One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 Myogenin_Rep1_motifs50/results/discovered_motifs/local_words_6nt_m21/peak-motifs_local_words_6nt_m21.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_m21/peak-motifs_local_words_6nt_m21_vs_db_jaspar_core_nonredundant_vertebrates

One-to-n matrix alignment; reference matrix: local_words_6nt_m21_shift0 ; 7 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
local_words_6nt_m21_shift0 (local_words_6nt_m21local_words_6nt_m21)
; local_words_6nt_m21 (local_words_6nt_m21local_words_6nt_m21); m=0 (reference); ncol1=24; shift=0; ncol=24; sysmCCACAGCTGTCACAGGTGbc ; Alignment reference a 6 9 4 21 3 6 32 0 40 0 0 1 0 0 3 36 0 33 1 0 3 3 5 7 c 12 13 17 10 30 28 3 37 0 2 37 2 0 4 31 1 36 2 2 9 2 2 10 15 g 13 6 10 6 2 2 2 2 0 38 2 0 39 2 4 1 3 2 35 28 4 35 12 9 t 9 12 9 3 5 4 3 1 0 0 1 37 1 34 2 2 1 3 2 3 31 0 13 9

MA1485.1_shift3 (FERD3L)
; local_words_6nt_m21 versus MA1485.1 (FERD3L); m=1/6; ncol2=14; w=14; offset=3; strand=D; shift=3; score=0.483539; ---GyrmCAGCTGTyAC------- ; cor=; Ncor= a 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 0 c 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 0 g 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 0 t 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 0

MA0832.1_rc_shift3 (Tcf21_rc)
; local_words_6nt_m21 versus MA0832.1_rc (Tcf21_rc); m=2/6; ncol2=14; w=14; offset=3; strand=R; shift=3; score=0.444995; ---ryAACAGCTGTTry------- ; cor=; Ncor= a 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 0 c 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 0 g 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 0 t 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 0

MA1641.1_shift4 (MYF5)
; local_words_6nt_m21 versus MA1641.1 (MYF5); m=3/6; ncol2=12; w=12; offset=4; strand=D; shift=4; score=0.429657; ----gvaCAGCTGtbc-------- ; cor=; Ncor= a 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 0 0 0 0 0 c 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 0 0 0 0 0 g 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 0 0 0 0 0 t 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 0 0 0 0 0

MA1619.1_shift4 (Ptf1a(var.2))
; local_words_6nt_m21 versus MA1619.1 (Ptf1a(var.2)); m=4/6; ncol2=12; w=12; offset=4; strand=D; shift=4; score=0.427179; ----rmaCAGCTGtky-------- ; cor=; Ncor= a 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 0 0 0 0 0 c 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 0 0 0 0 0 g 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 0 0 0 0 0 t 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 0 0 0 0 0

MA1621.1_shift3 (Rbpjl)
; local_words_6nt_m21 versus MA1621.1 (Rbpjl); m=5/6; ncol2=14; w=14; offset=3; strand=D; shift=3; score=0.409778; ---svmaCACCTGtsyc------- ; cor=; Ncor= a 0 0 0 2006.0 2466.0 3369.0 6005.0 139.0 9386.0 84.0 234.0 63.0 102.0 569.0 1539.0 2273.0 2082.0 0 0 0 0 0 0 0 c 0 0 0 2881.0 2427.0 3117.0 1373.0 9273.0 70.0 8533.0 9005.0 144.0 131.0 1718.0 3247.0 2884.0 3003.0 0 0 0 0 0 0 0 g 0 0 0 2476.0 2549.0 1802.0 1492.0 103.0 110.0 672.0 317.0 132.0 9295.0 1581.0 2687.0 1958.0 2281.0 0 0 0 0 0 0 0 t 0 0 0 2289.0 2210.0 1364.0 782.0 137.0 86.0 363.0 96.0 9313.0 124.0 5784.0 2179.0 2537.0 2286.0 0 0 0 0 0 0 0

MA0796.1_rc_shift4 (TGIF1_rc)
; local_words_6nt_m21 versus MA0796.1_rc (TGIF1_rc); m=6/6; ncol2=12; w=12; offset=4; strand=R; shift=4; score=0.403652; ----TGACAGCTGTCA-------- ; cor=; Ncor= a 0 0 0 0 33.0 17.0 12656.0 9.0 12775.0 12.0 963.0 4.0 7.0 0.0 4.0 13221.0 0 0 0 0 0 0 0 0 c 0 0 0 0 32.0 13.0 3.0 13261.0 8.0 2520.0 12673.0 22.0 5.0 20.0 13499.0 1.0 0 0 0 0 0 0 0 0 g 0 0 0 0 17.0 13485.0 24.0 13.0 62.0 10562.0 20.0 5.0 13304.0 3.0 8.0 19.0 0 0 0 0 0 0 0 0 t 0 0 0 0 9034.0 36.0 45.0 11.0 1.0 452.0 14.0 8861.0 1.0 8828.0 9.0 39.0 0 0 0 0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
local_words_6nt_m21_shift0 (local_words_6nt_m21local_words_6nt_m21)				; local_words_6nt_m21 (local_words_6nt_m21local_words_6nt_m21); m=0 (reference); ncol1=24; shift=0; ncol=24; sysmCCACAGCTGTCACAGGTGbc ; Alignment reference a 6 9 4 21 3 6 32 0 40 0 0 1 0 0 3 36 0 33 1 0 3 3 5 7 c 12 13 17 10 30 28 3 37 0 2 37 2 0 4 31 1 36 2 2 9 2 2 10 15 g 13 6 10 6 2 2 2 2 0 38 2 0 39 2 4 1 3 2 35 28 4 35 12 9 t 9 12 9 3 5 4 3 1 0 0 1 37 1 34 2 2 1 3 2 3 31 0 13 9
MA1485.1_shift3 (FERD3L)				; local_words_6nt_m21 versus MA1485.1 (FERD3L); m=1/6; ncol2=14; w=14; offset=3; strand=D; shift=3; score=0.483539; ---GyrmCAGCTGTyAC------- ; cor=; Ncor= a 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 0 c 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 0 g 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 0 t 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 0
MA0832.1_rc_shift3 (Tcf21_rc)				; local_words_6nt_m21 versus MA0832.1_rc (Tcf21_rc); m=2/6; ncol2=14; w=14; offset=3; strand=R; shift=3; score=0.444995; ---ryAACAGCTGTTry------- ; cor=; Ncor= a 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 0 c 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 0 g 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 0 t 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 0
MA1641.1_shift4 (MYF5)				; local_words_6nt_m21 versus MA1641.1 (MYF5); m=3/6; ncol2=12; w=12; offset=4; strand=D; shift=4; score=0.429657; ----gvaCAGCTGtbc-------- ; cor=; Ncor= a 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 0 0 0 0 0 c 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 0 0 0 0 0 g 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 0 0 0 0 0 t 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 0 0 0 0 0
MA1619.1_shift4 (Ptf1a(var.2))				; local_words_6nt_m21 versus MA1619.1 (Ptf1a(var.2)); m=4/6; ncol2=12; w=12; offset=4; strand=D; shift=4; score=0.427179; ----rmaCAGCTGtky-------- ; cor=; Ncor= a 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 0 0 0 0 0 c 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 0 0 0 0 0 g 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 0 0 0 0 0 t 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 0 0 0 0 0
MA1621.1_shift3 (Rbpjl)				; local_words_6nt_m21 versus MA1621.1 (Rbpjl); m=5/6; ncol2=14; w=14; offset=3; strand=D; shift=3; score=0.409778; ---svmaCACCTGtsyc------- ; cor=; Ncor= a 0 0 0 2006.0 2466.0 3369.0 6005.0 139.0 9386.0 84.0 234.0 63.0 102.0 569.0 1539.0 2273.0 2082.0 0 0 0 0 0 0 0 c 0 0 0 2881.0 2427.0 3117.0 1373.0 9273.0 70.0 8533.0 9005.0 144.0 131.0 1718.0 3247.0 2884.0 3003.0 0 0 0 0 0 0 0 g 0 0 0 2476.0 2549.0 1802.0 1492.0 103.0 110.0 672.0 317.0 132.0 9295.0 1581.0 2687.0 1958.0 2281.0 0 0 0 0 0 0 0 t 0 0 0 2289.0 2210.0 1364.0 782.0 137.0 86.0 363.0 96.0 9313.0 124.0 5784.0 2179.0 2537.0 2286.0 0 0 0 0 0 0 0
MA0796.1_rc_shift4 (TGIF1_rc)				; local_words_6nt_m21 versus MA0796.1_rc (TGIF1_rc); m=6/6; ncol2=12; w=12; offset=4; strand=R; shift=4; score=0.403652; ----TGACAGCTGTCA-------- ; cor=; Ncor= a 0 0 0 0 33.0 17.0 12656.0 9.0 12775.0 12.0 963.0 4.0 7.0 0.0 4.0 13221.0 0 0 0 0 0 0 0 0 c 0 0 0 0 32.0 13.0 3.0 13261.0 8.0 2520.0 12673.0 22.0 5.0 20.0 13499.0 1.0 0 0 0 0 0 0 0 0 g 0 0 0 0 17.0 13485.0 24.0 13.0 62.0 10562.0 20.0 5.0 13304.0 3.0 8.0 19.0 0 0 0 0 0 0 0 0 t 0 0 0 0 9034.0 36.0 45.0 11.0 1.0 452.0 14.0 8861.0 1.0 8828.0 9.0 39.0 0 0 0 0 0 0 0 0