One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep1_motifs50/results/discovered_motifs/local_words_6nt_m38/peak-motifs_local_words_6nt_m38.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_6nt_m38/peak-motifs_local_words_6nt_m38_vs_db_jaspar_core_nonredundant_vertebrates

One-to-n matrix alignment; reference matrix: local_words_6nt_m38_shift0 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
local_words_6nt_m38_shift0 (local_words_6nt_m38local_words_6nt_m38)
; local_words_6nt_m38 (local_words_6nt_m38local_words_6nt_m38); m=0 (reference); ncol1=24; shift=0; ncol=24; cksCCACAGCTGyCACAGsTGCcr ; Alignment reference a 8 8 4 6 2 48 0 55 1 0 1 0 0 1 52 0 49 0 3 4 1 2 10 26 c 30 8 20 44 48 2 55 1 1 55 0 0 24 52 1 52 2 0 26 3 3 42 27 6 g 6 15 27 4 2 5 1 0 54 0 0 56 1 3 1 3 1 54 23 6 49 8 6 14 t 12 25 5 2 4 1 0 0 0 1 55 0 31 0 2 1 4 2 4 43 3 4 13 10

MA1485.1_shift2 (FERD3L)
; local_words_6nt_m38 versus MA1485.1 (FERD3L); m=1/5; ncol2=14; w=14; offset=2; strand=D; shift=2; score=0.482485; --GyrmCAGCTGTyAC-------- ; cor=; Ncor= a 0 0 2158.0 450.0 14384.0 15390.0 36.0 29605.0 0.0 3649.0 81.0 0.0 1268.0 103.0 29605.0 0.0 0 0 0 0 0 0 0 0 c 0 0 68.0 20049.0 2443.0 9363.0 29605.0 126.0 841.0 29605.0 129.0 0.0 3878.0 8664.0 809.0 29605.0 0 0 0 0 0 0 0 0 g 0 0 29605.0 348.0 12703.0 3142.0 0.0 118.0 29605.0 471.0 210.0 29605.0 3395.0 5920.0 9815.0 0.0 0 0 0 0 0 0 0 0 t 0 0 225.0 9557.0 74.0 1710.0 0.0 144.0 4691.0 0.0 29605.0 0.0 21065.0 14919.0 958.0 48.0 0 0 0 0 0 0 0 0

MA0499.2_rc_shift11 (MYOD1_rc)
; local_words_6nt_m38 versus MA0499.2_rc (MYOD1_rc); m=2/5; ncol2=13; w=13; offset=11; strand=R; shift=11; score=0.42389; -----------rkrACAGGTGcwg ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 9358.0 8151.0 9000.0 29644.0 238.0 33130.0 330.0 1226.0 587.0 269.0 2245.0 9291.0 7728.0 c 0 0 0 0 0 0 0 0 0 0 0 7495.0 6202.0 4440.0 1699.0 33468.0 366.0 932.0 7336.0 849.0 354.0 21884.0 8444.0 8118.0 g 0 0 0 0 0 0 0 0 0 0 0 11760.0 10485.0 19052.0 2555.0 386.0 563.0 32504.0 25275.0 583.0 33328.0 5622.0 7103.0 11279.0 t 0 0 0 0 0 0 0 0 0 0 0 5687.0 9462.0 1808.0 402.0 208.0 241.0 534.0 463.0 32281.0 349.0 4549.0 9462.0 7175.0

MA1641.1_shift3 (MYF5)
; local_words_6nt_m38 versus MA1641.1 (MYF5); m=3/5; ncol2=12; w=12; offset=3; strand=D; shift=3; score=0.412593; ---gvaCAGCTGtbc--------- ; cor=; Ncor= a 0 0 0 2698.0 3507.0 7490.0 95.0 10965.0 100.0 223.0 129.0 42.0 578.0 1572.0 2554.0 0 0 0 0 0 0 0 0 0 c 0 0 0 2700.0 2986.0 1368.0 10911.0 47.0 230.0 10657.0 68.0 161.0 1775.0 3146.0 3258.0 0 0 0 0 0 0 0 0 0 g 0 0 0 3258.0 3145.0 1774.0 161.0 69.0 10658.0 230.0 47.0 10912.0 1368.0 2985.0 2701.0 0 0 0 0 0 0 0 0 0 t 0 0 0 2554.0 1572.0 578.0 43.0 129.0 222.0 100.0 10966.0 95.0 7489.0 3507.0 2697.0 0 0 0 0 0 0 0 0 0

MA1619.1_shift3 (Ptf1a(var.2))
; local_words_6nt_m38 versus MA1619.1 (Ptf1a(var.2)); m=4/5; ncol2=12; w=12; offset=3; strand=D; shift=3; score=0.412556; ---rmaCAGCTGtky--------- ; cor=; Ncor= a 0 0 0 1869.0 1978.0 4346.0 49.0 7119.0 34.0 224.0 26.0 27.0 535.0 1221.0 1602.0 0 0 0 0 0 0 0 0 0 c 0 0 0 1803.0 2430.0 1070.0 7149.0 41.0 307.0 6697.0 66.0 27.0 1312.0 1632.0 1977.0 0 0 0 0 0 0 0 0 0 g 0 0 0 1974.0 1629.0 1308.0 28.0 65.0 6689.0 299.0 40.0 7150.0 1065.0 2426.0 1803.0 0 0 0 0 0 0 0 0 0 t 0 0 0 1607.0 1216.0 529.0 27.0 28.0 223.0 33.0 7121.0 49.0 4341.0 1974.0 1871.0 0 0 0 0 0 0 0 0 0

MA0745.2_rc_shift11 (SNAI2_rc)
; local_words_6nt_m38 versus MA0745.2_rc (SNAI2_rc); m=5/5; ncol2=13; w=13; offset=11; strand=R; shift=11; score=0.403562; -----------rykACAGGTGcrt ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 17906.0 8917.0 8747.0 37272.0 126.0 45229.0 344.0 234.0 227.0 622.0 2359.0 16344.0 9958.0 c 0 0 0 0 0 0 0 0 0 0 0 8219.0 12297.0 6281.0 1263.0 45257.0 196.0 487.0 326.0 424.0 323.0 26742.0 9490.0 11169.0 g 0 0 0 0 0 0 0 0 0 0 0 13476.0 11016.0 18771.0 6467.0 254.0 313.0 44739.0 45144.0 202.0 44463.0 6393.0 12314.0 10031.0 t 0 0 0 0 0 0 0 0 0 0 0 6215.0 13586.0 12017.0 814.0 179.0 78.0 246.0 112.0 44963.0 408.0 10322.0 7668.0 14658.0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
local_words_6nt_m38_shift0 (local_words_6nt_m38local_words_6nt_m38)				; local_words_6nt_m38 (local_words_6nt_m38local_words_6nt_m38); m=0 (reference); ncol1=24; shift=0; ncol=24; cksCCACAGCTGyCACAGsTGCcr ; Alignment reference a 8 8 4 6 2 48 0 55 1 0 1 0 0 1 52 0 49 0 3 4 1 2 10 26 c 30 8 20 44 48 2 55 1 1 55 0 0 24 52 1 52 2 0 26 3 3 42 27 6 g 6 15 27 4 2 5 1 0 54 0 0 56 1 3 1 3 1 54 23 6 49 8 6 14 t 12 25 5 2 4 1 0 0 0 1 55 0 31 0 2 1 4 2 4 43 3 4 13 10
MA1485.1_shift2 (FERD3L)				; local_words_6nt_m38 versus MA1485.1 (FERD3L); m=1/5; ncol2=14; w=14; offset=2; strand=D; shift=2; score=0.482485; --GyrmCAGCTGTyAC-------- ; cor=; Ncor= a 0 0 2158.0 450.0 14384.0 15390.0 36.0 29605.0 0.0 3649.0 81.0 0.0 1268.0 103.0 29605.0 0.0 0 0 0 0 0 0 0 0 c 0 0 68.0 20049.0 2443.0 9363.0 29605.0 126.0 841.0 29605.0 129.0 0.0 3878.0 8664.0 809.0 29605.0 0 0 0 0 0 0 0 0 g 0 0 29605.0 348.0 12703.0 3142.0 0.0 118.0 29605.0 471.0 210.0 29605.0 3395.0 5920.0 9815.0 0.0 0 0 0 0 0 0 0 0 t 0 0 225.0 9557.0 74.0 1710.0 0.0 144.0 4691.0 0.0 29605.0 0.0 21065.0 14919.0 958.0 48.0 0 0 0 0 0 0 0 0
MA0499.2_rc_shift11 (MYOD1_rc)				; local_words_6nt_m38 versus MA0499.2_rc (MYOD1_rc); m=2/5; ncol2=13; w=13; offset=11; strand=R; shift=11; score=0.42389; -----------rkrACAGGTGcwg ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 9358.0 8151.0 9000.0 29644.0 238.0 33130.0 330.0 1226.0 587.0 269.0 2245.0 9291.0 7728.0 c 0 0 0 0 0 0 0 0 0 0 0 7495.0 6202.0 4440.0 1699.0 33468.0 366.0 932.0 7336.0 849.0 354.0 21884.0 8444.0 8118.0 g 0 0 0 0 0 0 0 0 0 0 0 11760.0 10485.0 19052.0 2555.0 386.0 563.0 32504.0 25275.0 583.0 33328.0 5622.0 7103.0 11279.0 t 0 0 0 0 0 0 0 0 0 0 0 5687.0 9462.0 1808.0 402.0 208.0 241.0 534.0 463.0 32281.0 349.0 4549.0 9462.0 7175.0
MA1641.1_shift3 (MYF5)				; local_words_6nt_m38 versus MA1641.1 (MYF5); m=3/5; ncol2=12; w=12; offset=3; strand=D; shift=3; score=0.412593; ---gvaCAGCTGtbc--------- ; cor=; Ncor= a 0 0 0 2698.0 3507.0 7490.0 95.0 10965.0 100.0 223.0 129.0 42.0 578.0 1572.0 2554.0 0 0 0 0 0 0 0 0 0 c 0 0 0 2700.0 2986.0 1368.0 10911.0 47.0 230.0 10657.0 68.0 161.0 1775.0 3146.0 3258.0 0 0 0 0 0 0 0 0 0 g 0 0 0 3258.0 3145.0 1774.0 161.0 69.0 10658.0 230.0 47.0 10912.0 1368.0 2985.0 2701.0 0 0 0 0 0 0 0 0 0 t 0 0 0 2554.0 1572.0 578.0 43.0 129.0 222.0 100.0 10966.0 95.0 7489.0 3507.0 2697.0 0 0 0 0 0 0 0 0 0
MA1619.1_shift3 (Ptf1a(var.2))				; local_words_6nt_m38 versus MA1619.1 (Ptf1a(var.2)); m=4/5; ncol2=12; w=12; offset=3; strand=D; shift=3; score=0.412556; ---rmaCAGCTGtky--------- ; cor=; Ncor= a 0 0 0 1869.0 1978.0 4346.0 49.0 7119.0 34.0 224.0 26.0 27.0 535.0 1221.0 1602.0 0 0 0 0 0 0 0 0 0 c 0 0 0 1803.0 2430.0 1070.0 7149.0 41.0 307.0 6697.0 66.0 27.0 1312.0 1632.0 1977.0 0 0 0 0 0 0 0 0 0 g 0 0 0 1974.0 1629.0 1308.0 28.0 65.0 6689.0 299.0 40.0 7150.0 1065.0 2426.0 1803.0 0 0 0 0 0 0 0 0 0 t 0 0 0 1607.0 1216.0 529.0 27.0 28.0 223.0 33.0 7121.0 49.0 4341.0 1974.0 1871.0 0 0 0 0 0 0 0 0 0
MA0745.2_rc_shift11 (SNAI2_rc)				; local_words_6nt_m38 versus MA0745.2_rc (SNAI2_rc); m=5/5; ncol2=13; w=13; offset=11; strand=R; shift=11; score=0.403562; -----------rykACAGGTGcrt ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 0 0 17906.0 8917.0 8747.0 37272.0 126.0 45229.0 344.0 234.0 227.0 622.0 2359.0 16344.0 9958.0 c 0 0 0 0 0 0 0 0 0 0 0 8219.0 12297.0 6281.0 1263.0 45257.0 196.0 487.0 326.0 424.0 323.0 26742.0 9490.0 11169.0 g 0 0 0 0 0 0 0 0 0 0 0 13476.0 11016.0 18771.0 6467.0 254.0 313.0 44739.0 45144.0 202.0 44463.0 6393.0 12314.0 10031.0 t 0 0 0 0 0 0 0 0 0 0 0 6215.0 13586.0 12017.0 814.0 179.0 78.0 246.0 112.0 44963.0 408.0 10322.0 7668.0 14658.0