AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00680_bsub_reg_300.orf -o00680_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 katA 300 vegetative catalase 1 #2 yraG 248 similar to spore coat protein #3 glyA 206 serine hydroxymethyltransferase #4 ywlF 156 alternate gene name: ipc-32d; similar to ribose 5-phosphate epimerase (pentose phosphate) #5 ywlE 75 alternate gene name: ipc-31d; similar to protein-tyrosine-phosphatase #6 ywlD 78 alternate gene name: ipc-30d; similar to hypothetical proteins #7 ywlC 156 alternate gene name: ipc-29d; similar to hypothetical proteins #8 ywlB 66 alternate gene name: ipc-28d #9 spoIIR 140 alternate gene name: ipc-27d, csfX #10 katX 128 catalase #11 katB 200 catalase 2 Motif number 1 TCCGATATGTCAACTCTTTTTTAAATACGATT 1 48 1 CCTCTTTTTT 0.96896 -253 ATTGATGTAACCTCCTTTTATCAACGTTACA 2 228 0 ATCCTTTTAT 0.610695 -21 CATAGCCAGTCTTTTCTTTTATTTTAAGATAG 3 19 1 CTTCTTTTAT 0.947242 -188 TATCCGTATCCTGTTCTTTGTTTTTACCATCA 3 169 0 CTTCTTTGTT 0.901738 -38 CGCAGCCTGTCCGCTCTTTGATTCACACCATA 4 85 0 CCTCTTTGAT 0.861485 -72 TGATGCGGCCCGCCCGCTTTATTGACCGCGCA 4 113 0 CCCGCTTTAT 0.758349 -44 ACGGCGACTTCGTTTCTTTTATTGGTATA 5 8 0 CTTCTTTTAT 0.947242 -68 ACGAAGTCGCCGTTTCTTTTTTCTTCATATAT 5 27 1 CTTCTTTTTT 0.966395 -49 GTCAGTCACCCCTTATTTTTCTCTATTA 5 58 0 CCCCTTATTT 0.815622 -18 GTCAGATGTTCTAACCCTTTTTGGACACGCAT 6 16 1 CACCCTTTTT 0.669052 -63 CTTGGACACGCCCCGCTTTTTTAGCCTATGCG 6 43 0 CCGCTTTTTT 0.930664 -36 CATACTTATCCACTTCTTTATTAGCGTTGTCC 7 25 1 CTTCTTTATT 0.697862 -132 TTGTGGATAACGCTTGTTTTATTACAGGACAT 7 62 1 CTTGTTTTAT 0.813999 -95 ACGCGTAAAACAATCGTTTTATTGTTGTGAAT 7 118 1 CTCGTTTTAT 0.905793 -39 CCGTTCACCCCGTTTTTGCGTTCTTTC 8 50 0 CCCCGTTTTT 0.88496 -17 CCGTTCCTCTCCGTGCTTTGTTTCTAGCCCTA 9 110 0 CTGCTTTGTT 0.797811 -31 GAATCGACCTCTCCTTTTACCGATTTTTGT 10 9 1 CTCCTTTTAC 0.790399 -120 GATTTTAAAACAGCCGTTTTTTTTGATCTGCT 10 59 0 CCCGTTTTTT 0.943557 -70 TGGTTGGCCCTCCTTTTTTGAACGGTAAC 10 110 0 CTCCTTTTTT 0.984419 -19 GTAAGCGCTTCCATCCTTTCTTTCTGTGAAGA 11 43 1 CTCCTTTCTT 0.882645 -158 GTCTGCTCCCCCTTTTTAAAACGAAAC 11 184 0 CCCCCTTTTT 0.95375 -17 * ********* Masking position 8 Map Score: 25.1328 Number of sites scoring better than the average of aligned sites = 1832 Number in coding regions = 1392 Number in noncoding regions = 440 Number of orfs with sites within 600 bp upstream = 449 Fraction of orfs with sites within 600 bp upstream = 0.0721169 Motif number 2 ATTTTTGATATCCTTGTTTATCACTTACTCT 1 77 1 TCCTTTTTAT 0.82366 -224 AAATAATTTTTCCTTCTCTATTTGCGAAACA 1 111 0 TCCTTTCTAT 0.901738 -190 TTTATACACATACTTATCCACTTCTTTATTA 7 17 1 TACTTTCCAC 0.899762 -140 TTCTTTATTAGCGTTGTCCACAATTTGTGGA 7 38 1 GCGTTTCCAC 0.983806 -119 AATAAAACAAGCGTTATCCACAAATTGTGGA 7 54 0 GCGTTTCCAC 0.983806 -103 CTGACCAAACTCCTTATTCACAACAATAAAA 7 134 0 TCCTTTTCAC 0.978993 -23 TCCCAGGCTCTCCTTGTCCATAATAGGGCTA 9 87 1 TCCTTTCCAT 0.978993 -54 TTTGAAATAAGCCTTCTTCACAGAAAGAAAG 11 58 0 GCCTTTTCAC 0.983606 -143 TTTACCCGTGGCGTTCTTCATATAAACTGCT 11 140 0 GCGTTTTCAT 0.940256 -61 ***** ***** Masking position 5 Map Score: 10.1616 Number of sites scoring better than the average of aligned sites = 445 Number in coding regions = 372 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 3 TCAAAAATCGTATTTAAAAAAGAGTTGACA 1 55 0 TATTTAAAAA 0.671791 -246 TAGAGATAACTATTTTATAATAATTATAAA 1 219 1 TATTTTATAA 0.886308 -82 AAGTCAATATTATTTTATAATTATTATAAA 1 232 0 TATTTTATAA 0.886308 -69 TATCATTTTTTGTTTTAAGAATCGCTGTTT 2 157 0 TGTTTTAAGA 0.961451 -92 TCTTTTCTTTTATTTTAAGATAGTGAAATA 3 28 1 TATTTTAAGA 0.948543 -179 TGTAAAAGATTATTTTTAAAAAATCTAAAT 3 113 0 TATTTTTAAA 0.810319 -94 GGATAACGCTTGTTTTATTACAGGACATCT 7 66 1 TGTTTTATTA 0.684709 -91 GAGGCAAATCTATTTTTAGACCAGATGA 8 9 0 TATTTTTAGA 0.822326 -58 GGTACGATAGTGTTTTAGGAGGTTTAAG 9 9 0 TGTTTTAGGA 0.869268 -132 AAAAAACGGCTGTTTTAAAATCTTTCCATT 10 69 1 TGTTTTAAAA 0.95838 -60 TAGAATGTTTCGTTTTAAAAAGGGGGAGCA 11 178 1 CGTTTTAAAA 0.813137 -23 ********** Masking position 10 Map Score: 6.43195 Number of sites scoring better than the average of aligned sites = 337 Number in coding regions = 255 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 4 CATGTTATTCAAACAAAAAAACA 1 4 0 AAACAAAAAA 0.810766 -297 ATAAACAAGGATATCAAAAATCGTATTTAA 1 68 0 ATATCAAAAA 0.877604 -233 CAATTTAATGATACCAAAGAAACCTGACAG 2 51 1 ATACCAAAGA 0.896375 -198 GCGATTCTTAAAACAAAAAATGATACCGAG 2 162 1 AAACAAAAAA 0.810766 -87 AAGTTGAAGCATACAGAAAATACACTCGGT 2 186 0 ATACAGAAAA 0.709363 -63 ATATTCGTTTTTACCAATAAAAATTTAGAT 3 91 1 TTACCAATAA 0.762124 -116 TATACCAATAAAAGAAACGAA 5 2 1 ATACCAATAA 0.92019 -74 TTCCCGAAGCAGATCAAAAAAAACGGCTGT 10 52 1 AGATCAAAAA 0.802385 -77 ATGGAAGCGCTTACCAAAAAAGCTGTTGAA 11 27 0 TTACCAAAAA 0.92019 -174 ATTTATATGTAGACCAAAAATCCTAATGAG 11 104 1 AGACCAAAAA 0.959164 -97 ********** Masking position 7 Map Score: 5.58457 Number of sites scoring better than the average of aligned sites = 381 Number in coding regions = 290 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 5 AAGACTGGCTATGCAGTCCTT 3 2 0 ATGCAGTCCT 0.916637 -205 AGGACTGCATAGCCAGTCTTTTCTTTTATT 3 12 1 AGCCAGTCTT 0.854306 -195 TCCTATCCGTATCCTGTTCTTTGTTTTTAC 3 174 0 ATCCTGTTCT 0.931281 -33 CAGCGAGATCCTCTCCTATCCGTATCC 3 190 0 ATCCTCTCCT 0.985678 -17 TTGACCGCGCAGCCTGTCCGCTCTTTGATT 4 94 0 AGCCTGTCCG 0.965215 -63 ACACATACTTATCCACTTCTTTATTAGCGT 7 22 1 ATCCACTTCT 0.876679 -135 CGTTTATCCCAGGCTCTCCTTGTCCATAAT 9 81 1 AGGCTCTCCT 0.945302 -60 GTCCCCACCGTTCCTCTCCGTGCTTTGTTT 9 119 0 TTCCTCTCCG 0.841349 -22 AAGCGCTTCCATCCTTTCTTTCTGTGAAGA 11 45 1 ATCCTTTCTT 0.721981 -156 ********** Masking position 7 Map Score: 3.80876 Number of sites scoring better than the average of aligned sites = 646 Number in coding regions = 541 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 112 Fraction of orfs with sites within 600 bp upstream = 0.0179891 Motif number 6 ATTATGTTCTTATAAATTCCAAGAGGTGAT 1 278 1 TATAAATTCC 0.894123 -23 TATGACATGGACTAAACTGCACTTAAATCT 2 116 0 ACTAAACTGC 0.953959 -133 AAGATAGTGAAATAAATTCCGAACTTTAAA 3 44 1 AATAAATTCC 0.894123 -163 TAAGTATGTGTATAAACTGCAC 7 3 0 TATAAACTGC 0.961527 -154 TTCTGACCAAACTCCTTATTCACAA 7 142 0 ACCAAACTCC 0.883396 -15 GCGTTCTTCATATAAACTGCTAATCCGCTC 11 131 0 TATAAACTGC 0.961527 -70 ********** Masking position 5 Map Score: 1.37415 Number of sites scoring better than the average of aligned sites = 66 Number in coding regions = 52 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 7 GAATAACATGTTAATTCAAATTATTCCGAT 1 24 1 TTAATTCAAA 0.567263 -277 TATGTCAACTCTTTTTTAAATACGATTTTT 1 53 1 CTTTTTTAAA 0.595419 -248 ATAGAGATAACTATTTTATAATAATTATAA 1 218 1 CTATTTTATA 0.655977 -83 AAAGTCAATATTATTTTATAATTATTATAA 1 233 0 TTATTTTATA 0.721971 -68 GTATCATTTTTTGTTTTAAGAATCGCTGTT 2 158 0 TTGTTTTAAG 0.884795 -91 GTCTTTTCTTTTATTTTAAGATAGTGAAAT 3 27 1 TTATTTTAAG 0.903248 -180 TAACTTAAATTTAATTTAAAGTTCGGAATT 3 58 0 TTAATTTAAA 0.721919 -149 ATGTAAAAGATTATTTTTAAAAAATCTAAA 3 114 0 TTATTTTTAA 0.803208 -93 TGAGGCAAATCTATTTTTAGACCAGATGA 8 10 0 CTATTTTTAG 0.68758 -57 TCTCCGTGCTTTGTTTCTAGCCCTATTATG 9 105 0 TTGTTTCTAG 0.554516 -36 AAAAAAACGGCTGTTTTAAAATCTTTCCAT 10 68 1 CTGTTTTAAA 0.884795 -61 TGAAGAAGGCTTATTTCAAATGTGTATGAC 11 69 1 TTATTTCAAA 0.865198 -132 GTAGAATGTTTCGTTTTAAAAAGGGGGAGC 11 177 1 TCGTTTTAAA 0.622595 -24 ********** Masking position 5 Map Score: 2.66115 Number of sites scoring better than the average of aligned sites = 716 Number in coding regions = 532 Number in noncoding regions = 184 Number of orfs with sites within 600 bp upstream = 196 Fraction of orfs with sites within 600 bp upstream = 0.0314809 Motif number 8 CGGACAGGCTGCGCGGTCAATAAAGCGGGC 4 104 1 GCGCGGTCAA 0.974267 -53 TTTAGCCTATGCGTGTCCAAAAAGGGTTAG 6 26 0 GCGTGTCCAA 0.986523 -53 AAAAAGCGGGGCGTGTCCAAGGGGGTTATT 6 54 1 GCGTGTCCAA 0.986523 -25 TTCTTTATTAGCGTTGTCCACAATTTGTGG 7 38 1 GCGTTGTCCA 0.875188 -119 TTTTTGGTAAGCGCTTCCATCCTTTCTTTC 11 37 1 GCGCTTCCAT 0.914235 -164 ********** Masking position 3 Map Score: 0.153964 Number of sites scoring better than the average of aligned sites = 130 Number in coding regions = 121 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 9 CAAGCAGAGTAAGTGATAAACAAGGATATC 1 83 0 AAGTGATAAA 0.623884 -218 TAATAATTTTTGGAGAAATAATTTTTCCTT 1 127 0 TGGAGAAATA 0.737947 -174 GTATCGAAATTGTTGAAAAACCTTGTTGTA 1 175 0 TGTTGAAAAA 0.691843 -126 TATCGATTAATAGAGATAACTATTTTATAA 1 209 1 TAGAGATAAC 0.720286 -92 AAATTCCAAGAGGTGATAAC 1 291 1 AGGTGATAAC 0.773656 -10 TATTTTAAGATAGTGAAATAAATTCCGAAC 3 38 1 TAGTGAAATA 0.788002 -169 AAATTTTTATTGGTAAAAACGAATATTAAT 3 87 0 TGGTAAAAAC 0.826264 -120 ACAATAGTGATGGTAAAAACAAAGAACAGG 3 162 1 TGGTAAAAAC 0.826264 -45 GAGTAGAATATAGTGAAAAGCACATCATAT 4 58 1 TAGTGAAAAG 0.821736 -99 TCATATATAATAGAGAAAAATAAGGGGTGA 5 51 1 TAGAGAAAAA 0.85647 -25 TAAACGTGCAGGGTGAAAAAAATCTAGCAA 9 57 0 GGGTGAAAAA 0.869407 -84 ********** Masking position 6 Map Score: 0.332293 Number of sites scoring better than the average of aligned sites = 1662 Number in coding regions = 1402 Number in noncoding regions = 260 Number of orfs with sites within 600 bp upstream = 280 Fraction of orfs with sites within 600 bp upstream = 0.0449727 Motif number 10 ********** No masking Map Score: 2.95118e-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 ********** No masking Map Score: 2.95118e-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: 2.95118e-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