One-to-n alignments
Command: compare-matrices -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/09/15/compare-matrices_2025-09-15.164012_GihXmp/compare-matrices_query_matrices.transfac -file2 $RSAT/public_html/motif_databases/Athamap/Athamap_2015-11-06.tf -format2 tf -strand DR -lth cor 0.7 -lth Ncor 0.4 -uth match_rank 50 -return cor,Ncor,logoDP,NsEucl,NSW,match_rank,matrix_id,matrix_name,width,strand,offset,consensus,alignments_1ton -o $RSAT/public_html/tmp/www-data/2025/09/15/compare-matrices_2025-09-15.164012_GihXmp/compare-matrices.tab
One-to-n matrix alignment; reference matrix: tcp4_c1_m17_assembly_17_shift1 ; 3 matrices ; sort_field=rank_mean
| Matrix name | Aligned logos | cor |
Ncor |
logoDP |
NsEucl |
NSW |
rcor |
rNcor |
rlogoDP |
rNsEucl |
rNSW |
rank_mean |
match_rank |
Aligned matrices |
|---|
| tcp4_c1_m17_assembly_17_shift1 (assembly_17) |
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; tcp4_c1_m17_assembly_17 (assembly_17); m=0 (reference); ncol1=10; shift=1; ncol=11; -waAGGACAwd
; Alignment reference
a 0 95 115 263 0 0 263 0 263 105 94
c 0 43 28 0 0 0 0 263 0 47 32
g 0 46 61 0 263 263 0 0 0 38 70
t 0 79 59 0 0 0 0 0 0 73 67
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| 5027_ID1_Athamap_20091028__rc_shift0 (5027_ID1_Athamap_20091028__rc) |
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0.780 |
0.709 |
0.745 |
0.900 |
0.899 |
2 |
1 |
5 |
2 |
2 |
2.400 |
1 |
; tcp4_c1_m17_assembly_17 versus 5027_ID1_Athamap_20091028__rc; m=1/2; ncol2=11; w=-1; offset=-1; strand=R; shift=0; score= 2.4; AwwrsGACAAA
; cor=0.780; Ncor=0.709; logoDP=0.745; NsEucl=0.900; NSW=0.899; rcor=2; rNcor=1; rlogoDP=5; rNsEucl=2; rNSW=2; rank_mean=2.400; match_rank=1
a 11 9 9 9 2 1 14 1 14 15 12
c 0 0 0 0 8 0 1 14 0 0 0
g 1 1 2 6 5 14 0 0 1 0 3
t 3 5 4 0 0 0 0 0 0 0 0
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| 5047_ZmHOX2a_1__Athamap_20091028__rc_shift1 (5047_ZmHOX2a_1__Athamap_20091028__rc) |
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0.904 |
0.633 |
0.148 |
0.916 |
0.950 |
1 |
4 |
6 |
1 |
1 |
2.600 |
3 |
; tcp4_c1_m17_assembly_17 versus 5047_ZmHOX2a_1__Athamap_20091028__rc; m=2/2; ncol2=7; w=0; offset=0; strand=R; shift=1; score= 2.6; -ttAGGAy---
; cor=0.904; Ncor=0.633; logoDP=0.148; NsEucl=0.916; NSW=0.950; rcor=1; rNcor=4; rlogoDP=6; rNsEucl=1; rNSW=1; rank_mean=2.600; match_rank=3
a 0 8 6 38 0 0 38 7 0 0 0
c 0 3 8 0 0 0 0 16 0 0 0
g 0 6 7 0 38 38 0 4 0 0 0
t 0 21 17 0 0 0 0 11 0 0 0
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One-to-n matrix alignment; reference matrix: tcp4_c1_m16_assembly_16_shift0 ; 2 matrices ; sort_field=rank_mean
| Matrix name | Aligned logos | cor |
Ncor |
logoDP |
NsEucl |
NSW |
rcor |
rNcor |
rlogoDP |
rNsEucl |
rNSW |
rank_mean |
match_rank |
Aligned matrices |
|---|
| tcp4_c1_m16_assembly_16_shift0 (assembly_16) |
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; tcp4_c1_m16_assembly_16 (assembly_16); m=0 (reference); ncol1=10; shift=0; ncol=10; wwCAAAAGww
; Alignment reference
a 410 391 0 1043 1043 1043 1043 0 413 397
c 170 191 1043 0 0 0 0 0 149 155
g 190 147 0 0 0 0 0 1043 176 167
t 273 314 0 0 0 0 0 0 305 324
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| 337_M00353_TRANSFAC_2012.1__DOF2_Athamap_20091028__shift0 (337_M00353_TRANSFAC_2012.1__DOF2_Athamap_20091028_) |
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0.754 |
0.685 |
7.807 |
0.899 |
0.898 |
3 |
2 |
1 |
3 |
3 |
2.400 |
2 |
; tcp4_c1_m16_assembly_16 versus 337_M00353_TRANSFAC_2012.1__DOF2_Athamap_20091028_; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 2.4; mmwwAAAGcr
; cor=0.754; Ncor=0.685; logoDP=7.807; NsEucl=0.899; NSW=0.898; rcor=3; rNcor=2; rlogoDP=1; rNsEucl=3; rNSW=3; rank_mean=2.400; match_rank=2
a 7 7 7 7 21 21 21 0 3 7
c 7 6 3 2 0 0 0 0 12 4
g 2 4 4 2 0 0 0 21 2 6
t 5 4 7 10 0 0 0 0 4 4
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One-to-n matrix alignment; reference matrix: tcp4_c1_m14_assembly_14_shift0 ; 2 matrices ; sort_field=rank_mean
| Matrix name | Aligned logos | cor |
Ncor |
logoDP |
NsEucl |
NSW |
rcor |
rNcor |
rlogoDP |
rNsEucl |
rNSW |
rank_mean |
match_rank |
Aligned matrices |
|---|
| tcp4_c1_m14_assembly_14_shift0 (assembly_14) |
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; tcp4_c1_m14_assembly_14 (assembly_14); m=0 (reference); ncol1=10; shift=0; ncol=10; waAGAAAGww
; Alignment reference
a 381 440 951 0 951 951 951 0 461 373
c 146 100 0 0 0 0 0 0 123 114
g 178 231 0 951 0 0 0 951 123 210
t 246 180 0 0 0 0 0 0 244 254
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| 337_M00353_TRANSFAC_2012.1__DOF2_Athamap_20091028__shift0 (337_M00353_TRANSFAC_2012.1__DOF2_Athamap_20091028_) |
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0.737 |
0.670 |
7.755 |
0.895 |
0.889 |
4 |
3 |
2 |
4 |
4 |
3.400 |
4 |
; tcp4_c1_m14_assembly_14 versus 337_M00353_TRANSFAC_2012.1__DOF2_Athamap_20091028_; m=1/1; ncol2=11; w=0; offset=0; strand=D; shift=0; score= 3.4; mmwwAAAGcr
; cor=0.737; Ncor=0.670; logoDP=7.755; NsEucl=0.895; NSW=0.889; rcor=4; rNcor=3; rlogoDP=2; rNsEucl=4; rNSW=4; rank_mean=3.400; match_rank=4
a 7 7 7 7 21 21 21 0 3 7
c 7 6 3 2 0 0 0 0 12 4
g 2 4 4 2 0 0 0 21 2 6
t 5 4 7 10 0 0 0 0 4 4
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One-to-n matrix alignment; reference matrix: tcp4_c1_m8_assembly_8_shift1 ; 2 matrices ; sort_field=rank_mean
| Matrix name | Aligned logos | cor |
Ncor |
logoDP |
NsEucl |
NSW |
rcor |
rNcor |
rlogoDP |
rNsEucl |
rNSW |
rank_mean |
match_rank |
Aligned matrices |
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| tcp4_c1_m8_assembly_8_shift1 (assembly_8) |
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; tcp4_c1_m8_assembly_8 (assembly_8); m=0 (reference); ncol1=11; shift=1; ncol=12; -waACCACAAww
; Alignment reference
a 0 1172 1341 2999 335 403 3125 537 3084 3047 1306 1281
c 0 663 660 89 2658 2652 72 2500 109 98 637 592
g 0 486 528 67 84 102 32 115 41 34 520 487
t 0 991 783 157 235 155 83 160 78 133 849 952
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| 5027_ID1_Athamap_20091028__rc_shift0 (5027_ID1_Athamap_20091028__rc) |
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0.713 |
0.594 |
1.196 |
0.891 |
0.880 |
5 |
5 |
4 |
5 |
5 |
4.800 |
5 |
; tcp4_c1_m8_assembly_8 versus 5027_ID1_Athamap_20091028__rc; m=1/1; ncol2=11; w=-1; offset=-1; strand=R; shift=0; score= 4.8; AwwrsGACAAA-
; cor=0.713; Ncor=0.594; logoDP=1.196; NsEucl=0.891; NSW=0.880; rcor=5; rNcor=5; rlogoDP=4; rNsEucl=5; rNSW=5; rank_mean=4.800; match_rank=5
a 11 9 9 9 2 1 14 1 14 15 12 0
c 0 0 0 0 8 0 1 14 0 0 0 0
g 1 1 2 6 5 14 0 0 1 0 3 0
t 3 5 4 0 0 0 0 0 0 0 0 0
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One-to-n matrix alignment; reference matrix: tcp4_c1_m11_assembly_11_shift0 ; 2 matrices ; sort_field=rank_mean
| Matrix name | Aligned logos | cor |
Ncor |
logoDP |
NsEucl |
NSW |
rcor |
rNcor |
rlogoDP |
rNsEucl |
rNSW |
rank_mean |
match_rank |
Aligned matrices |
|---|
| tcp4_c1_m11_assembly_11_shift0 (assembly_11) |
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; tcp4_c1_m11_assembly_11 (assembly_11); m=0 (reference); ncol1=12; shift=0; ncol=12; wwTGAGCTGAww
; Alignment reference
a 116 146 20 15 409 22 38 18 30 371 147 159
c 62 61 12 6 2 12 344 4 18 17 64 59
g 79 62 15 367 7 357 11 3 350 11 77 89
t 165 153 375 34 4 31 29 397 24 23 134 115
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| 5048_ZmHOX2a_2__Athamap_20091028__shift2 (5048_ZmHOX2a_2__Athamap_20091028_) |
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0.701 |
0.409 |
4.054 |
0.852 |
0.847 |
6 |
6 |
3 |
6 |
6 |
5.400 |
6 |
; tcp4_c1_m11_assembly_11 versus 5048_ZmHOX2a_2__Athamap_20091028_; m=1/1; ncol2=7; w=0; offset=2; strand=D; shift=2; score= 5.4; --tGATCkg---
; cor=0.701; Ncor=0.409; logoDP=4.054; NsEucl=0.852; NSW=0.847; rcor=6; rNcor=6; rlogoDP=3; rNsEucl=6; rNSW=6; rank_mean=5.400; match_rank=6
a 0 0 5 0 27 0 0 0 3 0 0 0
c 0 0 2 0 0 0 27 4 4 0 0 0
g 0 0 5 27 0 0 0 7 14 0 0 0
t 0 0 15 0 0 27 0 16 6 0 0 0
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