One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2021/02/16/peak-motifs.2021-02-16.144431_2021-02-16.144431_tXA9Xd/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/Jaspar_2020/nonredundant/JASPAR2020_CORE_vertebrates_non-redundant_pfms.tf -mode matches -strand DR -uth offset_rank 1 -lth w 5 -lth Wr 0.3 -lth cor 0.7 -lth Ncor 0.4 -return matrix_name,matrix_id,cor,Ncor,width,strand,offset,alignments_1ton -sort Ncor -quick -o $RSAT/public_html/tmp/www-data/2021/02/16/peak-motifs.2021-02-16.144431_2021-02-16.144431_tXA9Xd/results/discovered_motifs/positions_6nt_m1/peak-motifs_positions_6nt_m1_vs_db_jaspar_core_nonredundant_vertebrates

One-to-n matrix alignment; reference matrix: positions_6nt_m1_shift0 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
positions_6nt_m1_shift0 (positions_6nt_m1)
; positions_6nt_m1; m=0 (reference); ncol1=24; shift=0; ncol=24; ydyatwTGCATATGCAwatryayr ; Alignment reference a 139 199 105 312 70 227 37 64 50 644 45 604 39 42 122 617 299 438 132 222 173 278 144 209 c 189 144 244 151 173 69 58 18 586 10 45 22 21 41 504 13 113 34 113 124 229 143 200 160 g 168 182 127 115 35 119 14 508 34 21 20 45 8 578 19 57 73 172 151 274 127 166 167 190 t 218 189 238 136 436 299 605 124 44 39 604 43 646 53 69 27 229 70 318 94 185 127 203 155

MA0507.1_rc_shift9 (POU2F2_rc)
; positions_6nt_m1 versus MA0507.1_rc (POU2F2_rc); m=1/5; ncol2=13; w=13; offset=9; strand=R; shift=9; score=0.472555; ---------wyATGCAAATkmr-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 1225.0 476.0 2285.0 0.0 16.0 132.0 2287.0 2029.0 2287.0 251.0 442.0 898.0 835.0 0 0 c 0 0 0 0 0 0 0 0 0 107.0 613.0 0.0 0.0 0.0 1997.0 0.0 0.0 0.0 1.0 415.0 593.0 402.0 0 0 g 0 0 0 0 0 0 0 0 0 361.0 39.0 2.0 30.0 2271.0 0.0 0.0 2.0 0.0 19.0 825.0 266.0 635.0 0 0 t 0 0 0 0 0 0 0 0 0 594.0 1159.0 0.0 2257.0 0.0 158.0 0.0 256.0 0.0 2016.0 605.0 530.0 415.0 0 0

MA0627.2_rc_shift1 (POU2F3_rc)
; positions_6nt_m1 versus MA0627.2_rc (POU2F3_rc); m=2/5; ncol2=13; w=13; offset=1; strand=R; shift=1; score=0.448842; -wwATTTGCATatw---------- ; cor=; Ncor= a 0 17245.0 15909.0 43338.0 330.0 3276.0 896.0 3716.0 2827.0 53366.0 931.0 37593.0 13775.0 16525.0 0 0 0 0 0 0 0 0 0 0 c 0 7941.0 13237.0 4098.0 233.0 804.0 138.0 1079.0 51971.0 1251.0 354.0 3029.0 8770.0 10722.0 0 0 0 0 0 0 0 0 0 0 g 0 11936.0 10595.0 3478.0 164.0 567.0 80.0 50288.0 251.0 322.0 194.0 6885.0 6824.0 11383.0 0 0 0 0 0 0 0 0 0 0 t 0 18907.0 16288.0 5115.0 55302.0 51382.0 54915.0 946.0 980.0 1090.0 54550.0 8522.0 26660.0 17399.0 0 0 0 0 0 0 0 0 0 0

MA0142.1_rc_shift3 (Pou5f1::Sox2_rc)
; positions_6nt_m1 versus MA0142.1_rc (Pou5f1::Sox2_rc); m=3/5; ncol2=15; w=15; offset=3; strand=R; shift=3; score=0.439087; ---aTtTGCATrwsAAwr------ ; cor=; Ncor= a 0 0 0 837.0 53.0 92.0 269.0 196.0 104.0 1332.0 80.0 612.0 907.0 63.0 1231.0 1270.0 701.0 389.0 0 0 0 0 0 0 c 0 0 0 207.0 75.0 315.0 30.0 129.0 1239.0 15.0 24.0 186.0 29.0 825.0 79.0 36.0 28.0 66.0 0 0 0 0 0 0 g 0 0 0 119.0 33.0 68.0 16.0 1029.0 16.0 5.0 30.0 365.0 18.0 363.0 12.0 50.0 58.0 846.0 0 0 0 0 0 0 t 0 0 0 198.0 1200.0 887.0 1050.0 14.0 10.0 17.0 1235.0 206.0 415.0 118.0 47.0 11.0 579.0 63.0 0 0 0 0 0 0

MA0784.1_rc_shift0 (POU1F1_rc)
; positions_6nt_m1 versus MA0784.1_rc (POU1F1_rc); m=4/5; ncol2=14; w=14; offset=0; strand=R; shift=0; score=0.418074; cTmATTwGCATAwt---------- ; cor=; Ncor= a 547.0 273.0 1287.0 2128.0 3.0 85.0 861.0 536.0 176.0 2128.0 19.0 2128.0 1000.0 397.0 0 0 0 0 0 0 0 0 0 0 c 2128.0 194.0 840.0 40.0 0.0 82.0 7.0 164.0 2128.0 26.0 32.0 108.0 187.0 273.0 0 0 0 0 0 0 0 0 0 0 g 479.0 174.0 241.0 37.0 10.0 11.0 12.0 2128.0 11.0 74.0 14.0 83.0 123.0 247.0 0 0 0 0 0 0 0 0 0 0 t 736.0 2128.0 222.0 76.0 2128.0 2128.0 1267.0 98.0 28.0 45.0 2128.0 276.0 1128.0 1211.0 0 0 0 0 0 0 0 0 0 0

MA0786.1_rc_shift1 (POU3F1_rc)
; positions_6nt_m1 versus MA0786.1_rc (POU3F1_rc); m=5/5; ncol2=12; w=12; offset=1; strand=R; shift=1; score=0.400107; -wmATTwrCATAw----------- ; cor=; Ncor= a 0 961.0 1167.0 2471.0 63.0 284.0 1048.0 1119.0 232.0 2471.0 21.0 2471.0 1437.0 0 0 0 0 0 0 0 0 0 0 0 c 0 452.0 620.0 128.0 25.0 130.0 21.0 413.0 2471.0 21.0 26.0 128.0 322.0 0 0 0 0 0 0 0 0 0 0 0 g 0 478.0 302.0 95.0 20.0 103.0 1.0 2471.0 13.0 53.0 7.0 186.0 126.0 0 0 0 0 0 0 0 0 0 0 0 t 0 1510.0 382.0 259.0 2471.0 2471.0 1423.0 170.0 37.0 44.0 2471.0 505.0 1034.0 0 0 0 0 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
positions_6nt_m1_shift0 (positions_6nt_m1)				; positions_6nt_m1; m=0 (reference); ncol1=24; shift=0; ncol=24; ydyatwTGCATATGCAwatryayr ; Alignment reference a 139 199 105 312 70 227 37 64 50 644 45 604 39 42 122 617 299 438 132 222 173 278 144 209 c 189 144 244 151 173 69 58 18 586 10 45 22 21 41 504 13 113 34 113 124 229 143 200 160 g 168 182 127 115 35 119 14 508 34 21 20 45 8 578 19 57 73 172 151 274 127 166 167 190 t 218 189 238 136 436 299 605 124 44 39 604 43 646 53 69 27 229 70 318 94 185 127 203 155
MA0507.1_rc_shift9 (POU2F2_rc)				; positions_6nt_m1 versus MA0507.1_rc (POU2F2_rc); m=1/5; ncol2=13; w=13; offset=9; strand=R; shift=9; score=0.472555; ---------wyATGCAAATkmr-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 1225.0 476.0 2285.0 0.0 16.0 132.0 2287.0 2029.0 2287.0 251.0 442.0 898.0 835.0 0 0 c 0 0 0 0 0 0 0 0 0 107.0 613.0 0.0 0.0 0.0 1997.0 0.0 0.0 0.0 1.0 415.0 593.0 402.0 0 0 g 0 0 0 0 0 0 0 0 0 361.0 39.0 2.0 30.0 2271.0 0.0 0.0 2.0 0.0 19.0 825.0 266.0 635.0 0 0 t 0 0 0 0 0 0 0 0 0 594.0 1159.0 0.0 2257.0 0.0 158.0 0.0 256.0 0.0 2016.0 605.0 530.0 415.0 0 0
MA0627.2_rc_shift1 (POU2F3_rc)				; positions_6nt_m1 versus MA0627.2_rc (POU2F3_rc); m=2/5; ncol2=13; w=13; offset=1; strand=R; shift=1; score=0.448842; -wwATTTGCATatw---------- ; cor=; Ncor= a 0 17245.0 15909.0 43338.0 330.0 3276.0 896.0 3716.0 2827.0 53366.0 931.0 37593.0 13775.0 16525.0 0 0 0 0 0 0 0 0 0 0 c 0 7941.0 13237.0 4098.0 233.0 804.0 138.0 1079.0 51971.0 1251.0 354.0 3029.0 8770.0 10722.0 0 0 0 0 0 0 0 0 0 0 g 0 11936.0 10595.0 3478.0 164.0 567.0 80.0 50288.0 251.0 322.0 194.0 6885.0 6824.0 11383.0 0 0 0 0 0 0 0 0 0 0 t 0 18907.0 16288.0 5115.0 55302.0 51382.0 54915.0 946.0 980.0 1090.0 54550.0 8522.0 26660.0 17399.0 0 0 0 0 0 0 0 0 0 0
MA0142.1_rc_shift3 (Pou5f1::Sox2_rc)				; positions_6nt_m1 versus MA0142.1_rc (Pou5f1::Sox2_rc); m=3/5; ncol2=15; w=15; offset=3; strand=R; shift=3; score=0.439087; ---aTtTGCATrwsAAwr------ ; cor=; Ncor= a 0 0 0 837.0 53.0 92.0 269.0 196.0 104.0 1332.0 80.0 612.0 907.0 63.0 1231.0 1270.0 701.0 389.0 0 0 0 0 0 0 c 0 0 0 207.0 75.0 315.0 30.0 129.0 1239.0 15.0 24.0 186.0 29.0 825.0 79.0 36.0 28.0 66.0 0 0 0 0 0 0 g 0 0 0 119.0 33.0 68.0 16.0 1029.0 16.0 5.0 30.0 365.0 18.0 363.0 12.0 50.0 58.0 846.0 0 0 0 0 0 0 t 0 0 0 198.0 1200.0 887.0 1050.0 14.0 10.0 17.0 1235.0 206.0 415.0 118.0 47.0 11.0 579.0 63.0 0 0 0 0 0 0
MA0784.1_rc_shift0 (POU1F1_rc)				; positions_6nt_m1 versus MA0784.1_rc (POU1F1_rc); m=4/5; ncol2=14; w=14; offset=0; strand=R; shift=0; score=0.418074; cTmATTwGCATAwt---------- ; cor=; Ncor= a 547.0 273.0 1287.0 2128.0 3.0 85.0 861.0 536.0 176.0 2128.0 19.0 2128.0 1000.0 397.0 0 0 0 0 0 0 0 0 0 0 c 2128.0 194.0 840.0 40.0 0.0 82.0 7.0 164.0 2128.0 26.0 32.0 108.0 187.0 273.0 0 0 0 0 0 0 0 0 0 0 g 479.0 174.0 241.0 37.0 10.0 11.0 12.0 2128.0 11.0 74.0 14.0 83.0 123.0 247.0 0 0 0 0 0 0 0 0 0 0 t 736.0 2128.0 222.0 76.0 2128.0 2128.0 1267.0 98.0 28.0 45.0 2128.0 276.0 1128.0 1211.0 0 0 0 0 0 0 0 0 0 0
MA0786.1_rc_shift1 (POU3F1_rc)				; positions_6nt_m1 versus MA0786.1_rc (POU3F1_rc); m=5/5; ncol2=12; w=12; offset=1; strand=R; shift=1; score=0.400107; -wmATTwrCATAw----------- ; cor=; Ncor= a 0 961.0 1167.0 2471.0 63.0 284.0 1048.0 1119.0 232.0 2471.0 21.0 2471.0 1437.0 0 0 0 0 0 0 0 0 0 0 0 c 0 452.0 620.0 128.0 25.0 130.0 21.0 413.0 2471.0 21.0 26.0 128.0 322.0 0 0 0 0 0 0 0 0 0 0 0 g 0 478.0 302.0 95.0 20.0 103.0 1.0 2471.0 13.0 53.0 7.0 186.0 126.0 0 0 0 0 0 0 0 0 0 0 0 t 0 1510.0 382.0 259.0 2471.0 2471.0 1423.0 170.0 37.0 44.0 2471.0 505.0 1034.0 0 0 0 0 0 0 0 0 0 0 0