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/DMMPMM_drosophila/dmmpmm_PCM.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_DMMPMM_drosophila.tab
One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m7_shift0 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_7nt_mkv5_m7_shift0 (oligos_7nt_mkv5_m7) |
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; 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
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| Trl_shift1 (Trl) |
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; oligos_7nt_mkv5_m7 versus Trl; m=1/1; ncol2=13; w=0; offset=1; strand=D; shift=1; score=0.726651; -TtkykCTCtCtct
; cor=; Ncor=
a 0 10 15 4 0 7 0 4 2 6 13 9 4 18
c 0 10 8 19 41 3 72 0 56 12 56 16 47 3
g 0 0 13 24 10 27 5 11 8 9 1 6 9 14
t 0 57 41 30 26 40 0 62 11 50 7 46 17 42
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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) |
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; 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
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| Trl_rc_shift3 (Trl_rc) |
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; dyads_m2 versus Trl_rc; m=1/1; ncol2=13; w=0; offset=3; strand=R; shift=3; score=0.641698; ---agaGaGAGmrmaA-
; cor=; Ncor=
a 0 0 0 42 17 46 7 50 11 62 0 40 26 30 41 57 0
c 0 0 0 14 9 6 1 9 8 11 5 27 10 24 13 0 0
g 0 0 0 3 47 16 56 12 56 0 72 3 41 19 8 10 0
t 0 0 0 18 4 9 13 6 2 4 0 7 0 4 15 10 0
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One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m8_shift0 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6nt_mkv4_m8_shift0 (oligos_6nt_mkv4_m8) |
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; 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
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| pan_shift0 (pan) |
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; oligos_6nt_mkv4_m8 versus pan; m=1/1; ncol2=6; w=0; offset=0; strand=D; shift=0; score=0.527626; WtCAAA----
; cor=; Ncor=
a 18.72 5.2 3.12 20.8 23.92 23.92 0 0 0 0
c 0 4.16 20.8 0 1.04 0 0 0 0 0
g 0 0 1.04 0 0 0 0 0 0 0
t 7.28 16.64 1.04 5.2 1.04 2.08 0 0 0 0
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One-to-n matrix alignment; reference matrix: dyads_m4_shift0 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| dyads_m4_shift0 (dyads_m4) |
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; dyads_m4; m=0 (reference); ncol1=13; shift=0; ncol=13; camACACACrCaC
; Alignment reference
a 692 1932 1963 3124 46 3190 60 3155 31 986 38 2067 370
c 1862 667 1096 52 3156 14 3160 33 3190 50 3147 251 2240
g 346 403 68 60 25 53 18 45 21 2134 51 608 304
t 369 267 142 33 42 12 31 36 27 99 33 343 355
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| twi_shift2 (twi) |
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; dyads_m4 versus twi; m=1/1; ncol2=8; w=0; offset=2; strand=D; shift=2; score=0.479318; --mACAyaTG---
; cor=; Ncor=
a 0 0 10.6667 12.8 0 16 1.06667 10.6667 0 1.06667 0 0 0
c 0 0 5.33333 3.2 16 0 7.46667 3.2 3.2 0 0 0 0
g 0 0 0 0 0 0 1.06667 2.13333 1.06667 13.8667 0 0 0
t 0 0 0 0 0 0 6.4 0 11.7333 1.06667 0 0 0
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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) |
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; 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
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| twi_shift4 (twi) |
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; dyads_m6 versus twi; m=1/1; ncol2=8; w=0; offset=4; strand=D; shift=4; score=0.440078; ----mACAyaTG-
; cor=; Ncor=
a 0 0 0 0 10.6667 12.8 0 16 1.06667 10.6667 0 1.06667 0
c 0 0 0 0 5.33333 3.2 16 0 7.46667 3.2 3.2 0 0
g 0 0 0 0 0 0 0 0 1.06667 2.13333 1.06667 13.8667 0
t 0 0 0 0 0 0 0 0 6.4 0 11.7333 1.06667 0
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One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m3_shift0 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_6nt_mkv4_m3_shift0 (oligos_6nt_mkv4_m3) |
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; oligos_6nt_mkv4_m3; m=0 (reference); ncol1=12; shift=0; ncol=12; mrCTGTCAaamg
; Alignment reference
a 526 362 41 28 74 16 39 1314 942 891 393 301
c 353 229 1319 34 50 45 1321 36 139 210 434 341
g 252 522 20 27 1237 28 21 34 168 140 278 427
t 281 299 32 1323 51 1323 31 28 163 171 307 343
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| gt_shift4 (gt) |
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; oligos_6nt_mkv4_m3 versus gt; m=1/1; ncol2=7; w=0; offset=4; strand=D; shift=4; score=0.427456; ----GTmAwAW-
; cor=; Ncor=
a 0 0 0 0 0 1 5 8 3 8 6 0
c 0 0 0 0 1 1 3 0 0 0 0 0
g 0 0 0 0 7 0 0 0 0 0 0 0
t 0 0 0 0 0 6 0 0 5 0 2 0
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One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m1_shift0 ; 2 matrices ; sort_field=Ncor
| Matrix name | Aligned logos | cor |
Ncor |
Aligned matrices |
|---|
| oligos_7nt_mkv5_m1_shift0 (oligos_7nt_mkv5_m1) |
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; oligos_7nt_mkv5_m1; m=0 (reference); ncol1=11; shift=0; ncol=11; maAACACAAmm
; Alignment reference
a 623 573 1802 1747 96 1720 81 1680 1767 555 640
c 544 437 1 22 1609 67 1586 57 20 518 599
g 384 449 28 54 61 58 114 51 39 350 326
t 329 421 49 57 114 35 99 92 54 457 315
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| eve_shift4 (eve) |
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; oligos_7nt_mkv5_m1 versus eve; m=1/1; ncol2=8; w=0; offset=4; strand=D; shift=4; score=0.42504; ----mACaaTw
; cor=; Ncor=
a 0 0 0 0 8 18 1 13 13 0 9
c 0 0 0 0 9 0 16 3 0 1 1
g 0 0 0 0 3 2 0 4 3 0 1
t 0 0 0 0 0 0 3 0 4 19 9
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