AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -ifadR_bsub_opreg_300.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 yhfI 151 similar to hypothetical proteins #2 yhfK 64 similar to hypothetical proteins #3 yhfL 116 similar to long-chain fatty-acid-CoA ligase #4 mmgB 149 3-hydroxybutyryl-CoA dehydrogenase #5 mmgA 137 acetyl-CoA acetyltransferase #6 yqiK 78 similar to glycerophosphodiester phosphodiesterase #7 yqiH 300 alternate gene name: yzpA; similar to lipoprotein #8 lcfA 188 long chain acyl-CoA synthetase #9 yshC 73 similar to DNA polymerase beta #10 yshA 133 yshA #11 yusL 267 similar to 3-hydroxyacyl-CoA dehydrogenase #12 yusM 300 similar to proline dehydrogenase Motif number 1 CCATTTTTCTTGAAAAAAGCATGTTTTAAA 1 86 0 TGAAAAAAGC 0.92429 -66 ATGGGTATATTGAAGGAGGACCAATTTTTT 1 112 1 TGAAGGAGGA 0.859159 -40 ATAGAGAAACAGAAAAAAACACTCAAGAGC 3 35 0 AGAAAAAAAC 0.875129 -82 TCTATAATGGAGAAGAAAGCTTGGCTTCAA 3 60 1 AGAAGAAAGC 0.956187 -57 AACATGATGAAAAAGGGGATTTGA 4 5 1 TGATGAAAAA 0.575503 -145 AATAGTTGTTAGAAGGAGGCTGTTTGACGC 5 17 1 AGAAGGAGGC 0.939815 -121 CATGAATGAATGAAAAAAGAAGGCTGCGTC 5 42 0 TGAAAAAAGA 0.840801 -96 ATACATTCATAGAAGACAACTAGAAATTGT 5 85 1 AGAAGACAAC 0.846962 -53 AAAAATTAGCGGAAAGAAGCAACTTTTTAT 7 91 0 GGAAAGAAGC 0.839476 -210 TTCTGGTCAAAGATAAAAGCCAAACATCAG 7 267 1 AGATAAAAGC 0.805722 -34 GACGGAGAATAGATGGAAAAGCTTGCGAAA 8 14 1 AGATGGAAAA 0.534967 -175 TCATATTATGAGAAAAAGAAAGATTTACCT 8 96 1 AGAAAAAGAA 0.738981 -93 GGCAAAAAAAAGAAAAAGAAAGGTAAATCT 8 116 0 AGAAAAAGAA 0.738981 -73 CCATCATACTTGAAAAAAACTTCTCCGGAC 9 24 0 TGAAAAAAAC 0.863547 -50 TTTTCAAGTATGATGGAAACATATGTGAAC 9 38 1 TGATGGAAAC 0.705991 -36 TTACGGCGGCGGAAAACGGACAAGTCAAAA 11 72 0 GGAAAACGGA 0.574242 -196 TGACTGCCGCTGAAGACGGATTTTTTTTCT 11 142 1 TGAAGACGGA 0.795692 -126 ATGGTACGAGAGAAAAAAAATCCGTCTTCA 11 152 0 AGAAAAAAAA 0.751975 -116 TTGCTCGCGATGAAAAAAGCGCATTTCATG 12 100 0 TGAAAAAAGC 0.92429 -201 TCGAAATAACGGAAGGCGGCATTTGAGATT 12 171 1 GGAAGGCGGC 0.794083 -130 ACTCCCAGTCTGAAGGAAACTATAAAATGA 12 240 0 TGAAGGAAAC 0.886722 -61 GGTGTTTTGAAGATGACGGCGGGAGGGAGT 12 278 1 AGATGACGGC 0.753587 -23 ********** Masking position 3 Map Score: 21.6453 Number of sites scoring better than the average of aligned sites = 4353 Number in coding regions = 3855 Number in noncoding regions = 498 Number of orfs with sites within 600 bp upstream = 464 Fraction of orfs with sites within 600 bp upstream = 0.0745262 Motif number 2 TGCTCAAACAGCCGCCGACGCGGCTTTTATGTG 4 88 1 GCCCGACGCG 0.954047 -62 TCCTGCCTCCGCGGCCTCTGGATT 4 136 0 CTCCTCCGCG 0.900825 -14 TAGAAGGAGGCTGTTTGACGCAGCCTTCTTTTT 5 26 1 CGTTGACGCG 0.982933 -112 TGCGAAAATACTGCTCGCCGCAGCGGGAATCTT 8 37 1 CGTCGCCGCG 0.995744 -152 ATGGAAAGACGAGCCTCCCGCTGTTATGATACA 10 53 0 GGCTCCCGCG 0.990383 -81 CATAATGCAGCTGCTTCCCACGGCTGCTT 11 7 0 CGTTCCCACG 0.875787 -261 TTTGACTTGTCCGTTTTCCGCCGCCGTAATGCT 11 73 1 CGTTTCCGCG 0.97597 -195 AGGGAGATGCCGGTCCGACTCAGCATTACGGCG 11 94 0 CGCCGACTCG 0.930488 -174 GCTCGCCGCGCTGACTGCCGCTGAAGACGGATT 11 131 1 CGCTGCCGCG 0.997713 -137 CATGATGCATGTGTCCGACGCGGTCGAGTTCTT 12 36 1 GGCCGACGCG 0.98865 -265 GGCGGCATTTGAGATTGCTGCTGATTATCCATT 12 185 1 GGTTGCTGCG 0.883356 -116 CCGACTCCCTCCCGCCGTCATCTTCAA 12 284 0 CCCTCCCGCG 0.979628 -17 * * ******* * Masking position 11 Map Score: 17.6696 Number of sites scoring better than the average of aligned sites = 814 Number in coding regions = 753 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 3 TCCCTCTTTCCCCTTTGTAGTGATTTCA 1 7 1 TTCCCCTTTT 0.828434 -145 CCTCCTTCAATATACCCATTTTTCTTGAAAAA 1 99 0 TTACCCATTT 0.792722 -53 GAATCCCTCCTGCCTCCATTATTTCAAAAACA 2 41 0 TCCTCCATTT 0.808501 -24 GCCAAGCTTTCTTCTCCATTATAGAGAAACAG 3 53 0 CTCTCCATTT 0.851861 -64 ATAATGAATGACTATTCATTCACTTAAGGGGT 3 89 1 ATATTCATTA 0.578675 -28 TTTCCATTCAAATCCCCTTTTTCATCATGTT 4 10 0 ATCCCCTTTT 0.903619 -140 CCTTCTAACAACTATTCATTTT 5 1 0 ATATTCATTT 0.846693 -137 TGTTTGACGCAGCCTTCTTTTTTCATTCATTC 5 37 1 ACCTTCTTTT 0.651808 -101 ACCCTAAAGTTTTCTCCATTATACTTATTTTG 6 44 0 TTCTCCATTT 0.940216 -35 AATATCCTTTAAAAGGTTACGC 7 1 1 ATATCCTTTA 0.787592 -300 GAAGCAACTTTTTATTCATTTTAAAAAATTTG 7 74 0 TTATTCATTT 0.739887 -227 GTCTTTACAAATTCTCCATTCTGGTCAAAGAT 7 249 1 ATCTCCATTT 0.96829 -52 GTAATAATCTCCTTTTTTTACACTTTT 10 6 1 ATCTCCTTTT 0.959961 -128 TGCTTTAATATTCTTTGATAGTGATCAT 12 7 1 ATATTCTTTA 0.518864 -294 TGAGATACAAATGATCCTTTGTCGAAATAACG 12 150 1 AGATCCTTTT 0.685038 -151 ATTGCTGCTGATTATCCATTGTGATCCTCCTT 12 198 1 ATATCCATTT 0.949972 -103 * ******** * Masking position 9 Map Score: 12.4532 Number of sites scoring better than the average of aligned sites = 934 Number in coding regions = 691 Number in noncoding regions = 243 Number of orfs with sites within 600 bp upstream = 299 Fraction of orfs with sites within 600 bp upstream = 0.0480244 Motif number 4 GGGTATATTGAAGGAGGACCAATTTTTTTG 1 114 1 AAGGAGGACC 0.906876 -38 GCGGATGTATGATGTGAATCCAGAGGCCGC 4 120 1 GATGTGAATC 0.862342 -30 TCTTCTGAATGAGGTGAAACC 5 127 1 GAGGTGAAAC 0.977324 -11 TTTAGGGTTTGAGGTGAAACG 6 68 1 GAGGTGAAAC 0.977324 -11 AAGAAAAAGAAAGGTAAATCTTTCTTTTTC 8 107 0 AAGGTAAATC 0.79802 -82 CTATAATGATAAGGTGGATCTCTAAAATCG 8 155 1 AAGGTGGATC 0.971973 -34 TCGCGGAATGGAGGAGAAACG 10 123 1 GAGGAGAAAC 0.964114 -11 ACAGAAACCAAAGGAGGATCACAATGGATA 12 210 0 AAGGAGGATC 0.955787 -91 ********** Masking position 8 Map Score: 8.06137 Number of sites scoring better than the average of aligned sites = 218 Number in coding regions = 162 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 5 GTGAATCCCTCCTGCCTCCATTATTTCAA 2 46 0 TCCTGCCTCC 0.973882 -19 GAATTGCTCAAACAGCCGCCGACGCGGCTT 4 84 1 AACAGCCGCC 0.991119 -66 ATCCGCACATAAAAGCCGCGTCGGCGGCTG 4 96 0 AAAAGCCGCG 0.878789 -54 TCCTGCCTCCGCGGCCTCTG 4 140 0 TCCTGCCTCC 0.973882 -10 GGCTGCGTCAAACAGCCTCCTTCTAACAAC 5 21 0 AACAGCCTCC 0.989296 -117 GAATGGAAAGACGAGCCTCCCGCTGTTATG 10 58 0 ACGAGCCTCC 0.969417 -76 CAGCAATCTCAAATGCCGCCTTCCGTTATT 12 175 0 AAATGCCGCC 0.966624 -126 ********** Masking position 5 Map Score: 6.517 Number of sites scoring better than the average of aligned sites = 355 Number in coding regions = 288 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 6 TCGTTTGAAAGAGCGGTTGTGTTTTTGAAA 2 22 1 GAGCGGTTGT 0.977971 -43 GTCAGATGGGGAGCGGAATTGCTCAAACAG 4 69 1 GAGCGGAATT 0.947064 -81 CGGCTTTTATGTGCGGATGTATGATGTGAA 4 108 1 GTGCGGATGT 0.851748 -42 GAAAGATAACGAGCAGATTTGTCTATGAGG 7 148 0 GAGCAGATTT 0.968564 -153 CCGCTGCGGCGAGCAGTATTTTCGCAAGCT 8 33 0 GAGCAGTATT 0.947629 -156 AAATCGAAAGGGGAGGTTTT 8 179 1 GGGAGGTTTT 0.904118 -10 CTCCGGACAAGAGAAGTTTTT 9 2 0 GAGAAGTTTT 0.950789 -72 CTCTTGTCCGGAGAAGTTTTTTTCAAGTAT 9 19 1 GAGAAGTTTT 0.950789 -55 ********** Masking position 10 Map Score: 6.04017 Number of sites scoring better than the average of aligned sites = 416 Number in coding regions = 353 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 7 GTTTGAGCAATTCCGCTCCCCATCTGACCTG 4 66 0 TCCGCTCCCC 0.972868 -84 CCGTCAAACGATTTGCTCACCCTATTCTCAA 7 46 1 ATTGCTCACC 0.941785 -255 AAATCATGGAACTTGCTCGCCTGCATTCGCG 7 216 1 ATTGCTCGCC 0.988294 -85 CTTGCGAAAATACTGCTCGCCGCAGCGGGAA 8 35 1 TCTGCTCGCC 0.990287 -154 ATCATAATGCAGCTGCTTCCCACGGCTGCTT 11 11 0 ACTGCTTCCC 0.9 -257 GCATCTCCCTTTACGCTCGCCGCGCTGACTG 11 117 1 TACGCTCGCC 0.945257 -151 CTGAACTGGAATTTGCTCGCGATGAAAAAAG 12 111 0 ATTGCTCGCG 0.941963 -190 * ********* Masking position 7 Map Score: 3.50765 Number of sites scoring better than the average of aligned sites = 265 Number in coding regions = 234 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 8 TTAAACATTGTATCAAAACAGTTATTGATT 1 61 0 TATCAAAACA 0.957673 -91 CCTCCTATCTTTTCAAAAAAATTGGTCCTC 1 127 0 TTTCAAAAAA 0.672255 -25 TTCATGCCCGTTTCAAAGCATACATTCATA 5 66 1 TTTCAAAGCA 0.949834 -72 TCCACCTTATCATTATAGCAGATGGACGGC 8 143 0 CATTATAGCA 0.76654 -46 TATACCAGTGTATCATAACAGCGGGAGGCT 10 45 1 TATCATAACA 0.910543 -89 TCCTAGTTCTTATCATAACACGTTTATTAA 10 90 0 TATCATAACA 0.910543 -44 TATCAAAGAATATTAAAGCA 12 1 0 TATTAAAGCA 0.910578 -300 TCATGATCACTATCAAAGAATATTAAAGCA 12 11 0 TATCAAAGAA 0.86188 -290 CAGGATCAAACGTTAAAGCAAGAACTCGAC 12 58 0 CGTTAAAGCA 0.690517 -243 CCGCCGTCATCTTCAAAACACCTGTATATA 12 270 0 CTTCAAAACA 0.894223 -31 ********** Masking position 5 Map Score: 4.46173 Number of sites scoring better than the average of aligned sites = 573 Number in coding regions = 492 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 9 TCCCTCTTTCCCCTTTGTAGTGA 1 4 1 CTCTTTCCCC 0.943967 -148 GTGAATCCCTCCTGCCTCCATTATTTCA 2 47 0 CTCCTGCCTC 0.89045 -18 TCTCCCACCCCTTAAGTGAAT 3 106 0 CTCCCACCCC 0.944123 -11 TCCTGCCTCCGCGGCCTCTGGA 4 138 0 CTGCCTCCGC 0.806367 -12 TAAAAAGTTGCTTCTTTCCGCTAATTTTTT 7 92 1 CTTCTTTCCG 0.797514 -209 TTTACAAATTCTCCATTCTGGTCAAAGATA 7 252 1 CTCCATTCTG 0.751328 -49 TCCATCTATTCTCCGTCCCC 8 1 0 CTCCGTCCCC 0.9756 -188 AAAAACTTCTCTTGTCCGGAGAAGTTTT 9 9 1 CTCTTGTCCG 0.726878 -65 CGTTTCTCCTCCATTCCGCGAGAATCCT 10 116 0 CTCCATTCCG 0.94588 -18 CATAATGCAGCTGCTTCCCACGGCTGCTT 11 10 0 CTGCTTCCCA 0.818957 -258 CCGACTCCCTCCCGCCGTCATCTT 12 287 0 CTCCCTCCCG 0.990756 -14 ********** Masking position 2 Map Score: 5.57239 Number of sites scoring better than the average of aligned sites = 572 Number in coding regions = 465 Number in noncoding regions = 107 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 Motif number 10 AATGTCCTCCTATCTTTTCAAAAAAATTG 1 133 0 CCTATTTTTC 0.956176 -19 TCCCTCCTGCCTCCATTATTTCAAAAACACAAC 2 37 0 CCATTTTTCA 0.628602 -28 AGATAGACAGCGCTTACAATTTCTAGTTGTCTT 5 97 0 CCTACATTTC 0.860272 -41 TCACCTCAAACCCTAAAGTTTTCTCCATTATAC 6 52 0 CCAAATTTTC 0.748045 -27 TCACCCTATTCTCAAATTTTTTAAAATGAATAA 7 62 1 CCAATTTTTA 0.658026 -239 TGCTTCTTTCCGCTAATTTTTTCTAATTGGCGC 7 100 1 CCAATTTTTC 0.943076 -201 GGCTATACGACCCGATCATTTCCTGTTGTTAGA 7 176 0 CCATCTTTCC 0.952682 -125 GCAGTATTTTCGCAAGCTTTTCCATCTATTCTC 8 18 0 CCAGCTTTCC 0.861015 -171 AGAAAGGTAAATCTTTCTTTTTCTCATAATATG 8 97 0 ACTTCTTTTC 0.751376 -92 AGAAAGATTTACCTTTCTTTTTCTTTTTTTTGC 8 112 1 ACTTCTTTTC 0.751376 -77 CCCAGACGTTCACATATGTTTCCATCATACTTG 9 42 0 CCTATTTTCC 0.956958 -32 GTAATAATCTCCTTTTTTTACACTTTTCGCT 10 9 1 CCTTTTTTAC 0.748045 -125 TTTTTTTTCTCTCGTACCATTCCCTTCACCTCC 11 162 1 CCTACATTCC 0.862519 -106 CATTGTGATCCTCCTTTGGTTTCTGTTCATTTT 12 214 1 CCTTTGTTTC 0.763769 -87 * * *** ***** Masking position 10 Map Score: 5.74034 Number of sites scoring better than the average of aligned sites = 1514 Number in coding regions = 1302 Number in noncoding regions = 212 Number of orfs with sites within 600 bp upstream = 243 Fraction of orfs with sites within 600 bp upstream = 0.0390299 Motif number 11 ATTCATTCACTTAAGGGGTGGGAGA 3 102 1 TTAAGGGGTG 0.865488 -15 GGCGCAGGTCAGATGGGGAGCGGAATTGCT 4 62 1 AGATGGGGAG 0.744969 -88 ATGTGCGGATGTATGATGTGAATCCAGAGG 4 116 1 GTATGATGTG 0.723823 -34 TCTATCTTCTGAATGAGGTGAAACC 5 123 1 GAATGAGGTG 0.9584 -15 AAACTTTAGGGTTTGAGGTGAAACG 6 64 1 GTTTGAGGTG 0.808467 -15 AAAAATTTGAGAATAGGGTGAGCAAATCGT 7 53 0 GAATAGGGTG 0.91202 -248 CCAAACATCAGGAAGAGGTGGTCAT 7 286 1 GGAAGAGGTG 0.961156 -15 TCTGCTATAATGATAAGGTGGATCTCTAAA 8 151 1 TGATAAGGTG 0.668075 -38 CTCTAAAATCGAAAGGGGAGGTTTT 8 174 1 GAAAGGGGAG 0.919113 -15 CGCGGCGAGCGTAAAGGGAGATGCCGGTCC 11 111 0 GTAAAGGGAG 0.806753 -157 ********** Masking position 8 Map Score: 3.19441 Number of sites scoring better than the average of aligned sites = 610 Number in coding regions = 438 Number in noncoding regions = 172 Number of orfs with sites within 600 bp upstream = 152 Fraction of orfs with sites within 600 bp upstream = 0.0244137 Motif number 12 CATTCATAGAAGACAACTAGAAATTGTAAG 5 88 1 AGACAACTAG 0.908588 -50 TTCAGAAGATAGACAGCGCTTACAATTTCT 5 106 0 AGACAGCGCT 0.960276 -32 GTTGTTAGAAAGATAACGAGCAGATTTGTC 7 155 0 AGATAACGAG 0.908588 -146 GAATTTGTAAAGACAACGCGAATGCAGGCG 7 233 0 AGACAACGCG 0.991516 -68 CTTCAGCGGCAGTCAGCGCGGCGAGCGTAA 11 127 0 AGTCAGCGCG 0.974584 -141 ********** Masking position 5 Map Score: 0.587051 Number of sites scoring better than the average of aligned sites = 118 Number in coding regions = 110 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 13 ********** No masking Map Score: 1.77879e-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 14 ********** No masking Map Score: 1.77879e-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: 1.77879e-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