AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_borburg.txt -z/home/amcguire/genomes/borburg.fna -iphoB_bbur_opreg_300.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 TCATATTATAATAAATAAAAATATTTTAAAAA 2 21 0 ATAAAAAAAT 0.938341 -59 TTAAAATTAAAAACCAATTACTG 2 67 0 TAAATAAAAA 0.923471 -13 CTCGCAAAACTTAACATATAAATCTAGTAGTA 3 19 1 TTAATATAAA 0.90242 -144 ATTTATACCAAAAAATTAAAATATTTGCTATT 3 51 1 AAAATAAAAT 0.847886 -112 ACTTTATTGATTAAGTTATAATTGAGGAATAA 3 81 0 TTAATATAAT 0.917015 -82 TATAATAGCATTAATTTAAAATAAGTCAATTA 3 120 0 TTAATAAAAT 0.979114 -43 TTAAATTAAAGAAAAAAAAACTTGACT 4 6 1 TTAAAAAAAA 0.970541 -84 AACAATGTATTTAATAAAAGATACATAAAAAT 5 146 1 TTAAAAAGAT 0.798155 -155 TGTAGGCTATTTAACAAAAAAAGAATTTGAAT 5 229 1 TTAAAAAAAA 0.970539 -72 ATATTGGGATATAATTTAAAATCTAGGGATTC 5 257 0 ATAATAAAAT 0.947793 -44 ATTAAGGCTTTAAAAATAAAAACT 5 287 1 TAAATAAAAA 0.92347 -14 TTATAATTATTTAAGGAAAAATTATTTTT 6 8 0 TTAAAAAAAT 0.975209 -186 CAACTCTTATTAAATCTAAAATTAGATTAACA 6 90 0 TAAATAAAAT 0.935097 -104 ATAAACTTTCTTAATCAAACAACTCTTATTAA 6 109 0 TTAAAAACAA 0.768119 -85 TTATTTTTGTTTAATATAAAATGTTGTGTTAA 6 137 1 TTAATAAAAT 0.979107 -57 AGGCATTTACATAAATAATAATATTAAGTATA 7 14 1 ATAAAATAAT 0.781732 -65 TTTATATTTTTTAAGAAAATAAATTTTACAGG 8 15 0 TTAAAAATAA 0.690802 -140 ATTTTCTTAAAAAATATAAAAACTTAAATACA 8 27 1 AAAATAAAAA 0.823582 -128 TTGTTTTTTTTTAAATAAAAAATATAATCTGT 8 56 0 TTAAAAAAAA 0.97054 -99 AACAATTCTTTTAAAGAAAACTAACATAAACT 8 83 1 TTAAAAAACT 0.78185 -72 GAAAACTAACATAAACTAAAAACAAAAACAAT 8 98 1 ATAATAAAAA 0.938342 -57 TCAATACACATTAAGCTATAATTTAGGC 8 137 1 TTAATATAAT 0.91705 -18 **** ****** Masking position 8 Map Score: 36.652 Number of sites scoring better than the average of aligned sites = 1339 Number in coding regions = 784 Number in noncoding regions = 555 Number of orfs with sites within 600 bp upstream = 132 Fraction of orfs with sites within 600 bp upstream = 0.0212014 Motif number 2 ATATTTTAAAAAAAGGTCAATT 2 1 0 AAAGTCAATT 0.70617 -79 TATTATAATAAATAAAAATATTTTAAAAAAAG 2 18 0 ATAAAATATT 0.631978 -62 ATTTATACCAAAAAATTAAAATATTTGCTATT 3 51 1 AAAATAAAAT 0.712384 -112 TAATTGAGGAATAATAGCAAATATTTTAATTT 3 63 0 AAATGCAAAT 0.395176 -100 AACTTAATCAATAAAGTTAATTTGTAATTGAC 3 96 1 AAAATTAATT 0.790411 -67 ATTAATTTAAAATAAGTCAATTACAAATTAAC 3 111 0 ATAATCAATT 0.93454 -52 CTTATTTTAAATTAATGCTATTATATACTTAA 3 127 1 ATAAGCTATT 0.821657 -36 GATCAAGTCAAGTAATACAATTTAACATTGGC 4 41 1 ATAAACAATT 0.934618 -49 CAACATATATAATAATAAAATTTCACACTGGG 5 22 1 ATAAAAAATT 0.790083 -279 TGCAATAGGTATAATGTCAATTCCCTGATCTG 5 63 0 AAATTCAATT 0.7409 -238 CAGCATATCTAACAAAGCTATTCTAAAAACAC 5 106 1 ACAAGCTATT 0.573444 -195 AAGCTATTCTAAAAACACTAATCAAAAACAAT 5 120 1 AAAAACTAAT 0.846008 -181 GCTATTTAACAAAAAAAGAATTTGAATCCCTA 5 234 1 AAAAAGAATT 0.688682 -67 AATTATAAGCATAAAAGCAATTTTTCCAAAAT 6 32 1 AAAAGCAATT 0.945895 -162 CTAAAATTAGATTAACACTATTTAATAATCAA 6 75 0 ATAAACTATT 0.874942 -119 TGTTTGATTAAGAAAGTTTATTTTTGTTTAAT 6 120 1 AAAATTTATT 0.696356 -74 TCGCCTGTAAACATAATCTATTTTAACACAAC 6 159 0 AATATCTATT 0.474083 -35 CATTTACATAAATAATAATATTAAGTATAATC 7 17 1 ATAAAATATT 0.631978 -62 TTATGGCTGTATTAATACAAATCAAGATTATA 7 42 0 ATAAACAAAT 0.829673 -37 ATATTTTTTAAGAAAATAAATTTTACAGGAGG 8 12 0 AAAATAAATT 0.877893 -143 TAAAAAATATAAAAACTTAAATACAGATTATA 8 34 1 AAAATTAAAT 0.564828 -121 TTTTTTAAATAAAAAATATAATCTGTATTTAA 8 50 0 AAAATATAAT 0.600037 -105 TTTTATTTAAAAAAAAACAATTCTTTTAAAGA 8 68 1 AAAAACAATT 0.963398 -87 TAAACTAAAAACAAAAACAATTTATCATTCAA 8 109 1 AAAAACAATT 0.963475 -46 * *** ****** Masking position 12 Map Score: 25.0798 Number of sites scoring better than the average of aligned sites = 1609 Number in coding regions = 1074 Number in noncoding regions = 535 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 3 AATAAAAATATTTTAAAAAAAGGTCAATT 2 10 0 TTTTAAAAAA 0.514783 -70 CATATTATAATAAATAAAAATATTTTAAAA 2 22 0 TAAATAAAAA 0.594622 -58 TAGTAATTTATACCAAAAAATTAAAATATT 3 46 1 TACCAAAAAA 0.839548 -117 TGCTATTATATACTTAAACAAAGGAGTTTG 3 142 1 TACTTAAACA 0.760745 -21 ATTCACAACATATATAATAATAAAATTTCA 5 17 1 TATATAATAA 0.768099 -284 ATTGACAGCATATCTAACAAAGCTATTCTA 5 101 1 TATCTAACAA 0.863114 -200 AAAAACAATGTATTTAATAAAAGATACATA 5 143 1 TATTTAATAA 0.827069 -158 TAATAAAAGATACATAAAAATCGAACCATC 5 157 1 TACATAAAAA 0.918971 -144 TCGAACCATCTACCAAAAAAATACTTCAAA 5 177 1 TACCAAAAAA 0.839548 -124 CTCTGTAGGCTATTTAACAAAAAAAGAATT 5 226 1 TATTTAACAA 0.899572 -75 AGATTAACACTATTTAATAATCAATTCTGT 6 69 0 TATTTAATAA 0.827069 -125 CAACATTTTATATTAAACAAAAATAAACTT 6 133 0 TATTAAACAA 0.79333 -61 AAAAGGCATTTACATAAATAATAATATTAA 7 11 1 TACATAAATA 0.527472 -68 AAAATTTATTTTCTTAAAAAATATAAAAAC 8 20 1 TTCTTAAAAA 0.725083 -135 TTATATTTTTTATTTAAAAAAAAACAATTC 8 61 1 TATTTAAAAA 0.768735 -94 ********** Masking position 6 Map Score: 12.8852 Number of sites scoring better than the average of aligned sites = 962 Number in coding regions = 575 Number in noncoding regions = 387 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 4 AATTGACCTTTTTTTAAAATATT 2 2 1 ATTGCCTTTT 0.738597 -78 TTTTTTTAAAATATTTTTATTTATTATAATAT 2 19 1 ATATTTTATT 0.503921 -61 AATTAACTTTATTGATTAAGTTATAATTGAGG 3 86 0 ATTGTTAATT 0.769036 -77 TTAATTTGTAATTGACTTATTTTAAATTAATG 3 112 1 ATTGCTTATT 0.914715 -51 TAAGTATATAATAGCATTAATTTAAAATAAGT 3 126 0 ATAGATTATT 0.722169 -37 CCAATGTTAAATTGTATTACTTGACTTGATCT 4 40 0 ATTGATTATT 0.872139 -50 TATTAAATACATTGTTTTTGATTAGTGTTTTT 5 130 0 ATTGTTTTAT 0.773246 -171 AGGGATTCAAATTCTTTTTTTGTTAAATAGCC 5 233 0 ATTCTTTTTG 0.53871 -68 TTTTGGAAAAATTGCTTTTATGCTTATAATTA 6 31 0 ATTGTTTTTG 0.909092 -163 TTAAACAAAAATAAACTTTCTTAATCAAACAA 6 119 0 ATAACTTTTT 0.524402 -75 TTGTGTTAAAATAGATTATGTTTACAGGCGAA 6 160 1 ATAGTTATTT 0.711289 -34 CTCCTGTAAAATTTATTTTCTTAAAAAATATA 8 13 1 ATTTTTTTTT 0.838072 -142 TTAAATACAGATTATATTTTTTATTTAAAAAA 8 50 1 ATTAATTTTT 0.647754 -105 CTTTAAAAGAATTGTTTTTTTTTAAATAAAAA 8 67 0 ATTGTTTTTT 0.973856 -88 TGAATGATAAATTGTTTTTGTTTTTAGTTTAT 8 108 0 ATTGTTTTTT 0.973857 -47 **** **** ** Masking position 1 Map Score: 8.71254 Number of sites scoring better than the average of aligned sites = 1741 Number in coding regions = 1187 Number in noncoding regions = 554 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 5 AAATATTTTAATTTTTTGGTATAAATTACT 3 47 0 ATTTTTTGGT 0.622101 -116 TTAACTTTATTGATTAAGTTATAATTGAGG 3 86 0 TGATTAAGTT 0.595401 -77 CAAACTCCTTTGTTTAAGTATATAATAGCA 3 142 0 TGTTTAAGTA 0.339988 -21 TCTTAAGTCAAGTTTTTTTTTCTTTAATTT 4 13 0 AGTTTTTTTT 0.895383 -77 TTAAATACATTGTTTTTGATTAGTGTTTTT 5 130 0 TGTTTTTGAT 0.729284 -171 GTTTGAAGTATTTTTTTGGTAGATGGTTCG 5 178 0 TTTTTTTGGT 0.622101 -123 CCTATTGTGCTGTTTATGGTTTGAAGTATT 5 196 0 TGTTTATGGT 0.914553 -105 ATTCAAATTCTTTTTTTGTTAAATAGCCTA 5 231 0 TTTTTTTGTT 0.819041 -70 AGTTTTTATTTTTAAAGCCT 5 291 0 AGTTTTTATT 0.788282 -10 TGATTAAGAAAGTTTATTTTTGTTTAATAT 6 124 1 AGTTTATTTT 0.895377 -70 GTGTTAAAATAGATTATGTTTACAGGCGAA 6 162 1 AGATTATGTT 0.864169 -32 CCTCCTGTAAAATTTATTTTCTTAAAAAAT 8 12 1 AATTTATTTT 0.478648 -143 ATATAATCTGTATTTAAGTTTTTATATTTT 8 37 0 TATTTAAGTT 0.422117 -118 ACTTAAATACAGATTATATTTTTTATTTAA 8 48 1 AGATTATATT 0.445939 -107 TTAAAAGAATTGTTTTTTTTTAAATAAAAA 8 67 0 TGTTTTTTTT 0.895383 -88 AGTTTATGTTAGTTTTCTTTAAAAGAATTG 8 85 0 AGTTTTCTTT 0.537303 -70 TTTTGTTTTTAGTTTATGTTAGTTTTCTTT 8 95 0 AGTTTATGTT 0.967134 -60 AATGATAAATTGTTTTTGTTTTTAGTTTAT 8 108 0 TGTTTTTGTT 0.967135 -47 ********** Masking position 5 Map Score: 13.3778 Number of sites scoring better than the average of aligned sites = 1530 Number in coding regions = 1052 Number in noncoding regions = 478 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 6 GTTAATTTCCTTAAATCTAACTTAA 1 8 0 CCTTAAATCT 0.949784 -18 CTTGACTTGATCTTAAGTCAAGTTTTTTTT 4 23 0 TCTTAAGTCA 0.870396 -67 TAAAAGAATCCCTTAAAGCTCATGCCAATG 4 66 0 CCTTAAAGCT 0.958055 -24 TATATCCCAATATTAAGGCTTTAAAAATAA 5 276 1 TATTAAGGCT 0.949784 -25 AAACAACTCTTATTAAATCTAAAATTAGAT 6 95 0 TATTAAATCT 0.883497 -99 TAAATAATAATATTAAGTATAATCTTGATT 7 25 1 TATTAAGTAT 0.670139 -54 ATTCCAACCTCCTTATGGCTGTATTAATAC 7 56 0 CCTTATGGCT 0.907352 -23 ********** Masking position 5 Map Score: 1.74231 Number of sites scoring better than the average of aligned sites = 188 Number in coding regions = 135 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 7 ATTGTAGATTTATCAGTAATTGGTTTTTAA 2 54 1 TATCAGTAAT 0.627366 -26 CATATAAATCTAGTAGTAATTTATACCAAA 3 33 1 TAGTAGTAAT 0.913114 -130 AAGTATATAATAGCATTAATTTAAAATAAG 3 127 0 TAGCATTAAT 0.913113 -36 CAATGTTAAATTGTATTACTTGACTTGATC 4 41 0 TTGTATTACT 0.843006 -49 CAGTGTGAAATTTTATTATTATATATGTTG 5 22 0 TTTTATTATT 0.676737 -279 GATTATTAAATAGTGTTAATCTAATTTTAG 6 77 1 TAGTGTTAAT 0.913114 -117 ATATAAAATGTTGTGTTAAAATAGATTATG 6 150 1 TTGTGTTAAA 0.573506 -44 TTATACTTAATATTATTATTTATGTAAATG 7 17 0 TATTATTATT 0.720625 -62 TAATCTTGATTTGTATTAATACAGCCATAA 7 44 1 TTGTATTAAT 0.945801 -35 ********** Masking position 7 Map Score: 1.46789 Number of sites scoring better than the average of aligned sites = 507 Number in coding regions = 311 Number in noncoding regions = 196 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 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 Motif number 9 ********** 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 10 ********** 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