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/idmmpmm_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_IDMMPMM_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_rc_shift1 (Kr_rc) |
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0.969 |
0.711 |
2.138 |
0.095 |
0.953 |
0.544 |
0.975 |
1 |
2 |
1 |
2 |
1 |
1 |
1 |
1.286 |
1 |
; positions_6nt_m1 versus Kr_rc; m=1/1; ncol2=11; w=11; offset=1; strand=R; shift=1; score= 1.2857; -yrAAaGGGTta---
; cor=0.969; Ncor=0.711; logoDP=2.138; NIcor=0.095; NsEucl=0.953; SSD=0.544; NSW=0.975; rcor=1; rNcor=2; rlogoDP=1; rNIcor=2; rNsEucl=1; rSSD=1; rNSW=1; rank_mean=1.286; match_rank=1
a | 0 41.2239 122.207 250.55 255.546 173.904 0 41.8348 42.4092 16.3753 47.7674 157.647 0 0 0
c | 0 105.041 41.2178 0 10.3333 45.6551 0 0 8.06 5.93559 17.977 28.7388 0 0 0
g | 0 52.2137 85.1102 28.4501 2.06667 35.0057 266.548 226.987 225.999 30.0548 29.6445 40.4672 0 0 0
t | 0 80.521 30.4651 0 11.0536 24.4353 12.4517 10.1783 2.53167 226.634 183.611 52.1469 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_rc_shift1 (Kr_rc) |
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0.966 |
0.708 |
2.082 |
0.090 |
0.951 |
0.571 |
0.974 |
2 |
3 |
3 |
3 |
2 |
2 |
2 |
2.429 |
2 |
; positions_7nt_m1 versus Kr_rc; m=1/1; ncol2=11; w=11; offset=1; strand=R; shift=1; score= 2.4286; -yrAAaGGGTta---
; cor=0.966; Ncor=0.708; logoDP=2.082; NIcor=0.090; NsEucl=0.951; SSD=0.571; NSW=0.974; rcor=2; rNcor=3; rlogoDP=3; rNIcor=3; rNsEucl=2; rSSD=2; rNSW=2; rank_mean=2.429; match_rank=2
a | 0 41.2239 122.207 250.55 255.546 173.904 0 41.8348 42.4092 16.3753 47.7674 157.647 0 0 0
c | 0 105.041 41.2178 0 10.3333 45.6551 0 0 8.06 5.93559 17.977 28.7388 0 0 0
g | 0 52.2137 85.1102 28.4501 2.06667 35.0057 266.548 226.987 225.999 30.0548 29.6445 40.4672 0 0 0
t | 0 80.521 30.4651 0 11.0536 24.4353 12.4517 10.1783 2.53167 226.634 183.611 52.1469 0 0 0
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One-to-n matrix alignment; reference matrix: positions_7nt_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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| positions_7nt_m2_shift0 (positions_7nt_m2) |
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; positions_7nt_m2; m=0 (reference); ncol1=20; shift=0; ncol=20; wwAATwwwwwwwwTwTwAww
; Alignment reference
a | 1198 1305 2806 3297 188 1654 1534 1888 2133 1805 2054 1138 2494 149 1670 193 1340 2771 1162 1178
c | 661 685 268 118 85 58 57 49 77 64 46 89 59 109 39 140 77 282 659 648
g | 708 645 154 125 98 62 50 47 69 51 73 79 75 114 59 130 74 234 685 665
t | 1192 1124 531 219 3388 1985 2118 1775 1480 1839 1586 2453 1131 3387 1991 3296 2268 472 1253 1268
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| bab1_rc_shift0 (bab1_rc) |
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0.765 |
0.535 |
2.102 |
0.202 |
0.928 |
2.036 |
0.927 |
4 |
4 |
2 |
1 |
3 |
4 |
3 |
3.000 |
3 |
; positions_7nt_m2 versus bab1_rc; m=1/1; ncol2=14; w=14; offset=0; strand=R; shift=0; score= 3; AywATwATAwAtAT------
; cor=0.765; Ncor=0.535; logoDP=2.102; NIcor=0.202; NsEucl=0.928; SSD=2.036; NSW=0.927; rcor=4; rNcor=4; rlogoDP=2; rNIcor=1; rNsEucl=3; rSSD=4; rNSW=3; rank_mean=3.000; match_rank=3
a | 23.8333 5.95833 15.5833 30.5556 3.66667 17.4167 31.1667 3.66667 25.3611 12.5278 24.1389 7.33333 27.1944 1.22222 0 0 0 0 0 0
c | 3.36111 9.625 0 0 6.72222 0.611111 1.83333 0 0 0.611111 3.36111 6.11111 0.916667 3.05556 0 0 0 0 0 0
g | 0.916667 0.763889 1.22222 1.83333 0 1.83333 0 0.611111 1.22222 0 1.83333 3.66667 3.36111 5.5 0 0 0 0 0 0
t | 4.88889 16.6528 16.1944 0.611111 22.6111 13.1389 0 28.7222 6.41667 19.8611 3.66667 15.8889 1.52778 23.2222 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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| sna_rc_shift0 (sna_rc) |
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0.796 |
0.717 |
0.166 |
-0.225 |
0.897 |
1.717 |
0.905 |
3 |
1 |
4 |
4 |
4 |
3 |
4 |
3.286 |
4 |
; positions_6nt_m3 versus sna_rc; m=1/1; ncol2=9; w=9; offset=0; strand=R; shift=0; score= 3.2857; arCAGGTks-
; cor=0.796; Ncor=0.717; logoDP=0.166; NIcor=-0.225; NsEucl=0.897; SSD=1.717; NSW=0.905; rcor=3; rNcor=1; rlogoDP=4; rNIcor=4; rNsEucl=4; rSSD=3; rNSW=4; rank_mean=3.286; match_rank=4
a | 142.347 141.178 0.522917 241.825 51.8638 12.6261 0 30.6144 25.4898 0
c | 39.4755 1.56875 249.431 8.12898 0.522917 0 0 0 80.7859 0
g | 60.8105 90.2934 0.522917 0.522917 183.791 238.374 7.60606 156.419 95.8839 0
t | 8.36667 17.9598 0.522917 0.522917 14.8223 0 243.394 63.967 48.8404 0
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