One-to-n alignments

Command: compare-matrices  -v 1 -format1 transfac -file1 $RSAT/public_html/tmp/www-data/2019/07/08/compare-matrices_2019-07-08.175744_cfc2aO/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/2019/07/08/compare-matrices_2019-07-08.175744_cfc2aO/compare-matrices.tab

One-to-n matrix alignment; reference matrix: dyads_test_vs_ctrl_m2_shift10 ; 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

TBP3.ampDAP_M0621_AthalianaCistrome_rc_shift11 (TBP3.ampDAP:M0621:AthalianaCistrome_rc) 0.844 0.802 0.537 0.951 0.954 5 1 14 2 3 5.000 3
; dyads_test_vs_ctrl_m2 versus TBP3.ampDAP_M0621_AthalianaCistrome_rc (TBP3.ampDAP:M0621:AthalianaCistrome_rc); m=3/15; ncol2=19; w=19; offset=1; strand=R; shift=11; score= 5; -----------maamhhtaARCCCTAAwyy ; cor=0.844; Ncor=0.802; logoDP=0.537; NsEucl=0.951; NSW=0.954; rcor=5; rNcor=1; rlogoDP=14; rNsEucl=2; rNSW=3; rank_mean=5.000; 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

TRP2_MA1356.1_JASPAR_shift11 (TRP2:MA1356.1:JASPAR) 0.804 0.728 8.742 0.923 0.887 9 3 2 11 11 7.200 5
; dyads_test_vs_ctrl_m2 versus TRP2_MA1356.1_JASPAR (TRP2:MA1356.1:JASPAR); m=5/15; ncol2=20; w=19; offset=1; strand=D; shift=11; score= 7.2; -----------AAACCCTAAACCCTAAACC ; cor=0.804; Ncor=0.728; logoDP=8.742; NsEucl=0.923; NSW=0.887; rcor=9; rNcor=3; rlogoDP=2; rNsEucl=11; rNSW=11; rank_mean=7.200; match_rank=5 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

TRP2.ampDAP_M0612_AthalianaCistrome_shift11 (TRP2.ampDAP:M0612:AthalianaCistrome) 0.843 0.728 9.073 0.933 0.914 6 2 1 5 9 4.600 2
; dyads_test_vs_ctrl_m2 versus TRP2.ampDAP_M0612_AthalianaCistrome (TRP2.ampDAP:M0612:AthalianaCistrome); m=2/15; ncol2=21; w=19; offset=1; strand=D; shift=11; score= 4.6; -----------AAACCCTAAACCCTAAACC ; cor=0.843; Ncor=0.728; logoDP=9.073; NsEucl=0.933; NSW=0.914; rcor=6; rNcor=2; rlogoDP=1; rNsEucl=5; rNSW=9; rank_mean=4.600; 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

AT1G72740_MA1353.1_JASPAR_shift15 (AT1G72740:MA1353.1:JASPAR) 0.906 0.680 7.778 0.949 0.961 2 4 4 3 2 3.000 1
; dyads_test_vs_ctrl_m2 versus AT1G72740_MA1353.1_JASPAR (AT1G72740:MA1353.1:JASPAR); m=1/15; ncol2=15; w=15; offset=5; strand=D; shift=15; score= 3; ---------------cctAAACCCTAAwyc ; cor=0.906; Ncor=0.680; logoDP=7.778; NsEucl=0.949; NSW=0.961; rcor=2; rNcor=4; rlogoDP=4; rNsEucl=3; rNSW=2; rank_mean=3.000; match_rank=1 a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 62 69 59 214 282 282 10 0 0 0 289 242 138 9 37 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 154 159 46 3 3 0 281 291 291 0 0 0 41 129 157 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 23 34 51 22 2 9 0 0 0 0 1 49 2 16 27 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 52 29 135 52 4 0 0 0 0 291 1 0 110 137 70

dyads_test_vs_ctrl_m2_shift10 (dyads_test_vs_ctrl_m2)
; dyads_test_vs_ctrl_m2; m=0 (reference); ncol1=20; shift=10; ncol=30; ----------waarcccAAAACCCTAammy ; Alignment reference a 0 0 0 0 0 0 0 0 0 0 114 127 177 78 43 27 55 233 273 278 264 13 13 8 29 229 189 89 95 75 c 0 0 0 0 0 0 0 0 0 0 67 70 42 72 187 203 160 12 12 10 18 277 272 280 23 34 28 130 97 101 g 0 0 0 0 0 0 0 0 0 0 36 35 31 85 29 39 15 6 8 6 8 5 5 1 6 11 51 27 36 42 t 0 0 0 0 0 0 0 0 0 0 85 70 52 67 43 33 72 51 9 8 12 7 12 13 244 28 34 56 74 84

Matrix name	cor	Ncor ▴	logoDP	NsEucl	NSW	rcor	rNcor	rlogoDP	rNsEucl	rNSW	rank_mean	match_rank	Aligned matrices
TBP3.ampDAP_M0621_AthalianaCistrome_rc_shift11 (TBP3.ampDAP:M0621:AthalianaCistrome_rc)	0.844	0.802	0.537	0.951	0.954	5	1	14	2	3	5.000	3	; dyads_test_vs_ctrl_m2 versus TBP3.ampDAP_M0621_AthalianaCistrome_rc (TBP3.ampDAP:M0621:AthalianaCistrome_rc); m=3/15; ncol2=19; w=19; offset=1; strand=R; shift=11; score= 5; -----------maamhhtaARCCCTAAwyy ; cor=0.844; Ncor=0.802; logoDP=0.537; NsEucl=0.951; NSW=0.954; rcor=5; rNcor=1; rlogoDP=14; rNsEucl=2; rNSW=3; rank_mean=5.000; 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
TRP2_MA1356.1_JASPAR_shift11 (TRP2:MA1356.1:JASPAR)	0.804	0.728	8.742	0.923	0.887	9	3	2	11	11	7.200	5	; dyads_test_vs_ctrl_m2 versus TRP2_MA1356.1_JASPAR (TRP2:MA1356.1:JASPAR); m=5/15; ncol2=20; w=19; offset=1; strand=D; shift=11; score= 7.2; -----------AAACCCTAAACCCTAAACC ; cor=0.804; Ncor=0.728; logoDP=8.742; NsEucl=0.923; NSW=0.887; rcor=9; rNcor=3; rlogoDP=2; rNsEucl=11; rNSW=11; rank_mean=7.200; match_rank=5 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
TRP2.ampDAP_M0612_AthalianaCistrome_shift11 (TRP2.ampDAP:M0612:AthalianaCistrome)	0.843	0.728	9.073	0.933	0.914	6	2	1	5	9	4.600	2	; dyads_test_vs_ctrl_m2 versus TRP2.ampDAP_M0612_AthalianaCistrome (TRP2.ampDAP:M0612:AthalianaCistrome); m=2/15; ncol2=21; w=19; offset=1; strand=D; shift=11; score= 4.6; -----------AAACCCTAAACCCTAAACC ; cor=0.843; Ncor=0.728; logoDP=9.073; NsEucl=0.933; NSW=0.914; rcor=6; rNcor=2; rlogoDP=1; rNsEucl=5; rNSW=9; rank_mean=4.600; 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
AT1G72740_MA1353.1_JASPAR_shift15 (AT1G72740:MA1353.1:JASPAR)	0.906	0.680	7.778	0.949	0.961	2	4	4	3	2	3.000	1	; dyads_test_vs_ctrl_m2 versus AT1G72740_MA1353.1_JASPAR (AT1G72740:MA1353.1:JASPAR); m=1/15; ncol2=15; w=15; offset=5; strand=D; shift=15; score= 3; ---------------cctAAACCCTAAwyc ; cor=0.906; Ncor=0.680; logoDP=7.778; NsEucl=0.949; NSW=0.961; rcor=2; rNcor=4; rlogoDP=4; rNsEucl=3; rNSW=2; rank_mean=3.000; match_rank=1 a 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 62 69 59 214 282 282 10 0 0 0 289 242 138 9 37 c 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 154 159 46 3 3 0 281 291 291 0 0 0 41 129 157 g 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 23 34 51 22 2 9 0 0 0 0 1 49 2 16 27 t 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 52 29 135 52 4 0 0 0 0 291 1 0 110 137 70
dyads_test_vs_ctrl_m2_shift10 (dyads_test_vs_ctrl_m2)													; dyads_test_vs_ctrl_m2; m=0 (reference); ncol1=20; shift=10; ncol=30; ----------waarcccAAAACCCTAammy ; Alignment reference a 0 0 0 0 0 0 0 0 0 0 114 127 177 78 43 27 55 233 273 278 264 13 13 8 29 229 189 89 95 75 c 0 0 0 0 0 0 0 0 0 0 67 70 42 72 187 203 160 12 12 10 18 277 272 280 23 34 28 130 97 101 g 0 0 0 0 0 0 0 0 0 0 36 35 31 85 29 39 15 6 8 6 8 5 5 1 6 11 51 27 36 42 t 0 0 0 0 0 0 0 0 0 0 85 70 52 67 43 33 72 51 9 8 12 7 12 13 244 28 34 56 74 84