One-to-n alignments
Command: compare-matrices -v 1 -format transfac -file $RSAT/public_html/tmp/wwwrun/2014/09/06/peak-motifs.2014-09-06.123915_2014-09-06.123915_sfIm4F/results/discovered_motifs/peak-motifs_motifs_discovered.tf -distinct -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 $RSAT/public_html/tmp/wwwrun/2014/09/06/peak-motifs.2014-09-06.123915_2014-09-06.123915_sfIm4F/results/discovered_motifs/peak-motifs_motifs_disco_compa.tab
One-to-n matrix alignment; reference matrix: oligos_7nt_test_vs_ctrl_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 |
|---|
| oligos_7nt_test_vs_ctrl_m1_shift0 (oligos_7nt_test_vs_ctrl_m1) |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
; oligos_7nt_test_vs_ctrl_m1; m=0 (reference); ncol1=24; shift=0; ncol=24; TykGGCCAGyCCAAAGTCCArGAy
; Alignment reference
a 0 0 0 0 0 0 0 2 0 0 0 0 2 2 2 0 0 0 0 2 1 0 2 0
c 0 1 0 0 0 2 2 0 0 1 2 2 0 0 0 0 0 2 2 0 0 0 0 1
g 0 0 1 2 2 0 0 0 2 0 0 0 0 0 0 2 0 0 0 0 1 2 0 0
t 2 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 2 0 0 0 0 0 0 1
|
| oligos_7nt_test_vs_ctrl_m4_shift0 (oligos_7nt_test_vs_ctrl_m4) |
 |
0.850 |
0.850 |
32.070 |
0.856 |
0.938 |
4.500 |
0.906 |
2 |
1 |
1 |
1 |
1 |
6 |
3 |
2.143 |
1 |
; oligos_7nt_test_vs_ctrl_m1 versus oligos_7nt_test_vs_ctrl_m4; m=1/1; ncol2=24; w=24; offset=0; strand=D; shift=0; score= 2.1429; TmGGkCCAGkCCAAAGwCCAArwk
; cor=0.850; Ncor=0.850; logoDP=32.070; NIcor=0.856; NsEucl=0.938; SSD=4.500; NSW=0.906; rcor=2; rNcor=1; rlogoDP=1; rNIcor=1; rNsEucl=1; rSSD=6; rNSW=3; rank_mean=2.143; match_rank=1
a 0 1 0 0 0 0 0 2 0 0 0 0 2 2 2 0 1 0 0 2 2 1 1 0
c 0 1 0 0 0 2 2 0 0 0 2 2 0 0 0 0 0 2 2 0 0 0 0 0
g 0 0 2 2 1 0 0 0 2 1 0 0 0 0 0 2 0 0 0 0 0 1 0 1
t 2 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 1 1
|
One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m5_shift11 ; 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 |
|---|
| oligos_6nt_test_vs_ctrl_m5_shift11 (oligos_6nt_test_vs_ctrl_m5) |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
; oligos_6nt_test_vs_ctrl_m5; m=0 (reference); ncol1=12; shift=11; ncol=23; -----------cmAAGGTCAGrr
; Alignment reference
a 0 0 0 0 0 0 0 0 0 0 0 139 297 715 715 0 0 0 0 715 0 220 200
c 0 0 0 0 0 0 0 0 0 0 0 264 201 0 0 0 0 0 715 0 0 145 133
g 0 0 0 0 0 0 0 0 0 0 0 154 130 0 0 715 715 0 0 0 715 200 212
t 0 0 0 0 0 0 0 0 0 0 0 158 87 0 0 0 0 715 0 0 0 150 170
|
| oligos_8nt_test_vs_ctrl_m2_shift0 (oligos_8nt_test_vs_ctrl_m2) |
 |
0.897 |
0.468 |
14.223 |
0.455 |
0.930 |
1.408 |
0.941 |
1 |
7 |
3 |
5 |
2 |
1 |
1 |
2.857 |
2 |
; oligos_6nt_test_vs_ctrl_m5 versus oligos_8nt_test_vs_ctrl_m2; m=1/1; ncol2=23; w=12; offset=-11; strand=D; shift=0; score= 2.8571; myTCCArrGmCCAAAGGkCAGvh
; cor=0.897; Ncor=0.468; logoDP=14.223; NIcor=0.455; NsEucl=0.930; SSD=1.408; NSW=0.941; rcor=1; rNcor=7; rlogoDP=3; rNIcor=5; rNsEucl=2; rSSD=1; rNSW=1; rank_mean=2.857; match_rank=2
a 2 0 0 0 0 3 2 2 0 2 0 0 3 3 3 0 0 0 0 3 0 1 1
c 1 2 0 3 3 0 0 0 0 1 3 3 0 0 0 0 0 0 3 0 0 1 1
g 0 0 0 0 0 0 1 1 3 0 0 0 0 0 0 3 3 1 0 0 3 1 0
t 0 1 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 0 1
|
One-to-n matrix alignment; reference matrix: oligos_8nt_test_vs_ctrl_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 |
|---|
| oligos_8nt_test_vs_ctrl_m1_shift0 (oligos_8nt_test_vs_ctrl_m1) |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
; oligos_8nt_test_vs_ctrl_m1; m=0 (reference); ncol1=21; shift=0; ncol=21; ymAAGTCCAAAGTCCAGGGrw
; Alignment reference
a 3 5 15 18 0 1 0 0 18 17 16 0 0 0 2 15 1 3 0 6 6
c 6 7 0 0 0 1 18 18 0 0 0 2 1 18 16 0 1 0 0 3 4
g 3 4 2 0 17 1 0 0 0 1 2 15 3 0 0 0 14 14 15 7 3
t 6 2 1 0 1 15 0 0 0 0 0 1 14 0 0 3 2 1 3 2 5
|
| oligos_8nt_test_vs_ctrl_m3_shift4 (oligos_8nt_test_vs_ctrl_m3) |
 |
0.820 |
0.664 |
10.736 |
0.640 |
0.929 |
2.909 |
0.914 |
3 |
5 |
5 |
3 |
3 |
3 |
2 |
3.429 |
3 |
; oligos_8nt_test_vs_ctrl_m1 versus oligos_8nt_test_vs_ctrl_m3; m=1/2; ncol2=17; w=17; offset=4; strand=D; shift=4; score= 3.4286; ----ksCCAGAGTCCAGGGwt
; cor=0.820; Ncor=0.664; logoDP=10.736; NIcor=0.640; NsEucl=0.929; SSD=2.909; NSW=0.914; rcor=3; rNcor=5; rlogoDP=5; rNIcor=3; rNsEucl=3; rSSD=3; rNSW=2; rank_mean=3.429; match_rank=3
a 0 0 0 0 17 13 6 0 84 5 84 0 0 0 0 74 4 4 9 31 19
c 0 0 0 0 13 28 68 88 3 2 2 1 1 87 88 3 4 6 4 19 18
g 0 0 0 0 32 30 9 0 1 82 2 88 4 0 1 5 77 77 72 15 17
t 0 0 0 0 28 19 7 2 2 1 2 1 85 3 1 8 5 3 5 25 36
|
| oligos_8nt_test_vs_ctrl_m4_rc_shift1 (oligos_8nt_test_vs_ctrl_m4_rc) |
 |
0.779 |
0.741 |
2.169 |
-0.105 |
0.928 |
4.131 |
0.897 |
5 |
2 |
6 |
6 |
4 |
5 |
5 |
4.714 |
5 |
; oligos_8nt_test_vs_ctrl_m1 versus oligos_8nt_test_vs_ctrl_m4_rc; m=2/2; ncol2=20; w=20; offset=1; strand=R; shift=1; score= 4.7143; -vbAGGGCAAAGTCCAGGGrd
; cor=0.779; Ncor=0.741; logoDP=2.169; NIcor=-0.105; NsEucl=0.928; SSD=4.131; NSW=0.897; rcor=5; rNcor=2; rlogoDP=6; rNIcor=6; rNsEucl=4; rSSD=5; rNSW=5; rank_mean=4.714; match_rank=5
a 0 14 5 33 3 1 4 2 38 35 38 1 1 1 0 36 6 4 5 12 10
c 0 10 13 1 0 0 3 34 2 1 0 0 0 36 40 0 0 2 3 8 3
g 0 10 11 0 37 38 33 3 0 4 1 39 2 2 0 1 34 30 28 12 15
t 0 6 11 6 0 1 0 1 0 0 1 0 37 1 0 3 0 4 4 8 12
|
One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m3_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 |
|---|
| oligos_6nt_test_vs_ctrl_m3_shift1 (oligos_6nt_test_vs_ctrl_m3) |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
; oligos_6nt_test_vs_ctrl_m3; m=0 (reference); ncol1=11; shift=1; ncol=12; -mdGGGTCAGrr
; Alignment reference
a 0 425 502 0 0 0 0 0 1513 0 452 396
c 0 446 86 0 0 0 0 1513 0 0 285 256
g 0 284 466 1513 1513 1513 0 0 0 1513 477 526
t 0 358 459 0 0 0 1513 0 0 0 299 335
|
| oligos_6nt_test_vs_ctrl_m5_shift0 (oligos_6nt_test_vs_ctrl_m5) |
 |
0.767 |
0.703 |
11.593 |
0.705 |
0.895 |
2.673 |
0.878 |
7 |
3 |
4 |
2 |
7 |
2 |
6 |
4.429 |
4 |
; oligos_6nt_test_vs_ctrl_m3 versus oligos_6nt_test_vs_ctrl_m5; m=1/1; ncol2=12; w=11; offset=-1; strand=D; shift=0; score= 4.4286; cmAAGGTCAGrr
; cor=0.767; Ncor=0.703; logoDP=11.593; NIcor=0.705; NsEucl=0.895; SSD=2.673; NSW=0.878; rcor=7; rNcor=3; rlogoDP=4; rNIcor=2; rNsEucl=7; rSSD=2; rNSW=6; rank_mean=4.429; match_rank=4
a 139 297 715 715 0 0 0 0 715 0 220 200
c 264 201 0 0 0 0 0 715 0 0 145 133
g 154 130 0 0 715 715 0 0 0 715 200 212
t 158 87 0 0 0 0 715 0 0 0 150 170
|
One-to-n matrix alignment; reference matrix: oligos_8nt_test_vs_ctrl_m3_shift3 ; 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 |
|---|
| oligos_8nt_test_vs_ctrl_m3_shift3 (oligos_8nt_test_vs_ctrl_m3) |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
; oligos_8nt_test_vs_ctrl_m3; m=0 (reference); ncol1=17; shift=3; ncol=20; ---ksCCAGAGTCCAGGGwt
; Alignment reference
a 0 0 0 17 13 6 0 84 5 84 0 0 0 0 74 4 4 9 31 19
c 0 0 0 13 28 68 88 3 2 2 1 1 87 88 3 4 6 4 19 18
g 0 0 0 32 30 9 0 1 82 2 88 4 0 1 5 77 77 72 15 17
t 0 0 0 28 19 7 2 2 1 2 1 85 3 1 8 5 3 5 25 36
|
| oligos_8nt_test_vs_ctrl_m4_rc_shift0 (oligos_8nt_test_vs_ctrl_m4_rc) |
 |
0.782 |
0.665 |
1.415 |
-0.138 |
0.922 |
3.488 |
0.897 |
4 |
4 |
7 |
7 |
5 |
4 |
4 |
5.000 |
6 |
; oligos_8nt_test_vs_ctrl_m3 versus oligos_8nt_test_vs_ctrl_m4_rc; m=1/1; ncol2=20; w=17; offset=-3; strand=R; shift=0; score= 5; vbAGGGCAAAGTCCAGGGrd
; cor=0.782; Ncor=0.665; logoDP=1.415; NIcor=-0.138; NsEucl=0.922; SSD=3.488; NSW=0.897; rcor=4; rNcor=4; rlogoDP=7; rNIcor=7; rNsEucl=5; rSSD=4; rNSW=4; rank_mean=5.000; match_rank=6
a 14 5 33 3 1 4 2 38 35 38 1 1 1 0 36 6 4 5 12 10
c 10 13 1 0 0 3 34 2 1 0 0 0 36 40 0 0 2 3 8 3
g 10 11 0 37 38 33 3 0 4 1 39 2 2 0 1 34 30 28 12 15
t 6 11 6 0 1 0 1 0 0 1 0 37 1 0 3 0 4 4 8 12
|
One-to-n matrix alignment; reference matrix: oligos_6nt_test_vs_ctrl_m2_shift4 ; 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 |
|---|
| oligos_6nt_test_vs_ctrl_m2_shift4 (oligos_6nt_test_vs_ctrl_m2) |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
; oligos_6nt_test_vs_ctrl_m2; m=0 (reference); ncol1=23; shift=4; ncol=27; ----ATCCAAAGTCCAGAGCAGGGAAT
; Alignment reference
a 0 0 0 0 1 0 0 0 1 1 1 0 0 0 0 1 0 1 0 0 1 0 0 0 1 1 0
c 0 0 0 0 0 0 1 1 0 0 0 0 0 1 1 0 0 0 0 1 0 0 0 0 0 0 0
g 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 1 0 0 1 1 1 0 0 0
t 0 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1
|
| oligos_8nt_test_vs_ctrl_m1_shift0 (oligos_8nt_test_vs_ctrl_m1) |
|
0.773 |
0.487 |
17.440 |
0.475 |
0.906 |
5.160 |
0.848 |
6 |
6 |
2 |
4 |
6 |
7 |
7 |
5.429 |
7 |
; oligos_6nt_test_vs_ctrl_m2 versus oligos_8nt_test_vs_ctrl_m1; m=1/1; ncol2=21; w=17; offset=-4; strand=D; shift=0; score= 5.4286; ymAAGTCCAAAGTCCAGGGrw------
; cor=0.773; Ncor=0.487; logoDP=17.440; NIcor=0.475; NsEucl=0.906; SSD=5.160; NSW=0.848; rcor=6; rNcor=6; rlogoDP=2; rNIcor=4; rNsEucl=6; rSSD=7; rNSW=7; rank_mean=5.429; match_rank=7
a 3 5 15 18 0 1 0 0 18 17 16 0 0 0 2 15 1 3 0 6 6 0 0 0 0 0 0
c 6 7 0 0 0 1 18 18 0 0 0 2 1 18 16 0 1 0 0 3 4 0 0 0 0 0 0
g 3 4 2 0 17 1 0 0 0 1 2 15 3 0 0 0 14 14 15 7 3 0 0 0 0 0 0
t 6 2 1 0 1 15 0 0 0 0 0 1 14 0 0 3 2 1 3 2 5 0 0 0 0 0 0
|