AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00271_bsub_reg_100.orf -o00271_bsub_100.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 metS 300 methionyl-tRNA synthetase #2 yjcI 300 similar to cystathionine gamma-synthase #3 metC 300 cobalamin-independent methionine synthase #4 ykrB 300 similar to formylmethionine deformylase #5 yloD 233 similar to guanylate kinase #6 yloI 80 similar to pantothenate metabolism flavoprotein #7 def 26 polypeptide deformylase #8 metB 300 homoserine O-succinyltransferase #9 yrhA 64 similar to cysteine synthase #10 yrrT 192 yrrT #11 metK 300 S-adenosylmethionine synthetase Motif number 1 GCTCCCGCCCAAAGGACGAGAGCGGCGATAA 1 250 0 AAAGGCGAGA 0.888088 -51 TCTTATCGTGAGAGGTGGAGGGACTGGCCCT 2 124 1 AGAGGGGAGG 0.993516 -177 TTTTACATATAAAGGAGGAGAAACA 3 286 1 AAAGGGGAGA 0.988759 -15 TGGCGTAATTAAAAGAGGAGGTTATGTAATA 4 13 1 AAAAGGGAGG 0.918953 -288 TGGATATGGTTACGGCGGAGGCTGCTGCAGT 4 48 1 TACGGGGAGG 0.976062 -253 AGCTGCTTATTTAGGTGGAGGCTGTTGCTAA 4 171 1 TTAGGGGAGG 0.967248 -130 AAATCATCCGATTGGCGGAGATGATATTGCC 5 117 0 ATTGGGGAGA 0.896832 -117 TGTAAAGTGCAGAGGGGGAGAATTCA 6 65 1 AGAGGGGAGA 0.986369 -16 CTATACGTGTTGAGGGGGAAACAACAGAAAA 8 209 0 TGAGGGGAAA 0.715282 -92 ACGGGGAAATAATGGAGGTGGCACG 8 286 1 AATGGGGTGG 0.866985 -15 TTTAGAGAAAAACGGAGGAGAACGTTCTCCC 9 15 0 AACGGGGAGA 0.97123 -50 CAACCTCTATTAAGGAGGAGGACATAT 9 48 1 TAAGGGGAGG 0.990675 -17 ATGACTTGTGAAAGCTGGAGGGTCAAGAC 10 9 0 AAAGCGGAGG 0.970984 -184 CGGGAGGCCTTGTGCAGGAGGAAGCAAATC 11 281 1 TGTGCGGAGG 0.848081 -20 ***** ***** Masking position 8 Map Score: 21.2437 Number of sites scoring better than the average of aligned sites = 532 Number in coding regions = 386 Number in noncoding regions = 146 Number of orfs with sites within 600 bp upstream = 160 Fraction of orfs with sites within 600 bp upstream = 0.0256987 Motif number 2 CTATTATCCTACTAAAAATCCTTTTAAATCAAGAC 1 18 1 AAAAACCTTT 0.919555 -283 AAAATTCGACACGAACAGACTTTTTTTATTTTCAT 1 94 1 AAACACTTTT 0.93427 -207 AATAATTAAAATTAAAAATCTTTAATGAAAATAAA 1 118 0 AAAAACTTTA 0.555498 -183 CCTTTTCAAAATAAAAACCCCTTCTTCATAAGAAG 2 261 0 AAAAACCTTT 0.919555 -40 AAAATTAATAACATTTTCTCTTATCGAGAGT 3 7 1 AAACATTCTT 0.756076 -294 GTGTTTTACGTAGAAAAGCCTCTTTCTCTCATGGG 3 189 1 TAAAACTCTT 0.826557 -112 TTTTCTCACAACAAAAAGCCTCTTTCCCATGAGAG 3 214 0 AAAAACTCTT 0.956511 -87 CCTTTATATGTAAAACACTCTCTTTCACCCGCGGA 3 266 0 TAACACTCTT 0.884634 -35 TCTATAAAACATTACAATTCCCTCTTACATCTTTG 8 120 1 AACAACCCTT 0.869582 -181 AATAAAACGCACTGACACGCCTTTTGGTTTCACAG 8 167 0 AGACACCTTT 0.801428 -134 AGGGGGAAACAACAGAAAACTCTTTAAATAAAACG 8 193 0 AAGAACTCTT 0.736521 -108 GTTTTTCTCTAAAAACAACCTCTATTAAGGAGGAG 9 33 1 AAACACTCTT 0.972591 -32 AAAAGCAGGTACTAAAACACTTTGTGTATTTTATG 10 84 0 AAAAACTTTT 0.898218 -109 GGATTAATGATGGAACAGTTCCTATAATACCACAT 10 125 0 TAACATCCTT 0.465215 -68 GAGCTGGCGGAGGGACAGGCCCTATGAAGCCCAGC 11 15 1 AGACACCCTT 0.909749 -286 GAAAGGCACAAAGACCAAACCCTTTCCTCGATGGA 11 145 1 AACCACCCTT 0.914811 -156 TATTTATGAAATAAAAAAACCTTTTCCATCGAGGA 11 169 0 AAAAACCTTT 0.919555 -132 AAATATGCCAATTAACATTCTCTAATATAACTGTA 11 199 1 AAACACTCTA 0.834105 -102 * **** **** * Masking position 13 Map Score: 17.5152 Number of sites scoring better than the average of aligned sites = 675 Number in coding regions = 516 Number in noncoding regions = 159 Number of orfs with sites within 600 bp upstream = 162 Fraction of orfs with sites within 600 bp upstream = 0.0260199 Motif number 3 AATGCAAAACAAGCCGGTTGCTGAGGTTTCTAA 2 154 0 ACCGGTGCTG 0.98228 -147 ATTTGCAAAGCGCCAAGGTGCTAAATCCAGCAA 2 184 1 CCAAGTGCTA 0.903623 -117 AATGGTATTACGGTCGGTTGCTGTTGGGGTCAA 3 61 0 CTCGGTGCTG 0.871976 -240 ATGTCTCATAAGGCACGGTGCTAATTCCATCAG 3 130 1 ACACGTGCTA 0.948247 -171 TCACCCGCGGATACAGGCTGCTAAGAGGTTTTC 3 244 0 ACAGGTGCTA 0.991011 -57 CAAACGGATGATTCAGGATGCAAGAGACCGCGG 5 176 1 ACAGGTGCAA 0.939695 -58 AACCTACATGATATAGGTTGCTACTTGTGCTA 6 10 0 ATAGGTGCTA 0.968989 -71 AACCTATATCATGTAGGTTGTTATTTTTTTCCG 6 24 1 ATAGGTGTTA 0.731898 -57 AATAACAGAGAAACCGGTTGCTGGGCTTCATAG 11 36 0 ACCGGTGCTG 0.98248 -265 TGAGTGAGACAACCAAGGTGCTAACCTGTTGCA 11 82 1 ACAAGTGCTA 0.956143 -219 * **** ***** Masking position 9 Map Score: 9.62236 Number of sites scoring better than the average of aligned sites = 234 Number in coding regions = 208 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 4 TAATCAAATGAAATAAAAAACTTTGGTTCGA 1 55 0 AATAAAAAAC 0.957028 -246 TCTTTAATGAAAATAAAAAAAGTCTGTTCGT 1 104 0 AATAAAAAAA 0.877799 -197 AATTGCGCTAATATAAAACAATCAGAAAATT 2 81 1 AATAAAACAA 0.906013 -220 TATCTTCCAAGCATAAAAAACGCTTGCTGGA 2 209 0 GATAAAAAAC 0.925653 -92 TCCCTTTTCAAAATAAAAACCCCTTCTTCAT 2 267 0 AATAAAAACC 0.807471 -34 AGGCTTTTCTACGTAAAACACTGCCTCTCTC 3 179 0 AGTAAAACAC 0.911956 -122 CCTCCTTTATATGTAAAACACTCTCTTTCAC 3 273 0 AGTAAAACAC 0.911954 -28 TTAACAGAATGAATAAAACAACGATTAGCGC 4 130 0 GATAAAACAA 0.843483 -171 TAGAATGATAAGATAAAAAACGAGCCATATG 8 93 0 AATAAAAAAC 0.957028 -208 AAAACTCTTTAAATAAAACGCACTGACACGC 8 182 0 AATAAAACGC 0.849132 -119 ATATGAGATGGCATAAAATACACAAAGTGTT 10 73 1 GATAAAATAC 0.721038 -120 CATATTTATGAAATAAAAAAACCTTTTCCAT 11 175 0 AATAAAAAAA 0.877799 -126 * ********* Masking position 6 Map Score: 11.0149 Number of sites scoring better than the average of aligned sites = 241 Number in coding regions = 167 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 5 GCGCCAAGGTGCTAAATCCAGCAAGCGTTT 2 193 1 GCTAAATCCA 0.927558 -108 AAGGCACGGTGCTAATTCCATCAGATTGTG 3 139 1 GCTAATTCCA 0.69647 -162 CTCCGCCGTAACCATATCCATACATATTAC 4 38 0 ACCATATCCA 0.909232 -263 ATCCGCAGCCACCATATCCGTAACCACCAT 4 80 0 ACCATATCCG 0.951646 -221 TGCGGCCGTAGCCATATCCGCAGCCACCAT 4 95 0 GCCATATCCG 0.990094 -206 AAATTGACCAGCCATATACGGCTGGTCATT 4 214 1 GCCATATACG 0.951645 -87 AGATGATATTGCCAAATCCGATATTAATCA 5 100 0 GCCAAATCCG 0.987139 -134 GCTAATTGACGCTACATACGGACGAAGAAC 5 212 1 GCTACATACG 0.842456 -22 CGTGCCACCTCCATTATTTCCCC 8 288 0 GCCACCTCCA 0.918044 -13 ********** Masking position 4 Map Score: 7.41314 Number of sites scoring better than the average of aligned sites = 494 Number in coding regions = 456 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 6 GAATGTCAAAAAGCTCCCGCCCAAAGGACGA 1 262 0 AGCTCCCGCC 0.868101 -39 TGAGAGGTGGAGGGACTGGCCCTTAGAAACC 2 132 1 AGGACTGGCC 0.985959 -169 GAGTTGGGCGAGGGATTGGCCTTTTGACCCC 3 38 1 AGGATTGGCC 0.901076 -263 GATTAGCGCAAAGGTGCGGCCGTAGCCATAT 4 108 0 AGGTGCGGCC 0.936005 -193 ACAGCATGAAATTGACCAGCCATATACGGCT 4 206 1 ATGACCAGCC 0.96485 -95 CAACGAAACGAATGACCAGCCGTATATGGCT 4 223 0 ATGACCAGCC 0.96485 -78 AATAAAACGCACTGACACGCCTTTTGGTTTC 8 171 0 ATGACACGCC 0.934842 -130 GAGCTGGCGGAGGGACAGGCCCTATGAAGCC 11 15 1 AGGACAGGCC 0.98596 -286 * ********* Masking position 1 Map Score: 3.7481 Number of sites scoring better than the average of aligned sites = 184 Number in coding regions = 167 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 7 AATATTCATATATGATTTGCACTTATCGCCG 1 228 1 TTGATTTGCA 0.839625 -73 TTTTTGACATTCTGATTAGGAGGTTTCAAG 1 281 1 TTGATTAGGA 0.729584 -20 TGAAATAAACTGTGAATTGCGCTAATATAAA 2 67 1 TTGAATTGCG 0.968206 -234 TTGTTTTGCATTTGCAAAGCGCCAAGGTGCT 2 175 1 TTGCAAAGCG 0.852401 -126 GGGTTTTTATTTTGAAAAGGGAAGGTGTCAG 2 276 1 TTGAAAAGGG 0.92721 -25 GTAATACCATTGTGAAATGGGGCGCACTGCT 3 83 1 TTGAAATGGG 0.92721 -218 GAATCATCCGTTTGATTGGCGCAGACTCCGG 5 159 0 TTGATTGGCG 0.877991 -75 ATGTTTACATTTTGAATTGCGATTTAAA 8 8 0 TTGAATTGCG 0.968206 -293 TACCACATATTCTGAAAAGCAGGTACTAAAA 10 102 0 TTGAAAAGCA 0.890121 -91 * ********* Masking position 3 Map Score: 2.87848 Number of sites scoring better than the average of aligned sites = 308 Number in coding regions = 259 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 8 GGTTTCTAAGGGCCAGTCCCTCCACCTCTC 2 133 0 GGCCAGTCCC 0.996316 -168 GGGGTCAAAAGGCCAATCCCTCGCCCAACT 3 39 0 GGCCAATCCC 0.994262 -262 GGCTTCATAGGGCCTGTCCCTCCGCCAGCT 11 16 0 GGCCTGTCCC 0.99065 -285 AAGGCACAAAGACCAAACCCTTTCCTCGAT 11 147 1 GACCAAACCC 0.945972 -154 ********** Masking position 4 Map Score: 2.79708 Number of sites scoring better than the average of aligned sites = 28 Number in coding regions = 20 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 9 ATATGATTTGCACTTATCGCCGCTCTCGTC 1 237 1 CACTTATCGC 0.843048 -64 AAATCGATATTTCTTATCGTGAGAGGTGGA 2 113 1 TTCTTATCGT 0.762349 -188 ATAACATTTTCTCTTATCGAGAGTTGGGCG 3 18 1 CTCTTATCGA 0.809985 -283 AGACTGATGTCTCATAAGGCACGGTGCTAA 3 124 1 CTCATAAGGC 0.876672 -177 TGAACTGACGCTCATATCGTTAGGTTTCTT 8 54 0 CTCATATCGT 0.9167 -247 TCATTATCAATTCATATGGCTCGTTTTTTA 8 81 1 TTCATATGGC 0.950202 -220 AAGCTTATACTTCATATGACTTGTGAAAGC 10 25 0 TTCATATGAC 0.61899 -168 TTTATGCCATCTCATATTGCGCATTGACCG 10 60 0 CTCATATTGC 0.896327 -133 GTTGCTGGGCTTCATAGGGCCTGTCCCTCC 11 23 0 TTCATAGGGC 0.818123 -278 GTGCCTTTCACTCTTATCGCTCAAGGAATC 11 124 0 CTCTTATCGC 0.974472 -177 ********** Masking position 5 Map Score: 4.76291 Number of sites scoring better than the average of aligned sites = 313 Number in coding regions = 267 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 10 ********** No masking Map Score: -4.64452e-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 AGAGATGAGAGAGGCAGTGTTTTACGTAGA 3 173 1 GAGGCAGTGT 0.86997 -128 ATGAGAGAAAGAGGCTTTTCTACGTAAAAC 3 191 0 GAGGCTTTTC 0.903269 -110 TCATGGGAAAGAGGCTTTTTGTTGTGAGAA 3 217 1 GAGGCTTTTT 0.97559 -84 AGGCTGCTAAGAGGTTTTCTCACAACAAAA 3 233 0 GAGGTTTTCT 0.901611 -68 ATTAAAAGAGGAGGTTATGTAATATGTATG 4 20 1 GAGGTTATGT 0.870106 -281 TATTTAGGTGGAGGCTGTTGCTAACCACAC 4 178 1 GAGGCTGTTG 0.885087 -123 TTTTTTCCGTGCGGTTTTGTAAAGTGCAGA 6 48 1 GCGGTTTTGT 0.870616 -33 CTCCTTAATAGAGGTTGTTTTTAGAGAAAA 9 35 0 GAGGTTGTTT 0.953858 -30 CTCGATGGAAAAGGTTTTTTTATTTCATAA 11 171 1 AAGGTTTTTT 0.68648 -130 GGTCTTTCGGGAGGCCTTGTGCAGGAGGAA 11 274 1 GAGGCCTTGT 0.923207 -27 ********** Masking position 8 Map Score: 3.9493 Number of sites scoring better than the average of aligned sites = 370 Number in coding regions = 264 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 12 ********** No masking Map Score: -4.64452e-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 GCCCTGAAAAAGAATAATTAAAATTAAAAATCTT 1 131 0 AATATTAAAT 0.914316 -170 CTTAGCCTTTAAGATCAAGAATATATACATACGC 1 163 0 AATAAGAAAT 0.907102 -138 ATAAAGGATAAATATAAATAATATTCATATATGA 1 209 1 AATAATAAAT 0.945171 -92 AAAATTAATAACATTTTCTCTTAT 3 1 1 AATAATAAAT 0.945192 -300 AGCAGCTCCGACAATGATTAACAGAATGAATAAA 4 144 0 AATATTAAAG 0.858907 -157 GATGACGATTAAACTGATTAATATCGGATTTGGC 5 86 1 ACTATTAAAT 0.740597 -148 GAAAATTCCTATAATGAAGAAAATTAAACGGGGA 8 259 1 AATAAGAAAT 0.907085 -42 TCAGTTGAACATAATAAATAACAGAGAAACCGGT 11 51 0 AATAATAAAG 0.907092 -250 * ** ***** ** Masking position 7 Map Score: 0.560657 Number of sites scoring better than the average of aligned sites = 191 Number in coding regions = 145 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 14 TATATACATACGCCCTGAAAAAGAATAATTAAAA 1 142 0 CCCCTGAAAA 0.970204 -159 TGTCAAAAAGCTCCCGCCCAAAGGACGAGAGCGG 1 256 0 CCCCGCAAAG 0.956757 -45 AACGGTTCGGCACACGAAGAAAAAAGTGTTGAAA 2 38 1 CCACGAAAAA 0.935282 -263 CCCTCCACCTCTCACGATAAGAAATATCGATTTC 2 112 0 CCACGAAGAA 0.840871 -189 CACTCTCTTTCACCCGCGGATACAGGCTGCTAAG 3 252 0 CCCCGCATAA 0.973146 -49 CTTCTACGTTCCCCCTGTAAAATAGACGTCTCTA 5 53 0 CCCCTGAAAA 0.970204 -181 TTTACAAAACCGCACGGAAAAAAATAACAACCTA 6 37 0 CCACGGAAAA 0.970204 -44 ACGGAACTCGCTCCCTCTTATACAATGTACAGTT 11 227 0 CCCCTCATAA 0.93406 -74 * ***** *** * Masking position 10 Map Score: 1.58417 Number of sites scoring better than the average of aligned sites = 157 Number in coding regions = 138 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 15 ********** No masking Map Score: -4.64452e-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