One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep1_motifs50/results/discovered_motifs/local_words_8nt_m3/peak-motifs_local_words_8nt_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_8nt_m3/peak-motifs_local_words_8nt_m3_vs_db_jaspar_core_nonredundant_vertebrates

One-to-n matrix alignment; reference matrix: local_words_8nt_m3_shift0 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
local_words_8nt_m3_shift0 (local_words_8nt_m3local_words_8nt_m3)
; local_words_8nt_m3 (local_words_8nt_m3local_words_8nt_m3); m=0 (reference); ncol1=24; shift=0; ncol=24; mgsTGACAGCTGCCAGCTGyCAss ; Alignment reference a 12 9 2 2 0 30 0 38 0 0 4 0 4 2 42 2 0 0 0 6 1 33 8 9 c 14 8 16 3 4 8 40 2 5 41 0 2 36 42 1 4 40 0 1 11 39 4 14 13 g 8 17 25 1 40 2 2 2 38 3 1 41 3 0 0 36 4 0 43 4 1 2 15 16 t 10 10 1 38 0 4 2 2 1 0 39 1 1 0 1 2 0 44 0 23 3 5 7 6

MA0796.1_rc_shift3 (TGIF1_rc)
; local_words_8nt_m3 versus MA0796.1_rc (TGIF1_rc); m=1/5; ncol2=12; w=12; offset=3; strand=R; shift=3; score=0.440118; ---TGACAGCTGTCA--------- ; cor=; Ncor= a 0 0 0 33.0 17.0 12656.0 9.0 12775.0 12.0 963.0 4.0 7.0 0.0 4.0 13221.0 0 0 0 0 0 0 0 0 0 c 0 0 0 32.0 13.0 3.0 13261.0 8.0 2520.0 12673.0 22.0 5.0 20.0 13499.0 1.0 0 0 0 0 0 0 0 0 0 g 0 0 0 17.0 13485.0 24.0 13.0 62.0 10562.0 20.0 5.0 13304.0 3.0 8.0 19.0 0 0 0 0 0 0 0 0 0 t 0 0 0 9034.0 36.0 45.0 11.0 1.0 452.0 14.0 8861.0 1.0 8828.0 9.0 39.0 0 0 0 0 0 0 0 0 0

MA1571.1_rc_shift10 (TGIF2LX_rc)
; local_words_8nt_m3 versus MA1571.1_rc (TGIF2LX_rc); m=2/5; ncol2=12; w=12; offset=10; strand=R; shift=10; score=0.435438; ----------TGACAgcTGTCA-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 232.0 66.0 2539.0 22.0 2539.0 38.0 362.0 40.0 59.0 428.0 47.0 2539.0 0 0 c 0 0 0 0 0 0 0 0 0 0 361.0 172.0 72.0 2539.0 23.0 554.0 1566.0 316.0 29.0 132.0 2539.0 145.0 0 0 g 0 0 0 0 0 0 0 0 0 0 132.0 2539.0 127.0 23.0 318.0 1568.0 575.0 18.0 2539.0 64.0 187.0 355.0 0 0 t 0 0 0 0 0 0 0 0 0 0 2539.0 45.0 428.0 64.0 37.0 380.0 37.0 2539.0 32.0 2539.0 52.0 237.0 0 0

MA0797.1_shift3 (TGIF2)
; local_words_8nt_m3 versus MA0797.1 (TGIF2); m=3/5; ncol2=12; w=12; offset=3; strand=D; shift=3; score=0.43466; ---TGACAGsTGTCA--------- ; cor=; Ncor= a 0 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 c 0 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 g 0 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 t 0 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

MA1572.1_shift10 (TGIF2LY)
; local_words_8nt_m3 versus MA1572.1 (TGIF2LY); m=4/5; ncol2=12; w=12; offset=10; strand=D; shift=10; score=0.430883; ----------TGACAgcTGTCA-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 736.0 162.0 5209.0 123.0 5209.0 130.0 1033.0 140.0 175.0 1084.0 135.0 5209.0 0 0 c 0 0 0 0 0 0 0 0 0 0 836.0 270.0 163.0 5209.0 37.0 1267.0 2850.0 848.0 61.0 371.0 5209.0 362.0 0 0 g 0 0 0 0 0 0 0 0 0 0 415.0 5209.0 349.0 66.0 833.0 2794.0 1188.0 73.0 5209.0 145.0 259.0 807.0 0 0 t 0 0 0 0 0 0 0 0 0 0 5209.0 104.0 1197.0 144.0 110.0 1018.0 138.0 5209.0 121.0 5209.0 172.0 679.0 0 0

MA0783.1_rc_shift3 (PKNOX2_rc)
; local_words_8nt_m3 versus MA0783.1_rc (PKNOX2_rc); m=5/5; ncol2=12; w=12; offset=3; strand=R; shift=3; score=0.418449; ---TGACAsCTGTCA--------- ; cor=; Ncor= a 0 0 0 9.0 3.0 1167.0 0.0 1204.0 0.0 118.0 4.0 9.0 6.0 0.0 1192.0 0 0 0 0 0 0 0 0 0 c 0 0 0 21.0 6.0 5.0 1370.0 0.0 702.0 1298.0 1.0 0.0 13.0 1389.0 9.0 0 0 0 0 0 0 0 0 0 g 0 0 0 1.0 1265.0 29.0 1.0 4.0 304.0 0.0 0.0 1250.0 3.0 6.0 0.0 0 0 0 0 0 0 0 0 0 t 0 0 0 1190.0 11.0 10.0 3.0 0.0 39.0 7.0 1169.0 0.0 1124.0 1.0 37.0 0 0 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
local_words_8nt_m3_shift0 (local_words_8nt_m3local_words_8nt_m3)				; local_words_8nt_m3 (local_words_8nt_m3local_words_8nt_m3); m=0 (reference); ncol1=24; shift=0; ncol=24; mgsTGACAGCTGCCAGCTGyCAss ; Alignment reference a 12 9 2 2 0 30 0 38 0 0 4 0 4 2 42 2 0 0 0 6 1 33 8 9 c 14 8 16 3 4 8 40 2 5 41 0 2 36 42 1 4 40 0 1 11 39 4 14 13 g 8 17 25 1 40 2 2 2 38 3 1 41 3 0 0 36 4 0 43 4 1 2 15 16 t 10 10 1 38 0 4 2 2 1 0 39 1 1 0 1 2 0 44 0 23 3 5 7 6
MA0796.1_rc_shift3 (TGIF1_rc)				; local_words_8nt_m3 versus MA0796.1_rc (TGIF1_rc); m=1/5; ncol2=12; w=12; offset=3; strand=R; shift=3; score=0.440118; ---TGACAGCTGTCA--------- ; cor=; Ncor= a 0 0 0 33.0 17.0 12656.0 9.0 12775.0 12.0 963.0 4.0 7.0 0.0 4.0 13221.0 0 0 0 0 0 0 0 0 0 c 0 0 0 32.0 13.0 3.0 13261.0 8.0 2520.0 12673.0 22.0 5.0 20.0 13499.0 1.0 0 0 0 0 0 0 0 0 0 g 0 0 0 17.0 13485.0 24.0 13.0 62.0 10562.0 20.0 5.0 13304.0 3.0 8.0 19.0 0 0 0 0 0 0 0 0 0 t 0 0 0 9034.0 36.0 45.0 11.0 1.0 452.0 14.0 8861.0 1.0 8828.0 9.0 39.0 0 0 0 0 0 0 0 0 0
MA1571.1_rc_shift10 (TGIF2LX_rc)				; local_words_8nt_m3 versus MA1571.1_rc (TGIF2LX_rc); m=2/5; ncol2=12; w=12; offset=10; strand=R; shift=10; score=0.435438; ----------TGACAgcTGTCA-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 232.0 66.0 2539.0 22.0 2539.0 38.0 362.0 40.0 59.0 428.0 47.0 2539.0 0 0 c 0 0 0 0 0 0 0 0 0 0 361.0 172.0 72.0 2539.0 23.0 554.0 1566.0 316.0 29.0 132.0 2539.0 145.0 0 0 g 0 0 0 0 0 0 0 0 0 0 132.0 2539.0 127.0 23.0 318.0 1568.0 575.0 18.0 2539.0 64.0 187.0 355.0 0 0 t 0 0 0 0 0 0 0 0 0 0 2539.0 45.0 428.0 64.0 37.0 380.0 37.0 2539.0 32.0 2539.0 52.0 237.0 0 0
MA0797.1_shift3 (TGIF2)				; local_words_8nt_m3 versus MA0797.1 (TGIF2); m=3/5; ncol2=12; w=12; offset=3; strand=D; shift=3; score=0.43466; ---TGACAGsTGTCA--------- ; cor=; Ncor= a 0 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 c 0 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 g 0 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 t 0 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
MA1572.1_shift10 (TGIF2LY)				; local_words_8nt_m3 versus MA1572.1 (TGIF2LY); m=4/5; ncol2=12; w=12; offset=10; strand=D; shift=10; score=0.430883; ----------TGACAgcTGTCA-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 736.0 162.0 5209.0 123.0 5209.0 130.0 1033.0 140.0 175.0 1084.0 135.0 5209.0 0 0 c 0 0 0 0 0 0 0 0 0 0 836.0 270.0 163.0 5209.0 37.0 1267.0 2850.0 848.0 61.0 371.0 5209.0 362.0 0 0 g 0 0 0 0 0 0 0 0 0 0 415.0 5209.0 349.0 66.0 833.0 2794.0 1188.0 73.0 5209.0 145.0 259.0 807.0 0 0 t 0 0 0 0 0 0 0 0 0 0 5209.0 104.0 1197.0 144.0 110.0 1018.0 138.0 5209.0 121.0 5209.0 172.0 679.0 0 0
MA0783.1_rc_shift3 (PKNOX2_rc)				; local_words_8nt_m3 versus MA0783.1_rc (PKNOX2_rc); m=5/5; ncol2=12; w=12; offset=3; strand=R; shift=3; score=0.418449; ---TGACAsCTGTCA--------- ; cor=; Ncor= a 0 0 0 9.0 3.0 1167.0 0.0 1204.0 0.0 118.0 4.0 9.0 6.0 0.0 1192.0 0 0 0 0 0 0 0 0 0 c 0 0 0 21.0 6.0 5.0 1370.0 0.0 702.0 1298.0 1.0 0.0 13.0 1389.0 9.0 0 0 0 0 0 0 0 0 0 g 0 0 0 1.0 1265.0 29.0 1.0 4.0 304.0 0.0 0.0 1250.0 3.0 6.0 0.0 0 0 0 0 0 0 0 0 0 t 0 0 0 1190.0 11.0 10.0 3.0 0.0 39.0 7.0 1169.0 0.0 1124.0 1.0 37.0 0 0 0 0 0 0 0 0 0