AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00330_bbur_reg_100.orf -o00330_bbur_100.ace -a/home/amcguire/genomes/ORF_borburg.txt -z/home/amcguire/genomes/borburg.fna -g0.28 -x5 -e Parameter values: expect = 5 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.28 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: BB0595 21 B. burgdorferi predicted coding region BB0595 Input sequences: #1 BB0402 52 prolyl-tRNA synthetase (proS) #2 BB0403 165 B. burgdorferi predicted coding region BB0403 #3 BB0596 268 methyl-accepting chemotaxis protein (mcp-2) #4 BB0608 116 aminoacyl-histidine dipeptidase (pepD) #5 BB0841 178 arginine deiminase (arcA) #6 BB0842 64 ornithine carbamoyltransferase, catabolic (arcB) Motif number 1 CACTTCTTTAAAAAACTAAATAATTATAT 1 10 0 AAAAACTAAA 0.9627 -43 AATTTATCCCAAAAATTTAAATATTAAGTT 2 12 1 AAAAATTTAA 0.939706 -154 TTTATAGATTAAAAACTTAATATTTAAATT 2 25 0 AAAAACTTAA 0.945493 -141 TTTTTAATCTATAAACAAATAGTATATCAA 2 40 1 ATAAACAAAT 0.361563 -126 TTTCAAATTCAAAACTTTGATATACTATTT 2 56 0 AAAACTTTGA 0.752886 -110 TAAATTAATTATAAATAAGATTTAGTAGAT 2 115 1 ATAAATAAGA 0.4296 -51 TATAAGTTTAATAACAATAAATTATCTACT 2 138 0 ATAACAATAA 0.361744 -28 CTCCAAACATAAATATTAGTATGATTAAAA 3 18 1 AAATATTAGT 0.515713 -251 AGTATGATTAAAATCTTAAAACAAAACTTT 3 35 1 AAATCTTAAA 0.8979 -234 TCACCTTCATAAATCATATATAAATAATTA 3 64 1 AAATCATATA 0.4022 -205 TTTTCTTTCTAAATCTTAAAGATTAAATCC 3 118 1 AAATCTTAAA 0.8979 -151 AATTATTTGCAAATATTTGAAGGATTTAAT 3 139 0 AAATATTTGA 0.762582 -130 AAATATTTGCAAATAATTATTTTATTATTT 3 151 1 AAATAATTAT 0.574649 -118 GCATGTAGCTAAATAATAAAATAATTATTT 3 161 0 AAATAATAAA 0.90027 -108 ATATATAATTATATAATAAAACATGTAGAA 3 191 1 ATATAATAAA 0.768546 -78 GTAGAATACTAAAAATTTAATGTTTTAAAA 3 215 1 AAAAATTTAA 0.939706 -54 TTAATGTTTTAAAAATTTTATGAAAAAACA 3 231 1 AAAAATTTTA 0.665128 -38 AATTTTATGAAAAAACAAAATTTTGAGGAG 3 244 1 AAAAACAAAA 0.873553 -25 AATTCATTCAATAAATTCAATAATATTGG 4 10 0 ATAAATTCAA 0.765404 -107 TAATAATATAATATACTAAATTAATCTTTA 4 40 0 ATATACTAAA 0.855695 -77 ATTATTAATTATAAATTAAATCCAAGTATA 4 63 1 ATAAATTAAA 0.897261 -54 TGATTAAATTAAATCCATAAATATACTTGG 4 84 0 AAATCCATAA 0.632164 -33 AATTATGCTAAAATACTAATC 5 2 0 AAATACTAAT 0.782278 -177 AAACATAAACAAAAAATTATGCTAAAATAC 5 16 0 AAAAAATTAT 0.682747 -163 CTTCAAATCAAAAACATAAACAAAAAATTA 5 27 0 AAAACATAAA 0.895421 -152 AAAGTTCTAAAAAACTTCAAATCAAAAACA 5 41 0 AAAACTTCAA 0.84018 -138 TAAAAAATTGAAAAAATAAAAGTTCTAAAA 5 59 0 AAAAAATAAA 0.935287 -120 AATATAATATAAATATAAAAAATTGAAAAA 5 74 0 AAATATAAAA 0.798931 -105 TAATAATATTAAAAATATAATATAAATATA 5 87 0 AAAAATATAA 0.809748 -92 TTTATATTAAAAAACATCAACTATTTTTAA 5 114 0 AAAACATCAA 0.761724 -65 GTTTTTTAATATAAACTATAGTATTTTAAT 5 129 1 ATAAACTATA 0.544293 -50 GAAAATTGTCATATATTAAAATACTATAGT 5 143 0 ATATATTAAA 0.845188 -36 TCAAGTTTTTAAAAACTCATTTAACTCATG 6 29 0 AAAAACTCAT 0.682313 -36 ATGAGTTTTTAAAAACTTGATTGTAAAGGT 6 39 1 AAAAACTTGA 0.848135 -26 ********** Masking position 3 Map Score: 36.5917 Number of sites scoring better than the average of aligned sites = 7512 Number in coding regions = 4927 Number in noncoding regions = 2585 Number of orfs with sites within 600 bp upstream = 265 Fraction of orfs with sites within 600 bp upstream = 0.0425634 Motif number 2 ATATAATTATTTAGTTTTTTAAAGAA 1 4 1 TTTTTTAGTT 0.677281 -49 GATTAAAAACTTAATATTTAAATTTTTGGGATA 2 16 0 TATTTTAAAT 0.926793 -150 CTAAATCTTATTTATAATTAATTTAGCCTTACT 2 107 0 TATATTAATT 0.941449 -59 TAAGATTTAGTAGATAATTTATTGTTATTAAAC 2 130 1 TATATTTATT 0.915707 -36 AAGCTTTGTATAAGTTTAATAACAATAAATT 2 145 0 TAATTTAATA 0.846722 -21 AAGTTTTGTTTTAAGATTTTAATCATACTAATA 3 31 0 TAGTTTTAAT 0.574096 -238 TTTATGAAGGTGAAAGTTTTGTTTTAAGATTTT 3 44 0 TAATTTTGTT 0.814803 -225 TCATAAATCATATATAAATAATTACTAATAACA 3 70 1 TATAATAATT 0.669919 -199 TTTCTAAATCTTAAAGATTAAATCCTTCAAATA 3 123 1 TAAATTAAAT 0.768249 -146 TATTTGCAAATAATTATTTTATTATTTAGCTAC 3 154 1 TTTTTTTATT 0.824916 -115 TTTAGCTACATGCATATATAATTATATAATAAA 3 178 1 TATTATAATT 0.821591 -91 TTTAGTATTCTACATGTTTTATTATATAATTAT 3 195 0 TATTTTTATT 0.960998 -74 ATAAAATTTTTAAAACATTAAATTTTTAGTATT 3 219 0 TAAATTAAAT 0.768248 -50 TAAGTCTCCTCAAAATTTTGTTTTTTCATAAA 3 247 0 TAATTTTGTT 0.814796 -22 ATATACTAAATTAATCTTTAAATTCATTCAATA 4 27 0 TATTTTAAAT 0.926794 -90 TTTAGTATATTATATTATTAATTATAAATTAAA 4 50 1 TATATTAATT 0.941485 -67 TGAAGTTTTTTAGAACTTTTATTTTTTCAATTT 5 52 1 TAATTTTATT 0.936023 -127 TTTTATTTTTTCAATTTTTTATATTTATATTAT 5 68 1 TATTTTTATA 0.86687 -111 ATATTTATATTATATTTTTAATATTATTAAAAA 5 88 1 TATTTTAATA 0.905498 -91 ATATAAACTATAGTATTTTAATATATGACAATT 5 137 1 TTATTTAATA 0.52217 -42 * ** ******* Masking position 9 Map Score: 21.6796 Number of sites scoring better than the average of aligned sites = 2456 Number in coding regions = 1519 Number in noncoding regions = 937 Number of orfs with sites within 600 bp upstream = 171 Fraction of orfs with sites within 600 bp upstream = 0.0274655 Motif number 3 CCTTACTTAAAATAATATCAAAACAGCATTTC 2 82 0 AATAATATAA 0.960929 -84 AGGCTAAATTAATTATAAATAAGATTTAGTAG 2 111 1 AATTATAAAA 0.705655 -55 CACCTTCATAAATCATATATAAATAATTACTA 3 65 1 AATCATATAA 0.883288 -204 ATAATAAAATAATTATTTGCAAATATTTGAAG 3 147 0 AATTATTTAA 0.705655 -122 CATATATAATTATATAATAAAACATGTAGAAT 3 190 1 TATATAATAA 0.740168 -79 ATGTTTTAAAAATTTTATGAAAAAACAAAATT 3 234 1 AATTTTATAA 0.966093 -35 CCAATATTATTGAATTTATTGAAT 4 3 1 AATATTATAA 0.971314 -114 TATAATTAATAATATAATATACTAAATTAATC 4 44 0 AATATAATAC 0.808516 -73 ATTAATTATAAATTAAATCCAAGTATATTTAT 4 66 1 AATTAAATAA 0.937637 -51 TTATGGATTTAATTTAATCAAAGGAAAGTTAT 4 94 1 AATTTAATAA 0.953913 -23 TAATATTAAAAATATAATATAAATATAAAAAA 5 82 0 AATATAATAA 0.960931 -97 TTATATTTTTAATATTATTAAAAATAGTTGAT 5 97 1 AATATTATAA 0.971308 -82 ******** ** Masking position 2 Map Score: 12.7213 Number of sites scoring better than the average of aligned sites = 979 Number in coding regions = 567 Number in noncoding regions = 412 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 4 AAATTATCCTCAATAAAGCATT 1 41 0 AATTATCTCA 0.89346 -12 AAATTTATCCCAAAAATTTAAAT 2 2 1 AATTATCCAA 0.868155 -164 ATTTATAATTAATTTAGCCTTACTTAAAATAA 2 99 0 AATTAGCTTA 0.908883 -67 TTTAGTAGATAATTTATTGTTATTAAACTTAT 2 135 1 AATTATGTTA 0.755025 -31 ATTGTTATTAAACTTATACAAAGCTT 2 150 1 AATTATCAAA 0.947391 -16 TTTAAGATTTTAATCATACTAATATTTATGTT 3 23 0 TATCATCTAA 0.703559 -246 TCACCTTCATAAATCATATATAAATAATTACT 3 64 1 AATCATTATA 0.492957 -205 AACAATTGGCAAATTAGACTTTTCTTTCTAAA 3 99 1 AATTAGCTTT 0.727307 -170 CTTAAAGATTAAATCCTTCAAATATTTGCAAA 3 132 1 AATCCTCAAA 0.667421 -137 TTAATCTTTAAATTCATTCAATAAATTCAATA 4 18 0 AATCATCAAT 0.799074 -99 ATAATATACTAAATTAATCTTTAAATTCATTC 4 31 0 AATTAACTTT 0.63423 -86 ACTTGGATTTAATTTATAATTAATAATATAAT 4 58 0 AATTATATTA 0.656902 -59 TTATGGATTTAATTTAATCAAAGGAAAGTTAT 4 94 1 AATTAACAAA 0.786238 -23 CATAAACAAAAAATTATGCTAAAATACTAATC 5 11 0 AATTATCTAA 0.969284 -168 AAACTCATTTAACTCATGCTTAAACATGCTTA 6 15 0 AATCATCTTA 0.962843 -50 ** **** **** Masking position 2 Map Score: 7.67757 Number of sites scoring better than the average of aligned sites = 721 Number in coding regions = 486 Number in noncoding regions = 235 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 5 TAAAAAACTAAATAATTATAT 1 2 0 AATAATTATA 0.524298 -51 TTAAAAACTTAATATTTAAATTTTTGGGAT 2 17 0 AATATTTAAA 0.747597 -149 TTAATTTAGCCTTACTTAAAATAATATCAA 2 93 0 CTTACTTAAA 0.86962 -73 TCTACTAAATCTTATTTATAATTAATTTAG 2 114 0 CTTATTTATA 0.609873 -52 AAAAGCTCTCCAAACATAAATATTAGTATG 3 11 1 CAAACATAAA 0.684113 -258 AGATTTTAATCATACTAATATTTATGTTTG 3 21 0 CATACTAATA 0.871881 -248 CTTCATAAATCATATATAAATAATTACTAA 3 68 1 CATATATAAA 0.907406 -201 TATTTAGCTACATGCATATATAATTATATA 3 176 1 CATGCATATA 0.895763 -93 AAACATGTAGAATACTAAAAATTTAATGTT 3 209 1 AATACTAAAA 0.66844 -60 AAATTAAATCCATAAATATACTTGGATTTA 4 79 0 CATAAATATA 0.775078 -38 AACAAAAAATTATGCTAAAATACTAATC 5 9 0 TATGCTAAAA 0.438624 -170 AAATCAAAAACATAAACAAAAAATTATGCT 5 23 0 CATAAACAAA 0.496135 -156 TTCAATTTTTTATATTTATATTATATTTTT 5 77 1 TATATTTATA 0.444408 -102 TGAAAATTGTCATATATTAAAATACTATAG 5 144 0 CATATATTAA 0.462451 -35 CATGCTTAAACATGCTTAAATA 6 3 0 CATGCTTAAA 0.958265 -62 TCATTTAACTCATGCTTAAACATGCTTAAA 6 13 0 CATGCTTAAA 0.958265 -52 ********** Masking position 10 Map Score: 7.92604 Number of sites scoring better than the average of aligned sites = 972 Number in coding regions = 654 Number in noncoding regions = 318 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 6 ********** No masking Map Score: 1.59405e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 7 ********** No masking Map Score: 1.59405e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 8 ********** No masking Map Score: 1.59405e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0