One-to-n alignments

Command: compare-matrices  -v 1 -mode matches -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2025/05/16/peak-motifs.2025-05-16.184046_2025-05-16.184046_ZEi16E/results/discovered_motifs/oligos_7nt_mkv2_m3/peak-motifs_oligos_7nt_mkv2_m3.tf -format2 tf -file2 $RSAT/public_html/motif_databases/JASPAR/Jaspar_2024/JASPAR2024_CORE_vertebrates_non-redundant_pfms_transfac.txt -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 $RSAT/public_html/tmp/www-data/2025/05/16/peak-motifs.2025-05-16.184046_2025-05-16.184046_ZEi16E/results/discovered_motifs/oligos_7nt_mkv2_m3/peak-motifs_oligos_7nt_mkv2_m3_vs_db_JASPAR2024_CORE_vertebrates_non-redundant

One-to-n matrix alignment; reference matrix: oligos_7nt_mkv2_m3_shift2 ; 13 matrices ; sort_field=Ncor

Matrix name Aligned logos cor Ncor Aligned matrices
oligos_7nt_mkv2_m3_shift2 (oligos_7nt_mkv2_m3)
; oligos_7nt_mkv2_m3; m=0 (reference); ncol1=11; shift=2; ncol=13; --vwCTTGAACty ; Alignment reference a 0 0 6 8 0 1 0 0 21 20 1 5 3 c 0 0 7 3 22 1 2 0 0 0 19 4 11 g 0 0 9 3 0 0 3 21 0 2 0 3 1 t 0 0 0 8 0 20 17 1 1 0 2 10 7

MA1541.2_rc_shift0 (NR6A1_rc)
; oligos_7nt_mkv2_m3 versus MA1541.2_rc (NR6A1_rc); m=1/12; ncol2=14; w=-2; offset=-2; strand=R; shift=0; score=0.638146; YGamCTTGAmCTT ; cor=; Ncor= a 41.0 254.0 896.0 373.0 62.0 65.0 14.0 40.0 896.0 453.0 62.0 51.0 11.0 c 359.0 109.0 355.0 524.0 896.0 35.0 2.0 29.0 26.0 443.0 896.0 72.0 44.0 g 20.0 896.0 185.0 11.0 15.0 96.0 0.0 896.0 74.0 12.0 9.0 91.0 4.0 t 896.0 39.0 91.0 29.0 21.0 896.0 896.0 7.0 1.0 19.0 13.0 896.0 896.0

MA1540.3_rc_shift0 (NR5A1_rc)
; oligos_7nt_mkv2_m3 versus MA1540.3_rc (NR5A1_rc); m=2/12; ncol2=12; w=-2; offset=-2; strand=R; shift=0; score=0.632868; TGaCCTTGAact- ; cor=; Ncor= a 198.0 247.0 3173.0 117.0 85.0 111.0 92.0 120.0 3843.0 2845.0 606.0 721.0 0 c 154.0 112.0 171.0 4440.0 4461.0 160.0 125.0 189.0 130.0 729.0 2825.0 633.0 0 g 144.0 4271.0 964.0 53.0 45.0 86.0 193.0 4316.0 564.0 747.0 558.0 398.0 0 t 4201.0 67.0 389.0 87.0 106.0 4340.0 4287.0 72.0 160.0 376.0 708.0 2945.0 0

MA0693.4_rc_shift6 (Vdr_rc)
; oligos_7nt_mkv2_m3 versus MA0693.4_rc (Vdr_rc); m=3/12; ncol2=7; w=0; offset=4; strand=R; shift=6; score=0.60031; ------TGAACTc ; cor=; Ncor= a 0 0 0 0 0 0 750.0 2057.0 35628.0 35489.0 1110.0 813.0 2150.0 c 0 0 0 0 0 0 826.0 406.0 574.0 1555.0 36028.0 1137.0 25359.0 g 0 0 0 0 0 0 661.0 34477.0 655.0 520.0 599.0 644.0 4678.0 t 0 0 0 0 0 0 36305.0 1602.0 1685.0 978.0 805.0 35948.0 6355.0

MA1581.2_shift3 (ZBTB6)
; oligos_7nt_mkv2_m3 versus MA1581.2 (ZBTB6); m=4/12; ncol2=9; w=0; offset=1; strand=D; shift=3; score=0.595776; ---sCTTGAGCC- ; cor=; Ncor= a 0 0 0 312.0 94.0 29.0 207.0 13.0 2158.0 58.0 56.0 102.0 0 c 0 0 0 1157.0 2080.0 104.0 45.0 59.0 28.0 20.0 2087.0 1814.0 0 g 0 0 0 593.0 25.0 52.0 409.0 2148.0 20.0 2135.0 38.0 88.0 0 t 0 0 0 165.0 28.0 2042.0 1566.0 7.0 21.0 14.0 46.0 223.0 0

MA1649.2_shift4 (ZBTB12)
; oligos_7nt_mkv2_m3 versus MA1649.2 (ZBTB12); m=5/12; ncol2=7; w=0; offset=2; strand=D; shift=4; score=0.559933; ----CTrGAAC-- ; cor=; Ncor= a 0 0 0 0 144.0 130.0 1841.0 86.0 4475.0 4508.0 51.0 0 0 c 0 0 0 0 4377.0 216.0 73.0 80.0 114.0 65.0 4511.0 0 0 g 0 0 0 0 175.0 190.0 2797.0 4478.0 106.0 103.0 50.0 0 0 t 0 0 0 0 71.0 4231.0 56.0 123.0 72.0 91.0 155.0 0 0

MA1994.2_shift2 (Nkx2-1)
; oligos_7nt_mkv2_m3 versus MA1994.2 (Nkx2-1); m=6/12; ncol2=7; w=0; offset=0; strand=D; shift=2; score=0.54592; --CACTTGA---- ; cor=; Ncor= a 0 0 289.0 15478.0 168.0 369.0 252.0 895.0 15245.0 0 0 0 0 c 0 0 14886.0 275.0 15640.0 162.0 518.0 657.0 243.0 0 0 0 0 g 0 0 181.0 146.0 118.0 605.0 315.0 14172.0 213.0 0 0 0 0 t 0 0 886.0 343.0 316.0 15106.0 15157.0 518.0 541.0 0 0 0 0

MA1534.2_shift6 (NR1I3)
; oligos_7nt_mkv2_m3 versus MA1534.2 (NR1I3); m=7/12; ncol2=8; w=0; offset=4; strand=D; shift=6; score=0.538472; ------TGAACTt ; cor=; Ncor= a 0 0 0 0 0 0 162.0 6626.0 48424.0 48424.0 0.0 0.0 14101.0 c 0 0 0 0 0 0 11168.0 100.0 2613.0 2972.0 48424.0 1870.0 15443.0 g 0 0 0 0 0 0 0.0 48424.0 342.0 0.0 0.0 0.0 3267.0 t 0 0 0 0 0 0 48424.0 0.0 791.0 0.0 0.0 48424.0 34323.0

MA2003.2_shift1 (NKX2-4)
; oligos_7nt_mkv2_m3 versus MA2003.2 (NKX2-4); m=8/12; ncol2=8; w=-1; offset=-1; strand=D; shift=1; score=0.463379; -cCACTTsA---- ; cor=; Ncor= a 0 385.0 14.0 1185.0 0.0 0.0 52.0 243.0 1185.0 0 0 0 0 c 0 1185.0 1185.0 127.0 1185.0 25.0 409.0 545.0 56.0 0 0 0 0 g 0 485.0 7.0 17.0 0.0 1.0 13.0 640.0 57.0 0 0 0 0 t 0 61.0 129.0 207.0 0.0 1185.0 1185.0 58.0 153.0 0 0 0 0

MA0673.2_shift1 (NKX2-8)
; oligos_7nt_mkv2_m3 versus MA0673.2 (NKX2-8); m=9/12; ncol2=8; w=-1; offset=-1; strand=D; shift=1; score=0.456893; -sCACTYsA---- ; cor=; Ncor= a 0 1942.0 70.0 8562.0 14.0 0.0 23.0 1738.0 8562.0 0 0 0 0 c 0 3529.0 8562.0 595.0 8562.0 91.0 3197.0 2267.0 908.0 0 0 0 0 g 0 2843.0 0.0 0.0 0.0 0.0 0.0 4286.0 696.0 0 0 0 0 t 0 249.0 2155.0 516.0 110.0 8562.0 8562.0 271.0 2158.0 0 0 0 0

MA0505.3_shift0 (Nr5A2)
; oligos_7nt_mkv2_m3 versus MA0505.3 (Nr5A2); m=10/12; ncol2=9; w=-2; offset=-2; strand=D; shift=0; score=0.444951; TGaCCTTGA---- ; cor=; Ncor= a 4020.0 2032.0 19888.0 327.0 299.0 364.0 266.0 340.0 26370.0 0 0 0 0 c 3118.0 869.0 1185.0 29854.0 29734.0 694.0 338.0 870.0 645.0 0 0 0 0 g 2303.0 27158.0 6736.0 124.0 166.0 359.0 285.0 29010.0 2402.0 0 0 0 0 t 21101.0 483.0 2733.0 237.0 343.0 29125.0 29653.0 322.0 1125.0 0 0 0 0

MA0672.2_shift1 (NKX2-3)
; oligos_7nt_mkv2_m3 versus MA0672.2 (NKX2-3); m=11/12; ncol2=8; w=-1; offset=-1; strand=D; shift=1; score=0.436016; -sCACTTra---- ; cor=; Ncor= a 0 2025.0 38.0 9278.0 8.0 0.0 0.0 4241.0 9278.0 0 0 0 0 c 0 9278.0 9278.0 98.0 9278.0 0.0 939.0 1451.0 917.0 0 0 0 0 g 0 4499.0 0.0 16.0 0.0 18.0 0.0 5037.0 1831.0 0 0 0 0 t 0 140.0 132.0 250.0 0.0 9278.0 9278.0 343.0 2437.0 0 0 0 0

MA1536.2_rc_shift6 (NR2C2_rc)
; oligos_7nt_mkv2_m3 versus MA1536.2_rc (NR2C2_rc); m=12/12; ncol2=6; w=0; offset=4; strand=R; shift=6; score=0.403463; ------YGACCy- ; cor=; Ncor= a 0 0 0 0 0 0 0.0 4406.0 18628.0 4790.0 1341.0 0.0 0 c 0 0 0 0 0 0 6639.0 1643.0 1588.0 18628.0 18628.0 8395.0 0 g 0 0 0 0 0 0 0.0 18628.0 0.0 0.0 236.0 719.0 0 t 0 0 0 0 0 0 18628.0 0.0 0.0 0.0 0.0 10232.0 0

Matrix name	Aligned logos	cor	Ncor	Aligned matrices
oligos_7nt_mkv2_m3_shift2 (oligos_7nt_mkv2_m3)				; oligos_7nt_mkv2_m3; m=0 (reference); ncol1=11; shift=2; ncol=13; --vwCTTGAACty ; Alignment reference a 0 0 6 8 0 1 0 0 21 20 1 5 3 c 0 0 7 3 22 1 2 0 0 0 19 4 11 g 0 0 9 3 0 0 3 21 0 2 0 3 1 t 0 0 0 8 0 20 17 1 1 0 2 10 7
MA1541.2_rc_shift0 (NR6A1_rc)				; oligos_7nt_mkv2_m3 versus MA1541.2_rc (NR6A1_rc); m=1/12; ncol2=14; w=-2; offset=-2; strand=R; shift=0; score=0.638146; YGamCTTGAmCTT ; cor=; Ncor= a 41.0 254.0 896.0 373.0 62.0 65.0 14.0 40.0 896.0 453.0 62.0 51.0 11.0 c 359.0 109.0 355.0 524.0 896.0 35.0 2.0 29.0 26.0 443.0 896.0 72.0 44.0 g 20.0 896.0 185.0 11.0 15.0 96.0 0.0 896.0 74.0 12.0 9.0 91.0 4.0 t 896.0 39.0 91.0 29.0 21.0 896.0 896.0 7.0 1.0 19.0 13.0 896.0 896.0
MA1540.3_rc_shift0 (NR5A1_rc)				; oligos_7nt_mkv2_m3 versus MA1540.3_rc (NR5A1_rc); m=2/12; ncol2=12; w=-2; offset=-2; strand=R; shift=0; score=0.632868; TGaCCTTGAact- ; cor=; Ncor= a 198.0 247.0 3173.0 117.0 85.0 111.0 92.0 120.0 3843.0 2845.0 606.0 721.0 0 c 154.0 112.0 171.0 4440.0 4461.0 160.0 125.0 189.0 130.0 729.0 2825.0 633.0 0 g 144.0 4271.0 964.0 53.0 45.0 86.0 193.0 4316.0 564.0 747.0 558.0 398.0 0 t 4201.0 67.0 389.0 87.0 106.0 4340.0 4287.0 72.0 160.0 376.0 708.0 2945.0 0
MA0693.4_rc_shift6 (Vdr_rc)				; oligos_7nt_mkv2_m3 versus MA0693.4_rc (Vdr_rc); m=3/12; ncol2=7; w=0; offset=4; strand=R; shift=6; score=0.60031; ------TGAACTc ; cor=; Ncor= a 0 0 0 0 0 0 750.0 2057.0 35628.0 35489.0 1110.0 813.0 2150.0 c 0 0 0 0 0 0 826.0 406.0 574.0 1555.0 36028.0 1137.0 25359.0 g 0 0 0 0 0 0 661.0 34477.0 655.0 520.0 599.0 644.0 4678.0 t 0 0 0 0 0 0 36305.0 1602.0 1685.0 978.0 805.0 35948.0 6355.0
MA1581.2_shift3 (ZBTB6)				; oligos_7nt_mkv2_m3 versus MA1581.2 (ZBTB6); m=4/12; ncol2=9; w=0; offset=1; strand=D; shift=3; score=0.595776; ---sCTTGAGCC- ; cor=; Ncor= a 0 0 0 312.0 94.0 29.0 207.0 13.0 2158.0 58.0 56.0 102.0 0 c 0 0 0 1157.0 2080.0 104.0 45.0 59.0 28.0 20.0 2087.0 1814.0 0 g 0 0 0 593.0 25.0 52.0 409.0 2148.0 20.0 2135.0 38.0 88.0 0 t 0 0 0 165.0 28.0 2042.0 1566.0 7.0 21.0 14.0 46.0 223.0 0
MA1649.2_shift4 (ZBTB12)				; oligos_7nt_mkv2_m3 versus MA1649.2 (ZBTB12); m=5/12; ncol2=7; w=0; offset=2; strand=D; shift=4; score=0.559933; ----CTrGAAC-- ; cor=; Ncor= a 0 0 0 0 144.0 130.0 1841.0 86.0 4475.0 4508.0 51.0 0 0 c 0 0 0 0 4377.0 216.0 73.0 80.0 114.0 65.0 4511.0 0 0 g 0 0 0 0 175.0 190.0 2797.0 4478.0 106.0 103.0 50.0 0 0 t 0 0 0 0 71.0 4231.0 56.0 123.0 72.0 91.0 155.0 0 0
MA1994.2_shift2 (Nkx2-1)				; oligos_7nt_mkv2_m3 versus MA1994.2 (Nkx2-1); m=6/12; ncol2=7; w=0; offset=0; strand=D; shift=2; score=0.54592; --CACTTGA---- ; cor=; Ncor= a 0 0 289.0 15478.0 168.0 369.0 252.0 895.0 15245.0 0 0 0 0 c 0 0 14886.0 275.0 15640.0 162.0 518.0 657.0 243.0 0 0 0 0 g 0 0 181.0 146.0 118.0 605.0 315.0 14172.0 213.0 0 0 0 0 t 0 0 886.0 343.0 316.0 15106.0 15157.0 518.0 541.0 0 0 0 0
MA1534.2_shift6 (NR1I3)				; oligos_7nt_mkv2_m3 versus MA1534.2 (NR1I3); m=7/12; ncol2=8; w=0; offset=4; strand=D; shift=6; score=0.538472; ------TGAACTt ; cor=; Ncor= a 0 0 0 0 0 0 162.0 6626.0 48424.0 48424.0 0.0 0.0 14101.0 c 0 0 0 0 0 0 11168.0 100.0 2613.0 2972.0 48424.0 1870.0 15443.0 g 0 0 0 0 0 0 0.0 48424.0 342.0 0.0 0.0 0.0 3267.0 t 0 0 0 0 0 0 48424.0 0.0 791.0 0.0 0.0 48424.0 34323.0
MA2003.2_shift1 (NKX2-4)				; oligos_7nt_mkv2_m3 versus MA2003.2 (NKX2-4); m=8/12; ncol2=8; w=-1; offset=-1; strand=D; shift=1; score=0.463379; -cCACTTsA---- ; cor=; Ncor= a 0 385.0 14.0 1185.0 0.0 0.0 52.0 243.0 1185.0 0 0 0 0 c 0 1185.0 1185.0 127.0 1185.0 25.0 409.0 545.0 56.0 0 0 0 0 g 0 485.0 7.0 17.0 0.0 1.0 13.0 640.0 57.0 0 0 0 0 t 0 61.0 129.0 207.0 0.0 1185.0 1185.0 58.0 153.0 0 0 0 0
MA0673.2_shift1 (NKX2-8)				; oligos_7nt_mkv2_m3 versus MA0673.2 (NKX2-8); m=9/12; ncol2=8; w=-1; offset=-1; strand=D; shift=1; score=0.456893; -sCACTYsA---- ; cor=; Ncor= a 0 1942.0 70.0 8562.0 14.0 0.0 23.0 1738.0 8562.0 0 0 0 0 c 0 3529.0 8562.0 595.0 8562.0 91.0 3197.0 2267.0 908.0 0 0 0 0 g 0 2843.0 0.0 0.0 0.0 0.0 0.0 4286.0 696.0 0 0 0 0 t 0 249.0 2155.0 516.0 110.0 8562.0 8562.0 271.0 2158.0 0 0 0 0
MA0505.3_shift0 (Nr5A2)				; oligos_7nt_mkv2_m3 versus MA0505.3 (Nr5A2); m=10/12; ncol2=9; w=-2; offset=-2; strand=D; shift=0; score=0.444951; TGaCCTTGA---- ; cor=; Ncor= a 4020.0 2032.0 19888.0 327.0 299.0 364.0 266.0 340.0 26370.0 0 0 0 0 c 3118.0 869.0 1185.0 29854.0 29734.0 694.0 338.0 870.0 645.0 0 0 0 0 g 2303.0 27158.0 6736.0 124.0 166.0 359.0 285.0 29010.0 2402.0 0 0 0 0 t 21101.0 483.0 2733.0 237.0 343.0 29125.0 29653.0 322.0 1125.0 0 0 0 0
MA0672.2_shift1 (NKX2-3)				; oligos_7nt_mkv2_m3 versus MA0672.2 (NKX2-3); m=11/12; ncol2=8; w=-1; offset=-1; strand=D; shift=1; score=0.436016; -sCACTTra---- ; cor=; Ncor= a 0 2025.0 38.0 9278.0 8.0 0.0 0.0 4241.0 9278.0 0 0 0 0 c 0 9278.0 9278.0 98.0 9278.0 0.0 939.0 1451.0 917.0 0 0 0 0 g 0 4499.0 0.0 16.0 0.0 18.0 0.0 5037.0 1831.0 0 0 0 0 t 0 140.0 132.0 250.0 0.0 9278.0 9278.0 343.0 2437.0 0 0 0 0
MA1536.2_rc_shift6 (NR2C2_rc)				; oligos_7nt_mkv2_m3 versus MA1536.2_rc (NR2C2_rc); m=12/12; ncol2=6; w=0; offset=4; strand=R; shift=6; score=0.403463; ------YGACCy- ; cor=; Ncor= a 0 0 0 0 0 0 0.0 4406.0 18628.0 4790.0 1341.0 0.0 0 c 0 0 0 0 0 0 6639.0 1643.0 1588.0 18628.0 18628.0 8395.0 0 g 0 0 0 0 0 0 0.0 18628.0 0.0 0.0 236.0 719.0 0 t 0 0 0 0 0 0 18628.0 0.0 0.0 0.0 0.0 10232.0 0