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/DMMPMM_drosophila/dmmpmm_PCM.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_DMMPMM_drosophila.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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| Kr_shift2 (Kr) |
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0.967 |
0.645 |
5.916 |
0.643 |
0.943 |
0.658 |
0.967 |
1 |
3 |
2 |
3 |
1 |
1 |
1 |
1.714 |
1 |
; positions_6nt_m1 versus Kr; m=1/1; ncol2=10; w=10; offset=2; strand=D; shift=2; score= 1.7143; --aAAaGGGTta---
; cor=0.967; Ncor=0.645; logoDP=5.916; NIcor=0.643; NsEucl=0.943; SSD=0.658; NSW=0.967; rcor=1; rNcor=3; rlogoDP=2; rNIcor=3; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.714; match_rank=1
a | 0 0 24 38 33 23 2 5 6 3 6 27 0 0 0
c | 0 0 7 3 8 10 0 0 4 0 5 6 0 0 0
g | 0 0 9 3 2 7 41 39 34 2 4 7 0 0 0
t | 0 0 5 1 2 5 2 1 1 40 30 5 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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| Kr_shift2 (Kr) |
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0.966 |
0.644 |
5.908 |
0.641 |
0.943 |
0.659 |
0.967 |
2 |
4 |
3 |
4 |
2 |
2 |
2 |
2.714 |
2 |
; positions_7nt_m1 versus Kr; m=1/1; ncol2=10; w=10; offset=2; strand=D; shift=2; score= 2.7143; --aAAaGGGTta---
; cor=0.966; Ncor=0.644; logoDP=5.908; NIcor=0.641; NsEucl=0.943; SSD=0.659; NSW=0.967; rcor=2; rNcor=4; rlogoDP=3; rNIcor=4; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=2.714; match_rank=2
a | 0 0 24 38 33 23 2 5 6 3 6 27 0 0 0
c | 0 0 7 3 8 10 0 0 4 0 5 6 0 0 0
g | 0 0 9 3 2 7 41 39 34 2 4 7 0 0 0
t | 0 0 5 1 2 5 2 1 1 40 30 5 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=13; yckCTCkCKCtc-
; Alignment reference
a | 576 599 23 0 0 0 0 0 0 0 798 520 0
c | 1281 2822 4 5043 0 5043 0 5043 0 5043 816 2766 0
g | 950 581 1788 0 0 0 1653 0 1290 0 972 752 0
t | 2236 1041 3228 0 5043 0 3390 0 3753 0 2457 1005 0
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| Trl_shift0 (Trl) |
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0.821 |
0.757 |
3.792 |
0.727 |
0.924 |
1.679 |
0.930 |
4 |
1 |
4 |
1 |
3 |
5 |
3 |
3.000 |
3 |
; positions_7nt_m3 versus Trl; m=1/1; ncol2=13; w=12; offset=0; strand=D; shift=0; score= 3; TtkykCTCtCtct
; cor=0.821; Ncor=0.757; logoDP=3.792; NIcor=0.727; NsEucl=0.924; SSD=1.679; NSW=0.930; rcor=4; rNcor=1; rlogoDP=4; rNIcor=1; rNsEucl=3; rSSD=5; rNSW=3; rank_mean=3.000; match_rank=3
a | 10 15 4 0 7 0 4 2 6 13 9 4 18
c | 10 8 19 41 3 72 0 56 12 56 16 47 3
g | 0 13 24 10 27 5 11 8 9 1 6 9 14
t | 57 41 30 26 40 0 62 11 50 7 46 17 42
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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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| sna_shift0 (sna) |
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0.788 |
0.709 |
6.730 |
0.685 |
0.896 |
1.767 |
0.902 |
6 |
2 |
1 |
2 |
5 |
6 |
6 |
4.000 |
4 |
; positions_6nt_m3 versus sna; m=1/1; ncol2=9; w=9; offset=0; strand=D; shift=0; score= 4; AdCArGTdr-
; cor=0.788; Ncor=0.709; logoDP=6.730; NIcor=0.685; NsEucl=0.896; SSD=1.767; NSW=0.902; rcor=6; rNcor=2; rlogoDP=1; rNIcor=2; rNsEucl=5; rSSD=6; rNSW=6; rank_mean=4.000; match_rank=4
a | 9 4 0 10 4 0 0 3 3 0
c | 2 0 11 0 0 0 0 0 2 0
g | 0 4 0 1 6 11 2 5 6 0
t | 0 3 0 0 1 0 9 3 0 0
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One-to-n matrix alignment; reference matrix: oligos_7nt_mkv5_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_7nt_mkv5_m1_shift0 (oligos_7nt_mkv5_m1) |
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; oligos_7nt_mkv5_m1; m=0 (reference); ncol1=12; shift=0; ncol=12; wwTATYTkKAww
; Alignment reference
a | 1274 1387 0 4484 0 0 0 0 0 4484 1227 1330
c | 685 584 0 0 0 1204 0 0 0 0 707 1019
g | 685 1071 0 0 0 0 0 1682 1241 0 715 758
t | 1840 1442 4484 0 4484 3280 4484 2802 3243 0 1835 1377
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| Antp_rc_shift0 (Antp_rc) |
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0.858 |
0.429 |
3.592 |
0.239 |
0.890 |
0.875 |
0.927 |
3 |
6 |
5 |
5 |
6 |
3 |
4 |
4.571 |
5 |
; oligos_7nt_mkv5_m1 versus Antp_rc; m=1/2; ncol2=6; w=6; offset=0; strand=R; shift=0; score= 4.5714; wTTATk------
; cor=0.858; Ncor=0.429; logoDP=3.592; NIcor=0.239; NsEucl=0.890; SSD=0.875; NSW=0.927; rcor=3; rNcor=6; rlogoDP=5; rNIcor=5; rNsEucl=6; rSSD=3; rNSW=4; rank_mean=4.571; match_rank=5
a | 10.5 0 0 18 0 0 0 0 0 0 0 0
c | 0 0 1.5 0 0 3 0 0 0 0 0 0
g | 0 0 0 0 0 4.5 0 0 0 0 0 0
t | 7.5 18 16.5 0 18 10.5 0 0 0 0 0 0
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| br-Z1_rc_shift4 (br-Z1_rc) |
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0.802 |
0.535 |
1.425 |
0.089 |
0.901 |
1.244 |
0.922 |
5 |
5 |
6 |
6 |
4 |
4 |
5 |
5.000 |
6 |
; oligos_7nt_mkv5_m1 versus br-Z1_rc; m=2/2; ncol2=8; w=8; offset=4; strand=R; shift=4; score= 5; ----TTwGtAty
; cor=0.802; Ncor=0.535; logoDP=1.425; NIcor=0.089; NsEucl=0.901; SSD=1.244; NSW=0.922; rcor=5; rNcor=5; rlogoDP=6; rNIcor=6; rNsEucl=4; rSSD=4; rNSW=5; rank_mean=5.000; match_rank=6
a | 0 0 0 0 0 0 7.41176 0 0 14.8235 3.17647 0
c | 0 0 0 0 0 0 0 2.11765 3.17647 1.05882 3.17647 7.41176
g | 0 0 0 0 0 2.11765 1.05882 12.7059 3.17647 0 0 0
t | 0 0 0 0 18 15.8824 9.52941 3.17647 11.6471 2.11765 11.6471 10.5882
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