AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00900_bsub_reg_300.orf -o00900_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 Input sequences: #1 mmgC 27 acyl-CoA dehydrogenase #2 mmgB 149 3-hydroxybutyryl-CoA dehydrogenase #3 mmgA 137 acetyl-CoA acetyltransferase #4 yqiK 78 similar to glycerophosphodiester phosphodiesterase #5 yqiH 300 alternate gene name: yzpA; similar to lipoprotein #6 yqiC 85 similar to exodeoxyribonuclease VII (small subunit) #7 yqiB 137 similar to exodeoxyribonuclease VII (large subunit) #8 yqhZ 263 similar to transcription termination #9 accB 155 acetyl-CoA carboxylase subunit (biotin carboxyl carrier subunit) #10 spoIIIAC 22 spoIIIAC #11 spoIIIAA 75 spoIIIAA #12 yqhV 144 alternate gene name: yqgE #13 efp 24 elongation factor P #14 yqhS 86 similar to 3-dehydroquinate dehydratase #15 yqhR 226 yqhR #16 ywjF 154 similar to hypothetical proteins Motif number 1 ACATCCGCACATAAAAGCCGCGTCGGCGGCTG 2 96 0 AAAAACCGCG 0.944461 -54 GAATGAATGAAAAAAGAAGGCTGCGTCAAACA 3 37 0 AAAAGAGGCT 0.949744 -101 CCATAACTAAAGAAAACCCGCCCTGGCTTTAG 7 84 0 AAAAACCGCC 0.944461 -54 GTCTAAAAACTCCTCTCCTAAGCATT 7 122 0 AAAACCCTCT 0.926638 -16 CAAAGCATGAAGAAAGCCGGCTTACATAGCCG 8 75 1 AAAAGCGGCT 0.993348 -189 ACGTTCATGAAGAAACTCGGCTATGTAAGCCG 8 92 0 AAAACCGGCT 0.983101 -172 GAATGAGGGAAAAAAGCCCGCTAAACAAGCGG 9 11 1 AAAAGCCGCT 0.996114 -145 ACAGCAACGCAAAAAGCCCGCTTGTTTAGCGG 9 28 0 AAAAGCCGCT 0.996114 -128 GAGGCTTGTCATAAAGTCTGCCTCACATCATA 11 14 1 AAAAGCTGCC 0.950909 -62 AAAGGAAAAAAGAAGTCTGTTCCCAAAT 12 7 1 AAAAGAGTCT 0.705109 -138 TTGGGCACAAAAAAAGCCTGCTCCCATTTGGG 12 32 0 AAAAGCTGCT 0.980571 -113 CTATTGTACAGGAAACACCGCTAAACCTCTAG 15 60 1 GAAACCCGCT 0.940284 -167 CTTTTTACTGATAAAGACCGCGATCCCCTACC 16 122 0 AAAAGCCGCG 0.989937 -33 * **** ***** Masking position 5 Map Score: 21.6995 Number of sites scoring better than the average of aligned sites = 646 Number in coding regions = 543 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 2 AACATGATGAAAAAGGGGATTTGAATG 2 1 1 AAAGGAAGGG 0.986879 -149 TTCATTTTAAAAAATTTGAGAATAGGGTGAGCAAATC 5 55 0 AAATAATGGG 0.967441 -246 TCTTTCTAACAACAGGAAATGATCGGGTCGTATAGCC 5 172 1 AAAGAATGGG 0.984995 -129 ATGACATTTGAAGAAGCGATGAAAGGGCTTGAGAGCA 6 33 1 AAAGAAAGGG 0.971466 -53 TAGGAGCCTGAAGAAGCGGGTATCGTGCTCATATTCA 7 50 0 AAAGGATGTG 0.912324 -88 ATGGCTTAACACGAAACCAAGGGGAGGGCGGCCC 8 8 1 AAAGAAAGGG 0.971466 -256 GGTGTGTGAAAATATTCGGTAATAGGGTAAAAAAACC 8 146 1 AAATGATGGG 0.984995 -118 GTATAAAAGAAAGATTCTGTTTTTGGGCACAAAAAAA 12 49 0 AAATGTTGGG 0.902311 -96 TATCATATAAAAAAATGGGAGGTTGGGAGAGTGCT 12 120 1 AAATGGTGGG 0.961823 -25 CTGCGAGTAAAATTTGAAAATAACGGGTATAATGCAT 15 134 0 AATGAAAGGG 0.797712 -93 TAATCTTATACAGATTCGGGGGTAGGGGATCGCGGTC 16 102 1 CAATGGTGGG 0.812206 -53 CTTTATCAGTAAAAAGGGGGAATTGGA 16 138 1 AAAGGATGGA 0.912324 -17 ** * * * ** *** Masking position 2 Map Score: 12.017 Number of sites scoring better than the average of aligned sites = 213 Number in coding regions = 162 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 3 TTCAAATCCCCTTTTTCATCATGTT 2 3 0 CTTTTTCCTG 0.956955 -147 GCAGCCTTCTTTTTTCATTCATTCATGCCCGTT 3 45 1 TTTTTCACTT 0.896587 -93 AAAGAAGCAACTTTTTATTCATTTTAAAAAATT 5 76 0 CTTTTTACTT 0.870803 -225 TTTCCGCTAATTTTTTCTAATTGGCGCCTCAAT 5 106 1 TTTTTTCATG 0.741698 -195 TGTTTCATTTTTTTTCACGTCTG 6 1 0 TTTTTCATTG 0.763265 -85 ATCTCCCTCTTCAAGCTTTGATACAATGC 6 67 0 CTCTTCACTT 0.864107 -19 AGGGCGGGTTTTCTTTAGTTATGGTGCAGGAAT 7 92 1 TTCTTTATTG 0.657034 -46 GCCCTTTGGTTTTTTTACACGTTACCCTTTATT 8 41 1 TTTTTTACTT 0.873107 -223 TAAGCCGGCTTTCTTCATGCTTTGAAATAAAGG 8 66 0 TTCTTCACTT 0.866511 -198 CTTTGATCCTCTTTATCCGCTTGTCGTTAAGCC 8 231 0 CTTTATCCTG 0.655437 -33 TTTCTTTCTCCTTTGATCCTCTTT 8 250 0 TTCTTTCCTT 0.892286 -14 TTAGCGGGCTTTTTTCCCTCATTC 9 2 0 TTTTTCCCTT 0.933072 -154 TGTATAATCCTTTTCCAGTATGATAAAATGTT 14 10 1 CTTTTCCTTG 0.835488 -77 ACCTGCCTATTTCTTTAGGATTGCTAACCATTT 15 18 1 TTCTTTAATG 0.572095 -209 GCTATGGCAATTTTTTCAGCCTGTCAATCTAGA 15 87 0 TTTTTTCCTG 0.957797 -140 CATAGCCTTGCTTTTCCTACATGCATTATACCC 15 114 1 CTTTTCCCTG 0.965532 -113 ******* * ** Masking position 4 Map Score: 12.6318 Number of sites scoring better than the average of aligned sites = 1632 Number in coding regions = 1413 Number in noncoding regions = 219 Number of orfs with sites within 600 bp upstream = 232 Fraction of orfs with sites within 600 bp upstream = 0.0372631 Motif number 4 GCAGGTCAGATGGGGAGCGGAATTGCTCAAA 2 65 1 TGGGAGCGGA 0.850711 -85 TAACAACAGGAAATGATCGGGTCGTATAGCC 5 178 1 AATGATCGGG 0.780004 -123 CCCGCCTTGAATATGAGCACGATACCCGCTT 7 43 1 AATGAGCACG 0.891666 -95 CACGAAACCAAGGGGAGGGCGGCCCTTTGGT 8 20 1 AGGGAGGGCG 0.989088 -244 TGTTCATCTTACAGGAGCGGACTTGTGAATT 9 73 0 AAGGAGCGGA 0.976996 -83 AATTTCATACATAGGAGTGCGATTGT 9 140 1 AAGGAGTGCG 0.963557 -16 ACGTGAGGGGAGCAAAAATAA 10 1 1 AGTGAGGGGA 0.88026 -22 CAATCGGTAGAAAGGAGGAGGCTCTG 11 60 1 AAGGAGGAGG 0.961887 -16 CTGTTCCCAAATGGGAGCAGGCTTTTTTTGT 12 27 1 AGGGAGCAGG 0.977371 -118 TTGGAATATAGGAGGACATTAAAC 13 8 1 AAGGAGGACA 0.902653 -17 TTTACTACGGAAAGGAGTGCCGGT 16 4 0 AAGGAGTGCC 0.813989 -151 ATTCGGGGGTAGGGGATCGCGGTCTTTATCA 16 115 1 AGGGATCGCG 0.948993 -40 * ********* Masking position 6 Map Score: 9.39364 Number of sites scoring better than the average of aligned sites = 767 Number in coding regions = 611 Number in noncoding regions = 156 Number of orfs with sites within 600 bp upstream = 150 Fraction of orfs with sites within 600 bp upstream = 0.0240925 Motif number 5 AGCCGCGTCGGCGGCTGTTTGAGCAATTCCGC 2 81 0 GCGGTGTTGA 0.99041 -69 GCTTTTATGTGCGGATGTATGATGTGAATCCA 2 110 1 GCGGTGTTGA 0.99041 -40 TTGTTAGAAGGAGGCTGTTTGACGCAGCCTTC 3 22 1 GAGGTGTTGA 0.987687 -116 CTCTAGGATTAAGGCTGTATCAAT 4 3 0 AAGGTGTTCA 0.927285 -76 AAATCGTTTGACGGGTGGGTCAGCCAAGCGTA 5 28 0 ACGGTGGTCA 0.931234 -273 ATTTGTCTATGAGGATGGCTCTAATTGAGGCG 5 130 0 GAGGTGGTCT 0.893851 -171 TCTTACAGGAGCGGACTTGTGAATTCAACTCT 9 66 0 GCGGCTTTGA 0.826129 -90 AAAAAAATGGGAGGTTGGGAGAGTGCT 12 128 1 GAGGTGGAGA 0.912515 -17 TCCTTTTCGCGAGGGTTTCTCATGTAAAAAAT 14 57 0 GAGGTTTTCA 0.927285 -30 **** *** *** Masking position 4 Map Score: 6.31725 Number of sites scoring better than the average of aligned sites = 295 Number in coding regions = 251 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 6 ATGTGCGGATGTATGATGTGAATCCAGAGGCCGC 2 116 1 GATGGTGAAC 0.993015 -34 TTCTATGAATGTATGCTTTGAAACGGGCATGAAT 3 65 0 GATGTTGAAC 0.958816 -73 TCTATCTTCTGAATGAGGTGAAACC 3 123 1 GATGGTGAAC 0.993015 -15 AAACTTTAGGGTTTGAGGTGAAACG 4 64 1 GTTGGTGAAC 0.964872 -15 CCTCCCCTTGGTTTCGTGTTAAGCCAT 8 4 0 GTTCGTTAAC 0.873851 -260 CTCTTTATCCGCTTGTCGTTAAGCCACAAAGAGA 8 222 0 GTTGGTTAAC 0.967809 -42 TCTTTAAAATGTATGATGTGAGGCAGACTTTATG 11 23 0 GATGGTGAGC 0.982107 -53 * *** ***** * Masking position 11 Map Score: 7.03212 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 41 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 7 CCTGCTCCCATTTGGGAACAGACTTCTTTT 12 18 0 TTTGGGAACA 0.981667 -127 AGATTCTGTTTTTGGGCACAAAAAAAGCCT 12 45 0 TTTGGGCACA 0.993917 -100 CATTTCATTTTTTGGGCACACTTTAACTGG 15 200 1 TTTGGGCACA 0.993917 -27 ATTCCTGCTGTTCGGGCACACTACCTTTAC 16 30 0 TTCGGGCACA 0.991976 -125 ********** Masking position 8 Map Score: 5.86497 Number of sites scoring better than the average of aligned sites = 9 Number in coding regions = 5 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 8 TACATTCATAGAAGACAACTAGAAATTGTAAG 3 86 1 GAAGACAATG 0.8255 -52 ACCTCATTCAGAAGATAGACAGCGCTTACAAT 3 110 0 GAAGATAGCG 0.855876 -28 CTGTTGTTAGAAAGATAACGAGCAGATTTGTC 5 155 0 AAAGATAAGG 0.894896 -146 GAGAATTTGTAAAGACAACGCGAATGCAGGCG 5 233 0 AAAGACAAGG 0.963501 -68 GTCAAAGATAAAAGCCAAACATCAGGAAGAGG 5 272 1 AAAGCCAACT 0.772904 -29 TCAGGCTCCTAAAGCCAGGGCGGGTTTTCTTT 7 76 1 AAAGCCAGGG 0.93141 -62 GGCTTAACACGAAACCAAGGGGAGGGCGGCCC 8 13 1 GAAACCAAGG 0.880937 -251 AACGTGTAAAAAAACCAAAGGGCCGCCCTCCC 8 32 0 AAAACCAAGG 0.842652 -232 TTCAAAGCATGAAGAAAGCCGGCTTACATAGC 8 73 1 GAAGAAAGCG 0.643489 -191 TTTGTGGCTTAACGACAAGCGGATAAAGAGGA 8 226 1 AACGACAACG 0.806335 -38 ACATTTTAAAGAAGCCAATCGGTAGAAAGGAG 11 45 1 GAAGCCAACG 0.973797 -31 AGTAAAATTTGAAAATAACGGGTATAATGCAT 15 134 0 GAAAATAAGG 0.700775 -93 TATTTATCATAAAGATAATCTTATACAGATTC 16 87 1 AAAGATAACT 0.5186 -68 ******** * * Masking position 7 Map Score: 5.35629 Number of sites scoring better than the average of aligned sites = 1834 Number in coding regions = 1675 Number in noncoding regions = 159 Number of orfs with sites within 600 bp upstream = 148 Fraction of orfs with sites within 600 bp upstream = 0.0237713 Motif number 9 CCTCTGGATTCACATCATACATCCGCACAT 2 116 0 CACATCATAC 0.979471 -34 GGTTTCACCTCATTCAGAAGATAGA 3 123 0 CACCTCATTC 0.977036 -15 CGTTTCACCTCAAACCCTAAAGTTT 4 64 0 CACCTCAAAC 0.970304 -15 ATGACCACCTCTTCCTGATGTTTGG 5 286 0 CACCTCTTCC 0.950412 -15 AAGTCTGCCTCACATCATACATTTTAAAGA 11 27 1 CACATCATAC 0.979471 -49 ********** Masking position 5 Map Score: 3.47018 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 39 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 10 AGACAACTAGAAATTGTAAGCGCTGTCTATC 3 98 1 AAATTGTAGC 0.871752 -40 ATATCCTTTAAAAGGTTACGCTTGGCTGACC 5 12 1 AAAGGTTCGC 0.913284 -289 AAATTTGAGAATAGGGTGAGCAAATCGTTTG 5 50 0 ATAGGGTAGC 0.880153 -251 TTCACAGGCGAAATGTTTACCCGCCTTGAAT 7 24 1 AAATGTTACC 0.923647 -114 GCTTTGAAATAAAGGGTAACGTGTAAAAAAA 8 50 0 AAAGGGTACG 0.92127 -214 CAGTATGATAAAATGTTCACGAGAAGTGAAC 14 26 1 AAATGTTACG 0.763858 -61 CTCATGTAAAAAATGTTCACTTCTCGTGAAC 14 40 0 AAATGTTACT 0.542528 -47 GAGTGAAAGGAAATGGTTAGCAATCCTAAAG 15 30 0 AAATGGTAGC 0.96484 -197 CTGTCAATCTAGAGGTTTAGCGGTGTTTCCT 15 69 0 AGAGGTTAGC 0.851253 -158 CAGCTGCCAAAAAGTGTGAGCTTTTTTATTG 15 168 1 AAAGTGTAGC 0.928205 -59 ACCTCCAGTTAAAGTGTGCCCAAAAAATGAA 15 203 0 AAAGTGTCCC 0.806213 -24 ******* *** Masking position 3 Map Score: 4.35424 Number of sites scoring better than the average of aligned sites = 536 Number in coding regions = 442 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 11 ATGAATGAATGAAAAAAGAAGGCTGCGTCA 3 41 0 GAAAAAAGAA 0.946559 -97 CAGACGTGAAAAAAAATGAAACATGACATT 6 11 1 AAAAAATGAA 0.951214 -75 CCTGCACCATAACTAAAGAAAACCCGCCCT 7 92 0 AACTAAAGAA 0.75256 -46 AGTAACCTATAAAAAAAGAAATTTCATACA 9 121 1 AAAAAAAGAA 0.96902 -35 AAAGGAAAAAAGAAGTCTGTTCCC 12 5 1 GAAAAAAGAA 0.946559 -140 TTTTGTGCCCAAAAACAGAATCTTTCTTTT 12 52 1 AAAAACAGAA 0.892564 -93 AAGTGTGCCCAAAAAATGAAATGTCAATAA 15 193 0 AAAAAATGAA 0.951214 -34 TCTTTATGATAAATAATGAATGAGTGTTCA 16 72 0 AAATAATGAA 0.877117 -83 ********** Masking position 5 Map Score: 7.65477 Number of sites scoring better than the average of aligned sites = 536 Number in coding regions = 408 Number in noncoding regions = 128 Number of orfs with sites within 600 bp upstream = 136 Fraction of orfs with sites within 600 bp upstream = 0.0218439 Motif number 12 CAGGTCAGATGGGGAGCGGAATTGCTCAAA 2 66 1 GGGGAGCGGA 0.913402 -84 TCGTTTGACGGGTGGGTCAGCCAAGCGTAA 5 27 0 GGTGGGTCAG 0.642038 -274 TTGAGAATAGGGTGAGCAAATCGTTTGACG 5 47 0 GGTGAGCAAA 0.964115 -254 CGCGAATGCAGGCGAGCAAGTTCCATGATT 5 217 0 GGCGAGCAAG 0.983426 -84 TCATATTCAAGGCGGGTAAACATTTCGCCT 7 29 0 GGCGGGTAAA 0.930552 -109 ACGTGAGGGGAGCAAAAATAAA 10 7 1 GGGGAGCAAA 0.983749 -16 TGTTCCCAAATGGGAGCAGGCTTTTTTTGT 12 28 1 TGGGAGCAGG 0.884859 -117 TTTTGGCAGCTGCGAGTAAAATTTGAAAAT 15 150 0 TGCGAGTAAA 0.844046 -77 ********** Masking position 6 Map Score: 1.52424 Number of sites scoring better than the average of aligned sites = 350 Number in coding regions = 289 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 13 AATCATGGTAGCTGGCGCAGGTCAGATGGGG 2 49 1 GCTGGGCAGG 0.991969 -101 GCTTTTATGTGCGGATGTATGATGTGAATCC 2 110 1 GCGGAGTATG 0.898335 -40 TCCAGAGGCCGCGGAGGCAGGA 2 138 1 GCGGAGCAGG 0.99508 -12 TAAAGACAACGCGAATGCAGGCGAGCAAGTT 5 225 0 GCGAAGCAGG 0.957635 -76 TTTCTTTAGTTATGGTGCAGGAATGCTTAGG 7 101 1 TATGGGCAGG 0.816201 -37 CTGTTCCCAAATGGGAGCAGGCTTTTTTTGT 12 27 1 ATGGGGCAGG 0.865647 -118 GCTCTAGCTTGCTGAAGTAGTCTTGTCATTT 12 88 0 GCTGAGTAGT 0.775435 -57 TTATACAGATTCGGGGGTAGGGGATCGCGGT 16 107 1 TCGGGGTAGG 0.971621 -48 ***** ***** Masking position 9 Map Score: 3.06061 Number of sites scoring better than the average of aligned sites = 598 Number in coding regions = 536 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 14 ********** No masking Map Score: -4.43846e-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 15 ********** No masking Map Score: -4.43846e-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