; offset=4; strand=R; shift=5; score=0.607714; -----TATCAcww ; cor=; Ncor= a 0 0 0 0 0 0 27 0 0 22 3 7 9 c 0 0 0 0 0 1 0 0 27 0 16 3 2 g 0 0 0 0 0 0 0 0 0 5 4 4 4 t 0 0 0 0 0 26 0 27 0 0 4 13 12
Six4_SOLEXA_FBgn0027364_rc_shift5 (Six4_SOLEXA_FBgn0027364_rc)				; oligos_6nt_mkv4_m6 versus Six4_SOLEXA_FBgn0027364_rc; m=6/13; ncol2=8; w=0; offset=4; strand=R; shift=5; score=0.579365; -----TaTCAhww ; cor=; Ncor= a 0 0 0 0 0 0 383 0 38 599 194 203 181 c 0 0 0 0 0 0 126 0 556 0 167 83 116 g 0 0 0 0 0 40 128 0 0 38 84 91 93 t 0 0 0 0 0 597 0 637 43 0 192 260 247
GATAe_SANGER_5_FBgn0038391_rc_shift3 (GATAe_SANGER_5_FBgn0038391_rc)				; oligos_6nt_mkv4_m6 versus GATAe_SANGER_5_FBgn0038391_rc; m=7/13; ncol2=7; w=0; offset=2; strand=R; shift=3; score=0.572773; ---CTTATCw--- ; cor=; Ncor= a 0 0 0 0 0 0 19 0 0 9 0 0 0 c 0 0 0 15 0 0 0 0 19 0 0 0 0 g 0 0 0 4 0 0 0 0 0 2 0 0 0 t 0 0 0 0 19 19 0 19 0 8 0 0 0
pnr_SANGER_5_FBgn0003117_rc_shift4 (pnr_SANGER_5_FBgn0003117_rc)				; oligos_6nt_mkv4_m6 versus pnr_SANGER_5_FBgn0003117_rc; m=8/13; ncol2=7; w=0; offset=3; strand=R; shift=4; score=0.561174; ----TTATCwg-- ; cor=; Ncor= a 0 0 0 0 0 0 16 0 0 7 3 0 0 c 0 0 0 0 0 0 0 0 17 0 3 0 0 g 0 0 0 0 0 0 0 0 0 0 9 0 0 t 0 0 0 0 16 17 1 17 0 10 2 0 0
br_SOLEXA_10_FBgn0000210_rc_shift0 (br_SOLEXA_10_FBgn0000210_rc)				; oligos_6nt_mkv4_m6 versus br_SOLEXA_10_FBgn0000210_rc; m=9/13; ncol2=11; w=-1; offset=-1; strand=R; shift=0; score=0.541536; ytTCTAATCab-- ; cor=; Ncor= a 47 73 2 0 0 359 353 37 8 147 44 0 0 c 125 21 37 362 0 0 1 0 344 41 118 0 0 g 32 54 1 0 0 0 4 21 1 78 87 0 0 t 156 212 322 0 362 3 4 304 9 86 89 0 0
So_Cell_FBgn0003460_rc_shift5 (So_Cell_FBgn0003460_rc)				; oligos_6nt_mkv4_m6 versus So_Cell_FBgn0003460_rc; m=10/13; ncol2=7; w=0; offset=4; strand=R; shift=5; score=0.527048; -----TATCAyt- ; cor=; Ncor= a 0 0 0 0 0 0 26 0 0 26 3 6 0 c 0 0 0 0 0 0 1 0 27 1 10 5 0 g 0 0 0 0 0 0 0 0 0 0 1 4 0 t 0 0 0 0 0 27 0 27 0 0 13 12 0
exd_SOLEXA_2_FBgn0000611_rc_shift4 (exd_SOLEXA_2_FBgn0000611_rc)				; oligos_6nt_mkv4_m6 versus exd_SOLEXA_2_FBgn0000611_rc; m=11/13; ncol2=8; w=0; offset=3; strand=R; shift=4; score=0.474868; ----wyrTCAaa- ; cor=; Ncor= a 0 0 0 0 483 259 1228 0 0 2672 1314 1025 0 c 0 0 0 0 145 914 86 0 2672 0 598 458 0 g 0 0 0 0 91 14 1169 0 0 0 204 568 0 t 0 0 0 0 474 1470 189 2672 0 0 539 587 0
Six4_SOLEXA_2_FBgn0027364_rc_shift3 (Six4_SOLEXA_2_FBgn0027364_rc)				; oligos_6nt_mkv4_m6 versus Six4_SOLEXA_2_FBgn0027364_rc; m=12/13; ncol2=8; w=0; offset=2; strand=R; shift=3; score=0.474572; ---sgTaTCAy-- ; cor=; Ncor= a 0 0 0 136 239 0 1624 0 143 2272 633 0 0 c 0 0 0 210 58 0 644 0 2488 74 695 0 0 g 0 0 0 377 1021 89 257 0 0 204 413 0 0 t 0 0 0 83 209 2542 106 2631 0 52 824 0 0
br_SANGER_10_FBgn0000210_rc_shift2 (br_SANGER_10_FBgn0000210_rc)				; oligos_6nt_mkv4_m6 versus br_SANGER_10_FBgn0000210_rc; m=13/13; ncol2=7; w=0; offset=1; strand=R; shift=2; score=0.420056; --TCTAATC---- ; cor=; Ncor= a 0 0 0 0 0 12 12 0 0 0 0 0 0 c 0 0 0 11 0 0 0 0 11 0 0 0 0 g 0 0 0 1 0 0 0 0 0 0 0 0 0 t 0 0 12 0 12 0 0 12 1 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m7_shift1 (dyads_m7)				; dyads_m7; m=0 (reference); ncol1=15; shift=1; ncol=16; -camACACACACrCac ; Alignment reference a 0 746 2162 2054 3563 103 3664 76 3641 88 3518 93 1154 127 2089 496 c 0 2128 728 1297 97 3543 51 3629 30 3616 79 3585 176 3437 446 2402 g 0 453 495 139 100 64 94 52 113 38 139 81 2268 151 757 435 t 0 523 465 360 90 140 41 93 66 108 114 91 252 135 558 517
klu_SOLEXA_5_FBgn0013469_rc_shift0 (klu_SOLEXA_5_FBgn0013469_rc)				; dyads_m7 versus klu_SOLEXA_5_FBgn0013469_rc; m=1/3; ncol2=15; w=-1; offset=-1; strand=R; shift=0; score=0.630841; mmmmmCACCCmCrCm- ; cor=; Ncor= a 132 156 135 134 155 9 378 3 3 5 315 2 226 54 156 0 c 152 168 188 204 298 491 6 491 485 472 168 493 10 360 138 0 g 82 90 85 64 24 0 48 0 5 0 6 1 230 5 54 0 t 91 79 95 101 26 3 71 9 10 26 14 7 37 33 75 0
klu_SANGER_10_FBgn0013469_rc_shift4 (klu_SANGER_10_FBgn0013469_rc)				; dyads_m7 versus klu_SANGER_10_FBgn0013469_rc; m=2/3; ncol2=11; w=0; offset=3; strand=R; shift=4; score=0.55567; ----mCACCCmCrCa- ; cor=; Ncor= a 0 0 0 0 7 0 18 0 0 0 13 0 9 0 12 0 c 0 0 0 0 11 20 0 20 20 19 7 20 0 16 2 0 g 0 0 0 0 2 0 0 0 0 0 0 0 10 0 2 0 t 0 0 0 0 0 0 2 0 0 1 0 0 1 3 2 0
CG16778_SANGER_5_FBgn0003715_shift5 (CG16778_SANGER_5_FBgn0003715)				; dyads_m7 versus CG16778_SANGER_5_FBgn0003715; m=3/3; ncol2=8; w=0; offset=4; strand=D; shift=5; score=0.436799; -----CACAyAYG--- ; cor=; Ncor= a 0 0 0 0 0 0 18 0 20 0 17 0 0 0 0 0 c 0 0 0 0 0 15 1 20 0 9 0 6 1 0 0 0 g 0 0 0 0 0 2 0 0 0 0 3 0 18 0 0 0 t 0 0 0 0 0 1 0 0 0 11 0 14 1 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv5_m4_shift3 (oligos_7nt_mkv5_m4)				; oligos_7nt_mkv5_m4; m=0 (reference); ncol1=13; shift=3; ncol=16; ---caCACAcACACac ; Alignment reference a 0 0 0 1616 5949 121 8874 84 8611 2218 8784 54 8849 112 5929 1185 c 0 0 0 5506 794 8776 44 8848 265 5812 99 8906 48 8808 804 5541 g 0 0 0 663 1558 47 67 42 67 257 96 17 101 57 1381 1022 t 0 0 0 1242 726 83 42 53 84 740 48 50 29 50 913 1279
klu_SANGER_10_FBgn0013469_rc_shift4 (klu_SANGER_10_FBgn0013469_rc)				; oligos_7nt_mkv5_m4 versus klu_SANGER_10_FBgn0013469_rc; m=1/6; ncol2=11; w=0; offset=1; strand=R; shift=4; score=0.624937; ----mCACCCmCrCa- ; cor=; Ncor= a 0 0 0 0 7 0 18 0 0 0 13 0 9 0 12 0 c 0 0 0 0 11 20 0 20 20 19 7 20 0 16 2 0 g 0 0 0 0 2 0 0 0 0 0 0 0 10 0 2 0 t 0 0 0 0 0 0 2 0 0 1 0 0 1 3 2 0
klu_SOLEXA_5_FBgn0013469_rc_shift0 (klu_SOLEXA_5_FBgn0013469_rc)				; oligos_7nt_mkv5_m4 versus klu_SOLEXA_5_FBgn0013469_rc; m=2/6; ncol2=15; w=-3; offset=-3; strand=R; shift=0; score=0.534019; mmmmmCACCCmCrCm- ; cor=; Ncor= a 132 156 135 134 155 9 378 3 3 5 315 2 226 54 156 0 c 152 168 188 204 298 491 6 491 485 472 168 493 10 360 138 0 g 82 90 85 64 24 0 48 0 5 0 6 1 230 5 54 0 t 91 79 95 101 26 3 71 9 10 26 14 7 37 33 75 0
CG5953_SANGER_5_FBgn0032587_shift6 (CG5953_SANGER_5_FBgn0032587)				; oligos_7nt_mkv5_m4 versus CG5953_SANGER_5_FBgn0032587; m=3/6; ncol2=8; w=0; offset=3; strand=D; shift=6; score=0.492643; ------aCAAACAy-- ; cor=; Ncor= a 0 0 0 0 0 0 10 0 16 16 16 0 16 1 0 0 c 0 0 0 0 0 0 3 16 0 0 0 16 0 5 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 3 0 0 0 0 0 0 10 0 0
Ci_SANGER_5_FBgn0004859_shift1 (Ci_SANGER_5_FBgn0004859)				; oligos_7nt_mkv5_m4 versus Ci_SANGER_5_FBgn0004859; m=4/6; ncol2=11; w=-2; offset=-2; strand=D; shift=1; score=0.433596; -rGMCCACMCAC---- ; cor=; Ncor= a 0 6 0 8 2 1 8 0 3 0 10 0 0 0 0 0 c 0 0 0 3 9 10 2 10 8 11 0 9 0 0 0 0 g 0 4 11 0 0 0 0 0 0 0 1 2 0 0 0 0 t 0 1 0 0 0 0 1 1 0 0 0 0 0 0 0 0
CG12029_SANGER_10_FBgn0035454_rc_shift1 (CG12029_SANGER_10_FBgn0035454_rc)				; oligos_7nt_mkv5_m4 versus CG12029_SANGER_10_FBgn0035454_rc; m=5/6; ncol2=11; w=-2; offset=-2; strand=R; shift=1; score=0.43286; -RCCACACCCac---- ; cor=; Ncor= a 0 5 4 0 16 0 17 0 0 0 13 4 0 0 0 0 c 0 0 14 20 2 20 0 20 20 20 3 11 0 0 0 0 g 0 15 2 0 2 0 2 0 0 0 0 1 0 0 0 0 t 0 0 0 0 0 0 1 0 0 0 4 4 0 0 0 0
CG16778_SANGER_5_FBgn0003715_shift9 (CG16778_SANGER_5_FBgn0003715)				; oligos_7nt_mkv5_m4 versus CG16778_SANGER_5_FBgn0003715; m=6/6; ncol2=8; w=0; offset=6; strand=D; shift=9; score=0.418046; ---------CACAyAY ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 18 0 20 0 17 0 c 0 0 0 0 0 0 0 0 0 15 1 20 0 9 0 6 g 0 0 0 0 0 0 0 0 0 2 0 0 0 0 3 0 t 0 0 0 0 0 0 0 0 0 1 0 0 0 11 0 14

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m4_shift2 (dyads_m4)				; dyads_m4; m=0 (reference); ncol1=13; shift=2; ncol=15; --camACACACrCaC ; Alignment reference a 0 0 692 1932 1963 3124 46 3190 60 3155 31 986 38 2067 370 c 0 0 1862 667 1096 52 3156 14 3160 33 3190 50 3147 251 2240 g 0 0 346 403 68 60 25 53 18 45 21 2134 51 608 304 t 0 0 369 267 142 33 42 12 31 36 27 99 33 343 355
klu_SANGER_10_FBgn0013469_rc_shift3 (klu_SANGER_10_FBgn0013469_rc)				; dyads_m4 versus klu_SANGER_10_FBgn0013469_rc; m=1/5; ncol2=11; w=0; offset=1; strand=R; shift=3; score=0.601875; ---mCACCCmCrCa- ; cor=; Ncor= a 0 0 0 7 0 18 0 0 0 13 0 9 0 12 0 c 0 0 0 11 20 0 20 20 19 7 20 0 16 2 0 g 0 0 0 2 0 0 0 0 0 0 0 10 0 2 0 t 0 0 0 0 0 2 0 0 1 0 0 1 3 2 0
CG16778_SANGER_5_FBgn0003715_shift4 (CG16778_SANGER_5_FBgn0003715)				; dyads_m4 versus CG16778_SANGER_5_FBgn0003715; m=2/5; ncol2=8; w=0; offset=2; strand=D; shift=4; score=0.455999; ----CACAyAYG--- ; cor=; Ncor= a 0 0 0 0 0 18 0 20 0 17 0 0 0 0 0 c 0 0 0 0 15 1 20 0 9 0 6 1 0 0 0 g 0 0 0 0 2 0 0 0 0 3 0 18 0 0 0 t 0 0 0 0 1 0 0 0 11 0 14 1 0 0 0
Ci_SANGER_5_FBgn0004859_shift0 (Ci_SANGER_5_FBgn0004859)				; dyads_m4 versus Ci_SANGER_5_FBgn0004859; m=3/5; ncol2=11; w=-2; offset=-2; strand=D; shift=0; score=0.420771; rGMCCACMCAC---- ; cor=; Ncor= a 6 0 8 2 1 8 0 3 0 10 0 0 0 0 0 c 0 0 3 9 10 2 10 8 11 0 9 0 0 0 0 g 4 11 0 0 0 0 0 0 0 1 2 0 0 0 0 t 1 0 0 0 0 1 1 0 0 0 0 0 0 0 0
foxo_SANGER_10_FBgn0038197_rc_shift1 (foxo_SANGER_10_FBgn0038197_rc)				; dyads_m4 versus foxo_SANGER_10_FBgn0038197_rc; m=4/5; ncol2=9; w=-1; offset=-1; strand=R; shift=1; score=0.420181; -ycrwAAACA----- ; cor=; Ncor= a 0 0 3 8 8 16 16 20 0 20 0 0 0 0 0 c 0 6 12 0 0 1 4 0 18 0 0 0 0 0 0 g 0 3 3 11 0 0 0 0 0 0 0 0 0 0 0 t 0 11 2 1 12 3 0 0 2 0 0 0 0 0 0
CG5953_SANGER_5_FBgn0032587_shift1 (CG5953_SANGER_5_FBgn0032587)				; dyads_m4 versus CG5953_SANGER_5_FBgn0032587; m=5/5; ncol2=8; w=-1; offset=-1; strand=D; shift=1; score=0.408791; -aCAAACAy------ ; cor=; Ncor= a 0 10 0 16 16 16 0 16 1 0 0 0 0 0 0 c 0 3 16 0 0 0 16 0 5 0 0 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 3 0 0 0 0 0 0 10 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv5_m3_shift5 (oligos_7nt_mkv5_m3)				; oligos_7nt_mkv5_m3; m=0 (reference); ncol1=12; shift=5; ncol=17; -----caCCAmCACCac ; Alignment reference a 0 0 0 0 0 537 1591 66 86 2670 1679 63 2659 69 354 1474 675 c 0 0 0 0 0 1526 481 2678 2677 71 919 2713 103 2669 2209 633 1190 g 0 0 0 0 0 300 368 59 42 43 104 15 52 63 104 430 431 t 0 0 0 0 0 489 412 49 47 68 150 61 38 51 185 315 556
CG10267_SANGER_5_FBgn0037446_shift6 (CG10267_SANGER_5_FBgn0037446)				; oligos_7nt_mkv5_m3 versus CG10267_SANGER_5_FBgn0037446; m=1/4; ncol2=10; w=0; offset=1; strand=D; shift=6; score=0.601382; ------whyAACACTR- ; cor=; Ncor= a 0 0 0 0 0 0 8 6 1 16 16 1 16 0 0 11 0 c 0 0 0 0 0 0 0 6 10 0 0 14 0 16 0 0 0 g 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 5 0 t 0 0 0 0 0 0 7 4 5 0 0 1 0 0 16 0 0
Aef1_FlyReg_FBgn0005694_shift8 (Aef1_FlyReg_FBgn0005694)				; oligos_7nt_mkv5_m3 versus Aef1_FlyReg_FBgn0005694; m=2/4; ncol2=8; w=0; offset=3; strand=D; shift=8; score=0.48462; --------CAACwACw- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 3 3 0 2 3 0 2 0 c 0 0 0 0 0 0 0 0 3 0 0 3 0 0 3 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 1 0
CG31782-F9-11_SOLEXA_FBgn0051782_rc_shift3 (CG31782-F9-11_SOLEXA_FBgn0051782_rc)				; oligos_7nt_mkv5_m3 versus CG31782-F9-11_SOLEXA_FBgn0051782_rc; m=3/4; ncol2=11; w=-2; offset=-2; strand=R; shift=3; score=0.457205; ---ctCACCacyaa--- ; cor=; Ncor= a 0 0 0 269 617 42 2023 0 0 1676 407 471 1282 1413 0 0 0 c 0 0 0 1324 287 1979 143 2554 2552 582 1464 954 350 486 0 0 0 g 0 0 0 584 195 25 0 0 0 27 305 289 438 420 0 0 0 t 0 0 0 375 1453 506 386 0 1 269 377 838 482 234 0 0 0
klu_SOLEXA_5_FBgn0013469_rc_shift0 (klu_SOLEXA_5_FBgn0013469_rc)				; oligos_7nt_mkv5_m3 versus klu_SOLEXA_5_FBgn0013469_rc; m=4/4; ncol2=15; w=-5; offset=-5; strand=R; shift=0; score=0.412172; mmmmmCACCCmCrCm-- ; cor=; Ncor= a 132 156 135 134 155 9 378 3 3 5 315 2 226 54 156 0 0 c 152 168 188 204 298 491 6 491 485 472 168 493 10 360 138 0 0 g 82 90 85 64 24 0 48 0 5 0 6 1 230 5 54 0 0 t 91 79 95 101 26 3 71 9 10 26 14 7 37 33 75 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv4_m9_shift5 (oligos_6nt_mkv4_m9)				; oligos_6nt_mkv4_m9; m=0 (reference); ncol1=11; shift=5; ncol=16; -----mycCCACAGcv ; Alignment reference a 0 0 0 0 0 351 293 194 0 22 1229 47 1193 25 335 370 c 0 0 0 0 0 446 514 929 1366 1252 59 1259 95 36 476 370 g 0 0 0 0 0 285 244 167 14 74 64 49 67 1298 267 380 t 0 0 0 0 0 320 351 112 22 54 50 47 47 43 324 282
lola-PL_SOLEXA_FBgn0005630_shift4 (lola-PL_SOLEXA_FBgn0005630)				; oligos_6nt_mkv4_m9 versus lola-PL_SOLEXA_FBgn0005630; m=1/5; ncol2=14; w=-1; offset=-1; strand=D; shift=4; score=0.598127; ----kgmmCCACcgkg ; cor=; Ncor= a 0 0 0 0 357 215 944 808 0 0 2061 0 361 407 457 281 c 0 0 0 0 322 163 968 793 2061 2061 0 2061 1099 481 334 387 g 0 0 0 0 600 1232 0 137 0 0 0 0 123 834 690 939 t 0 0 0 0 780 447 148 322 0 0 0 0 476 337 576 452
lola-PL_SANGER_2.5_FBgn0005630_rc_shift4 (lola-PL_SANGER_2.5_FBgn0005630_rc)				; oligos_6nt_mkv4_m9 versus lola-PL_SANGER_2.5_FBgn0005630_rc; m=2/5; ncol2=9; w=-1; offset=-1; strand=R; shift=4; score=0.546944; ----TGmcCCACm--- ; cor=; Ncor= a 0 0 0 0 2 0 4 2 0 0 11 0 4 0 0 0 c 0 0 0 0 0 0 7 5 11 11 0 11 6 0 0 0 g 0 0 0 0 0 9 0 2 0 0 0 0 0 0 0 0 t 0 0 0 0 8 2 0 2 0 0 0 0 1 0 0 0
lmd_SOLEXA_5_FBgn0039039_rc_shift0 (lmd_SOLEXA_5_FBgn0039039_rc)				; oligos_6nt_mkv4_m9 versus lmd_SOLEXA_5_FBgn0039039_rc; m=3/5; ncol2=15; w=-5; offset=-5; strand=R; shift=0; score=0.453161; mmgmCCCCCcrCrga- ; cor=; Ncor= a 181 206 90 318 20 45 33 3 14 77 284 3 199 113 143 0 c 196 192 128 182 516 522 516 574 550 384 30 421 130 30 72 0 g 97 85 242 70 0 0 0 0 0 0 249 134 162 339 46 0 t 78 80 117 7 41 10 28 0 13 116 14 19 86 72 56 0
Opa_SANGER_5_FBgn0003002_shift1 (Opa_SANGER_5_FBgn0003002)				; oligos_6nt_mkv4_m9 versus Opa_SANGER_5_FBgn0003002; m=4/5; ncol2=13; w=-4; offset=-4; strand=D; shift=1; score=0.44943; -mkmmMCCCCmCyR-- ; cor=; Ncor= a 0 7 2 4 4 3 1 0 0 0 8 0 0 3 0 0 c 0 3 0 5 7 9 9 12 11 12 3 11 8 0 0 0 g 0 1 5 2 1 0 2 0 1 0 1 1 0 9 0 0 t 0 1 5 1 0 0 0 0 0 0 0 0 4 0 0 0
lmd_SANGER_5_FBgn0039039_rc_shift0 (lmd_SANGER_5_FBgn0039039_rc)				; oligos_6nt_mkv4_m9 versus lmd_SANGER_5_FBgn0039039_rc; m=5/5; ncol2=14; w=-5; offset=-5; strand=R; shift=0; score=0.419373; mmkaCCCCCCrCmG-- ; cor=; Ncor= a 10 8 1 13 0 0 0 0 0 1 11 0 9 3 0 0 c 8 9 3 5 20 22 22 22 22 16 1 18 7 1 0 0 g 2 3 11 4 0 0 0 0 0 0 10 4 3 15 0 0 t 1 2 7 0 2 0 0 0 0 5 0 0 3 2 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv5_m5_shift3 (oligos_7nt_mkv5_m5)				; oligos_7nt_mkv5_m5; m=0 (reference); ncol1=14; shift=3; ncol=17; ---caCACGCACACmca ; Alignment reference a 0 0 0 460 1509 205 2555 45 520 37 2687 35 2652 46 968 624 1177 c 0 0 0 1722 359 2317 95 2713 96 2718 45 2733 70 2700 1562 1283 628 g 0 0 0 280 595 123 87 48 2153 40 64 21 60 67 155 526 545 t 0 0 0 389 388 206 114 45 82 56 55 62 69 38 166 418 501
klu_SANGER_10_FBgn0013469_rc_shift4 (klu_SANGER_10_FBgn0013469_rc)				; oligos_7nt_mkv5_m5 versus klu_SANGER_10_FBgn0013469_rc; m=1/7; ncol2=11; w=0; offset=1; strand=R; shift=4; score=0.585532; ----mCACCCmCrCa-- ; cor=; Ncor= a 0 0 0 0 7 0 18 0 0 0 13 0 9 0 12 0 0 c 0 0 0 0 11 20 0 20 20 19 7 20 0 16 2 0 0 g 0 0 0 0 2 0 0 0 0 0 0 0 10 0 2 0 0 t 0 0 0 0 0 0 2 0 0 1 0 0 1 3 2 0 0
klu_SOLEXA_5_FBgn0013469_rc_shift0 (klu_SOLEXA_5_FBgn0013469_rc)				; oligos_7nt_mkv5_m5 versus klu_SOLEXA_5_FBgn0013469_rc; m=2/7; ncol2=15; w=-3; offset=-3; strand=R; shift=0; score=0.532574; mmmmmCACCCmCrCm-- ; cor=; Ncor= a 132 156 135 134 155 9 378 3 3 5 315 2 226 54 156 0 0 c 152 168 188 204 298 491 6 491 485 472 168 493 10 360 138 0 0 g 82 90 85 64 24 0 48 0 5 0 6 1 230 5 54 0 0 t 91 79 95 101 26 3 71 9 10 26 14 7 37 33 75 0 0
tgo_ss_SANGER_5_FBgn0003513_rc_shift3 (tgo_ss_SANGER_5_FBgn0003513_rc)				; oligos_7nt_mkv5_m5 versus tgo_ss_SANGER_5_FBgn0003513_rc; m=3/7; ncol2=8; w=0; offset=0; strand=R; shift=3; score=0.44245; ---GTCACGCA------ ; cor=; Ncor= a 0 0 0 2 0 0 10 0 1 0 9 0 0 0 0 0 0 c 0 0 0 0 0 10 0 9 0 10 0 0 0 0 0 0 0 g 0 0 0 8 0 0 0 1 9 0 1 0 0 0 0 0 0 t 0 0 0 0 10 0 0 0 0 0 0 0 0 0 0 0 0
tgo_ss_SANGER_5_FBgn0015014_rc_shift3 (tgo_ss_SANGER_5_FBgn0015014_rc)				; oligos_7nt_mkv5_m5 versus tgo_ss_SANGER_5_FBgn0015014_rc; m=4/7; ncol2=8; w=0; offset=0; strand=R; shift=3; score=0.44245; ---GTCACGCA------ ; cor=; Ncor= a 0 0 0 2 0 0 10 0 1 0 9 0 0 0 0 0 0 c 0 0 0 0 0 10 0 9 0 10 0 0 0 0 0 0 0 g 0 0 0 8 0 0 0 1 9 0 1 0 0 0 0 0 0 t 0 0 0 0 10 0 0 0 0 0 0 0 0 0 0 0 0
CG12029_SANGER_10_FBgn0035454_rc_shift1 (CG12029_SANGER_10_FBgn0035454_rc)				; oligos_7nt_mkv5_m5 versus CG12029_SANGER_10_FBgn0035454_rc; m=5/7; ncol2=11; w=-2; offset=-2; strand=R; shift=1; score=0.424923; -RCCACACCCac----- ; cor=; Ncor= a 0 5 4 0 16 0 17 0 0 0 13 4 0 0 0 0 0 c 0 0 14 20 2 20 0 20 20 20 3 11 0 0 0 0 0 g 0 15 2 0 2 0 2 0 0 0 0 1 0 0 0 0 0 t 0 0 0 0 0 0 1 0 0 0 4 4 0 0 0 0 0
Ci_SANGER_5_FBgn0004859_shift1 (Ci_SANGER_5_FBgn0004859)				; oligos_7nt_mkv5_m5 versus Ci_SANGER_5_FBgn0004859; m=6/7; ncol2=11; w=-2; offset=-2; strand=D; shift=1; score=0.412168; -rGMCCACMCAC----- ; cor=; Ncor= a 0 6 0 8 2 1 8 0 3 0 10 0 0 0 0 0 0 c 0 0 0 3 9 10 2 10 8 11 0 9 0 0 0 0 0 g 0 4 11 0 0 0 0 0 0 0 1 2 0 0 0 0 0 t 0 1 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0
CG16778_SANGER_5_FBgn0003715_shift9 (CG16778_SANGER_5_FBgn0003715)				; oligos_7nt_mkv5_m5 versus CG16778_SANGER_5_FBgn0003715; m=7/7; ncol2=8; w=0; offset=6; strand=D; shift=9; score=0.405763; ---------CACAyAYG ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 18 0 20 0 17 0 0 c 0 0 0 0 0 0 0 0 0 15 1 20 0 9 0 6 1 g 0 0 0 0 0 0 0 0 0 2 0 0 0 0 3 0 18 t 0 0 0 0 0 0 0 0 0 1 0 0 0 11 0 14 1

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv5_m10_shift4 (oligos_7nt_mkv5_m10)				; oligos_7nt_mkv5_m10; m=0 (reference); ncol1=11; shift=4; ncol=15; ----rrCAGAGACrg ; Alignment reference a 0 0 0 0 510 713 119 1668 35 1626 74 1599 123 732 432 c 0 0 0 0 439 367 1422 60 33 93 37 80 1348 348 434 g 0 0 0 0 525 496 207 55 1666 59 1613 85 267 487 665 t 0 0 0 0 329 227 55 20 69 25 79 39 65 236 272
Adf1_SANGER_5_FBgn0000054_shift0 (Adf1_SANGER_5_FBgn0000054)				; oligos_7nt_mkv5_m10 versus Adf1_SANGER_5_FBgn0000054; m=1/3; ncol2=15; w=-4; offset=-4; strand=D; shift=0; score=0.582795; ymcmRGCAGAGmhrm ; cor=; Ncor= a 1 7 2 4 3 0 0 11 0 8 0 7 4 5 7 c 5 3 6 7 0 0 11 0 1 1 0 3 4 2 4 g 0 1 2 0 8 10 0 0 10 2 11 1 0 3 0 t 5 0 1 0 0 1 0 0 0 0 0 0 3 1 0
CG13897_SANGER_5_FBgn0035160_shift2 (CG13897_SANGER_5_FBgn0035160)				; oligos_7nt_mkv5_m10 versus CG13897_SANGER_5_FBgn0035160; m=2/3; ncol2=11; w=-2; offset=-2; strand=D; shift=2; score=0.514126; --wsrrCAGACAs-- ; cor=; Ncor= a 0 0 5 2 8 9 0 17 0 17 0 17 4 0 0 c 0 0 4 8 0 0 13 0 0 0 17 0 8 0 0 g 0 0 0 7 8 7 4 0 17 0 0 0 5 0 0 t 0 0 8 0 1 1 0 0 0 0 0 0 0 0 0
bin_FlyReg_FBgn0045759_shift2 (bin_FlyReg_FBgn0045759)				; oligos_7nt_mkv5_m10 versus bin_FlyReg_FBgn0045759; m=3/3; ncol2=10; w=-2; offset=-2; strand=D; shift=2; score=0.463785; --TAAACArmGA--- ; cor=; Ncor= a 0 0 0 4 4 4 0 5 3 2 0 4 0 0 0 c 0 0 0 0 0 1 5 0 0 2 0 0 0 0 0 g 0 0 0 0 0 0 0 0 2 1 5 1 0 0 0 t 0 0 5 1 1 0 0 0 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv4_m8_shift3 (oligos_6nt_mkv4_m8)				; oligos_6nt_mkv4_m8; m=0 (reference); ncol1=10; shift=3; ncol=13; ---mrCAAAACam ; Alignment reference a 0 0 0 588 575 0 1505 1527 1517 1531 0 700 535 c 0 0 0 401 285 1520 0 0 0 0 1533 288 428 g 0 0 0 275 408 0 3 0 1 0 0 317 327 t 0 0 0 269 265 13 25 6 15 2 0 228 243
Ara_Cell_FBgn0015904_shift4 (Ara_Cell_FBgn0015904)				; oligos_6nt_mkv4_m8 versus Ara_Cell_FBgn0015904; m=1/11; ncol2=8; w=0; offset=1; strand=D; shift=4; score=0.582067; ----raAwwACA- ; cor=; Ncor= a 0 0 0 0 12 16 24 14 23 34 0 34 0 c 0 0 0 0 5 7 1 0 0 0 34 0 0 g 0 0 0 0 10 6 1 5 0 0 0 0 0 t 0 0 0 0 7 5 8 15 11 0 0 0 0
grh_FlyReg_FBgn0259211_rc_shift4 (grh_FlyReg_FBgn0259211_rc)				; oligos_6nt_mkv4_m8 versus grh_FlyReg_FBgn0259211_rc; m=2/11; ncol2=10; w=0; offset=1; strand=R; shift=4; score=0.580747; ----rbwrAACMA ; cor=; Ncor= a 0 0 0 0 4 0 4 4 8 7 1 2 7 c 0 0 0 0 0 3 1 1 0 0 6 6 0 g 0 0 0 0 3 2 1 3 0 1 0 0 1 t 0 0 0 0 1 3 2 0 0 0 1 0 0
pan_FlyReg_FBgn0085432_rc_shift2 (pan_FlyReg_FBgn0085432_rc)				; oligos_6nt_mkv4_m8 versus pan_FlyReg_FBgn0085432_rc; m=3/11; ncol2=8; w=-1; offset=-1; strand=R; shift=2; score=0.502901; --kWTCAAAr--- ; cor=; Ncor= a 0 0 4 17 3 3 23 22 20 8 0 0 0 c 0 0 3 0 5 20 0 1 0 3 0 0 0 g 0 0 11 0 0 2 0 0 3 10 0 0 0 t 0 0 7 8 17 0 2 2 2 4 0 0 0
jim_F1-9_SOLEXA_2.5_FBgn0027339_shift1 (jim_F1-9_SOLEXA_2.5_FBgn0027339)				; oligos_6nt_mkv4_m8 versus jim_F1-9_SOLEXA_2.5_FBgn0027339; m=4/11; ncol2=15; w=-2; offset=-2; strand=D; shift=1; score=0.489351; -rmAAaAAAAmma ; cor=; Ncor= a 0 202 124 372 414 259 411 369 349 412 159 154 240 c 0 60 190 26 6 104 1 52 5 0 222 122 55 g 0 102 43 6 0 0 4 2 64 11 40 74 74 t 0 25 50 19 3 60 7 0 5 0 2 73 54
Exd_Cell_FBgn0000611_rc_shift2 (Exd_Cell_FBgn0000611_rc)				; oligos_6nt_mkv4_m8 versus Exd_Cell_FBgn0000611_rc; m=5/11; ncol2=8; w=-1; offset=-1; strand=R; shift=2; score=0.464969; --yRTCAAAa--- ; cor=; Ncor= a 0 0 0 5 0 0 17 17 14 5 0 0 0 c 0 0 6 0 0 17 0 0 2 4 0 0 0 g 0 0 0 12 0 0 0 0 0 4 0 0 0 t 0 0 11 0 17 0 0 0 1 4 0 0 0
Ara_SOLEXA_FBgn0015904_shift6 (Ara_SOLEXA_FBgn0015904)				; oligos_6nt_mkv4_m8 versus Ara_SOLEXA_FBgn0015904; m=6/11; ncol2=6; w=0; offset=3; strand=D; shift=6; score=0.445715; ------awwACA- ; cor=; Ncor= a 0 0 0 0 0 0 155 97 193 313 0 313 0 c 0 0 0 0 0 0 36 0 0 0 313 0 0 g 0 0 0 0 0 0 44 45 38 0 0 0 0 t 0 0 0 0 0 0 78 171 82 0 0 0 0
exd_FlyReg_FBgn0000611_rc_shift0 (exd_FlyReg_FBgn0000611_rc)				; oligos_6nt_mkv4_m8 versus exd_FlyReg_FBgn0000611_rc; m=7/11; ncol2=10; w=-3; offset=-3; strand=R; shift=0; score=0.433853; twrawyrAAA--- ; cor=; Ncor= a 1 4 3 3 3 1 2 6 5 5 0 0 0 c 1 0 1 1 0 3 1 0 0 1 0 0 0 g 1 0 2 1 0 0 2 0 0 0 0 0 0 t 3 2 0 1 3 2 1 0 1 0 0 0 0
Mirr_SOLEXA_FBgn0014343_shift6 (Mirr_SOLEXA_FBgn0014343)				; oligos_6nt_mkv4_m8 versus Mirr_SOLEXA_FBgn0014343; m=8/11; ncol2=6; w=0; offset=3; strand=D; shift=6; score=0.425234; ------wwwACA- ; cor=; Ncor= a 0 0 0 0 0 0 550 410 782 1415 0 1415 0 c 0 0 0 0 0 0 158 93 0 0 1415 0 0 g 0 0 0 0 0 0 327 282 204 0 0 0 0 t 0 0 0 0 0 0 380 630 429 0 0 0 0
sage_da_SANGER_5_FBgn0037672_shift6 (sage_da_SANGER_5_FBgn0037672)				; oligos_6nt_mkv4_m8 versus sage_da_SANGER_5_FBgn0037672; m=9/11; ncol2=11; w=0; offset=3; strand=D; shift=6; score=0.416231; ------rAAMCAs ; cor=; Ncor= a 0 0 0 0 0 0 12 17 21 16 0 23 0 c 0 0 0 0 0 0 0 3 2 6 23 0 10 g 0 0 0 0 0 0 6 3 0 1 0 0 9 t 0 0 0 0 0 0 5 0 0 0 0 0 4
Side_SANGER_5_FBgn0032741_shift6 (Side_SANGER_5_FBgn0032741)				; oligos_6nt_mkv4_m8 versus Side_SANGER_5_FBgn0032741; m=10/11; ncol2=11; w=0; offset=3; strand=D; shift=6; score=0.416231; ------rAAMCAs ; cor=; Ncor= a 0 0 0 0 0 0 12 17 21 16 0 23 0 c 0 0 0 0 0 0 0 3 2 6 23 0 10 g 0 0 0 0 0 0 6 3 0 1 0 0 9 t 0 0 0 0 0 0 5 0 0 0 0 0 4
sage_da_SANGER_5_FBgn0000413_shift6 (sage_da_SANGER_5_FBgn0000413)				; oligos_6nt_mkv4_m8 versus sage_da_SANGER_5_FBgn0000413; m=11/11; ncol2=11; w=0; offset=3; strand=D; shift=6; score=0.416231; ------rAAMCAs ; cor=; Ncor= a 0 0 0 0 0 0 12 17 21 16 0 23 0 c 0 0 0 0 0 0 0 3 2 6 23 0 10 g 0 0 0 0 0 0 6 3 0 1 0 0 9 t 0 0 0 0 0 0 5 0 0 0 0 0 4

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m3_shift0 (dyads_m3)				; dyads_m3; m=0 (reference); ncol1=14; shift=0; ncol=14; agCAGCAGCAGCag ; Alignment reference a 3023 732 205 4256 205 120 4427 196 120 4310 275 188 3102 833 c 572 721 4047 152 229 4354 108 164 4365 138 232 4152 534 744 g 704 2845 257 245 4149 96 157 4245 93 192 4045 171 729 2643 t 468 469 258 114 184 197 75 162 189 127 215 256 402 547
odd_NAR_FBgn0002985_shift0 (odd_NAR_FBgn0002985)				; dyads_m3 versus odd_NAR_FBgn0002985; m=1/5; ncol2=11; w=0; offset=0; strand=D; shift=0; score=0.570072; mmCAGTAGCAv--- ; cor=; Ncor= a 7 10 0 12 0 0 15 0 0 11 5 0 0 0 c 5 5 14 0 0 0 0 0 15 3 4 0 0 0 g 0 0 1 3 15 0 0 15 0 1 6 0 0 0 t 3 0 0 0 0 15 0 0 0 0 0 0 0 0
odd_NBT_5_FBgn0002985_rc_shift0 (odd_NBT_5_FBgn0002985_rc)				; dyads_m3 versus odd_NBT_5_FBgn0002985_rc; m=2/5; ncol2=9; w=0; offset=0; strand=R; shift=0; score=0.46271; wMCAGTAGC----- ; cor=; Ncor= a 9 16 0 18 0 0 23 0 0 0 0 0 0 0 c 5 6 23 0 0 0 0 0 23 0 0 0 0 0 g 0 0 0 5 23 0 0 23 0 0 0 0 0 0 t 9 1 0 0 0 23 0 0 0 0 0 0 0 0
odd_NBT_1.5_FBgn0002985_rc_shift0 (odd_NBT_1.5_FBgn0002985_rc)				; dyads_m3 versus odd_NBT_1.5_FBgn0002985_rc; m=3/5; ncol2=9; w=0; offset=0; strand=R; shift=0; score=0.461044; wmCrGWAGC----- ; cor=; Ncor= a 8 6 1 12 0 6 20 0 0 0 0 0 0 0 c 2 11 21 0 0 0 0 2 19 0 0 0 0 0 g 2 2 0 10 22 0 0 20 1 0 0 0 0 0 t 10 3 0 0 0 16 2 0 2 0 0 0 0 0
CG11504_SANGER_5_FBgn0039733_shift5 (CG11504_SANGER_5_FBgn0039733)				; dyads_m3 versus CG11504_SANGER_5_FBgn0039733; m=4/5; ncol2=9; w=0; offset=5; strand=D; shift=5; score=0.453636; -----YmGCAACAT ; cor=; Ncor= a 0 0 0 0 0 0 11 0 1 20 19 1 20 2 c 0 0 0 0 0 14 5 1 19 0 0 19 0 4 g 0 0 0 0 0 0 1 19 0 0 0 0 0 0 t 0 0 0 0 0 6 3 0 0 0 1 0 0 14
bowl_SANGER_5_FBgn0004893_shift1 (bowl_SANGER_5_FBgn0004893)				; dyads_m3 versus bowl_SANGER_5_FBgn0004893; m=5/5; ncol2=8; w=0; offset=1; strand=D; shift=1; score=0.416262; -mCrGwAGY----- ; cor=; Ncor= a 0 4 0 7 0 5 12 0 0 0 0 0 0 0 c 0 7 12 1 0 0 0 0 8 0 0 0 0 0 g 0 0 0 4 12 1 0 12 0 0 0 0 0 0 t 0 0 0 0 0 6 0 0 3 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv5_m1_shift3 (oligos_7nt_mkv5_m1)				; oligos_7nt_mkv5_m1; m=0 (reference); ncol1=11; shift=3; ncol=14; ---maAACACAAmm ; Alignment reference a 0 0 0 623 573 1802 1747 96 1720 81 1680 1767 555 640 c 0 0 0 544 437 1 22 1609 67 1586 57 20 518 599 g 0 0 0 384 449 28 54 61 58 114 51 39 350 326 t 0 0 0 329 421 49 57 114 35 99 92 54 457 315
CG10267_SANGER_5_FBgn0037446_shift2 (CG10267_SANGER_5_FBgn0037446)				; oligos_7nt_mkv5_m1 versus CG10267_SANGER_5_FBgn0037446; m=1/15; ncol2=10; w=-1; offset=-1; strand=D; shift=2; score=0.565316; --whyAACACTR-- ; cor=; Ncor= a 0 0 8 6 1 16 16 1 16 0 0 11 0 0 c 0 0 0 6 10 0 0 14 0 16 0 0 0 0 g 0 0 1 0 0 0 0 0 0 0 0 5 0 0 t 0 0 7 4 5 0 0 1 0 0 16 0 0 0
lola-PJ_SOLEXA_FBgn0005630_rc_shift0 (lola-PJ_SOLEXA_FBgn0005630_rc)				; oligos_7nt_mkv5_m1 versus lola-PJ_SOLEXA_FBgn0005630_rc; m=2/15; ncol2=15; w=-3; offset=-3; strand=R; shift=0; score=0.542897; mamvcArCATAAma ; cor=; Ncor= a 949 1076 776 839 556 2611 1471 0 2787 0 2752 2331 1167 928 c 872 696 1136 870 1665 49 0 2787 0 0 2 147 860 656 g 518 608 521 771 335 7 1227 0 0 2 9 254 494 560 t 446 405 352 305 229 117 87 0 0 2784 22 53 264 640
jim_F1-9_SOLEXA_2.5_FBgn0027339_shift3 (jim_F1-9_SOLEXA_2.5_FBgn0027339)				; oligos_7nt_mkv5_m1 versus jim_F1-9_SOLEXA_2.5_FBgn0027339; m=3/15; ncol2=15; w=0; offset=0; strand=D; shift=3; score=0.535592; ---rmAAaAAAAmm ; cor=; Ncor= a 0 0 0 202 124 372 414 259 411 369 349 412 159 154 c 0 0 0 60 190 26 6 104 1 52 5 0 222 122 g 0 0 0 102 43 6 0 0 4 2 64 11 40 74 t 0 0 0 25 50 19 3 60 7 0 5 0 2 73
Sox15_SANGER_5_FBgn0005613_shift6 (Sox15_SANGER_5_FBgn0005613)				; oligos_7nt_mkv5_m1 versus Sox15_SANGER_5_FBgn0005613; m=4/15; ncol2=8; w=0; offset=3; strand=D; shift=6; score= 0.532; ------aaACAATr ; cor=; Ncor= a 0 0 0 0 0 0 12 13 21 0 21 21 3 6 c 0 0 0 0 0 0 1 2 0 21 0 0 0 0 g 0 0 0 0 0 0 5 2 0 0 0 0 0 14 t 0 0 0 0 0 0 3 4 0 0 0 0 18 1
Ara_Cell_FBgn0015904_shift3 (Ara_Cell_FBgn0015904)				; oligos_7nt_mkv5_m1 versus Ara_Cell_FBgn0015904; m=5/15; ncol2=8; w=0; offset=0; strand=D; shift=3; score=0.51772; ---raAwwACA--- ; cor=; Ncor= a 0 0 0 12 16 24 14 23 34 0 34 0 0 0 c 0 0 0 5 7 1 0 0 0 34 0 0 0 0 g 0 0 0 10 6 1 5 0 0 0 0 0 0 0 t 0 0 0 7 5 8 15 11 0 0 0 0 0 0
Mirr_SOLEXA_FBgn0014343_shift3 (Mirr_SOLEXA_FBgn0014343)				; oligos_7nt_mkv5_m1 versus Mirr_SOLEXA_FBgn0014343; m=6/15; ncol2=6; w=0; offset=0; strand=D; shift=3; score=0.498442; ---wwwACA----- ; cor=; Ncor= a 0 0 0 550 410 782 1415 0 1415 0 0 0 0 0 c 0 0 0 158 93 0 0 1415 0 0 0 0 0 0 g 0 0 0 327 282 204 0 0 0 0 0 0 0 0 t 0 0 0 380 630 429 0 0 0 0 0 0 0 0
Ara_SOLEXA_FBgn0015904_shift3 (Ara_SOLEXA_FBgn0015904)				; oligos_7nt_mkv5_m1 versus Ara_SOLEXA_FBgn0015904; m=7/15; ncol2=6; w=0; offset=0; strand=D; shift=3; score=0.49709; ---awwACA----- ; cor=; Ncor= a 0 0 0 155 97 193 313 0 313 0 0 0 0 0 c 0 0 0 36 0 0 0 313 0 0 0 0 0 0 g 0 0 0 44 45 38 0 0 0 0 0 0 0 0 t 0 0 0 78 171 82 0 0 0 0 0 0 0 0
Caup_SOLEXA_FBgn0015919_shift3 (Caup_SOLEXA_FBgn0015919)				; oligos_7nt_mkv5_m1 versus Caup_SOLEXA_FBgn0015919; m=8/15; ncol2=6; w=0; offset=0; strand=D; shift=3; score=0.485439; ---wtwACA----- ; cor=; Ncor= a 0 0 0 999 577 1415 2904 2 2904 0 0 0 0 0 c 0 0 0 460 201 0 0 2902 0 0 0 0 0 0 g 0 0 0 626 639 511 0 0 0 0 0 0 0 0 t 0 0 0 819 1487 978 0 0 0 0 0 0 0 0
foxo_SANGER_10_FBgn0038197_rc_shift2 (foxo_SANGER_10_FBgn0038197_rc)				; oligos_7nt_mkv5_m1 versus foxo_SANGER_10_FBgn0038197_rc; m=9/15; ncol2=9; w=-1; offset=-1; strand=R; shift=2; score=0.472208; --ycrwAAACA--- ; cor=; Ncor= a 0 0 0 3 8 8 16 16 20 0 20 0 0 0 c 0 0 6 12 0 0 1 4 0 18 0 0 0 0 g 0 0 3 3 11 0 0 0 0 0 0 0 0 0 t 0 0 11 2 1 12 3 0 0 2 0 0 0 0
lola-PJ_SANGER_5_FBgn0005630_shift5 (lola-PJ_SANGER_5_FBgn0005630)				; oligos_7nt_mkv5_m1 versus lola-PJ_SANGER_5_FBgn0005630; m=10/15; ncol2=7; w=0; offset=2; strand=D; shift=5; score=0.471638; -----ArCATAA-- ; cor=; Ncor= a 0 0 0 0 0 11 5 0 12 0 12 12 0 0 c 0 0 0 0 0 0 0 12 0 0 0 0 0 0 g 0 0 0 0 0 0 7 0 0 0 0 0 0 0 t 0 0 0 0 0 1 0 0 0 12 0 0 0 0
CG5953_SANGER_5_FBgn0032587_shift2 (CG5953_SANGER_5_FBgn0032587)				; oligos_7nt_mkv5_m1 versus CG5953_SANGER_5_FBgn0032587; m=11/15; ncol2=8; w=-1; offset=-1; strand=D; shift=2; score=0.44424; --aCAAACAy---- ; cor=; Ncor= a 0 0 10 0 16 16 16 0 16 1 0 0 0 0 c 0 0 3 16 0 0 0 16 0 5 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 3 0 0 0 0 0 0 10 0 0 0 0
Mirr_Cell_FBgn0014343_shift1 (Mirr_Cell_FBgn0014343)				; oligos_7nt_mkv5_m1 versus Mirr_Cell_FBgn0014343; m=12/15; ncol2=8; w=-2; offset=-2; strand=D; shift=1; score=0.428582; -waawAACA----- ; cor=; Ncor= a 0 18 18 22 20 29 41 0 41 0 0 0 0 0 c 0 6 4 7 1 0 0 41 0 0 0 0 0 0 g 0 6 10 6 1 2 0 0 0 0 0 0 0 0 t 0 11 9 6 19 10 0 0 0 0 0 0 0 0
Caup_Cell_FBgn0015919_shift1 (Caup_Cell_FBgn0015919)				; oligos_7nt_mkv5_m1 versus Caup_Cell_FBgn0015919; m=13/15; ncol2=8; w=-2; offset=-2; strand=D; shift=1; score=0.422059; -cwwtAACA----- ; cor=; Ncor= a 0 4 9 8 4 14 19 0 19 0 0 0 0 0 c 0 9 0 0 1 0 0 19 0 0 0 0 0 0 g 0 2 3 4 2 2 0 0 0 0 0 0 0 0 t 0 4 7 7 12 3 0 0 0 0 0 0 0 0
slp2_SANGER_5_FBgn0004567_shift2 (slp2_SANGER_5_FBgn0004567)				; oligos_7nt_mkv5_m1 versus slp2_SANGER_5_FBgn0004567; m=14/15; ncol2=8; w=-1; offset=-1; strand=D; shift=2; score=0.415498; --rTAAACAa---- ; cor=; Ncor= a 0 0 6 0 18 18 18 0 18 11 0 0 0 0 c 0 0 0 1 0 0 0 18 0 3 0 0 0 0 g 0 0 12 0 0 0 0 0 0 3 0 0 0 0 t 0 0 0 17 0 0 0 0 0 1 0 0 0 0
bin_SANGER_5_FBgn0045759_shift2 (bin_SANGER_5_FBgn0045759)				; oligos_7nt_mkv5_m1 versus bin_SANGER_5_FBgn0045759; m=15/15; ncol2=7; w=-1; offset=-1; strand=D; shift=2; score=0.400116; --rTAAACA----- ; cor=; Ncor= a 0 0 9 0 20 20 20 0 19 0 0 0 0 0 c 0 0 0 0 0 0 0 20 0 0 0 0 0 0 g 0 0 10 0 0 0 0 0 0 0 0 0 0 0 t 0 0 1 20 0 0 0 0 1 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv4_m1_shift6 (oligos_6nt_mkv4_m1)				; oligos_6nt_mkv4_m1; m=0 (reference); ncol1=11; shift=6; ncol=17; ------cycCCACAAmm ; Alignment reference a 0 0 0 0 0 0 354 335 306 0 2 1250 50 1267 1364 427 379 c 0 0 0 0 0 0 516 530 804 1437 1382 94 1304 72 17 444 541 g 0 0 0 0 0 0 254 207 179 0 16 42 44 36 33 264 277 t 0 0 0 0 0 0 320 372 155 7 44 58 46 69 30 309 247
lola-PL_SOLEXA_FBgn0005630_shift5 (lola-PL_SOLEXA_FBgn0005630)				; oligos_6nt_mkv4_m1 versus lola-PL_SOLEXA_FBgn0005630; m=1/4; ncol2=14; w=-1; offset=-1; strand=D; shift=5; score=0.555117; -----kgmmCCACcgkg ; cor=; Ncor= a 0 0 0 0 0 357 215 944 808 0 0 2061 0 361 407 457 281 c 0 0 0 0 0 322 163 968 793 2061 2061 0 2061 1099 481 334 387 g 0 0 0 0 0 600 1232 0 137 0 0 0 0 123 834 690 939 t 0 0 0 0 0 780 447 148 322 0 0 0 0 476 337 576 452
lola-PL_SANGER_2.5_FBgn0005630_rc_shift5 (lola-PL_SANGER_2.5_FBgn0005630_rc)				; oligos_6nt_mkv4_m1 versus lola-PL_SANGER_2.5_FBgn0005630_rc; m=2/4; ncol2=9; w=-1; offset=-1; strand=R; shift=5; score=0.544368; -----TGmcCCACm--- ; cor=; Ncor= a 0 0 0 0 0 2 0 4 2 0 0 11 0 4 0 0 0 c 0 0 0 0 0 0 0 7 5 11 11 0 11 6 0 0 0 g 0 0 0 0 0 0 9 0 2 0 0 0 0 0 0 0 0 t 0 0 0 0 0 8 2 0 2 0 0 0 0 1 0 0 0
Lag1_Cell_FBgn0040918_shift9 (Lag1_Cell_FBgn0040918)				; oligos_6nt_mkv4_m1 versus Lag1_Cell_FBgn0040918; m=3/4; ncol2=10; w=0; offset=3; strand=D; shift=9; score=0.440737; ---------CyACyAaa ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 17 1 0 18 12 10 c 0 0 0 0 0 0 0 0 0 19 9 2 18 12 0 0 3 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 4 4 t 0 0 0 0 0 0 0 0 0 0 10 0 0 7 0 3 2
CG7368_SOLEXA_2.5_FBgn0036179_rc_shift0 (CG7368_SOLEXA_2.5_FBgn0036179_rc)				; oligos_6nt_mkv4_m1 versus CG7368_SOLEXA_2.5_FBgn0036179_rc; m=4/4; ncol2=15; w=-6; offset=-6; strand=R; shift=0; score=0.400001; yyCCCCChCCCmChm-- ; cor=; Ncor= a 38 51 27 3 8 1 34 90 44 3 8 97 14 64 95 0 0 c 111 95 203 230 227 235 200 84 170 230 224 133 199 66 65 0 0 g 16 22 1 0 0 0 0 0 1 0 0 0 0 19 13 0 0 t 67 68 5 3 1 0 2 62 21 3 4 6 23 81 26 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m1_shift2 (positions_6nt_m1)				; positions_6nt_m1; m=0 (reference); ncol1=15; shift=2; ncol=17; --acACACrCACACrca ; Alignment reference a 0 0 2460 417 3456 98 3539 72 1434 73 3511 79 3438 73 998 561 1745 c 0 0 435 2532 54 3524 54 3551 73 3555 25 3556 91 3576 237 2074 601 g 0 0 560 284 179 63 121 74 2125 61 193 54 179 89 2345 565 858 t 0 0 350 572 116 120 91 108 173 116 76 116 97 67 225 605 601
klu_SOLEXA_5_FBgn0013469_rc_shift0 (klu_SOLEXA_5_FBgn0013469_rc)				; positions_6nt_m1 versus klu_SOLEXA_5_FBgn0013469_rc; m=1/3; ncol2=15; w=-2; offset=-2; strand=R; shift=0; score=0.541754; mmmmmCACCCmCrCm-- ; cor=; Ncor= a 132 156 135 134 155 9 378 3 3 5 315 2 226 54 156 0 0 c 152 168 188 204 298 491 6 491 485 472 168 493 10 360 138 0 0 g 82 90 85 64 24 0 48 0 5 0 6 1 230 5 54 0 0 t 91 79 95 101 26 3 71 9 10 26 14 7 37 33 75 0 0
klu_SANGER_10_FBgn0013469_rc_shift4 (klu_SANGER_10_FBgn0013469_rc)				; positions_6nt_m1 versus klu_SANGER_10_FBgn0013469_rc; m=2/3; ncol2=11; w=0; offset=2; strand=R; shift=4; score=0.535556; ----mCACCCmCrCa-- ; cor=; Ncor= a 0 0 0 0 7 0 18 0 0 0 13 0 9 0 12 0 0 c 0 0 0 0 11 20 0 20 20 19 7 20 0 16 2 0 0 g 0 0 0 0 2 0 0 0 0 0 0 0 10 0 2 0 0 t 0 0 0 0 0 0 2 0 0 1 0 0 1 3 2 0 0
CG12029_SANGER_10_FBgn0035454_rc_shift1 (CG12029_SANGER_10_FBgn0035454_rc)				; positions_6nt_m1 versus CG12029_SANGER_10_FBgn0035454_rc; m=3/3; ncol2=11; w=-1; offset=-1; strand=R; shift=1; score=0.471629; -RCCACACCCac----- ; cor=; Ncor= a 0 5 4 0 16 0 17 0 0 0 13 4 0 0 0 0 0 c 0 0 14 20 2 20 0 20 20 20 3 11 0 0 0 0 0 g 0 15 2 0 2 0 2 0 0 0 0 1 0 0 0 0 0 t 0 0 0 0 0 0 1 0 0 0 4 4 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m6_shift1 (dyads_m6)				; dyads_m6; m=0 (reference); ncol1=13; shift=1; ncol=14; -camACACACAyac ; Alignment reference a 0 641 1787 1910 2920 40 2982 31 2973 30 2915 148 1847 393 c 0 1706 619 936 41 2945 17 2942 28 2937 41 987 432 1939 g 0 346 362 48 33 15 30 21 19 24 30 98 415 351 t 0 345 270 144 44 38 9 44 18 47 52 1805 344 355
CG16778_SANGER_5_FBgn0003715_shift5 (CG16778_SANGER_5_FBgn0003715)				; dyads_m6 versus CG16778_SANGER_5_FBgn0003715; m=1/3; ncol2=8; w=0; offset=4; strand=D; shift=5; score=0.503517; -----CACAyAYG- ; cor=; Ncor= a 0 0 0 0 0 0 18 0 20 0 17 0 0 0 c 0 0 0 0 0 15 1 20 0 9 0 6 1 0 g 0 0 0 0 0 2 0 0 0 0 3 0 18 0 t 0 0 0 0 0 1 0 0 0 11 0 14 1 0
CG5953_SANGER_5_FBgn0032587_shift4 (CG5953_SANGER_5_FBgn0032587)				; dyads_m6 versus CG5953_SANGER_5_FBgn0032587; m=2/3; ncol2=8; w=0; offset=3; strand=D; shift=4; score=0.486142; ----aCAAACAy-- ; cor=; Ncor= a 0 0 0 0 10 0 16 16 16 0 16 1 0 0 c 0 0 0 0 3 16 0 0 0 16 0 5 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 3 0 0 0 0 0 0 10 0 0
foxo_SANGER_10_FBgn0038197_rc_shift0 (foxo_SANGER_10_FBgn0038197_rc)				; dyads_m6 versus foxo_SANGER_10_FBgn0038197_rc; m=3/3; ncol2=9; w=-1; offset=-1; strand=R; shift=0; score=0.421793; ycrwAAACA----- ; cor=; Ncor= a 0 3 8 8 16 16 20 0 20 0 0 0 0 0 c 6 12 0 0 1 4 0 18 0 0 0 0 0 0 g 3 3 11 0 0 0 0 0 0 0 0 0 0 0 t 11 2 1 12 3 0 0 2 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv5_m6_shift0 (oligos_7nt_mkv5_m6)				; oligos_7nt_mkv5_m6; m=0 (reference); ncol1=17; shift=0; ncol=17; tgsTGCTGyTGCTGytg ; Alignment reference a 167 226 113 47 59 58 27 40 40 30 21 38 39 45 109 190 250 c 335 230 1115 82 31 1919 38 44 1312 37 40 1972 68 82 1155 261 291 g 355 1425 770 45 2066 113 50 2073 102 35 2098 89 51 2015 200 279 1342 t 1343 319 202 2026 44 110 2085 43 746 2098 41 101 2042 58 736 1470 317
odd_NAR_FBgn0002985_rc_shift5 (odd_NAR_FBgn0002985_rc)				; oligos_7nt_mkv5_m6 versus odd_NAR_FBgn0002985_rc; m=1/3; ncol2=11; w=0; offset=5; strand=R; shift=5; score=0.459648; -----bTGCTACTGkk- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 15 0 0 0 0 3 0 c 0 0 0 0 0 6 1 0 15 0 0 15 3 1 0 0 0 g 0 0 0 0 0 4 3 15 0 0 0 0 0 14 5 5 0 t 0 0 0 0 0 5 11 0 0 15 0 0 12 0 10 7 0
Aef1_SANGER_5_FBgn0005694_rc_shift1 (Aef1_SANGER_5_FBgn0005694_rc)				; oligos_7nt_mkv5_m6 versus Aef1_SANGER_5_FBgn0005694_rc; m=2/3; ncol2=11; w=0; offset=1; strand=R; shift=1; score=0.453241; -GKTGTTGTTGy----- ; cor=; Ncor= a 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 0 g 0 9 3 0 12 0 0 12 0 0 12 2 0 0 0 0 0 t 0 2 9 12 0 12 12 0 12 12 0 6 0 0 0 0 0
CG11504_SANGER_5_FBgn0039733_rc_shift5 (CG11504_SANGER_5_FBgn0039733_rc)				; oligos_7nt_mkv5_m6 versus CG11504_SANGER_5_FBgn0039733_rc; m=3/3; ncol2=9; w=0; offset=5; strand=R; shift=5; score=0.406288; -----ATGTTGCkR--- ; cor=; Ncor= a 0 0 0 0 0 14 0 0 1 0 0 0 3 6 0 0 0 c 0 0 0 0 0 0 0 0 0 0 0 19 1 0 0 0 0 g 0 0 0 0 0 4 0 19 0 0 19 1 5 14 0 0 0 t 0 0 0 0 0 2 20 1 19 20 1 0 11 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m9_shift0 (dyads_m9)				; dyads_m9; m=0 (reference); ncol1=14; shift=0; ncol=14; caAACACACACmca ; Alignment reference a 665 1337 1976 2446 92 2530 67 2498 59 2477 62 891 527 1266 c 1305 637 478 94 2450 56 2487 87 2538 99 2482 1505 1329 555 g 367 345 63 67 43 57 48 47 32 30 70 152 464 441 t 356 374 176 86 108 50 91 61 64 87 79 145 373 431
CG5953_SANGER_5_FBgn0032587_shift3 (CG5953_SANGER_5_FBgn0032587)				; dyads_m9 versus CG5953_SANGER_5_FBgn0032587; m=1/3; ncol2=8; w=0; offset=3; strand=D; shift=3; score=0.414153; ---aCAAACAy--- ; cor=; Ncor= a 0 0 0 10 0 16 16 16 0 16 1 0 0 0 c 0 0 0 3 16 0 0 0 16 0 5 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 3 0 0 0 0 0 0 10 0 0 0
CG16778_SANGER_5_FBgn0003715_shift4 (CG16778_SANGER_5_FBgn0003715)				; dyads_m9 versus CG16778_SANGER_5_FBgn0003715; m=2/3; ncol2=8; w=0; offset=4; strand=D; shift=4; score=0.407586; ----CACAyAYG-- ; cor=; Ncor= a 0 0 0 0 0 18 0 20 0 17 0 0 0 0 c 0 0 0 0 15 1 20 0 9 0 6 1 0 0 g 0 0 0 0 2 0 0 0 0 3 0 18 0 0 t 0 0 0 0 1 0 0 0 11 0 14 1 0 0
Ara_Cell_FBgn0015904_shift0 (Ara_Cell_FBgn0015904)				; dyads_m9 versus Ara_Cell_FBgn0015904; m=3/3; ncol2=8; w=0; offset=0; strand=D; shift=0; score=0.40058; raAwwACA------ ; cor=; Ncor= a 12 16 24 14 23 34 0 34 0 0 0 0 0 0 c 5 7 1 0 0 0 34 0 0 0 0 0 0 0 g 10 6 1 5 0 0 0 0 0 0 0 0 0 0 t 7 5 8 15 11 0 0 0 0 0 0 0 0 0