AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00330_bbur_reg_300.orf -o00330_bbur_300.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 BB0605 70 serine-type D-Ala-D-Ala carboxypeptidase (dacA) #5 BB0608 116 aminoacyl-histidine dipeptidase (pepD) #6 BB0841 178 arginine deiminase (arcA) #7 BB0842 64 ornithine carbamoyltransferase, catabolic (arcB) Motif number 1 ATATAATTATTTAGTTTTTTAAAGAAGTG 1 10 1 TTTAGTTTTT 0.956137 -43 AACTTAATATTTAAATTTTTGGGATAAATT 2 12 0 TTAAATTTTT 0.967847 -154 AATTTAAATATTAAGTTTTTAATCTATAAA 2 25 1 TTAAGTTTTT 0.972851 -141 AATGCTGTTTTGATATTATTTTAAGTAAGG 2 84 1 TGATATTATT 0.737025 -82 ATCTACTAAATCTTATTTATAATTAATTTA 2 115 0 TCTTATTTAT 0.699551 -51 GTAGATAATTTATTGTTATTAAACTTATAC 2 139 1 TATTGTTATT 0.668889 -27 TTAATCATACTAATATTTATGTTTGGAGAG 3 16 0 TAATATTTAT 0.85047 -253 AAGTTTTGTTTTAAGATTTTAATCATACTA 3 34 0 TTAAGATTTT 0.787765 -235 CAAATAATTATTTTATTATTTAGCTACATG 3 160 1 TTTTATTATT 0.824122 -109 TTTTAAAACATTAAATTTTTAGTATTCTAC 3 215 0 TTAAATTTTT 0.967847 -54 TGTTTTTTCATAAAATTTTTAAAACATTAA 3 231 0 TAAAATTTTT 0.917969 -38 CTCCTCAAAATTTTGTTTTTTCATAAAATT 3 244 0 TTTTGTTTTT 0.962482 -25 TAAAATTATATATTATTTATTGATTGTTAA 4 41 0 TATTATTTAT 0.77578 -30 GTTGTAATATTAAAATTATATATTATTTA 4 52 0 TTAAAATTAT 0.574287 -19 ATTTAGTATATTATATTATTAATTATAAAT 5 49 1 TTATATTATT 0.885127 -68 TATACTTGGATTTAATTTATAATTAATAAT 5 63 0 TTTAATTTAT 0.887538 -54 AATTTTTTGTTTATGTTTTTGATTTGAAGT 6 28 1 TTATGTTTTT 0.976845 -151 GTTTTTGATTTGAAGTTTTTTAGAACTTTT 6 42 1 TGAAGTTTTT 0.928767 -137 TTTTTAGAACTTTTATTTTTTCAATTTTTT 6 58 1 TTTTATTTTT 0.956672 -121 TTTCAATTTTTTATATTTATATTATATTTT 6 76 1 TTATATTTAT 0.938754 -103 TATATTTATATTATATTTTTAATATTATTA 6 87 1 TTATATTTTT 0.973189 -92 TAAAAATAGTTGATGTTTTTTAATATAAAC 6 115 1 TGATGTTTTT 0.938816 -64 ATTAAAATACTATAGTTTATATTAAAAAAC 6 129 0 TATAGTTTAT 0.77354 -50 ACCTTTACAATCAAGTTTTTAAAAACTCAT 7 39 0 TCAAGTTTTT 0.899509 -26 ********** Masking position 7 Map Score: 36.9396 Number of sites scoring better than the average of aligned sites = 3172 Number in coding regions = 2099 Number in noncoding regions = 1073 Number of orfs with sites within 600 bp upstream = 176 Fraction of orfs with sites within 600 bp upstream = 0.0282686 Motif number 2 ATATAATTATTTAGTTTTTTAAAGAAGTGAA 1 11 1 TTAGTTTTTA 0.895709 -42 GATTAAAAACTTAATATTTAAATTTTTGGGA 2 18 0 TTAATATTTA 0.976649 -148 TATTAAGTTTTTAATCTATAAACAAATAGTA 2 33 1 TTAATCTATA 0.913437 -133 CTATAAACAAATAGTATATCAAAGTTTTGAA 2 48 1 ATAGTATATA 0.832475 -118 TGCTGTTTTGATATTATTTTAAGTAAGGCTA 2 86 1 ATATTATTTA 0.746413 -80 TAAATAAGATTTAGTAGATAATTTATTGTTA 2 126 1 TTAGTAGATA 0.661061 -40 AAGTTTTGTTTTAAGATTTTAATCATACTAA 3 33 0 TTAAGATTTA 0.793189 -236 TTAGTAATTATTTATATATGATTTATGAAGG 3 67 0 TTTATATATA 0.837492 -202 TTTGAAGGATTTAATCTTTAAGATTTAGAAA 3 123 0 TTAATCTTTA 0.935382 -146 TTGCAAATAATTATTTTATTATTTAGCTACA 3 157 1 TTATTTTATA 0.725315 -112 TCTACATGTTTTATTATATAATTATATATGC 3 189 0 TTATTATATA 0.90861 -80 CATTAAATTTTTAGTATTCTACATGTTTTAT 3 206 0 TTAGTATTCA 0.765697 -63 TACTAAAAATTTAATGTTTTAAAAATTTTAT 3 221 1 TTAATGTTTA 0.845701 -48 CAATCAATAAATAATATATAATTTTAATATT 4 45 1 ATAATATATA 0.87563 -26 ATATATAATTTTAATATTACAAC 4 58 1 TTAATATTAA 0.911334 -13 ATATACTAAATTAATCTTTAAATTCATTCAA 5 29 0 TTAATCTTTA 0.935382 -88 AAAGATTAATTTAGTATATTATATTATTAAT 5 41 1 TTAGTATATA 0.959044 -76 ATACTTGGATTTAATTTATAATTAATAATAT 5 61 0 TTAATTTATA 0.895432 -56 GATTAGTATTTTAGCATAATTTT 6 3 1 TTAGTATTTA 0.97015 -176 TTTAGAACTTTTATTTTTTCAATTTTTTATA 6 60 1 TTATTTTTTA 0.785592 -119 ATTTTTTATATTTATATTATATTTTTAATAT 6 81 1 TTTATATTAA 0.614875 -98 ACTATTTTTAATAATATTAAAAATATAATAT 6 94 0 ATAATATTAA 0.685657 -85 AATACTATAGTTTATATTAAAAAACATCAAC 6 123 0 TTTATATTAA 0.61483 -56 CTATAGTATTTTAATATATGACAATTTTCAT 6 144 1 TTAATATATA 0.970734 -35 ********* * Masking position 2 Map Score: 34.6262 Number of sites scoring better than the average of aligned sites = 1057 Number in coding regions = 641 Number in noncoding regions = 416 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 3 AAGCATTTCACTTCTTTAAAAAACTAAATA 1 18 0 CTTCTTTAAA 0.763115 -35 TTAAAAACTTAATATTTAAATTTTTGGGAT 2 17 0 AATATTTAAA 0.938144 -149 TTAAGTTTTTAATCTATAAACAAATAGTAT 2 35 1 AATCTATAAA 0.917086 -131 TTAATTTAGCCTTACTTAAAATAATATCAA 2 93 0 CTTACTTAAA 0.611447 -73 GTATGATTAAAATCTTAAAACAAAACTTTC 3 36 1 AATCTTAAAA 0.893052 -233 CTTCATAAATCATATATAAATAATTACTAA 3 68 1 CATATATAAA 0.832299 -201 TGAAGGATTTAATCTTTAAGATTTAGAAAG 3 122 0 AATCTTTAAG 0.756675 -147 TTAAAGATTAAATCCTTCAAATATTTGCAA 3 133 1 AATCCTTCAA 0.758434 -136 AAACATGTAGAATACTAAAAATTTAATGTT 3 209 1 AATACTAAAA 0.803115 -60 CTAAAAATTTAATGTTTTAAAAATTTTATG 3 223 1 AATGTTTTAA 0.619675 -46 TGTAATTAACAATCAATAAATAATATATAA 4 36 1 AATCAATAAA 0.561619 -35 GTTGTAATATTAAAATTATATATTA 4 56 0 AATATTAAAA 0.820403 -15 ATACTAAATTAATCTTTAAATTCATTCAAT 5 28 0 AATCTTTAAA 0.965187 -89 GATTAAATTAAATCCATAAATATACTTGGA 5 83 0 AATCCATAAA 0.908062 -34 TATTTTTAATAATATTAAAAATATAATATA 6 93 0 AATATTAAAA 0.820403 -86 TGAAAATTGTCATATATTAAAATACTATAG 6 144 0 CATATATTAA 0.428246 -35 CATGCTTAAACATGCTTAAATA 7 3 0 CATGCTTAAA 0.887783 -62 TCATTTAACTCATGCTTAAACATGCTTAAA 7 13 0 CATGCTTAAA 0.887783 -52 ********** Masking position 3 Map Score: 19.724 Number of sites scoring better than the average of aligned sites = 1508 Number in coding regions = 992 Number in noncoding regions = 516 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 4 TAAAAAACTAAATAATTATAT 1 2 0 AATAATTATA 0.582283 -51 TTAAAAACTTAATATTTAAATTTTTGGGAT 2 17 0 AATATTTAAA 0.48931 -149 GTAAGGCTAAATTAATTATAAATAAGATTT 2 108 1 ATTAATTATA 0.764031 -58 GTTTTAAGATTTTAATCATACTAATATTTA 3 27 0 TTTAATCATA 0.86507 -242 TTTCACCTTCATAAATCATATATAAATAAT 3 62 1 ATAAATCATA 0.556278 -207 GTTATTAGTAATTATTTATATATGATTTAT 3 72 0 ATTATTTATA 0.874267 -197 AATATTTGCAAATAATTATTTTATTATTTA 3 152 1 AATAATTATT 0.4401 -117 TACATGCATATATAATTATATAATAAAACA 3 184 1 TATAATTATA 0.498774 -85 ATGGCTCCTTTTTAATTGTATTGTAATTAA 4 15 1 TTTAATTGTA 0.743062 -56 ATAAATAATATATAATTTTAATATTACAAC 4 51 1 TATAATTTTA 0.448959 -20 ATATTATATTATTAATTATAAATTAAATCC 5 56 1 ATTAATTATA 0.764031 -61 ATGGATTTAATTTAATCAAAGGAAAGTTAT 5 96 1 TTTAATCAAA 0.647354 -21 TTCAATTTTTTATATTTATATTATATTTTT 6 77 1 TATATTTATA 0.663658 -102 ATCAACTATTTTTAATAATATTAAAAATAT 6 99 0 TTTAATAATA 0.712165 -80 ********** Masking position 4 Map Score: 13.112 Number of sites scoring better than the average of aligned sites = 452 Number in coding regions = 232 Number in noncoding regions = 220 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 5 CTTAATATTTAAATTTTTGGGATAAATTT 2 10 0 AAATTTTTGG 0.84121 -156 ATAGTATATCAAAGTTTTGAATTTGAAATG 2 58 1 AAAGTTTTGA 0.889201 -108 TTTAGTAGATAATTTATTGTTATTAAACTT 2 135 1 AATTTATTGT 0.787545 -31 CTCCAAACATAAATATTAGTATGATTAAAA 3 18 1 AAATATTAGT 0.588712 -251 TATGAAGGTGAAAGTTTTGTTTTAAGATTT 3 45 0 AAAGTTTTGT 0.820698 -224 AATTATTTGCAAATATTTGAAGGATTTAAT 3 139 0 AAATATTTGA 0.939565 -130 ATAATAAAATAATTATTTGCAAATATTTGA 3 149 0 AATTATTTGC 0.664921 -120 TAAAACATTAAATTTTTAGTATTCTACATG 3 212 0 AATTTTTAGT 0.588716 -57 TTTTTTCATAAAATTTTTAAAACATTAAAT 3 229 0 AAATTTTTAA 0.573143 -40 ATGAAAAAACAAAATTTTGAGGAGACTTA 3 250 1 AAAATTTTGA 0.881417 -19 AATTATATATTATTTATTGATTGTTAATTA 4 38 0 TATTTATTGA 0.357372 -33 AATATTATTGAATTTATTGAATGAATTTAA 5 13 1 AATTTATTGA 0.866654 -104 ATTTTAGCATAATTTTTTGTTTATGTTTTT 6 18 1 AATTTTTTGT 0.898654 -161 ATATAAATATAAAAAATTGAAAAAATAAAA 6 68 0 AAAAAATTGA 0.655364 -111 ATATTATTAAAAATAGTTGATGTTTTTTAA 6 108 1 AAATAGTTGA 0.745405 -71 ATGAGTTTTTAAAAACTTGATTGTAAAGGT 7 39 1 AAAAACTTGA 0.461454 -26 ********** Masking position 7 Map Score: 9.05934 Number of sites scoring better than the average of aligned sites = 2012 Number in coding regions = 1425 Number in noncoding regions = 587 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 6 AAATTATCCTCAATAAAGCA 1 43 0 AAATTATCCT 0.974398 -10 AAATTTATCCCAAAAATTTAA 2 2 1 AATTTATCCC 0.932962 -164 ATTTATAATTAATTTAGCCTTACTTAAAAT 2 101 0 AATTTAGCCT 0.969272 -65 AACAATTGGCAAATTAGACTTTTCTTTCTA 3 99 1 AAATTAGACT 0.933341 -170 ACTTGGATTTAATTTATAATTAATAATATA 5 60 0 AATTTATAAT 0.723169 -57 CATAAACAAAAAATTATGCTAAAATACTAA 6 13 0 AAATTATGCT 0.934202 -166 ********** Masking position 5 Map Score: 2.00234 Number of sites scoring better than the average of aligned sites = 120 Number in coding regions = 83 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 7 ATAAATTATCTACTAAATCTTATTTATAATT 2 121 0 TACTAATCTT 0.816057 -45 AAGCTTTGTATAAGTTTAATAACAAT 2 150 0 TTGTAAAGTT 0.945734 -16 ATATTTATGTTTGGAGAGCTTTT 3 3 0 TTGGAAGCTT 0.877453 -266 AGACTTTTCTTTCTAAATCTTAAAGATTAAA 3 114 1 TTCTAATCTT 0.961175 -155 ATTTTTAGTATTCTACATGTTTTATTATATA 3 200 0 TTCTAATGTT 0.961175 -69 GCATAATTTTTTGTTTATGTTTTTGATTTGA 6 24 1 TTGTTATGTT 0.853528 -155 ATTTGAAGTTTTTTAGAACTTTTATTTTTTC 6 49 1 TTTTAAACTT 0.769564 -130 AAAAACTTGATTGTAAAGGTTGGTGG 7 49 1 TTGTAAGGTT 0.964232 -16 ***** ***** Masking position 7 Map Score: 2.68418 Number of sites scoring better than the average of aligned sites = 199 Number in coding regions = 123 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 8 ********** No masking Map Score: -1.24102e-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 9 ********** No masking Map Score: -1.24102e-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 10 ********** No masking Map Score: -1.24102e-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