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/DrosophilaTFs/DrosophilaTFs_2015-11-06.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_DrosophilaTFs.tab

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m6_shift3 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m6_shift3 (oligos_6nt_mkv4_m6)
; oligos_6nt_mkv4_m6; m=0 (reference); ncol1=12; shift=3; ncol=15; ---yyCTTATCagym ; Alignment reference a 0 0 0 258 185 81 30 34 1157 9 27 667 140 266 331 c 0 0 0 411 359 1020 64 33 44 19 1173 127 207 383 328 g 0 0 0 231 277 65 39 16 8 37 9 266 679 226 283 t 0 0 0 339 418 73 1106 1156 30 1174 30 179 213 364 297

4988_srp_DrosophilaTF_1.1__rc_shift3 (4988_srp_DrosophilaTF_1.1__rc)
; oligos_6nt_mkv4_m6 versus 4988_srp_DrosophilaTF_1.1__rc; m=1/3; ncol2=10; w=0; offset=0; strand=R; shift=3; score=0.760079; ---rysTTATCrm-- ; cor=; Ncor= a 0 0 0 28 3 9 0 0 1 0 0 37 28 0 0 c 0 0 0 19 41 56 3 0 0 0 1 0 50 0 0 g 0 0 0 34 9 35 0 0 0 0 0 44 13 0 0 t 0 0 0 19 47 0 97 1 0 1 0 19 9 0 0

4978_pnr_DrosophilaTF_1.1__rc_shift0 (4978_pnr_DrosophilaTF_1.1__rc)
; oligos_6nt_mkv4_m6 versus 4978_pnr_DrosophilaTF_1.1__rc; m=2/3; ncol2=18; w=-3; offset=-3; strand=R; shift=0; score=0.625142; vbcyscTTATCdsmm ; cor=; Ncor= a 42 17 23 20 6 16 10 0 1 0 0 42 22 40 33 c 25 33 31 40 50 63 10 0 0 0 1 0 34 27 34 g 25 25 23 7 31 21 10 0 0 0 0 32 33 13 13 t 8 25 23 33 13 0 70 1 0 1 0 26 11 20 20

4945_TFAM_DrosophilaTF_1.1__shift6 (4945_TFAM_DrosophilaTF_1.1_)
; oligos_6nt_mkv4_m6 versus 4945_TFAM_DrosophilaTF_1.1_; m=3/3; ncol2=5; w=0; offset=3; strand=D; shift=6; score=0.412265; ------TTATC---- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 82 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 18 0 0 0 0 t 0 0 0 0 0 0 1 1 0 1 0 0 0 0 0

One-to-n matrix alignment; reference matrix: dyads_m3_shift0 ; 2 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

4933_Adf1_DrosophilaTF_1.1__rc_shift0 (4933_Adf1_DrosophilaTF_1.1__rc)
; dyads_m3 versus 4933_Adf1_DrosophilaTF_1.1__rc; m=1/1; ncol2=12; w=0; offset=0; strand=R; shift=0; score=0.705504; drCrGmrGsAGC-- ; cor=; Ncor= a 33 50 0 50 0 50 50 0 0 1 0 0 0 0 c 0 0 1 0 0 50 0 0 50 0 0 1 0 0 g 33 50 0 50 1 0 50 1 50 0 1 0 0 0 t 34 0 0 0 0 0 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m6_shift0 ; 2 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

4933_Adf1_DrosophilaTF_1.1__shift4 (4933_Adf1_DrosophilaTF_1.1_)
; oligos_7nt_mkv5_m6 versus 4933_Adf1_DrosophilaTF_1.1_; m=1/1; ncol2=12; w=0; offset=4; strand=D; shift=4; score=0.568981; ----GCTsCykCyGyh- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 34 0 c 0 0 0 0 0 1 0 50 1 50 0 1 50 0 50 33 0 g 0 0 0 0 1 0 0 50 0 0 50 0 0 1 0 0 0 t 0 0 0 0 0 0 1 0 0 50 50 0 50 0 50 33 0

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m2_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv5_m2_shift0 (oligos_7nt_mkv5_m2)
; oligos_7nt_mkv5_m2; m=0 (reference); ncol1=11; shift=0; ncol=11; hhCCACACCmm ; Alignment reference a 610 665 56 47 1899 120 1884 31 37 665 597 c 779 651 2175 2075 185 2039 272 2139 2175 670 740 g 352 414 33 72 129 81 56 70 39 560 463 t 597 608 74 144 125 98 126 98 87 443 538

4936_Dip3_DrosophilaTF_1.1__shift2 (4936_Dip3_DrosophilaTF_1.1_)
; oligos_7nt_mkv5_m2 versus 4936_Dip3_DrosophilaTF_1.1_; m=1/1; ncol2=12; w=0; offset=2; strand=D; shift=2; score=0.524266; --cCwsrycwk ; cor=; Ncor= a 0 0 4 4 46 19 35 7 12 35 19 c 0 0 64 73 11 42 19 58 65 12 8 g 0 0 8 4 12 31 27 4 4 15 27 t 0 0 24 19 31 8 19 31 19 38 46

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m4_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m4_shift0 (oligos_6nt_mkv4_m4)
; oligos_6nt_mkv4_m4; m=0 (reference); ncol1=11; shift=0; ncol=11; ammAACACCmc ; Alignment reference a 603 434 886 1461 1470 34 1378 0 0 542 381 c 379 473 435 6 49 1453 126 1550 1575 416 540 g 284 341 132 31 32 32 22 11 3 328 294 t 322 340 135 90 37 69 62 27 10 302 373

4954_br-Z4_DrosophilaTF_1.1__shift0 (4954_br-Z4_DrosophilaTF_1.1_)
; oligos_6nt_mkv4_m4 versus 4954_br-Z4_DrosophilaTF_1.1_; m=1/1; ncol2=7; w=0; offset=0; strand=D; shift=0; score=0.517034; rkAAAsA---- ; cor=; Ncor= a 50 0 1 1 1 0 1 0 0 0 0 c 0 0 0 0 0 50 0 0 0 0 0 g 50 50 0 0 0 50 0 0 0 0 0 t 0 50 0 0 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m8_shift0 ; 3 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m8_shift0 (oligos_6nt_mkv4_m8)
; oligos_6nt_mkv4_m8; m=0 (reference); ncol1=10; shift=0; ncol=10; mrCAAAACam ; Alignment reference a 588 575 0 1505 1527 1517 1531 0 700 535 c 401 285 1520 0 0 0 0 1533 288 428 g 275 408 0 3 0 1 0 0 317 327 t 269 265 13 25 6 15 2 0 228 243

4953_br-Z3_DrosophilaTF_1.1__shift3 (4953_br-Z3_DrosophilaTF_1.1_)
; oligos_6nt_mkv4_m8 versus 4953_br-Z3_DrosophilaTF_1.1_; m=1/2; ncol2=9; w=0; offset=3; strand=D; shift=3; score=0.510925; ---wAAACww ; cor=; Ncor= a 0 0 0 50 1 1 1 0 50 50 c 0 0 0 0 0 0 0 1 0 0 g 0 0 0 0 0 0 0 0 0 0 t 0 0 0 50 0 0 0 0 50 50

4958_croc_DrosophilaTF_1.1__shift1 (4958_croc_DrosophilaTF_1.1_)
; oligos_6nt_mkv4_m8 versus 4958_croc_DrosophilaTF_1.1_; m=2/2; ncol2=6; w=0; offset=1; strand=D; shift=1; score=0.422479; -rTAAAA--- ; cor=; Ncor= a 0 67 0 1 1 80 1 0 0 0 c 0 0 0 0 0 20 0 0 0 0 g 0 33 0 0 0 0 0 0 0 0 t 0 0 1 0 0 0 0 0 0 0

One-to-n matrix alignment; reference matrix: dyads_m6_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m6_shift0 (dyads_m6)
; dyads_m6; m=0 (reference); ncol1=13; shift=0; ncol=13; camACACACAyac ; Alignment reference a 641 1787 1910 2920 40 2982 31 2973 30 2915 148 1847 393 c 1706 619 936 41 2945 17 2942 28 2937 41 987 432 1939 g 346 362 48 33 15 30 21 19 24 30 98 415 351 t 345 270 144 44 38 9 44 18 47 52 1805 344 355

4983_sd_DrosophilaTF_1.1__rc_shift5 (4983_sd_DrosophilaTF_1.1__rc)
; dyads_m6 versus 4983_sd_DrosophilaTF_1.1__rc; m=1/1; ncol2=9; w=0; offset=5; strand=R; shift=5; score=0.437052; -----AnAmATny ; cor=; Ncor= a 0 0 0 0 0 1 25 1 50 1 0 25 0 c 0 0 0 0 0 0 25 0 50 0 0 25 50 g 0 0 0 0 0 0 25 0 0 0 0 25 0 t 0 0 0 0 0 0 25 0 0 0 1 25 50

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m1_shift0 ; 2 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m1_shift0 (oligos_6nt_mkv4_m1)
; oligos_6nt_mkv4_m1; m=0 (reference); ncol1=11; shift=0; ncol=11; cycCCACAAmm ; Alignment reference a 354 335 306 0 2 1250 50 1267 1364 427 379 c 516 530 804 1437 1382 94 1304 72 17 444 541 g 254 207 179 0 16 42 44 36 33 264 277 t 320 372 155 7 44 58 46 69 30 309 247

4934_Aef1_DrosophilaTF_1.1__shift3 (4934_Aef1_DrosophilaTF_1.1_)
; oligos_6nt_mkv4_m1 versus 4934_Aef1_DrosophilaTF_1.1_; m=1/1; ncol2=6; w=0; offset=3; strand=D; shift=3; score=0.415469; ---CAACAA-- ; cor=; Ncor= a 0 0 0 0 1 1 0 1 1 0 0 c 0 0 0 1 0 0 1 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 0 t 0 0 0 0 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv4_m6_shift3 (oligos_6nt_mkv4_m6)				; oligos_6nt_mkv4_m6; m=0 (reference); ncol1=12; shift=3; ncol=15; ---yyCTTATCagym ; Alignment reference a 0 0 0 258 185 81 30 34 1157 9 27 667 140 266 331 c 0 0 0 411 359 1020 64 33 44 19 1173 127 207 383 328 g 0 0 0 231 277 65 39 16 8 37 9 266 679 226 283 t 0 0 0 339 418 73 1106 1156 30 1174 30 179 213 364 297
4988_srp_DrosophilaTF_1.1__rc_shift3 (4988_srp_DrosophilaTF_1.1__rc)				; oligos_6nt_mkv4_m6 versus 4988_srp_DrosophilaTF_1.1__rc; m=1/3; ncol2=10; w=0; offset=0; strand=R; shift=3; score=0.760079; ---rysTTATCrm-- ; cor=; Ncor= a 0 0 0 28 3 9 0 0 1 0 0 37 28 0 0 c 0 0 0 19 41 56 3 0 0 0 1 0 50 0 0 g 0 0 0 34 9 35 0 0 0 0 0 44 13 0 0 t 0 0 0 19 47 0 97 1 0 1 0 19 9 0 0
4978_pnr_DrosophilaTF_1.1__rc_shift0 (4978_pnr_DrosophilaTF_1.1__rc)				; oligos_6nt_mkv4_m6 versus 4978_pnr_DrosophilaTF_1.1__rc; m=2/3; ncol2=18; w=-3; offset=-3; strand=R; shift=0; score=0.625142; vbcyscTTATCdsmm ; cor=; Ncor= a 42 17 23 20 6 16 10 0 1 0 0 42 22 40 33 c 25 33 31 40 50 63 10 0 0 0 1 0 34 27 34 g 25 25 23 7 31 21 10 0 0 0 0 32 33 13 13 t 8 25 23 33 13 0 70 1 0 1 0 26 11 20 20
4945_TFAM_DrosophilaTF_1.1__shift6 (4945_TFAM_DrosophilaTF_1.1_)				; oligos_6nt_mkv4_m6 versus 4945_TFAM_DrosophilaTF_1.1_; m=3/3; ncol2=5; w=0; offset=3; strand=D; shift=6; score=0.412265; ------TTATC---- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 c 0 0 0 0 0 0 0 0 0 0 82 0 0 0 0 g 0 0 0 0 0 0 0 0 0 0 18 0 0 0 0 t 0 0 0 0 0 0 1 1 0 1 0 0 0 0 0