One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep1_motifs50/results/discovered_motifs/local_words_6nt_m2/peak-motifs_local_words_6nt_m2.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_m2/peak-motifs_local_words_6nt_m2_vs_db_jaspar_core_nonredundant_vertebrates

One-to-n matrix alignment; reference matrix: local_words_6nt_m2_shift0 ; 5 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
local_words_6nt_m2_shift0 (local_words_6nt_m2local_words_6nt_m2)
; local_words_6nt_m2 (local_words_6nt_m2local_words_6nt_m2); m=0 (reference); ncol1=24; shift=0; ncol=24; dsTGGCAGCAGCTGCTGCCAGCcc ; Alignment reference a 25 12 7 7 7 2 70 3 0 94 3 0 4 0 0 8 2 4 9 77 3 9 18 18 c 16 33 5 4 7 89 8 13 99 1 3 98 0 0 91 3 8 87 82 8 17 72 47 36 g 29 44 10 86 80 8 5 82 0 0 93 2 1 100 5 4 87 5 4 7 73 13 15 23 t 30 11 78 3 6 1 17 2 1 5 1 0 95 0 4 85 3 4 5 8 7 6 20 23

MA1529.1_rc_shift2 (NHLH2_rc)
; local_words_6nt_m2 versus MA1529.1_rc (NHLH2_rc); m=1/4; ncol2=18; w=18; offset=2; strand=R; shift=2; score=0.527886; --gkGrCGCAGCTGCKrCcc---- ; cor=; Ncor= a 0 0 4228.0 3330.0 2533.0 13503.0 740.0 1230.0 0.0 21358.0 0.0 1054.0 1.0 5.0 2634.0 151.0 5394.0 2763.0 5198.0 4143.0 0 0 0 0 c 0 0 2264.0 1579.0 1183.0 1520.0 20977.0 275.0 21363.0 3.0 2266.0 20096.0 26.0 2.0 18930.0 671.0 4908.0 18450.0 13903.0 9732.0 0 0 0 0 g 0 0 11271.0 13462.0 18351.0 7207.0 204.0 20611.0 2.0 14.0 20268.0 2459.0 0.0 21359.0 2324.0 15451.0 6141.0 1065.0 2219.0 2655.0 0 0 0 0 t 0 0 3601.0 6392.0 3766.0 1184.0 210.0 693.0 0.0 0.0 525.0 6.0 21364.0 2.0 2378.0 5603.0 4921.0 3741.0 4312.0 4834.0 0 0 0 0

MA1485.1_shift4 (FERD3L)
; local_words_6nt_m2 versus MA1485.1 (FERD3L); m=2/4; ncol2=14; w=14; offset=4; strand=D; shift=4; score=0.447106; ----GyrmCAGCTGTyAC------ ; cor=; Ncor= a 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 0 0 0 0 c 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 0 0 0 0 g 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 0 0 0 0 t 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 0 0 0 0

MA0500.2_shift5 (MYOG)
; local_words_6nt_m2 versus MA0500.2 (MYOG); m=3/4; ncol2=12; w=12; offset=5; strand=D; shift=5; score=0.427555; -----sarCAGCTGyts------- ; cor=; Ncor= a 0 0 0 0 0 5310.0 8428.0 7159.0 86.0 21782.0 95.0 167.0 163.0 182.0 1667.0 4667.0 5018.0 0 0 0 0 0 0 0 c 0 0 0 0 0 6381.0 3754.0 2730.0 21988.0 176.0 130.0 21964.0 238.0 102.0 10792.0 5497.0 5660.0 0 0 0 0 0 0 0 g 0 0 0 0 0 5596.0 5483.0 10790.0 101.0 236.0 21963.0 131.0 179.0 21985.0 2706.0 3718.0 6369.0 0 0 0 0 0 0 0 t 0 0 0 0 0 5070.0 4692.0 1678.0 182.0 163.0 169.0 95.0 21777.0 88.0 7192.0 8475.0 5310.0 0 0 0 0 0 0 0

MA0832.1_rc_shift4 (Tcf21_rc)
; local_words_6nt_m2 versus MA0832.1_rc (Tcf21_rc); m=4/4; ncol2=14; w=14; offset=4; strand=R; shift=4; score=0.413665; ----ryAACAGCTGTTry------ ; cor=; Ncor= a 0 0 0 0 60.0 19.0 171.0 171.0 0.0 171.0 1.0 2.0 0.0 0.0 0.0 3.0 46.0 17.0 0 0 0 0 0 0 c 0 0 0 0 32.0 80.0 0.0 20.0 171.0 0.0 1.0 171.0 0.0 0.0 0.0 23.0 22.0 70.0 0 0 0 0 0 0 g 0 0 0 0 49.0 23.0 23.0 4.0 0.0 0.0 171.0 0.0 1.0 171.0 10.0 1.0 76.0 29.0 0 0 0 0 0 0 t 0 0 0 0 30.0 50.0 5.0 0.0 0.0 0.0 0.0 0.0 171.0 0.0 171.0 171.0 28.0 55.0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
local_words_6nt_m2_shift0 (local_words_6nt_m2local_words_6nt_m2)				; local_words_6nt_m2 (local_words_6nt_m2local_words_6nt_m2); m=0 (reference); ncol1=24; shift=0; ncol=24; dsTGGCAGCAGCTGCTGCCAGCcc ; Alignment reference a 25 12 7 7 7 2 70 3 0 94 3 0 4 0 0 8 2 4 9 77 3 9 18 18 c 16 33 5 4 7 89 8 13 99 1 3 98 0 0 91 3 8 87 82 8 17 72 47 36 g 29 44 10 86 80 8 5 82 0 0 93 2 1 100 5 4 87 5 4 7 73 13 15 23 t 30 11 78 3 6 1 17 2 1 5 1 0 95 0 4 85 3 4 5 8 7 6 20 23
MA1529.1_rc_shift2 (NHLH2_rc)				; local_words_6nt_m2 versus MA1529.1_rc (NHLH2_rc); m=1/4; ncol2=18; w=18; offset=2; strand=R; shift=2; score=0.527886; --gkGrCGCAGCTGCKrCcc---- ; cor=; Ncor= a 0 0 4228.0 3330.0 2533.0 13503.0 740.0 1230.0 0.0 21358.0 0.0 1054.0 1.0 5.0 2634.0 151.0 5394.0 2763.0 5198.0 4143.0 0 0 0 0 c 0 0 2264.0 1579.0 1183.0 1520.0 20977.0 275.0 21363.0 3.0 2266.0 20096.0 26.0 2.0 18930.0 671.0 4908.0 18450.0 13903.0 9732.0 0 0 0 0 g 0 0 11271.0 13462.0 18351.0 7207.0 204.0 20611.0 2.0 14.0 20268.0 2459.0 0.0 21359.0 2324.0 15451.0 6141.0 1065.0 2219.0 2655.0 0 0 0 0 t 0 0 3601.0 6392.0 3766.0 1184.0 210.0 693.0 0.0 0.0 525.0 6.0 21364.0 2.0 2378.0 5603.0 4921.0 3741.0 4312.0 4834.0 0 0 0 0
MA1485.1_shift4 (FERD3L)				; local_words_6nt_m2 versus MA1485.1 (FERD3L); m=2/4; ncol2=14; w=14; offset=4; strand=D; shift=4; score=0.447106; ----GyrmCAGCTGTyAC------ ; cor=; Ncor= a 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 0 0 0 0 c 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 0 0 0 0 g 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 0 0 0 0 t 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 0 0 0 0
MA0500.2_shift5 (MYOG)				; local_words_6nt_m2 versus MA0500.2 (MYOG); m=3/4; ncol2=12; w=12; offset=5; strand=D; shift=5; score=0.427555; -----sarCAGCTGyts------- ; cor=; Ncor= a 0 0 0 0 0 5310.0 8428.0 7159.0 86.0 21782.0 95.0 167.0 163.0 182.0 1667.0 4667.0 5018.0 0 0 0 0 0 0 0 c 0 0 0 0 0 6381.0 3754.0 2730.0 21988.0 176.0 130.0 21964.0 238.0 102.0 10792.0 5497.0 5660.0 0 0 0 0 0 0 0 g 0 0 0 0 0 5596.0 5483.0 10790.0 101.0 236.0 21963.0 131.0 179.0 21985.0 2706.0 3718.0 6369.0 0 0 0 0 0 0 0 t 0 0 0 0 0 5070.0 4692.0 1678.0 182.0 163.0 169.0 95.0 21777.0 88.0 7192.0 8475.0 5310.0 0 0 0 0 0 0 0
MA0832.1_rc_shift4 (Tcf21_rc)				; local_words_6nt_m2 versus MA0832.1_rc (Tcf21_rc); m=4/4; ncol2=14; w=14; offset=4; strand=R; shift=4; score=0.413665; ----ryAACAGCTGTTry------ ; cor=; Ncor= a 0 0 0 0 60.0 19.0 171.0 171.0 0.0 171.0 1.0 2.0 0.0 0.0 0.0 3.0 46.0 17.0 0 0 0 0 0 0 c 0 0 0 0 32.0 80.0 0.0 20.0 171.0 0.0 1.0 171.0 0.0 0.0 0.0 23.0 22.0 70.0 0 0 0 0 0 0 g 0 0 0 0 49.0 23.0 23.0 4.0 0.0 0.0 171.0 0.0 1.0 171.0 10.0 1.0 76.0 29.0 0 0 0 0 0 0 t 0 0 0 0 30.0 50.0 5.0 0.0 0.0 0.0 0.0 0.0 171.0 0.0 171.0 171.0 28.0 55.0 0 0 0 0 0 0