AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i256_bsub_mtub_300.orf -o256_bsub_mtub_300.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.55 -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 = 0.55 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 ylxM 176 similar to hypothetical proteins #2 rpsP 105 ribosomal protein S16 (BS17) #3 ylqD 121 ylqD #4 rplS 130 ribosomal protein L19 #5 ylqF 142 similar to hypothetical proteins #6 rnh 70 ribonuclease H #7 ylqG 31 ylqG #8 sucC 172 succinyl-CoA synthetase (beta subunit) #9 sucD 28 succinyl-CoA synthetase (alpha subunit) #10 smf 60 DNA processing Smf protein homolog #11 topA 187 DNA topoisomerase I #12 gid 75 glucose-inhibited division protein #13 codV 67 integrase/recombinase Motif number 1 TGTATATGAACCCTATTTTAAGGAGGATTT 1 13 0 CCCTATTTTA 0.947656 -164 TTGAGCTCTCCCCTTTGTTAAGTCAAATCC 1 157 0 CCCTTTGTTA 0.934873 -20 CCGGCACCTCCCCTTTTTTTACACGCAAAA 3 22 1 CCCTTTTTTT 0.977111 -100 TATCAGTTTACCCTTTTTTTGCGTGTAAAA 3 38 0 CCCTTTTTTT 0.977111 -84 CACCAAGCTCCCCGCTTTTAAAACTTTTAC 3 100 0 CCCGCTTTTA 0.958291 -22 CTGTAACAAGCTCTTTTTTTATACAGAATT 5 38 1 CTCTTTTTTT 0.885574 -105 AAATGCGGGTCTTTATTTTTTCTTGGCTGA 6 21 1 CTTTATTTTT 0.572265 -50 TATTCCCCATCCTTCTTTGAAATTTATGTT 8 17 1 CCTTCTTTGA 0.915607 -156 TGACGGCTGTCCCTTTTTTA 10 1 0 CCCTTTTTTA 0.98018 -60 CAAGGCTGTTCCTGCTTTTTCTAACAAAAG 10 29 1 CCTGCTTTTT 0.903523 -32 AGATTGACCTCCTTTTGTTAGAAAAAGCAG 10 40 0 CCTTTTGTTA 0.87144 -21 GAGGTGTTCTCTCTCTTTTCAAGATATTTC 11 153 0 CTCTCTTTTC 0.792165 -35 GTCTTGCTCACCTTCTTTGTGTGTTAAAAG 12 22 1 CCTTCTTTGT 0.903523 -54 TTATTCAAGGCCTTCTTTTAACACACAAAG 12 36 0 CCTTCTTTTA 0.973943 -40 ********** Masking position 6 Map Score: 20.3808 Number of sites scoring better than the average of aligned sites = 1053 Number in coding regions = 768 Number in noncoding regions = 285 Number of orfs with sites within 600 bp upstream = 292 Fraction of orfs with sites within 600 bp upstream = 0.0469001 Motif number 2 TTGAGCTCTCCCCTTTGTTAAGTC 1 163 0 GCTCTCCCCT 0.951748 -14 AGGTGCCGGCCCTCTCCCTT 3 1 0 CCTCTCCCTT 0.985498 -121 AGAGGGCCGGCACCTCCCCTTTTTTTACAC 3 16 1 CACCTCCCCT 0.938825 -106 ATGATTCATTGTTGTCCTTTATGTATTTTA 5 90 0 GTTGTCCTTT 0.574629 -53 GTGACACGAACACCGCCTTTATCTTCAGTA 5 123 0 CACCGCCTTT 0.747037 -20 TTTCTCTTCTCCCTTACTGTATGTA 6 56 0 CTTCTCCCTT 0.930464 -15 CTAAAATATTCCCCATCCTTCTTTGAAATT 8 11 1 CCCCATCCTT 0.858866 -162 TATTTGGTCCCCTGCCTTTCATTCTTTC 9 11 0 CCCCTGCCTT 0.954357 -18 AGCCTTGACGGCTGTCCCTTTTTTA 10 6 0 GCTGTCCCTT 0.950913 -55 AGCCGTCAAGGCTGTTCCTGCTTTTTCTAA 10 23 1 GCTGTTCCTG 0.690829 -38 TAGATTGACCTCCTTTTGTTAGAAAA 10 45 0 GACCTCCTTT 0.949299 -16 GGGTCTTGCTCACCTTCTTTGTGTGTTAAA 12 20 1 CACCTTCTTT 0.881521 -56 TATTATTCAAGGCCTTCTTTTAACACACAA 12 38 0 GGCCTTCTTT 0.770206 -38 CCATTTAAAAGCCCTTCCTGGGGAGGTATT 13 44 1 GCCCTTCCTG 0.943177 -24 ********** Masking position 7 Map Score: 10.2651 Number of sites scoring better than the average of aligned sites = 1600 Number in coding regions = 1105 Number in noncoding regions = 495 Number of orfs with sites within 600 bp upstream = 498 Fraction of orfs with sites within 600 bp upstream = 0.0799872 Motif number 3 TAATCGCCGCTTTGACAAGATAAAAACTTGACAGTGTCAT 1 87 1 TTAAGTATTG 0.988642 -90 GTGTTTTTTCTTAACAACGGTTTTATCATGTATAACCGA 2 10 0 TTCAGTAATG 0.885717 -96 AAAAAACACTTTACAAACACTTTTATCATTGTTAATATAC 2 41 1 TTAAATAATT 0.640981 -65 CCGAAAATATTTCAACAAGATAGTATATTAACAATGATAA 2 63 0 TTAAGTATTA 0.930605 -43 CGAGTAAAAGTTTTAAAAGCGGGGAGCTTGGTGCG 3 97 1 TTAAGGATTG 0.937277 -25 ATTTTATTGCATAGGCTATGAAATTGTGATAAGATA 4 7 1 TTAAGTATTG 0.988642 -124 AGCTCTTTTTTTATACAGAATTTGAAAATGCCGGACAGGC 5 46 1 TTAAATAATG 0.953348 -97 TTTAAAAAGGTGCCTCCTTGTCCATGGTGA 7 12 0 TTAAGTTTTG 0.909765 -20 AATTTATGTTTTTAATAAAGTAAAAGTTTGAATGTTTAGA 8 37 1 TTAAATATTG 0.975248 -136 TTTAGTTTTGTTACATAAGTTAGGAGGATGGGAA 8 149 1 TTAAGTAATG 0.97833 -24 ATGACGTTCATGATAAAGAATGAAATGTTGAAAGCCAAAT 11 89 1 TGAAATATTG 0.871199 -99 TCTCTCTCTTTTCAAGATATTTCAATTTTATTTTTGCAGC 11 136 0 TTAAATATTA 0.858559 -52 ** * * * * * *** Masking position 7 Map Score: 10.7331 Number of sites scoring better than the average of aligned sites = 213 Number in coding regions = 165 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 4 CACTGTCAAGTTTTTATCTTGTCAAAGCGGCG 1 91 0 TTTTTATTGT 0.716364 -86 TTACAAACACTTTTATCATTGTTAATATACTA 2 51 1 TTTTATTTGT 0.904635 -55 CGTCCAGGCTTTTCTATTTTGCCTAAGCTTCT 3 67 0 TTTCTATTGC 0.866133 -55 GGAACATCGTTTTCAAGCTTGCAGCGGATAAG 4 67 0 TTTCAATTGC 0.96653 -64 AGTATGCATGATTCATTGTTGTCCTTTATGTA 5 95 0 ATTCATTTGT 0.887319 -48 CTTCTTTGAAATTTATGTTTTTAATAAAGTAA 8 28 1 ATTTATTTTT 0.613434 -145 CCTTCTAAACATTCAAACTTTTACTTTATTAA 8 48 0 ATTCAATTTT 0.751133 -125 GCGCAGTCTATTTTAGTTTTGTTACATAAGTT 8 138 1 TTTTAGTTGT 0.776212 -35 GTCCCCTGCCTTTCATTCTTTC 9 1 0 TTTCATTTTC 0.886853 -28 AATAGTGAGGATTTAAAGTTGCATATTGTTTT 11 46 1 ATTTAATTGC 0.903452 -142 TTTATTTGGCTTTCAACATTTCATTCTTTATC 11 100 0 TTTCAATTTC 0.903046 -88 GATATTTCAATTTTATTTTTGCAGCTGTCTTT 11 129 0 TTTTATTTGC 0.938206 -59 ****** **** Masking position 9 Map Score: 7.25277 Number of sites scoring better than the average of aligned sites = 956 Number in coding regions = 796 Number in noncoding regions = 160 Number of orfs with sites within 600 bp upstream = 171 Fraction of orfs with sites within 600 bp upstream = 0.0274655 Motif number 5 AAAAATCCTCCTTAAAATAGGGTT 1 5 1 ATCCTCCTTA 0.976294 -172 GCAGCGGATAAGCCCGCTTAAGCCACAAGT 4 49 0 AGCCCGCTTA 0.92549 -82 AATATTCCCCATCCTTCTTTGAAATTTATG 8 15 1 ATCCTTCTTT 0.766117 -158 AAATCTTTTAATCCTTCTAAACATTCAAAC 8 62 0 ATCCTTCTAA 0.927306 -111 TTCCCATCCTCCTAACTTATGTAAC 8 158 0 ATCCTCCTAA 0.966377 -15 TTTCATCCCCCTCAAGAGGTGTTC 11 174 0 ATCCCCCTCA 0.98449 -14 GGTGAGCAAGACCCTGCTCACCG 12 4 0 ACCCTGCTCA 0.952213 -72 GGTATCACAAATCGCGCTCAGGTTGCAATC 13 16 0 ATCGCGCTCA 0.913079 -52 ********** Masking position 1 Map Score: 4.92221 Number of sites scoring better than the average of aligned sites = 340 Number in coding regions = 262 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 6 TTTACTAGCACCTCCGAAAATATT 2 92 0 CTAGCACCTC 0.95703 -14 AGGGAGAGGGCCGGCACCTCCCCTTTTTTT 3 12 1 CCGGCACCTC 0.981864 -110 CGCACCAAGCTCCCCGCTTTTAAAA 3 107 0 CAAGCTCCCC 0.914123 -15 GCCACAAAAACCGGCACAGCGGAACATCGT 4 89 0 CCGGCACAGC 0.963351 -42 TGAGCAAGACCCTGCTCACCG 12 2 0 CCTGCTCACC 0.98046 -74 TGAGCAGGGTCTTGCTCACCTTCTTTGTGT 12 14 1 CTTGCTCACC 0.969617 -62 CTTTCACATCTCCTAGTTTA 12 66 0 CTTTCACATC 0.774161 -10 ********** Masking position 5 Map Score: 2.94069 Number of sites scoring better than the average of aligned sites = 553 Number in coding regions = 507 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 7 AGTGTTTGTAAAGTGTTTTTTCTTAACAAC 2 32 0 AAGTGTTTTT 0.852016 -74 ACAATGATAAAAGTGTTTGTAAAGTGTTTT 2 43 0 AAGTGTTTGT 0.928519 -63 TTTTGTGGCCAAGAGCATCTGTTGGAAGGA 4 110 1 AAGAGCATCT 0.905859 -21 AACGAACGAAAAGAGCTTGTTACCTGTAAC 5 15 1 AAGAGCTTGT 0.984143 -128 TGTATAAAAAAAGAGCTTGTTACAGGTAAC 5 33 0 AAGAGCTTGT 0.984143 -110 TTTATTATTCAAGGCCTTCTTTTAACACAC 12 40 0 AAGGCCTTCT 0.906734 -36 CCTCCCCAGGAAGGGCTTTTAAATGGTATC 13 40 0 AAGGGCTTTT 0.968709 -28 ********** Masking position 2 Map Score: 4.86091 Number of sites scoring better than the average of aligned sites = 393 Number in coding regions = 354 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 8 GAACCCTATTTTAAGGAGGATTTTT 1 6 0 TTAAGGAGGA 0.937617 -171 GTTGAAATATTTTCGGAGGTGCTAGTAAA 2 87 1 TTTCGGAGGT 0.906461 -19 AAGAGCATCTGTTGGAAGGAG 4 120 1 GTTGGAAGGA 0.902643 -11 AGTTTGAATGTTTAGAAGGATTAAAAGATT 8 61 1 TTTAGAAGGA 0.930985 -112 TGTTACATAAGTTAGGAGGATGGGAA 8 157 1 GTTAGGAGGA 0.976188 -16 AGAACACCTCTTGAGGGGGATGAAA 11 173 1 TTGAGGGGGA 0.926548 -15 AAAGCCCTTCCTGGGGAGGTATTAGGC 13 51 1 CTGGGGAGGT 0.86946 -17 ********** Masking position 2 Map Score: 0.984973 Number of sites scoring better than the average of aligned sites = 345 Number in coding regions = 221 Number in noncoding regions = 124 Number of orfs with sites within 600 bp upstream = 142 Fraction of orfs with sites within 600 bp upstream = 0.0228076 Motif number 9 ********** No masking Map Score: -1.88842e-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 10 ********** No masking Map Score: -1.88842e-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 11 ********** No masking Map Score: -1.88842e-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