One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep1_motifs50/results/discovered_motifs/local_words_6nt_m8/peak-motifs_local_words_6nt_m8.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_m8/peak-motifs_local_words_6nt_m8_vs_db_jaspar_core_nonredundant_vertebrates

One-to-n matrix alignment; reference matrix: local_words_6nt_m8_shift0 ; 4 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
local_words_6nt_m8_shift0 (local_words_6nt_m8local_words_6nt_m8)
; local_words_6nt_m8 (local_words_6nt_m8local_words_6nt_m8); m=0 (reference); ncol1=24; shift=0; ncol=24; dsaGCTGGCAGCAGCTGCAGCcrc ; Alignment reference a 15 11 30 2 3 1 1 3 1 43 1 0 44 1 0 1 0 1 39 0 1 4 20 4 c 8 20 4 0 41 6 2 0 45 1 1 51 2 0 48 1 2 43 5 0 46 30 12 24 g 15 15 12 46 4 9 45 46 2 4 49 0 0 49 2 2 49 7 5 49 2 10 13 12 t 13 5 5 3 3 35 3 2 3 3 0 0 5 1 1 47 0 0 2 2 2 7 6 11

MA1529.1_shift5 (NHLH2)
; local_words_6nt_m8 versus MA1529.1 (NHLH2); m=1/3; ncol2=18; w=18; offset=5; strand=D; shift=5; score=0.532292; -----ggGyMGCAGCTGCGyCmc- ; cor=; Ncor= a 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 0 c 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 0 g 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 0 t 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 0

MA1485.1_rc_shift7 (FERD3L_rc)
; local_words_6nt_m8 versus MA1485.1_rc (FERD3L_rc); m=2/3; ncol2=14; w=14; offset=7; strand=R; shift=7; score=0.418293; -------GTrACAGCTGkyrC--- ; cor=; Ncor= a 0 0 0 0 0 0 0 48.0 958.0 14919.0 21065.0 0.0 29605.0 0.0 4691.0 144.0 0.0 1710.0 74.0 9557.0 225.0 0 0 0 c 0 0 0 0 0 0 0 0.0 9815.0 5920.0 3395.0 29605.0 210.0 471.0 29605.0 118.0 0.0 3142.0 12703.0 348.0 29605.0 0 0 0 g 0 0 0 0 0 0 0 29605.0 809.0 8664.0 3878.0 0.0 129.0 29605.0 841.0 126.0 29605.0 9363.0 2443.0 20049.0 68.0 0 0 0 t 0 0 0 0 0 0 0 0.0 29605.0 103.0 1268.0 0.0 81.0 3649.0 0.0 29605.0 36.0 15390.0 14384.0 450.0 2158.0 0 0 0

MA0500.2_rc_shift8 (MYOG_rc)
; local_words_6nt_m8 versus MA0500.2_rc (MYOG_rc); m=3/3; ncol2=12; w=12; offset=8; strand=R; shift=8; score=0.404663; --------sarCAGCTGyts---- ; cor=; Ncor= a 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 0 c 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 0 g 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 0 t 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 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
local_words_6nt_m8_shift0 (local_words_6nt_m8local_words_6nt_m8)				; local_words_6nt_m8 (local_words_6nt_m8local_words_6nt_m8); m=0 (reference); ncol1=24; shift=0; ncol=24; dsaGCTGGCAGCAGCTGCAGCcrc ; Alignment reference a 15 11 30 2 3 1 1 3 1 43 1 0 44 1 0 1 0 1 39 0 1 4 20 4 c 8 20 4 0 41 6 2 0 45 1 1 51 2 0 48 1 2 43 5 0 46 30 12 24 g 15 15 12 46 4 9 45 46 2 4 49 0 0 49 2 2 49 7 5 49 2 10 13 12 t 13 5 5 3 3 35 3 2 3 3 0 0 5 1 1 47 0 0 2 2 2 7 6 11
MA1529.1_shift5 (NHLH2)				; local_words_6nt_m8 versus MA1529.1 (NHLH2); m=1/3; ncol2=18; w=18; offset=5; strand=D; shift=5; score=0.532292; -----ggGyMGCAGCTGCGyCmc- ; cor=; Ncor= a 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 0 c 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 0 g 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 0 t 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 0
MA1485.1_rc_shift7 (FERD3L_rc)				; local_words_6nt_m8 versus MA1485.1_rc (FERD3L_rc); m=2/3; ncol2=14; w=14; offset=7; strand=R; shift=7; score=0.418293; -------GTrACAGCTGkyrC--- ; cor=; Ncor= a 0 0 0 0 0 0 0 48.0 958.0 14919.0 21065.0 0.0 29605.0 0.0 4691.0 144.0 0.0 1710.0 74.0 9557.0 225.0 0 0 0 c 0 0 0 0 0 0 0 0.0 9815.0 5920.0 3395.0 29605.0 210.0 471.0 29605.0 118.0 0.0 3142.0 12703.0 348.0 29605.0 0 0 0 g 0 0 0 0 0 0 0 29605.0 809.0 8664.0 3878.0 0.0 129.0 29605.0 841.0 126.0 29605.0 9363.0 2443.0 20049.0 68.0 0 0 0 t 0 0 0 0 0 0 0 0.0 29605.0 103.0 1268.0 0.0 81.0 3649.0 0.0 29605.0 36.0 15390.0 14384.0 450.0 2158.0 0 0 0
MA0500.2_rc_shift8 (MYOG_rc)				; local_words_6nt_m8 versus MA0500.2_rc (MYOG_rc); m=3/3; ncol2=12; w=12; offset=8; strand=R; shift=8; score=0.404663; --------sarCAGCTGyts---- ; cor=; Ncor= a 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 0 c 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 0 g 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 0 t 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 0