One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep1_motifs50/results/discovered_motifs/local_words_7nt_m3/peak-motifs_local_words_7nt_m3.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_7nt_m3/peak-motifs_local_words_7nt_m3_vs_db_jaspar_core_nonredundant_vertebrates

One-to-n matrix alignment; reference matrix: local_words_7nt_m3_shift0 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
local_words_7nt_m3_shift0 (local_words_7nt_m3local_words_7nt_m3)
; local_words_7nt_m3 (local_words_7nt_m3local_words_7nt_m3); m=0 (reference); ncol1=24; shift=0; ncol=24; ssTGaCAGCTGGCAGCTGTCAsck ; Alignment reference a 6 8 5 3 24 0 45 0 2 1 0 1 1 39 0 1 2 2 4 0 39 2 10 10 c 16 15 2 1 4 44 0 4 37 0 0 3 41 1 3 39 2 2 2 40 1 25 18 9 g 14 14 4 40 11 1 0 41 4 1 43 37 3 0 42 5 2 41 8 4 3 16 8 14 t 9 8 34 1 6 0 0 0 2 43 2 4 0 5 0 0 39 0 31 1 2 2 9 12

MA0796.1_shift9 (TGIF1)
; local_words_7nt_m3 versus MA0796.1 (TGIF1); m=1/5; ncol2=12; w=12; offset=9; strand=D; shift=9; score=0.439559; ---------TGACAGCTGTCA--- ; cor=; Ncor= a 0 0 0 0 0 0 0 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 c 0 0 0 0 0 0 0 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 g 0 0 0 0 0 0 0 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 t 0 0 0 0 0 0 0 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

MA1571.1_shift2 (TGIF2LX)
; local_words_7nt_m3 versus MA1571.1 (TGIF2LX); m=2/5; ncol2=12; w=12; offset=2; strand=D; shift=2; score=0.435188; --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

MA0797.1_rc_shift9 (TGIF2_rc)
; local_words_7nt_m3 versus MA0797.1_rc (TGIF2_rc); m=3/5; ncol2=12; w=12; offset=9; strand=R; shift=9; score=0.433871; ---------TGACAsCTGTCA--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 420.0 113.0 11801.0 83.0 11801.0 91.0 2690.0 41.0 156.0 155.0 52.0 11801.0 0 0 0 c 0 0 0 0 0 0 0 0 0 395.0 136.0 123.0 11801.0 57.0 4341.0 11801.0 270.0 51.0 396.0 11801.0 153.0 0 0 0 g 0 0 0 0 0 0 0 0 0 172.0 11801.0 621.0 77.0 410.0 7459.0 262.0 25.0 11801.0 34.0 48.0 421.0 0 0 0 t 0 0 0 0 0 0 0 0 0 11801.0 70.0 601.0 150.0 71.0 1501.0 324.0 11801.0 127.0 11801.0 97.0 477.0 0 0 0

MA1572.1_rc_shift2 (TGIF2LY_rc)
; local_words_7nt_m3 versus MA1572.1_rc (TGIF2LY_rc); m=4/5; ncol2=12; w=12; offset=2; strand=R; shift=2; score=0.430547; --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_shift9 (PKNOX2)
; local_words_7nt_m3 versus MA0783.1 (PKNOX2); m=5/5; ncol2=12; w=12; offset=9; strand=D; shift=9; score=0.417537; ---------TGACAGsTGTCA--- ; cor=; Ncor= a 0 0 0 0 0 0 0 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 c 0 0 0 0 0 0 0 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 g 0 0 0 0 0 0 0 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 t 0 0 0 0 0 0 0 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

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
local_words_7nt_m3_shift0 (local_words_7nt_m3local_words_7nt_m3)				; local_words_7nt_m3 (local_words_7nt_m3local_words_7nt_m3); m=0 (reference); ncol1=24; shift=0; ncol=24; ssTGaCAGCTGGCAGCTGTCAsck ; Alignment reference a 6 8 5 3 24 0 45 0 2 1 0 1 1 39 0 1 2 2 4 0 39 2 10 10 c 16 15 2 1 4 44 0 4 37 0 0 3 41 1 3 39 2 2 2 40 1 25 18 9 g 14 14 4 40 11 1 0 41 4 1 43 37 3 0 42 5 2 41 8 4 3 16 8 14 t 9 8 34 1 6 0 0 0 2 43 2 4 0 5 0 0 39 0 31 1 2 2 9 12
MA0796.1_shift9 (TGIF1)				; local_words_7nt_m3 versus MA0796.1 (TGIF1); m=1/5; ncol2=12; w=12; offset=9; strand=D; shift=9; score=0.439559; ---------TGACAGCTGTCA--- ; cor=; Ncor= a 0 0 0 0 0 0 0 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 c 0 0 0 0 0 0 0 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 g 0 0 0 0 0 0 0 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 t 0 0 0 0 0 0 0 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
MA1571.1_shift2 (TGIF2LX)				; local_words_7nt_m3 versus MA1571.1 (TGIF2LX); m=2/5; ncol2=12; w=12; offset=2; strand=D; shift=2; score=0.435188; --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
MA0797.1_rc_shift9 (TGIF2_rc)				; local_words_7nt_m3 versus MA0797.1_rc (TGIF2_rc); m=3/5; ncol2=12; w=12; offset=9; strand=R; shift=9; score=0.433871; ---------TGACAsCTGTCA--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 420.0 113.0 11801.0 83.0 11801.0 91.0 2690.0 41.0 156.0 155.0 52.0 11801.0 0 0 0 c 0 0 0 0 0 0 0 0 0 395.0 136.0 123.0 11801.0 57.0 4341.0 11801.0 270.0 51.0 396.0 11801.0 153.0 0 0 0 g 0 0 0 0 0 0 0 0 0 172.0 11801.0 621.0 77.0 410.0 7459.0 262.0 25.0 11801.0 34.0 48.0 421.0 0 0 0 t 0 0 0 0 0 0 0 0 0 11801.0 70.0 601.0 150.0 71.0 1501.0 324.0 11801.0 127.0 11801.0 97.0 477.0 0 0 0
MA1572.1_rc_shift2 (TGIF2LY_rc)				; local_words_7nt_m3 versus MA1572.1_rc (TGIF2LY_rc); m=4/5; ncol2=12; w=12; offset=2; strand=R; shift=2; score=0.430547; --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_shift9 (PKNOX2)				; local_words_7nt_m3 versus MA0783.1 (PKNOX2); m=5/5; ncol2=12; w=12; offset=9; strand=D; shift=9; score=0.417537; ---------TGACAGsTGTCA--- ; cor=; Ncor= a 0 0 0 0 0 0 0 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 c 0 0 0 0 0 0 0 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 g 0 0 0 0 0 0 0 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 t 0 0 0 0 0 0 0 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