One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep2_motifs50/results/discovered_motifs/local_words_6nt_m5/peak-motifs_local_words_6nt_m5.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/local_words_6nt_m5/peak-motifs_local_words_6nt_m5_vs_db_jaspar_core_nonredundant_vertebrates

One-to-n matrix alignment; reference matrix: local_words_6nt_m5_shift0 ; 6 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
local_words_6nt_m5_shift0 (local_words_6nt_m5local_words_6nt_m5)
; local_words_6nt_m5 (local_words_6nt_m5local_words_6nt_m5); m=0 (reference); ncol1=23; shift=0; ncol=24; cwGCtGCTGCaGCAGCTGCcgcc- ; Alignment reference a 4 31 1 4 21 2 3 11 8 3 72 4 0 83 1 1 2 0 1 14 21 10 26 0 c 73 26 8 102 13 3 99 9 2 101 13 1 112 7 1 112 8 6 104 65 25 62 42 0 g 23 26 100 5 13 106 7 12 100 5 7 106 2 4 111 0 5 107 2 14 53 22 27 0 t 14 31 5 3 67 3 5 82 4 5 22 3 0 20 1 1 99 1 7 21 15 20 19 0

MA1529.1_shift6 (NHLH2)
; local_words_6nt_m5 versus MA1529.1 (NHLH2); m=1/5; ncol2=18; w=17; offset=6; strand=D; shift=6; score=0.504967; ------ggGyMGCAGCTGCGyCmc ; cor=; Ncor= a 0 0 0 0 0 0 4834.0 4312.0 3741.0 4921.0 5603.0 2378.0 2.0 21364.0 6.0 525.0 0.0 0.0 693.0 210.0 1184.0 3766.0 6392.0 3601.0 c 0 0 0 0 0 0 2655.0 2219.0 1065.0 6141.0 15451.0 2324.0 21359.0 0.0 2459.0 20268.0 14.0 2.0 20611.0 204.0 7207.0 18351.0 13462.0 11271.0 g 0 0 0 0 0 0 9732.0 13903.0 18450.0 4908.0 671.0 18930.0 2.0 26.0 20096.0 2266.0 3.0 21363.0 275.0 20977.0 1520.0 1183.0 1579.0 2264.0 t 0 0 0 0 0 0 4143.0 5198.0 2763.0 5394.0 151.0 2634.0 5.0 1.0 1054.0 0.0 21358.0 0.0 1230.0 740.0 13503.0 2533.0 3330.0 4228.0

MA0500.2_rc_shift9 (MYOG_rc)
; local_words_6nt_m5 versus MA0500.2_rc (MYOG_rc); m=2/5; ncol2=12; w=12; offset=9; strand=R; shift=9; score=0.450772; ---------sarCAGCTGyts--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 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 c 0 0 0 0 0 0 0 0 0 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 g 0 0 0 0 0 0 0 0 0 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 t 0 0 0 0 0 0 0 0 0 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

MA1485.1_shift8 (FERD3L)
; local_words_6nt_m5 versus MA1485.1 (FERD3L); m=3/5; ncol2=14; w=14; offset=8; strand=D; shift=8; score=0.448773; --------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

MA1631.1_shift9 (ASCL1(var.2))
; local_words_6nt_m5 versus MA1631.1 (ASCL1(var.2)); m=4/5; ncol2=13; w=13; offset=9; strand=D; shift=9; score=0.431602; ---------cdgCACCTGCysc-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 6833.0 8952.0 5836.0 184.0 32315.0 163.0 196.0 368.0 251.0 399.0 4490.0 7083.0 5972.0 0 0 c 0 0 0 0 0 0 0 0 0 11805.0 7998.0 6654.0 33562.0 563.0 30169.0 33402.0 740.0 445.0 28844.0 17883.0 10555.0 11996.0 0 0 g 0 0 0 0 0 0 0 0 0 8371.0 8601.0 18576.0 321.0 860.0 3209.0 607.0 492.0 33411.0 2719.0 2966.0 8939.0 8356.0 0 0 t 0 0 0 0 0 0 0 0 0 7347.0 8805.0 3290.0 289.0 618.0 815.0 151.0 32756.0 249.0 2394.0 9017.0 7779.0 8032.0 0 0

MA0830.2_shift9 (TCF4)
; local_words_6nt_m5 versus MA0830.2 (TCF4); m=5/5; ncol2=13; w=13; offset=9; strand=D; shift=9; score=0.419426; ---------cggCACCTGccss-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 6048.0 7034.0 4168.0 243.0 27023.0 216.0 356.0 372.0 251.0 1694.0 5534.0 6413.0 5133.0 0 0 c 0 0 0 0 0 0 0 0 0 10052.0 6754.0 5062.0 28686.0 635.0 26765.0 27724.0 1016.0 540.0 18935.0 12872.0 8658.0 9843.0 0 0 g 0 0 0 0 0 0 0 0 0 7140.0 8618.0 18498.0 321.0 1295.0 1733.0 1197.0 679.0 28432.0 5281.0 4933.0 7964.0 7662.0 0 0 t 0 0 0 0 0 0 0 0 0 6225.0 7059.0 1737.0 215.0 512.0 751.0 188.0 27398.0 242.0 3555.0 6126.0 6430.0 6827.0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
local_words_6nt_m5_shift0 (local_words_6nt_m5local_words_6nt_m5)				; local_words_6nt_m5 (local_words_6nt_m5local_words_6nt_m5); m=0 (reference); ncol1=23; shift=0; ncol=24; cwGCtGCTGCaGCAGCTGCcgcc- ; Alignment reference a 4 31 1 4 21 2 3 11 8 3 72 4 0 83 1 1 2 0 1 14 21 10 26 0 c 73 26 8 102 13 3 99 9 2 101 13 1 112 7 1 112 8 6 104 65 25 62 42 0 g 23 26 100 5 13 106 7 12 100 5 7 106 2 4 111 0 5 107 2 14 53 22 27 0 t 14 31 5 3 67 3 5 82 4 5 22 3 0 20 1 1 99 1 7 21 15 20 19 0
MA1529.1_shift6 (NHLH2)				; local_words_6nt_m5 versus MA1529.1 (NHLH2); m=1/5; ncol2=18; w=17; offset=6; strand=D; shift=6; score=0.504967; ------ggGyMGCAGCTGCGyCmc ; cor=; Ncor= a 0 0 0 0 0 0 4834.0 4312.0 3741.0 4921.0 5603.0 2378.0 2.0 21364.0 6.0 525.0 0.0 0.0 693.0 210.0 1184.0 3766.0 6392.0 3601.0 c 0 0 0 0 0 0 2655.0 2219.0 1065.0 6141.0 15451.0 2324.0 21359.0 0.0 2459.0 20268.0 14.0 2.0 20611.0 204.0 7207.0 18351.0 13462.0 11271.0 g 0 0 0 0 0 0 9732.0 13903.0 18450.0 4908.0 671.0 18930.0 2.0 26.0 20096.0 2266.0 3.0 21363.0 275.0 20977.0 1520.0 1183.0 1579.0 2264.0 t 0 0 0 0 0 0 4143.0 5198.0 2763.0 5394.0 151.0 2634.0 5.0 1.0 1054.0 0.0 21358.0 0.0 1230.0 740.0 13503.0 2533.0 3330.0 4228.0
MA0500.2_rc_shift9 (MYOG_rc)				; local_words_6nt_m5 versus MA0500.2_rc (MYOG_rc); m=2/5; ncol2=12; w=12; offset=9; strand=R; shift=9; score=0.450772; ---------sarCAGCTGyts--- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 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 c 0 0 0 0 0 0 0 0 0 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 g 0 0 0 0 0 0 0 0 0 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 t 0 0 0 0 0 0 0 0 0 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
MA1485.1_shift8 (FERD3L)				; local_words_6nt_m5 versus MA1485.1 (FERD3L); m=3/5; ncol2=14; w=14; offset=8; strand=D; shift=8; score=0.448773; --------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
MA1631.1_shift9 (ASCL1(var.2))				; local_words_6nt_m5 versus MA1631.1 (ASCL1(var.2)); m=4/5; ncol2=13; w=13; offset=9; strand=D; shift=9; score=0.431602; ---------cdgCACCTGCysc-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 6833.0 8952.0 5836.0 184.0 32315.0 163.0 196.0 368.0 251.0 399.0 4490.0 7083.0 5972.0 0 0 c 0 0 0 0 0 0 0 0 0 11805.0 7998.0 6654.0 33562.0 563.0 30169.0 33402.0 740.0 445.0 28844.0 17883.0 10555.0 11996.0 0 0 g 0 0 0 0 0 0 0 0 0 8371.0 8601.0 18576.0 321.0 860.0 3209.0 607.0 492.0 33411.0 2719.0 2966.0 8939.0 8356.0 0 0 t 0 0 0 0 0 0 0 0 0 7347.0 8805.0 3290.0 289.0 618.0 815.0 151.0 32756.0 249.0 2394.0 9017.0 7779.0 8032.0 0 0
MA0830.2_shift9 (TCF4)				; local_words_6nt_m5 versus MA0830.2 (TCF4); m=5/5; ncol2=13; w=13; offset=9; strand=D; shift=9; score=0.419426; ---------cggCACCTGccss-- ; cor=; Ncor= a 0 0 0 0 0 0 0 0 0 6048.0 7034.0 4168.0 243.0 27023.0 216.0 356.0 372.0 251.0 1694.0 5534.0 6413.0 5133.0 0 0 c 0 0 0 0 0 0 0 0 0 10052.0 6754.0 5062.0 28686.0 635.0 26765.0 27724.0 1016.0 540.0 18935.0 12872.0 8658.0 9843.0 0 0 g 0 0 0 0 0 0 0 0 0 7140.0 8618.0 18498.0 321.0 1295.0 1733.0 1197.0 679.0 28432.0 5281.0 4933.0 7964.0 7662.0 0 0 t 0 0 0 0 0 0 0 0 0 6225.0 7059.0 1737.0 215.0 512.0 751.0 188.0 27398.0 242.0 3555.0 6126.0 6430.0 6827.0 0 0