One-to-n alignments

Command: compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/03/30/compare-matrices_2026-03-30.174248_p7BlRJ/compare-matrices_query_matrices.transfac -file2 $RSAT/public_html/motif_databases/JASPAR/Jaspar_2024/JASPAR2024_CORE_vertebrates_non-redundant_pfms_transfac.txt -format2 tf -strand DR -lth cor 0.7 -lth Ncor 0.4 -uth match_rank 50 -return cor,Ncor,logoDP,NsEucl,NSW,match_rank,matrix_id,matrix_name,width,strand,offset,consensus,alignments_1ton -o $RSAT/public_html/tmp/www-data/2026/03/30/compare-matrices_2026-03-30.174248_p7BlRJ/compare-matrices.tab

One-to-n matrix alignment; reference matrix: assembly_5_shift4 ; 20 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NsEucl NSW rcor rNcor rlogoDP rNsEucl rNSW rank_mean match_rank Aligned matrices
assembly_5_shift4 (assembly_5)
; assembly_5; m=0 (reference); ncol1=10; shift=4; ncol=14; ----gsCCAGGArg ; Alignment reference a 0 0 0 0 6 4 0 0 25 0 0 25 9 6 c 0 0 0 0 5 7 25 25 0 0 0 0 5 6 g 0 0 0 0 8 10 0 0 0 25 25 0 7 8 t 0 0 0 0 6 4 0 0 0 0 0 0 4 5

MA1992.2_shift7 (Ikzf3) 0.895 0.522 7.011 0.908 0.940 1 13 4 3 2 4.600 1
; assembly_5 versus MA1992.2 (Ikzf3); m=1/19; ncol2=9; w=0; offset=3; strand=D; shift=7; score= 4.6; -------CAGGAAG ; cor=0.895; Ncor=0.522; logoDP=7.011; NsEucl=0.908; NSW=0.940; rcor=1; rNcor=13; rlogoDP=4; rNsEucl=3; rNSW=2; rank_mean=4.600; match_rank=1 a 0 0 0 0 0 0 0 51.0 1054.0 4.0 18.0 1130.0 1058.0 102.0 c 0 0 0 0 0 0 0 998.0 62.0 7.0 16.0 25.0 12.0 45.0 g 0 0 0 0 0 0 0 103.0 48.0 1166.0 1141.0 22.0 20.0 1011.0 t 0 0 0 0 0 0 0 31.0 19.0 6.0 8.0 6.0 93.0 25.0

MA0473.4_shift7 (ELF1) 0.880 0.513 6.742 0.901 0.931 2 16 6 5 4 6.600 2
; assembly_5 versus MA0473.4 (ELF1); m=2/19; ncol2=9; w=0; offset=3; strand=D; shift=7; score= 6.6; -------CAGGAAG ; cor=0.880; Ncor=0.513; logoDP=6.742; NsEucl=0.901; NSW=0.931; rcor=2; rNcor=16; rlogoDP=6; rNsEucl=5; rNSW=4; rank_mean=6.600; match_rank=2 a 0 0 0 0 0 0 0 3094.0 42164.0 320.0 649.0 45930.0 45243.0 4063.0 c 0 0 0 0 0 0 0 37923.0 4038.0 421.0 505.0 796.0 705.0 1570.0 g 0 0 0 0 0 0 0 4819.0 932.0 46642.0 45970.0 676.0 779.0 41738.0 t 0 0 0 0 0 0 0 1934.0 636.0 387.0 646.0 368.0 1043.0 399.0

MA2330.1_shift5 (ZBTB24) 0.832 0.681 5.293 0.906 0.920 11 2 14 4 7 7.600 3
; assembly_5 versus MA2330.1 (ZBTB24); m=3/19; ncol2=10; w=0; offset=1; strand=D; shift=5; score= 7.6; -----cCCAGGACC ; cor=0.832; Ncor=0.681; logoDP=5.293; NsEucl=0.906; NSW=0.920; rcor=11; rNcor=2; rlogoDP=14; rNsEucl=4; rNSW=7; rank_mean=7.600; match_rank=3 a 0 0 0 0 0 65.0 58.0 28.0 667.0 25.0 49.0 629.0 41.0 84.0 c 0 0 0 0 0 534.0 662.0 750.0 53.0 35.0 67.0 70.0 705.0 641.0 g 0 0 0 0 0 127.0 47.0 24.0 62.0 738.0 677.0 57.0 49.0 48.0 t 0 0 0 0 0 102.0 61.0 26.0 46.0 30.0 35.0 72.0 33.0 55.0

MA2326.1_shift8 (IKZF2) 0.861 0.517 7.121 0.875 0.907 5 14 3 19 14 11.000 5
; assembly_5 versus MA2326.1 (IKZF2); m=4/19; ncol2=6; w=0; offset=4; strand=D; shift=8; score= 11; --------AGGAAG ; cor=0.861; Ncor=0.517; logoDP=7.121; NsEucl=0.875; NSW=0.907; rcor=5; rNcor=14; rlogoDP=3; rNsEucl=19; rNSW=14; rank_mean=11.000; match_rank=5 a 0 0 0 0 0 0 0 0 11101.0 2.0 5.0 11264.0 11159.0 21.0 c 0 0 0 0 0 0 0 0 208.0 127.0 7.0 25.0 191.0 57.0 g 0 0 0 0 0 0 0 0 79.0 11244.0 11270.0 17.0 26.0 11273.0 t 0 0 0 0 0 0 0 0 6.0 21.0 112.0 88.0 18.0 43.0

MA0761.3_shift6 (ETV1) 0.774 0.563 7.199 0.875 0.875 17 8 1 20 17 12.600 6
; assembly_5 versus MA0761.3 (ETV1); m=5/19; ncol2=9; w=0; offset=2; strand=D; shift=6; score= 12.6; ------aCAGGAAG ; cor=0.774; Ncor=0.563; logoDP=7.199; NsEucl=0.875; NSW=0.875; rcor=17; rNcor=8; rlogoDP=1; rNsEucl=20; rNSW=17; rank_mean=12.600; match_rank=6 a 0 0 0 0 0 0 22801.0 1848.0 33305.0 231.0 378.0 36130.0 33368.0 4235.0 c 0 0 0 0 0 0 4339.0 32139.0 3064.0 275.0 271.0 471.0 486.0 1307.0 g 0 0 0 0 0 0 6015.0 2389.0 573.0 36483.0 36121.0 375.0 412.0 31256.0 t 0 0 0 0 0 0 4184.0 963.0 397.0 350.0 569.0 363.0 3073.0 541.0

MA0640.3_rc_shift7 (ELF3_rc) 0.857 0.500 1.192 0.894 0.921 7 19 32 8 6 14.400 8
; assembly_5 versus MA0640.3_rc (ELF3_rc); m=6/19; ncol2=9; w=0; offset=3; strand=R; shift=7; score= 14.4; -------cAGGAAG ; cor=0.857; Ncor=0.500; logoDP=1.192; NsEucl=0.894; NSW=0.921; rcor=7; rNcor=19; rlogoDP=32; rNsEucl=8; rNSW=6; rank_mean=14.400; match_rank=8 a 0 0 0 0 0 0 0 8528.0 44422.0 475.0 793.0 46173.0 45195.0 4633.0 c 0 0 0 0 0 0 0 28319.0 1989.0 473.0 566.0 954.0 768.0 1365.0 g 0 0 0 0 0 0 0 9278.0 1315.0 47107.0 46481.0 943.0 1368.0 41950.0 t 0 0 0 0 0 0 0 2377.0 776.0 447.0 662.0 432.0 1171.0 554.0

MA0598.4_rc_shift7 (EHF_rc) 0.850 0.496 1.332 0.892 0.919 9 21 30 9 8 15.400 9
; assembly_5 versus MA0598.4_rc (EHF_rc); m=7/19; ncol2=9; w=0; offset=3; strand=R; shift=7; score= 15.4; -------cAGGAAG ; cor=0.850; Ncor=0.496; logoDP=1.332; NsEucl=0.892; NSW=0.919; rcor=9; rNcor=21; rlogoDP=30; rNsEucl=9; rNSW=8; rank_mean=15.400; match_rank=9 a 0 0 0 0 0 0 0 2629.0 12794.0 112.0 201.0 14865.0 14622.0 1706.0 c 0 0 0 0 0 0 0 9061.0 1538.0 101.0 139.0 199.0 152.0 377.0 g 0 0 0 0 0 0 0 2983.0 608.0 14997.0 14833.0 164.0 167.0 13116.0 t 0 0 0 0 0 0 0 695.0 428.0 158.0 195.0 140.0 427.0 169.0

MA0474.4_shift6 (Erg) 0.764 0.509 7.184 0.872 0.869 20 17 2 22 22 16.600 11
; assembly_5 versus MA0474.4 (Erg); m=8/19; ncol2=10; w=0; offset=2; strand=D; shift=6; score= 16.6; ------aCAGGAAG ; cor=0.764; Ncor=0.509; logoDP=7.184; NsEucl=0.872; NSW=0.869; rcor=20; rNcor=17; rlogoDP=2; rNsEucl=22; rNSW=22; rank_mean=16.600; match_rank=11 a 0 0 0 0 0 0 19688.0 1837.0 26773.0 170.0 297.0 29248.0 27881.0 4894.0 c 0 0 0 0 0 0 2742.0 24759.0 2559.0 133.0 265.0 355.0 370.0 1173.0 g 0 0 0 0 0 0 4936.0 2732.0 463.0 29562.0 29221.0 274.0 277.0 23600.0 t 0 0 0 0 0 0 2695.0 733.0 266.0 196.0 278.0 184.0 1533.0 394.0

MA2332.1_shift6 (ZNF175) 0.754 0.549 6.245 0.871 0.866 22 9 9 24 25 17.800 12
; assembly_5 versus MA2332.1 (ZNF175); m=9/19; ncol2=9; w=0; offset=2; strand=D; shift=6; score= 17.8; ------aCAGGAAG ; cor=0.754; Ncor=0.549; logoDP=6.245; NsEucl=0.871; NSW=0.866; rcor=22; rNcor=9; rlogoDP=9; rNsEucl=24; rNSW=25; rank_mean=17.800; match_rank=12 a 0 0 0 0 0 0 923.0 114.0 1333.0 26.0 44.0 1399.0 1343.0 99.0 c 0 0 0 0 0 0 177.0 1138.0 66.0 26.0 12.0 32.0 32.0 44.0 g 0 0 0 0 0 0 207.0 142.0 42.0 1397.0 1373.0 21.0 28.0 1309.0 t 0 0 0 0 0 0 169.0 82.0 35.0 27.0 47.0 24.0 73.0 24.0

MA1972.1_shift0 (ZFP14) 0.730 0.487 4.722 0.896 0.893 28 25 17 6 15 18.200 14
; assembly_5 versus MA1972.1 (ZFP14); m=10/19; ncol2=15; w=-4; offset=-4; strand=D; shift=0; score= 18.2; GGAGGcmctGGAry ; cor=0.730; Ncor=0.487; logoDP=4.722; NsEucl=0.896; NSW=0.893; rcor=28; rNcor=25; rlogoDP=17; rNsEucl=6; rNSW=15; rank_mean=18.200; match_rank=14 a 137.739 118.631 994.427 0.796178 86.7834 233.28 354.299 134.554 223.726 121.815 7.16561 978.503 596.338 150.478 c 13.535 0.796178 3.98089 0.796178 220.541 545.382 351.115 675.955 207.803 0.796178 0.796178 0.796178 89.9682 268.312 g 832.006 876.592 0.796178 994.427 691.879 172.771 64.4904 93.1529 182.325 755.573 991.242 19.9045 309.713 246.019 t 16.7197 3.98089 0.796178 3.98089 0.796178 48.5669 230.096 96.3376 386.146 121.815 0.796178 0.796178 3.98089 335.191

MA1715.1_rc_shift3 (ZNF707_rc) 0.745 0.497 1.315 0.885 0.869 23 20 31 10 23 21.400 21
; assembly_5 versus MA1715.1_rc (ZNF707_rc); m=11/19; ncol2=15; w=-1; offset=-1; strand=R; shift=3; score= 21.4; ---GTACCAGRAGT ; cor=0.745; Ncor=0.497; logoDP=1.315; NsEucl=0.885; NSW=0.869; rcor=23; rNcor=20; rlogoDP=31; rNsEucl=10; rNSW=23; rank_mean=21.400; match_rank=21 a 0 0 0 82.0 110.0 995.0 19.0 67.0 1052.0 57.0 321.0 1139.0 32.0 26.0 c 0 0 0 121.0 49.0 58.0 1066.0 1033.0 5.0 9.0 11.0 2.0 5.0 17.0 g 0 0 0 819.0 145.0 64.0 15.0 15.0 83.0 1079.0 821.0 11.0 1111.0 5.0 t 0 0 0 135.0 853.0 40.0 57.0 42.0 17.0 12.0 4.0 5.0 9.0 1109.0

MA1729.2_shift6 (ZNF680) 0.744 0.458 6.815 0.865 0.855 25 28 5 26 30 22.800 25
; assembly_5 versus MA1729.2 (ZNF680); m=12/19; ncol2=11; w=0; offset=2; strand=D; shift=6; score= 22.8; ------CCAAGAAG ; cor=0.744; Ncor=0.458; logoDP=6.815; NsEucl=0.865; NSW=0.855; rcor=25; rNcor=28; rlogoDP=5; rNsEucl=26; rNSW=30; rank_mean=22.800; match_rank=25 a 0 0 0 0 0 0 418.0 1120.0 5394.0 4522.0 43.0 5681.0 5479.0 494.0 c 0 0 0 0 0 0 4870.0 4324.0 60.0 17.0 14.0 23.0 13.0 40.0 g 0 0 0 0 0 0 133.0 69.0 208.0 1116.0 5691.0 44.0 203.0 5144.0 t 0 0 0 0 0 0 345.0 253.0 104.0 111.0 18.0 18.0 71.0 88.0

MA0062.4_rc_shift6 (GABPA_rc) 0.761 0.507 0.464 0.873 0.870 21 18 40 21 21 24.200 26
; assembly_5 versus MA0062.4_rc (GABPA_rc); m=13/19; ncol2=10; w=0; offset=2; strand=R; shift=6; score= 24.2; ------aCAGGAAG ; cor=0.761; Ncor=0.507; logoDP=0.464; NsEucl=0.873; NSW=0.870; rcor=21; rNcor=18; rlogoDP=40; rNsEucl=21; rNSW=21; rank_mean=24.200; match_rank=26 a 0 0 0 0 0 0 40409.0 5012.0 57654.0 859.0 1558.0 61754.0 59186.0 6717.0 c 0 0 0 0 0 0 7720.0 51920.0 4561.0 520.0 1150.0 1633.0 965.0 2169.0 g 0 0 0 0 0 0 12006.0 6328.0 1542.0 63107.0 61373.0 1230.0 1443.0 55664.0 t 0 0 0 0 0 0 5344.0 2219.0 1722.0 993.0 1398.0 862.0 3885.0 929.0

MA1508.2_shift5 (IKZF1) 0.706 0.565 6.698 0.857 0.835 40 7 7 30 42 25.200 28
; assembly_5 versus MA1508.2 (IKZF1); m=14/19; ncol2=8; w=0; offset=1; strand=D; shift=5; score= 25.2; -----AACAGGAA- ; cor=0.706; Ncor=0.565; logoDP=6.698; NsEucl=0.857; NSW=0.835; rcor=40; rNcor=7; rlogoDP=7; rNsEucl=30; rNSW=42; rank_mean=25.200; match_rank=28 a 0 0 0 0 0 8122.0 9137.0 673.0 10194.0 125.0 418.0 10323.0 10254.0 0 c 0 0 0 0 0 1158.0 473.0 8678.0 212.0 106.0 178.0 247.0 114.0 0 g 0 0 0 0 0 1007.0 956.0 1272.0 252.0 10569.0 10185.0 297.0 261.0 0 t 0 0 0 0 0 631.0 352.0 295.0 260.0 118.0 137.0 51.0 289.0 0

MA0671.2_shift4 (NFIX) 0.741 0.445 4.911 0.853 0.871 26 34 16 35 20 26.200 29
; assembly_5 versus MA0671.2 (NFIX); m=15/19; ncol2=6; w=0; offset=0; strand=D; shift=4; score= 26.2; ----tGCCAr---- ; cor=0.741; Ncor=0.445; logoDP=4.911; NsEucl=0.853; NSW=0.871; rcor=26; rNcor=34; rlogoDP=16; rNsEucl=35; rNSW=20; rank_mean=26.200; match_rank=29 a 0 0 0 0 11279.0 132.0 3.0 0.0 32864.0 32864.0 0 0 0 0 c 0 0 0 0 9695.0 186.0 32864.0 32864.0 2230.0 1356.0 0 0 0 0 g 0 0 0 0 5911.0 32864.0 3257.0 0.0 180.0 12688.0 0 0 0 0 t 0 0 0 0 32864.0 2539.0 29.0 0.0 110.0 2399.0 0 0 0 0

MA0136.4_shift7 (Elf5) 0.726 0.462 6.346 0.851 0.844 30 27 8 36 36 27.400 31
; assembly_5 versus MA0136.4 (Elf5); m=16/19; ncol2=8; w=0; offset=3; strand=D; shift=7; score= 27.4; -------AAGGAAG ; cor=0.726; Ncor=0.462; logoDP=6.346; NsEucl=0.851; NSW=0.844; rcor=30; rNcor=27; rlogoDP=8; rNsEucl=36; rNSW=36; rank_mean=27.400; match_rank=31 a 0 0 0 0 0 0 0 29427.0 38778.0 512.0 587.0 40896.0 40552.0 2609.0 c 0 0 0 0 0 0 0 6065.0 978.0 182.0 510.0 580.0 389.0 1234.0 g 0 0 0 0 0 0 0 5204.0 2049.0 41025.0 40626.0 390.0 481.0 37803.0 t 0 0 0 0 0 0 0 1450.0 341.0 427.0 423.0 280.0 724.0 500.0

MA0750.3_shift7 (ZBTB7A) 0.718 0.419 5.912 0.849 0.841 33 39 10 38 38 31.600 37
; assembly_5 versus MA0750.3 (ZBTB7A); m=17/19; ncol2=9; w=0; offset=3; strand=D; shift=7; score= 31.6; -------CCGGAAG ; cor=0.718; Ncor=0.419; logoDP=5.912; NsEucl=0.849; NSW=0.841; rcor=33; rNcor=39; rlogoDP=10; rNsEucl=38; rNSW=38; rank_mean=31.600; match_rank=37 a 0 0 0 0 0 0 0 477.0 2490.0 173.0 114.0 13854.0 13719.0 629.0 c 0 0 0 0 0 0 0 12469.0 11293.0 210.0 163.0 274.0 343.0 711.0 g 0 0 0 0 0 0 0 1496.0 624.0 14130.0 14239.0 335.0 261.0 13112.0 t 0 0 0 0 0 0 0 199.0 234.0 128.0 125.0 178.0 318.0 189.0

MA2329.1_rc_shift7 (ZBTB11_rc) 0.704 0.411 1.702 0.845 0.832 43 42 25 42 43 39.000 44
; assembly_5 versus MA2329.1_rc (ZBTB11_rc); m=18/19; ncol2=9; w=0; offset=3; strand=R; shift=7; score= 39; -------CCGGAAG ; cor=0.704; Ncor=0.411; logoDP=1.702; NsEucl=0.845; NSW=0.832; rcor=43; rNcor=42; rlogoDP=25; rNsEucl=42; rNSW=43; rank_mean=39.000; match_rank=44 a 0 0 0 0 0 0 0 91.0 319.0 27.0 9.0 2293.0 2176.0 106.0 c 0 0 0 0 0 0 0 2030.0 1977.0 25.0 15.0 31.0 101.0 84.0 g 0 0 0 0 0 0 0 230.0 74.0 2328.0 2342.0 33.0 39.0 2192.0 t 0 0 0 0 0 0 0 44.0 25.0 15.0 29.0 38.0 79.0 13.0

MA0076.3_rc_shift7 (ELK4_rc) 0.712 0.415 0.528 0.845 0.831 34 40 38 44 44 40.000 45
; assembly_5 versus MA0076.3_rc (ELK4_rc); m=19/19; ncol2=9; w=0; offset=3; strand=R; shift=7; score= 40; -------CCGGAAG ; cor=0.712; Ncor=0.415; logoDP=0.528; NsEucl=0.845; NSW=0.831; rcor=34; rNcor=40; rlogoDP=38; rNsEucl=44; rNSW=44; rank_mean=40.000; match_rank=45 a 0 0 0 0 0 0 0 83.0 512.0 0.0 0.0 3427.0 3419.0 723.0 c 0 0 0 0 0 0 0 2843.0 2915.0 0.0 0.0 0.0 0.0 16.0 g 0 0 0 0 0 0 0 501.0 0.0 3427.0 3427.0 0.0 0.0 2688.0 t 0 0 0 0 0 0 0 0.0 0.0 0.0 0.0 0.0 8.0 0.0

Matrix name	cor	Ncor	logoDP	NsEucl	NSW	rcor	rNcor	rlogoDP	rNsEucl	rNSW	rank_mean	match_rank	Aligned matrices
assembly_5_shift4 (assembly_5)													; assembly_5; m=0 (reference); ncol1=10; shift=4; ncol=14; ----gsCCAGGArg ; Alignment reference a 0 0 0 0 6 4 0 0 25 0 0 25 9 6 c 0 0 0 0 5 7 25 25 0 0 0 0 5 6 g 0 0 0 0 8 10 0 0 0 25 25 0 7 8 t 0 0 0 0 6 4 0 0 0 0 0 0 4 5
MA1992.2_shift7 (Ikzf3)	0.895	0.522	7.011	0.908	0.940	1	13	4	3	2	4.600	1	; assembly_5 versus MA1992.2 (Ikzf3); m=1/19; ncol2=9; w=0; offset=3; strand=D; shift=7; score= 4.6; -------CAGGAAG ; cor=0.895; Ncor=0.522; logoDP=7.011; NsEucl=0.908; NSW=0.940; rcor=1; rNcor=13; rlogoDP=4; rNsEucl=3; rNSW=2; rank_mean=4.600; match_rank=1 a 0 0 0 0 0 0 0 51.0 1054.0 4.0 18.0 1130.0 1058.0 102.0 c 0 0 0 0 0 0 0 998.0 62.0 7.0 16.0 25.0 12.0 45.0 g 0 0 0 0 0 0 0 103.0 48.0 1166.0 1141.0 22.0 20.0 1011.0 t 0 0 0 0 0 0 0 31.0 19.0 6.0 8.0 6.0 93.0 25.0
MA0473.4_shift7 (ELF1)	0.880	0.513	6.742	0.901	0.931	2	16	6	5	4	6.600	2	; assembly_5 versus MA0473.4 (ELF1); m=2/19; ncol2=9; w=0; offset=3; strand=D; shift=7; score= 6.6; -------CAGGAAG ; cor=0.880; Ncor=0.513; logoDP=6.742; NsEucl=0.901; NSW=0.931; rcor=2; rNcor=16; rlogoDP=6; rNsEucl=5; rNSW=4; rank_mean=6.600; match_rank=2 a 0 0 0 0 0 0 0 3094.0 42164.0 320.0 649.0 45930.0 45243.0 4063.0 c 0 0 0 0 0 0 0 37923.0 4038.0 421.0 505.0 796.0 705.0 1570.0 g 0 0 0 0 0 0 0 4819.0 932.0 46642.0 45970.0 676.0 779.0 41738.0 t 0 0 0 0 0 0 0 1934.0 636.0 387.0 646.0 368.0 1043.0 399.0
MA2330.1_shift5 (ZBTB24)	0.832	0.681	5.293	0.906	0.920	11	2	14	4	7	7.600	3	; assembly_5 versus MA2330.1 (ZBTB24); m=3/19; ncol2=10; w=0; offset=1; strand=D; shift=5; score= 7.6; -----cCCAGGACC ; cor=0.832; Ncor=0.681; logoDP=5.293; NsEucl=0.906; NSW=0.920; rcor=11; rNcor=2; rlogoDP=14; rNsEucl=4; rNSW=7; rank_mean=7.600; match_rank=3 a 0 0 0 0 0 65.0 58.0 28.0 667.0 25.0 49.0 629.0 41.0 84.0 c 0 0 0 0 0 534.0 662.0 750.0 53.0 35.0 67.0 70.0 705.0 641.0 g 0 0 0 0 0 127.0 47.0 24.0 62.0 738.0 677.0 57.0 49.0 48.0 t 0 0 0 0 0 102.0 61.0 26.0 46.0 30.0 35.0 72.0 33.0 55.0
MA2326.1_shift8 (IKZF2)	0.861	0.517	7.121	0.875	0.907	5	14	3	19	14	11.000	5	; assembly_5 versus MA2326.1 (IKZF2); m=4/19; ncol2=6; w=0; offset=4; strand=D; shift=8; score= 11; --------AGGAAG ; cor=0.861; Ncor=0.517; logoDP=7.121; NsEucl=0.875; NSW=0.907; rcor=5; rNcor=14; rlogoDP=3; rNsEucl=19; rNSW=14; rank_mean=11.000; match_rank=5 a 0 0 0 0 0 0 0 0 11101.0 2.0 5.0 11264.0 11159.0 21.0 c 0 0 0 0 0 0 0 0 208.0 127.0 7.0 25.0 191.0 57.0 g 0 0 0 0 0 0 0 0 79.0 11244.0 11270.0 17.0 26.0 11273.0 t 0 0 0 0 0 0 0 0 6.0 21.0 112.0 88.0 18.0 43.0
MA0761.3_shift6 (ETV1)	0.774	0.563	7.199	0.875	0.875	17	8	1	20	17	12.600	6	; assembly_5 versus MA0761.3 (ETV1); m=5/19; ncol2=9; w=0; offset=2; strand=D; shift=6; score= 12.6; ------aCAGGAAG ; cor=0.774; Ncor=0.563; logoDP=7.199; NsEucl=0.875; NSW=0.875; rcor=17; rNcor=8; rlogoDP=1; rNsEucl=20; rNSW=17; rank_mean=12.600; match_rank=6 a 0 0 0 0 0 0 22801.0 1848.0 33305.0 231.0 378.0 36130.0 33368.0 4235.0 c 0 0 0 0 0 0 4339.0 32139.0 3064.0 275.0 271.0 471.0 486.0 1307.0 g 0 0 0 0 0 0 6015.0 2389.0 573.0 36483.0 36121.0 375.0 412.0 31256.0 t 0 0 0 0 0 0 4184.0 963.0 397.0 350.0 569.0 363.0 3073.0 541.0
MA0640.3_rc_shift7 (ELF3_rc)	0.857	0.500	1.192	0.894	0.921	7	19	32	8	6	14.400	8	; assembly_5 versus MA0640.3_rc (ELF3_rc); m=6/19; ncol2=9; w=0; offset=3; strand=R; shift=7; score= 14.4; -------cAGGAAG ; cor=0.857; Ncor=0.500; logoDP=1.192; NsEucl=0.894; NSW=0.921; rcor=7; rNcor=19; rlogoDP=32; rNsEucl=8; rNSW=6; rank_mean=14.400; match_rank=8 a 0 0 0 0 0 0 0 8528.0 44422.0 475.0 793.0 46173.0 45195.0 4633.0 c 0 0 0 0 0 0 0 28319.0 1989.0 473.0 566.0 954.0 768.0 1365.0 g 0 0 0 0 0 0 0 9278.0 1315.0 47107.0 46481.0 943.0 1368.0 41950.0 t 0 0 0 0 0 0 0 2377.0 776.0 447.0 662.0 432.0 1171.0 554.0
MA0598.4_rc_shift7 (EHF_rc)	0.850	0.496	1.332	0.892	0.919	9	21	30	9	8	15.400	9	; assembly_5 versus MA0598.4_rc (EHF_rc); m=7/19; ncol2=9; w=0; offset=3; strand=R; shift=7; score= 15.4; -------cAGGAAG ; cor=0.850; Ncor=0.496; logoDP=1.332; NsEucl=0.892; NSW=0.919; rcor=9; rNcor=21; rlogoDP=30; rNsEucl=9; rNSW=8; rank_mean=15.400; match_rank=9 a 0 0 0 0 0 0 0 2629.0 12794.0 112.0 201.0 14865.0 14622.0 1706.0 c 0 0 0 0 0 0 0 9061.0 1538.0 101.0 139.0 199.0 152.0 377.0 g 0 0 0 0 0 0 0 2983.0 608.0 14997.0 14833.0 164.0 167.0 13116.0 t 0 0 0 0 0 0 0 695.0 428.0 158.0 195.0 140.0 427.0 169.0
MA0474.4_shift6 (Erg)	0.764	0.509	7.184	0.872	0.869	20	17	2	22	22	16.600	11	; assembly_5 versus MA0474.4 (Erg); m=8/19; ncol2=10; w=0; offset=2; strand=D; shift=6; score= 16.6; ------aCAGGAAG ; cor=0.764; Ncor=0.509; logoDP=7.184; NsEucl=0.872; NSW=0.869; rcor=20; rNcor=17; rlogoDP=2; rNsEucl=22; rNSW=22; rank_mean=16.600; match_rank=11 a 0 0 0 0 0 0 19688.0 1837.0 26773.0 170.0 297.0 29248.0 27881.0 4894.0 c 0 0 0 0 0 0 2742.0 24759.0 2559.0 133.0 265.0 355.0 370.0 1173.0 g 0 0 0 0 0 0 4936.0 2732.0 463.0 29562.0 29221.0 274.0 277.0 23600.0 t 0 0 0 0 0 0 2695.0 733.0 266.0 196.0 278.0 184.0 1533.0 394.0
MA2332.1_shift6 (ZNF175)	0.754	0.549	6.245	0.871	0.866	22	9	9	24	25	17.800	12	; assembly_5 versus MA2332.1 (ZNF175); m=9/19; ncol2=9; w=0; offset=2; strand=D; shift=6; score= 17.8; ------aCAGGAAG ; cor=0.754; Ncor=0.549; logoDP=6.245; NsEucl=0.871; NSW=0.866; rcor=22; rNcor=9; rlogoDP=9; rNsEucl=24; rNSW=25; rank_mean=17.800; match_rank=12 a 0 0 0 0 0 0 923.0 114.0 1333.0 26.0 44.0 1399.0 1343.0 99.0 c 0 0 0 0 0 0 177.0 1138.0 66.0 26.0 12.0 32.0 32.0 44.0 g 0 0 0 0 0 0 207.0 142.0 42.0 1397.0 1373.0 21.0 28.0 1309.0 t 0 0 0 0 0 0 169.0 82.0 35.0 27.0 47.0 24.0 73.0 24.0
MA1972.1_shift0 (ZFP14)	0.730	0.487	4.722	0.896	0.893	28	25	17	6	15	18.200	14	; assembly_5 versus MA1972.1 (ZFP14); m=10/19; ncol2=15; w=-4; offset=-4; strand=D; shift=0; score= 18.2; GGAGGcmctGGAry ; cor=0.730; Ncor=0.487; logoDP=4.722; NsEucl=0.896; NSW=0.893; rcor=28; rNcor=25; rlogoDP=17; rNsEucl=6; rNSW=15; rank_mean=18.200; match_rank=14 a 137.739 118.631 994.427 0.796178 86.7834 233.28 354.299 134.554 223.726 121.815 7.16561 978.503 596.338 150.478 c 13.535 0.796178 3.98089 0.796178 220.541 545.382 351.115 675.955 207.803 0.796178 0.796178 0.796178 89.9682 268.312 g 832.006 876.592 0.796178 994.427 691.879 172.771 64.4904 93.1529 182.325 755.573 991.242 19.9045 309.713 246.019 t 16.7197 3.98089 0.796178 3.98089 0.796178 48.5669 230.096 96.3376 386.146 121.815 0.796178 0.796178 3.98089 335.191
MA1715.1_rc_shift3 (ZNF707_rc)	0.745	0.497	1.315	0.885	0.869	23	20	31	10	23	21.400	21	; assembly_5 versus MA1715.1_rc (ZNF707_rc); m=11/19; ncol2=15; w=-1; offset=-1; strand=R; shift=3; score= 21.4; ---GTACCAGRAGT ; cor=0.745; Ncor=0.497; logoDP=1.315; NsEucl=0.885; NSW=0.869; rcor=23; rNcor=20; rlogoDP=31; rNsEucl=10; rNSW=23; rank_mean=21.400; match_rank=21 a 0 0 0 82.0 110.0 995.0 19.0 67.0 1052.0 57.0 321.0 1139.0 32.0 26.0 c 0 0 0 121.0 49.0 58.0 1066.0 1033.0 5.0 9.0 11.0 2.0 5.0 17.0 g 0 0 0 819.0 145.0 64.0 15.0 15.0 83.0 1079.0 821.0 11.0 1111.0 5.0 t 0 0 0 135.0 853.0 40.0 57.0 42.0 17.0 12.0 4.0 5.0 9.0 1109.0
MA1729.2_shift6 (ZNF680)	0.744	0.458	6.815	0.865	0.855	25	28	5	26	30	22.800	25	; assembly_5 versus MA1729.2 (ZNF680); m=12/19; ncol2=11; w=0; offset=2; strand=D; shift=6; score= 22.8; ------CCAAGAAG ; cor=0.744; Ncor=0.458; logoDP=6.815; NsEucl=0.865; NSW=0.855; rcor=25; rNcor=28; rlogoDP=5; rNsEucl=26; rNSW=30; rank_mean=22.800; match_rank=25 a 0 0 0 0 0 0 418.0 1120.0 5394.0 4522.0 43.0 5681.0 5479.0 494.0 c 0 0 0 0 0 0 4870.0 4324.0 60.0 17.0 14.0 23.0 13.0 40.0 g 0 0 0 0 0 0 133.0 69.0 208.0 1116.0 5691.0 44.0 203.0 5144.0 t 0 0 0 0 0 0 345.0 253.0 104.0 111.0 18.0 18.0 71.0 88.0
MA0062.4_rc_shift6 (GABPA_rc)	0.761	0.507	0.464	0.873	0.870	21	18	40	21	21	24.200	26	; assembly_5 versus MA0062.4_rc (GABPA_rc); m=13/19; ncol2=10; w=0; offset=2; strand=R; shift=6; score= 24.2; ------aCAGGAAG ; cor=0.761; Ncor=0.507; logoDP=0.464; NsEucl=0.873; NSW=0.870; rcor=21; rNcor=18; rlogoDP=40; rNsEucl=21; rNSW=21; rank_mean=24.200; match_rank=26 a 0 0 0 0 0 0 40409.0 5012.0 57654.0 859.0 1558.0 61754.0 59186.0 6717.0 c 0 0 0 0 0 0 7720.0 51920.0 4561.0 520.0 1150.0 1633.0 965.0 2169.0 g 0 0 0 0 0 0 12006.0 6328.0 1542.0 63107.0 61373.0 1230.0 1443.0 55664.0 t 0 0 0 0 0 0 5344.0 2219.0 1722.0 993.0 1398.0 862.0 3885.0 929.0
MA1508.2_shift5 (IKZF1)	0.706	0.565	6.698	0.857	0.835	40	7	7	30	42	25.200	28	; assembly_5 versus MA1508.2 (IKZF1); m=14/19; ncol2=8; w=0; offset=1; strand=D; shift=5; score= 25.2; -----AACAGGAA- ; cor=0.706; Ncor=0.565; logoDP=6.698; NsEucl=0.857; NSW=0.835; rcor=40; rNcor=7; rlogoDP=7; rNsEucl=30; rNSW=42; rank_mean=25.200; match_rank=28 a 0 0 0 0 0 8122.0 9137.0 673.0 10194.0 125.0 418.0 10323.0 10254.0 0 c 0 0 0 0 0 1158.0 473.0 8678.0 212.0 106.0 178.0 247.0 114.0 0 g 0 0 0 0 0 1007.0 956.0 1272.0 252.0 10569.0 10185.0 297.0 261.0 0 t 0 0 0 0 0 631.0 352.0 295.0 260.0 118.0 137.0 51.0 289.0 0
MA0671.2_shift4 (NFIX)	0.741	0.445	4.911	0.853	0.871	26	34	16	35	20	26.200	29	; assembly_5 versus MA0671.2 (NFIX); m=15/19; ncol2=6; w=0; offset=0; strand=D; shift=4; score= 26.2; ----tGCCAr---- ; cor=0.741; Ncor=0.445; logoDP=4.911; NsEucl=0.853; NSW=0.871; rcor=26; rNcor=34; rlogoDP=16; rNsEucl=35; rNSW=20; rank_mean=26.200; match_rank=29 a 0 0 0 0 11279.0 132.0 3.0 0.0 32864.0 32864.0 0 0 0 0 c 0 0 0 0 9695.0 186.0 32864.0 32864.0 2230.0 1356.0 0 0 0 0 g 0 0 0 0 5911.0 32864.0 3257.0 0.0 180.0 12688.0 0 0 0 0 t 0 0 0 0 32864.0 2539.0 29.0 0.0 110.0 2399.0 0 0 0 0
MA0136.4_shift7 (Elf5)	0.726	0.462	6.346	0.851	0.844	30	27	8	36	36	27.400	31	; assembly_5 versus MA0136.4 (Elf5); m=16/19; ncol2=8; w=0; offset=3; strand=D; shift=7; score= 27.4; -------AAGGAAG ; cor=0.726; Ncor=0.462; logoDP=6.346; NsEucl=0.851; NSW=0.844; rcor=30; rNcor=27; rlogoDP=8; rNsEucl=36; rNSW=36; rank_mean=27.400; match_rank=31 a 0 0 0 0 0 0 0 29427.0 38778.0 512.0 587.0 40896.0 40552.0 2609.0 c 0 0 0 0 0 0 0 6065.0 978.0 182.0 510.0 580.0 389.0 1234.0 g 0 0 0 0 0 0 0 5204.0 2049.0 41025.0 40626.0 390.0 481.0 37803.0 t 0 0 0 0 0 0 0 1450.0 341.0 427.0 423.0 280.0 724.0 500.0
MA0750.3_shift7 (ZBTB7A)	0.718	0.419	5.912	0.849	0.841	33	39	10	38	38	31.600	37	; assembly_5 versus MA0750.3 (ZBTB7A); m=17/19; ncol2=9; w=0; offset=3; strand=D; shift=7; score= 31.6; -------CCGGAAG ; cor=0.718; Ncor=0.419; logoDP=5.912; NsEucl=0.849; NSW=0.841; rcor=33; rNcor=39; rlogoDP=10; rNsEucl=38; rNSW=38; rank_mean=31.600; match_rank=37 a 0 0 0 0 0 0 0 477.0 2490.0 173.0 114.0 13854.0 13719.0 629.0 c 0 0 0 0 0 0 0 12469.0 11293.0 210.0 163.0 274.0 343.0 711.0 g 0 0 0 0 0 0 0 1496.0 624.0 14130.0 14239.0 335.0 261.0 13112.0 t 0 0 0 0 0 0 0 199.0 234.0 128.0 125.0 178.0 318.0 189.0
MA2329.1_rc_shift7 (ZBTB11_rc)	0.704	0.411	1.702	0.845	0.832	43	42	25	42	43	39.000	44	; assembly_5 versus MA2329.1_rc (ZBTB11_rc); m=18/19; ncol2=9; w=0; offset=3; strand=R; shift=7; score= 39; -------CCGGAAG ; cor=0.704; Ncor=0.411; logoDP=1.702; NsEucl=0.845; NSW=0.832; rcor=43; rNcor=42; rlogoDP=25; rNsEucl=42; rNSW=43; rank_mean=39.000; match_rank=44 a 0 0 0 0 0 0 0 91.0 319.0 27.0 9.0 2293.0 2176.0 106.0 c 0 0 0 0 0 0 0 2030.0 1977.0 25.0 15.0 31.0 101.0 84.0 g 0 0 0 0 0 0 0 230.0 74.0 2328.0 2342.0 33.0 39.0 2192.0 t 0 0 0 0 0 0 0 44.0 25.0 15.0 29.0 38.0 79.0 13.0
MA0076.3_rc_shift7 (ELK4_rc)	0.712	0.415	0.528	0.845	0.831	34	40	38	44	44	40.000	45	; assembly_5 versus MA0076.3_rc (ELK4_rc); m=19/19; ncol2=9; w=0; offset=3; strand=R; shift=7; score= 40; -------CCGGAAG ; cor=0.712; Ncor=0.415; logoDP=0.528; NsEucl=0.845; NSW=0.831; rcor=34; rNcor=40; rlogoDP=38; rNsEucl=44; rNSW=44; rank_mean=40.000; match_rank=45 a 0 0 0 0 0 0 0 83.0 512.0 0.0 0.0 3427.0 3419.0 723.0 c 0 0 0 0 0 0 0 2843.0 2915.0 0.0 0.0 0.0 0.0 16.0 g 0 0 0 0 0 0 0 501.0 0.0 3427.0 3427.0 0.0 0.0 2688.0 t 0 0 0 0 0 0 0 0.0 0.0 0.0 0.0 0.0 8.0 0.0

One-to-n matrix alignment; reference matrix: assembly_2_shift1 ; 5 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NsEucl NSW rcor rNcor rlogoDP rNsEucl rNSW rank_mean match_rank Aligned matrices
assembly_2_shift1 (assembly_2)
; assembly_2; m=0 (reference); ncol1=11; shift=1; ncol=12; -ktCAGAGACwk ; Alignment reference a 0 9 11 0 50 1 51 6 44 6 20 8 c 0 12 12 54 0 1 0 2 6 42 8 11 g 0 17 11 0 0 53 0 46 1 4 11 17 t 0 17 21 1 5 0 4 1 4 3 16 19

MA1731.2_rc_shift3 (ZNF768_rc) 0.858 0.702 1.102 0.912 0.930 6 1 34 2 5 9.600 4
; assembly_2 versus MA1731.2_rc (ZNF768_rc); m=1/4; ncol2=9; w=0; offset=2; strand=R; shift=3; score= 9.6; ---CAGAGAgGs ; cor=0.858; Ncor=0.702; logoDP=1.102; NsEucl=0.912; NSW=0.930; rcor=6; rNcor=1; rlogoDP=34; rNsEucl=2; rNSW=5; rank_mean=9.600; match_rank=4 a 0 0 0 1.0 987.0 1.0 945.0 20.0 917.0 123.0 141.0 43.0 c 0 0 0 973.0 11.0 11.0 43.0 29.0 11.0 179.0 62.0 268.0 g 0 0 0 25.0 1.0 987.0 6.0 950.0 39.0 655.0 768.0 478.0 t 0 0 0 1.0 1.0 1.0 6.0 1.0 34.0 43.0 29.0 211.0

MA1726.2_shift1 (ZNF331) 0.705 0.640 5.486 0.883 0.864 42 4 12 13 27 19.600 16
; assembly_2 versus MA1726.2 (ZNF331); m=2/4; ncol2=10; w=0; offset=0; strand=D; shift=1; score= 19.6; -TGCAGAGCCc- ; cor=0.705; Ncor=0.640; logoDP=5.486; NsEucl=0.883; NSW=0.864; rcor=42; rNcor=4; rlogoDP=12; rNsEucl=13; rNSW=27; rank_mean=19.600; match_rank=16 a 0 152.0 12.0 17.0 864.0 16.0 1098.0 64.0 18.0 165.0 163.0 0 c 0 61.0 14.0 1114.0 28.0 10.0 23.0 11.0 1103.0 845.0 660.0 0 g 0 83.0 1115.0 9.0 44.0 1121.0 19.0 1075.0 15.0 42.0 146.0 0 t 0 857.0 12.0 13.0 217.0 6.0 13.0 3.0 17.0 101.0 184.0 0

MA1998.2_rc_shift3 (Prdm14_rc) 0.708 0.515 0.357 0.864 0.851 37 15 43 28 33 31.200 34
; assembly_2 versus MA1998.2_rc (Prdm14_rc); m=3/4; ncol2=8; w=0; offset=2; strand=R; shift=3; score= 31.2; ---TAGAGACC- ; cor=0.708; Ncor=0.515; logoDP=0.357; NsEucl=0.864; NSW=0.851; rcor=37; rNcor=15; rlogoDP=43; rNsEucl=28; rNSW=33; rank_mean=31.200; match_rank=34 a 0 0 0 384.0 13232.0 788.0 11967.0 503.0 11682.0 530.0 826.0 0 c 0 0 0 393.0 128.0 891.0 183.0 562.0 1234.0 12447.0 11199.0 0 g 0 0 0 505.0 278.0 12030.0 1276.0 12509.0 381.0 571.0 1081.0 0 t 0 0 0 12559.0 203.0 132.0 415.0 267.0 544.0 293.0 735.0 0

MA1579.2_shift0 (ZBTB26) 0.703 0.410 5.040 0.847 0.837 44 43 15 40 40 36.400 43
; assembly_2 versus MA1579.2 (ZBTB26); m=4/4; ncol2=8; w=-1; offset=-1; strand=D; shift=0; score= 36.4; cTCCAGAA---- ; cor=0.703; Ncor=0.410; logoDP=5.040; NsEucl=0.847; NSW=0.837; rcor=44; rNcor=43; rlogoDP=15; rNsEucl=40; rNSW=40; rank_mean=36.400; match_rank=43 a 274.0 9.0 20.0 5.0 1535.0 27.0 1582.0 1134.0 0 0 0 0 c 872.0 5.0 1592.0 1503.0 17.0 3.0 22.0 138.0 0 0 0 0 g 123.0 5.0 12.0 13.0 49.0 1581.0 9.0 223.0 0 0 0 0 t 358.0 1608.0 3.0 106.0 26.0 16.0 14.0 132.0 0 0 0 0

Matrix name	cor	Ncor	logoDP	NsEucl	NSW	rcor	rNcor	rlogoDP	rNsEucl	rNSW	rank_mean	match_rank	Aligned matrices
assembly_2_shift1 (assembly_2)													; assembly_2; m=0 (reference); ncol1=11; shift=1; ncol=12; -ktCAGAGACwk ; Alignment reference a 0 9 11 0 50 1 51 6 44 6 20 8 c 0 12 12 54 0 1 0 2 6 42 8 11 g 0 17 11 0 0 53 0 46 1 4 11 17 t 0 17 21 1 5 0 4 1 4 3 16 19
MA1731.2_rc_shift3 (ZNF768_rc)	0.858	0.702	1.102	0.912	0.930	6	1	34	2	5	9.600	4	; assembly_2 versus MA1731.2_rc (ZNF768_rc); m=1/4; ncol2=9; w=0; offset=2; strand=R; shift=3; score= 9.6; ---CAGAGAgGs ; cor=0.858; Ncor=0.702; logoDP=1.102; NsEucl=0.912; NSW=0.930; rcor=6; rNcor=1; rlogoDP=34; rNsEucl=2; rNSW=5; rank_mean=9.600; match_rank=4 a 0 0 0 1.0 987.0 1.0 945.0 20.0 917.0 123.0 141.0 43.0 c 0 0 0 973.0 11.0 11.0 43.0 29.0 11.0 179.0 62.0 268.0 g 0 0 0 25.0 1.0 987.0 6.0 950.0 39.0 655.0 768.0 478.0 t 0 0 0 1.0 1.0 1.0 6.0 1.0 34.0 43.0 29.0 211.0
MA1726.2_shift1 (ZNF331)	0.705	0.640	5.486	0.883	0.864	42	4	12	13	27	19.600	16	; assembly_2 versus MA1726.2 (ZNF331); m=2/4; ncol2=10; w=0; offset=0; strand=D; shift=1; score= 19.6; -TGCAGAGCCc- ; cor=0.705; Ncor=0.640; logoDP=5.486; NsEucl=0.883; NSW=0.864; rcor=42; rNcor=4; rlogoDP=12; rNsEucl=13; rNSW=27; rank_mean=19.600; match_rank=16 a 0 152.0 12.0 17.0 864.0 16.0 1098.0 64.0 18.0 165.0 163.0 0 c 0 61.0 14.0 1114.0 28.0 10.0 23.0 11.0 1103.0 845.0 660.0 0 g 0 83.0 1115.0 9.0 44.0 1121.0 19.0 1075.0 15.0 42.0 146.0 0 t 0 857.0 12.0 13.0 217.0 6.0 13.0 3.0 17.0 101.0 184.0 0
MA1998.2_rc_shift3 (Prdm14_rc)	0.708	0.515	0.357	0.864	0.851	37	15	43	28	33	31.200	34	; assembly_2 versus MA1998.2_rc (Prdm14_rc); m=3/4; ncol2=8; w=0; offset=2; strand=R; shift=3; score= 31.2; ---TAGAGACC- ; cor=0.708; Ncor=0.515; logoDP=0.357; NsEucl=0.864; NSW=0.851; rcor=37; rNcor=15; rlogoDP=43; rNsEucl=28; rNSW=33; rank_mean=31.200; match_rank=34 a 0 0 0 384.0 13232.0 788.0 11967.0 503.0 11682.0 530.0 826.0 0 c 0 0 0 393.0 128.0 891.0 183.0 562.0 1234.0 12447.0 11199.0 0 g 0 0 0 505.0 278.0 12030.0 1276.0 12509.0 381.0 571.0 1081.0 0 t 0 0 0 12559.0 203.0 132.0 415.0 267.0 544.0 293.0 735.0 0
MA1579.2_shift0 (ZBTB26)	0.703	0.410	5.040	0.847	0.837	44	43	15	40	40	36.400	43	; assembly_2 versus MA1579.2 (ZBTB26); m=4/4; ncol2=8; w=-1; offset=-1; strand=D; shift=0; score= 36.4; cTCCAGAA---- ; cor=0.703; Ncor=0.410; logoDP=5.040; NsEucl=0.847; NSW=0.837; rcor=44; rNcor=43; rlogoDP=15; rNsEucl=40; rNSW=40; rank_mean=36.400; match_rank=43 a 274.0 9.0 20.0 5.0 1535.0 27.0 1582.0 1134.0 0 0 0 0 c 872.0 5.0 1592.0 1503.0 17.0 3.0 22.0 138.0 0 0 0 0 g 123.0 5.0 12.0 13.0 49.0 1581.0 9.0 223.0 0 0 0 0 t 358.0 1608.0 3.0 106.0 26.0 16.0 14.0 132.0 0 0 0 0

One-to-n matrix alignment; reference matrix: assembly_4_shift1 ; 6 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NsEucl NSW rcor rNcor rlogoDP rNsEucl rNSW rank_mean match_rank Aligned matrices
assembly_4_shift1 (assembly_4)
; assembly_4; m=0 (reference); ncol1=11; shift=1; ncol=12; -krAAAATGTwa ; Alignment reference a 0 14 16 51 55 49 52 3 3 3 15 19 c 0 8 13 3 2 6 2 0 1 1 11 13 g 0 21 18 4 1 1 2 3 53 6 14 12 t 0 15 11 0 0 2 2 52 1 48 18 14

MA0095.4_shift2 (Yy1) 0.790 0.575 5.367 0.882 0.889 15 6 13 14 16 12.800 7
; assembly_4 versus MA0095.4 (Yy1); m=1/5; ncol2=8; w=0; offset=1; strand=D; shift=2; score= 12.8; --CAAAATGG-- ; cor=0.790; Ncor=0.575; logoDP=5.367; NsEucl=0.882; NSW=0.889; rcor=15; rNcor=6; rlogoDP=13; rNsEucl=14; rNSW=16; rank_mean=12.800; match_rank=7 a 0 0 3123.0 41529.0 39666.0 30769.0 41506.0 689.0 561.0 1597.0 0 0 c 0 0 33122.0 926.0 1447.0 2536.0 746.0 241.0 165.0 971.0 0 0 g 0 0 3684.0 287.0 1320.0 8658.0 712.0 708.0 42263.0 39612.0 0 0 t 0 0 3419.0 606.0 915.0 1385.0 384.0 41710.0 359.0 1168.0 0 0

MA1707.2_rc_shift5 (DMRTA1_rc) 0.861 0.431 0.542 0.912 0.946 4 35 37 1 1 15.600 10
; assembly_4 versus MA1707.2_rc (DMRTA1_rc); m=2/5; ncol2=10; w=0; offset=4; strand=R; shift=5; score= 15.6; -----awTGTAw ; cor=0.861; Ncor=0.431; logoDP=0.542; NsEucl=0.912; NSW=0.946; rcor=4; rNcor=35; rlogoDP=37; rNsEucl=1; rNSW=1; rank_mean=15.600; match_rank=10 a 0 0 0 0 0 2671.0 2671.0 342.0 0.0 0.0 2671.0 1595.0 c 0 0 0 0 0 585.0 587.0 39.0 0.0 15.0 0.0 1.0 g 0 0 0 0 0 650.0 299.0 0.0 2671.0 4.0 89.0 761.0 t 0 0 0 0 0 588.0 1392.0 2671.0 2.0 2671.0 771.0 1076.0

MA2124.1_rc_shift0 (Hmga1_rc) 0.849 0.495 1.118 0.885 0.907 10 22 33 11 13 17.800 13
; assembly_4 versus MA2124.1_rc (Hmga1_rc); m=3/5; ncol2=8; w=-1; offset=-1; strand=R; shift=0; score= 17.8; wTAAAAAT---- ; cor=0.849; Ncor=0.495; logoDP=1.118; NsEucl=0.885; NSW=0.907; rcor=10; rNcor=22; rlogoDP=33; rNsEucl=11; rNSW=13; rank_mean=17.800; match_rank=13 a 11340.0 542.0 24333.0 24654.0 24779.0 24269.0 24172.0 496.0 0 0 0 0 c 2438.0 358.0 294.0 237.0 138.0 303.0 421.0 188.0 0 0 0 0 g 2348.0 473.0 409.0 264.0 194.0 200.0 393.0 71.0 0 0 0 0 t 9680.0 24433.0 770.0 651.0 695.0 1034.0 820.0 25051.0 0 0 0 0

MA0160.3_shift4 (NR4A2) 0.729 0.530 4.197 0.871 0.868 29 11 21 23 24 21.600 22
; assembly_4 versus MA0160.3 (NR4A2); m=4/5; ncol2=8; w=0; offset=3; strand=D; shift=4; score= 21.6; ----AAAGGTCA ; cor=0.729; Ncor=0.530; logoDP=4.197; NsEucl=0.871; NSW=0.868; rcor=29; rNcor=11; rlogoDP=21; rNsEucl=23; rNSW=24; rank_mean=21.600; match_rank=22 a 0 0 0 0 209.0 209.0 209.0 0.0 0.0 6.0 0.0 209.0 c 0 0 0 0 0.0 0.0 5.0 0.0 0.0 22.0 209.0 4.0 g 0 0 0 0 28.0 1.0 1.0 160.0 209.0 21.0 1.0 40.0 t 0 0 0 0 22.0 18.0 0.0 49.0 2.0 209.0 14.0 0.0

MA1112.3_shift4 (NR4A1) 0.720 0.523 4.344 0.865 0.854 32 12 20 27 31 24.400 27
; assembly_4 versus MA1112.3 (NR4A1); m=5/5; ncol2=8; w=0; offset=3; strand=D; shift=4; score= 24.4; ----AAAGGTCA ; cor=0.720; Ncor=0.523; logoDP=4.344; NsEucl=0.865; NSW=0.854; rcor=32; rNcor=12; rlogoDP=20; rNsEucl=27; rNSW=31; rank_mean=24.400; match_rank=27 a 0 0 0 0 14313.0 15268.0 15684.0 427.0 300.0 365.0 70.0 15126.0 c 0 0 0 0 236.0 117.0 62.0 92.0 166.0 824.0 14949.0 151.0 g 0 0 0 0 823.0 333.0 128.0 12434.0 14964.0 1358.0 151.0 329.0 t 0 0 0 0 555.0 209.0 53.0 2974.0 497.0 13380.0 757.0 321.0

Matrix name	cor	Ncor	logoDP	NsEucl	NSW	rcor	rNcor	rlogoDP	rNsEucl	rNSW	rank_mean	match_rank	Aligned matrices
assembly_4_shift1 (assembly_4)													; assembly_4; m=0 (reference); ncol1=11; shift=1; ncol=12; -krAAAATGTwa ; Alignment reference a 0 14 16 51 55 49 52 3 3 3 15 19 c 0 8 13 3 2 6 2 0 1 1 11 13 g 0 21 18 4 1 1 2 3 53 6 14 12 t 0 15 11 0 0 2 2 52 1 48 18 14
MA0095.4_shift2 (Yy1)	0.790	0.575	5.367	0.882	0.889	15	6	13	14	16	12.800	7	; assembly_4 versus MA0095.4 (Yy1); m=1/5; ncol2=8; w=0; offset=1; strand=D; shift=2; score= 12.8; --CAAAATGG-- ; cor=0.790; Ncor=0.575; logoDP=5.367; NsEucl=0.882; NSW=0.889; rcor=15; rNcor=6; rlogoDP=13; rNsEucl=14; rNSW=16; rank_mean=12.800; match_rank=7 a 0 0 3123.0 41529.0 39666.0 30769.0 41506.0 689.0 561.0 1597.0 0 0 c 0 0 33122.0 926.0 1447.0 2536.0 746.0 241.0 165.0 971.0 0 0 g 0 0 3684.0 287.0 1320.0 8658.0 712.0 708.0 42263.0 39612.0 0 0 t 0 0 3419.0 606.0 915.0 1385.0 384.0 41710.0 359.0 1168.0 0 0
MA1707.2_rc_shift5 (DMRTA1_rc)	0.861	0.431	0.542	0.912	0.946	4	35	37	1	1	15.600	10	; assembly_4 versus MA1707.2_rc (DMRTA1_rc); m=2/5; ncol2=10; w=0; offset=4; strand=R; shift=5; score= 15.6; -----awTGTAw ; cor=0.861; Ncor=0.431; logoDP=0.542; NsEucl=0.912; NSW=0.946; rcor=4; rNcor=35; rlogoDP=37; rNsEucl=1; rNSW=1; rank_mean=15.600; match_rank=10 a 0 0 0 0 0 2671.0 2671.0 342.0 0.0 0.0 2671.0 1595.0 c 0 0 0 0 0 585.0 587.0 39.0 0.0 15.0 0.0 1.0 g 0 0 0 0 0 650.0 299.0 0.0 2671.0 4.0 89.0 761.0 t 0 0 0 0 0 588.0 1392.0 2671.0 2.0 2671.0 771.0 1076.0
MA2124.1_rc_shift0 (Hmga1_rc)	0.849	0.495	1.118	0.885	0.907	10	22	33	11	13	17.800	13	; assembly_4 versus MA2124.1_rc (Hmga1_rc); m=3/5; ncol2=8; w=-1; offset=-1; strand=R; shift=0; score= 17.8; wTAAAAAT---- ; cor=0.849; Ncor=0.495; logoDP=1.118; NsEucl=0.885; NSW=0.907; rcor=10; rNcor=22; rlogoDP=33; rNsEucl=11; rNSW=13; rank_mean=17.800; match_rank=13 a 11340.0 542.0 24333.0 24654.0 24779.0 24269.0 24172.0 496.0 0 0 0 0 c 2438.0 358.0 294.0 237.0 138.0 303.0 421.0 188.0 0 0 0 0 g 2348.0 473.0 409.0 264.0 194.0 200.0 393.0 71.0 0 0 0 0 t 9680.0 24433.0 770.0 651.0 695.0 1034.0 820.0 25051.0 0 0 0 0
MA0160.3_shift4 (NR4A2)	0.729	0.530	4.197	0.871	0.868	29	11	21	23	24	21.600	22	; assembly_4 versus MA0160.3 (NR4A2); m=4/5; ncol2=8; w=0; offset=3; strand=D; shift=4; score= 21.6; ----AAAGGTCA ; cor=0.729; Ncor=0.530; logoDP=4.197; NsEucl=0.871; NSW=0.868; rcor=29; rNcor=11; rlogoDP=21; rNsEucl=23; rNSW=24; rank_mean=21.600; match_rank=22 a 0 0 0 0 209.0 209.0 209.0 0.0 0.0 6.0 0.0 209.0 c 0 0 0 0 0.0 0.0 5.0 0.0 0.0 22.0 209.0 4.0 g 0 0 0 0 28.0 1.0 1.0 160.0 209.0 21.0 1.0 40.0 t 0 0 0 0 22.0 18.0 0.0 49.0 2.0 209.0 14.0 0.0
MA1112.3_shift4 (NR4A1)	0.720	0.523	4.344	0.865	0.854	32	12	20	27	31	24.400	27	; assembly_4 versus MA1112.3 (NR4A1); m=5/5; ncol2=8; w=0; offset=3; strand=D; shift=4; score= 24.4; ----AAAGGTCA ; cor=0.720; Ncor=0.523; logoDP=4.344; NsEucl=0.865; NSW=0.854; rcor=32; rNcor=12; rlogoDP=20; rNsEucl=27; rNSW=31; rank_mean=24.400; match_rank=27 a 0 0 0 0 14313.0 15268.0 15684.0 427.0 300.0 365.0 70.0 15126.0 c 0 0 0 0 236.0 117.0 62.0 92.0 166.0 824.0 14949.0 151.0 g 0 0 0 0 823.0 333.0 128.0 12434.0 14964.0 1358.0 151.0 329.0 t 0 0 0 0 555.0 209.0 53.0 2974.0 497.0 13380.0 757.0 321.0

One-to-n matrix alignment; reference matrix: assembly_3_shift1 ; 16 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NsEucl NSW rcor rNcor rlogoDP rNsEucl rNSW rank_mean match_rank Aligned matrices
assembly_3_shift1 (assembly_3)
; assembly_3; m=0 (reference); ncol1=10; shift=1; ncol=11; -wvAGTGATth ; Alignment reference a 0 8 6 15 0 0 0 15 0 3 4 c 0 0 4 0 0 0 0 0 0 3 6 g 0 3 5 0 15 0 15 0 0 3 1 t 0 4 0 0 0 15 0 0 15 6 4

MA0914.2_rc_shift1 (ISL2_rc) 0.821 0.492 1.426 0.877 0.910 14 23 29 17 11 18.800 15
; assembly_3 versus MA0914.2_rc (ISL2_rc); m=1/15; ncol2=6; w=0; offset=0; strand=R; shift=1; score= 18.8; -TAAkTG---- ; cor=0.821; Ncor=0.492; logoDP=1.426; NsEucl=0.877; NSW=0.910; rcor=14; rNcor=23; rlogoDP=29; rNsEucl=17; rNSW=11; rank_mean=18.800; match_rank=15 a 0 1354.0 5631.0 5631.0 398.0 248.0 1019.0 0 0 0 0 c 0 59.0 13.0 169.0 171.0 134.0 126.0 0 0 0 0 g 0 206.0 718.0 130.0 5631.0 162.0 5631.0 0 0 0 0 t 0 5631.0 278.0 218.0 3161.0 5631.0 160.0 0 0 0 0

MA0063.3_rc_shift0 (NKX2-5_rc) 0.851 0.464 0.461 0.882 0.916 8 26 41 15 9 19.800 17
; assembly_3 versus MA0063.3_rc (NKX2-5_rc); m=2/15; ncol2=7; w=-1; offset=-1; strand=R; shift=0; score= 19.8; TTGAGTG---- ; cor=0.851; Ncor=0.464; logoDP=0.461; NsEucl=0.882; NSW=0.916; rcor=8; rNcor=26; rlogoDP=41; rNsEucl=15; rNSW=9; rank_mean=19.800; match_rank=17 a 250.0 288.0 841.0 5166.0 153.0 74.0 322.0 0 0 0 0 c 98.0 217.0 62.0 61.0 49.0 76.0 24.0 0 0 0 0 g 165.0 120.0 4319.0 82.0 5098.0 48.0 5002.0 0 0 0 0 t 4931.0 4819.0 222.0 135.0 144.0 5246.0 96.0 0 0 0 0

MA0038.3_rc_shift0 (GFI1_rc) 0.744 0.677 0.849 0.884 0.866 24 3 36 12 26 20.200 18
; assembly_3 versus MA0038.3_rc (GFI1_rc); m=3/15; ncol2=11; w=-1; offset=-1; strand=R; shift=0; score= 20.2; tGChGTGATTk ; cor=0.744; Ncor=0.677; logoDP=0.849; NsEucl=0.884; NSW=0.866; rcor=24; rNcor=3; rlogoDP=36; rNsEucl=12; rNSW=26; rank_mean=20.200; match_rank=18 a 4134.0 3702.0 888.0 13996.0 0.0 1594.0 10.0 30161.0 1.0 0.0 565.0 c 4079.0 0.0 27514.0 8349.0 3888.0 0.0 0.0 0.0 0.0 0.0 812.0 g 5221.0 27891.0 266.0 54.0 27769.0 0.0 30139.0 0.0 0.0 2.0 10155.0 t 16713.0 292.0 2294.0 7748.0 838.0 29255.0 15.0 0.0 30150.0 30168.0 19146.0

MA1639.2_rc_shift5 (MEIS1_rc) 0.870 0.402 0.255 0.895 0.934 3 45 44 7 3 20.400 19
; assembly_3 versus MA1639.2_rc (MEIS1_rc); m=4/15; ncol2=9; w=0; offset=4; strand=R; shift=5; score= 20.4; -----TGATTk ; cor=0.870; Ncor=0.402; logoDP=0.255; NsEucl=0.895; NSW=0.934; rcor=3; rNcor=45; rlogoDP=44; rNsEucl=7; rNSW=3; rank_mean=20.400; match_rank=19 a 0 0 0 0 0 872.0 152.0 6459.0 218.0 304.0 609.0 c 0 0 0 0 0 152.0 61.0 63.0 192.0 33.0 252.0 g 0 0 0 0 0 279.0 6367.0 87.0 214.0 336.0 3580.0 t 0 0 0 0 0 5433.0 156.0 127.0 6112.0 6063.0 2295.0

MA1523.2_rc_shift0 (MSANTD3_rc) 0.831 0.453 0.507 0.878 0.910 12 29 39 16 10 21.200 20
; assembly_3 versus MA1523.2_rc (MSANTD3_rc); m=5/15; ncol2=7; w=-1; offset=-1; strand=R; shift=0; score= 21.2; kTGAGTG---- ; cor=0.831; Ncor=0.453; logoDP=0.507; NsEucl=0.878; NSW=0.910; rcor=12; rNcor=29; rlogoDP=39; rNsEucl=16; rNSW=10; rank_mean=21.200; match_rank=20 a 96.0 59.0 60.0 954.0 45.0 16.0 180.0 0 0 0 0 c 63.0 24.0 29.0 0.0 27.0 2.0 31.0 0 0 0 0 g 568.0 140.0 862.0 7.0 896.0 0.0 723.0 0 0 0 0 t 271.0 775.0 47.0 37.0 31.0 980.0 64.0 0 0 0 0

MA2336.1_rc_shift3 (ZSCAN21_rc) 0.765 0.536 2.185 0.858 0.858 19 10 23 29 28 21.800 23
; assembly_3 versus MA2336.1_rc (ZSCAN21_rc); m=6/15; ncol2=7; w=0; offset=2; strand=R; shift=3; score= 21.8; ---AGTGCTT- ; cor=0.765; Ncor=0.536; logoDP=2.185; NsEucl=0.858; NSW=0.858; rcor=19; rNcor=10; rlogoDP=23; rNsEucl=29; rNSW=28; rank_mean=21.800; match_rank=23 a 0 0 0 885.0 11.0 11.0 154.0 41.0 10.0 65.0 0 c 0 0 0 16.0 30.0 22.0 32.0 853.0 25.0 55.0 0 g 0 0 0 9.0 881.0 21.0 744.0 25.0 16.0 124.0 0 t 0 0 0 37.0 25.0 893.0 17.0 28.0 896.0 703.0 0

MA2339.1_rc_shift5 (Nanog_rc) 0.826 0.450 0.943 0.876 0.908 13 31 35 18 12 21.800 24
; assembly_3 versus MA2339.1_rc (Nanog_rc); m=7/15; ncol2=7; w=0; offset=4; strand=R; shift=5; score= 21.8; -----TGATTG ; cor=0.826; Ncor=0.450; logoDP=0.943; NsEucl=0.876; NSW=0.908; rcor=13; rNcor=31; rlogoDP=35; rNsEucl=18; rNSW=12; rank_mean=21.800; match_rank=24 a 0 0 0 0 0 277.0 746.0 8209.0 303.0 907.0 1130.0 c 0 0 0 0 0 180.0 149.0 124.0 196.0 365.0 93.0 g 0 0 0 0 0 131.0 7421.0 96.0 206.0 400.0 7298.0 t 0 0 0 0 0 8076.0 348.0 235.0 7959.0 6992.0 143.0

MA1644.2_rc_shift5 (NFYC_rc) 0.769 0.420 1.578 0.855 0.874 18 38 27 31 18 26.400 30
; assembly_3 versus MA1644.2_rc (NFYC_rc); m=8/15; ncol2=7; w=0; offset=4; strand=R; shift=5; score= 26.4; -----TGATTG ; cor=0.769; Ncor=0.420; logoDP=1.578; NsEucl=0.855; NSW=0.874; rcor=18; rNcor=38; rlogoDP=27; rNsEucl=31; rNSW=18; rank_mean=26.400; match_rank=30 a 0 0 0 0 0 188.0 396.0 12912.0 374.0 412.0 245.0 c 0 0 0 0 0 891.0 1464.0 71.0 549.0 103.0 111.0 g 0 0 0 0 0 711.0 11224.0 374.0 376.0 325.0 12880.0 t 0 0 0 0 0 11826.0 532.0 259.0 12317.0 12776.0 380.0

MA1994.2_rc_shift0 (Nkx2-1_rc) 0.779 0.425 0.438 0.854 0.872 16 36 42 34 19 29.400 32
; assembly_3 versus MA1994.2_rc (Nkx2-1_rc); m=9/15; ncol2=7; w=-1; offset=-1; strand=R; shift=0; score= 29.4; TCAAGTG---- ; cor=0.779; Ncor=0.425; logoDP=0.438; NsEucl=0.854; NSW=0.872; rcor=16; rNcor=36; rlogoDP=42; rNsEucl=34; rNSW=19; rank_mean=29.400; match_rank=32 a 541.0 518.0 15157.0 15106.0 316.0 343.0 886.0 0 0 0 0 c 213.0 14172.0 315.0 605.0 118.0 146.0 181.0 0 0 0 0 g 243.0 657.0 518.0 162.0 15640.0 275.0 14886.0 0 0 0 0 t 15245.0 895.0 252.0 369.0 168.0 15478.0 289.0 0 0 0 0

MA0122.4_rc_shift0 (Nkx3-2_rc) 0.708 0.579 0.154 0.871 0.849 38 5 45 25 35 29.600 33
; assembly_3 versus MA0122.4_rc (Nkx3-2_rc); m=10/15; ncol2=10; w=-1; offset=-1; strand=R; shift=0; score= 29.6; tTAAGTGktt- ; cor=0.708; Ncor=0.579; logoDP=0.154; NsEucl=0.871; NSW=0.849; rcor=38; rNcor=5; rlogoDP=45; rNsEucl=25; rNSW=35; rank_mean=29.600; match_rank=33 a 2241.0 325.0 9919.0 10109.0 94.0 212.0 218.0 1033.0 2359.0 2088.0 0 c 1368.0 68.0 68.0 29.0 10.0 19.0 23.0 1504.0 1154.0 1466.0 0 g 991.0 147.0 138.0 32.0 9965.0 82.0 9900.0 5079.0 1109.0 952.0 0 t 5620.0 9680.0 95.0 50.0 151.0 9907.0 79.0 2604.0 5598.0 5714.0 0

MA0673.2_rc_shift0 (NKX2-8_rc) 0.710 0.452 1.554 0.855 0.852 36 30 28 32 32 31.600 36
; assembly_3 versus MA0673.2_rc (NKX2-8_rc); m=11/15; ncol2=8; w=-1; offset=-1; strand=R; shift=0; score= 31.6; TsRAGTGs--- ; cor=0.710; Ncor=0.452; logoDP=1.554; NsEucl=0.855; NSW=0.852; rcor=36; rNcor=30; rlogoDP=28; rNsEucl=32; rNSW=32; rank_mean=31.600; match_rank=36 a 2158.0 271.0 8562.0 8562.0 110.0 516.0 2155.0 249.0 0 0 0 c 696.0 4286.0 0.0 0.0 0.0 0.0 0.0 2843.0 0 0 0 g 908.0 2267.0 3197.0 91.0 8562.0 595.0 8562.0 3529.0 0 0 0 t 8562.0 1738.0 23.0 0.0 14.0 8562.0 70.0 1942.0 0 0 0

MA2003.2_rc_shift0 (NKX2-4_rc) 0.707 0.450 1.694 0.854 0.851 39 32 26 33 34 32.800 38
; assembly_3 versus MA2003.2_rc (NKX2-4_rc); m=12/15; ncol2=8; w=-1; offset=-1; strand=R; shift=0; score= 32.8; TsAAGTGg--- ; cor=0.707; Ncor=0.450; logoDP=1.694; NsEucl=0.854; NSW=0.851; rcor=39; rNcor=32; rlogoDP=26; rNsEucl=33; rNSW=34; rank_mean=32.800; match_rank=38 a 153.0 58.0 1185.0 1185.0 0.0 207.0 129.0 61.0 0 0 0 c 57.0 640.0 13.0 1.0 0.0 17.0 7.0 485.0 0 0 0 g 56.0 545.0 409.0 25.0 1185.0 127.0 1185.0 1185.0 0 0 0 t 1185.0 243.0 52.0 0.0 0.0 1185.0 14.0 385.0 0 0 0

MA0610.2_rc_shift5 (DMRT3_rc) 0.737 0.402 3.000 0.845 0.856 27 44 22 43 29 33.000 39
; assembly_3 versus MA0610.2_rc (DMRT3_rc); m=13/15; ncol2=7; w=0; offset=4; strand=R; shift=5; score= 33; -----tGATAC ; cor=0.737; Ncor=0.402; logoDP=3.000; NsEucl=0.845; NSW=0.856; rcor=27; rNcor=44; rlogoDP=22; rNsEucl=43; rNSW=29; rank_mean=33.000; match_rank=39 a 0 0 0 0 0 97.0 0.0 694.0 0.0 999.0 0.0 c 0 0 0 0 0 97.0 0.0 104.0 0.0 0.0 999.0 g 0 0 0 0 0 188.0 999.0 0.0 0.0 0.0 0.0 t 0 0 0 0 0 618.0 0.0 202.0 999.0 0.0 0.0

MA0124.3_rc_shift1 (Nkx3-1_rc) 0.702 0.491 4.674 0.842 0.826 45 24 18 45 45 35.400 41
; assembly_3 versus MA0124.3_rc (Nkx3-1_rc); m=14/15; ncol2=7; w=0; offset=0; strand=R; shift=1; score= 35.4; -TAAGTGg--- ; cor=0.702; Ncor=0.491; logoDP=4.674; NsEucl=0.842; NSW=0.826; rcor=45; rNcor=24; rlogoDP=18; rNsEucl=45; rNSW=45; rank_mean=35.400; match_rank=41 a 0 523.0 5335.0 5335.0 9.0 88.0 336.0 275.0 0 0 0 c 0 173.0 0.0 0.0 9.0 10.0 10.0 1776.0 0 0 0 g 0 273.0 254.0 1.0 5335.0 28.0 5335.0 5335.0 0 0 0 t 0 5335.0 0.0 0.0 59.0 5335.0 0.0 981.0 0 0 0

MA0672.2_rc_shift0 (NKX2-3_rc) 0.706 0.449 2.012 0.847 0.837 41 33 24 41 41 36.000 42
; assembly_3 versus MA0672.2_rc (NKX2-3_rc); m=15/15; ncol2=8; w=-1; offset=-1; strand=R; shift=0; score= 36; tyAAGTGs--- ; cor=0.706; Ncor=0.449; logoDP=2.012; NsEucl=0.847; NSW=0.837; rcor=41; rNcor=33; rlogoDP=24; rNsEucl=41; rNSW=41; rank_mean=36.000; match_rank=42 a 2437.0 343.0 9278.0 9278.0 0.0 250.0 132.0 140.0 0 0 0 c 1831.0 5037.0 0.0 18.0 0.0 16.0 0.0 4499.0 0 0 0 g 917.0 1451.0 939.0 0.0 9278.0 98.0 9278.0 9278.0 0 0 0 t 9278.0 4241.0 0.0 0.0 8.0 9278.0 38.0 2025.0 0 0 0

Matrix name	cor	Ncor	logoDP	NsEucl	NSW	rcor	rNcor	rlogoDP	rNsEucl	rNSW	rank_mean	match_rank	Aligned matrices
assembly_3_shift1 (assembly_3)													; assembly_3; m=0 (reference); ncol1=10; shift=1; ncol=11; -wvAGTGATth ; Alignment reference a 0 8 6 15 0 0 0 15 0 3 4 c 0 0 4 0 0 0 0 0 0 3 6 g 0 3 5 0 15 0 15 0 0 3 1 t 0 4 0 0 0 15 0 0 15 6 4
MA0914.2_rc_shift1 (ISL2_rc)	0.821	0.492	1.426	0.877	0.910	14	23	29	17	11	18.800	15	; assembly_3 versus MA0914.2_rc (ISL2_rc); m=1/15; ncol2=6; w=0; offset=0; strand=R; shift=1; score= 18.8; -TAAkTG---- ; cor=0.821; Ncor=0.492; logoDP=1.426; NsEucl=0.877; NSW=0.910; rcor=14; rNcor=23; rlogoDP=29; rNsEucl=17; rNSW=11; rank_mean=18.800; match_rank=15 a 0 1354.0 5631.0 5631.0 398.0 248.0 1019.0 0 0 0 0 c 0 59.0 13.0 169.0 171.0 134.0 126.0 0 0 0 0 g 0 206.0 718.0 130.0 5631.0 162.0 5631.0 0 0 0 0 t 0 5631.0 278.0 218.0 3161.0 5631.0 160.0 0 0 0 0
MA0063.3_rc_shift0 (NKX2-5_rc)	0.851	0.464	0.461	0.882	0.916	8	26	41	15	9	19.800	17	; assembly_3 versus MA0063.3_rc (NKX2-5_rc); m=2/15; ncol2=7; w=-1; offset=-1; strand=R; shift=0; score= 19.8; TTGAGTG---- ; cor=0.851; Ncor=0.464; logoDP=0.461; NsEucl=0.882; NSW=0.916; rcor=8; rNcor=26; rlogoDP=41; rNsEucl=15; rNSW=9; rank_mean=19.800; match_rank=17 a 250.0 288.0 841.0 5166.0 153.0 74.0 322.0 0 0 0 0 c 98.0 217.0 62.0 61.0 49.0 76.0 24.0 0 0 0 0 g 165.0 120.0 4319.0 82.0 5098.0 48.0 5002.0 0 0 0 0 t 4931.0 4819.0 222.0 135.0 144.0 5246.0 96.0 0 0 0 0
MA0038.3_rc_shift0 (GFI1_rc)	0.744	0.677	0.849	0.884	0.866	24	3	36	12	26	20.200	18	; assembly_3 versus MA0038.3_rc (GFI1_rc); m=3/15; ncol2=11; w=-1; offset=-1; strand=R; shift=0; score= 20.2; tGChGTGATTk ; cor=0.744; Ncor=0.677; logoDP=0.849; NsEucl=0.884; NSW=0.866; rcor=24; rNcor=3; rlogoDP=36; rNsEucl=12; rNSW=26; rank_mean=20.200; match_rank=18 a 4134.0 3702.0 888.0 13996.0 0.0 1594.0 10.0 30161.0 1.0 0.0 565.0 c 4079.0 0.0 27514.0 8349.0 3888.0 0.0 0.0 0.0 0.0 0.0 812.0 g 5221.0 27891.0 266.0 54.0 27769.0 0.0 30139.0 0.0 0.0 2.0 10155.0 t 16713.0 292.0 2294.0 7748.0 838.0 29255.0 15.0 0.0 30150.0 30168.0 19146.0
MA1639.2_rc_shift5 (MEIS1_rc)	0.870	0.402	0.255	0.895	0.934	3	45	44	7	3	20.400	19	; assembly_3 versus MA1639.2_rc (MEIS1_rc); m=4/15; ncol2=9; w=0; offset=4; strand=R; shift=5; score= 20.4; -----TGATTk ; cor=0.870; Ncor=0.402; logoDP=0.255; NsEucl=0.895; NSW=0.934; rcor=3; rNcor=45; rlogoDP=44; rNsEucl=7; rNSW=3; rank_mean=20.400; match_rank=19 a 0 0 0 0 0 872.0 152.0 6459.0 218.0 304.0 609.0 c 0 0 0 0 0 152.0 61.0 63.0 192.0 33.0 252.0 g 0 0 0 0 0 279.0 6367.0 87.0 214.0 336.0 3580.0 t 0 0 0 0 0 5433.0 156.0 127.0 6112.0 6063.0 2295.0
MA1523.2_rc_shift0 (MSANTD3_rc)	0.831	0.453	0.507	0.878	0.910	12	29	39	16	10	21.200	20	; assembly_3 versus MA1523.2_rc (MSANTD3_rc); m=5/15; ncol2=7; w=-1; offset=-1; strand=R; shift=0; score= 21.2; kTGAGTG---- ; cor=0.831; Ncor=0.453; logoDP=0.507; NsEucl=0.878; NSW=0.910; rcor=12; rNcor=29; rlogoDP=39; rNsEucl=16; rNSW=10; rank_mean=21.200; match_rank=20 a 96.0 59.0 60.0 954.0 45.0 16.0 180.0 0 0 0 0 c 63.0 24.0 29.0 0.0 27.0 2.0 31.0 0 0 0 0 g 568.0 140.0 862.0 7.0 896.0 0.0 723.0 0 0 0 0 t 271.0 775.0 47.0 37.0 31.0 980.0 64.0 0 0 0 0
MA2336.1_rc_shift3 (ZSCAN21_rc)	0.765	0.536	2.185	0.858	0.858	19	10	23	29	28	21.800	23	; assembly_3 versus MA2336.1_rc (ZSCAN21_rc); m=6/15; ncol2=7; w=0; offset=2; strand=R; shift=3; score= 21.8; ---AGTGCTT- ; cor=0.765; Ncor=0.536; logoDP=2.185; NsEucl=0.858; NSW=0.858; rcor=19; rNcor=10; rlogoDP=23; rNsEucl=29; rNSW=28; rank_mean=21.800; match_rank=23 a 0 0 0 885.0 11.0 11.0 154.0 41.0 10.0 65.0 0 c 0 0 0 16.0 30.0 22.0 32.0 853.0 25.0 55.0 0 g 0 0 0 9.0 881.0 21.0 744.0 25.0 16.0 124.0 0 t 0 0 0 37.0 25.0 893.0 17.0 28.0 896.0 703.0 0
MA2339.1_rc_shift5 (Nanog_rc)	0.826	0.450	0.943	0.876	0.908	13	31	35	18	12	21.800	24	; assembly_3 versus MA2339.1_rc (Nanog_rc); m=7/15; ncol2=7; w=0; offset=4; strand=R; shift=5; score= 21.8; -----TGATTG ; cor=0.826; Ncor=0.450; logoDP=0.943; NsEucl=0.876; NSW=0.908; rcor=13; rNcor=31; rlogoDP=35; rNsEucl=18; rNSW=12; rank_mean=21.800; match_rank=24 a 0 0 0 0 0 277.0 746.0 8209.0 303.0 907.0 1130.0 c 0 0 0 0 0 180.0 149.0 124.0 196.0 365.0 93.0 g 0 0 0 0 0 131.0 7421.0 96.0 206.0 400.0 7298.0 t 0 0 0 0 0 8076.0 348.0 235.0 7959.0 6992.0 143.0
MA1644.2_rc_shift5 (NFYC_rc)	0.769	0.420	1.578	0.855	0.874	18	38	27	31	18	26.400	30	; assembly_3 versus MA1644.2_rc (NFYC_rc); m=8/15; ncol2=7; w=0; offset=4; strand=R; shift=5; score= 26.4; -----TGATTG ; cor=0.769; Ncor=0.420; logoDP=1.578; NsEucl=0.855; NSW=0.874; rcor=18; rNcor=38; rlogoDP=27; rNsEucl=31; rNSW=18; rank_mean=26.400; match_rank=30 a 0 0 0 0 0 188.0 396.0 12912.0 374.0 412.0 245.0 c 0 0 0 0 0 891.0 1464.0 71.0 549.0 103.0 111.0 g 0 0 0 0 0 711.0 11224.0 374.0 376.0 325.0 12880.0 t 0 0 0 0 0 11826.0 532.0 259.0 12317.0 12776.0 380.0
MA1994.2_rc_shift0 (Nkx2-1_rc)	0.779	0.425	0.438	0.854	0.872	16	36	42	34	19	29.400	32	; assembly_3 versus MA1994.2_rc (Nkx2-1_rc); m=9/15; ncol2=7; w=-1; offset=-1; strand=R; shift=0; score= 29.4; TCAAGTG---- ; cor=0.779; Ncor=0.425; logoDP=0.438; NsEucl=0.854; NSW=0.872; rcor=16; rNcor=36; rlogoDP=42; rNsEucl=34; rNSW=19; rank_mean=29.400; match_rank=32 a 541.0 518.0 15157.0 15106.0 316.0 343.0 886.0 0 0 0 0 c 213.0 14172.0 315.0 605.0 118.0 146.0 181.0 0 0 0 0 g 243.0 657.0 518.0 162.0 15640.0 275.0 14886.0 0 0 0 0 t 15245.0 895.0 252.0 369.0 168.0 15478.0 289.0 0 0 0 0
MA0122.4_rc_shift0 (Nkx3-2_rc)	0.708	0.579	0.154	0.871	0.849	38	5	45	25	35	29.600	33	; assembly_3 versus MA0122.4_rc (Nkx3-2_rc); m=10/15; ncol2=10; w=-1; offset=-1; strand=R; shift=0; score= 29.6; tTAAGTGktt- ; cor=0.708; Ncor=0.579; logoDP=0.154; NsEucl=0.871; NSW=0.849; rcor=38; rNcor=5; rlogoDP=45; rNsEucl=25; rNSW=35; rank_mean=29.600; match_rank=33 a 2241.0 325.0 9919.0 10109.0 94.0 212.0 218.0 1033.0 2359.0 2088.0 0 c 1368.0 68.0 68.0 29.0 10.0 19.0 23.0 1504.0 1154.0 1466.0 0 g 991.0 147.0 138.0 32.0 9965.0 82.0 9900.0 5079.0 1109.0 952.0 0 t 5620.0 9680.0 95.0 50.0 151.0 9907.0 79.0 2604.0 5598.0 5714.0 0
MA0673.2_rc_shift0 (NKX2-8_rc)	0.710	0.452	1.554	0.855	0.852	36	30	28	32	32	31.600	36	; assembly_3 versus MA0673.2_rc (NKX2-8_rc); m=11/15; ncol2=8; w=-1; offset=-1; strand=R; shift=0; score= 31.6; TsRAGTGs--- ; cor=0.710; Ncor=0.452; logoDP=1.554; NsEucl=0.855; NSW=0.852; rcor=36; rNcor=30; rlogoDP=28; rNsEucl=32; rNSW=32; rank_mean=31.600; match_rank=36 a 2158.0 271.0 8562.0 8562.0 110.0 516.0 2155.0 249.0 0 0 0 c 696.0 4286.0 0.0 0.0 0.0 0.0 0.0 2843.0 0 0 0 g 908.0 2267.0 3197.0 91.0 8562.0 595.0 8562.0 3529.0 0 0 0 t 8562.0 1738.0 23.0 0.0 14.0 8562.0 70.0 1942.0 0 0 0
MA2003.2_rc_shift0 (NKX2-4_rc)	0.707	0.450	1.694	0.854	0.851	39	32	26	33	34	32.800	38	; assembly_3 versus MA2003.2_rc (NKX2-4_rc); m=12/15; ncol2=8; w=-1; offset=-1; strand=R; shift=0; score= 32.8; TsAAGTGg--- ; cor=0.707; Ncor=0.450; logoDP=1.694; NsEucl=0.854; NSW=0.851; rcor=39; rNcor=32; rlogoDP=26; rNsEucl=33; rNSW=34; rank_mean=32.800; match_rank=38 a 153.0 58.0 1185.0 1185.0 0.0 207.0 129.0 61.0 0 0 0 c 57.0 640.0 13.0 1.0 0.0 17.0 7.0 485.0 0 0 0 g 56.0 545.0 409.0 25.0 1185.0 127.0 1185.0 1185.0 0 0 0 t 1185.0 243.0 52.0 0.0 0.0 1185.0 14.0 385.0 0 0 0
MA0610.2_rc_shift5 (DMRT3_rc)	0.737	0.402	3.000	0.845	0.856	27	44	22	43	29	33.000	39	; assembly_3 versus MA0610.2_rc (DMRT3_rc); m=13/15; ncol2=7; w=0; offset=4; strand=R; shift=5; score= 33; -----tGATAC ; cor=0.737; Ncor=0.402; logoDP=3.000; NsEucl=0.845; NSW=0.856; rcor=27; rNcor=44; rlogoDP=22; rNsEucl=43; rNSW=29; rank_mean=33.000; match_rank=39 a 0 0 0 0 0 97.0 0.0 694.0 0.0 999.0 0.0 c 0 0 0 0 0 97.0 0.0 104.0 0.0 0.0 999.0 g 0 0 0 0 0 188.0 999.0 0.0 0.0 0.0 0.0 t 0 0 0 0 0 618.0 0.0 202.0 999.0 0.0 0.0
MA0124.3_rc_shift1 (Nkx3-1_rc)	0.702	0.491	4.674	0.842	0.826	45	24	18	45	45	35.400	41	; assembly_3 versus MA0124.3_rc (Nkx3-1_rc); m=14/15; ncol2=7; w=0; offset=0; strand=R; shift=1; score= 35.4; -TAAGTGg--- ; cor=0.702; Ncor=0.491; logoDP=4.674; NsEucl=0.842; NSW=0.826; rcor=45; rNcor=24; rlogoDP=18; rNsEucl=45; rNSW=45; rank_mean=35.400; match_rank=41 a 0 523.0 5335.0 5335.0 9.0 88.0 336.0 275.0 0 0 0 c 0 173.0 0.0 0.0 9.0 10.0 10.0 1776.0 0 0 0 g 0 273.0 254.0 1.0 5335.0 28.0 5335.0 5335.0 0 0 0 t 0 5335.0 0.0 0.0 59.0 5335.0 0.0 981.0 0 0 0
MA0672.2_rc_shift0 (NKX2-3_rc)	0.706	0.449	2.012	0.847	0.837	41	33	24	41	41	36.000	42	; assembly_3 versus MA0672.2_rc (NKX2-3_rc); m=15/15; ncol2=8; w=-1; offset=-1; strand=R; shift=0; score= 36; tyAAGTGs--- ; cor=0.706; Ncor=0.449; logoDP=2.012; NsEucl=0.847; NSW=0.837; rcor=41; rNcor=33; rlogoDP=24; rNsEucl=41; rNSW=41; rank_mean=36.000; match_rank=42 a 2437.0 343.0 9278.0 9278.0 0.0 250.0 132.0 140.0 0 0 0 c 1831.0 5037.0 0.0 18.0 0.0 16.0 0.0 4499.0 0 0 0 g 917.0 1451.0 939.0 0.0 9278.0 98.0 9278.0 9278.0 0 0 0 t 9278.0 4241.0 0.0 0.0 8.0 9278.0 38.0 2025.0 0 0 0

One-to-n matrix alignment; reference matrix: assembly_1_shift0 ; 3 matrices ; sort_field=rank_mean

Matrix name Aligned logos cor Ncor logoDP NsEucl NSW rcor rNcor rlogoDP rNsEucl rNSW rank_mean match_rank Aligned matrices
assembly_1_shift0 (assembly_1)
; assembly_1; m=0 (reference); ncol1=12; shift=0; ncol=12; rvATATCTAGch ; Alignment reference a 5 4 15 1 13 1 0 1 15 0 2 5 c 2 5 0 0 0 2 14 1 0 0 7 4 g 5 4 0 0 1 1 0 0 0 15 3 0 t 3 2 0 14 1 11 1 13 0 0 3 6

MA1153.2_shift3 (Smad4) 0.724 0.423 5.882 0.847 0.837 31 37 11 39 39 31.400 35
; assembly_1 versus MA1153.2 (Smad4); m=1/2; ncol2=7; w=0; offset=3; strand=D; shift=3; score= 31.4; ---yGTCTrG-- ; cor=0.724; Ncor=0.423; logoDP=5.882; NsEucl=0.847; NSW=0.837; rcor=31; rNcor=37; rlogoDP=11; rNsEucl=39; rNSW=39; rank_mean=31.400; match_rank=35 a 0 0 0 88.0 0.0 0.0 0.0 0.0 596.0 0.0 0 0 c 0 0 0 250.0 0.0 0.0 1000.0 0.0 0.0 0.0 0 0 g 0 0 0 81.0 1000.0 0.0 0.0 0.0 404.0 1000.0 0 0 t 0 0 0 581.0 0.0 1000.0 0.0 1000.0 0.0 0.0 0 0

MA0036.4_shift1 (GATA2) 0.711 0.415 4.517 0.850 0.843 35 41 19 37 37 33.800 40
; assembly_1 versus MA0036.4 (GATA2); m=2/2; ncol2=7; w=0; offset=1; strand=D; shift=1; score= 33.8; -CTTATCT---- ; cor=0.711; Ncor=0.415; logoDP=4.517; NsEucl=0.850; NSW=0.843; rcor=35; rNcor=41; rlogoDP=19; rNsEucl=37; rNSW=37; rank_mean=33.800; match_rank=40 a 0 940.0 444.0 417.0 14098.0 145.0 96.0 2373.0 0 0 0 0 c 0 10607.0 259.0 34.0 14.0 77.0 13786.0 492.0 0 0 0 0 g 0 1223.0 150.0 21.0 43.0 48.0 126.0 367.0 0 0 0 0 t 0 1443.0 13360.0 13741.0 58.0 13943.0 205.0 10981.0 0 0 0 0