AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00272_bbur_reg_300.orf -o00272_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 BB0087 120 L-lactate dehydrogenase (ldh) #2 BB0088 159 GTP-binding membrane protein (lepA) #3 BB0089 71 B. burgdorferi predicted coding region BB0089 #4 BB0093 21 V-type ATPase, subunit B (atpB) #5 BB0094 85 V-type ATPase, subunit A (atpA) #6 BB0096 183 V-type ATPase, subunit E, putative #7 BB0100 156 glutamate racemase (murI) #8 BB0599 51 cysteinyl-tRNA synthetase (cysS) Motif number 1 CATACCTTTAAAAATTAAAAACAAAT 1 7 0 AAAATTAAAA 0.950849 -114 TTAAATAAGTAATGATAAAAATATTCTATC 1 62 0 AATGATAAAA 0.879283 -59 AACTATATACAAAACTAATTTTAAATAAGT 1 82 0 AAAACTAATT 0.622045 -39 ATTACTCCATTAAATTAAAACTATATACAA 1 100 0 TAAATTAAAA 0.811955 -21 ACTACAAGTCAAAATTTAAAAAT 2 4 0 AAAATTTAAA 0.667002 -156 TTTTCTTACGAATACTAATACTACTTCCCC 2 39 0 AATACTAATA 0.881265 -121 TTCAAAAAGCTAAAATAATATCTGATCGTG 2 126 1 TAAAATAATA 0.789545 -34 TATTAAAAGAAATAATAAATCAAAA 3 6 0 AATAATAAAT 0.94294 -66 GAGAAAATTTAATATTAAAAGAAATAATAA 3 18 0 AATATTAAAA 0.969523 -54 AATAATAAATATATTAAATT 3 62 0 AATAATAAAT 0.94294 -10 AACTATTAGAAATAATACAACCA 6 4 0 AATAATACAA 0.879287 -180 AAGTTGGCACAATAATACTTCTTTAAAGAA 6 47 0 AATAATACTT 0.617364 -137 AAAATTTTACAATATTAAAAAACATATCAA 6 75 0 AATATTAAAA 0.969523 -109 TAAAATTTTTGATATTAAAAATTTATTTTA 6 96 1 GATATTAAAA 0.761831 -88 TAAAAAAGCATAAAATAAATTTTTAATATC 6 106 0 TAAAATAAAT 0.692326 -78 CATATAAGATAAAAATAATAACCTAACACT 6 154 0 AAAAATAATA 0.943835 -30 TTGATTTAACAATATTAATAAGTTAAGTAT 7 16 0 AATATTAATA 0.950809 -141 AGTTTTAAGCTATAATAAAATTGATTTAAC 7 36 0 TATAATAAAA 0.910222 -121 CAAGAATTAAAATAATAAAAATTGTTAAAT 7 81 0 AATAATAAAA 0.978445 -76 AAATATTAACAAAGTTAATATCAAGAATTA 7 102 0 AAAGTTAATA 0.65327 -55 TAACTTTGTTAATATTTATACTTTACTTTT 7 115 1 AATATTTATA 0.665036 -42 TACAAAATAATAATCACCCCTAAAA 7 142 0 AATAATAATC 0.755126 -15 ACGTACTTAATAATAAATTAGATTTTTT 8 9 1 AATAATAAAT 0.94294 -43 TCAAAATTGAAAAAATAAAAAATCTAATTT 8 25 0 AAAAATAAAA 0.965104 -27 ********** Masking position 6 Map Score: 36.1742 Number of sites scoring better than the average of aligned sites = 3104 Number in coding regions = 1966 Number in noncoding regions = 1138 Number of orfs with sites within 600 bp upstream = 214 Fraction of orfs with sites within 600 bp upstream = 0.034372 Motif number 2 ATTTGTTTTTAATTTTTAAA 1 1 1 ATTTGTTTTT 0.921247 -120 TATTTTTATCATTACTTATTTAAAATTAGT 1 69 1 ATTACTTATT 0.803183 -52 CTTATTTAAAATTAGTTTTGTATATAGTTT 1 83 1 ATTAGTTTTG 0.653919 -38 GCAATAATGCAAAAGTTTTTCTTACGAATA 2 55 0 AAAAGTTTTT 0.768591 -105 CAGATATTATTTTAGCTTTTTGAATAAATC 2 120 0 TTTAGCTTTT 0.885472 -40 TATTCATTTAAATTCCTTTT 5 1 0 AATTCCTTTT 0.739589 -85 CTCCAACGACTTTTCCTTTTGTATTCATTT 5 22 0 TTTTCCTTTT 0.82655 -64 CTTTAAAGAATATACTTATTCTCAACTATT 6 27 0 TATACTTATT 0.600713 -157 TGCCAACTTGATATGTTTTTTAATATTGTA 6 68 1 ATATGTTTTT 0.877435 -116 ATTGTAAAATTTTTGATATTAAAAATTTAT 6 92 1 TTTTGATATT 0.418806 -92 AAAATTTATTTTATGCTTTTTTAAAGTTTT 6 113 1 TTATGCTTTT 0.788469 -71 CCTAAATACTTAACTTATTAATATTGTTA 7 10 1 TTAACTTATT 0.662315 -147 ATTATAGCTTAAAACTTTTTTTAAAAAAAA 7 50 1 AAAACTTTTT 0.768059 -107 AAAAATTGTTAAATGTTTTTTTTAAAAAAA 7 65 0 AAATGTTTTT 0.769872 -92 ATATTTATACTTTACTTTTTAGGGGTGATT 7 126 1 TTTACTTTTT 0.901507 -31 TTAATAATAAATTAGATTTTTTATTTTTTC 8 17 1 ATTAGATTTT 0.769199 -35 ********** Masking position 7 Map Score: 11.1987 Number of sites scoring better than the average of aligned sites = 2829 Number in coding regions = 1839 Number in noncoding regions = 990 Number of orfs with sites within 600 bp upstream = 160 Fraction of orfs with sites within 600 bp upstream = 0.0256987 Motif number 3 AATCACATACCTTTAAAAATTAAAAACAAA 1 12 0 CTTTAAAAAT 0.945892 -109 ATCATTACTTATTTAAAATTAGTTTTGTAT 1 76 1 ATTTAAAATT 0.906172 -45 ACAAGTCAAAATTTAAAAAT 2 1 0 ATTTAAAAAT 0.725741 -159 GTAAGAAAAACTTTTGCATTATTGCACACA 2 60 1 CTTTTGCATT 0.658021 -100 TTGACTTTTAAAATCACGATCAGA 2 146 0 CTTTTAAAAT 0.721771 -14 ATTTCTTTTAATATTAAATTTTCTCGTAAT 3 23 1 ATATTAAATT 0.736577 -49 AATAATAAATATATTAAATTAACTCATAAA 3 52 0 ATATTAAATT 0.736577 -20 CTTTTGTATTCATTTAAATTCCTTTT 5 7 0 CATTTAAATT 0.613671 -79 AATATCAAAAATTTTACAATATTAAAAAAC 6 82 0 ATTTTACAAT 0.709295 -102 AATTTTTGATATTAAAAATTTATTTTATGC 6 99 1 ATTAAAAATT 0.666695 -85 GCAAACAAAACTTTAAAAAAGCATAAAATA 6 119 0 CTTTAAAAAA 0.703234 -65 AATAAAATTGATTTAACAATATTAATAAGT 7 23 0 ATTTAACAAT 0.930412 -134 TAAAAAAAACATTTAACAATTTTTATTATT 7 71 1 ATTTAACAAT 0.930412 -86 ********** Masking position 8 Map Score: 12.7384 Number of sites scoring better than the average of aligned sites = 1114 Number in coding regions = 740 Number in noncoding regions = 374 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 4 TGCCAATCACATACCTTTAAAAATTAAAAAC 1 15 0 ATACCTTAAA 0.883149 -106 TTTTATCATTACTTATTTAAAATTAGTTTTG 1 72 1 ACTTATTAAA 0.936302 -49 AATTACTCCATTAAATTAAAACTAT 1 106 0 ACTCCATAAA 0.78353 -15 TAGCTGATCGATTTATTCAAAAAGCTAAAAT 2 111 1 ATTTATTAAA 0.93981 -49 TTGATTTATTATTTCTTTTAATATTAAATTT 3 13 1 ATTTCTTTAA 0.844622 -59 ATATATATTTCTCCAAACCCC 4 5 0 ATTTCTCAAA 0.942593 -17 TTCCTTTTGTATTCATTTAAATTCCTTTT 5 9 0 ATTCATTAAA 0.917916 -77 GCACAATAATACTTCTTTAAAGAATATACTT 6 40 0 ACTTCTTAAA 0.975615 -144 TAAATACTTAACTTATTAATATTGTTAAATC 7 13 1 ACTTATTATA 0.651293 -144 CAATTTTATTATAGCTTAAAACTTTTTTTAA 7 43 1 ATAGCTTAAA 0.738176 -114 ACATTTCTCAAAATTGAAAAAAT 8 39 0 ATTTCTCAAA 0.94259 -13 ******* *** Masking position 1 Map Score: 9.3588 Number of sites scoring better than the average of aligned sites = 670 Number in coding regions = 470 Number in noncoding regions = 200 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 5 ACAAAACTAATTTTAAATAAGTAATGATAA 1 74 0 TTTTAAATAA 0.395919 -47 TATTTTAGCTTTTTGAATAAATCGATCAGC 2 113 0 TTTTGAATAA 0.713348 -47 AACTCATAAATTACGAGAAAATTTAATATT 3 32 0 TTACGAGAAA 0.74199 -40 TTCTCGTAATTTATGAGTTAATTTAATATA 3 43 1 TTATGAGTTA 0.592042 -29 GGGGTTTGGAGAAATATATAT 4 5 1 TTTGGAGAAA 0.672649 -17 TTATTCTCAACTATTAGAAATAATACAACC 6 12 0 CTATTAGAAA 0.758047 -172 AAATTTTACAATATTAAAAAACATATCAAG 6 74 0 ATATTAAAAA 0.714202 -110 AAAATTTTTGATATTAAAAATTTATTTTAT 6 97 1 ATATTAAAAA 0.714202 -87 AACCTAACACTTATTAGCAAACAAAACTTT 6 135 0 TTATTAGCAA 0.777088 -49 TGATTTAACAATATTAATAAGTTAAGTATT 7 15 0 ATATTAATAA 0.635555 -142 CTTAAAACTTTTTTTAAAAAAAACATTTAA 7 57 1 TTTTTAAAAA 0.491066 -100 AAAATCTAATTTATTATTAAGTACGT 8 7 0 TTATTATTAA 0.525172 -45 ATTTTTTCAATTTTGAGAAATGT 8 39 1 TTTTGAGAAA 0.900476 -13 ********** Masking position 6 Map Score: 2.86355 Number of sites scoring better than the average of aligned sites = 2161 Number in coding regions = 1446 Number in noncoding regions = 715 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 6 ********** No masking Map Score: -3.03101e-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 7 ********** No masking Map Score: -3.03101e-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: -3.03101e-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