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_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 yitJ 300 similar to hypothetical proteins #2 metC 300 cobalamin-independent methionine synthase #3 metB 300 homoserine O-succinyltransferase #4 glyA 206 serine hydroxymethyltransferase #5 ywlF 156 alternate gene name: ipc-32d; similar to ribose 5-phosphate epimerase (pentose phosphate) #6 ywlE 75 alternate gene name: ipc-31d; similar to protein-tyrosine-phosphatase #7 ywlD 78 alternate gene name: ipc-30d; similar to hypothetical proteins #8 ywlC 156 alternate gene name: ipc-29d; similar to hypothetical proteins #9 ywlB 66 alternate gene name: ipc-28d #10 spoIIR 140 alternate gene name: ipc-27d, csfX Motif number 1 GGTAAATTTGGAGAAAGGGAAAAACGCCAGA 1 34 1 GGAAAGGGAA 0.837488 -267 CGTTCTTATCAAGAGAAGCAGAGGGACTGGC 1 102 1 AGAGAAGCAG 0.914419 -199 ACATCAGCAAGGAAAAAAGAGAAATAAAAAA 1 262 0 GAAAAAAGAG 0.881071 -39 TTGCTGATGTGAATAAAGGAGGCAGACA 1 283 1 GATAAAGGAG 0.826572 -18 CAGTCTCGGCGCGAAAAGCAGTGCGCCCCAT 2 99 0 GGAAAAGCAG 0.968677 -202 TCTGAGAGATGAGAGAGGCAGTGTTTTACGT 2 169 1 GGAGAGGCAG 0.93748 -132 TCTTTCCCATGAGAGAAAGAGGCTTTTCTAC 2 198 0 GGAGAAAGAG 0.97413 -103 TCTTTCTCTCATGGGAAAGAGGCTTTTTGTT 2 209 1 AGGGAAAGAG 0.684131 -92 CTGTATCCGCGGGTGAAAGAGAGTGTTTTAC 2 261 1 GGTGAAAGAG 0.937588 -40 AGTGTTTTACATATAAAGGAGGAGAAACA 2 282 1 AATAAAGGAG 0.505233 -19 TTTCAAAGATGTAAGAGGGAATTGTAATGTT 3 127 0 GAAGAGGGAA 0.725013 -174 TACGTGTTGAGGGGGAAACAACAGAAAACTC 3 206 0 GGGGAAACAA 0.790741 -95 CAATAGTGATGGTAAAAACAAAGAACAGGAT 4 163 1 GTAAAAACAA 0.503427 -44 TGCAAATCCTGCGTGAAGGAGTAGAATATAG 5 40 1 GGTGAAGGAG 0.960357 -117 GTAGAATATAGTGAAAAGCACATCATATGGT 5 60 1 GGAAAAGCAC 0.766832 -97 ACACGCTGGGAGGAAAAGCAG 5 146 1 AGAAAAGCAG 0.868867 -11 TTATATATGAAGAAAAAAGAAACGGCGACTT 6 30 0 AAAAAAAGAA 0.419435 -46 AGGATTACACGCGTAAAACAATCGTTTTATT 8 110 1 GGTAAAACAA 0.776902 -47 CTCATAGATTGGAAGAAAGAACGCAAAAACG 9 36 1 GAAGAAAGAA 0.844663 -31 CCATAATAGGGCTAGAAACAAAGCACGGAGA 10 104 1 GTAGAAACAA 0.620471 -37 * ********* Masking position 6 Map Score: 14.6277 Number of sites scoring better than the average of aligned sites = 2991 Number in coding regions = 2450 Number in noncoding regions = 541 Number of orfs with sites within 600 bp upstream = 496 Fraction of orfs with sites within 600 bp upstream = 0.0796659 Motif number 2 TTCTCTTGATAAGAACGGATATGAAATTTTCGTG 1 85 0 AAAACGGAGA 0.938049 -216 AACAGCTTGGAAGATAAGAAGAGACAAAATCACT 1 202 1 AAATAAGAGA 0.914961 -99 TCACATCAGCAAGGAAAAAAGAGAAATAAAAAAA 1 261 0 AAGAAAAAGA 0.735991 -40 GTGTTTTACATATAAAGGAGGAGAAACA 2 283 1 TAAAAGGAGA 0.768155 -18 TCAAAATGTAAACATCAATTAAGAACTCATAAGA 3 24 1 AAATCAATGA 0.312289 -277 ATAGAATGATAAGATAAAAAACGAGCCATATGAA 3 91 0 AAATAAAAGA 0.869979 -210 ACTATCTTAAAATAAAAGAAAAGACTGGCTATGC 4 18 0 AAAAAAGAGA 0.968484 -189 CGTTTTTACCAATAAAAATTTAGATTTTTTAAAA 4 96 1 AAAAAAATGA 0.768343 -111 TGATGGTAAAAACAAAGAACAGGATACGGATAGG 4 169 1 AAAAAGAAGA 0.960128 -38 ATATGGTGTGAATCAAAGAGCGGACAGGCTGCGC 5 84 1 AACAAAGAGA 0.891889 -73 TATACCAATAAAAGAAACGAAGTCGCCGTT 6 7 1 AAAAAAGAGA 0.968484 -69 ATATATGAAGAAAAAAGAAACGGCGACTTCGTTT 6 25 0 AAAAAGAAGC 0.753319 -51 ATAATAGAGAAAAATAAGGGGTGACTGAC 6 57 1 AAATAAGGGA 0.61082 -19 GGACAACGCTAATAAAGAAGTGGATAAGTATGTG 8 23 0 AAAAAGAAGA 0.960128 -134 CATAGATTGGAAGAAAGAACGCAAAAACGGGGTG 9 38 1 AAAAAGAAAA 0.560019 -29 GCTAGAAACAAAGCACGGAGAGGAACGGTGGGGA 10 114 1 AACACGGAGA 0.802562 -27 ** ****** ** Masking position 2 Map Score: 10.3953 Number of sites scoring better than the average of aligned sites = 1375 Number in coding regions = 1080 Number in noncoding regions = 295 Number of orfs with sites within 600 bp upstream = 300 Fraction of orfs with sites within 600 bp upstream = 0.048185 Motif number 3 TATCAAGAGAAGCAGAGGGACTGGCCCGACGAA 1 108 1 AGCAGGGCTG 0.985533 -193 CGGCGCGAAAAGCAGTGCGCCCCATTTCACAAT 2 91 0 AGCAGGGCCC 0.990829 -210 AAAACCTCTTAGCAGCCTGTATCCGCGGGTGAA 2 245 1 AGCAGCGATC 0.952992 -56 TGAATCAAAGAGCGGACAGGCTGCGCGGTCAAT 5 92 1 AGCGGCGCTG 0.990751 -65 CGGTCAATAAAGCGGGCGGGCCGCATCACACAC 5 117 1 AGCGGCGCCG 0.994149 -40 AGGCTAAAAAAGCGGGGCGTGTCCAAGGGGGTT 7 48 1 AGCGGGGGTC 0.980193 -31 AGAACGCAAAAACGGGGTGAACGG 9 53 1 AACGGGGACG 0.968367 -14 CACGGAGAGGAACGGTGGGGACCG 10 127 1 AACGGGGACC 0.968367 -14 ***** * * *** Masking position 1 Map Score: 6.92886 Number of sites scoring better than the average of aligned sites = 314 Number in coding regions = 287 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 4 TCCTCTTAAGAAGAAGACTTTGTCAGTGATT 1 229 0 AAGAAGCTTT 0.870783 -72 TCTTCTTCTTAAGAGGACTTTTTTTATTTCT 1 243 1 AAGAGGCTTT 0.981104 -58 CCATGAGAGAAAGAGGCTTTTCTACGTAAAA 2 192 0 AAGAGGTTTT 0.98636 -109 TCTCATGGGAAAGAGGCTTTTTGTTGTGAGA 2 215 1 AAGAGGTTTT 0.98636 -86 ACAGGCTGCTAAGAGGTTTTCTCACAACAAA 2 234 0 AAGAGGTTTC 0.960489 -67 GCGGGTGAAAGAGAGTGTTTTACATATAAAG 2 269 1 GAGAGTTTTT 0.90498 -32 GTTTTATTTAAAGAGTTTTCTGTTGTTTCCC 3 194 1 AAGAGTTTCT 0.904988 -107 GCCGATGTAAAAGATTATTTTTAAAAAATCT 4 117 0 AAGATTTTTT 0.82277 -90 ****** **** Masking position 4 Map Score: 5.88939 Number of sites scoring better than the average of aligned sites = 163 Number in coding regions = 119 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 5 CTGAAGCTTCGTCGGGCCAGTCCCTCTGCTTCT 1 115 0 GTGCCAGTCC 0.915344 -186 AAACCTCTTAGCAGCCTGTATCCGCGGGTGAAA 2 246 1 GCCTGTATCC 0.845049 -55 AAGGACTGCATAGCCAGTCTTTTCTTTTAT 4 8 1 GCGCCAGTCT 0.915316 -199 GAGATCCTCTCCTATCCGTATCCTGTTCTTTGT 4 180 0 CCCCGTATCC 0.945293 -27 TTTATTGACCGCGCAGCCTGTCCGCTCTTTGAT 5 95 0 GCGCCTGTCC 0.996074 -62 GCTTTTTTAGCCTATGCGTGTCCAAAAAGGGTT 7 28 0 CCGCGTGTCC 0.99193 -51 GGCTAAAAAAGCGGGGCGTGTCCAAGGGGGTTA 7 49 1 GCGCGTGTCC 0.99713 -30 TTTATCCCAGGCTCTCCTTGTCCATAATAGGGC 10 83 1 GCCCTTGTCC 0.976141 -58 ** ******** Masking position 11 Map Score: 4.78273 Number of sites scoring better than the average of aligned sites = 205 Number in coding regions = 181 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 6 AGATATCTGGCGTTTTTCCCTTTCTCCAAA 1 40 0 CGTTTTTCCC 0.985035 -261 TGTCTGCCTCCTTTATTCACATCAGCAAGG 1 281 0 CTTTATTCAC 0.769444 -20 CAACAAAAAGCCTCTTTCCCATGAGAGAAA 2 211 0 CCTCTTTCCC 0.844746 -90 TATTAATATTCGTTTTTACCAATAAAAATT 4 86 1 CGTTTTTACC 0.865823 -121 TCTTTATTAGCGTTGTCCACAATTTGTGGA 8 39 1 CGTTGTCCAC 0.925644 -118 ATAAAACAAGCGTTATCCACAAATTGTGGA 8 54 0 CGTTATCCAC 0.955001 -103 TGACCAAACTCCTTATTCACAACAATAAAA 8 134 0 CCTTATTCAC 0.901019 -23 CCGTTCACCCCGTTTTTGCGT 9 56 0 CGTTCACCCC 0.885438 -11 TCACCCTGCACGTTTATCCCAGGCTCTCCT 10 71 1 CGTTTATCCC 0.954129 -70 ********** Masking position 3 Map Score: 4.23917 Number of sites scoring better than the average of aligned sites = 484 Number in coding regions = 429 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 7 TACCATTGTGAAATGGGGCGCACTGCTTTT 2 87 1 AAATGGGGCG 0.972076 -214 CTGATGTCTCATAAGGCACGGTGCTAATTC 2 127 1 ATAAGGCACG 0.819975 -174 TTATCAATTCATATGGCTCGTTTTTTATCT 3 84 1 ATATGGCTCG 0.855717 -217 CTGTGAAACCAAAAGGCGTGTCAGTGCGTT 3 167 1 AAAAGGCGTG 0.972845 -134 ATAGATTGAAAATTGGCGTGAAAATTCCTA 3 240 1 AATTGGCGTG 0.893159 -61 AAAGCACATCATATGGTGTGAATCAAAGAG 5 74 1 ATATGGTGTG 0.899386 -83 ATAGAGAAAAATAAGGGGTGACTGAC 6 60 1 ATAAGGGGTG 0.964633 -16 AAGAACGCAAAAACGGGGTGAACGG 9 52 1 AAACGGGGTG 0.941173 -15 ********** Masking position 1 Map Score: 3.98117 Number of sites scoring better than the average of aligned sites = 297 Number in coding regions = 263 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 8 GTGATTTTGTCTCTTCTTATCTTCCAAGCT 1 205 0 CTCTTCTTAT 0.738885 -96 CTTAAGAGGACTTTTTTTATTTCTCTTTTT 1 250 1 CTTTTTTTAT 0.72008 -51 CATATCGTTAGGTTTCTTATGAGTTCTTAA 3 42 0 GGTTTCTTAT 0.756254 -259 TCATATGGCTCGTTTTTTATCTTATCATTC 3 92 1 CGTTTTTTAT 0.912166 -209 CGTGTCAGTGCGTTTTATTTAAAGAGTTTT 3 183 1 CGTTTTATTT 0.813791 -118 ATTATTTCCCCGTTTAATTTTCTTCATTAT 3 269 0 CGTTTAATTT 0.633652 -32 CATAGCCAGTCTTTTCTTTTATTTTAAGAT 4 19 1 CTTTTCTTTT 0.917775 -188 ACGGCGACTTCGTTTCTTTTATTGGTATA 6 10 0 CGTTTCTTTT 0.97829 -66 ACGAAGTCGCCGTTTCTTTTTTCTTCATAT 6 27 1 CGTTTCTTTT 0.97829 -49 TTGTGGATAACGCTTGTTTTATTACAGGAC 8 62 1 CGCTTGTTTT 0.891017 -95 AACAATAAAACGATTGTTTTACGCGTGTAA 8 114 0 CGATTGTTTT 0.749838 -43 ********** Masking position 5 Map Score: 7.50117 Number of sites scoring better than the average of aligned sites = 849 Number in coding regions = 701 Number in noncoding regions = 148 Number of orfs with sites within 600 bp upstream = 157 Fraction of orfs with sites within 600 bp upstream = 0.0252168 Motif number 9 CTTGCTGGATTTAGCACCTTGGTCATGGCTG 1 167 0 TTACACCTTG 0.957309 -134 CCAGCAAGCTCGAACAGCTTGGAAGATAAGA 1 190 1 CGACAGCTTG 0.952888 -111 TCTGATGGAATTAGCACCGTGCCTTATGAGA 2 133 0 TTACACCGTG 0.960329 -168 AGAAAACCTCTTAGCAGCCTGTATCCGCGGG 2 243 1 TTACAGCCTG 0.982864 -58 CTTTATTGACCGCGCAGCCTGTCCGCTCTTT 5 98 0 CGCCAGCCTG 0.955264 -59 CTGCTTTTCCTCCCAGCGTGTGTGATGCGG 5 137 0 CTCCAGCGTG 0.962892 -20 ATAAATAAGATTAACAGCTTGCTAGATTTTT 10 39 1 TTACAGCTTG 0.973321 -102 TGCTAGATTTTTTTCACCCTGCACGTTTATC 10 58 1 TTTCACCCTG 0.896898 -83 *** ******* Masking position 6 Map Score: 6.65527 Number of sites scoring better than the average of aligned sites = 234 Number in coding regions = 214 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 10 CCGACCGTAATACCATTGTGAAATGGGGCG 2 77 1 TACCATTGTG 0.930757 -224 GCTAATTCCATCAGATTGTGTCTGAGAGAT 2 149 1 TCAGATTGTG 0.882288 -152 TCTTTTATTTTAAGATAGTGAAATAAATTC 4 33 1 TAAGATAGTG 0.959724 -174 AAAAACCATGTACAATAGTGATGGTAAAAA 4 151 1 TACAATAGTG 0.926734 -56 TTATTTATGGTACGATAGTGTTTTAGGAGG 10 17 0 TACGATAGTG 0.981097 -124 ********** Masking position 5 Map Score: 0.530463 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 48 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 11 ********** No masking Map Score: -4.04056e-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: -4.04056e-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: -4.04056e-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