AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00710_bbur_reg_100.orf -o00710_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 BB0057 72 glyceraldehyde 3-phosphate dehydrogenase (gap) #2 BB0060 83 conserved hypothetical protein #3 BB0061 73 thioredoxin (trxA) #4 BB0347 183 fibronectin/fibrinogen-binding protein, putative #5 BB0348 97 pyruvate kinase (pyk) #6 BB0445 166 fructose-bisphosphate aldolase (fba) #7 BB0657 133 ribose 5-phosphate isomerase (rpi) Motif number 1 TCTAGTAAGAATAAAATCAAAAAATTGGAG 1 45 1 ATAAAATCAA 0.944534 -28 TTTGCAAAATAAAATAATTTAATTGCTA 2 9 1 ATAAAATAAT 0.955135 -75 TAAATATACCCTAAAATAATCCACATATAA 2 62 0 CTAAAATAAT 0.71375 -22 ATTAAATATACCCTAAAATA 2 74 0 ATTAAATATA 0.854219 -10 TATATCACAAATACAATATTAATAATAAGG 3 22 0 ATACAATATT 0.681784 -52 CCCTATCGACTTAAAATTATATCACAAATA 3 39 0 TTAAAATTAT 0.764093 -35 AAAACTACATTTAAACTATTTATTGTCAAT 4 47 1 TTAAACTATT 0.782726 -137 TTTATTGTCAATAAACTTTATTTCCATAAT 4 65 1 ATAAACTTTA 0.885843 -119 TATCATGGAAATAAACTATTATTAATAGTA 4 101 1 ATAAACTATT 0.928863 -83 AGTTTAATACATAAAATAAAAATTTAAAGC 4 133 1 ATAAAATAAA 0.96236 -51 TGAATTTTTTACAAAATATTGTTATTCAAT 5 37 1 ACAAAATATT 0.69084 -61 GACAAAAAGCATAAAATTTATAAAAGTGGA 5 67 1 ATAAAATTTA 0.940475 -31 TTTTAAACTTTTTTATGCAAAA 6 3 1 TTAAACTTTT 0.663383 -164 ATGCAAAATAATAAATTTTTAATAAATTTT 6 25 1 ATAAATTTTT 0.657682 -142 AAAACCAAACATAAAATTTATTAAAAATTT 6 37 0 ATAAAATTTA 0.940475 -130 ATAAATAATTATTAAATCAAAACCAAACAT 6 55 0 ATTAAATCAA 0.775208 -112 AATTTAAATCAAAAAATAAATAATTATTAA 6 70 0 AAAAAATAAA 0.600085 -97 ATTTTTTGATTTAAATTCAATTCAACTTCT 6 83 1 TTAAATTCAA 0.467841 -84 AATGCCTATAATAAATTATACACCTAAGAA 6 109 0 ATAAATTATA 0.840474 -58 TAGGCATTTGATAAAAGAAAAAATAAAATG 6 131 1 ATAAAAGAAA 0.681707 -36 GTATTGGTAAATAAAATAAT 7 1 0 ATAAAATAAT 0.955135 -133 ATAAATTAGCATAAAATCTAGTCAAGATTT 7 39 1 ATAAAATCTA 0.948592 -95 ATTACTAAGGTTTAAATCTTGACTAGATTT 7 52 0 TTTAAATCTT 0.486967 -82 AACCTTAGTAATTAAATAATGATATACTTT 7 70 1 ATTAAATAAT 0.82429 -64 TCCTTGCTTGATAAACTTAAAGCTTAATGT 7 105 0 ATAAACTTAA 0.870602 -29 ********** Masking position 5 Map Score: 27.3315 Number of sites scoring better than the average of aligned sites = 2498 Number in coding regions = 1544 Number in noncoding regions = 954 Number of orfs with sites within 600 bp upstream = 203 Fraction of orfs with sites within 600 bp upstream = 0.0326052 Motif number 2 TAAATCACAAATTAACAACAAGTGTCAAA 1 10 0 ATTAACAACA 0.680133 -63 TTCTTACTAGAATTATTAAATCACAAATTA 1 26 0 AATTATTAAA 0.807299 -47 TAATTCTAGTAAGAATAAAATCAAAAAATT 1 41 1 AAGAATAAAA 0.703637 -32 TGCTATAGCAATTAATCATACTTGTAAGTT 2 34 1 ATTAATCATA 0.704018 -50 AATAATAAGGAATTATAAGAA 3 2 0 AATTATAAGA 0.814771 -72 CAAATACAATATTAATAATAAGGAATTATA 3 15 0 ATTAATAATA 0.93828 -59 GCTTAAGCTTAATAATAAGAGTTCATAGA 4 10 0 AATAATAAGA 0.895673 -174 AGCTTAAGCTATTAACAAAACTACATTTAA 4 31 1 ATTAACAAAA 0.910627 -153 AATAAAGTTTATTGACAATAAATAGTTTAA 4 57 0 ATTGACAATA 0.725377 -127 AACTAGTACTATTAATAATAGTTTATTTCC 4 107 0 ATTAATAATA 0.93828 -77 TTTGTCATTGAATAACAATATTTTGTAAAA 5 43 0 AATAACAATA 0.916993 -55 ATTGTTATTCAATGACAAAAAGCATAAAAT 5 54 1 AATGACAAAA 0.782369 -44 AAAGCATAAAATTTATAAAAGTGGAGGAAG 5 72 1 ATTTATAAAA 0.895629 -26 TTTTATGCAAAATAATAAATTTTTAATAAA 6 21 1 AATAATAAAT 0.51738 -146 CAAACATAAAATTTATTAAAAATTTATTAT 6 32 0 ATTTATTAAA 0.775884 -135 AAAAATAAATAATTATTAAATCAAAACCAA 6 59 0 AATTATTAAA 0.807299 -108 TAGGTGTATAATTTATTATAGGCATTTGAT 6 113 1 ATTTATTATA 0.753923 -54 TGATAAAAGAAAAAATAAAATGGAAAGGAG 6 139 1 AAAAATAAAA 0.615678 -28 TACCAATACTAATAATTATAAATTAGCATA 7 22 1 AATAATTATA 0.881362 -112 TTAGTAATTAAATAATGATATACTTTAAAA 7 74 1 AATAATGATA 0.744472 -60 ********** Masking position 5 Map Score: 20.133 Number of sites scoring better than the average of aligned sites = 2037 Number in coding regions = 1209 Number in noncoding regions = 828 Number of orfs with sites within 600 bp upstream = 160 Fraction of orfs with sites within 600 bp upstream = 0.0256987 Motif number 3 TGTTGTTAATTTGTGATTTAATAATTCTAGT 1 20 1 TTTGATTTAA 0.972067 -53 TCCTCCAATTTTTTGATTTTATTCTTACTAG 1 46 0 TTTGATTTTA 0.956968 -27 AATATTGTATTTGTGATATAATTTTAAGTCG 3 32 1 TTTGATATAA 0.917849 -42 ATTATTAAGCTTAAGCTATTAACAAAACTAC 4 24 1 TTAGCTATTA 0.84094 -160 AAGCTTTAAATTTTTATTTTATGTATTAAAC 4 134 0 TTTTATTTTA 0.737789 -50 GTGTTTATATCTAAGCTTTAAATTTTTATTT 4 146 0 CTAGCTTTAA 0.928618 -38 CAAAACTTTACTTTGCTATAAGCAGTGT 5 8 0 CTTGCTATAA 0.900279 -90 TTTATAAATTTTATGCTTTTTGTCATTGAAT 5 60 0 TTTGCTTTTT 0.791137 -38 TTATGTTTGGTTTTGATTTAATAATTATTTA 6 53 1 TTTGATTTAA 0.972067 -114 ATTATTTATTTTTTGATTTAAATTCAATTCA 6 76 1 TTTGATTTAA 0.972067 -91 TCCATTTTATTTTTTCTTTTATCAAATGCCT 6 132 0 TTTTCTTTTA 0.818297 -35 TATTTAATTACTAAGGTTTAAATCTTGACTA 7 57 0 CTAGGTTTAA 0.714322 -77 TTAAAATACATTAAGCTTTAAGTTTATCAAG 7 98 1 TTAGCTTTAA 0.960789 -36 ** ******** Masking position 7 Map Score: 18.4918 Number of sites scoring better than the average of aligned sites = 717 Number in coding regions = 462 Number in noncoding regions = 255 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 4 TAAATTATTTTATTTTGCAAA 2 2 0 TATTTTGCAA 0.949564 -82 ATATTTTACATGCCCCCCTAT 3 63 0 TATTTTACAT 0.924434 -11 TCAATAAACTTTATTTCCATAATACTACAT 4 72 1 TTATTTCCAT 0.910982 -112 TAATAATAGTTTATTTCCATGATATGTAGT 4 95 0 TTATTTCCAT 0.910982 -89 TTCAAAACTTTACTTTGCTATAAGCAGTGT 5 11 0 TACTTTGCTA 0.747705 -87 AAGTTTTGAATTTTTTACAAAATATTGTTA 5 31 1 TTTTTTACAA 0.83892 -67 AAAAATTTATTATTTTGCATAAAAAAGTTT 6 15 0 TATTTTGCAT 0.964991 -152 TTATATCACTCCTTTCCATTTTATTTTTT 6 148 0 TCCTTTCCAT 0.944715 -19 ATTATTTTATTTACCAATACTAATAAT 7 8 1 TATTTACCAA 0.811675 -126 AAATTCTTTTCCTTGCTTGATAAA 7 120 0 TCTTTTCCTT 0.893487 -14 ********** Masking position 5 Map Score: 6.50659 Number of sites scoring better than the average of aligned sites = 628 Number in coding regions = 449 Number in noncoding regions = 179 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 5 ********** No masking Map Score: -4.73059e-14 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 6 ********** No masking Map Score: -4.73059e-14 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: -4.73059e-14 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