One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep2_motifs50/results/discovered_motifs/oligos_7nt_mkv4_m40/peak-motifs_oligos_7nt_mkv4_m40.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_Rep2_motifs50/results/discovered_motifs/oligos_7nt_mkv4_m40/peak-motifs_oligos_7nt_mkv4_m40_vs_db_jaspar_core_nonredundant_vertebrates

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv4_m40_shift2 ; 9 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv4_m40_shift2 (oligos_7nt_mkv4_m40oligos_7nt_mkv4_m40)
; oligos_7nt_mkv4_m40 (oligos_7nt_mkv4_m40oligos_7nt_mkv4_m40); m=0 (reference); ncol1=11; shift=2; ncol=13; --ssCGyGCGCss ; Alignment reference a 0 0 23 29 1 4 15 12 1 2 1 30 27 c 0 0 130 79 264 3 89 11 269 1 262 93 101 g 0 0 89 142 6 267 50 243 3 270 4 127 115 t 0 0 32 24 3 0 120 8 1 1 7 24 31

MA0506.1_shift1 (NRF1)
; oligos_7nt_mkv4_m40 versus MA0506.1 (NRF1); m=1/8; ncol2=11; w=10; offset=-1; strand=D; shift=1; score=0.674874; -GCGCmTGCGCr- ; cor=; Ncor= a 0 602.0 623.0 196.0 0.0 1514.0 0.0 0.0 0.0 0.0 74.0 2245.0 0 c 0 375.0 4001.0 189.0 4016.0 1862.0 403.0 0.0 4338.0 349.0 4550.0 804.0 0 g 0 3647.0 0.0 4239.0 468.0 935.0 528.0 4624.0 0.0 4275.0 0.0 1575.0 0 t 0 0.0 0.0 0.0 140.0 313.0 3693.0 0.0 286.0 0.0 0.0 0.0 0

MA0632.2_shift3 (TCFL5)
; oligos_7nt_mkv4_m40 versus MA0632.2 (TCFL5); m=2/8; ncol2=10; w=10; offset=1; strand=D; shift=3; score=0.668205; ---kCrCGCGCmc ; cor=; Ncor= a 0 0 0 2810.0 0.0 72543.0 0.0 1566.0 1765.0 3520.0 1593.0 72543.0 10588.0 c 0 0 0 10582.0 72543.0 0.0 72543.0 0.0 57092.0 657.0 72543.0 44394.0 47538.0 g 0 0 0 22297.0 0.0 29710.0 0.0 72543.0 0.0 72543.0 4594.0 19096.0 5747.0 t 0 0 0 36854.0 0.0 9359.0 1643.0 0.0 15451.0 0.0 635.0 25921.0 8670.0

MA0131.2_shift1 (HINFP)
; oligos_7nt_mkv4_m40 versus MA0131.2 (HINFP); m=3/8; ncol2=12; w=11; offset=-1; strand=D; shift=1; score=0.647461; -carCGTCCGCgk ; cor=; Ncor= a 0 23.0 285.0 276.0 1.0 0.0 0.0 0.0 0.0 0.0 1.0 85.0 77.0 c 0 340.0 131.0 45.0 388.0 14.0 0.0 404.0 413.0 31.0 395.0 55.0 84.0 g 0 106.0 113.0 217.0 97.0 484.0 0.0 13.0 0.0 472.0 15.0 188.0 154.0 t 0 100.0 53.0 17.0 7.0 10.0 470.0 0.0 3.0 21.0 12.0 97.0 107.0

MA1650.1_rc_shift3 (ZBTB14_rc)
; oligos_7nt_mkv4_m40 versus MA1650.1_rc (ZBTB14_rc); m=4/8; ncol2=12; w=10; offset=1; strand=R; shift=3; score=0.629739; ---ssGTGCGCGG ; cor=; Ncor= a 0 0 0 606.0 508.0 123.0 0.0 52.0 67.0 82.0 62.0 59.0 73.0 c 0 0 0 1239.0 1451.0 651.0 10.0 261.0 4043.0 319.0 4098.0 155.0 614.0 g 0 0 0 2260.0 1618.0 3674.0 37.0 4178.0 305.0 4078.0 294.0 4292.0 3525.0 t 0 0 0 442.0 970.0 99.0 4500.0 56.0 132.0 68.0 93.0 41.0 335.0

MA0006.1_shift2 (Ahr::Arnt)
; oligos_7nt_mkv4_m40 versus MA0006.1 (Ahr::Arnt); m=5/8; ncol2=6; w=6; offset=0; strand=D; shift=2; score=0.468421; --yGCGTG----- ; cor=; Ncor= a 0 0 3.0 0.0 0.0 0.0 0.0 0.0 0 0 0 0 0 c 0 0 8.0 0.0 23.0 0.0 0.0 0.0 0 0 0 0 0 g 0 0 2.0 23.0 0.0 23.0 0.0 24.0 0 0 0 0 0 t 0 0 11.0 1.0 1.0 1.0 24.0 0.0 0 0 0 0 0

MA0259.1_shift1 (ARNT::HIF1A)
; oligos_7nt_mkv4_m40 versus MA0259.1 (ARNT::HIF1A); m=6/8; ncol2=8; w=7; offset=-1; strand=D; shift=1; score=0.452233; -vbACGTGc---- ; cor=; Ncor= a 0 27.0 10.0 78.0 0.0 0.0 0.0 0.0 18.0 0 0 0 0 c 0 28.0 29.0 2.0 103.0 0.0 0.0 0.0 51.0 0 0 0 0 g 0 49.0 34.0 23.0 0.0 104.0 0.0 104.0 20.0 0 0 0 0 t 0 0.0 31.0 1.0 1.0 0.0 104.0 0.0 15.0 0 0 0 0

MA1560.1_rc_shift0 (SOHLH2_rc)
; oligos_7nt_mkv4_m40 versus MA1560.1_rc (SOHLH2_rc); m=7/8; ncol2=10; w=8; offset=-2; strand=R; shift=0; score=0.430952; ygCACGTGcr--- ; cor=; Ncor= a 224.0 153.0 4.0 1212.0 15.0 7.0 0.0 70.0 276.0 313.0 0 0 0 c 369.0 172.0 1212.0 0.0 1212.0 11.0 41.0 29.0 1212.0 184.0 0 0 0 g 239.0 1212.0 4.0 65.0 0.0 1212.0 0.0 1212.0 264.0 485.0 0 0 0 t 381.0 272.0 41.0 36.0 14.0 0.0 1212.0 45.0 172.0 230.0 0 0 0

MA0004.1_shift2 (Arnt)
; oligos_7nt_mkv4_m40 versus MA0004.1 (Arnt); m=8/8; ncol2=6; w=6; offset=0; strand=D; shift=2; score=0.413496; --CACGTG----- ; cor=; Ncor= a 0 0 4.0 19.0 0.0 0.0 0.0 0.0 0 0 0 0 0 c 0 0 16.0 0.0 20.0 0.0 0.0 0.0 0 0 0 0 0 g 0 0 0.0 1.0 0.0 20.0 0.0 20.0 0 0 0 0 0 t 0 0 0.0 0.0 0.0 0.0 20.0 0.0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv4_m40_shift2 (oligos_7nt_mkv4_m40oligos_7nt_mkv4_m40)				; oligos_7nt_mkv4_m40 (oligos_7nt_mkv4_m40oligos_7nt_mkv4_m40); m=0 (reference); ncol1=11; shift=2; ncol=13; --ssCGyGCGCss ; Alignment reference a 0 0 23 29 1 4 15 12 1 2 1 30 27 c 0 0 130 79 264 3 89 11 269 1 262 93 101 g 0 0 89 142 6 267 50 243 3 270 4 127 115 t 0 0 32 24 3 0 120 8 1 1 7 24 31
MA0506.1_shift1 (NRF1)				; oligos_7nt_mkv4_m40 versus MA0506.1 (NRF1); m=1/8; ncol2=11; w=10; offset=-1; strand=D; shift=1; score=0.674874; -GCGCmTGCGCr- ; cor=; Ncor= a 0 602.0 623.0 196.0 0.0 1514.0 0.0 0.0 0.0 0.0 74.0 2245.0 0 c 0 375.0 4001.0 189.0 4016.0 1862.0 403.0 0.0 4338.0 349.0 4550.0 804.0 0 g 0 3647.0 0.0 4239.0 468.0 935.0 528.0 4624.0 0.0 4275.0 0.0 1575.0 0 t 0 0.0 0.0 0.0 140.0 313.0 3693.0 0.0 286.0 0.0 0.0 0.0 0
MA0632.2_shift3 (TCFL5)				; oligos_7nt_mkv4_m40 versus MA0632.2 (TCFL5); m=2/8; ncol2=10; w=10; offset=1; strand=D; shift=3; score=0.668205; ---kCrCGCGCmc ; cor=; Ncor= a 0 0 0 2810.0 0.0 72543.0 0.0 1566.0 1765.0 3520.0 1593.0 72543.0 10588.0 c 0 0 0 10582.0 72543.0 0.0 72543.0 0.0 57092.0 657.0 72543.0 44394.0 47538.0 g 0 0 0 22297.0 0.0 29710.0 0.0 72543.0 0.0 72543.0 4594.0 19096.0 5747.0 t 0 0 0 36854.0 0.0 9359.0 1643.0 0.0 15451.0 0.0 635.0 25921.0 8670.0
MA0131.2_shift1 (HINFP)				; oligos_7nt_mkv4_m40 versus MA0131.2 (HINFP); m=3/8; ncol2=12; w=11; offset=-1; strand=D; shift=1; score=0.647461; -carCGTCCGCgk ; cor=; Ncor= a 0 23.0 285.0 276.0 1.0 0.0 0.0 0.0 0.0 0.0 1.0 85.0 77.0 c 0 340.0 131.0 45.0 388.0 14.0 0.0 404.0 413.0 31.0 395.0 55.0 84.0 g 0 106.0 113.0 217.0 97.0 484.0 0.0 13.0 0.0 472.0 15.0 188.0 154.0 t 0 100.0 53.0 17.0 7.0 10.0 470.0 0.0 3.0 21.0 12.0 97.0 107.0
MA1650.1_rc_shift3 (ZBTB14_rc)				; oligos_7nt_mkv4_m40 versus MA1650.1_rc (ZBTB14_rc); m=4/8; ncol2=12; w=10; offset=1; strand=R; shift=3; score=0.629739; ---ssGTGCGCGG ; cor=; Ncor= a 0 0 0 606.0 508.0 123.0 0.0 52.0 67.0 82.0 62.0 59.0 73.0 c 0 0 0 1239.0 1451.0 651.0 10.0 261.0 4043.0 319.0 4098.0 155.0 614.0 g 0 0 0 2260.0 1618.0 3674.0 37.0 4178.0 305.0 4078.0 294.0 4292.0 3525.0 t 0 0 0 442.0 970.0 99.0 4500.0 56.0 132.0 68.0 93.0 41.0 335.0
MA0006.1_shift2 (Ahr::Arnt)				; oligos_7nt_mkv4_m40 versus MA0006.1 (Ahr::Arnt); m=5/8; ncol2=6; w=6; offset=0; strand=D; shift=2; score=0.468421; --yGCGTG----- ; cor=; Ncor= a 0 0 3.0 0.0 0.0 0.0 0.0 0.0 0 0 0 0 0 c 0 0 8.0 0.0 23.0 0.0 0.0 0.0 0 0 0 0 0 g 0 0 2.0 23.0 0.0 23.0 0.0 24.0 0 0 0 0 0 t 0 0 11.0 1.0 1.0 1.0 24.0 0.0 0 0 0 0 0
MA0259.1_shift1 (ARNT::HIF1A)				; oligos_7nt_mkv4_m40 versus MA0259.1 (ARNT::HIF1A); m=6/8; ncol2=8; w=7; offset=-1; strand=D; shift=1; score=0.452233; -vbACGTGc---- ; cor=; Ncor= a 0 27.0 10.0 78.0 0.0 0.0 0.0 0.0 18.0 0 0 0 0 c 0 28.0 29.0 2.0 103.0 0.0 0.0 0.0 51.0 0 0 0 0 g 0 49.0 34.0 23.0 0.0 104.0 0.0 104.0 20.0 0 0 0 0 t 0 0.0 31.0 1.0 1.0 0.0 104.0 0.0 15.0 0 0 0 0
MA1560.1_rc_shift0 (SOHLH2_rc)				; oligos_7nt_mkv4_m40 versus MA1560.1_rc (SOHLH2_rc); m=7/8; ncol2=10; w=8; offset=-2; strand=R; shift=0; score=0.430952; ygCACGTGcr--- ; cor=; Ncor= a 224.0 153.0 4.0 1212.0 15.0 7.0 0.0 70.0 276.0 313.0 0 0 0 c 369.0 172.0 1212.0 0.0 1212.0 11.0 41.0 29.0 1212.0 184.0 0 0 0 g 239.0 1212.0 4.0 65.0 0.0 1212.0 0.0 1212.0 264.0 485.0 0 0 0 t 381.0 272.0 41.0 36.0 14.0 0.0 1212.0 45.0 172.0 230.0 0 0 0
MA0004.1_shift2 (Arnt)				; oligos_7nt_mkv4_m40 versus MA0004.1 (Arnt); m=8/8; ncol2=6; w=6; offset=0; strand=D; shift=2; score=0.413496; --CACGTG----- ; cor=; Ncor= a 0 0 4.0 19.0 0.0 0.0 0.0 0.0 0 0 0 0 0 c 0 0 16.0 0.0 20.0 0.0 0.0 0.0 0 0 0 0 0 g 0 0 0.0 1.0 0.0 20.0 0.0 20.0 0 0 0 0 0 t 0 0 0.0 0.0 0.0 0.0 20.0 0.0 0 0 0 0 0