AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -imetR_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 yitJ 300 similar to hypothetical proteins #2 metC 300 cobalamin-independent methionine synthase #3 metB 300 homoserine O-succinyltransferase #4 glyA 206 serine hydroxymethyltransferase Motif number 1 TATCTTTTGGCACTTCCTGACACGAAAATTTCAT 1 65 1 CACTCCTCCG 0.990827 -236 GGGCCAGTCCCTCTGCTTCTCTTGATAAGAACGG 1 101 0 CTCTCTTCTG 0.990317 -200 GTGATTTTGTCTCTTCTTATCTTCCAAGCTGTTC 1 201 0 CTCTCTTCTC 0.944221 -100 TTTTTTATTTCTCTTTTTTCCTTGCTGATGTGAA 1 262 1 CTCTTTTCTG 0.974078 -39 GTCAAAAGGCCAATCCCTCGCCCAACTCTCGATA 2 32 0 CAATCCTCCA 0.706012 -269 AAATGGGGCGCACTGCTTTTCGCGCCGAGACTGA 2 97 1 CACTCTTCCG 0.991416 -204 CTACGTAAAACACTGCCTCTCTCATCTCTCAGAC 2 168 0 CACTCCTCCA 0.968232 -133 GTAGAAAAGCCTCTTTCTCTCATGGGAAAGAGGC 2 198 1 CTCTTCTCTG 0.972332 -103 ATGTAAAACACTCTCTTTCACCCGCGGATACAGG 2 260 0 CTCTTTTCCG 0.980555 -41 TTTTTACCATCACTATTGTACATGGTTTTTAAGG 4 147 0 CACTTTGCTG 0.868327 -60 CAGCGAGATCCTCTCCTATCCGTATCCTGTTCTT 4 183 0 CTCTCTACTA 0.802398 -24 **** *** * ** Masking position 4 Map Score: 13.4712 Number of sites scoring better than the average of aligned sites = 313 Number in coding regions = 269 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 2 AGATATCTTTTGGCACTTCCTGACACGAAAATTTCATAT 1 62 1 TGACTCAAAA 0.825084 -239 CTGCTTCTCTTGATAAGAACGGATATGAAATTTTCGTGT 1 84 0 TGAAACAAAA 0.987859 -217 AGATAAGAAGAGACAAAATCACTGACAAAGTCTTCTTCT 1 213 1 AGAAACTAAA 0.939207 -88 CACATCAGCAAGGAAAAAAGAGAAATAAAAAAAGTCCTC 1 255 0 AGAAAGAAAA 0.766707 -46 CTTTTTGTTGTGAGAAAACCTCTTAGCAGCCTGTATCCG 2 231 1 TGAAACTAAG 0.975352 -70 CAATTCAAAATGTAAACATCAATTAAGAACTCATAAGAA 3 20 1 TGAAACTAAA 0.982325 -281 TTTTATAGAATGATAAGATAAAAAACGAGCCATATGAAT 3 90 0 TGAAAAAAAG 0.850289 -211 AAAATTGGCGTGAAAATTCCTATAATGAAGAAAATTAAA 3 248 1 TGAATCTAAA 0.939207 -53 AAATTTTTATTGGTAAAAACGAATATTAATAACTTAAAT 4 78 0 TGAAACAAAA 0.987858 -129 ACAATAGTGATGGTAAAAACAAAGAACAGGATACGGATA 4 162 1 TGAAACAAAG 0.983032 -45 ** ** * * * * ** Masking position 5 Map Score: 6.97396 Number of sites scoring better than the average of aligned sites = 252 Number in coding regions = 211 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 3 AAAAACGCCAGATATCTTTTGGCACTTCCTG 1 53 1 GTATCTTTTG 0.854208 -248 CCATTACACCGGTTGCTGAAGCTTCGTCGGG 1 132 0 GTTGCTGAAG 0.952197 -169 TCTCTTTTTTCCTTGCTGATGTGAATAAAGG 1 271 1 CTTGCTGATG 0.948573 -30 TATTACGGTCGGTTGCTGTTGGGGTCAAAAG 2 58 0 GTTGCTGTTG 0.992059 -243 TGGGAAAGAGGCTTTTTGTTGTGAGAAAACC 2 220 1 GTTTTTGTTG 0.930648 -81 CATATCGTTAGGTTTCTTATGAGTTCTTAAT 3 41 0 GTTTCTTATG 0.955897 -260 TATTTAAAGAGTTTTCTGTTGTTTCCCCCTC 3 198 1 GTTTCTGTTG 0.990427 -103 * ********* Masking position 7 Map Score: 5.03734 Number of sites scoring better than the average of aligned sites = 454 Number in coding regions = 424 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 4 TGTCTGCCTCCTTTATTCACATCAGC 1 285 0 CCTCCTTTAT 0.977158 -16 TAAAACACTGCCTCTCTCATCTCTCAGACA 2 167 0 CCTCTCTCAT 0.978984 -134 CGTAGAAAAGCCTCTTTCTCTCATGGGAAA 2 197 1 CCTCTTTCTC 0.89057 -104 CAACAAAAAGCCTCTTTCCCATGAGAGAAA 2 211 0 CCTCTTTCCC 0.923441 -90 TGTTTCTCCTCCTTTATATGTAAAACA 2 284 0 CCTCCTTTAT 0.977158 -17 ATTACAATTCCCTCTTACATCTTTGAAAAT 3 130 1 CCTCTTACAT 0.934945 -171 CGTGCCACCTCCATTATTTCCCCGTTT 3 284 0 CCTCCATTAT 0.913447 -17 CAGCGAGATCCTCTCCTATCCGTATCCTG 4 188 0 CCTCTCCTAT 0.900365 -19 ********** Masking position 3 Map Score: 6.46983 Number of sites scoring better than the average of aligned sites = 374 Number in coding regions = 260 Number in noncoding regions = 114 Number of orfs with sites within 600 bp upstream = 138 Fraction of orfs with sites within 600 bp upstream = 0.0221651 Motif number 5 CTTGCTGGATTTAGCACCTTGGTCATGGCTG 1 167 0 TTAGCACCTG 0.995975 -134 TCTGATGGAATTAGCACCGTGCCTTATGAGA 2 133 0 TTAGCACCTG 0.996008 -168 AGAAAACCTCTTAGCAGCCTGTATCCGCGGG 2 243 1 TTAGCAGCTG 0.992627 -58 ******** ** Masking position 6 Map Score: 1.50587 Number of sites scoring better than the average of aligned sites = 9 Number in coding regions = 2 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 6 TTAAGAGGACTTTTTTTATTTCTCTTTTTTC 1 251 1 TTTTTTTATT 0.806193 -50 GAGAGAGGCAGTGTTTTACGTAGAAAAGCCT 2 179 1 GTGTTTTACT 0.972753 -122 GTGAAAGAGAGTGTTTTACATATAAAGGAGG 2 273 1 GTGTTTTACT 0.972734 -28 CATATGGCTCGTTTTTTATCTTATCATTCTA 3 93 1 GTTTTTTATT 0.924872 -208 GGGAATTGTAATGTTTTATAGAATGATAAGA 3 111 0 ATGTTTTATG 0.765793 -190 GCGTGTCAGTGCGTTTTATTTAAAGAGTTTT 3 182 1 GCGTTTTATT 0.906338 -119 AGCCAGTCTTTTCTTTTATTTTAAGATAGTG 4 22 1 TTCTTTTATT 0.865491 -185 TTTAAAAATAATCTTTTACATCGGCCTTAAA 4 123 1 ATCTTTTACT 0.863111 -84 ********* * Masking position 8 Map Score: 2.36363 Number of sites scoring better than the average of aligned sites = 463 Number in coding regions = 358 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 Motif number 7 CAGTCCCTCTGCTTCTCTTGATAAGAACGG 1 101 0 GCTTCTCTTG 0.887836 -200 CTTGGTCATGGCTGATCGCCATTACACCGG 1 151 0 GCTGATCGCC 0.956591 -150 TATCTTCCAAGCTGTTCGAGCTTGCTGGAT 1 188 0 GCTGTTCGAG 0.964123 -113 TTTTGTCTCTTCTTATCTTCCAAGCTGTTC 1 201 0 TCTTATCTTC 0.737023 -100 TAACATTTTCTCTTATCGAGAGTTGGGCGA 2 19 1 TCTTATCGAG 0.915926 -282 GGGGCGCACTGCTTTTCGCGCCGAGACTGA 2 101 1 GCTTTTCGCG 0.97733 -200 AGAGAAAGAGGCTTTTCTACGTAAAACACT 2 188 0 GCTTTTCTAC 0.936392 -113 ********** Masking position 6 Map Score: 1.08349 Number of sites scoring better than the average of aligned sites = 692 Number in coding regions = 634 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 8 AAGAGAAGCAGAGGGACTGGCCCGACGAAGC 1 112 1 GAGGACTGGC 0.988333 -189 AGAAGAGACAAAATCACTGACAAAGTCTTCT 1 218 1 AATCACTGAC 0.938824 -83 AGAGTTGGGCGAGGGATTGGCCTTTTGACCC 2 37 1 GAGGATTGGC 0.916606 -264 TTTTCTACGTAAAACACTGCCTCTCTCATCT 2 175 0 AAACACTGCC 0.940735 -126 ATGAATTGATAATGAACTGACGCTCATATCG 3 65 0 AAGAACTGAC 0.952734 -236 CTTTAAATAAAACGCACTGACACGCCTTTTG 3 176 0 AAGCACTGAC 0.987667 -125 AAAATAAAAGAAAAGACTGGCTATGCAGTCC 4 13 0 AAAGACTGGC 0.977036 -194 ** ******** Masking position 6 Map Score: 4.3579 Number of sites scoring better than the average of aligned sites = 246 Number in coding regions = 227 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 9 CCAAGCTGTTCGAGCTTGCTGGATTTAGCAC 1 181 0 CGGCTTGCTG 0.962617 -120 CTTTTCGCGCCGAGACTGATGTCTCATAAGG 2 112 1 CGGACTGATG 0.977701 -189 GAATTAGCACCGTGCCTTATGAGACATCAGT 2 126 0 CGGCCTTATG 0.995305 -175 AGATAAAAAACGAGCCATATGAATTGATAAT 3 83 0 CGGCCATATG 0.984734 -218 AACGCACTGACACGCCTTTTGGTTTCACAGT 3 166 0 CAGCCTTTTG 0.941496 -135 ** ******** Masking position 10 Map Score: 0.63068 Number of sites scoring better than the average of aligned sites = 125 Number in coding regions = 109 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 10 ATATCTGGCGTTTTTCCCTTTCTCCAAATTTA 1 36 0 TTTTCCCTTC 0.987302 -265 GGACTTTTTTTATTTCTCTTTTTTCCTTGCTG 1 257 1 TTTTCTCTTT 0.903976 -44 TAAAACACTCTCTTTCACCCGCGGATACAGGC 2 259 0 TTTTCACCGC 0.963047 -42 TGTTTCTCCTCCTTTATATGTA 2 289 0 TTTTCTCCCC 0.963047 -12 AGTTTTCTGTTGTTTCCCCCTCAACACGTATA 3 207 1 TTTTCCCCTC 0.993812 -94 CCACCTCCATTATTTCCCCGTTTAATTTTCTT 3 275 0 TTTTCCCCTT 0.977683 -26 GTTCGGAATTTATTTCACTATCTTAAAATAAA 4 36 0 TTTTCACTTC 0.971839 -171 * ******* ** Masking position 5 Map Score: 6.26062 Number of sites scoring better than the average of aligned sites = 174 Number in coding regions = 144 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 11 ********** No masking Map Score: 1.67931e-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: 1.67931e-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: 1.67931e-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