One-to-n alignments

Command: compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2019/07/04/compare-matrices_2019-07-04.133944_SG6Qfh/compare-matrices_query_matrices.transfac -file2 $RSAT/public_html/motif_databases/footprintDB/footprintDB.plants.motif.tf -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/2019/07/04/compare-matrices_2019-07-04.133944_SG6Qfh/compare-matrices.tab

One-to-n matrix alignment; reference matrix: dyads_test_vs_ctrl_m1_shift10 ; 15 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

dyads_test_vs_ctrl_m1_shift10 (dyads_test_vs_ctrl_m1)
; dyads_test_vs_ctrl_m1; m=0 (reference); ncol1=20; shift=10; ncol=30; ----------hmaccCtAAAACCCTAammh ; Alignment reference a 0 0 0 0 0 0 0 0 0 0 82 79 106 51 34 19 35 173 200 213 199 3 5 6 11 167 134 74 68 61 c 0 0 0 0 0 0 0 0 0 0 60 64 44 100 110 156 44 10 10 4 12 215 207 205 11 24 26 84 71 79 g 0 0 0 0 0 0 0 0 0 0 22 32 20 23 33 22 11 4 7 2 4 1 2 3 1 11 35 14 30 21 t 0 0 0 0 0 0 0 0 0 0 57 46 51 47 44 24 131 34 4 2 6 2 7 7 198 19 26 49 52 60

TRP2.ampDAP_M0612_AthalianaCistrome_shift11 (TRP2.ampDAP:M0612:AthalianaCistrome) 0.799 0.690 10.207 0.926 0.897 8 2 1 5 9 5.000 2
; dyads_test_vs_ctrl_m1 versus TRP2.ampDAP_M0612_AthalianaCistrome (TRP2.ampDAP:M0612:AthalianaCistrome); m=2/14; ncol2=21; w=19; offset=1; strand=D; shift=11; score= 5; -----------AAACCCTAAACCCTAAACC ; cor=0.799; Ncor=0.690; logoDP=10.207; NsEucl=0.926; NSW=0.897; rcor=8; rNcor=2; rlogoDP=1; rNsEucl=5; rNSW=9; rank_mean=5.000; match_rank=2 a 0 0 0 0 0 0 0 0 0 0 0 90 85 87 0 9 7 12 103 104 101 2 1 0 5 99 99 97 7 14 c 0 0 0 0 0 0 0 0 0 0 0 3 2 1 85 88 75 2 0 0 3 102 103 102 0 0 0 0 80 75 g 0 0 0 0 0 0 0 0 0 0 0 2 4 1 5 5 5 1 1 0 0 0 0 0 0 4 3 2 1 1 t 0 0 0 0 0 0 0 0 0 0 0 9 13 15 14 2 17 89 0 0 0 0 0 2 99 1 2 5 16 14

TBP3.ampDAP_M0621_AthalianaCistrome_rc_shift11 (TBP3.ampDAP:M0621:AthalianaCistrome_rc) 0.837 0.795 0.503 0.949 0.950 7 1 13 2 3 5.200 3
; dyads_test_vs_ctrl_m1 versus TBP3.ampDAP_M0621_AthalianaCistrome_rc (TBP3.ampDAP:M0621:AthalianaCistrome_rc); m=3/14; ncol2=19; w=19; offset=1; strand=R; shift=11; score= 5.2; -----------maamhhtaARCCCTAAwyy ; cor=0.837; Ncor=0.795; logoDP=0.503; NsEucl=0.949; NSW=0.950; rcor=7; rNcor=1; rlogoDP=13; rNsEucl=2; rNSW=3; rank_mean=5.200; match_rank=3 a 0 0 0 0 0 0 0 0 0 0 0 126 140 138 102 76 73 50 167 197 186 11 5 0 0 251 231 93 23 51 c 0 0 0 0 0 0 0 0 0 0 0 64 39 30 66 96 83 37 4 2 3 239 237 239 18 3 1 57 71 95 g 0 0 0 0 0 0 0 0 0 0 0 21 48 33 26 19 23 38 35 2 66 1 3 13 5 1 21 9 7 24 t 0 0 0 0 0 0 0 0 0 0 0 44 28 54 61 64 76 130 49 54 0 4 10 3 232 0 2 96 154 85

TBP3_MA1355.1_JASPAR_shift12 (TBP3:MA1355.1:JASPAR) 0.779 0.667 7.113 0.937 0.929 9 4 8 4 8 6.600 5
; dyads_test_vs_ctrl_m1 versus TBP3_MA1355.1_JASPAR (TBP3:MA1355.1:JASPAR); m=5/14; ncol2=19; w=18; offset=2; strand=D; shift=12; score= 6.6; ------------awwwhtwwrCCCTAAwtw ; cor=0.779; Ncor=0.667; logoDP=7.113; NsEucl=0.937; NSW=0.929; rcor=9; rNcor=4; rlogoDP=8; rNsEucl=4; rNSW=8; rank_mean=6.600; match_rank=5 a 0 0 0 0 0 0 0 0 0 0 0 0 266 277 262 237 171 119 302 378 335 42 0 0 0 572 483 191 95 144 c 0 0 0 0 0 0 0 0 0 0 0 0 105 76 91 114 148 80 9 3 0 530 572 572 0 0 0 87 117 137 g 0 0 0 0 0 0 0 0 0 0 0 0 68 68 58 47 43 76 86 1 237 0 0 0 0 0 87 12 25 59 t 0 0 0 0 0 0 0 0 0 0 0 0 133 151 161 174 210 297 175 190 0 0 0 0 572 0 2 282 335 232

TRP2_MA1356.1_JASPAR_shift11 (TRP2:MA1356.1:JASPAR) 0.751 0.680 9.776 0.916 0.865 10 3 2 11 11 7.400 7
; dyads_test_vs_ctrl_m1 versus TRP2_MA1356.1_JASPAR (TRP2:MA1356.1:JASPAR); m=7/14; ncol2=20; w=19; offset=1; strand=D; shift=11; score= 7.4; -----------AAACCCTAAACCCTAAACC ; cor=0.751; Ncor=0.680; logoDP=9.776; NsEucl=0.916; NSW=0.865; rcor=10; rNcor=3; rlogoDP=2; rNsEucl=11; rNSW=11; rank_mean=7.400; match_rank=7 a 0 0 0 0 0 0 0 0 0 0 0 72 72 72 0 6 0 3 72 76 75 0 2 2 2 73 68 73 1 7 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 66 63 65 1 0 0 0 75 74 71 0 0 6 0 69 62 g 0 0 0 0 0 0 0 0 0 0 0 1 2 0 2 2 1 1 0 0 0 1 0 3 3 1 0 2 0 2 t 0 0 0 0 0 0 0 0 0 0 0 3 2 4 8 5 10 71 4 0 1 0 0 0 71 2 2 1 6 5

Matrix name	cor	Ncor	logoDP	NsEucl	NSW	rcor	rNcor	rlogoDP	rNsEucl	rNSW	rank_mean	match_rank	Aligned matrices
dyads_test_vs_ctrl_m1_shift10 (dyads_test_vs_ctrl_m1)													; dyads_test_vs_ctrl_m1; m=0 (reference); ncol1=20; shift=10; ncol=30; ----------hmaccCtAAAACCCTAammh ; Alignment reference a 0 0 0 0 0 0 0 0 0 0 82 79 106 51 34 19 35 173 200 213 199 3 5 6 11 167 134 74 68 61 c 0 0 0 0 0 0 0 0 0 0 60 64 44 100 110 156 44 10 10 4 12 215 207 205 11 24 26 84 71 79 g 0 0 0 0 0 0 0 0 0 0 22 32 20 23 33 22 11 4 7 2 4 1 2 3 1 11 35 14 30 21 t 0 0 0 0 0 0 0 0 0 0 57 46 51 47 44 24 131 34 4 2 6 2 7 7 198 19 26 49 52 60
TRP2.ampDAP_M0612_AthalianaCistrome_shift11 (TRP2.ampDAP:M0612:AthalianaCistrome)	0.799	0.690	10.207	0.926	0.897	8	2	1	5	9	5.000	2	; dyads_test_vs_ctrl_m1 versus TRP2.ampDAP_M0612_AthalianaCistrome (TRP2.ampDAP:M0612:AthalianaCistrome); m=2/14; ncol2=21; w=19; offset=1; strand=D; shift=11; score= 5; -----------AAACCCTAAACCCTAAACC ; cor=0.799; Ncor=0.690; logoDP=10.207; NsEucl=0.926; NSW=0.897; rcor=8; rNcor=2; rlogoDP=1; rNsEucl=5; rNSW=9; rank_mean=5.000; match_rank=2 a 0 0 0 0 0 0 0 0 0 0 0 90 85 87 0 9 7 12 103 104 101 2 1 0 5 99 99 97 7 14 c 0 0 0 0 0 0 0 0 0 0 0 3 2 1 85 88 75 2 0 0 3 102 103 102 0 0 0 0 80 75 g 0 0 0 0 0 0 0 0 0 0 0 2 4 1 5 5 5 1 1 0 0 0 0 0 0 4 3 2 1 1 t 0 0 0 0 0 0 0 0 0 0 0 9 13 15 14 2 17 89 0 0 0 0 0 2 99 1 2 5 16 14
TBP3.ampDAP_M0621_AthalianaCistrome_rc_shift11 (TBP3.ampDAP:M0621:AthalianaCistrome_rc)	0.837	0.795	0.503	0.949	0.950	7	1	13	2	3	5.200	3	; dyads_test_vs_ctrl_m1 versus TBP3.ampDAP_M0621_AthalianaCistrome_rc (TBP3.ampDAP:M0621:AthalianaCistrome_rc); m=3/14; ncol2=19; w=19; offset=1; strand=R; shift=11; score= 5.2; -----------maamhhtaARCCCTAAwyy ; cor=0.837; Ncor=0.795; logoDP=0.503; NsEucl=0.949; NSW=0.950; rcor=7; rNcor=1; rlogoDP=13; rNsEucl=2; rNSW=3; rank_mean=5.200; match_rank=3 a 0 0 0 0 0 0 0 0 0 0 0 126 140 138 102 76 73 50 167 197 186 11 5 0 0 251 231 93 23 51 c 0 0 0 0 0 0 0 0 0 0 0 64 39 30 66 96 83 37 4 2 3 239 237 239 18 3 1 57 71 95 g 0 0 0 0 0 0 0 0 0 0 0 21 48 33 26 19 23 38 35 2 66 1 3 13 5 1 21 9 7 24 t 0 0 0 0 0 0 0 0 0 0 0 44 28 54 61 64 76 130 49 54 0 4 10 3 232 0 2 96 154 85
TBP3_MA1355.1_JASPAR_shift12 (TBP3:MA1355.1:JASPAR)	0.779	0.667	7.113	0.937	0.929	9	4	8	4	8	6.600	5	; dyads_test_vs_ctrl_m1 versus TBP3_MA1355.1_JASPAR (TBP3:MA1355.1:JASPAR); m=5/14; ncol2=19; w=18; offset=2; strand=D; shift=12; score= 6.6; ------------awwwhtwwrCCCTAAwtw ; cor=0.779; Ncor=0.667; logoDP=7.113; NsEucl=0.937; NSW=0.929; rcor=9; rNcor=4; rlogoDP=8; rNsEucl=4; rNSW=8; rank_mean=6.600; match_rank=5 a 0 0 0 0 0 0 0 0 0 0 0 0 266 277 262 237 171 119 302 378 335 42 0 0 0 572 483 191 95 144 c 0 0 0 0 0 0 0 0 0 0 0 0 105 76 91 114 148 80 9 3 0 530 572 572 0 0 0 87 117 137 g 0 0 0 0 0 0 0 0 0 0 0 0 68 68 58 47 43 76 86 1 237 0 0 0 0 0 87 12 25 59 t 0 0 0 0 0 0 0 0 0 0 0 0 133 151 161 174 210 297 175 190 0 0 0 0 572 0 2 282 335 232
TRP2_MA1356.1_JASPAR_shift11 (TRP2:MA1356.1:JASPAR)	0.751	0.680	9.776	0.916	0.865	10	3	2	11	11	7.400	7	; dyads_test_vs_ctrl_m1 versus TRP2_MA1356.1_JASPAR (TRP2:MA1356.1:JASPAR); m=7/14; ncol2=20; w=19; offset=1; strand=D; shift=11; score= 7.4; -----------AAACCCTAAACCCTAAACC ; cor=0.751; Ncor=0.680; logoDP=9.776; NsEucl=0.916; NSW=0.865; rcor=10; rNcor=3; rlogoDP=2; rNsEucl=11; rNSW=11; rank_mean=7.400; match_rank=7 a 0 0 0 0 0 0 0 0 0 0 0 72 72 72 0 6 0 3 72 76 75 0 2 2 2 73 68 73 1 7 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 66 63 65 1 0 0 0 75 74 71 0 0 6 0 69 62 g 0 0 0 0 0 0 0 0 0 0 0 1 2 0 2 2 1 1 0 0 0 1 0 3 3 1 0 2 0 2 t 0 0 0 0 0 0 0 0 0 0 0 3 2 4 8 5 10 71 4 0 1 0 0 0 71 2 2 1 6 5