AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00252_bbur_reg_100.orf -o00252_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 Input sequences: #1 BB0101 156 asparaginyl-tRNA synthetase (asnS) #2 BB0158 153 antigen, S2, putative #3 BB0159 23 B. burgdorferi predicted coding region BB0159 #4 BB0160 47 alanine racemase (alr) #5 BB0224 68 B. burgdorferi predicted coding region BB0224 #6 BB0446 243 aspartyl-tRNA synthetase (aspS) #7 BB0608 116 aminoacyl-histidine dipeptidase (pepD) Motif number 1 CACCCCTAAAAAGTAAAGTATAAATATTAACAAA 1 25 1 AAGTAAATAA 0.879321 -132 TAATATCAAGAATTAAAATAATAAAAATTGTTAA 1 61 1 AATTAAAAAA 0.974283 -96 ACTTTTTTTAAAAAAAACATTTAACAATTTTTAT 1 81 0 AAAAAAATAA 0.836592 -76 TGTTTTTTTTAAAAAAAGTTTTAAGCTATAATAA 1 96 1 AAAAAAATAA 0.836592 -61 GCTATAATAAAATTGATTTAACAATATTAATAAG 1 120 1 AATTGATAAA 0.892754 -37 GATTTAACAATATTAATAAGTTAAGTATTTAGG 1 134 1 TATTAATTAA 0.795308 -23 GATATTGAAAGATTAAAAATAAAAAT 2 3 1 TATTGAATAA 0.671445 -151 GAAAGATTAAAAATAAAAATGCAATTTTAAATAA 2 17 1 AAATAAAGAA 0.831607 -137 ATGCAATTTTAAATAAAACCAAAAGCGACTTGAC 2 35 1 AAATAAAAAA 0.954826 -119 TTTAGGCGGTAATTAAAATTTACATTAAATCATA 2 96 0 AATTAAATCA 0.82641 -58 ACTACAAATTAATAGAAAAAAGATTTTTAC 4 7 1 AATTAATAAA 0.960764 -41 AAAAAAGAATAAATAATTGTTAAATCAGCTCGTT 5 30 0 AAATAATTAA 0.93867 -39 AAATGTAATGAATTGAATGAAAAATTGATAGACA 6 29 1 AATTGAAAAA 0.927951 -215 ATCGCAGAAAAAATAAAACTTGAATATTGCATTA 6 185 1 AAATAAATAA 0.959482 -59 AAATTCATTCAATAAATTCAATAATATTGG 7 7 0 AATAAATAAA 0.841117 -110 TAATATACTAAATTAATCTTTAAATTCATTCAAT 7 28 0 AATTAATTAA 0.96483 -89 TTTAATTTATAATTAATAATATAATATACTAAAT 7 49 0 AATTAATAAA 0.960763 -68 CCTTTGATTAAATTAAATCCATAAATATACTTGG 7 84 0 AATTAAAAAA 0.974283 -33 ******* * ** Masking position 6 Map Score: 26.0138 Number of sites scoring better than the average of aligned sites = 1508 Number in coding regions = 938 Number in noncoding regions = 570 Number of orfs with sites within 600 bp upstream = 126 Fraction of orfs with sites within 600 bp upstream = 0.0202377 Motif number 2 CTTTGTTAATATTTATACTTTACTTTTTAGGGGTGATT 1 22 0 ATTCTTTTTT 0.955055 -135 AACATTTAACAATTTTTATTATTTTAATTCTTGATATT 1 62 0 ATTATTTTAT 0.644447 -95 AGCATTCTATATTATTACTATGATTTAATGTAAATTTT 2 78 1 AATCTATTTA 0.687246 -76 TAGATCTTCTTCCTTTATACCATTTAAAG 2 135 0 ATTCTTTTAA 0.984477 -19 AAGATATTTCCTTTTGTTTTTAT 3 3 0 ATTCTTTTTT 0.955071 -21 TAGAAAAAAGATTTTTACTTCTCTAAGAGAGCTAA 4 23 1 ATTCTTTAAA 0.957533 -25 TTTAACAATTATTTATTCTTTTTTAGGAGGAATTGTTA 5 40 1 ATTCTTTAGA 0.874021 -29 AAAAGTTGAAATAAATGCTTGGGTAAAAAAAATTAGAC 6 64 1 AATCTTTAAA 0.889056 -180 GATCTTTAGAAGCTTTTCTTCATTTACCAGAACTTGAG 6 150 0 ATTCTTTTAC 0.936779 -94 TCTTTTGATCAACAGTCCTTGAATTTTAATGCAATATT 6 207 0 AATCTTTTTA 0.949931 -37 TTAAATCCATAAATATACTTGGATTTAATTTATAATTA 7 68 0 ATTCTTTTTA 0.981413 -49 AATAACTTTCCTTTGATTAAATTAAATCCAT 7 96 0 ATTCTTTTAA 0.984477 -21 * * * *** *** * Masking position 1 Map Score: 12.8936 Number of sites scoring better than the average of aligned sites = 578 Number in coding regions = 357 Number in noncoding regions = 221 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 3 TACTTTACTTTTTAGGGGTGATTATTATTTTGT 1 12 0 TTTAGTGATT 0.620522 -145 ATTTTAATTCTTGATATTAACTTTGTTAATATT 1 47 0 TTGATAACTT 0.934827 -110 TTAAATCAATTTTATTATAGCTTAAAACTTTTT 1 108 0 TTTATAGCTT 0.970729 -49 TTTGGTTTTATTTAAAATTGCATTTTTATTTTT 2 25 0 TTTATTGCAT 0.941958 -129 CGACTTGACTTTGACATTAGCATTCTATATTAT 2 60 1 TTGATAGCAT 0.974062 -94 ATTACTATGATTTAATGTAAATTTTAATTACCG 2 91 1 TTTATAAATT 0.849031 -63 AATCAGCTCGTTTATTCTAACATATTATATA 5 9 0 TTTATAACAT 0.959999 -60 ATGTAATGAATTGAATGAAAAATTGATAGACAA 6 31 1 TTGAAAAAAT 0.639047 -213 TCTAATTTTTTTTACCCAAGCATTTATTTCAAC 6 68 0 TTTAAAGCAT 0.926958 -176 CTTTTCTTCATTTACCAGAACTTGAGCTTTTTC 6 143 0 TTTAGAACTT 0.882315 -101 AAAATAAAACTTGAATATTGCATTAAAATTCAA 6 194 1 TTGATTGCAT 0.930321 -50 TATACTTGGATTTAATTTATAATTAATAATATA 7 60 0 TTTATATAAT 0.656281 -57 **** ****** Masking position 4 Map Score: 8.33179 Number of sites scoring better than the average of aligned sites = 487 Number in coding regions = 308 Number in noncoding regions = 179 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 4 TTAGGGGTGATTATTATTTTGTA 1 4 0 TTATTATTTT 0.897023 -153 TTTGTTAATATTTATACTTTACTTTTTAGG 1 29 0 TTTATACTTT 0.703603 -128 TTAACAATTTTTATTATTTTAATTCTTGAT 1 65 0 TTATTATTTT 0.897023 -92 AATACTTAACTTATTAATATTGTTAAATCA 1 133 0 TTATTAATAT 0.728353 -24 TAAAATTGCATTTTTATTTTTAATCTTTCA 2 16 0 TTTTTATTTT 0.931665 -138 GCATTCTATATTATTACTATGATTTAATGT 2 79 1 TTATTACTAT 0.863257 -75 TAGATCTTCTTCCTTTATACCATTTA 2 138 0 TTCTTCCTTT 0.931276 -16 AAGATATTTCCTTTTGTTTTTAT 3 10 0 TATTTCCTTT 0.742602 -14 AGTAAAAATCTTTTTTCTATTAATTTGTAG 4 12 0 TTTTTTCTAT 0.609036 -36 AGAAAAAAGATTTTTACTTCTCTAAGAGAG 4 24 1 TTTTTACTTC 0.874393 -24 TAACAATTATTTATTCTTTTTTAGGAGGAA 5 42 1 TTATTCTTTT 0.913703 -27 TGTCTATCAATTTTTCATTCAATTCATTAC 6 33 0 TTTTTCATTC 0.783105 -211 GAACTTGAGCTTTTTCATATCTGTCTCTTA 6 129 0 TTTTTCATAT 0.83674 -115 TTAGAAGCTTTTCTTCATTTACCAGAACTT 6 153 0 TTCTTCATTT 0.852571 -91 CAATATTCAAGTTTTATTTTTTCTGCGATC 6 184 0 GTTTTATTTT 0.649101 -60 ********** Masking position 5 Map Score: 13.4751 Number of sites scoring better than the average of aligned sites = 2609 Number in coding regions = 1744 Number in noncoding regions = 865 Number of orfs with sites within 600 bp upstream = 140 Fraction of orfs with sites within 600 bp upstream = 0.0224863 Motif number 5 AGTTAATATCAAGAATTAAAATAATAAAAAT 1 58 1 AAAATTAAAA 0.720857 -99 CAATTTTATTATAGCTTAAAACTTTTTTTAA 1 104 0 ATGCTTAAAA 0.950967 -53 CTATAATAAAATTGATTTAACAATATTAATA 1 121 1 ATGATTTAAC 0.75283 -36 GATATTGAAAGATTAAAAATAAAAATGC 2 8 1 AAGATTAAAA 0.866642 -146 GTAATTAAAATTTACATTAAATCATAGTAAT 2 91 0 TTACATTAAA 0.42203 -63 CCGCCTAAAAAAGGCTTTAAATGGTATAAAG 2 121 1 AAGCTTTAAA 0.925151 -33 ATTACATTTGATAACTTTAAACATAAC 6 7 0 ATACTTTAAA 0.913745 -237 AATGTAATGAATTGAATGAAAAATTGATAGA 6 30 1 ATGAATGAAA 0.815818 -214 AGTTCTGGTAAATGAAGAAAAGCTTCTAAAG 6 154 1 AAGAAGAAAA 0.63928 -90 GCTTCTAAAGATCGCAGAAAAAATAAAACTT 6 175 1 ATGCAGAAAA 0.840993 -69 AAACTTGAATATTGCATTAAAATTCAAGGAC 6 200 1 ATGCATTAAA 0.95815 -44 AATTTATTGAATGAATTTAAAGATTAATTTA 7 23 1 ATAATTTAAA 0.884417 -94 CTTTCCTTTGATTAAATTAAATCCATAAATA 7 91 0 ATAAATTAAA 0.851793 -26 ** ******** Masking position 9 Map Score: 9.11437 Number of sites scoring better than the average of aligned sites = 1049 Number in coding regions = 736 Number in noncoding regions = 313 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 6 TAATATTTATACTTTACTTTTTAGGGGTGA 1 24 0 ACTTTACTTT 0.934791 -133 TTTTATTTAAAATTGCATTTTTATTTTTAA 2 23 0 AATTGCATTT 0.895685 -131 ACCAAAAGCGACTTGACTTTGACATTAGCA 2 52 1 ACTTGACTTT 0.984292 -102 AAAAAATAAAACTTGAATATTGCATTAAAA 6 192 1 ACTTGAATAT 0.919728 -52 GATCAACAGTCCTTGAATTTTAATGCAATA 6 209 0 CCTTGAATTT 0.951633 -35 CCAATATTATTGAATTTATTGAATGAA 7 8 1 TATTGAATTT 0.752182 -109 CCATAAATATACTTGGATTTAATTTATAAT 7 70 0 ACTTGGATTT 0.958971 -47 AATAACTTTCCTTTGATTAAATTA 7 103 0 ACTTTCCTTT 0.906052 -14 ********** Masking position 4 Map Score: 6.81071 Number of sites scoring better than the average of aligned sites = 211 Number in coding regions = 136 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 7 ********** No masking Map Score: -3.17312e-13 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: -3.17312e-13 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: -3.17312e-13 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