AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i117_bsub_mtub_100.orf -o117_bsub_mtub_100.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 appD 191 oligopeptide ABC transporter (ATP-binding protein) #2 appA 87 oligopeptide ABC transporter (oligopeptide-binding protein) #3 appB 75 oligopeptide ABC transporter (permease) #4 oppA 300 oligopeptide ABC transporter (binding protein) #5 oppB 107 oligopeptide ABC transporter (permease) #6 dppA 128 dipeptide ABC transporter #7 oppB 206 oppB #8 dppA 300 dppA Motif number 1 CCCTCTCAAAGCTGTGCGGGCAACA 2 5 0 GCTGGCGGGC 0.807886 -83 GGGAGAAAACGCTCTCCCTCCCCTTTAAGGG 3 15 0 GCTCCCCTCC 0.871639 -61 ACCGCGATACCCGAGGAGGCCCGC 7 4 0 CCGAGAGGCC 0.724339 -203 CTCGGGTATCGCGGTGTGGACTTTGCTACTC 7 20 1 GCGGGTGGAC 0.830596 -187 TTAAAATTCACCGCGGCGTCGATCTGAGTAG 7 45 0 CCGCGCGTCG 0.87814 -162 CCGGATGGTTCCGCTCGGGCCGATTCTGATG 7 99 0 CCGCCGGGCC 0.939461 -108 CGGTTGATGGGGTCACCCGTGATCCGGATGG 7 122 0 GGTCCCCGTG 0.591868 -85 CCATCAACCGGCGCGCTGGCGGCACGCCATC 7 143 1 GCGCCTGGCG 0.989308 -64 GGACAGGGTAGCGAGCCCGGCGATGGCGTGC 7 164 0 GCGACCCGGC 0.960891 -43 CTGTCCCAATGCGACGCGGTGGTTGGGC 7 189 1 GCGAGCGGTG 0.968129 -18 TCGCGCGGGCTGCCTTCCTCGCC 8 3 1 GCGCGGCTGC 0.706814 -298 GGTGGTGTCGGCGCTGTGGCGAGGAAGGCAG 8 20 0 GCGCGTGGCG 0.987508 -281 CACGCCAACAGCGCCCGGTCGGGCGAGGTCT 8 71 1 GCGCCGGTCG 0.936701 -230 GCCCGGTCGGGCGAGGTCTTCCCTTGGGAAG 8 83 1 GCGAGTCTTC 0.578479 -218 CCCTTGGGAAGCGCAGTCGCGGTGGGTAGCC 8 103 1 GCGCGTCGCG 0.97859 -198 ACCGTCGTTCGCGATCCGGTGTTGGCTACCC 8 126 0 GCGACCGGTG 0.973218 -175 CAGAGTGCCGGCGAACCGGTGGGACGATGTT 8 171 0 GCGACCGGTG 0.973218 -130 GTGACCGTTAGCTACCACGCCACCCAGAGTG 8 195 0 GCTACACGCC 0.673889 -106 GGTAGCTAACGGTCACCGGCGAGTGTGTCGG 8 210 1 GGTCCCGGCG 0.89597 -91 GGCCTGGCCAGCGCAGCCGACACACTCGCCG 8 226 0 GCGCGCCGAC 0.966346 -75 CCGGTGAAGTGCGGCCTGGCCAGCGCAGCCG 8 238 0 GCGGCTGGCC 0.969765 -63 TCACCGGCTGGGGAGCCGGACTGCACAAGAA 8 262 1 GGGACCGGAC 0.818326 -39 **** ****** Masking position 2 Map Score: 27.174 Number of sites scoring better than the average of aligned sites = 3590 Number in coding regions = 3306 Number in noncoding regions = 284 Number of orfs with sites within 600 bp upstream = 158 Fraction of orfs with sites within 600 bp upstream = 0.0253774 Motif number 2 ATAAAGGGATTGCTTTCTCTTGAAAACGTTT 1 141 1 TCTTTCTCTT 0.800266 -51 AGCTCCCCTTTCCCCCCTCTTGTTGTCAAAC 1 168 0 TCCCCCTCTT 0.994593 -24 GCTAGCTCCCCTTTCCCCCCTCT 1 179 0 TGCTCCCCTT 0.969697 -13 GTAGTGTGCATACCCCCTCTCAAAGCTGTGC 2 19 0 TCCCCCTCTC 0.971943 -69 TAGATATTCCCCCTCTTGAAATGTTCG 2 71 0 TCCCCCTCTT 0.994593 -17 GAAAACGCTCTCCCTCCCCTTTAAGGGAAAT 3 11 0 TCCTCCCCTT 0.989065 -65 GGAGAGCGTTTTCTCCCTCTTCTGTTTTTAA 3 29 1 TCTCCCTCTT 0.989766 -47 ATACTTGTCCCCCTTTACTTTCCTT 3 61 0 TGTCCCCCTT 0.969697 -15 ACTTTTATTCTGTTCCGTCTTTTCTGATTAT 4 196 0 TTTCCGTCTT 0.787311 -105 ATATGGGGCTTTTCTCCCCATATACCTTGAG 5 34 0 TTCTCCCCAT 0.790205 -74 TTATATTGCATTTTTCCTCTTTTTTTAATAT 6 64 1 TTTTCCTCTT 0.943393 -65 * ********* Masking position 1 Map Score: 16.8352 Number of sites scoring better than the average of aligned sites = 420 Number in coding regions = 293 Number in noncoding regions = 127 Number of orfs with sites within 600 bp upstream = 123 Fraction of orfs with sites within 600 bp upstream = 0.0197559 Motif number 3 GCTCCCCTTTCCCCCCTCTTGTTGTCAAAC 1 168 0 CCCCCCTCTT 0.99392 -24 TAGTGTGCATACCCCCTCTCAAAGCTGTGC 2 19 0 ACCCCCTCTC 0.958847 -69 TAGATATTCCCCCTCTTGAAATGTTCG 2 71 0 TCCCCCTCTT 0.99498 -17 AAAACGCTCTCCCTCCCCTTTAAGGGAAAT 3 11 0 CCCTCCCCTT 0.955315 -65 GAGAGCGTTTTCTCCCTCTTCTGTTTTTAA 3 30 1 TCTCCCTCTT 0.982432 -46 ATACTTGTCCCCCTTTACTTTCCTTAT 3 59 0 TCCCCCTTTA 0.926159 -17 TATATTGCATTTTTCCTCTTTTTTTAATAT 6 65 1 TTTTCCTCTT 0.753919 -64 AACGCTCCTCCTTTTTTACTAAATT 6 114 0 TCCTCCTTTT 0.955525 -15 GCGCGGGCTGCCTTCCTCGCCACAGCGCCG 8 13 1 CCTTCCTCGC 0.875664 -288 ACACCACCGGTCCTCCTCGAGGATGCCGCA 8 43 1 TCCTCCTCGA 0.95137 -258 ********** Masking position 5 Map Score: 11.224 Number of sites scoring better than the average of aligned sites = 412 Number in coding regions = 258 Number in noncoding regions = 154 Number of orfs with sites within 600 bp upstream = 171 Fraction of orfs with sites within 600 bp upstream = 0.0274655 Motif number 4 CACTACATAAACAACAGCCTAGAAGAACGAA 2 44 1 ACAACAGCTA 0.625211 -44 AAGTTGTGGAAACTCAGGTTCATTTGTCTGA 4 223 1 AACTCAGGTC 0.811173 -78 GTGAATTTTAACAACCGGTTACCCAGTTTTC 7 65 1 ACAACCGGTA 0.920359 -142 CCGAGCGGAACCATCCGGATCACGGGTGACC 7 112 1 CCATCCGGTC 0.975667 -95 GCCCAACCACCGCGTCGCATTGGGAC 7 191 0 ACCACCGCTC 0.990332 -16 CAGCGCCGACACCACCGGTCCTCCTCGAGGA 8 35 1 ACCACCGGCC 0.986942 -266 ATGCCGCACGCCAACAGCGCCCGGTCGGGCG 8 65 1 CCAACAGCCC 0.862033 -236 GTGTTGGCTACCCACCGCGACTGCGCTTCCC 8 108 0 CCCACCGCAC 0.955888 -193 GTGGGTAGCCAACACCGGATCGCGAACGACG 8 124 1 AACACCGGTC 0.977548 -177 AAAACATCGTCCCACCGGTTCGCCGGCACTC 8 169 1 CCCACCGGTC 0.995778 -132 CCTTCTTGTGCAGTCCGGCTCCCCAGCCGGT 8 264 0 CAGTCCGGTC 0.817325 -37 ******** ** Masking position 5 Map Score: 11.5545 Number of sites scoring better than the average of aligned sites = 615 Number in coding regions = 553 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 5 TAATATTATTAATGAAATTCCATTATTTTATC 1 14 0 AATAAATTCA 0.927288 -178 GAATTTCATTAATAATATTACATTTATCCTAA 1 26 1 AATATATTCA 0.985195 -166 ATATTATTACAATCATTTTGCAAAATCAAGAA 1 62 0 AATATTTTCA 0.927288 -130 AAATGATTGTAATAATATACAACTATAAAATT 1 76 1 AATATATAAA 0.83291 -116 AGAAATAATAAATAATATTGAATTATCGAAAA 1 107 0 AATATATTAA 0.965293 -85 AAATTGATAAAATAATATTGCAATAAATTATT 4 112 1 AATATATTCA 0.986107 -189 GATTTTTCCCAGTTATATTGCATTTTTCCTCT 6 52 1 AGTATATTCA 0.949585 -77 TATTCTAACAAATTATATTAAAAAAAGAGGAA 6 77 0 AATATATTAA 0.965271 -52 *** ***** ** Masking position 5 Map Score: 8.28083 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 16 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 6 TCCCCCTTTACTTTCCTTATTAAAAACAGAAG 3 47 0 CTTTCCTATA 0.941538 -29 ATTGTTACAGCTTTTTTACAAAAATAATCAGA 4 173 1 CTTTTTTCAA 0.94079 -128 TCTGTTCCGTCTTTTCTGATTATTTTTGTAAA 4 187 0 CTTTTCTATA 0.966034 -114 GTATATGGGGCTTTTCTCCCCATATACCTTGA 5 35 0 CTTTTCTCCA 0.945036 -73 CCCCATATACCTTTCTTACTGATGGAGTATAA 5 57 1 CTTTCTTCTA 0.960903 -51 AAAGAGGATTCTTTTTTTATCACTGAATGATT 6 18 1 CTTTTTTATA 0.956693 -111 CATTTTTCCTCTTTTTTTAATATAATTTGTTA 6 72 1 CTTTTTTAAA 0.889955 -57 AACGCTCCTCCTTTTTTACTAAATTATGAATA 6 107 0 CTTTTTTCTA 0.977479 -22 GCGGTGTGGACTTTGCTACTCAGATCGACGCC 7 30 1 CTTTGCTCTA 0.945036 -177 ******* ** * Masking position 7 Map Score: 8.78744 Number of sites scoring better than the average of aligned sites = 232 Number in coding regions = 191 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 7 TCAAAGCTGTGCGGGCAACA 2 1 0 GCGGGCAACA 0.922618 -87 GCGGGCCTCCTCGGGTATCG 7 1 1 GCGGGCCTCC 0.984571 -206 CCCGGCGATGGCGTGCCGCCAGCGCGCCGG 7 150 0 GCGTGCCGCC 0.995718 -57 TCGCGCGGGCTGCCTTCCTCGCCA 8 5 1 GCGGGCTGCC 0.994103 -296 GGCGCTGTTGGCGTGCGGCATCCTCGAGGA 8 56 0 GCGTGCGGCA 0.983266 -245 ACGCCACCCAGAGTGCCGGCGAACCGGTGG 8 180 0 GAGTGCCGGC 0.934286 -121 ********** Masking position 5 Map Score: 6.00174 Number of sites scoring better than the average of aligned sites = 177 Number in coding regions = 160 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 8 TGCTTTAAATGGTAGAAGGATATTATGTTC 4 49 1 GGTAGAAGGA 0.921267 -252 AAGACCTCAAGGTATATGGGGAGAAAAGCC 5 29 1 GGTATATGGG 0.988909 -79 CAGTAAGAAAGGTATATGGGGCTTTTCTCC 5 48 0 GGTATATGGG 0.988909 -60 CCAGCGCGCCGGTTGATGGGGTCACCCGTG 7 132 0 GGTTGATGGG 0.987579 -75 AATGCGACGCGGTGGTTGGGC 7 196 1 GGTGGTTGGG 0.97284 -11 ********** Masking position 3 Map Score: 3.99121 Number of sites scoring better than the average of aligned sites = 28 Number in coding regions = 26 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 9 TTAATGAAATTCCATTATTTTATCCTT 1 5 0 TCAATTTTAT 0.524069 -187 TTTTGCAAAATCAAGAATTTTTTAGGATAAATG 1 46 0 TCAATTTTTT 0.874765 -146 TATTGAATTATCGAAAAATTTTATAGTTGTATA 1 91 0 TCAAATTTTA 0.690155 -101 CCTCTTGTTGTCAAACGTTTTCAAGAGAAAGCA 1 151 0 TCAGTTTTCA 0.945975 -41 GTTTTCTCCCTCTTCTGTTTTTAATAAGGAAAG 3 36 1 TCTGTTTTTA 0.965477 -40 AAAAACTTTTTCATGTGTTTTCTGCCCA 4 6 0 TCTGTTTTCT 0.874636 -295 TATTTAAACTTCGTTAGTTTTTCTTCCATGAAC 4 75 0 TCTGTTTTTC 0.867269 -226 AACCTGAGTTTCCACAACTTTTATTCTGTTCCG 4 210 0 TCAACTTTTA 0.767575 -91 TACCTTGAGGTCTTTTATTTTCAGACGTAGCC 5 10 0 TCTATTTTCA 0.916553 -98 GGGGAACACCTCCATGGTTTTTACATTTTTATA 5 84 0 TCAGTTTTTA 0.965477 -24 ATTGCATTTTTCCTCTTTTTTTAATATAATTTG 6 68 1 TCTTTTTTTA 0.884111 -61 AACGCTCCTCCTTTTTTACTAAATTATG 6 111 0 TCTTTTTTTA 0.884111 -18 ** * ******* Masking position 9 Map Score: 6.37328 Number of sites scoring better than the average of aligned sites = 683 Number in coding regions = 535 Number in noncoding regions = 148 Number of orfs with sites within 600 bp upstream = 159 Fraction of orfs with sites within 600 bp upstream = 0.0255381 Motif number 10 ********** No masking Map Score: 3.47699e-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: 3.47699e-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: 3.47699e-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