compare-matrices -v 1 -file1 DemoCompMat.txt -file2 $RSAT/data/motif_databases/JASPAR/jaspar_core_vertebrates_2009_10.tf -format transfac -lth Ncor2 0.7 -lth w 3 -mode profiles -return matrix_id,cor,Ncor,Ncor1,Ncor2,w,offset,strand -o benchmark_result_slow.tab Program version 1.117 Input files file2 $RSAT/data/motif_databases/JASPAR/jaspar_core_vertebrates_2009_10.tf file1 DemoCompMat.txt Output files match_table_txt benchmark_result_slow.tab html_index benchmark_result_slow_index.html output_prefix benchmark_result_slow match_table_html benchmark_result_slow.html Matrices file1 6 matrices DemoCompMat.txt file2 130 matrices $RSAT/data/motif_databases/JASPAR/jaspar_core_vertebrates_2009_10.tf file1 1 12 392 tgCATrACAAwr file1 2 12 565 wtATGCAAATgw file1 3 11 246 wtATGyTAAtk file1 4 20 233 byCwTTGwyATGCAaATGdr file1 5 21 56 srTATGyGCATATGCAwATrw file1 6 11 663 AAAAAAAAAAA file2 1 9 185 GCCcbrrGs file2 2 6 20 CACGTG file2 3 6 24 yGCGTG file2 4 22 24 hwwrGmACryyvtGTwCchrms file2 5 11 40 CTAGGTGTGAA file2 6 20 12 drvkcasygrwGcRkrrCsr file2 7 14 13 TGAmCTTTGmmCyt file2 8 12 39 rrrTGCAATmcc file2 9 8 10 TTTsGCGC file2 10 11 23 TTAyGTAAyrt file2 11 11 10 waRTdRWkbyc file2 12 10 28 varcCGGAAr file2 13 14 27 aAGAyAAGATAAba file2 14 14 28 bmaasRTAAACAaw file2 15 8 20 GTAAACAw file2 16 8 16 vshvwGTA file2 17 8 23 wwdayATA file2 18 5 53 gGATr file2 19 6 63 wGATwg file2 20 10 53 ymAATCacwg file2 21 11 18 tAwTGTTTATw file2 22 12 47 gwwTRTTTdTTY file2 23 12 31 ksdTrTTTrTwT file2 24 12 18 krTTACryAAth file2 25 14 21 gGTTAATwwTTamc file2 26 12 54 gCGCAGCTGCKy file2 27 12 20 rAAAryGAAAsy file2 28 18 12 sGAAAGyGAAAsyrwwwm file2 29 10 58 CTATTTwTAG file2 30 12 16 mrrCArCwGswG file2 31 6 20 yGGGGA file2 32 10 16 bkAKGGGkrr file2 33 10 17 rrmCACGTGr file2 34 11 21 rAsCACGTGGt file2 35 16 116 myyrrCCAATsrgmrs file2 36 10 38 GGGrmTTyCC file2 37 7 17 wTAAktg file2 38 20 28 sTrGGTCAcsgTGACCyAcW file2 39 8 31 wgTCAykb file2 40 30 21 rAAwawwwkcmmmwacymcmcymmcmcymc file2 41 14 43 TTyACGCwTsAvTk file2 42 12 18 hcATCAATCAww file2 43 10 25 wwcwAGGTCA file2 44 14 36 wwwAwbTAGGTCAr file2 45 20 11 MCMCmAMmCAmCMmCmmmsm file2 46 15 10 RGGTCAwcGrGTTCA file2 47 5 59 AATTA file2 48 9 20 ACCGGAAGy file2 49 9 76 rAACAATrG file2 50 9 31 yhyATTGTs file2 51 7 49 wsmGGAA file2 52 12 46 GCCCWTATAwGG file2 53 9 28 kwwaACAAw file2 54 7 23 wAACAAT file2 55 20 10 bayyTCCCAkmaTkCmwyGm file2 56 6 34 sATGAC file2 57 12 12 yRCATTCCwsbg file2 58 12 44 mgAmCAKMTGkT file2 59 10 29 srTCTGGmwt file2 60 7 30 CACGTGr file2 61 6 17 rCCATc file2 62 6 40 ywTCCk file2 63 8 51 grCvGTTG file2 64 10 17 sGGrmwTTCC file2 65 6 41 CACCTk file2 66 11 18 GGGGrwyYCCC file2 67 20 17 msGRACATGyCCGGGCATGT file2 68 10 18 gGGraTTTCC file2 69 15 389 sTATAWAwrssssss file2 70 10 59 wwmCwTwkvt file2 71 11 12 RGGGTwwCAGc file2 72 18 9 rrrAacAtwmyGTyCtrw file2 73 13 67 rGgbCAAAGkyCa file2 74 17 25 AAAGGTCAAAGGTCAAc file2 75 15 33 gsmmCCyWrGGkkkm file2 76 8 15 GCTGAcks file2 77 14 16 TGGCAssrwGCCAA file2 78 9 24 ytrAGTRsm file2 79 7 20 aTACTTA file2 80 8 38 TAATTrsy file2 81 6 16 mTCCAC file2 82 10 20 bwACGTCCGc file2 83 6 31 cTAATk file2 84 7 43 mCAAcms file2 85 13 20 wAATTAATTAwyy file2 86 9 44 waywTCCkk file2 87 19 913 ygrCCAsyAGrkGGCrsyr file2 88 18 2949 ctgskgsggrswGATAAg file2 89 12 3656 rgsyCAAGGTCA file2 90 15 1369 ywTTswyATGCAaAt file2 91 15 669 cywTTGTyaTgcaaA file2 92 10 613 TTCCaGGAAr file2 93 14 4090 CCrGyyyrarCCrG file2 94 14 481 sssgsCbvGGCCTs file2 95 10 227 mgCACGTGGc file2 96 11 897 TGTTTrCwywg file2 97 18 105 GGAAGGAAGGAAGGAAGG file2 98 11 993 CCGGAAGygvc file2 99 11 4000 rsWGATAAgrr file2 100 10 4349 wGGGyGkGGc file2 101 21 1606 tTCAGcACCatGGACAGckcC file2 102 11 2000 ktyTGTGGttw file2 103 15 2085 cayTTCChrGAAryc file2 104 10 438 msCACGTGGc file2 105 12 811 TRTTTACwywgg file2 106 20 475 vkscmaGGtCAcccTGaCCy file2 107 15 864 strGGgcArAGGkcA file2 108 11 20 rTGACwmAGCA file2 109 6 27 ATyAAA file2 110 7 26 TTTTCCA file2 111 12 9 yyAATrwTTAAC file2 112 10 25 mCyCmaGGGA file2 113 12 24 TGymwGGGGkcr file2 114 8 13 CAGGAArT file2 115 8 13 kGTAAACA file2 116 8 16 CdbwAATk file2 117 17 23 rGkTCAysgrsAGKTCA file2 118 8 14 aAGGTCAc file2 119 6 6912 yTGGCa file2 120 11 15 yGCGTGGGcGk file2 121 14 18 GGGGCCcwmGGGGG file2 122 7 23 cAAGCTT file2 123 7 42 AGGAAGT file2 124 8 11 TGACGYcA file2 125 7 18 TGAmTCA file2 126 10 35 CCCCkCCCCC file2 127 9 18 TtkygCAAy file2 128 18 357 cwrGGTCAsgkTGmCCys file2 129 8 104 vbACGTGc file2 130 6 22 CwTTGT Threshold values Parameter Lower Upper w 3 none ncor2 0.7 none Column content 1 id1 Identifier of the first matrix 2 id2 Identifier of the second matrix 3 name1 Name of the first matrix 4 name2 Name of the second matrix 5 cor Pearson coefficient of correlation between frequency matrices 6 Ncor Normalized correlation. Ncor = cor * Wr 7 Ncor1 Normalized correlation. Ncor1 = cor * w / w1 8 Ncor2 Normalized correlation. Ncor2 = cor * w / w2 9 w1 Width of the first matrix 10 w2 Width of the second matrix 11 w Alignment length (number of overlapping columns between matrix 1 and matrix 2, as a function of the offset) 12 W Total alignment length (overlapping + non-overlapping columns). W = w1 + w2 - w 13 Wr Relative alignment length (overlap divided by the total alignemnt length). Wr = w/W 14 wr1 Alignment length relative to the width of the first matrix. wr1 = w/w1 15 wr2 Alignment length relative to the width of the second matrix. wr2 = w/w2 16 strand "strand", i.e. orientation of matrix 2 relative to matrix 1 (D=direct; R=reverse) 17 offset shift of the second matrix relative to the first matrix (negative:left; positive: right) 18 consensus1 IUPAC consensus of matrix 1 (dots represent non-aligned columns) 19 consensus2 IUPAC consensus of matrix 2 (dots represent non-aligned columns)
| id1 | id2 | name1 | name2 | cor | Ncor | Ncor1 | Ncor2 | w1 | w2 | w | W | Wr | wr1 | wr2 | strand | offset | consensus1 | consensus2 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| oligos_7nt_mkv5_m1 | MA0067.1 | oligos_7nt_mkv5_m1 | Pax2 | 0.702 | 0.468 | 0.468 | 0.702 | 12 | 8 | 8 | 12 | 0.6667 | 0.6667 | 1.0000 | R | 1 | .gCATrACA... | VMRTGACW |
| oligos_7nt_mkv5_m1 | MA0077.1 | oligos_7nt_mkv5_m1 | SOX9 | 0.790 | 0.486 | 0.527 | 0.702 | 12 | 9 | 8 | 13 | 0.6154 | 0.6667 | 0.8889 | D | 4 | ....TrACAAwr | rAACAATr. |
| oligos_7nt_mkv5_m1 | MA0078.1 | oligos_7nt_mkv5_m1 | Sox17 | 0.914 | 0.457 | 0.533 | 0.711 | 12 | 9 | 7 | 14 | 0.5000 | 0.5833 | 0.7778 | R | 5 | .....rACAAwr | SACAATR.. |
| oligos_7nt_mkv5_m1 | MA0084.1 | oligos_7nt_mkv5_m1 | SRY | 0.745 | 0.559 | 0.559 | 0.745 | 12 | 9 | 9 | 12 | 0.7500 | 0.7500 | 1.0000 | D | 2 | ..CATrACAAw. | kwwaACAAw |
| oligos_7nt_mkv5_m1 | MA0087.1 | oligos_7nt_mkv5_m1 | Sox5 | 0.828 | 0.483 | 0.483 | 0.828 | 12 | 7 | 7 | 12 | 0.5833 | 0.5833 | 1.0000 | D | 4 | ....TrACAAw. | wAACAAT |
| oligos_7nt_mkv5_m1 | MA0089.1 | oligos_7nt_mkv5_m1 | NFE2L1::MafG | 0.842 | 0.421 | 0.421 | 0.842 | 12 | 6 | 6 | 12 | 0.5000 | 0.5000 | 1.0000 | D | 2 | ..CATrAC.... | sATGAC |
| oligos_7nt_mkv5_m1 | MA0142.1 | oligos_7nt_mkv5_m1 | Pou5f1 | 0.944 | 0.755 | 0.944 | 0.755 | 12 | 15 | 12 | 15 | 0.8000 | 1.0000 | 0.8000 | R | -3 | tgCATrACAAwr | ...TGCATRWSAAWR |
| oligos_7nt_mkv5_m1 | MA0143.1 | oligos_7nt_mkv5_m1 | Sox2 | 0.962 | 0.769 | 0.962 | 0.769 | 12 | 15 | 12 | 15 | 0.8000 | 1.0000 | 0.8000 | R | -2 | tgCATrACAAwr | ..TGCATRACAAWR. |
| oligos_7nt_mkv5_m1 | MA0442.1 | oligos_7nt_mkv5_m1 | SOX10 | 0.945 | 0.472 | 0.472 | 0.945 | 12 | 6 | 6 | 12 | 0.5000 | 0.5000 | 1.0000 | R | 6 | ......ACAAwr | ACAAWG |
| oligos_7nt_mkv5_m2 | MA0075.1 | oligos_7nt_mkv5_m2 | Prrx2 | 0.751 | 0.313 | 0.313 | 0.751 | 12 | 5 | 5 | 12 | 0.4167 | 0.4167 | 1.0000 | D | 7 | .......AATgw | AATTA |
| oligos_7nt_mkv5_m2 | MA0132.1 | oligos_7nt_mkv5_m2 | Pdx1 | 0.752 | 0.376 | 0.376 | 0.752 | 12 | 6 | 6 | 12 | 0.5000 | 0.5000 | 1.0000 | D | 5 | .....CAAATg. | cTAATk |
| oligos_7nt_mkv5_m3 | MA0075.1 | oligos_7nt_mkv5_m3 | Prrx2 | 0.886 | 0.403 | 0.403 | 0.886 | 11 | 5 | 5 | 11 | 0.4545 | 0.4545 | 1.0000 | R | 6 | ......TAAtk | TAATT |
| oligos_7nt_mkv5_m3 | MA0132.1 | oligos_7nt_mkv5_m3 | Pdx1 | 0.928 | 0.506 | 0.506 | 0.928 | 11 | 6 | 6 | 11 | 0.5455 | 0.5455 | 1.0000 | D | 5 | .....yTAAtk | cTAATk |
| positions_7nt_m1 | MA0077.1 | positions_7nt_m1 | SOX9 | 0.766 | 0.345 | 0.345 | 0.766 | 20 | 9 | 9 | 20 | 0.4500 | 0.4500 | 1.0000 | R | 1 | .yCwTTGwyA.......... | CYATTGTTY |
| positions_7nt_m1 | MA0078.1 | positions_7nt_m1 | Sox17 | 0.845 | 0.380 | 0.380 | 0.845 | 20 | 9 | 9 | 20 | 0.4500 | 0.4500 | 1.0000 | D | 0 | byCwTTGwy........... | yhyATTGTs |
| positions_7nt_m1 | MA0087.1 | positions_7nt_m1 | Sox5 | 0.807 | 0.282 | 0.282 | 0.807 | 20 | 7 | 7 | 20 | 0.3500 | 0.3500 | 1.0000 | R | 3 | ...wTTGwyA.......... | ATTGTTW |
| positions_7nt_m1 | MA0089.1 | positions_7nt_m1 | NFE2L1::MafG | 0.736 | 0.221 | 0.221 | 0.736 | 20 | 6 | 6 | 20 | 0.3000 | 0.3000 | 1.0000 | R | 6 | ......GwyATG........ | GTCATS |
| positions_7nt_m1 | MA0095.1 | positions_7nt_m1 | YY1 | 0.756 | 0.227 | 0.227 | 0.756 | 20 | 6 | 6 | 20 | 0.3000 | 0.3000 | 1.0000 | R | 14 | ..............aATGdr | GATGGY |
| positions_7nt_m1 | MA0142.1 | positions_7nt_m1 | Pou5f1 | 0.989 | 0.742 | 0.742 | 0.989 | 20 | 15 | 15 | 20 | 0.7500 | 0.7500 | 1.0000 | D | 2 | ..CwTTGwyATGCAaAT... | ywTTswyATGCAaAt |
| positions_7nt_m1 | MA0143.1 | positions_7nt_m1 | Sox2 | 0.948 | 0.711 | 0.711 | 0.948 | 20 | 15 | 15 | 20 | 0.7500 | 0.7500 | 1.0000 | D | 1 | .yCwTTGwyATGCAaA.... | cywTTGTyaTgcaaA |
| positions_7nt_m1 | MA0442.1 | positions_7nt_m1 | SOX10 | 0.947 | 0.284 | 0.284 | 0.947 | 20 | 6 | 6 | 20 | 0.3000 | 0.3000 | 1.0000 | D | 2 | ..CwTTGw............ | CwTTGT |
| positions_7nt_m2 | MA0033.1 | positions_7nt_m2 | FOXL1 | 0.757 | 0.288 | 0.288 | 0.757 | 21 | 8 | 8 | 21 | 0.3810 | 0.3810 | 1.0000 | R | 10 | ..........TATGCAwA... | TATRTHWW |
Host name caminante-6.local Job started 2013-03-05.165441 Job done 2013-03-05.165444 Seconds 3.41 user 3.41 system 0.02 cuser 0 ; csystem 0