One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep3_motifs50/results/discovered_motifs/dyads_m37/peak-motifs_dyads_m37.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_Rep3_motifs50/results/discovered_motifs/dyads_m37/peak-motifs_dyads_m37_vs_db_jaspar_core_nonredundant_vertebrates

One-to-n matrix alignment; reference matrix: dyads_m37_shift4 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
dyads_m37_shift4 (dyads_m37dyads_m37)
; dyads_m37 (dyads_m37dyads_m37); m=0 (reference); ncol1=11; shift=4; ncol=17; ----ksrCGyACGsv-- ; Alignment reference a 0 0 0 0 1 1 7 0 0 0 10 0 0 1 3 0 0 c 0 0 0 0 2 4 0 11 0 5 1 11 0 5 3 0 0 g 0 0 0 0 5 4 3 0 11 2 0 0 11 4 4 0 0 t 0 0 0 0 3 2 1 0 0 4 0 0 0 1 1 0 0

MA0131.2_rc_shift4 (HINFP_rc)
; dyads_m37 versus MA0131.2_rc (HINFP_rc); m=1/6; ncol2=12; w=11; offset=0; strand=R; shift=4; score=0.657259; ----mcGCGGACGytg- ; cor=; Ncor= a 0 0 0 0 107.0 97.0 12.0 21.0 3.0 0.0 470.0 10.0 7.0 17.0 53.0 100.0 0 c 0 0 0 0 154.0 188.0 15.0 472.0 0.0 13.0 0.0 484.0 97.0 217.0 113.0 106.0 0 g 0 0 0 0 84.0 55.0 395.0 31.0 413.0 404.0 0.0 14.0 388.0 45.0 131.0 340.0 0 t 0 0 0 0 77.0 85.0 1.0 0.0 0.0 0.0 0.0 0.0 1.0 276.0 285.0 23.0 0

MA0259.1_rc_shift4 (ARNT::HIF1A_rc)
; dyads_m37 versus MA0259.1_rc (ARNT::HIF1A_rc); m=2/6; ncol2=8; w=8; offset=0; strand=R; shift=4; score=0.51921; ----gCACGTvb----- ; cor=; Ncor= a 0 0 0 0 15.0 0.0 104.0 0.0 1.0 1.0 31.0 0.0 0 0 0 0 0 c 0 0 0 0 20.0 104.0 0.0 104.0 0.0 23.0 34.0 49.0 0 0 0 0 0 g 0 0 0 0 51.0 0.0 0.0 0.0 103.0 2.0 29.0 28.0 0 0 0 0 0 t 0 0 0 0 18.0 0.0 0.0 0.0 0.0 78.0 10.0 27.0 0 0 0 0 0

MA0006.1_rc_shift9 (Ahr::Arnt_rc)
; dyads_m37 versus MA0006.1_rc (Ahr::Arnt_rc); m=3/6; ncol2=6; w=6; offset=5; strand=R; shift=9; score=0.468433; ---------CACGCr-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0.0 24.0 1.0 1.0 1.0 11.0 0 0 c 0 0 0 0 0 0 0 0 0 24.0 0.0 23.0 0.0 23.0 2.0 0 0 g 0 0 0 0 0 0 0 0 0 0.0 0.0 0.0 23.0 0.0 8.0 0 0 t 0 0 0 0 0 0 0 0 0 0.0 0.0 0.0 0.0 0.0 3.0 0 0

MA0615.1_shift0 (Gmeb1)
; dyads_m37 versus MA0615.1 (Gmeb1); m=4/6; ncol2=17; w=11; offset=-4; strand=D; shift=0; score=0.464158; smkkkkRCGYmmgayrs ; cor=; Ncor= a 17.0 34.0 11.0 13.0 13.0 5.0 71.0 0.0 1.0 0.0 59.0 40.0 21.0 44.0 18.0 27.0 24.0 c 26.0 31.0 23.0 22.0 7.0 4.0 1.0 99.0 0.0 28.0 33.0 40.0 23.0 15.0 26.0 21.0 25.0 g 35.0 15.0 35.0 29.0 40.0 33.0 28.0 0.0 99.0 1.0 4.0 7.0 37.0 18.0 23.0 31.0 27.0 t 22.0 20.0 31.0 36.0 40.0 59.0 0.0 1.0 0.0 71.0 5.0 13.0 19.0 24.0 33.0 20.0 24.0

MA0604.1_shift3 (Atf1)
; dyads_m37 versus MA0604.1 (Atf1); m=5/6; ncol2=8; w=7; offset=-1; strand=D; shift=3; score=0.444684; ---rTGACGTa------ ; cor=; Ncor= a 0 0 0 462.0 24.0 0.0 1000.0 0.0 7.0 90.0 600.0 0 0 0 0 0 0 c 0 0 0 86.0 16.0 22.0 0.0 1000.0 0.0 198.0 138.0 0 0 0 0 0 0 g 0 0 0 387.0 0.0 803.0 0.0 0.0 993.0 0.0 163.0 0 0 0 0 0 0 t 0 0 0 65.0 960.0 175.0 0.0 0.0 0.0 712.0 100.0 0 0 0 0 0 0

MA0004.1_rc_shift9 (Arnt_rc)
; dyads_m37 versus MA0004.1_rc (Arnt_rc); m=6/6; ncol2=6; w=6; offset=5; strand=R; shift=9; score=0.401601; ---------CACGTG-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0.0 20.0 0.0 0.0 0.0 0.0 0 0 c 0 0 0 0 0 0 0 0 0 20.0 0.0 20.0 0.0 1.0 0.0 0 0 g 0 0 0 0 0 0 0 0 0 0.0 0.0 0.0 20.0 0.0 16.0 0 0 t 0 0 0 0 0 0 0 0 0 0.0 0.0 0.0 0.0 19.0 4.0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
dyads_m37_shift4 (dyads_m37dyads_m37)				; dyads_m37 (dyads_m37dyads_m37); m=0 (reference); ncol1=11; shift=4; ncol=17; ----ksrCGyACGsv-- ; Alignment reference a 0 0 0 0 1 1 7 0 0 0 10 0 0 1 3 0 0 c 0 0 0 0 2 4 0 11 0 5 1 11 0 5 3 0 0 g 0 0 0 0 5 4 3 0 11 2 0 0 11 4 4 0 0 t 0 0 0 0 3 2 1 0 0 4 0 0 0 1 1 0 0
MA0131.2_rc_shift4 (HINFP_rc)				; dyads_m37 versus MA0131.2_rc (HINFP_rc); m=1/6; ncol2=12; w=11; offset=0; strand=R; shift=4; score=0.657259; ----mcGCGGACGytg- ; cor=; Ncor= a 0 0 0 0 107.0 97.0 12.0 21.0 3.0 0.0 470.0 10.0 7.0 17.0 53.0 100.0 0 c 0 0 0 0 154.0 188.0 15.0 472.0 0.0 13.0 0.0 484.0 97.0 217.0 113.0 106.0 0 g 0 0 0 0 84.0 55.0 395.0 31.0 413.0 404.0 0.0 14.0 388.0 45.0 131.0 340.0 0 t 0 0 0 0 77.0 85.0 1.0 0.0 0.0 0.0 0.0 0.0 1.0 276.0 285.0 23.0 0
MA0259.1_rc_shift4 (ARNT::HIF1A_rc)				; dyads_m37 versus MA0259.1_rc (ARNT::HIF1A_rc); m=2/6; ncol2=8; w=8; offset=0; strand=R; shift=4; score=0.51921; ----gCACGTvb----- ; cor=; Ncor= a 0 0 0 0 15.0 0.0 104.0 0.0 1.0 1.0 31.0 0.0 0 0 0 0 0 c 0 0 0 0 20.0 104.0 0.0 104.0 0.0 23.0 34.0 49.0 0 0 0 0 0 g 0 0 0 0 51.0 0.0 0.0 0.0 103.0 2.0 29.0 28.0 0 0 0 0 0 t 0 0 0 0 18.0 0.0 0.0 0.0 0.0 78.0 10.0 27.0 0 0 0 0 0
MA0006.1_rc_shift9 (Ahr::Arnt_rc)				; dyads_m37 versus MA0006.1_rc (Ahr::Arnt_rc); m=3/6; ncol2=6; w=6; offset=5; strand=R; shift=9; score=0.468433; ---------CACGCr-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0.0 24.0 1.0 1.0 1.0 11.0 0 0 c 0 0 0 0 0 0 0 0 0 24.0 0.0 23.0 0.0 23.0 2.0 0 0 g 0 0 0 0 0 0 0 0 0 0.0 0.0 0.0 23.0 0.0 8.0 0 0 t 0 0 0 0 0 0 0 0 0 0.0 0.0 0.0 0.0 0.0 3.0 0 0
MA0615.1_shift0 (Gmeb1)				; dyads_m37 versus MA0615.1 (Gmeb1); m=4/6; ncol2=17; w=11; offset=-4; strand=D; shift=0; score=0.464158; smkkkkRCGYmmgayrs ; cor=; Ncor= a 17.0 34.0 11.0 13.0 13.0 5.0 71.0 0.0 1.0 0.0 59.0 40.0 21.0 44.0 18.0 27.0 24.0 c 26.0 31.0 23.0 22.0 7.0 4.0 1.0 99.0 0.0 28.0 33.0 40.0 23.0 15.0 26.0 21.0 25.0 g 35.0 15.0 35.0 29.0 40.0 33.0 28.0 0.0 99.0 1.0 4.0 7.0 37.0 18.0 23.0 31.0 27.0 t 22.0 20.0 31.0 36.0 40.0 59.0 0.0 1.0 0.0 71.0 5.0 13.0 19.0 24.0 33.0 20.0 24.0
MA0604.1_shift3 (Atf1)				; dyads_m37 versus MA0604.1 (Atf1); m=5/6; ncol2=8; w=7; offset=-1; strand=D; shift=3; score=0.444684; ---rTGACGTa------ ; cor=; Ncor= a 0 0 0 462.0 24.0 0.0 1000.0 0.0 7.0 90.0 600.0 0 0 0 0 0 0 c 0 0 0 86.0 16.0 22.0 0.0 1000.0 0.0 198.0 138.0 0 0 0 0 0 0 g 0 0 0 387.0 0.0 803.0 0.0 0.0 993.0 0.0 163.0 0 0 0 0 0 0 t 0 0 0 65.0 960.0 175.0 0.0 0.0 0.0 712.0 100.0 0 0 0 0 0 0
MA0004.1_rc_shift9 (Arnt_rc)				; dyads_m37 versus MA0004.1_rc (Arnt_rc); m=6/6; ncol2=6; w=6; offset=5; strand=R; shift=9; score=0.401601; ---------CACGTG-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0.0 20.0 0.0 0.0 0.0 0.0 0 0 c 0 0 0 0 0 0 0 0 0 20.0 0.0 20.0 0.0 1.0 0.0 0 0 g 0 0 0 0 0 0 0 0 0 0.0 0.0 0.0 20.0 0.0 16.0 0 0 t 0 0 0 0 0 0 0 0 0 0.0 0.0 0.0 0.0 19.0 4.0 0 0