AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -irpoN_bsub_opreg_100.orf -g0.435 -x5 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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 yckK 114 similar to glutamine ABC transporter (glutamine-binding protein) #2 acoR 115 transcriptional regulator #3 glnR 110 transcriptional regulator #4 glnA 60 glutamine synthetase #5 yqiY 80 similar to amino acid ABC transporter (permease) #6 yqiX 268 similar to amino acid ABC transporter (binding protein) #7 yqiR 152 similar to transcriptional regulator (sigma-L-dependent) #8 glnQ 155 glutamine ABC transporter (ATP-binding protein) #9 glnH 21 glutamine ABC transporter (glutamine-binding protein) #10 glnM 60 glutamine ABC transporter (integral membrane protein) #11 ytmM 29 similar to amino acid ABC transporter (permease) #12 ytmL 21 similar to amino acid ABC transporter (permease) #13 ytmI 152 similar to hypothetical proteins from B. subtilis #14 yufT 300 similar to NADH dehydrogenase #15 yxeN 22 similar to amino acid ABC transporter (permease) #16 yxeM 24 similar to amino acid ABC transporter (binding protein) #17 yxeK 185 similar to monooxygenase #18 rocR 240 transcriptional regulator (NtrC/NifA family) Motif number 1 ATTTTATTGAAATAAAAAATTAGCTTACAAATCT 1 68 0 AAAAAAATGC 0.803565 -47 AATAAAATCAACCAGAAAAGTGGGGAATAAG 1 94 1 AAGAAAAGGG 0.991568 -21 TAAAGGAAAAAGCAGGCGCATGGATA 2 3 1 AGAAAAAGGG 0.960782 -113 CGCTTTCAACAATAAAAAAGCAGGCGCCTTATAT 2 34 0 AAAAAAAGGG 0.986447 -82 TGAAACTAAGTTAAGAAAAGGAGGAAATTGAG 3 89 1 TAGAAAAGGG 0.963298 -22 AAATGTATATAGCAAAACAGTTGCTAACGGA 4 8 0 AAAAACAGGC 0.810011 -53 AAAAAGGCTCAACGAAAAAGTTGAGCCGCTTTTT 5 12 0 AGAAAAAGGA 0.820164 -69 CTTTTCTTACAGGAAAAAAGTTTCCTATTCAATA 5 45 0 AAAAAAAGTC 0.640109 -36 CTTTTTTCCTGTAAGAAAAGGAGACAAAGGCT 5 59 1 GAGAAAAGGA 0.687606 -22 AAATTTATGCACAAAAAAACCCGGGCTGCTTTGA 6 30 0 AAAAAAACGG 0.931065 -239 TTTTGTCAAGAGAAGAAAACGTGGTAACATAGGG 7 65 1 AAGAAAACGG 0.956183 -88 ACCCCTTTGTATGAAAAAATTTGCACACCTATTT 7 123 0 AAAAAAATGC 0.803565 -30 ACTTTTAATTTTCAGAAAAGTTTGATCATTTACT 8 100 1 TAGAAAAGTG 0.636847 -56 CAATCCTCCTATCAGAAAATTTGACCAAAAAGTA 8 130 0 AAGAAAATGA 0.770853 -26 AACAGAAATGGGGGAGCTTGT 9 1 1 AAGAAATGGG 0.868569 -21 ATTTTAATGATGAAAAACAGGAGGGAGCACA 13 8 0 TAAAACAGGG 0.72236 -145 AAATAAGTCTAACAAAAAAGAGGTTATTTGTATA 14 44 0 AAAAAAAGGT 0.804618 -257 CGTGGCAGCTTGCAGAAAAGTGCGATATAATTTG 14 122 1 TAGAAAAGCG 0.595792 -179 CTCGTTCTCAATTGAAAAATGCGCTATGTATAAA 14 179 0 AGAAAAATGC 0.579291 -122 TCAATTGAGAACGAGAAAAGGAGGTCTTATCTTT 14 198 1 AAGAAAAGGG 0.991568 -103 GATAAAAGCAAATAAAAAAGGCGATAAAATAGCA 14 247 0 AAAAAAAGGA 0.931267 -54 AAATAGAAAAGGCGGGAAAATCAA 16 2 1 AAGAAAAGGG 0.991568 -23 AACATGTTGAAACAGAAAACAAGGGGGAATTCAA 18 13 0 AAGAAAACGG 0.956183 -228 GCATTTATATAAAGGGAAAGCAGGATAACATGTT 18 39 0 AGGGAAAGGG 0.767273 -202 * ******* ** Masking position 7 Map Score: 32.0587 Number of sites scoring better than the average of aligned sites = 1971 Number in coding regions = 1490 Number in noncoding regions = 481 Number of orfs with sites within 600 bp upstream = 501 Fraction of orfs with sites within 600 bp upstream = 0.080469 Motif number 2 TTATATCCATGCGCCTGCTTTTTCCTTTA 2 10 0 GCGCCTGCTT 0.920743 -106 TGGATATAAGGCGCCTGCTTTTTTATTGTT 2 31 1 GCGCCTGCTT 0.920743 -85 TTCCTTGATCGCTCCTCCCTTACACGCCGT 2 96 0 GCTCCTCCCT 0.975912 -20 CTCAATTTCCTCCTTTTCTTAACTT 3 96 0 TTTCCTCCTT 0.902532 -15 TTGGTAAAATTCCTCCTCTTAAAAGGTA 4 43 0 ATTCCTCCTC 0.649585 -18 GATCCATTTCCCCCGTATTCATTACT 6 253 0 TTTCCCCCGT 0.838926 -16 ACAAGCTCCCCCATTTCTGTT 9 8 0 GCTCCCCCAT 0.966657 -14 GGGATGAGCATCGCCTGCTCATCCCGGGAT 10 16 0 TCGCCTGCTC 0.707603 -45 TCTTCTCCCCCCTCATCCGAAGA 11 17 0 TCTCCCCCCT 0.974897 -13 CACTGCTCCCTCTCTTTTTAC 12 8 0 GCTCCCTCTC 0.922554 -14 TGTGCTCCCTCCTGTTTTTCATC 13 4 1 GCTCCCTCCT 0.96033 -149 TTGATTTTCCCGCCTTTTCTATTT 16 10 0 TTTCCCGCCT 0.914434 -15 ATCAATGCCGTTCCCTCATGGTCACGCAA 17 10 1 GTTCCCTCAT 0.794353 -176 ATTTGAATTCCCCCTTGTTTTCTGTT 18 7 1 ATTCCCCCTT 0.895075 -234 ********** Masking position 5 Map Score: 12.4047 Number of sites scoring better than the average of aligned sites = 928 Number in coding regions = 715 Number in noncoding regions = 213 Number of orfs with sites within 600 bp upstream = 255 Fraction of orfs with sites within 600 bp upstream = 0.0409573 Motif number 3 AAGATTTTGTCTTATGAAAACCAAA 1 4 1 ATTTTGTCAT 0.740367 -111 CTCAATTTCCTCCTTTTCTTAACTTA 3 95 0 ATTTCCTCTT 0.829752 -16 TGCTATATACATTTTTACCTTTTAAGAGGAGG 4 28 1 ATTTTTACTT 0.726276 -33 ATCCCTTAATATTTATTCATATATCCTTGGAA 6 62 0 ATTTATTCAT 0.925327 -207 CTTTCCAGTGATCTCTTCTGATATTACTAGAT 6 127 0 ATCTCTTCAT 0.85874 -142 GTATTTGAATATTTATTCGTTAATTTGTATTT 6 215 0 ATTTATTCTA 0.62599 -54 AAACCCCTTTATCTTTTCATTTCCTTTATTGT 7 18 1 ATCTTTTCTT 0.885622 -135 TTGACAAAATATTTTTTCCGCTGGACAATAAA 7 42 0 ATTTTTTCCT 0.866076 -111 TGTTACCACGTTTTCTTCTCTTGACAAAATAT 7 62 0 TTTTCTTCTT 0.754516 -91 TTGCACACCTATTTATTCCGTTGCAATAATTT 7 105 0 ATTTATTCTT 0.948141 -48 AGGTGTGCAAATTTTTTCATACAAAGGGGTAT 7 127 1 ATTTTTTCAC 0.740367 -26 AGTCATGGACATTTTTTCACTTTTAATTTTCA 8 82 1 ATTTTTTCTT 0.968759 -74 TATATTTCTTCGGATGAGGGGGGAG 11 4 1 ATTTCTTCAT 0.960546 -26 GTTAAGATTAATTTTTTCTATTCAAGCGAAAA 17 45 0 ATTTTTTCTT 0.968759 -141 GTACATTTTGATTTATTCATATTAAACGACTA 17 102 1 ATTTATTCAT 0.925327 -84 TTTTCTTAATATTGCTTCTATTTTATAAAAAA 18 198 0 ATTGCTTCTT 0.819996 -43 ******** ** Masking position 2 Map Score: 12.3442 Number of sites scoring better than the average of aligned sites = 676 Number in coding regions = 568 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 130 Fraction of orfs with sites within 600 bp upstream = 0.0208802 Motif number 4 AATCCAGGAGAAATTTTTAAAAAAT 3 3 0 AAATTTTAAA 0.896054 -108 ATATCCTTGGAAATTTATGCACAAAAAAACCCG 6 41 0 AAATTTTCAA 0.843731 -228 AGCCTAAAGATAATTTTTAAAAATAGTATTGCA 6 162 1 TAATTTTAAA 0.935916 -107 GCGGAAAAAATATTTTGTCAAGAGAAGAAAACG 7 53 1 TATTTTTAAA 0.961168 -100 ATAGGTGTGCAAATTTTTTCATACAAAGGGGTA 7 125 1 AAATTTTCAA 0.843731 -28 TTTCACTTTTAATTTTCAGAAAAGTTTGATCAT 8 96 1 AATTTTAAAA 0.672865 -60 AGGAATTATATATTTTGTGAAGAGGAGTGACAA 13 128 1 TATTTTTAAA 0.961168 -25 TTTGACCGTATATTTTATACATAGCGCATTTTT 14 166 1 TATTTTTCAA 0.93706 -135 TCTTTTTGCGTATTTTGCCAAGAAGGGAATGAT 14 278 0 TATTTTCAAA 0.837905 -23 ATATTGCTTCTATTTTATAAAAAAACGGAGAGG 18 189 0 TATTTTTAAA 0.958731 -52 CTCCCTCAATTATTTTCTTAATATTGCTTCTAT 18 209 0 TATTTTTAAA 0.958731 -32 ****** * ** * Masking position 11 Map Score: 9.76554 Number of sites scoring better than the average of aligned sites = 229 Number in coding regions = 142 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 5 TATTGTAGGGGAAAAATAAAGCGCTTTCAA 2 59 0 GAAAAATAAA 0.944673 -57 TCCTCCTCTTAAAAGGTAAAAATGTATATA 4 31 0 AAAAGGTAAA 0.866226 -30 ATTACTAGATAAAAATTAAATCGCTGTACA 6 107 0 AAAAATTAAA 0.869856 -162 AAAGGAAATGAAAAGATAAAGGGGTTTTCT 7 15 0 AAAAGATAAA 0.887011 -138 ACTGACTAAAGAAACATAAAGAATAATTCC 8 48 0 GAAACATAAA 0.799572 -108 AAACTTTTCTGAAAATTAAAAGTGAAAAAA 8 93 0 GAAAATTAAA 0.862082 -63 AAATTTGACCAAAAAGTAAATGATCAAACT 8 118 0 AAAAAGTAAA 0.937731 -38 GACTAATCAAAAAAAGTAAACCTTCACTTC 13 46 0 AAAAAGTAAA 0.937731 -107 TTTATAGTATAAACAATAAAAGCTTAGTAA 13 92 1 AAACAATAAA 0.774686 -61 GCTTGAATAGAAAAAATTAATCTTAACTCA 17 50 1 AAAAAATTAA 0.698778 -136 TGAATAATGCGAAAAATAAACTCCTATATT 17 136 0 GAAAAATAAA 0.944673 -50 ********** Masking position 3 Map Score: 10.1855 Number of sites scoring better than the average of aligned sites = 466 Number in coding regions = 341 Number in noncoding regions = 125 Number of orfs with sites within 600 bp upstream = 152 Fraction of orfs with sites within 600 bp upstream = 0.0244137 Motif number 6 AACCAAATACTTACTCATACTAAAAAAAAGTTAT 1 29 1 TATCATTAAA 0.931118 -86 TTGGTAAAATTCCTCCTCTTAAAAGGTAAAAAT 4 38 0 TCTCCTTAAA 0.884721 -23 TATTTATTCATATATCCTTGGAAATTTATGCACA 6 51 0 TTTCCTGAAA 0.690074 -218 GCACACCTATTTATTCCGTTGCAATAATTTGCAC 7 101 0 TATCCGGCAA 0.890713 -52 ACATAAAGAATAATTCCTTGTAAACCTCAAAAGA 8 31 0 TATCCTTAAA 0.973547 -125 CTGCCTATTCACTCCTTATCAAATTGGGATGA 10 39 0 TATCCTTCAA 0.980152 -22 TTTTGTCACTCCTCTTCACAAAATATATA 13 134 0 TATCCTTCAC 0.90292 -19 ATATTTAAAATCAATCCTGATCAAGCTGAAGGAA 14 13 0 TATCCTTCAA 0.979926 -288 AAATTAATCTTAACTCATTGACAAACGTCCAAGA 17 63 1 TATCATACAA 0.740963 -123 ACATTTTGATTTATTCATATTAAACGACTAGGAA 17 104 1 TATCATTAAA 0.931129 -82 ATTTTTCGCATTATTCAGCCTAAAAACATGATAA 17 149 1 TATCAGTAAA 0.838419 -37 * * **** **** Masking position 13 Map Score: 6.3779 Number of sites scoring better than the average of aligned sites = 247 Number in coding regions = 201 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 7 CGGCGTGTAAGGGAGGAGCGATCAAGGAA 2 97 1 GGGAGGAGCG 0.987868 -19 TTGAGCATCCGGGTTGTTCGTCT 6 4 0 GGGTTGTTCG 0.946773 -265 TGGTAACATAGGGTTGTGCAAATTATTGCA 7 86 1 GGGTTGTGCA 0.984495 -67 CAACCATCCCGGGATGAGCAGGCGATGCTC 10 11 1 GGGATGAGCA 0.991629 -50 TTATCAAATTGGGATGAGCATCGCCTGCTC 10 26 0 GGGATGAGCA 0.991629 -35 AAATAATTGAGGGAGGTTCATACA 18 227 1 GGGAGGTTCA 0.970749 -14 ********** Masking position 6 Map Score: 7.13802 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 39 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 8 GTGATCTCTTCTGATATTACTAGATAAAAATTA 6 119 0 CTGATTTCAG 0.983316 -150 TATCTTTAGGCTTATCTTTCCAGTGATCTCTTC 6 141 0 CTTATTTCAG 0.986497 -128 TTTGCACAACCCTATGTTACCACGTTTTCTTCT 7 75 0 CCTATTTCAC 0.932888 -78 AAAAGGAGGTCTTATCTTTGCAGCTCTTACATC 14 213 1 CTTATTTGAG 0.943704 -88 AAAATAAACTCCTATATTCCTAGTCGTTTAATA 17 121 0 CCTATTTCAG 0.983772 -65 CAAAAACATTCTGATATTTCGAGCGAAAATTTC 18 130 1 CTGATTTCAG 0.98375 -111 ***** ** * ** Masking position 7 Map Score: 2.33862 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 28 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 9 TAAGTTAAGAAAAGGAGGAAATTGAG 3 95 1 AAAGGAGGAA 0.913386 -16 ATGAAAAGATAAAGGGGTTTTCTGAAG 7 8 0 AAAGGGGTTT 0.922313 -145 TTTTTCATACAAAGGGGTATCGGG 7 139 1 AAAGGGGTAT 0.936041 -14 AAATTTTCTGATAGGAGGATTGCG 8 142 1 ATAGGAGGAT 0.948967 -14 AGTCTAACAAAAAAGAGGTTATTTGTATAT 14 43 0 AAAAGAGGTT 0.824019 -258 GAGAACGAGAAAAGGAGGTCTTATCTTTGC 14 204 1 AAAGGAGGTC 0.926934 -97 GACTAGGAATATAGGAGTTTATTTTTCGCA 17 129 1 ATAGGAGTTT 0.88481 -57 AAACATGATAAAAGGAGTATCGCC 17 172 1 AAAGGAGTAT 0.967687 -14 ATATAAAGGGAAAGCAGGATAACATGTTGA 18 37 0 AAAGCAGGAT 0.895288 -204 ********** Masking position 3 Map Score: 7.0096 Number of sites scoring better than the average of aligned sites = 469 Number in coding regions = 213 Number in noncoding regions = 256 Number of orfs with sites within 600 bp upstream = 308 Fraction of orfs with sites within 600 bp upstream = 0.04947 Motif number 10 CTCAATTTCCTCCTTTTCTTAACTTAGTTT 3 91 0 CTCCTTTCTT 0.941688 -20 AGCCTTTGTCTCCTTTTCTTACAGGAAAAA 5 61 0 CTCCTTTCTT 0.941688 -20 CCTTTATCTTTTCATTTCCTTTATTGTCCAG 7 23 1 TTCATTTCTT 0.952092 -130 GTTACCACGTTTTCTTCTCTTGACAAAATAT 7 62 0 TTTCTTCCTT 0.891044 -91 GTCATGGACATTTTTTCACTTTTAATTTTCA 8 83 1 TTTTTTCCTT 0.673027 -73 GAAAAGTTTGATCATTTACTTTTTGGTCAAA 8 114 1 ATCATTTCTT 0.938509 -42 TATCGCCTTTTTTATTTGCTTTTATCATTCC 14 255 1 TTTATTTCTT 0.910033 -46 ATTTGCTTTTATCATTCCCTTCTTGGCAAAA 14 268 1 ATCATTCCTT 0.926411 -33 ACCTCCCTCAATTATTTTCTTAATATTGCTT 18 213 0 ATTATTTCTT 0.885953 -28 ******* *** Masking position 6 Map Score: 4.86523 Number of sites scoring better than the average of aligned sites = 510 Number in coding regions = 427 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 11 ********** No masking Map Score: 3.19987e-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: 3.19987e-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 13 ********** No masking Map Score: 3.19987e-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