One-to-n alignments
Command: compare-matrices -v 1 -mode matches -format1 transfac -file1 /home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_motifs/peak-motifs_motifs_discovered.tf -format2 tf -file2 /home/rsat/rsa-tools/public_html/data/motif_databases/JASPAR/jaspar_core_insects_2009_10.tf -mode matches -DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.75 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,logoDP,NIcor,NsEucl,SSD,NSW,match_rank,width,strand,offset,consensus,alignments_1ton -sort Ncor -o /home/rsat/rsa-tools/public_html/tmp/peak-motifs.2012_03_11.082424/results/discovered_vs_db/peak-motifs_motifs_vs_db_jaspar_core_insects.tab
One-to-n matrix alignment; reference matrix: positions_6nt_m1_shift0 ; 2 matrices ; sort_field=rank_mean
| Matrix name | Aligned logos | cor |
Ncor |
logoDP |
NIcor |
NsEucl |
SSD |
NSW |
rcor |
rNcor |
rlogoDP |
rNIcor |
rNsEucl |
rSSD |
rNSW |
rank_mean |
match_rank |
Aligned matrices |
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| positions_6nt_m1_shift0 (positions_6nt_m1) |
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; positions_6nt_m1; m=0 (reference); ncol1=15; shift=0; ncol=15; rrrAAAGGGTTAArd
; Alignment reference
a | 338 299 421 1039 1054 828 0 0 0 3 8 840 779 305 274
c | 216 265 122 1 2 15 1 0 0 0 4 1 89 195 240
g | 316 275 453 11 13 223 1073 1071 1074 27 1 232 103 393 287
t | 204 235 78 23 5 8 0 3 0 1044 1061 1 103 181 273
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| MA0452.1_shift1 (Kr) |
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0.953 |
0.699 |
8.659 |
0.701 |
0.950 |
0.608 |
0.972 |
2 |
2 |
2 |
2 |
1 |
5 |
1 |
2.143 |
1 |
; positions_6nt_m1 versus MA0452.1 (Kr); m=1/1; ncol2=11; w=11; offset=1; strand=D; shift=1; score= 2.1429; -crAAaGGGTTa---
; cor=0.953; Ncor=0.699; logoDP=8.659; NIcor=0.701; NsEucl=0.950; SSD=0.608; NSW=0.972; rcor=2; rNcor=2; rlogoDP=2; rNIcor=2; rNsEucl=1; rSSD=5; rNSW=1; rank_mean=2.143; match_rank=1
a | 0 3 11 24 30 18 0 2 2 0 4 20 0 0 0
c | 0 17 4 0 0 6 0 0 0 1 0 4 0 0 0
g | 0 5 10 7 0 7 31 29 29 7 5 3 0 0 0
t | 0 6 6 0 1 0 0 0 0 23 22 4 0 0 0
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One-to-n matrix alignment; reference matrix: positions_7nt_m1_shift0 ; 2 matrices ; sort_field=rank_mean
| Matrix name | Aligned logos | cor |
Ncor |
logoDP |
NIcor |
NsEucl |
SSD |
NSW |
rcor |
rNcor |
rlogoDP |
rNIcor |
rNsEucl |
rSSD |
rNSW |
rank_mean |
match_rank |
Aligned matrices |
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| positions_7nt_m1_shift0 (positions_7nt_m1) |
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; positions_7nt_m1; m=0 (reference); ncol1=15; shift=0; ncol=15; rrrAAAGGGTTAArd
; Alignment reference
a | 325 287 388 918 991 801 0 0 0 1 1 821 814 317 252
c | 201 244 235 0 1 5 0 0 0 0 0 0 49 162 228
g | 288 256 319 72 12 200 1008 1008 1008 10 0 187 73 370 271
t | 194 221 66 18 4 2 0 0 0 997 1007 0 72 159 257
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| MA0452.1_shift1 (Kr) |
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0.953 |
0.699 |
8.685 |
0.699 |
0.950 |
0.614 |
0.972 |
3 |
3 |
1 |
3 |
2 |
6 |
2 |
2.857 |
2 |
; positions_7nt_m1 versus MA0452.1 (Kr); m=1/1; ncol2=11; w=11; offset=1; strand=D; shift=1; score= 2.8571; -crAAaGGGTTa---
; cor=0.953; Ncor=0.699; logoDP=8.685; NIcor=0.699; NsEucl=0.950; SSD=0.614; NSW=0.972; rcor=3; rNcor=3; rlogoDP=1; rNIcor=3; rNsEucl=2; rSSD=6; rNSW=2; rank_mean=2.857; match_rank=2
a | 0 3 11 24 30 18 0 2 2 0 4 20 0 0 0
c | 0 17 4 0 0 6 0 0 0 1 0 4 0 0 0
g | 0 5 10 7 0 7 31 29 29 7 5 3 0 0 0
t | 0 6 6 0 1 0 0 0 0 23 22 4 0 0 0
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One-to-n matrix alignment; reference matrix: positions_7nt_m3_shift0 ; 2 matrices ; sort_field=rank_mean
| Matrix name | Aligned logos | cor |
Ncor |
logoDP |
NIcor |
NsEucl |
SSD |
NSW |
rcor |
rNcor |
rlogoDP |
rNIcor |
rNsEucl |
rSSD |
rNSW |
rank_mean |
match_rank |
Aligned matrices |
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| positions_7nt_m3_shift0 (positions_7nt_m3) |
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; positions_7nt_m3; m=0 (reference); ncol1=12; shift=0; ncol=12; yckCTCkCKCtc
; Alignment reference
a | 576 599 23 0 0 0 0 0 0 0 798 520
c | 1281 2822 4 5043 0 5043 0 5043 0 5043 816 2766
g | 950 581 1788 0 0 0 1653 0 1290 0 972 752
t | 2236 1041 3228 0 5043 0 3390 0 3753 0 2457 1005
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| MA0205.1_shift0 (Trl) |
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0.893 |
0.744 |
4.967 |
0.731 |
0.927 |
1.071 |
0.946 |
7 |
1 |
11 |
1 |
3 |
9 |
7 |
5.571 |
3 |
; positions_7nt_m3 versus MA0205.1 (Trl); m=1/1; ncol2=10; w=10; offset=0; strand=D; shift=0; score= 5.5714; yykCTCTCty--
; cor=0.893; Ncor=0.744; logoDP=4.967; NIcor=0.731; NsEucl=0.927; SSD=1.071; NSW=0.946; rcor=7; rNcor=1; rlogoDP=11; rNIcor=1; rNsEucl=3; rSSD=9; rNSW=7; rank_mean=5.571; match_rank=3
a | 4 6 12 0 3 1 13 5 7 9 0 0
c | 22 23 6 64 0 70 0 54 13 33 0 0
g | 9 11 30 3 14 0 2 7 11 10 0 0
t | 36 31 23 4 54 0 56 5 40 19 0 0
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One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m2_shift4 ; 5 matrices ; sort_field=rank_mean
| Matrix name | Aligned logos | cor |
Ncor |
logoDP |
NIcor |
NsEucl |
SSD |
NSW |
rcor |
rNcor |
rlogoDP |
rNIcor |
rNsEucl |
rSSD |
rNSW |
rank_mean |
match_rank |
Aligned matrices |
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| oligos_7nt_mkv5_m2_shift4 (oligos_7nt_mkv5_m2) |
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; oligos_7nt_mkv5_m2; m=0 (reference); ncol1=11; shift=4; ncol=15; ----waAACAyAAww
; Alignment reference
a | 0 0 0 0 2194 2297 6636 6636 0 6636 0 6636 6636 2283 2203
c | 0 0 0 0 1355 1342 0 0 5129 0 3468 0 0 1367 1387
g | 0 0 0 0 1234 1358 0 0 0 0 1211 0 0 1096 1135
t | 0 0 0 0 1853 1639 0 0 1507 0 1957 0 0 1890 1911
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| MA0233.1_shift5 (mirr) |
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0.930 |
0.423 |
5.396 |
0.419 |
0.913 |
0.382 |
0.962 |
4 |
9 |
9 |
8 |
5 |
2 |
4 |
5.857 |
4 |
; oligos_7nt_mkv5_m2 versus MA0233.1 (mirr); m=1/4; ncol2=5; w=5; offset=1; strand=D; shift=5; score= 5.8571; -----wAACA-----
; cor=0.930; Ncor=0.423; logoDP=5.396; NIcor=0.419; NsEucl=0.913; SSD=0.382; NSW=0.962; rcor=4; rNcor=9; rlogoDP=9; rNIcor=8; rNsEucl=5; rSSD=2; rNSW=4; rank_mean=5.857; match_rank=4
a | 0 0 0 0 0 20 29 41 0 41 0 0 0 0 0
c | 0 0 0 0 0 1 0 0 41 0 0 0 0 0 0
g | 0 0 0 0 0 1 2 0 0 0 0 0 0 0 0
t | 0 0 0 0 0 19 10 0 0 0 0 0 0 0 0
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| MA0210.1_shift5 (ara) |
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0.926 |
0.421 |
5.467 |
0.417 |
0.911 |
0.399 |
0.960 |
5 |
10 |
7 |
9 |
6 |
3 |
5 |
6.429 |
6 |
; oligos_7nt_mkv5_m2 versus MA0210.1 (ara); m=2/4; ncol2=5; w=5; offset=1; strand=D; shift=5; score= 6.4286; -----wwACA-----
; cor=0.926; Ncor=0.421; logoDP=5.467; NIcor=0.417; NsEucl=0.911; SSD=0.399; NSW=0.960; rcor=5; rNcor=10; rlogoDP=7; rNIcor=9; rNsEucl=6; rSSD=3; rNSW=5; rank_mean=6.429; match_rank=6
a | 0 0 0 0 0 14 23 34 0 34 0 0 0 0 0
c | 0 0 0 0 0 0 0 0 34 0 0 0 0 0 0
g | 0 0 0 0 0 5 0 0 0 0 0 0 0 0 0
t | 0 0 0 0 0 15 11 0 0 0 0 0 0 0 0
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| MA0217.1_shift5 (caup) |
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0.926 |
0.421 |
5.404 |
0.412 |
0.910 |
0.407 |
0.959 |
6 |
11 |
8 |
10 |
7 |
4 |
6 |
7.429 |
8 |
; oligos_7nt_mkv5_m2 versus MA0217.1 (caup); m=3/4; ncol2=5; w=5; offset=1; strand=D; shift=5; score= 7.4286; -----tAACA-----
; cor=0.926; Ncor=0.421; logoDP=5.404; NIcor=0.412; NsEucl=0.910; SSD=0.407; NSW=0.959; rcor=6; rNcor=11; rlogoDP=8; rNIcor=10; rNsEucl=7; rSSD=4; rNSW=6; rank_mean=7.429; match_rank=8
a | 0 0 0 0 0 4 14 19 0 19 0 0 0 0 0
c | 0 0 0 0 0 1 0 0 19 0 0 0 0 0 0
g | 0 0 0 0 0 2 2 0 0 0 0 0 0 0 0
t | 0 0 0 0 0 12 3 0 0 0 0 0 0 0 0
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| MA0458.1_rc_shift0 (slp1_rc) |
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0.866 |
0.404 |
0.606 |
-0.012 |
0.902 |
0.945 |
0.932 |
8 |
14 |
14 |
14 |
9 |
7 |
8 |
10.571 |
13 |
; oligos_7nt_mkv5_m2 versus MA0458.1_rc (slp1_rc); m=4/4; ncol2=11; w=7; offset=-4; strand=R; shift=0; score=10.5714; wryrtAAACAm----
; cor=0.866; Ncor=0.404; logoDP=0.606; NIcor=-0.012; NsEucl=0.902; SSD=0.945; NSW=0.932; rcor=8; rNcor=14; rlogoDP=14; rNIcor=14; rNsEucl=9; rSSD=7; rNSW=8; rank_mean=10.571; match_rank=13
a | 19 21 1 11 10 39 40 41 0 41 16 0 0 0 0
c | 4 3 15 7 4 2 1 0 38 0 14 0 0 0 0
g | 3 13 8 22 0 0 0 0 0 0 3 0 0 0 0
t | 15 4 17 1 27 0 0 0 3 0 8 0 0 0 0
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One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m1_shift0 ; 3 matrices ; sort_field=rank_mean
| Matrix name | Aligned logos | cor |
Ncor |
logoDP |
NIcor |
NsEucl |
SSD |
NSW |
rcor |
rNcor |
rlogoDP |
rNIcor |
rNsEucl |
rSSD |
rNSW |
rank_mean |
match_rank |
Aligned matrices |
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| oligos_6nt_mkv4_m1_shift0 (oligos_6nt_mkv4_m1) |
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; oligos_6nt_mkv4_m1; m=0 (reference); ncol1=11; shift=0; ncol=11; wkCTTATsArw
; Alignment reference
a | 474 394 0 0 0 1796 0 0 1796 611 473
c | 435 355 1796 0 0 0 0 1203 0 347 443
g | 342 496 0 0 0 0 0 593 0 458 295
t | 545 551 0 1796 1796 0 1796 0 0 380 585
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| MA0199.1_rc_shift4 (Optix_rc) |
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0.957 |
0.435 |
2.664 |
0.084 |
0.924 |
0.289 |
0.971 |
1 |
8 |
13 |
13 |
4 |
1 |
3 |
6.143 |
5 |
; oligos_6nt_mkv4_m1 versus MA0199.1_rc (Optix_rc); m=1/2; ncol2=5; w=5; offset=4; strand=R; shift=4; score= 6.1429; ----TATCA--
; cor=0.957; Ncor=0.435; logoDP=2.664; NIcor=0.084; NsEucl=0.924; SSD=0.289; NSW=0.971; rcor=1; rNcor=8; rlogoDP=13; rNIcor=13; rNsEucl=4; rSSD=1; rNSW=3; rank_mean=6.143; match_rank=5
a | 0 0 0 0 0 27 0 0 22 0 0
c | 0 0 0 0 1 0 0 27 0 0 0
g | 0 0 0 0 0 0 0 0 5 0 0
t | 0 0 0 0 26 0 27 0 0 0 0
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| MA0246.1_rc_shift3 (so_rc) |
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0.768 |
0.419 |
5.200 |
0.225 |
0.839 |
1.868 |
0.844 |
13 |
12 |
10 |
12 |
12 |
12 |
12 |
11.857 |
14 |
; oligos_6nt_mkv4_m1 versus MA0246.1_rc (so_rc); m=2/2; ncol2=6; w=6; offset=3; strand=R; shift=3; score=11.8571; ---GTATCA--
; cor=0.768; Ncor=0.419; logoDP=5.200; NIcor=0.225; NsEucl=0.839; SSD=1.868; NSW=0.844; rcor=13; rNcor=12; rlogoDP=10; rNIcor=12; rNsEucl=12; rSSD=12; rNSW=12; rank_mean=11.857; match_rank=14
a | 0 0 0 3 0 26 0 0 26 0 0
c | 0 0 0 0 0 1 0 27 1 0 0
g | 0 0 0 10 0 0 0 0 0 0 0
t | 0 0 0 0 27 0 27 0 0 0 0
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One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m3_shift0 ; 3 matrices ; sort_field=rank_mean
| Matrix name | Aligned logos | cor |
Ncor |
logoDP |
NIcor |
NsEucl |
SSD |
NSW |
rcor |
rNcor |
rlogoDP |
rNIcor |
rNsEucl |
rSSD |
rNSW |
rank_mean |
match_rank |
Aligned matrices |
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| oligos_6nt_mkv4_m3_shift0 (oligos_6nt_mkv4_m3) |
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; oligos_6nt_mkv4_m3; m=0 (reference); ncol1=10; shift=0; ncol=11; yaTACATAta-
; Alignment reference
a | 1566 3368 0 7443 0 7443 0 7443 1588 3283 0
c | 1981 835 0 0 7443 0 0 0 1762 858 0
g | 900 1799 0 0 0 0 0 0 757 1698 0
t | 2996 1441 7443 0 0 0 7443 0 3336 1604 0
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| MA0015.1_rc_shift1 (Cf2_II_rc) |
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0.825 |
0.675 |
6.525 |
0.570 |
0.902 |
1.544 |
0.914 |
10 |
4 |
5 |
4 |
8 |
11 |
10 |
7.429 |
7 |
; oligos_6nt_mkv4_m3 versus MA0015.1_rc (Cf2_II_rc); m=1/2; ncol2=10; w=9; offset=1; strand=R; shift=1; score= 7.4286; -ryAyATATAy
; cor=0.825; Ncor=0.675; logoDP=6.525; NIcor=0.570; NsEucl=0.902; SSD=1.544; NSW=0.914; rcor=10; rNcor=4; rlogoDP=5; rNIcor=4; rNsEucl=8; rSSD=11; rNSW=10; rank_mean=7.429; match_rank=7
a | 0 24 4 68 1 74 0 67 0 76 2
c | 0 15 20 1 36 1 0 4 4 1 40
g | 0 29 3 9 2 4 2 9 2 2 13
t | 0 12 53 2 41 1 78 0 74 1 25
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| MA0210.1_shift1 (ara) |
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0.828 |
0.414 |
6.119 |
0.401 |
0.859 |
1.000 |
0.900 |
9 |
13 |
6 |
11 |
11 |
8 |
11 |
9.857 |
11 |
; oligos_6nt_mkv4_m3 versus MA0210.1 (ara); m=2/2; ncol2=5; w=5; offset=1; strand=D; shift=1; score= 9.8571; -wwACA-----
; cor=0.828; Ncor=0.414; logoDP=6.119; NIcor=0.401; NsEucl=0.859; SSD=1.000; NSW=0.900; rcor=9; rNcor=13; rlogoDP=6; rNIcor=11; rNsEucl=11; rSSD=8; rNSW=11; rank_mean=9.857; match_rank=11
a | 0 14 23 34 0 34 0 0 0 0 0
c | 0 0 0 0 34 0 0 0 0 0 0
g | 0 5 0 0 0 0 0 0 0 0 0
t | 0 15 11 0 0 0 0 0 0 0 0
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One-to-n matrix alignment; reference matrix: positions_6nt_m3_shift0 ; 2 matrices ; sort_field=rank_mean
| Matrix name | Aligned logos | cor |
Ncor |
logoDP |
NIcor |
NsEucl |
SSD |
NSW |
rcor |
rNcor |
rlogoDP |
rNIcor |
rNsEucl |
rSSD |
rNSW |
rank_mean |
match_rank |
Aligned matrices |
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| positions_6nt_m3_shift0 (positions_6nt_m3) |
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; positions_6nt_m3; m=0 (reference); ncol1=10; shift=0; ncol=10; wrCAGGTAra
; Alignment reference
a | 1036 986 0 3557 0 0 0 3557 1228 1214
c | 764 745 3557 0 0 0 0 0 538 770
g | 860 1059 0 0 3557 3557 0 0 1249 762
t | 897 767 0 0 0 0 3557 0 542 811
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| MA0086.1_shift2 (sna) |
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0.777 |
0.466 |
8.354 |
0.471 |
0.837 |
1.924 |
0.840 |
12 |
5 |
3 |
5 |
13 |
13 |
13 |
9.143 |
9 |
; positions_6nt_m3 versus MA0086.1 (sna); m=1/1; ncol2=6; w=6; offset=2; strand=D; shift=2; score= 9.1429; --CAGGTG--
; cor=0.777; Ncor=0.466; logoDP=8.354; NIcor=0.471; NsEucl=0.837; SSD=1.924; NSW=0.840; rcor=12; rNcor=5; rlogoDP=3; rNIcor=5; rNsEucl=13; rSSD=13; rNSW=13; rank_mean=9.143; match_rank=9
a | 0 0 0 39 3 2 0 0 0 0
c | 0 0 39 0 0 0 0 0 0 0
g | 0 0 1 0 37 38 0 38 0 0
t | 0 0 0 1 0 0 40 2 0 0
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One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_m1_shift1 ; 2 matrices ; sort_field=rank_mean
| Matrix name | Aligned logos | cor |
Ncor |
logoDP |
NIcor |
NsEucl |
SSD |
NSW |
rcor |
rNcor |
rlogoDP |
rNIcor |
rNsEucl |
rSSD |
rNSW |
rank_mean |
match_rank |
Aligned matrices |
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| oligos_7nt_mkv5_m1_shift1 (oligos_7nt_mkv5_m1) |
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; oligos_7nt_mkv5_m1; m=0 (reference); ncol1=12; shift=1; ncol=13; -wwTATYTkKAww
; Alignment reference
a | 0 1274 1387 0 4484 0 0 0 0 0 4484 1227 1330
c | 0 685 584 0 0 0 1204 0 0 0 0 707 1019
g | 0 685 1071 0 0 0 0 0 1682 1241 0 715 758
t | 0 1840 1442 4484 0 4484 3280 4484 2802 3243 0 1835 1377
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| MA0011.1_shift0 (br_Z2) |
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0.822 |
0.443 |
4.369 |
0.437 |
0.893 |
1.126 |
0.920 |
11 |
7 |
12 |
7 |
10 |
10 |
9 |
9.429 |
10 |
; oligos_7nt_mkv5_m1 versus MA0011.1 (br_Z2); m=1/1; ncol2=8; w=7; offset=-1; strand=D; shift=0; score= 9.4286; wwCTAtTt-----
; cor=0.822; Ncor=0.443; logoDP=4.369; NIcor=0.437; NsEucl=0.893; SSD=1.126; NSW=0.920; rcor=11; rNcor=7; rlogoDP=12; rNIcor=7; rNsEucl=10; rSSD=10; rNSW=9; rank_mean=9.429; match_rank=10
a | 3 5 0 0 12 1 2 1 0 0 0 0 0
c | 1 2 10 1 0 1 0 2 0 0 0 0 0
g | 1 1 0 0 0 2 1 1 0 0 0 0 0
t | 7 4 2 11 0 8 9 8 0 0 0 0 0
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One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m2_shift0 ; 2 matrices ; sort_field=rank_mean
| Matrix name | Aligned logos | cor |
Ncor |
logoDP |
NIcor |
NsEucl |
SSD |
NSW |
rcor |
rNcor |
rlogoDP |
rNIcor |
rNsEucl |
rSSD |
rNSW |
rank_mean |
match_rank |
Aligned matrices |
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| oligos_6nt_mkv4_m2_shift0 (oligos_6nt_mkv4_m2) |
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; oligos_6nt_mkv4_m2; m=0 (reference); ncol1=10; shift=0; ncol=10; acAGATACaw
; Alignment reference
a | 1904 1156 4754 0 4754 0 4754 0 2319 1234
c | 841 1841 0 0 0 0 0 4754 563 1169
g | 931 929 0 4754 0 0 0 0 724 1054
t | 1078 828 0 0 0 4754 0 0 1148 1297
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| MA0246.1_shift2 (so) |
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0.762 |
0.457 |
8.307 |
0.458 |
0.832 |
2.038 |
0.830 |
14 |
6 |
4 |
6 |
14 |
14 |
14 |
10.286 |
12 |
; oligos_6nt_mkv4_m2 versus MA0246.1 (so); m=1/1; ncol2=6; w=6; offset=2; strand=D; shift=2; score=10.2857; --TGATAC--
; cor=0.762; Ncor=0.457; logoDP=8.307; NIcor=0.458; NsEucl=0.832; SSD=2.038; NSW=0.830; rcor=14; rNcor=6; rlogoDP=4; rNIcor=6; rNsEucl=14; rSSD=14; rNSW=14; rank_mean=10.286; match_rank=12
a | 0 0 0 0 27 0 27 0 0 0
c | 0 0 0 0 0 0 0 10 0 0
g | 0 0 1 27 0 1 0 0 0 0
t | 0 0 26 0 0 26 0 3 0 0
|