One-to-n alignments

Command: compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2026/03/29/compare-matrices_2026-03-29.155109_sgXuti/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 0.9 -lth Ncor 0.5 -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/2026/03/29/compare-matrices_2026-03-29.155109_sgXuti/compare-matrices.tab

One-to-n matrix alignment; reference matrix: assembly_4_shift0 ; 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_shift0 (assembly_4)
; assembly_4; m=0 (reference); ncol1=12; shift=0; ncol=12; wvAGTGAGTCaa ; Alignment reference a 5 4 15 1 0 0 15 0 1 1 8 10 c 2 5 0 0 0 1 0 0 1 12 3 0 g 3 4 0 14 1 14 0 15 2 1 1 2 t 5 2 0 0 14 0 0 0 11 1 3 3

MA0835.3_rc_shift4 (BATF3_rc) 0.952 0.555 4.935 0.935 0.970 1 4 9 1 1 3.200 1
; assembly_4 versus MA0835.3_rc (BATF3_rc); m=1/5; ncol2=7; w=0; offset=4; strand=R; shift=4; score= 3.2; ----TGAGTCA- ; cor=0.952; Ncor=0.555; logoDP=4.935; NsEucl=0.935; NSW=0.970; rcor=1; rNcor=4; rlogoDP=9; rNsEucl=1; rNSW=1; rank_mean=3.200; match_rank=1 a 0 0 0 0 235.0 282.0 11502.0 408.0 116.0 1238.0 11737.0 0 c 0 0 0 0 117.0 88.0 117.0 560.0 87.0 10420.0 37.0 0 g 0 0 0 0 84.0 10347.0 79.0 10589.0 92.0 62.0 59.0 0 t 0 0 0 0 11529.0 1248.0 267.0 408.0 11670.0 245.0 132.0 0

MA1988.2_rc_shift4 (Atf3_rc) 0.947 0.552 4.839 0.934 0.969 2 5 11 2 2 4.400 2
; assembly_4 versus MA1988.2_rc (Atf3_rc); m=2/5; ncol2=7; w=0; offset=4; strand=R; shift=4; score= 4.4; ----TGAGTCA- ; cor=0.947; Ncor=0.552; logoDP=4.839; NsEucl=0.934; NSW=0.969; rcor=2; rNcor=5; rlogoDP=11; rNsEucl=2; rNSW=2; rank_mean=4.400; match_rank=2 a 0 0 0 0 887.0 2087.0 50485.0 2262.0 547.0 3914.0 53085.0 0 c 0 0 0 0 1086.0 574.0 1365.0 4498.0 471.0 48774.0 357.0 0 g 0 0 0 0 673.0 46610.0 504.0 45670.0 356.0 443.0 669.0 0 t 0 0 0 0 52046.0 5421.0 2338.0 2262.0 53318.0 1561.0 581.0 0

MA0462.3_rc_shift4 (BATF::JUN_rc) 0.946 0.552 4.945 0.933 0.968 3 6 8 4 3 4.800 4
; assembly_4 versus MA0462.3_rc (BATF::JUN_rc); m=3/5; ncol2=7; w=0; offset=4; strand=R; shift=4; score= 4.8; ----TGAGTCA- ; cor=0.946; Ncor=0.552; logoDP=4.945; NsEucl=0.933; NSW=0.968; rcor=3; rNcor=6; rlogoDP=8; rNsEucl=4; rNSW=3; rank_mean=4.800; match_rank=4 a 0 0 0 0 558.0 907.0 36619.0 1399.0 320.0 3785.0 37330.0 0 c 0 0 0 0 424.0 522.0 539.0 4188.0 350.0 33135.0 182.0 0 g 0 0 0 0 318.0 32770.0 241.0 31168.0 204.0 400.0 275.0 0 t 0 0 0 0 36854.0 3955.0 755.0 1399.0 37280.0 834.0 367.0 0

MA1928.2_shift4 (BNC2) 0.945 0.551 5.252 0.932 0.968 4 7 6 5 4 5.200 5
; assembly_4 versus MA1928.2 (BNC2); m=4/5; ncol2=7; w=0; offset=4; strand=D; shift=4; score= 5.2; ----TGAGTCA- ; cor=0.945; Ncor=0.551; logoDP=5.252; NsEucl=0.932; NSW=0.968; rcor=4; rNcor=7; rlogoDP=6; rNsEucl=5; rNSW=4; rank_mean=5.200; match_rank=5 a 0 0 0 0 147.0 134.0 5303.0 227.0 86.0 216.0 5483.0 0 c 0 0 0 0 66.0 72.0 117.0 838.0 106.0 5238.0 54.0 0 g 0 0 0 0 96.0 5184.0 61.0 4332.0 80.0 112.0 56.0 0 t 0 0 0 0 5363.0 282.0 191.0 275.0 5400.0 106.0 79.0 0

MA1634.2_rc_shift4 (BATF_rc) 0.944 0.551 4.891 0.932 0.968 5 8 10 6 5 6.800 6
; assembly_4 versus MA1634.2_rc (BATF_rc); m=5/5; ncol2=7; w=0; offset=4; strand=R; shift=4; score= 6.8; ----TGAGTCA- ; cor=0.944; Ncor=0.551; logoDP=4.891; NsEucl=0.932; NSW=0.968; rcor=5; rNcor=8; rlogoDP=10; rNsEucl=6; rNSW=5; rank_mean=6.800; match_rank=6 a 0 0 0 0 754.0 1276.0 44736.0 2051.0 471.0 4682.0 45887.0 0 c 0 0 0 0 507.0 711.0 836.0 5573.0 341.0 40617.0 283.0 0 g 0 0 0 0 431.0 40279.0 306.0 37333.0 250.0 570.0 355.0 0 t 0 0 0 0 45316.0 4742.0 1130.0 2051.0 45946.0 1139.0 483.0 0

Matrix name	cor	Ncor	logoDP	NsEucl	NSW	rcor	rNcor	rlogoDP	rNsEucl	rNSW	rank_mean	match_rank	Aligned matrices
assembly_4_shift0 (assembly_4)													; assembly_4; m=0 (reference); ncol1=12; shift=0; ncol=12; wvAGTGAGTCaa ; Alignment reference a 5 4 15 1 0 0 15 0 1 1 8 10 c 2 5 0 0 0 1 0 0 1 12 3 0 g 3 4 0 14 1 14 0 15 2 1 1 2 t 5 2 0 0 14 0 0 0 11 1 3 3
MA0835.3_rc_shift4 (BATF3_rc)	0.952	0.555	4.935	0.935	0.970	1	4	9	1	1	3.200	1	; assembly_4 versus MA0835.3_rc (BATF3_rc); m=1/5; ncol2=7; w=0; offset=4; strand=R; shift=4; score= 3.2; ----TGAGTCA- ; cor=0.952; Ncor=0.555; logoDP=4.935; NsEucl=0.935; NSW=0.970; rcor=1; rNcor=4; rlogoDP=9; rNsEucl=1; rNSW=1; rank_mean=3.200; match_rank=1 a 0 0 0 0 235.0 282.0 11502.0 408.0 116.0 1238.0 11737.0 0 c 0 0 0 0 117.0 88.0 117.0 560.0 87.0 10420.0 37.0 0 g 0 0 0 0 84.0 10347.0 79.0 10589.0 92.0 62.0 59.0 0 t 0 0 0 0 11529.0 1248.0 267.0 408.0 11670.0 245.0 132.0 0
MA1988.2_rc_shift4 (Atf3_rc)	0.947	0.552	4.839	0.934	0.969	2	5	11	2	2	4.400	2	; assembly_4 versus MA1988.2_rc (Atf3_rc); m=2/5; ncol2=7; w=0; offset=4; strand=R; shift=4; score= 4.4; ----TGAGTCA- ; cor=0.947; Ncor=0.552; logoDP=4.839; NsEucl=0.934; NSW=0.969; rcor=2; rNcor=5; rlogoDP=11; rNsEucl=2; rNSW=2; rank_mean=4.400; match_rank=2 a 0 0 0 0 887.0 2087.0 50485.0 2262.0 547.0 3914.0 53085.0 0 c 0 0 0 0 1086.0 574.0 1365.0 4498.0 471.0 48774.0 357.0 0 g 0 0 0 0 673.0 46610.0 504.0 45670.0 356.0 443.0 669.0 0 t 0 0 0 0 52046.0 5421.0 2338.0 2262.0 53318.0 1561.0 581.0 0
MA0462.3_rc_shift4 (BATF::JUN_rc)	0.946	0.552	4.945	0.933	0.968	3	6	8	4	3	4.800	4	; assembly_4 versus MA0462.3_rc (BATF::JUN_rc); m=3/5; ncol2=7; w=0; offset=4; strand=R; shift=4; score= 4.8; ----TGAGTCA- ; cor=0.946; Ncor=0.552; logoDP=4.945; NsEucl=0.933; NSW=0.968; rcor=3; rNcor=6; rlogoDP=8; rNsEucl=4; rNSW=3; rank_mean=4.800; match_rank=4 a 0 0 0 0 558.0 907.0 36619.0 1399.0 320.0 3785.0 37330.0 0 c 0 0 0 0 424.0 522.0 539.0 4188.0 350.0 33135.0 182.0 0 g 0 0 0 0 318.0 32770.0 241.0 31168.0 204.0 400.0 275.0 0 t 0 0 0 0 36854.0 3955.0 755.0 1399.0 37280.0 834.0 367.0 0
MA1928.2_shift4 (BNC2)	0.945	0.551	5.252	0.932	0.968	4	7	6	5	4	5.200	5	; assembly_4 versus MA1928.2 (BNC2); m=4/5; ncol2=7; w=0; offset=4; strand=D; shift=4; score= 5.2; ----TGAGTCA- ; cor=0.945; Ncor=0.551; logoDP=5.252; NsEucl=0.932; NSW=0.968; rcor=4; rNcor=7; rlogoDP=6; rNsEucl=5; rNSW=4; rank_mean=5.200; match_rank=5 a 0 0 0 0 147.0 134.0 5303.0 227.0 86.0 216.0 5483.0 0 c 0 0 0 0 66.0 72.0 117.0 838.0 106.0 5238.0 54.0 0 g 0 0 0 0 96.0 5184.0 61.0 4332.0 80.0 112.0 56.0 0 t 0 0 0 0 5363.0 282.0 191.0 275.0 5400.0 106.0 79.0 0
MA1634.2_rc_shift4 (BATF_rc)	0.944	0.551	4.891	0.932	0.968	5	8	10	6	5	6.800	6	; assembly_4 versus MA1634.2_rc (BATF_rc); m=5/5; ncol2=7; w=0; offset=4; strand=R; shift=4; score= 6.8; ----TGAGTCA- ; cor=0.944; Ncor=0.551; logoDP=4.891; NsEucl=0.932; NSW=0.968; rcor=5; rNcor=8; rlogoDP=10; rNsEucl=6; rNSW=5; rank_mean=6.800; match_rank=6 a 0 0 0 0 754.0 1276.0 44736.0 2051.0 471.0 4682.0 45887.0 0 c 0 0 0 0 507.0 711.0 836.0 5573.0 341.0 40617.0 283.0 0 g 0 0 0 0 431.0 40279.0 306.0 37333.0 250.0 570.0 355.0 0 t 0 0 0 0 45316.0 4742.0 1130.0 2051.0 45946.0 1139.0 483.0 0

One-to-n matrix alignment; reference matrix: assembly_5_shift1 ; 2 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_shift1 (assembly_5)
; assembly_5; m=0 (reference); ncol1=12; shift=1; ncol=13; -wrAGTCAAGAar ; Alignment reference a 0 7 7 17 2 1 1 16 16 1 17 10 6 c 0 1 3 0 0 0 14 1 1 1 0 0 2 g 0 2 6 0 15 1 0 0 0 14 0 4 5 t 0 7 1 0 0 15 2 0 0 1 0 3 4

MA0676.1_shift0 (Nr2e1) 0.930 0.572 5.991 0.933 0.964 6 3 4 3 6 4.400 3
; assembly_5 versus MA0676.1 (Nr2e1); m=1/1; ncol2=9; w=-1; offset=-1; strand=D; shift=0; score= 4.4; aaAAGTCAA---- ; cor=0.930; Ncor=0.572; logoDP=5.991; NsEucl=0.933; NSW=0.964; rcor=6; rNcor=3; rlogoDP=4; rNsEucl=3; rNSW=6; rank_mean=4.400; match_rank=3 a 1118.0 1118.0 1118.0 1118.0 40.0 0.0 11.0 1118.0 1118.0 0 0 0 0 c 244.0 89.0 1.0 0.0 0.0 58.0 1118.0 0.0 131.0 0 0 0 0 g 191.0 448.0 101.0 74.0 1118.0 0.0 12.0 0.0 117.0 0 0 0 0 t 401.0 369.0 19.0 5.0 8.0 1118.0 112.0 0.0 247.0 0 0 0 0

Matrix name	Aligned logos	cor	Ncor	logoDP	NsEucl	NSW	rcor	rNcor	rlogoDP	rNsEucl	rNSW	rank_mean	match_rank	Aligned matrices
assembly_5_shift1 (assembly_5)														; assembly_5; m=0 (reference); ncol1=12; shift=1; ncol=13; -wrAGTCAAGAar ; Alignment reference a 0 7 7 17 2 1 1 16 16 1 17 10 6 c 0 1 3 0 0 0 14 1 1 1 0 0 2 g 0 2 6 0 15 1 0 0 0 14 0 4 5 t 0 7 1 0 0 15 2 0 0 1 0 3 4
MA0676.1_shift0 (Nr2e1)		0.930	0.572	5.991	0.933	0.964	6	3	4	3	6	4.400	3	; assembly_5 versus MA0676.1 (Nr2e1); m=1/1; ncol2=9; w=-1; offset=-1; strand=D; shift=0; score= 4.4; aaAAGTCAA---- ; cor=0.930; Ncor=0.572; logoDP=5.991; NsEucl=0.933; NSW=0.964; rcor=6; rNcor=3; rlogoDP=4; rNsEucl=3; rNSW=6; rank_mean=4.400; match_rank=3 a 1118.0 1118.0 1118.0 1118.0 40.0 0.0 11.0 1118.0 1118.0 0 0 0 0 c 244.0 89.0 1.0 0.0 0.0 58.0 1118.0 0.0 131.0 0 0 0 0 g 191.0 448.0 101.0 74.0 1118.0 0.0 12.0 0.0 117.0 0 0 0 0 t 401.0 369.0 19.0 5.0 8.0 1118.0 112.0 0.0 247.0 0 0 0 0

One-to-n matrix alignment; reference matrix: assembly_3_shift0 ; 2 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_shift0 (assembly_3)
; assembly_3; m=0 (reference); ncol1=11; shift=0; ncol=11; wcCCCAGCChy ; Alignment reference a 12 8 2 1 0 41 5 1 2 16 8 c 10 18 32 38 40 0 0 39 33 14 12 g 9 8 4 0 1 1 36 2 1 1 7 t 11 8 4 3 1 0 1 0 6 11 15

MA2341.1_shift2 (FEZF2) 0.916 0.666 5.165 0.927 0.957 10 1 7 8 9 7.000 7
; assembly_3 versus MA2341.1 (FEZF2); m=1/1; ncol2=8; w=0; offset=2; strand=D; shift=2; score= 7; --CCCAGCCT- ; cor=0.916; Ncor=0.666; logoDP=5.165; NsEucl=0.927; NSW=0.957; rcor=10; rNcor=1; rlogoDP=7; rNsEucl=8; rNSW=9; rank_mean=7.000; match_rank=7 a 0 0 17.0 5.0 4.0 231.0 6.0 8.0 7.0 14.0 0 c 0 0 202.0 206.0 258.0 15.0 8.0 224.0 247.0 10.0 0 g 0 0 10.0 9.0 0.0 14.0 251.0 28.0 2.0 8.0 0 t 0 0 36.0 45.0 3.0 5.0 0.0 5.0 9.0 233.0 0

Matrix name	Aligned logos	cor	Ncor	logoDP	NsEucl	NSW	rcor	rNcor	rlogoDP	rNsEucl	rNSW	rank_mean	match_rank	Aligned matrices
assembly_3_shift0 (assembly_3)														; assembly_3; m=0 (reference); ncol1=11; shift=0; ncol=11; wcCCCAGCChy ; Alignment reference a 12 8 2 1 0 41 5 1 2 16 8 c 10 18 32 38 40 0 0 39 33 14 12 g 9 8 4 0 1 1 36 2 1 1 7 t 11 8 4 3 1 0 1 0 6 11 15
MA2341.1_shift2 (FEZF2)		0.916	0.666	5.165	0.927	0.957	10	1	7	8	9	7.000	7	; assembly_3 versus MA2341.1 (FEZF2); m=1/1; ncol2=8; w=0; offset=2; strand=D; shift=2; score= 7; --CCCAGCCT- ; cor=0.916; Ncor=0.666; logoDP=5.165; NsEucl=0.927; NSW=0.957; rcor=10; rNcor=1; rlogoDP=7; rNsEucl=8; rNSW=9; rank_mean=7.000; match_rank=7 a 0 0 17.0 5.0 4.0 231.0 6.0 8.0 7.0 14.0 0 c 0 0 202.0 206.0 258.0 15.0 8.0 224.0 247.0 10.0 0 g 0 0 10.0 9.0 0.0 14.0 251.0 28.0 2.0 8.0 0 t 0 0 36.0 45.0 3.0 5.0 0.0 5.0 9.0 233.0 0

One-to-n matrix alignment; reference matrix: assembly_1_shift0 ; 2 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; kyCCTGGGCCmd ; Alignment reference a 1 0 0 0 0 0 1 0 1 0 4 4 c 3 5 14 13 0 0 0 0 13 13 8 2 g 4 3 1 0 0 15 13 15 1 0 0 4 t 7 7 0 2 15 0 1 0 0 2 3 5

MA1986.2_rc_shift3 (ZNF692_rc) 0.930 0.620 2.948 0.929 0.960 7 2 13 7 7 7.200 8
; assembly_1 versus MA1986.2_rc (ZNF692_rc); m=1/1; ncol2=8; w=0; offset=3; strand=R; shift=3; score= 7.2; ---sTGGGCCc- ; cor=0.930; Ncor=0.620; logoDP=2.948; NsEucl=0.929; NSW=0.960; rcor=7; rNcor=2; rlogoDP=13; rNsEucl=7; rNSW=7; rank_mean=7.200; match_rank=8 a 0 0 0 1192.0 0.0 21.0 17.0 22.0 26.0 13.0 1195.0 0 c 0 0 0 3703.0 210.0 176.0 241.0 7.0 10684.0 10642.0 6833.0 0 g 0 0 0 4998.0 0.0 10545.0 10446.0 10689.0 4.0 90.0 1314.0 0 t 0 0 0 852.0 10535.0 3.0 41.0 27.0 31.0 0.0 1403.0 0

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; kyCCTGGGCCmd ; Alignment reference a 1 0 0 0 0 0 1 0 1 0 4 4 c 3 5 14 13 0 0 0 0 13 13 8 2 g 4 3 1 0 0 15 13 15 1 0 0 4 t 7 7 0 2 15 0 1 0 0 2 3 5
MA1986.2_rc_shift3 (ZNF692_rc)		0.930	0.620	2.948	0.929	0.960	7	2	13	7	7	7.200	8	; assembly_1 versus MA1986.2_rc (ZNF692_rc); m=1/1; ncol2=8; w=0; offset=3; strand=R; shift=3; score= 7.2; ---sTGGGCCc- ; cor=0.930; Ncor=0.620; logoDP=2.948; NsEucl=0.929; NSW=0.960; rcor=7; rNcor=2; rlogoDP=13; rNsEucl=7; rNSW=7; rank_mean=7.200; match_rank=8 a 0 0 0 1192.0 0.0 21.0 17.0 22.0 26.0 13.0 1195.0 0 c 0 0 0 3703.0 210.0 176.0 241.0 7.0 10684.0 10642.0 6833.0 0 g 0 0 0 4998.0 0.0 10545.0 10446.0 10689.0 4.0 90.0 1314.0 0 t 0 0 0 852.0 10535.0 3.0 41.0 27.0 31.0 0.0 1403.0 0

One-to-n matrix alignment; reference matrix: assembly_2_shift0 ; 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_2_shift0 (assembly_2)
; assembly_2; m=0 (reference); ncol1=12; shift=0; ncol=12; rwAATTAAAcyy ; Alignment reference a 8 10 26 25 2 1 26 26 26 4 6 5 c 4 5 0 1 1 2 0 0 0 16 7 8 g 9 4 0 0 1 2 0 0 0 2 2 5 t 5 7 0 0 22 21 0 0 0 4 11 8

MA1519.2_shift0 (LHX5) 0.926 0.540 6.723 0.923 0.958 8 9 2 9 8 7.200 9
; assembly_2 versus MA1519.2 (LHX5); m=1/5; ncol2=7; w=0; offset=0; strand=D; shift=0; score= 7.2; sYAATTA----- ; cor=0.926; Ncor=0.540; logoDP=6.723; NsEucl=0.923; NSW=0.958; rcor=8; rNcor=9; rlogoDP=2; rNsEucl=9; rNSW=8; rank_mean=7.200; match_rank=9 a 394.0 0.0 7142.0 7142.0 0.0 0.0 7142.0 0 0 0 0 0 c 3420.0 2093.0 187.0 0.0 0.0 144.0 0.0 0 0 0 0 0 g 3721.0 0.0 0.0 0.0 0.0 28.0 160.0 0 0 0 0 0 t 1215.0 5049.0 0.0 0.0 7142.0 7142.0 0.0 0 0 0 0 0

MA0889.2_shift0 (GBX1) 0.920 0.536 6.393 0.921 0.957 9 10 3 10 10 8.400 10
; assembly_2 versus MA0889.2 (GBX1); m=2/5; ncol2=7; w=0; offset=0; strand=D; shift=0; score= 8.4; syAATTA----- ; cor=0.920; Ncor=0.536; logoDP=6.393; NsEucl=0.921; NSW=0.957; rcor=9; rNcor=10; rlogoDP=3; rNsEucl=10; rNSW=10; rank_mean=8.400; match_rank=10 a 1674.0 243.0 27339.0 27339.0 45.0 312.0 27339.0 0 0 0 0 0 c 14978.0 13543.0 589.0 172.0 128.0 438.0 50.0 0 0 0 0 0 g 6964.0 15.0 758.0 29.0 1.0 246.0 8.0 0 0 0 0 0 t 3723.0 13796.0 157.0 23.0 27339.0 27339.0 321.0 0 0 0 0 0

MA0075.4_shift0 (PRRX2) 0.908 0.530 6.754 0.914 0.948 11 11 1 12 12 9.400 11
; assembly_2 versus MA0075.4 (PRRX2); m=3/5; ncol2=7; w=0; offset=0; strand=D; shift=0; score= 9.4; cyAATTA----- ; cor=0.908; Ncor=0.530; logoDP=6.754; NsEucl=0.914; NSW=0.948; rcor=11; rNcor=11; rlogoDP=1; rNsEucl=12; rNSW=12; rank_mean=9.400; match_rank=11 a 778.0 122.0 6720.0 6720.0 0.0 0.0 6720.0 0 0 0 0 0 c 6720.0 2008.0 29.0 0.0 0.0 0.0 1.0 0 0 0 0 0 g 1613.0 131.0 3.0 0.0 0.0 0.0 399.0 0 0 0 0 0 t 1933.0 4711.0 0.0 0.0 6720.0 6720.0 0.0 0 0 0 0 0

MA0644.3_shift0 (ESX1) 0.908 0.530 5.860 0.918 0.953 12 12 5 11 11 10.200 12
; assembly_2 versus MA0644.3 (ESX1); m=4/5; ncol2=7; w=0; offset=0; strand=D; shift=0; score= 10.2; yyAATTA----- ; cor=0.908; Ncor=0.530; logoDP=5.860; NsEucl=0.918; NSW=0.953; rcor=12; rNcor=12; rlogoDP=5; rNsEucl=11; rNSW=11; rank_mean=10.200; match_rank=12 a 1070.0 589.0 19670.0 19670.0 0.0 47.0 19670.0 0 0 0 0 0 c 11980.0 7595.0 634.0 95.0 0.0 1009.0 0.0 0 0 0 0 0 g 2110.0 0.0 821.0 0.0 0.0 225.0 925.0 0 0 0 0 0 t 7690.0 12075.0 181.0 0.0 19670.0 19670.0 557.0 0 0 0 0 0

MA0621.2_rc_shift1 (mix-a_rc) 0.903 0.527 3.905 0.907 0.939 13 13 12 13 13 12.800 13
; assembly_2 versus MA0621.2_rc (mix-a_rc); m=5/5; ncol2=7; w=0; offset=1; strand=R; shift=1; score= 12.8; -TAATTAa---- ; cor=0.903; Ncor=0.527; logoDP=3.905; NsEucl=0.907; NSW=0.939; rcor=13; rNcor=13; rlogoDP=12; rNsEucl=13; rNSW=13; rank_mean=12.800; match_rank=13 a 0 21.0 1000.0 1000.0 0.0 0.0 1000.0 679.0 0 0 0 0 c 0 21.0 0.0 0.0 0.0 0.0 0.0 46.0 0 0 0 0 g 0 21.0 0.0 0.0 0.0 0.0 0.0 146.0 0 0 0 0 t 0 938.0 0.0 0.0 1000.0 1000.0 0.0 130.0 0 0 0 0

Matrix name	cor	Ncor	logoDP	NsEucl	NSW	rcor	rNcor	rlogoDP	rNsEucl	rNSW	rank_mean	match_rank	Aligned matrices
assembly_2_shift0 (assembly_2)													; assembly_2; m=0 (reference); ncol1=12; shift=0; ncol=12; rwAATTAAAcyy ; Alignment reference a 8 10 26 25 2 1 26 26 26 4 6 5 c 4 5 0 1 1 2 0 0 0 16 7 8 g 9 4 0 0 1 2 0 0 0 2 2 5 t 5 7 0 0 22 21 0 0 0 4 11 8
MA1519.2_shift0 (LHX5)	0.926	0.540	6.723	0.923	0.958	8	9	2	9	8	7.200	9	; assembly_2 versus MA1519.2 (LHX5); m=1/5; ncol2=7; w=0; offset=0; strand=D; shift=0; score= 7.2; sYAATTA----- ; cor=0.926; Ncor=0.540; logoDP=6.723; NsEucl=0.923; NSW=0.958; rcor=8; rNcor=9; rlogoDP=2; rNsEucl=9; rNSW=8; rank_mean=7.200; match_rank=9 a 394.0 0.0 7142.0 7142.0 0.0 0.0 7142.0 0 0 0 0 0 c 3420.0 2093.0 187.0 0.0 0.0 144.0 0.0 0 0 0 0 0 g 3721.0 0.0 0.0 0.0 0.0 28.0 160.0 0 0 0 0 0 t 1215.0 5049.0 0.0 0.0 7142.0 7142.0 0.0 0 0 0 0 0
MA0889.2_shift0 (GBX1)	0.920	0.536	6.393	0.921	0.957	9	10	3	10	10	8.400	10	; assembly_2 versus MA0889.2 (GBX1); m=2/5; ncol2=7; w=0; offset=0; strand=D; shift=0; score= 8.4; syAATTA----- ; cor=0.920; Ncor=0.536; logoDP=6.393; NsEucl=0.921; NSW=0.957; rcor=9; rNcor=10; rlogoDP=3; rNsEucl=10; rNSW=10; rank_mean=8.400; match_rank=10 a 1674.0 243.0 27339.0 27339.0 45.0 312.0 27339.0 0 0 0 0 0 c 14978.0 13543.0 589.0 172.0 128.0 438.0 50.0 0 0 0 0 0 g 6964.0 15.0 758.0 29.0 1.0 246.0 8.0 0 0 0 0 0 t 3723.0 13796.0 157.0 23.0 27339.0 27339.0 321.0 0 0 0 0 0
MA0075.4_shift0 (PRRX2)	0.908	0.530	6.754	0.914	0.948	11	11	1	12	12	9.400	11	; assembly_2 versus MA0075.4 (PRRX2); m=3/5; ncol2=7; w=0; offset=0; strand=D; shift=0; score= 9.4; cyAATTA----- ; cor=0.908; Ncor=0.530; logoDP=6.754; NsEucl=0.914; NSW=0.948; rcor=11; rNcor=11; rlogoDP=1; rNsEucl=12; rNSW=12; rank_mean=9.400; match_rank=11 a 778.0 122.0 6720.0 6720.0 0.0 0.0 6720.0 0 0 0 0 0 c 6720.0 2008.0 29.0 0.0 0.0 0.0 1.0 0 0 0 0 0 g 1613.0 131.0 3.0 0.0 0.0 0.0 399.0 0 0 0 0 0 t 1933.0 4711.0 0.0 0.0 6720.0 6720.0 0.0 0 0 0 0 0
MA0644.3_shift0 (ESX1)	0.908	0.530	5.860	0.918	0.953	12	12	5	11	11	10.200	12	; assembly_2 versus MA0644.3 (ESX1); m=4/5; ncol2=7; w=0; offset=0; strand=D; shift=0; score= 10.2; yyAATTA----- ; cor=0.908; Ncor=0.530; logoDP=5.860; NsEucl=0.918; NSW=0.953; rcor=12; rNcor=12; rlogoDP=5; rNsEucl=11; rNSW=11; rank_mean=10.200; match_rank=12 a 1070.0 589.0 19670.0 19670.0 0.0 47.0 19670.0 0 0 0 0 0 c 11980.0 7595.0 634.0 95.0 0.0 1009.0 0.0 0 0 0 0 0 g 2110.0 0.0 821.0 0.0 0.0 225.0 925.0 0 0 0 0 0 t 7690.0 12075.0 181.0 0.0 19670.0 19670.0 557.0 0 0 0 0 0
MA0621.2_rc_shift1 (mix-a_rc)	0.903	0.527	3.905	0.907	0.939	13	13	12	13	13	12.800	13	; assembly_2 versus MA0621.2_rc (mix-a_rc); m=5/5; ncol2=7; w=0; offset=1; strand=R; shift=1; score= 12.8; -TAATTAa---- ; cor=0.903; Ncor=0.527; logoDP=3.905; NsEucl=0.907; NSW=0.939; rcor=13; rNcor=13; rlogoDP=12; rNsEucl=13; rNSW=13; rank_mean=12.800; match_rank=13 a 0 21.0 1000.0 1000.0 0.0 0.0 1000.0 679.0 0 0 0 0 c 0 21.0 0.0 0.0 0.0 0.0 0.0 46.0 0 0 0 0 g 0 21.0 0.0 0.0 0.0 0.0 0.0 146.0 0 0 0 0 t 0 938.0 0.0 0.0 1000.0 1000.0 0.0 130.0 0 0 0 0