AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00052_bbur_reg_300.orf -o00052_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 Input sequences: #1 BB0004 246 phosphoglucomutase (femD) #2 BB0116 173 PTS system, maltose and glucose-specific IIABC component (malX) #3 BB0207 52 UTP--glucose-1-phosphate uridylyltransferase (gtaB) #4 BB0554 261 B. burgdorferi predicted coding region BB0554 #5 BB0557 138 phosphocarrier protein HPr (ptsH-2) #6 BB0630 81 1-phosphofructokinase (fruK) #7 BB0644 154 conserved hypothetical protein #8 BB0645 45 PTS system, glucose-specific IIBC component (ptsG) #9 BBB04_BBB05 276 BBB04: PTS system, cellobiose-specific IIC component (celB), BBB05: PTS system, cellobiose-specific IIA component (celC) #10 BBB29 300 PTS system, maltose and glucose-specific IIABC component (malX) Motif number 1 GTTAAAGTTGATAAAATTTTTTCTGAAATGATAC 1 72 0 AAAATTTTTT 0.599236 -175 TTGCTTATATTAATAAGCTTTTCTTTAAGGGTTT 1 124 0 TATACTTTTT 0.392575 -123 TTATACTTAAAAATTTGTTTTTTTGCTTATATTA 1 146 0 AATTTTTTTT 0.675191 -101 TAGTATAGCCACTTATGTTATTATACTTAAAAAT 1 166 0 ATTATTATTT 0.729797 -81 TTGCCTCCGTTTTATCACTTATTTATAAAAAATA 2 15 1 TTATCTTATT 0.652767 -159 AGTAAGGTATTATATATTTTTTATAAATAAGTGA 2 29 0 TTATTTTTTT 0.954327 -145 GCTTGATTTATCTAACCTTATTATTTGGCTTGTG 2 100 1 TTAATTATTT 0.913693 -74 TTGTGTAGTAAGTAAAGTTTTTTTTTGCAAAAAA 2 129 1 ATAATTTTTT 0.916257 -45 CTATTTTATTATAAAGCTTTTTTTGCAAAAAAAA 2 147 0 AAAATTTTTT 0.823532 -27 TATAGCAAAAATTTAATTTTATATATTCA 3 6 0 ATTATTTATT 0.728852 -47 AAATTTTTGCTATAATCTTATTTTAAGAGAGAAA 3 26 1 TTAATTATTT 0.913693 -27 GTGAATTTTTTATTAATTTATTTTAAGATTGTTG 4 144 1 TTTATTATTT 0.82548 -118 GTTTTATTTTTTAATCCTTTTTATTTATGCAATG 4 209 1 TAATTTTTTT 0.891215 -53 TTTTTACTAATTTAATTTTTTTGT 4 248 1 TTAATTTTTT 0.954351 -14 AAAGATAGTAATTAAACTTATTCTAACAA 5 6 0 ATAATTATTT 0.857692 -133 AAGTTTAATTACTATCTTTATTATGCTATATTTC 5 21 1 ATATTTATTT 0.858032 -118 TTTATTATGCTATATTTCTTATGTAAAGGGAATA 5 37 1 TTATCTTATT 0.652767 -102 GTAAAGGGAATATATAATTTATTTTTATGTATTA 5 59 1 TTATTTTATT 0.913623 -80 CCTCATTATGAATATTGTTTTTTTTGATTAACTT 5 102 0 ATATTTTTTT 0.922678 -37 CTTTATATATTATATAGTGTATATA 6 2 1 TTATATTATT 0.60887 -80 TACTATTTATTTAATTGATTTTATAAATCAAAGG 6 50 1 TAATATTTTT 0.546408 -32 GCCTAAATTATAGCTTAATGTGTATTGAATG 7 8 1 TATATTAATT 0.484195 -147 TATTGAATGATAAATTGTTTTTGTTTTTAGTTTA 7 33 1 TAATTTTTTT 0.891189 -122 TTTCTTTAAAAGAATTGTTTTTTTTTAAATAAAA 7 74 1 AAATTTTTTT 0.820944 -81 TTAAATACAGATTATATTTTTTATTTAAAAAAAA 7 92 0 ATATTTTTTT 0.919979 -63 TATAATCTGTATTTAAGTTTTTATATTTTTTAAG 7 110 1 ATTATTTTTT 0.839132 -45 ACCTCCTGTAAAATTTATTTTCTTAAAAAA 7 135 0 TTAATTTATT 0.913554 -20 TAAGGGTTAATTTATTTTTTATTTTAGGAGGGTT 8 20 1 TTATTTTATT 0.913693 -26 TTTCGATATTTTTATTGTTAATATCGTTTTCATA 9 21 1 TTATTTAATT 0.842786 -256 ATTTCATGTATTAATGATTTATATGCTTCATAAG 9 59 1 TAATTTTATT 0.805707 -218 ATAAGATTGGTTTTTATTTTTTCTTTCTAATTTT 9 88 1 TTTTTTTTTT 0.903298 -189 ATTTTTTCTTTCTAATTTTATTATTTTATTATAA 9 103 1 TTAATTATTT 0.913693 -174 TTTATTATTTTATTATAATATTCTAAATTGGATT 9 119 1 TTTAATATTT 0.410253 -158 CATTTTGGCTATTTTTTTTAATTTGCTGTATTAT 9 204 1 ATTTTTAATT 0.57767 -73 TTATTAGCTTTGTAAAAATTTTATTACGCTTTGC 10 95 1 TTAAATTTTT 0.7543 -206 CTGTTACGGTTCTTATGTTAATGTTTAATACAAT 10 253 0 TTTATTAATT 0.705493 -48 * *** ***** * Masking position 9 Map Score: 38.7136 Number of sites scoring better than the average of aligned sites = 5339 Number in coding regions = 3353 Number in noncoding regions = 1986 Number of orfs with sites within 600 bp upstream = 243 Fraction of orfs with sites within 600 bp upstream = 0.0390299 Motif number 2 GAATTAAGTTTTTCAAGTATCATTTCAGAAAAA 1 56 1 TTTAGTATAT 0.941378 -191 GGGTTTTGGTTTTAACTTATGAATGTTAAAGTT 1 97 0 TTTATTATAA 0.908742 -150 AAAAACAAATTTTTAAGTATAATAACATAAGTG 1 158 1 TTTAGTATAT 0.941377 -89 ATTGCTATAATTTTAATAATCAATAGTATAGCC 1 190 0 TTTATAATAA 0.899922 -57 ATTATAGATGTTTTCTGAATAAAAACAAGGACC 4 13 0 TTTCGAATAA 0.836718 -249 TAAGTGAATTTTTTATTAATTTATTTTAAGATT 4 141 1 TTTATAATTA 0.769413 -121 TATTAATTTATTTTAAGATTGTTGCATGTATTG 4 154 1 TTTAGATTTT 0.718384 -108 GTCGGATGTTTTTGAGGTTTTATTTTTTAATCC 4 193 1 TTTAGTTTAT 0.883896 -69 AATGTTAGGTTTTTACTAATTTAATTTTTTTGT 4 239 1 TTTATAATTA 0.769413 -23 TATAATTTATTTTTATGTATTATAATGTAAAAA 5 71 1 TTTAGTATAT 0.941378 -68 ATTTATTAAATTTTACTATTTATTTAATTGATT 6 37 1 TTTATATTAT 0.793796 -45 GATAATCTCCTTTGATTTATAAAATCAATTAAA 6 59 0 TTTATTATAA 0.908704 -23 ATAATCTGTATTTAAGTTTTTATATTTTTTAAG 7 111 1 TTTATTTTAT 0.809995 -44 TCATATGCTATTTCATGTATTAATGATTTATAT 9 50 1 TTTAGTATAA 0.94676 -227 TTCTTTCTAATTTTATTATTTTATTATAATATT 9 108 1 TTTATATTTA 0.612686 -169 TTTTTTTTAATTTGCTGTATTATTTCATTAGCT 9 215 1 TTTCGTATAT 0.83672 -62 TTCATTAGCTTTTGCGGAATTTAGTACGCCACC 9 238 1 TTTCGAATTA 0.655353 -39 TAATAGGATGTTTGACGTTTTAAATCGGTTGGA 10 202 0 TTTAGTTTAA 0.893962 -99 TTAAAGCTCATTTGATTAATAATAGGATGTTTG 10 221 0 TTTATAATAT 0.890351 -80 *** * **** ** Masking position 10 Map Score: 21.501 Number of sites scoring better than the average of aligned sites = 953 Number in coding regions = 625 Number in noncoding regions = 328 Number of orfs with sites within 600 bp upstream = 103 Fraction of orfs with sites within 600 bp upstream = 0.0165435 Motif number 3 TTTTGAATCCATTAAATATTTTCC 1 5 0 ATTAAATATT 0.914374 -242 TCTTGCCAGAATTAAGTTTTTCAAGTATCA 1 48 1 ATTAAGTTTT 0.79638 -199 GTTAAAGTTGATAAAATTTTTTCTGAAATG 1 76 0 ATAAAATTTT 0.834174 -171 GCTTATATTAATAAGCTTTTCTTTAAGGGT 1 126 0 ATAAGCTTTT 0.615404 -121 AAAGTAAGGTATTATATATTTTTTATAAAT 2 35 0 ATTATATATT 0.722695 -139 TCAAGATCAAATTAAATCTTGCTTGATTTA 2 80 1 ATTAAATCTT 0.878014 -94 AATATATAAAATTAAATTTTTGCTATAATC 3 13 1 ATTAAATTTT 0.961209 -40 GTTTTTACTAATTTAATTTTTTTGT 4 247 1 ATTTAATTTT 0.639529 -15 ATAAAAATAAATTATATATTCCCTTTACAT 5 57 0 ATTATATATT 0.722695 -82 GTTTTTTTTGATTAACTTTTTACATTATAA 5 90 0 ATTAACTTTT 0.953106 -49 ATATACATTTATTAAATTTTACTATTTATT 6 31 1 ATTAAATTTT 0.961209 -51 TTAAATACAGATTATATTTTTTATTTAAAA 7 96 0 ATTATATTTT 0.859475 -59 TTTTTAAGAAAATAAATTTTACAGGAGGT 7 136 1 AATAAATTTT 0.766551 -19 TAAAAAATAAATTAACCCTTAAGTTTAAAA 8 11 0 ATTAACCCTT 0.549343 -35 TAAATGGCTTATTAGCTTTTCATTTTGGCT 9 184 1 ATTAGCTTTT 0.887016 -93 GTATTATTTCATTAGCTTTTGCGGAATTTA 9 231 1 ATTAGCTTTT 0.887016 -46 TAATAAGAGAAATAACTATTGCAGCTAAAA 10 71 0 AATAACTATT 0.532118 -230 GCAAAGCGTAATAAAATTTTTACAAAGCTA 10 99 0 ATAAAATTTT 0.834174 -202 CTTTAATTGTATTAAACATTAACATAAGAA 10 248 1 ATTAAACATT 0.688278 -53 ********** Masking position 9 Map Score: 22.1647 Number of sites scoring better than the average of aligned sites = 838 Number in coding regions = 494 Number in noncoding regions = 344 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 4 GGAAAATATTTAATGGATTCAAAAGTA 1 8 1 ATTTAATGGA 0.638693 -239 TTCAGAAAAAATTTTATCAACTTTAACATT 1 79 1 ATTTTATCAA 0.56008 -168 TATTGCTATAATTTTAATAATCAATAGTAT 1 194 0 ATTTTAATAA 0.714791 -53 TATTATATATTTTTTATAAATAAGTGATAA 2 26 0 TTTTTATAAA 0.749435 -148 TTTTTATCTCTTTTGATAAATGGACAAATT 4 61 0 TTTTGATAAA 0.702268 -201 CCGGGGGCTATTTTTATTGACAAATAGTGC 4 94 1 TTTTTATTGA 0.772961 -168 TTAAGTGAATTTTTTATTAATTTATTTTAA 4 140 1 TTTTTATTAA 0.90896 -122 TTTTTAATCCTTTTTATTTATGCAATGTTA 4 216 1 TTTTTATTTA 0.601758 -46 CAATGTTAGGTTTTTACTAATTTAATTTTT 4 238 1 TTTTTACTAA 0.575897 -24 ATATAATTTATTTTTATGTATTATAATGTA 5 70 1 TTTTTATGTA 0.596803 -69 ATATTGTTTTTTTTGATTAACTTTTTACAT 5 95 0 TTTTGATTAA 0.880291 -44 AAATAGTAAAATTTAATAAATGTATATACA 6 28 0 ATTTAATAAA 0.630203 -54 TTTACTATTTATTTAATTGATTTTATAAAT 6 48 1 ATTTAATTGA 0.64344 -34 AAAACAATTCTTTTAAAGAAAACTAACATA 7 65 0 TTTTAAAGAA 0.740611 -90 AATTGTTTTTTTTTAAATAAAAAATATAAT 7 86 1 TTTTAAATAA 0.744552 -69 GTTTTTATATTTTTTAAGAAAATAAATTTT 7 126 1 TTTTTAAGAA 0.770779 -29 AATATCGAAATTTTAAAGAA 9 1 0 TTTTAAAGAA 0.740611 -276 CTCTAAACAAATTTGATGAAGATAAATCCA 9 147 0 ATTTGATGAA 0.829437 -130 CTAATAAGCCATTTAATTAACACTCTAAAC 9 169 0 ATTTAATTAA 0.841478 -108 ATTAAAGCTCATTTGATTAATAATAGGATG 10 225 0 ATTTGATTAA 0.832335 -76 ********** Masking position 4 Map Score: 14.9903 Number of sites scoring better than the average of aligned sites = 1840 Number in coding regions = 1164 Number in noncoding regions = 676 Number of orfs with sites within 600 bp upstream = 120 Fraction of orfs with sites within 600 bp upstream = 0.019274 Motif number 5 TGATTATTAAAATTATAGCAATAATATGAC 1 201 1 AATTATAGCA 0.967029 -46 ACCTTACTTTAATTGTAGCTTTTTCTCAAG 2 55 1 AATTGTAGCT 0.928895 -119 CTCAAGATCAAATTAAATCTTGCTTGATTT 2 79 1 AATTAAATCT 0.776747 -95 CTTAAAATAAGATTATAGCAAAAATTTAAT 3 23 0 GATTATAGCA 0.87266 -30 TAACATTATAAATTATAGATGTTTTCTGAA 4 27 0 AATTATAGAT 0.916694 -235 TTTACATAAGAAATATAGCATAATAAAGAT 5 34 0 AAATATAGCA 0.822172 -105 CATAAAAATAAATTATATATTCCCTTTACA 5 58 0 AATTATATAT 0.684212 -81 GCCTAAATTATAGCTTAATGTGTAT 7 6 1 AATTATAGCT 0.982382 -149 TGTTTAATACAATTAAAGCTCATTTGATTA 10 236 0 AATTAAAGCT 0.946435 -65 ********** Masking position 4 Map Score: 6.9781 Number of sites scoring better than the average of aligned sites = 198 Number in coding regions = 126 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 6 GTAAATTTCTTCTCATTGATATTCTA 1 231 0 TTTCTCTCAT 0.868407 -16 TTTGCCTCCGTTTTATCACTTATTTATAAAA 2 14 1 TTTTTCACTT 0.947501 -160 ATTTTTCTCTCTTAAAATAAGAT 3 40 0 TTTTTCTCTT 0.986515 -13 CCCCGGCTATTTTTATCTCTTTTGATAAATG 4 69 0 TTTTTCTCTT 0.986515 -193 GCTGCAATAGTTATTTCTCTTATTAGCTTTG 10 76 1 TTATTCTCTT 0.947501 -225 AAGAGCACCTTTTTTTCTCTTTATTGTTGAC 10 132 1 TTTTTCTCTT 0.986515 -169 **** ****** Masking position 6 Map Score: 6.4789 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 42 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 7 TTTAAGGGTTTTGGTTTTAACTTATGAATGTT 1 103 0 TTGTTTTACT 0.931102 -144 AATTTGTTTTTTTGCTTATATTAATAAGCTTT 1 137 0 TTGCTTAATT 0.621296 -110 AAGGTCCTTGTTTTTATTCAGAAAACAT 4 7 1 CTGTTTTATT 0.837041 -255 TGTTTTCAAATTAGTTTTAAGTGAATTTTTTA 4 124 1 TTGTTTTAGT 0.962765 -138 TATGCAATGTTAGGTTTTTACTAATTTAATTT 4 234 1 TAGTTTTACT 0.570835 -28 AATATATAATTTATTTTTATGTATTATAATGT 5 67 1 TTTTTTTTGT 0.62139 -72 ATGAATATTGTTTTTTTTGATTAACTTTTTAC 5 97 0 TTTTTTTATT 0.892617 -42 ATAAATTGTTTTTGTTTTTAGTTTATGTTAGT 7 42 1 TTGTTTTAGT 0.962765 -113 TTAGTTTATGTTAGTTTTCTTTAAAAGAATTG 7 59 1 TTGTTTTTTT 0.904471 -96 CTTTAAAAGAATTGTTTTTTTTTAAATAAAAA 7 77 1 ATGTTTTTTT 0.482366 -78 AAGGGTTAATTTATTTTTTATTTTAGGAGGGT 8 21 1 TTTTTTTATT 0.892617 -25 CTTCATAAGATTGGTTTTTATTTTTTCTTTCT 9 84 1 TTGTTTTATT 0.972385 -193 CTTCATCAAATTTGTTTAGAGTGTTAATTAAA 9 156 1 TTGTTTAAGT 0.817765 -121 ATTTTGGCTATTTTTTTTAATTTGCTGTATTA 9 205 1 TTTTTTTATT 0.892617 -72 ATTAATCAAATGAGCTTTAATTGTATTAAACA 10 234 1 TGGCTTTATT 0.579643 -67 ** ***** *** Masking position 6 Map Score: 13.0936 Number of sites scoring better than the average of aligned sites = 601 Number in coding regions = 379 Number in noncoding regions = 222 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 8 CTTAATTCTGGCAAGATTTGTCCTAATACTTT 1 32 0 GCAATTTGTC 0.98651 -215 ATTAAATCTTGCTTGATTTATCTAACCTTATT 2 90 1 GCTATTTATC 0.962908 -84 TATAATGTTAGCATAATTTGTCCATTTATCAA 4 47 1 GCAATTTGTC 0.986512 -215 ATAGCCCCCGGCTATTTTTATCTCTTTTGATA 4 73 0 GCTTTTTATC 0.843456 -189 TTTGAAAACAGCACTATTTGTCAATAAAAATA 4 102 0 GCAATTTGTC 0.986523 -160 CTAAATTATAGCTTAATGTGTATTGAATGATA 7 13 1 GCTATGTGTA 0.888897 -142 AATCAAATGAGCTTTAATTGTATTAAACATTA 10 237 1 GCTAATTGTA 0.843707 -64 *** ******* Masking position 9 Map Score: 3.30681 Number of sites scoring better than the average of aligned sites = 14 Number in coding regions = 10 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 9 ATGAATGTTAAAGTTGATAAAATTTTTTCT 1 82 0 AAGTTGATAA 0.625833 -165 CCTTAAAGAAAAGCTTATTAATATAAGCAA 1 128 1 AAGCTTATTA 0.416779 -119 TTATTAATATAAGCAAAAAAACAAATTTTT 1 142 1 AAGCAAAAAA 0.68499 -105 ATCTTAAAATAAATTAATAAAAAATTCACT 4 143 0 AAATTAATAA 0.678585 -119 TAGCATAATAAAGATAGTAATTAAACTTAT 5 19 0 AAGATAGTAA 0.52494 -120 ATAATGTAAAAAGTTAATCAAAAAAAACAA 5 92 1 AAGTTAATCA 0.645452 -47 TAAATAGTAAAATTTAATAAATGTATATAC 6 29 0 AATTTAATAA 0.595701 -53 AAACTAACATAAACTAAAAACAAAAACAAT 7 46 0 AAACTAAAAA 0.531842 -109 TATATTTTTTAAGAAAATAAATTTTACAGG 7 131 1 AAGAAAATAA 0.75631 -24 CAATCTTATGAAGCATATAAATCATTAATA 9 67 0 AAGCATATAA 0.701594 -210 ATATTATAATAAAATAATAAAATTAGAAAG 9 110 0 AAAATAATAA 0.618526 -167 CCAAAATGAAAAGCTAATAAGCCATTTAAT 9 182 0 AAGCTAATAA 0.970483 -95 AATTCCGCAAAAGCTAATGAAATAATACAG 9 229 0 AAGCTAATGA 0.912182 -48 AATTTTTACAAAGCTAATAAGAGAAATAAC 10 85 0 AAGCTAATAA 0.970483 -216 TCCTATTATTAATCAAATGAGCTTTAATTG 10 227 1 AATCAAATGA 0.354829 -74 ********** Masking position 2 Map Score: 5.01536 Number of sites scoring better than the average of aligned sites = 714 Number in coding regions = 472 Number in noncoding regions = 242 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 10 ********** No masking Map Score: 1.38088e-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 11 ********** No masking Map Score: 1.38088e-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 12 ********** No masking Map Score: 1.38088e-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