One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep1_motifs50/results/discovered_motifs/local_words_8nt_m7/peak-motifs_local_words_8nt_m7.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 Myogenin_Rep1_motifs50/results/discovered_motifs/local_words_8nt_m7/peak-motifs_local_words_8nt_m7_vs_db_jaspar_core_nonredundant_vertebrates

One-to-n matrix alignment; reference matrix: local_words_8nt_m7_shift0 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
local_words_8nt_m7_shift0 (local_words_8nt_m7local_words_8nt_m7)
; local_words_8nt_m7 (local_words_8nt_m7local_words_8nt_m7); m=0 (reference); ncol1=24; shift=0; ncol=24; rvTGACAGCTGCCAGCTGCTGCyk ; Alignment reference a 17 14 5 1 43 1 52 1 0 7 2 4 3 48 0 1 6 0 2 3 3 2 5 8 c 12 18 4 11 5 49 1 1 51 1 1 40 50 0 3 54 1 1 48 3 7 40 14 13 g 16 17 8 42 2 4 0 51 3 0 52 7 2 1 48 0 2 52 2 0 42 6 13 20 t 10 6 38 1 5 1 2 2 1 47 0 4 0 6 4 0 46 2 3 49 3 7 23 14

MA0796.1_shift2 (TGIF1)
; local_words_8nt_m7 versus MA0796.1 (TGIF1); m=1/6; ncol2=12; w=12; offset=2; strand=D; shift=2; score=0.443132; --TGACAGCTGTCA---------- ; cor=; Ncor= a 0 0 39.0 9.0 8828.0 1.0 8861.0 14.0 452.0 1.0 11.0 45.0 36.0 9034.0 0 0 0 0 0 0 0 0 0 0 c 0 0 19.0 8.0 3.0 13304.0 5.0 20.0 10562.0 62.0 13.0 24.0 13485.0 17.0 0 0 0 0 0 0 0 0 0 0 g 0 0 1.0 13499.0 20.0 5.0 22.0 12673.0 2520.0 8.0 13261.0 3.0 13.0 32.0 0 0 0 0 0 0 0 0 0 0 t 0 0 13221.0 4.0 0.0 7.0 4.0 963.0 12.0 12775.0 9.0 12656.0 17.0 33.0 0 0 0 0 0 0 0 0 0 0

MA0797.1_shift2 (TGIF2)
; local_words_8nt_m7 versus MA0797.1 (TGIF2); m=2/6; ncol2=12; w=12; offset=2; strand=D; shift=2; score=0.437803; --TGACAGsTGTCA---------- ; cor=; Ncor= a 0 0 477.0 97.0 11801.0 127.0 11801.0 324.0 1501.0 71.0 150.0 601.0 70.0 11801.0 0 0 0 0 0 0 0 0 0 0 c 0 0 421.0 48.0 34.0 11801.0 25.0 262.0 7459.0 410.0 77.0 621.0 11801.0 172.0 0 0 0 0 0 0 0 0 0 0 g 0 0 153.0 11801.0 396.0 51.0 270.0 11801.0 4341.0 57.0 11801.0 123.0 136.0 395.0 0 0 0 0 0 0 0 0 0 0 t 0 0 11801.0 52.0 155.0 156.0 41.0 2690.0 91.0 11801.0 83.0 11801.0 113.0 420.0 0 0 0 0 0 0 0 0 0 0

MA1571.1_shift2 (TGIF2LX)
; local_words_8nt_m7 versus MA1571.1 (TGIF2LX); m=3/6; ncol2=12; w=12; offset=2; strand=D; shift=2; score=0.437233; --TGACAgcTGTCA---------- ; cor=; Ncor= a 0 0 237.0 52.0 2539.0 32.0 2539.0 37.0 380.0 37.0 64.0 428.0 45.0 2539.0 0 0 0 0 0 0 0 0 0 0 c 0 0 355.0 187.0 64.0 2539.0 18.0 575.0 1568.0 318.0 23.0 127.0 2539.0 132.0 0 0 0 0 0 0 0 0 0 0 g 0 0 145.0 2539.0 132.0 29.0 316.0 1566.0 554.0 23.0 2539.0 72.0 172.0 361.0 0 0 0 0 0 0 0 0 0 0 t 0 0 2539.0 47.0 428.0 59.0 40.0 362.0 38.0 2539.0 22.0 2539.0 66.0 232.0 0 0 0 0 0 0 0 0 0 0

MA1572.1_rc_shift2 (TGIF2LY_rc)
; local_words_8nt_m7 versus MA1572.1_rc (TGIF2LY_rc); m=4/6; ncol2=12; w=12; offset=2; strand=R; shift=2; score=0.431051; --TGACAgcTGTCA---------- ; cor=; Ncor= a 0 0 679.0 172.0 5209.0 121.0 5209.0 138.0 1018.0 110.0 144.0 1197.0 104.0 5209.0 0 0 0 0 0 0 0 0 0 0 c 0 0 807.0 259.0 145.0 5209.0 73.0 1188.0 2794.0 833.0 66.0 349.0 5209.0 415.0 0 0 0 0 0 0 0 0 0 0 g 0 0 362.0 5209.0 371.0 61.0 848.0 2850.0 1267.0 37.0 5209.0 163.0 270.0 836.0 0 0 0 0 0 0 0 0 0 0 t 0 0 5209.0 135.0 1084.0 175.0 140.0 1033.0 130.0 5209.0 123.0 5209.0 162.0 736.0 0 0 0 0 0 0 0 0 0 0

MA0783.1_shift2 (PKNOX2)
; local_words_8nt_m7 versus MA0783.1 (PKNOX2); m=5/6; ncol2=12; w=12; offset=2; strand=D; shift=2; score=0.417877; --TGACAGsTGTCA---------- ; cor=; Ncor= a 0 0 37.0 1.0 1124.0 0.0 1169.0 7.0 39.0 0.0 3.0 10.0 11.0 1190.0 0 0 0 0 0 0 0 0 0 0 c 0 0 0.0 6.0 3.0 1250.0 0.0 0.0 304.0 4.0 1.0 29.0 1265.0 1.0 0 0 0 0 0 0 0 0 0 0 g 0 0 9.0 1389.0 13.0 0.0 1.0 1298.0 702.0 0.0 1370.0 5.0 6.0 21.0 0 0 0 0 0 0 0 0 0 0 t 0 0 1192.0 0.0 6.0 9.0 4.0 118.0 0.0 1204.0 0.0 1167.0 3.0 9.0 0 0 0 0 0 0 0 0 0 0

MA0499.2_rc_shift1 (MYOD1_rc)
; local_words_8nt_m7 versus MA0499.2_rc (MYOD1_rc); m=6/6; ncol2=13; w=13; offset=1; strand=R; shift=1; score=0.414242; -rkrACAGGTGcwg---------- ; cor=; Ncor= a 0 9358.0 8151.0 9000.0 29644.0 238.0 33130.0 330.0 1226.0 587.0 269.0 2245.0 9291.0 7728.0 0 0 0 0 0 0 0 0 0 0 c 0 7495.0 6202.0 4440.0 1699.0 33468.0 366.0 932.0 7336.0 849.0 354.0 21884.0 8444.0 8118.0 0 0 0 0 0 0 0 0 0 0 g 0 11760.0 10485.0 19052.0 2555.0 386.0 563.0 32504.0 25275.0 583.0 33328.0 5622.0 7103.0 11279.0 0 0 0 0 0 0 0 0 0 0 t 0 5687.0 9462.0 1808.0 402.0 208.0 241.0 534.0 463.0 32281.0 349.0 4549.0 9462.0 7175.0 0 0 0 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
local_words_8nt_m7_shift0 (local_words_8nt_m7local_words_8nt_m7)				; local_words_8nt_m7 (local_words_8nt_m7local_words_8nt_m7); m=0 (reference); ncol1=24; shift=0; ncol=24; rvTGACAGCTGCCAGCTGCTGCyk ; Alignment reference a 17 14 5 1 43 1 52 1 0 7 2 4 3 48 0 1 6 0 2 3 3 2 5 8 c 12 18 4 11 5 49 1 1 51 1 1 40 50 0 3 54 1 1 48 3 7 40 14 13 g 16 17 8 42 2 4 0 51 3 0 52 7 2 1 48 0 2 52 2 0 42 6 13 20 t 10 6 38 1 5 1 2 2 1 47 0 4 0 6 4 0 46 2 3 49 3 7 23 14
MA0796.1_shift2 (TGIF1)				; local_words_8nt_m7 versus MA0796.1 (TGIF1); m=1/6; ncol2=12; w=12; offset=2; strand=D; shift=2; score=0.443132; --TGACAGCTGTCA---------- ; cor=; Ncor= a 0 0 39.0 9.0 8828.0 1.0 8861.0 14.0 452.0 1.0 11.0 45.0 36.0 9034.0 0 0 0 0 0 0 0 0 0 0 c 0 0 19.0 8.0 3.0 13304.0 5.0 20.0 10562.0 62.0 13.0 24.0 13485.0 17.0 0 0 0 0 0 0 0 0 0 0 g 0 0 1.0 13499.0 20.0 5.0 22.0 12673.0 2520.0 8.0 13261.0 3.0 13.0 32.0 0 0 0 0 0 0 0 0 0 0 t 0 0 13221.0 4.0 0.0 7.0 4.0 963.0 12.0 12775.0 9.0 12656.0 17.0 33.0 0 0 0 0 0 0 0 0 0 0
MA0797.1_shift2 (TGIF2)				; local_words_8nt_m7 versus MA0797.1 (TGIF2); m=2/6; ncol2=12; w=12; offset=2; strand=D; shift=2; score=0.437803; --TGACAGsTGTCA---------- ; cor=; Ncor= a 0 0 477.0 97.0 11801.0 127.0 11801.0 324.0 1501.0 71.0 150.0 601.0 70.0 11801.0 0 0 0 0 0 0 0 0 0 0 c 0 0 421.0 48.0 34.0 11801.0 25.0 262.0 7459.0 410.0 77.0 621.0 11801.0 172.0 0 0 0 0 0 0 0 0 0 0 g 0 0 153.0 11801.0 396.0 51.0 270.0 11801.0 4341.0 57.0 11801.0 123.0 136.0 395.0 0 0 0 0 0 0 0 0 0 0 t 0 0 11801.0 52.0 155.0 156.0 41.0 2690.0 91.0 11801.0 83.0 11801.0 113.0 420.0 0 0 0 0 0 0 0 0 0 0
MA1571.1_shift2 (TGIF2LX)				; local_words_8nt_m7 versus MA1571.1 (TGIF2LX); m=3/6; ncol2=12; w=12; offset=2; strand=D; shift=2; score=0.437233; --TGACAgcTGTCA---------- ; cor=; Ncor= a 0 0 237.0 52.0 2539.0 32.0 2539.0 37.0 380.0 37.0 64.0 428.0 45.0 2539.0 0 0 0 0 0 0 0 0 0 0 c 0 0 355.0 187.0 64.0 2539.0 18.0 575.0 1568.0 318.0 23.0 127.0 2539.0 132.0 0 0 0 0 0 0 0 0 0 0 g 0 0 145.0 2539.0 132.0 29.0 316.0 1566.0 554.0 23.0 2539.0 72.0 172.0 361.0 0 0 0 0 0 0 0 0 0 0 t 0 0 2539.0 47.0 428.0 59.0 40.0 362.0 38.0 2539.0 22.0 2539.0 66.0 232.0 0 0 0 0 0 0 0 0 0 0
MA1572.1_rc_shift2 (TGIF2LY_rc)				; local_words_8nt_m7 versus MA1572.1_rc (TGIF2LY_rc); m=4/6; ncol2=12; w=12; offset=2; strand=R; shift=2; score=0.431051; --TGACAgcTGTCA---------- ; cor=; Ncor= a 0 0 679.0 172.0 5209.0 121.0 5209.0 138.0 1018.0 110.0 144.0 1197.0 104.0 5209.0 0 0 0 0 0 0 0 0 0 0 c 0 0 807.0 259.0 145.0 5209.0 73.0 1188.0 2794.0 833.0 66.0 349.0 5209.0 415.0 0 0 0 0 0 0 0 0 0 0 g 0 0 362.0 5209.0 371.0 61.0 848.0 2850.0 1267.0 37.0 5209.0 163.0 270.0 836.0 0 0 0 0 0 0 0 0 0 0 t 0 0 5209.0 135.0 1084.0 175.0 140.0 1033.0 130.0 5209.0 123.0 5209.0 162.0 736.0 0 0 0 0 0 0 0 0 0 0
MA0783.1_shift2 (PKNOX2)				; local_words_8nt_m7 versus MA0783.1 (PKNOX2); m=5/6; ncol2=12; w=12; offset=2; strand=D; shift=2; score=0.417877; --TGACAGsTGTCA---------- ; cor=; Ncor= a 0 0 37.0 1.0 1124.0 0.0 1169.0 7.0 39.0 0.0 3.0 10.0 11.0 1190.0 0 0 0 0 0 0 0 0 0 0 c 0 0 0.0 6.0 3.0 1250.0 0.0 0.0 304.0 4.0 1.0 29.0 1265.0 1.0 0 0 0 0 0 0 0 0 0 0 g 0 0 9.0 1389.0 13.0 0.0 1.0 1298.0 702.0 0.0 1370.0 5.0 6.0 21.0 0 0 0 0 0 0 0 0 0 0 t 0 0 1192.0 0.0 6.0 9.0 4.0 118.0 0.0 1204.0 0.0 1167.0 3.0 9.0 0 0 0 0 0 0 0 0 0 0
MA0499.2_rc_shift1 (MYOD1_rc)				; local_words_8nt_m7 versus MA0499.2_rc (MYOD1_rc); m=6/6; ncol2=13; w=13; offset=1; strand=R; shift=1; score=0.414242; -rkrACAGGTGcwg---------- ; cor=; Ncor= a 0 9358.0 8151.0 9000.0 29644.0 238.0 33130.0 330.0 1226.0 587.0 269.0 2245.0 9291.0 7728.0 0 0 0 0 0 0 0 0 0 0 c 0 7495.0 6202.0 4440.0 1699.0 33468.0 366.0 932.0 7336.0 849.0 354.0 21884.0 8444.0 8118.0 0 0 0 0 0 0 0 0 0 0 g 0 11760.0 10485.0 19052.0 2555.0 386.0 563.0 32504.0 25275.0 583.0 33328.0 5622.0 7103.0 11279.0 0 0 0 0 0 0 0 0 0 0 t 0 5687.0 9462.0 1808.0 402.0 208.0 241.0 534.0 463.0 32281.0 349.0 4549.0 9462.0 7175.0 0 0 0 0 0 0 0 0 0 0