AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00562_bsub_reg_300.orf -o00562_bsub_300.ace -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -g0.44 -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 = 0.44 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: iolG 22 myo-inositol 2-dehydrogenase Input sequences: #1 spoIIE 300 serine phosphatase #2 yabS 84 similar to hypothetical proteins #3 yabT 88 yabT #4 comQ 184 transcriptional regulator #5 degQ 300 alternate gene name: sacQ #6 iolD 203 alternate gene name: yxdD; myo-inositol catabolism #7 iolC 23 alternate gene name: yxdC; myo-inositol catabolism #8 iolB 74 alternate gene name: yxdB; myo-inositol catabolism #9 iolA 300 methylmalonate-semialdehyde dehydrogenase Motif number 1 TCGTTGCCTGTCATTATAGCGAAAGCACAGATAGGAT 1 249 0 TCTTAGAAGA 0.90017 -52 ATTCATTCCTCCTGGAGAATACGAGGATT 2 66 0 TCTTCCGAGA 0.980686 -19 GTCTTTTTTTTCGTTCTACCGATACAATAAATGGATA 4 28 1 TCTTCCAACA 0.98261 -157 TCTCAATAGGTCCTTATACTCAAAGGAATCACAACAA 5 128 0 TCTTACAAGA 0.95848 -173 TTTCGGCTCATTTTTCACCGAAAAGTATGCAAAAAAG 5 184 0 TTTTCCAAGA 0.975337 -117 TACCTAGGACTCGTTCACCATACACAATTCATTGATC 5 249 1 TCTTCCAACA 0.98261 -52 TAAGCGAATTTTCTTACCCACAAACGATCCCACCTTT 6 27 0 TTTTACAACA 0.889263 -177 GCTGATTAAATTCTTAAACCAGCAGTACATCCATGTA 6 78 1 TTTTACGAGA 0.908058 -126 CTGTTCGGACTCATTCTGCCAATAGAAAGAGGAGGGC 8 42 1 TCTTCCAAGA 0.991774 -33 ** *** * * ** * Masking position 5 Map Score: 8.81629 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 73 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 2 GCCGATTTTTTTCATTTTTAGACAACATTCCGGA 1 140 1 TTCTTTGACA 0.954545 -161 TGCCTTGATATTCGTTTATGAAAAGAATTTCCGG 1 169 0 TTCTTTAAAA 0.976428 -132 TATTGTTACCTTCTTTTGACAAAATCCTATCTGT 1 226 1 TTCTTAAAAA 0.91856 -75 CAGCAGGTTTTTCGTTTTTTAACAATCATATAAT 4 69 0 TTCTTTAACA 0.967207 -116 GACTATAGTCTTGCTTAGTGAAAATGCGAAACCC 5 14 1 TTGTTTAAAA 0.857523 -287 GTTTCCACACTCCTTTTTTTGAAAGATCAATGAA 5 276 0 TCCTTTGAAA 0.926911 -25 ATCGTGAAGATCCCTTCGACAAAAGGCTCTTCCT 6 122 0 TCCTTAAAAA 0.831926 -82 CTTCACGATTTTCGGTCATGGAAACGTATTAGGG 6 147 1 TTCGTTGAAA 0.860158 -57 CTTACTTCTCTTACTTGATTAAAAGATTAATATA 9 19 1 TTATTTAAAA 0.802406 -282 TATTGCCTCCTTCATTAGTAAACACATACACTTG 9 274 0 TTCTTTAACA 0.967206 -27 *** ** * **** Masking position 6 Map Score: 5.30107 Number of sites scoring better than the average of aligned sites = 364 Number in coding regions = 280 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 3 GATCCCCTCCGCCGCTACCATATTTGTTTGGCCCGTTG 1 2 1 ACCTCCATTT 0.98748 -299 GTTAAGACACCGCCCTTTCACGGCGGTAACACGGGTTCGAATCCCGT 1 57 1 CCTTCCACTT 0.977865 -244 ATCCTAACAAATCGGTTTCTCTTGCAGAAGCCGATTTTTTTCATTTT 1 111 1 ACTTCCACTT 0.990361 -190 TTCATATATTCCCATCTTCGCCAGAAGAAATTTGATTTATACGGAAG 2 13 0 CCCTCCATTT 0.97137 -72 GTGGAATGGAAACACTTATACATTGCGTAAACAGCTTGGTAAAGGGG 3 41 1 ACTTTCACTT 0.943794 -48 AAAACGAAAAACCTGCTGTCCTTTAAATGTCCCATTTAGTAAAATGG 4 85 1 ACCTTCGCTT 0.896693 -100 TCTGCTCAATAACGACTTCCCCCCTCCCATTCCATTTTACTAAATGG 4 116 0 ACCTCCACTT 0.995864 -69 GAATTTAATCAGCGCCTGCGCAGTTGTTAAGCGAATTTTCTTACCCA 6 44 0 ACCTCCACTT 0.995864 -160 ATCCTGCTCAAGCGCCTGCCCGATCCCTAATACGTTTCCATGACCGA 6 158 0 ACCTCCAATT 0.968972 -46 ACATACAAGCAACCATTTCATGCACAACAGGTTACTTTTTGGTCATT 9 124 0 ACTTCTATTT 0.746321 -177 * * ** * * * * ** Masking position 7 Map Score: 8.5906 Number of sites scoring better than the average of aligned sites = 257 Number in coding regions = 218 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 4 ACCAACGGGCCAAACAAATATGGTAGCGGC 1 21 0 CAAACAAATA 0.862311 -280 ACGGGTCATCCTAACAAATCGGTTTCTCTT 1 104 1 CTAACAAATC 0.909671 -197 GTCTAAAAATGAAAAAAATCGGCTTCTGCA 1 133 0 GAAAAAAATC 0.939248 -168 GTAACAATACCAAAGAAATCTTCGACGGTT 1 205 0 CAAAGAAATC 0.949838 -96 AAAAGACTTGGAAACAAGTCTTTTTTTTCG 4 11 1 GAAACAAGTC 0.913377 -174 TCCTTATACTCAAAGGAATCACAACAAGAA 5 125 0 CAAAGGAATC 0.797936 -176 GAAAAGTATGCAAAAAAGTCCTGCGTGACA 5 172 0 CAAAAAAGTC 0.907586 -129 CACACTATTAGTAACAGATCAAATACCTAG 5 226 1 GTAACAGATC 0.745618 -75 TTGAAAAAGATCGAGTAAAGGT 6 3 1 GAAAAAGATC 0.869242 -201 TCAAAAACACCAAAAAAATAAATGGCGGAT 9 179 0 CAAAAAAATA 0.797914 -122 ********** Masking position 4 Map Score: 6.02891 Number of sites scoring better than the average of aligned sites = 691 Number in coding regions = 610 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 5 GTCATTATAGCGAAAGCACAGATAGGATTT 1 247 0 CGAAAGCACA 0.953031 -54 TTATACATTGCGTAAACAGCTTGGTAAAGG 3 56 1 CGTAAACAGC 0.979168 -33 AAAAATGAGCCGAAAGCAGACACACTATTA 5 206 1 CGAAAGCAGA 0.939202 -95 CGTAAACAGCCACTCCTCAC 7 14 0 CGTAAACAGC 0.979168 -10 ATAAGTCAATCATAAACACTACATTTTTTC 9 64 0 CATAAACACT 0.809124 -237 TAAACGCTTTCAAAAACACCAAAAAAATAA 9 188 0 CAAAAACACC 0.928234 -113 CTCCTTCATTAGTAAACACATACACTTGTA 9 272 0 AGTAAACACA 0.835871 -29 ********** Masking position 5 Map Score: 2.46273 Number of sites scoring better than the average of aligned sites = 429 Number in coding regions = 402 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 6 ACACGGGTTCGAATCCCGTACGGGTCATCCTAA 1 85 1 GATCCGTCGG 0.989636 -216 AGATATGTTTAGATTCTGTCCGGATCAAGGAGA 4 160 1 AATCTGTCGG 0.949573 -25 GGACTTTTTTGCATACTTTTCGGTGAAAAATGA 5 181 1 GATCTTTCGG 0.985055 -120 AAAGATCAATGAATTGTGTATGGTGAACGAGTC 5 256 0 GATGTGTTGG 0.958882 -45 AGTAAAGGTGGGATCGTTTGTGGGTAAGAAAAT 6 24 1 GATGTTTTGG 0.901144 -180 CAGCGCACATGGACGCCGTTCGGCTGTTCGTCG 8 12 0 GACCCGTCGG 0.981842 -63 CGGCGTCCATGTGCGCTGTTCGGACTCATTCTG 8 27 1 GGCCTGTCGG 0.967086 -48 ATGCACAACAGGTTACTTTTTGGTCATTTCTTG 9 119 0 GTTCTTTTGG 0.842497 -182 * ** **** *** Masking position 9 Map Score: 3.81776 Number of sites scoring better than the average of aligned sites = 269 Number in coding regions = 243 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 7 ATAAACGAATATCAAGGCAGAAACCGTCGA 1 184 1 ATCAAGGCAG 0.962042 -117 TCCTCGTATTCTCCAGGAGGAATGAAT 2 68 1 CTCCAGGAGG 0.966202 -17 CCTCAAGCCGGGTACGACAAT 3 2 1 CTCAAGCCGG 0.93479 -87 TTCTGTCCGGATCAAGGAGAAA 4 173 1 ATCAAGGAGA 0.974137 -12 ACCCGTTAAAATCAAGGAGATTAAGAATCT 5 44 1 ATCAAGGAGA 0.974137 -257 TAATCTTTTAATCAAGTAAGAGAAGTAAGA 9 18 0 ATCAAGTAAG 0.853521 -283 GTGTTTACTAATGAAGGAGGCAATAAGA 9 283 1 ATGAAGGAGG 0.963694 -18 ********** Masking position 5 Map Score: 3.18645 Number of sites scoring better than the average of aligned sites = 394 Number in coding regions = 334 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 8 GCCGGGTACGACAATCAAAGGCAAGTGGAAT 3 17 1 ACAATAAAGG 0.913939 -72 AATCAAAGGCAAGTGGAATGGAAACACTTAT 3 29 1 AAGTGAATGG 0.847968 -60 TTCTACCGATACAATAAATGGATAAAGTATT 4 41 1 ACAATAATGG 0.943636 -144 ACTAAATGGGACATTTAAAGGACAGCAGGTT 4 94 0 ACATTAAAGG 0.943507 -91 CCATTTAGTAAAATGGAATGGGAGGGGGGAA 4 116 1 AAATGAATGG 0.954522 -69 ACATCCATGTAGATGGAAAGGAAGAGCCTTT 6 104 1 AGATGAAAGG 0.88477 -100 AACCTGTTGTGCATGAAATGGTTGCTTGTAT 9 138 1 GCATGAATGG 0.919204 -163 AAACACCAAAAAAATAAATGGCGGATGCATA 9 174 0 AAAATAATGG 0.891903 -127 ***** ***** Masking position 7 Map Score: 2.8181 Number of sites scoring better than the average of aligned sites = 306 Number in coding regions = 267 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 9 AGATGGGAATATATGAATCTGAGAATCCTC 2 43 1 ATATGAATCT 0.957938 -42 TATTTTTATTATATTAATCTTTTAATCAAG 9 32 0 ATATTAATCT 0.890489 -269 TTGTATGTAAATATGCATCCGCCATTTATT 9 163 1 ATATGCATCC 0.937499 -138 GTGGATATTGATATGAATCTATCCGGAACC 9 237 1 ATATGAATCT 0.957938 -64 ********** Masking position 4 Map Score: 0.705794 Number of sites scoring better than the average of aligned sites = 45 Number in coding regions = 32 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 10 ********** No masking Map Score: -7.64954e-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 11 ********** No masking Map Score: -7.64954e-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 12 ********** No masking Map Score: -7.64954e-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