One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep1_motifs50/results/discovered_motifs/local_words_7nt_m13/peak-motifs_local_words_7nt_m13.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_7nt_m13/peak-motifs_local_words_7nt_m13_vs_db_jaspar_core_nonredundant_vertebrates

One-to-n matrix alignment; reference matrix: local_words_7nt_m13_shift0 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
local_words_7nt_m13_shift0 (local_words_7nt_m13local_words_7nt_m13)
; local_words_7nt_m13 (local_words_7nt_m13local_words_7nt_m13); m=0 (reference); ncol1=24; shift=0; ncol=24; ccrCAGCTGCCACAGCTGyCAcmg ; Alignment reference a 26 35 47 17 130 9 15 14 6 10 8 132 0 145 1 0 5 1 12 0 126 11 47 26 c 68 62 24 108 7 6 126 6 10 120 136 8 152 3 8 145 1 4 41 137 12 104 48 37 g 34 29 64 14 6 136 6 6 134 4 4 4 1 3 142 2 1 149 3 11 8 30 22 74 t 27 29 20 16 12 4 8 129 5 21 7 11 2 4 4 8 148 1 99 7 9 10 38 18

MA1485.1_shift8 (FERD3L)
; local_words_7nt_m13 versus MA1485.1 (FERD3L); m=1/5; ncol2=14; w=14; offset=8; strand=D; shift=8; score=0.496127; --------GyrmCAGCTGTyAC-- ; cor=; Ncor= a 0 0 0 0 0 0 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 c 0 0 0 0 0 0 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 g 0 0 0 0 0 0 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 t 0 0 0 0 0 0 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

MA1641.1_shift9 (MYF5)
; local_words_7nt_m13 versus MA1641.1 (MYF5); m=2/5; ncol2=12; w=12; offset=9; strand=D; shift=9; score=0.418061; ---------gvaCAGCTGtbc--- ; cor=; Ncor= a 0 0 0 0 0 0 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 c 0 0 0 0 0 0 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 g 0 0 0 0 0 0 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 t 0 0 0 0 0 0 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

MA0832.1_shift8 (Tcf21)
; local_words_7nt_m13 versus MA0832.1 (Tcf21); m=3/5; ncol2=14; w=14; offset=8; strand=D; shift=8; score=0.417853; --------ryAACAGCTGTTry-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 55.0 28.0 171.0 171.0 0.0 171.0 0.0 0.0 0.0 0.0 0.0 5.0 50.0 30.0 0 0 c 0 0 0 0 0 0 0 0 29.0 76.0 1.0 10.0 171.0 1.0 0.0 171.0 0.0 0.0 4.0 23.0 23.0 49.0 0 0 g 0 0 0 0 0 0 0 0 70.0 22.0 23.0 0.0 0.0 0.0 171.0 1.0 0.0 171.0 20.0 0.0 80.0 32.0 0 0 t 0 0 0 0 0 0 0 0 17.0 46.0 3.0 0.0 0.0 0.0 2.0 1.0 171.0 0.0 171.0 171.0 19.0 60.0 0 0

MA1619.1_shift9 (Ptf1a(var.2))
; local_words_7nt_m13 versus MA1619.1 (Ptf1a(var.2)); m=4/5; ncol2=12; w=12; offset=9; strand=D; shift=9; score=0.417434; ---------rmaCAGCTGtky--- ; cor=; Ncor= a 0 0 0 0 0 0 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 c 0 0 0 0 0 0 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 g 0 0 0 0 0 0 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 t 0 0 0 0 0 0 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

MA0500.2_rc_shift0 (MYOG_rc)
; local_words_7nt_m13 versus MA0500.2_rc (MYOG_rc); m=5/5; ncol2=12; w=12; offset=0; strand=R; shift=0; score=0.409918; sarCAGCTGyts------------ ; cor=; Ncor= a 5310.0 8475.0 7192.0 88.0 21777.0 95.0 169.0 163.0 182.0 1678.0 4692.0 5070.0 0 0 0 0 0 0 0 0 0 0 0 0 c 6369.0 3718.0 2706.0 21985.0 179.0 131.0 21963.0 236.0 101.0 10790.0 5483.0 5596.0 0 0 0 0 0 0 0 0 0 0 0 0 g 5660.0 5497.0 10792.0 102.0 238.0 21964.0 130.0 176.0 21988.0 2730.0 3754.0 6381.0 0 0 0 0 0 0 0 0 0 0 0 0 t 5018.0 4667.0 1667.0 182.0 163.0 167.0 95.0 21782.0 86.0 7159.0 8428.0 5310.0 0 0 0 0 0 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
local_words_7nt_m13_shift0 (local_words_7nt_m13local_words_7nt_m13)				; local_words_7nt_m13 (local_words_7nt_m13local_words_7nt_m13); m=0 (reference); ncol1=24; shift=0; ncol=24; ccrCAGCTGCCACAGCTGyCAcmg ; Alignment reference a 26 35 47 17 130 9 15 14 6 10 8 132 0 145 1 0 5 1 12 0 126 11 47 26 c 68 62 24 108 7 6 126 6 10 120 136 8 152 3 8 145 1 4 41 137 12 104 48 37 g 34 29 64 14 6 136 6 6 134 4 4 4 1 3 142 2 1 149 3 11 8 30 22 74 t 27 29 20 16 12 4 8 129 5 21 7 11 2 4 4 8 148 1 99 7 9 10 38 18
MA1485.1_shift8 (FERD3L)				; local_words_7nt_m13 versus MA1485.1 (FERD3L); m=1/5; ncol2=14; w=14; offset=8; strand=D; shift=8; score=0.496127; --------GyrmCAGCTGTyAC-- ; cor=; Ncor= a 0 0 0 0 0 0 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 c 0 0 0 0 0 0 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 g 0 0 0 0 0 0 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 t 0 0 0 0 0 0 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
MA1641.1_shift9 (MYF5)				; local_words_7nt_m13 versus MA1641.1 (MYF5); m=2/5; ncol2=12; w=12; offset=9; strand=D; shift=9; score=0.418061; ---------gvaCAGCTGtbc--- ; cor=; Ncor= a 0 0 0 0 0 0 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 c 0 0 0 0 0 0 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 g 0 0 0 0 0 0 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 t 0 0 0 0 0 0 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
MA0832.1_shift8 (Tcf21)				; local_words_7nt_m13 versus MA0832.1 (Tcf21); m=3/5; ncol2=14; w=14; offset=8; strand=D; shift=8; score=0.417853; --------ryAACAGCTGTTry-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 55.0 28.0 171.0 171.0 0.0 171.0 0.0 0.0 0.0 0.0 0.0 5.0 50.0 30.0 0 0 c 0 0 0 0 0 0 0 0 29.0 76.0 1.0 10.0 171.0 1.0 0.0 171.0 0.0 0.0 4.0 23.0 23.0 49.0 0 0 g 0 0 0 0 0 0 0 0 70.0 22.0 23.0 0.0 0.0 0.0 171.0 1.0 0.0 171.0 20.0 0.0 80.0 32.0 0 0 t 0 0 0 0 0 0 0 0 17.0 46.0 3.0 0.0 0.0 0.0 2.0 1.0 171.0 0.0 171.0 171.0 19.0 60.0 0 0
MA1619.1_shift9 (Ptf1a(var.2))				; local_words_7nt_m13 versus MA1619.1 (Ptf1a(var.2)); m=4/5; ncol2=12; w=12; offset=9; strand=D; shift=9; score=0.417434; ---------rmaCAGCTGtky--- ; cor=; Ncor= a 0 0 0 0 0 0 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 c 0 0 0 0 0 0 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 g 0 0 0 0 0 0 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 t 0 0 0 0 0 0 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
MA0500.2_rc_shift0 (MYOG_rc)				; local_words_7nt_m13 versus MA0500.2_rc (MYOG_rc); m=5/5; ncol2=12; w=12; offset=0; strand=R; shift=0; score=0.409918; sarCAGCTGyts------------ ; cor=; Ncor= a 5310.0 8475.0 7192.0 88.0 21777.0 95.0 169.0 163.0 182.0 1678.0 4692.0 5070.0 0 0 0 0 0 0 0 0 0 0 0 0 c 6369.0 3718.0 2706.0 21985.0 179.0 131.0 21963.0 236.0 101.0 10790.0 5483.0 5596.0 0 0 0 0 0 0 0 0 0 0 0 0 g 5660.0 5497.0 10792.0 102.0 238.0 21964.0 130.0 176.0 21988.0 2730.0 3754.0 6381.0 0 0 0 0 0 0 0 0 0 0 0 0 t 5018.0 4667.0 1667.0 182.0 163.0 167.0 95.0 21782.0 86.0 7159.0 8428.0 5310.0 0 0 0 0 0 0 0 0 0 0 0 0