One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep1_motifs50/results/discovered_motifs/oligos_6nt_mkv4_m36/peak-motifs_oligos_6nt_mkv4_m36.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/oligos_6nt_mkv4_m36/peak-motifs_oligos_6nt_mkv4_m36_vs_db_jaspar_core_nonredundant_vertebrates

One-to-n matrix alignment; reference matrix: oligos_6nt_mkv4_m36_shift1 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_6nt_mkv4_m36_shift1 (oligos_6nt_mkv4_m36oligos_6nt_mkv4_m36)
; oligos_6nt_mkv4_m36 (oligos_6nt_mkv4_m36oligos_6nt_mkv4_m36); m=0 (reference); ncol1=10; shift=1; ncol=15; -ysTCACCAss---- ; Alignment reference a 0 1252 789 0 0 5279 0 0 5279 807 1283 0 0 0 0 c 0 1513 1891 0 5279 0 5279 5273 0 1742 1796 0 0 0 0 g 0 1166 1808 0 0 0 0 6 0 1829 1362 0 0 0 0 t 0 1348 791 5279 0 0 0 0 0 901 838 0 0 0 0

MA0117.2_rc_shift1 (Mafb_rc)
; oligos_6nt_mkv4_m36 versus MA0117.2_rc (Mafb_rc); m=1/3; ncol2=12; w=10; offset=0; strand=R; shift=1; score=0.596603; -hGTCAGCAwwwt-- ; cor=; Ncor= a 0 816.0 273.0 13.0 170.0 2182.0 7.0 5.0 2182.0 611.0 704.0 639.0 446.0 0 0 c 0 646.0 490.0 17.0 2182.0 2.0 5.0 2182.0 31.0 429.0 182.0 159.0 326.0 0 0 g 0 138.0 2182.0 13.0 13.0 36.0 2182.0 14.0 618.0 398.0 216.0 121.0 174.0 0 0 t 0 582.0 182.0 2182.0 45.0 31.0 295.0 2.0 264.0 744.0 1080.0 1263.0 1237.0 0 0

MA0842.2_rc_shift1 (NRL_rc)
; oligos_6nt_mkv4_m36 versus MA0842.2_rc (NRL_rc); m=2/3; ncol2=13; w=10; offset=0; strand=R; shift=1; score=0.544279; -cGTCAGCAywwtt- ; cor=; Ncor= a 0 5030.0 2394.0 0.0 1036.0 27228.0 14.0 0.0 27228.0 6741.0 13194.0 9761.0 6039.0 4130.0 0 c 0 14528.0 559.0 4.0 27228.0 0.0 22.0 27228.0 68.0 7983.0 822.0 635.0 3685.0 5588.0 0 g 0 1669.0 27228.0 0.0 0.0 8.0 27228.0 0.0 2768.0 5669.0 1314.0 319.0 838.0 3102.0 0 t 0 6001.0 47.0 27228.0 73.0 0.0 1008.0 1.0 581.0 6835.0 14033.0 17467.0 21189.0 14408.0 0

MA0659.2_shift0 (MAFG)
; oligos_6nt_mkv4_m36 versus MA0659.2 (MAFG); m=3/3; ncol2=15; w=10; offset=-1; strand=D; shift=0; score=0.468246; ragTCAGCAtTTytw ; cor=; Ncor= a 5651.0 12161.0 2200.0 273.0 696.0 20838.0 264.0 212.0 19623.0 4913.0 4021.0 3439.0 4248.0 4697.0 5905.0 c 2485.0 2067.0 3628.0 166.0 20232.0 71.0 270.0 20693.0 302.0 2566.0 1436.0 1448.0 5544.0 4852.0 4263.0 g 8586.0 2182.0 14148.0 198.0 130.0 174.0 19577.0 200.0 639.0 2848.0 1285.0 1051.0 1782.0 2712.0 3923.0 t 4679.0 4991.0 1425.0 20764.0 343.0 318.0 1290.0 296.0 837.0 11074.0 14659.0 15463.0 9827.0 9140.0 7310.0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_6nt_mkv4_m36_shift1 (oligos_6nt_mkv4_m36oligos_6nt_mkv4_m36)				; oligos_6nt_mkv4_m36 (oligos_6nt_mkv4_m36oligos_6nt_mkv4_m36); m=0 (reference); ncol1=10; shift=1; ncol=15; -ysTCACCAss---- ; Alignment reference a 0 1252 789 0 0 5279 0 0 5279 807 1283 0 0 0 0 c 0 1513 1891 0 5279 0 5279 5273 0 1742 1796 0 0 0 0 g 0 1166 1808 0 0 0 0 6 0 1829 1362 0 0 0 0 t 0 1348 791 5279 0 0 0 0 0 901 838 0 0 0 0
MA0117.2_rc_shift1 (Mafb_rc)				; oligos_6nt_mkv4_m36 versus MA0117.2_rc (Mafb_rc); m=1/3; ncol2=12; w=10; offset=0; strand=R; shift=1; score=0.596603; -hGTCAGCAwwwt-- ; cor=; Ncor= a 0 816.0 273.0 13.0 170.0 2182.0 7.0 5.0 2182.0 611.0 704.0 639.0 446.0 0 0 c 0 646.0 490.0 17.0 2182.0 2.0 5.0 2182.0 31.0 429.0 182.0 159.0 326.0 0 0 g 0 138.0 2182.0 13.0 13.0 36.0 2182.0 14.0 618.0 398.0 216.0 121.0 174.0 0 0 t 0 582.0 182.0 2182.0 45.0 31.0 295.0 2.0 264.0 744.0 1080.0 1263.0 1237.0 0 0
MA0842.2_rc_shift1 (NRL_rc)				; oligos_6nt_mkv4_m36 versus MA0842.2_rc (NRL_rc); m=2/3; ncol2=13; w=10; offset=0; strand=R; shift=1; score=0.544279; -cGTCAGCAywwtt- ; cor=; Ncor= a 0 5030.0 2394.0 0.0 1036.0 27228.0 14.0 0.0 27228.0 6741.0 13194.0 9761.0 6039.0 4130.0 0 c 0 14528.0 559.0 4.0 27228.0 0.0 22.0 27228.0 68.0 7983.0 822.0 635.0 3685.0 5588.0 0 g 0 1669.0 27228.0 0.0 0.0 8.0 27228.0 0.0 2768.0 5669.0 1314.0 319.0 838.0 3102.0 0 t 0 6001.0 47.0 27228.0 73.0 0.0 1008.0 1.0 581.0 6835.0 14033.0 17467.0 21189.0 14408.0 0
MA0659.2_shift0 (MAFG)				; oligos_6nt_mkv4_m36 versus MA0659.2 (MAFG); m=3/3; ncol2=15; w=10; offset=-1; strand=D; shift=0; score=0.468246; ragTCAGCAtTTytw ; cor=; Ncor= a 5651.0 12161.0 2200.0 273.0 696.0 20838.0 264.0 212.0 19623.0 4913.0 4021.0 3439.0 4248.0 4697.0 5905.0 c 2485.0 2067.0 3628.0 166.0 20232.0 71.0 270.0 20693.0 302.0 2566.0 1436.0 1448.0 5544.0 4852.0 4263.0 g 8586.0 2182.0 14148.0 198.0 130.0 174.0 19577.0 200.0 639.0 2848.0 1285.0 1051.0 1782.0 2712.0 3923.0 t 4679.0 4991.0 1425.0 20764.0 343.0 318.0 1290.0 296.0 837.0 11074.0 14659.0 15463.0 9827.0 9140.0 7310.0