AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_borburg.txt -z/home/amcguire/genomes/borburg.fna -iphoB_bbur_opreg_100.orf -g0.282 -x5 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 = 0.282 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 BB0044 25 B. burgdorferi predicted coding region BB0044 #2 BB0045 79 P115 protein #3 BB0215 162 phosphate ABC transporter, periplasmic phosphate-binding protein (pstS) #4 BB0216 89 phosphate ABC transporter, permease protein (pstC) #5 BB0217 300 phosphate ABC transporter, permease protein (pstA) #6 BB0533 193 phnP protein (phnP) #7 BB0642 78 spermidine/putrescine ABC transporter, ATP-binding protein (potA) #8 BB0643 154 conserved hypothetical protein Motif number 1 ATTGACCTTTTTTTAAAATATTTTTATTTA 2 12 1 TTTTAAAATA 0.905095 -68 TTTTAAAATATTTTTATTTATTATAATATG 2 22 1 TTTTTATTTA 0.963358 -58 AGTAATTGGTTTTTAATTTTAA 2 68 1 TTTTAATTTT 0.849331 -12 ATAGCAAATATTTTAATTTTTTGGTATAAA 3 52 0 TTTTAATTTT 0.849331 -111 ATTGATTAAGTTATAATTGAGGAATAATAG 3 78 0 TTATAATTGA 0.69628 -85 CAAATTAACTTTATTGATTAAGTTATAATT 3 90 0 TTATTGATTA 0.814254 -73 AATTGACTTATTTTAAATTAATGCTATTAT 3 121 1 TTTTAAATTA 0.94353 -42 TAAATTAATGCTATTATATACTTAAACAAA 3 134 1 CTATTATATA 0.676127 -29 GTTTTTTTTTCTTTAATTTAA 4 2 0 CTTTAATTTA 0.87393 -88 TTTTTAAAAGAATCCCTTAAA 4 79 0 TTTTAAAAGA 0.680494 -11 TGAAATTTTATTATTATATATGTTGTGAAT 5 17 0 TTATTATATA 0.871975 -284 TGATTAGTGTTTTTAGAATAGCTTTGTTAG 5 114 0 TTTTAGAATA 0.825894 -187 AAATACATTGTTTTTGATTAGTGTTTTTAG 5 128 0 TTTTTGATTA 0.90618 -173 TATGTATCTTTTATTAAATACATTGTTTTT 5 143 0 TTATTAAATA 0.83172 -158 GATGGTTCGATTTTTATGTATCTTTTATTA 5 157 0 TTTTTATGTA 0.757903 -144 AATCCCTAGATTTTAAATTATATCCCAATA 5 258 1 TTTTAAATTA 0.94353 -43 AGTTTTTATTTTTAAAGCCTTA 5 289 0 TTTTTATTTT 0.867601 -12 ACAGAATTGATTATTAAATAGTGTTAATCT 6 69 1 TTATTAAATA 0.83172 -125 GTTAATCTAATTTTAGATTTAATAAGAGTT 6 91 1 TTTTAGATTT 0.674347 -103 AGAAAGTTTATTTTTGTTTAATATAAAATG 6 130 1 TTTTTGTTTA 0.928962 -64 ATACTTAATATTATTATTTATGTAAATGCC 7 15 0 TTATTATTTA 0.922678 -64 TGTATTTAAGTTTTTATATTTTTTAAGAAA 8 29 0 TTTTTATATT 0.789052 -126 CAGATTATATTTTTTATTTAAAAAAAAACA 8 57 1 TTTTTATTTA 0.963358 -98 AAAAACAATTCTTTTAAAGAAAACTAACAT 8 80 1 CTTTTAAAGA 0.431396 -75 TTGTTTTTGTTTTTAGTTTATGTTAGTTTT 8 99 0 TTTTAGTTTA 0.918363 -56 ACACATTAAGCTATAATTTAGGC 8 142 1 CTATAATTTA 0.758811 -13 ********** Masking position 4 Map Score: 33.8368 Number of sites scoring better than the average of aligned sites = 2913 Number in coding regions = 1722 Number in noncoding regions = 1191 Number of orfs with sites within 600 bp upstream = 220 Fraction of orfs with sites within 600 bp upstream = 0.0353357 Motif number 2 TAATTTCCTTAAATCTAACTTAA 1 3 0 AAATCAACTT 0.854736 -23 TATAATAAATAAAAATATTTTAAAAAAAGGT 2 16 0 AAAAAATTTT 0.928833 -64 AAATTAAAGAAAAAAAAACTTGACTTAAGAT 4 13 1 AAAAAAACTT 0.781008 -77 TCAAGTCAAGTAATACAATTTAACATTGGCA 4 43 1 TAATAAATTT 0.913891 -47 ACATATATAATAATAAAATTTCACACTGGGG 5 24 1 TAATAAATTT 0.913891 -277 CATATCTAACAAAGCTATTCTAAAAACACTA 5 109 1 AAAGCATTCT 0.814824 -192 TATTTAACAAAAAAAGAATTTGAATCCCTAG 5 236 1 AAAAAAATTT 0.933453 -65 AAAAATAATTTTTCCTTAAAT 6 1 1 AAAAAAATTT 0.933453 -193 TATAAGCATAAAAGCAATTTTTCCAAAATAG 6 35 1 AAAGCATTTT 0.900524 -159 ATCAATTCTGTAAACTATTTTGGAAAAATTG 6 49 0 TAAACATTTT 0.906083 -145 CACTATTTAATAATCAATTCTGTAAACTATT 6 61 0 TAATCATTCT 0.854603 -133 TAAATAGTGTTAATCTAATTTTAGATTTAAT 6 83 1 TAATCAATTT 0.932194 -111 TATTAAACAAAAATAAACTTTCTTAATCAAA 6 122 0 AAATAACTTT 0.809013 -72 CCTGTAAACATAATCTATTTTAACACAACAT 6 157 0 TAATCATTTT 0.924703 -37 TTTTTTAAGAAAATAAATTTTACAGGAGGT 8 10 0 AAATAATTTT 0.941033 -145 TTTAAATAAAAAATATAATCTGTATTTAAGT 8 48 0 AAATAAATCT 0.908195 -107 TATTTAAAAAAAAACAATTCTTTTAAAGAAA 8 71 1 AAAACATTCT 0.899923 -84 AACTAAAAACAAAAACAATTTATCATTCAAT 8 111 1 AAAAAAATTT 0.933453 -44 ***** ***** Masking position 11 Map Score: 24.6341 Number of sites scoring better than the average of aligned sites = 1450 Number in coding regions = 977 Number in noncoding regions = 473 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 3 AATTGACCTTTTTTTAAAATAT 2 1 1 AATTGCCTTT 0.807404 -79 TTTTTAAAATATTTTTATTTATTATAATATGA 2 21 1 ATTTTATTTT 0.812833 -59 TAAATCTACAATTTCATATTATAATAAATAAA 2 34 0 ATTTCTATTT 0.554812 -46 ATTTATCAGTAATTGGTTTTTAATTTTAA 2 61 1 AATTGTTTTA 0.725565 -19 AATAGCAAATATTTTAATTTTTTGGTATAAAT 3 51 0 ATTTTATTTT 0.812833 -112 AAATTAAAATATTTGCTATTATTCCTCAATTA 3 63 1 ATTTGTATTT 0.852914 -100 GTCAATTACAAATTAACTTTATTGATTAAGTT 3 96 0 AATTACTTTT 0.693673 -67 GTTAATTTGTAATTGACTTATTTTAAATTAAT 3 111 1 AATTGCTTAT 0.896407 -52 GCCAATGTTAAATTGTATTACTTGACTTGATC 4 41 0 AATTGATTAT 0.88876 -49 CCCAGTGTGAAATTTTATTATTATATATGTTG 5 22 0 AATTTATTAT 0.718408 -279 CAGATCAGGGAATTGACATTATACCTATTGCA 5 63 1 AATTGCATTT 0.902972 -238 TAGGGATTCAAATTCTTTTTTTGTTAAATAGC 5 234 0 AATTCTTTTT 0.882465 -67 GAATCCCTAGATTTTAAATTATATCCCAATAT 5 257 1 ATTTTAATTT 0.58442 -44 ATTTTGGAAAAATTGCTTTTATGCTTATAATT 6 32 0 AATTGTTTTT 0.972172 -162 TATAATCTTGATTTGTATTAATACAGCCATAA 7 42 1 ATTTGATTAT 0.803735 -37 CCTCCTGTAAAATTTATTTTCTTAAAAAATAT 8 12 1 AATTTTTTTT 0.917748 -143 TCTTTAAAAGAATTGTTTTTTTTTAAATAAAA 8 68 0 AATTGTTTTT 0.972172 -87 TTGAATGATAAATTGTTTTTGTTTTTAGTTTA 8 109 0 AATTGTTTTT 0.972172 -46 ***** **** * Masking position 4 Map Score: 19.2903 Number of sites scoring better than the average of aligned sites = 1391 Number in coding regions = 941 Number in noncoding regions = 450 Number of orfs with sites within 600 bp upstream = 102 Fraction of orfs with sites within 600 bp upstream = 0.0163829 Motif number 4 TCGCAAAACTTAACATATAAATCTAGTAGT 3 20 1 TAACATATAA 0.522917 -143 TAGTAATTTATACCAAAAAATTAAAATATT 3 46 1 TACCAAAAAA 0.820307 -117 TAAATTAAAGAAAAAAAAACTTGACTTAAG 4 12 1 AAAAAAAAAC 0.874502 -78 TAAAAACACTAATCAAAAACAATGTATTTA 5 129 1 AATCAAAAAC 0.743933 -172 TTAATAAAAGATACATAAAAATCGAACCAT 5 156 1 ATACATAAAA 0.681364 -145 TCGAACCATCTACCAAAAAAATACTTCAAA 5 177 1 TACCAAAAAA 0.820307 -124 AAATACTTCAAACCATAAACAGCACAATAG 5 195 1 AACCATAAAC 0.934729 -106 GTAGGCTATTTAACAAAAAAAGAATTTGAA 5 230 1 TAACAAAAAA 0.921099 -71 TTAAGGCTTTAAAAATAAAAACT 5 288 1 AAAAATAAAA 0.869628 -13 AAATAATTATAAGCATAAAAGCAATTTTTC 6 28 1 AAGCATAAAA 0.804756 -166 TATATTAAACAAAAATAAACTTTCTTAATC 6 125 0 AAAAATAAAC 0.896323 -69 TATTTTTGTTTAATATAAAATGTTGTGTTA 6 138 1 TAATATAAAA 0.724122 -56 TTTCGCCTGTAAACATAATCTATTTTAACA 6 163 0 AAACATAATC 0.734855 -31 TTTTCTTAAAAAATATAAAAACTTAAATAC 8 28 1 AAATATAAAA 0.836671 -127 GTTTTTTTTTAAATAAAAAATATAATCTGT 8 56 0 AAATAAAAAA 0.805029 -99 TTTTTTATTTAAAAAAAAACAATTCTTTTA 8 66 1 AAAAAAAAAC 0.874502 -89 TAAAGAAAACTAACATAAACTAAAAACAAA 8 94 1 TAACATAAAC 0.949424 -61 CATAAACTAAAAACAAAAACAATTTATCAT 8 107 1 AAACAAAAAC 0.967232 -48 ********** Masking position 5 Map Score: 22.21 Number of sites scoring better than the average of aligned sites = 1088 Number in coding regions = 726 Number in noncoding regions = 362 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 5 GTTAATTTCCTTAAATCTAACTTAA 1 11 0 ATTTCTTAAA 0.969955 -15 TAATGCTATTATATACTTAAACAAAGGAGTT 3 139 1 ATATCTTAAA 0.964497 -24 TTTTTAAAAGAATCCCTTAAAGCTCATGCCA 4 69 0 AATCCTTAAA 0.877232 -21 ATTTAATAAAAGATACATAAAAATCGAACCA 5 154 1 AGATCATAAA 0.74188 -147 TCTACCAAAAAAATACTTCAAACCATAAACA 5 185 1 AAATCTTCAA 0.698488 -116 AAAAATAATTTTTCCTTAAATAATTATAAG 6 10 1 TTTTCTTAAA 0.803978 -184 TTAAATAATTATAAGCATAAAAGCAATTTTT 6 26 1 ATAACATAAA 0.773732 -168 AAAAGGCATTTACATAAATAATAATATT 7 8 1 ATTTCATAAA 0.927828 -71 TGTAAAATTTATTTTCTTAAAAAATATAAAA 8 17 1 ATTTCTTAAA 0.969948 -138 TAAAAAATATAAAAACTTAAATACAGATTAT 8 34 1 AAAACTTAAA 0.795389 -121 AAAAAAAACAATTCTTTTAAAGAAAACTAAC 8 77 1 ATTCTTTAAA 0.554241 -78 **** ****** Masking position 10 Map Score: 6.57644 Number of sites scoring better than the average of aligned sites = 492 Number in coding regions = 316 Number in noncoding regions = 176 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 6 ********** No masking Map Score: -3.45081e-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: -3.45081e-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: -3.45081e-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