AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00450_bsub_reg_100.orf -o00450_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 yacB 194 similar to hypothetical proteins #3 yacC 85 similar to hypothetical proteins #4 yacD 46 similar to protein secretion PrsA homolog #5 cysK 75 cysteine synthetase A #6 yitA 300 similar to sulfate adenylyltransferase #7 yjcI 300 similar to cystathionine gamma-synthase #8 ggt 184 gamma-glutamyltranspeptidase #9 yrhA 64 similar to cysteine synthase #10 yrrT 192 yrrT #11 ytkP 148 similar to cysteine synthase #12 metK 300 S-adenosylmethionine synthetase #13 yvgR 170 similar to sulfite reductase Motif number 1 TAATCAAATGAAATAAAAAACTTTGGTTCG 1 56 0 AAATAAAAAA 0.945644 -245 TCTTTAATGAAAATAAAAAAAGTCTGTTCG 1 105 0 AAATAAAAAA 0.945644 -196 AGAATAATTAAAATTAAAAATCTTTAATGA 1 125 0 AAATTAAAAA 0.724131 -176 CCAATCATTTACATAAAAAAACTGCCAGCG 2 43 0 ACATAAAAAA 0.949679 -152 CCCTTTTCTCAAATTAAAAACCCGCTAAAG 4 14 0 AAATTAAAAA 0.724131 -33 TAGATTATATACATAATACCAATACAAATA 5 34 1 ACATAATACC 0.449184 -42 TAAGTGCAGAAAAGAAAACAAGGAAACGTA 6 70 1 AAAGAAAACA 0.821093 -231 TTCGGCACACGAAGAAAAAAGTGTTGAAAT 7 43 1 GAAGAAAAAA 0.764705 -258 AATTGCGCTAATATAAAACAATCAGAAAAT 7 81 1 ATATAAAACA 0.68916 -220 TATCTTCCAAGCATAAAAAACGCTTGCTGG 7 210 0 GCATAAAAAA 0.87284 -91 TCCCTTTTCAAAATAAAAACCCCTTCTTCA 7 268 0 AAATAAAAAC 0.863529 -33 TCAATTCTGCACAGAAAAACGGCATTATGC 8 74 1 ACAGAAAAAC 0.779033 -111 TAATATCCTAACATAATAAACGTTTGTGCG 11 96 0 ACATAATAAA 0.813617 -53 ATTCCTTTCTGAATAAAACAAGTGTCATAT 11 125 0 GAATAAAACA 0.764705 -24 ACTCAGTTGAACATAATAAATAACAGAGAA 12 57 0 ACATAATAAA 0.813617 -244 CATATTTATGAAATAAAAAAACCTTTTCCA 12 176 0 AAATAAAAAA 0.945644 -125 CTTCATGTAAATAGAAAAAAGAGAAGGACT 13 20 0 ATAGAAAAAA 0.68916 -151 ********** Masking position 6 Map Score: 15.2569 Number of sites scoring better than the average of aligned sites = 1339 Number in coding regions = 868 Number in noncoding regions = 471 Number of orfs with sites within 600 bp upstream = 450 Fraction of orfs with sites within 600 bp upstream = 0.0722775 Motif number 2 TTAATTTGAGAAAAGGGGCTGAAAGCAGGT 4 27 1 AAAAGGGGCT 0.78011 -20 ACGAACCCCACGGAGGGGTATTAATCAACC 6 129 1 CGGAGGGGTA 0.837597 -172 TCGTGAGAGGTGGAGGGACTGGCCCTTAGA 7 129 1 TGGAGGGACT 0.866669 -172 CTTCATAAGAAGAAGGGGTTTAACGCTTCT 7 243 0 AGAAGGGGTT 0.931395 -58 CTTCTTATGAAGAAGGGGTTTTTATTTTGA 7 261 1 AGAAGGGGTT 0.931395 -40 ATACGGATTAAGAAGGGACTGCTAT 8 6 0 AGAAGGGACT 0.964933 -179 AGCTTCATATAGGAGGGAGAAC 8 173 1 AGGAGGGAGA 0.978051 -12 ACCTCTATTAAGGAGGAGGACATAT 9 50 1 AGGAGGAGGA 0.851743 -15 TAGCTGTCAAAGAAGGGAGTGTCAGACGG 11 10 0 AGAAGGGAGT 0.975991 -139 CCCGAGCTGGCGGAGGGACAGGCCCTATGA 12 12 1 CGGAGGGACA 0.912691 -289 TACATTGTATAAGAGGGAGCGAGTTCCGTA 12 232 1 AAGAGGGAGC 0.823759 -69 GGCCTTGTGCAGGAGGAAGCAAATC 12 286 1 AGGAGGAAGC 0.823759 -15 AGAGAAGGGAGTCCTTCTCTTT 13 3 1 AGAAGGGAGT 0.975991 -168 ********** Masking position 4 Map Score: 14.2444 Number of sites scoring better than the average of aligned sites = 472 Number in coding regions = 289 Number in noncoding regions = 183 Number of orfs with sites within 600 bp upstream = 210 Fraction of orfs with sites within 600 bp upstream = 0.0337295 Motif number 3 CTAAACCTCCTATACACTTCCTACGCGGTTTC 3 62 0 TAACCTTCCT 0.898589 -24 AACCTCCATTTATACGTTTCCTTGTTTTCTTT 6 80 0 TAACTTTCCT 0.848171 -221 AATGCAAAACAAGCCGGTTGCTGAGGTTTCTA 7 155 0 AACCGTTGCT 0.974511 -146 CCAAGCATAAAAAACGCTTGCTGGATTTAGCA 7 202 0 AAACCTTGCT 0.924992 -99 AAGAAGCGTTAAACCCCTTCTTCTTATGAAGA 7 242 1 AACCCTTCTT 0.880374 -59 TTCAAAATAAAAACCCCTTCTTCATAAGAAGA 7 260 0 AACCCTTCTT 0.880374 -41 GTCCCTTCTTAATCCGTATGCTGATTCTAATA 8 17 1 AACCTATGCT 0.736287 -168 AGTGTTTTCATACACTGTTCCTCTATCCGCAC 11 62 0 TAACGTTCCT 0.898589 -87 AATAACAGAGAAACCGGTTGCTGGGCTTCATA 12 37 0 AACCGTTGCT 0.974512 -264 ACCAAGGTGCTAACCTGTTGCAAGGTTGTATG 12 93 1 TACCGTTGCA 0.81628 -208 CACAAAGACCAAACCCTTTCCTCGATGGAAAA 12 151 1 AACCTTTCCT 0.970925 -150 TGAAATAAAAAAACCTTTTCCATCGAGGAAAG 12 166 0 AACCTTTCCA 0.882104 -135 ** ** ****** Masking position 2 Map Score: 9.10357 Number of sites scoring better than the average of aligned sites = 484 Number in coding regions = 425 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 4 AATTGGATGATTGTAAAAGCCGCAGCTGAGCCAATCAT 2 65 0 TTTAAAGAGG 0.981262 -130 TATCGATTTGTTTACAAATGAGCCGCTGATCGTGTATG 2 107 1 TTAAAAGCGG 0.910683 -88 TGTAGAATGTTTGTAAAAAGTAAAGTAGAGAAACTATT 2 149 1 TTTAAAAAGG 0.957171 -46 TGGAATTGATTTATGAAAGAAACCGCGTAGGAAGTGTA 3 44 1 TTTAAAACGT 0.803956 -42 TGACAAAAAATTTTGAAATTGATAGATTATATACATAA 5 12 1 TTTAAAAAGT 0.905099 -64 GGGGTTTTTATTTTGAAAAGGGAAGGTGTCAGCTAT 7 275 1 TTTAAAGAGG 0.981262 -26 AGGTTGTTTTTAGAGAAAAACGGAGGAGAACGTTCTCC 9 16 0 TAAAAAGAGG 0.769404 -49 TTCATATGACTTGTGAAAGCTGGAGGGTCAAGAC 10 7 0 TTTAAAGAGT 0.957171 -186 CTTATAGGAATTATTAAATATGGAGTGTGACAAAT 10 168 1 TTTAAAGAGT 0.957171 -25 AGCCTCTTTATTGATAAAATAATAGCTGTCAAAGAAGG 11 24 0 TTAAAAAAGG 0.910068 -125 ** * *** * ** * Masking position 8 Map Score: 6.02903 Number of sites scoring better than the average of aligned sites = 304 Number in coding regions = 254 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 5 ACTAAAAATCCTTTTAAATCAAGACTTTCGAACC 1 28 1 CTTAACAAGA 0.912639 -273 CCATCTTAGCCTTTAAGATCAAGAATATATACAT 1 167 0 CTTAACAAGA 0.912633 -134 ATTCCAGCCCTTTTAGGGTTAAGAATGGATCAAC 3 16 0 TTTGGTAAGA 0.911959 -70 ATCATTTCGATTCTCACATCAAGAACCTGCCA 6 9 0 TTTAACAAGA 0.816722 -292 GTCCCTCCACCTCTCACGATAAGAAATATCGATT 7 114 0 CTTAGTAAGA 0.97157 -187 GTTTTTTATGCTTGGAAGATAAGAAGAAGCGTTA 7 219 1 CTGAGTAAGA 0.960524 -82 CGCTGTAATTTTTTTACGCTAAGATTGTAACAAT 8 137 1 TTTAGTAAGA 0.935564 -48 CTTGTGAAAGCTGGAGGGTCAAGAC 10 2 0 CTGGGCAAGA 0.949417 -191 GCACAAACGTTTATTATGTTAGGATATTATATGA 11 97 1 TTTAGTAGGA 0.752562 -52 TGTATGATTCCTTGAGCGATAAGAGTGAAAGGCA 12 119 1 CTGGGTAAGA 0.945428 -182 ** * * * ***** Masking position 11 Map Score: 4.51052 Number of sites scoring better than the average of aligned sites = 147 Number in coding regions = 113 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 6 CTGTTCGTGTCGAATTTTGTCGTATATAATCAAATGAA 1 74 0 CGTTTTGTTA 0.821189 -227 CTTTTTTCTTCGTGTGCCGAACCGTTTAAAGAGAGAAA 7 26 0 CGTGCCGCTA 0.990607 -275 CAAAACAAGCCGGTTGCTGAGGTTTCTAAGGGCCAGTC 7 145 0 CGTGCTGTTA 0.992354 -156 GCATAAAAAACGCTTGCTGGATTTAGCACCTTGGCGCT 7 192 0 CGTGCTGTCA 0.975572 -109 CTTCTTAATCCGTATGCTGATTCTAATATAGCACATGG 8 21 1 CGTGCTGCTA 0.99366 -164 ACAGAGAAACCGGTTGCTGGGCTTCATAGGGCCTGTCC 12 27 0 CGTGCTGTTA 0.992354 -274 TAAGAGGGAGCGAGTTCCGTATCATATATACAAGGTCT 12 241 1 CGTTCCGCTA 0.96641 -60 ** ***** * ** Masking position 18 Map Score: 3.06914 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 53 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 7 GCAAAACAAGCCGGTTGCTGAGGTTTCTAA 7 154 0 CCGGTTGCTG 0.995278 -147 AGCATAAAAAACGCTTGCTGGATTTAGCAC 7 201 0 ACGCTTGCTG 0.969694 -100 CCTTCTTAATCCGTATGCTGATTCTAATAT 8 20 1 CCGTATGCTG 0.964632 -165 AACAGAGAAACCGGTTGCTGGGCTTCATAG 12 36 0 CCGGTTGCTG 0.995278 -265 ********** Masking position 6 Map Score: 2.53906 Number of sites scoring better than the average of aligned sites = 98 Number in coding regions = 90 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 8 AAATCAATTCCAGCCCTTTTAGGGTTAAGAA 3 25 0 CAGCCCTTTA 0.975678 -61 ACCTGCTTTCAGCCCCTTTTCTCAAATTAA 4 27 0 CAGCCCCTTT 0.949404 -20 AGTTTGACATCAGCGCCTTAACATCATTTCG 6 34 0 CAGCGCCTTA 0.985676 -267 CGTTTCCATTCAACGTGTTCAACCTCCATTT 6 101 0 CAACGTGTTA 0.747915 -200 TCGGCGGCTACAGCCCGTTAACAGGTTTTTT 6 246 1 CAGCCCGTTA 0.98414 -55 AAAAAAATTACAGCGTTTTCACAAGTGACAA 8 121 0 CAGCGTTTTA 0.936658 -64 TCTATCCGCACAGCCTCTTTATTGATAAAAT 11 42 0 CAGCCTCTTA 0.97766 -107 ********* * Masking position 2 Map Score: 4.82876 Number of sites scoring better than the average of aligned sites = 227 Number in coding regions = 211 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 9 ATAAATAATATTCATATATGATTTGCACTTATC 1 222 1 TTCAATTGAT 0.789049 -79 CGCGGTTTCTTTCATAAATCAATTCCAGCCCTT 3 38 0 TTCAAATCAT 0.921839 -48 ACGCGCACCCTTCAAAATGGCATGCGGGATCAC 6 162 0 TTCAAAGGCT 0.947992 -139 CTCTTTCACAACGGAATGATAATCTTT 6 284 0 TTCAAAGGAT 0.976954 -17 AGCATACGGATTAAGAAGGGACTGCTAT 8 6 0 TTAAAAGGAT 0.787399 -179 CGTTTTTCTGTGCAGAATTGATTATATTGATAT 8 62 0 TGCAAATGAT 0.919551 -123 TATTATATAGTGCATAATGCCGTTTTTCTGTGC 8 82 0 TGCAAAGCCT 0.776653 -103 TTACAGCGTTTTCACAAGTGACAAATGGTATAT 8 112 0 TTCAAATGAA 0.880803 -73 CCCTCCAGCTTTCACAAGTCATATGAAGTATAA 10 18 1 TTCAAATCAA 0.766273 -175 ACTTGTTTTATTCAGAAAGGAATGACA 11 132 1 TTCAAAGGAT 0.976954 -17 **** ** *** * Masking position 6 Map Score: 3.77163 Number of sites scoring better than the average of aligned sites = 434 Number in coding regions = 382 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 10 TCCTTTGGGCGGGAGCTTTTTGACATTCTG 1 265 1 GGGAGCTTTT 0.719028 -36 AGCGTCAGCCGGCAGTTTTTTTAGAAAGAA 2 17 0 GGCAGTTTTT 0.931448 -178 GGCTGACGCTGGCAGTTTTTTTATGTAAAT 2 37 1 GGCAGTTTTT 0.931448 -158 TGGCAGGTTCTTGATGTGAGA 6 2 1 GGCAGGTTCT 0.944891 -299 GTTTCTAAGGGCCAGTCCCTCCACCTCTCA 7 132 0 GCCAGTCCCT 0.91787 -169 ATAGCAGTCCCTTCTTAATCCG 8 3 1 AGCAGTCCCT 0.868748 -182 CTGGCGGAGGGACAGGCCCTATGAAGCCCA 12 18 1 GACAGGCCCT 0.880824 -283 AAGGTCTTTCGGGAGGCCTTGTGCAGGAGG 12 272 1 GGGAGGCCTT 0.963626 -29 AGAGAAGGGAGTCCTTCTCTTTTTTC 13 7 1 GGGAGTCCTT 0.964321 -164 ********** Masking position 4 Map Score: 3.71557 Number of sites scoring better than the average of aligned sites = 602 Number in coding regions = 501 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 11 TAAAAGCCGCAGCTGAGCCAATCATTTACA 2 60 0 AGCTGAGCCA 0.939377 -135 ACAAATGAGCCGCTGATCGTGTATGGTATT 2 120 1 CGCTGATCGT 0.917785 -75 ACATCGTTGATCCATTCTTAACCC 3 5 1 CGTTGATCCA 0.887489 -81 ACTCAGTGCAAGCTGATCCAGCTCTGCTTG 6 197 0 AGCTGATCCA 0.980529 -104 GTATTATAGGAACTGTTCCATCATTAATCC 10 130 1 AACTGTTCCA 0.913846 -63 TGTTTTCATACACTGTTCCTCTATCCGCAC 11 62 0 CACTGTTCCT 0.847847 -87 CAAAGTTATAAACTGATCGAAAATTGCATC 13 138 0 AACTGATCGA 0.911415 -33 ********** Masking position 4 Map Score: 1.35001 Number of sites scoring better than the average of aligned sites = 533 Number in coding regions = 508 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 12 TTTCAGGGCGTATGTATATATTCTTGATCT 1 156 1 TATGTATATA 0.898521 -145 GCAGTTTTTTTATGTAAATGATTGGCTCAG 2 48 1 TATGTAAATG 0.789651 -147 GTATTGGTATTATGTATATAATCTATCAAT 5 29 0 TATGTATATA 0.898521 -47 CCCGAAAGACCTTGTATATATGATACGGAA 12 255 0 CTTGTATATA 0.843237 -46 GGCTATGCTTCATGTAAATAGAAAAAAGAG 13 27 0 CATGTAAATA 0.942744 -144 TAGTTATCATCATGTAAATATATTTTACTT 13 79 1 CATGTAAATA 0.942744 -92 ********** Masking position 5 Map Score: 2.26064 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 35 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 13 ********** No masking Map Score: -5.82402e-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 CTTGAAACCTCCTAATCAGAAT 1 289 0 TGAAACCTCC 0.91634 -12 TAAACCTCCTATACACTTCCTACGCGGTTT 3 63 0 ATACACTTCC 0.63643 -23 TACTAAACCTCCTATACACTTC 3 74 0 CTAAACCTCC 0.907892 -12 TCTCGACACCTCAATTTCCGACT 5 63 0 CGACACCTCA 0.938891 -13 ATTCAACGTGTTCAACCTCCATTTATACGT 6 95 0 TTCAACCTCC 0.884171 -206 CGGTTGATTAATACCCCTCCGTGGGGTTCG 6 130 0 ATACCCCTCC 0.807091 -171 GGGCCAGTCCCTCCACCTCTCACGATAAGA 7 124 0 CTCCACCTCT 0.76495 -177 ACTGGCCCTTAGAAACCTCAGCAACCGGCT 7 146 1 AGAAACCTCA 0.823759 -155 ATAGCTGACACCTTCCCTTTTCAAA 7 286 0 TGACACCTTC 0.701416 -15 GTGTATTTTATGCCATCTCATATTGCGCAT 10 66 0 TGCCATCTCA 0.483877 -127 CGTATCCACCTCACAAAGTTATA 13 158 0 ATCCACCTCA 0.898648 -13 ********** Masking position 8 Map Score: 1.82373 Number of sites scoring better than the average of aligned sites = 698 Number in coding regions = 464 Number in noncoding regions = 234 Number of orfs with sites within 600 bp upstream = 249 Fraction of orfs with sites within 600 bp upstream = 0.0399936 Motif number 15 CTATTATCCTACTAAAAATCCTTTTAAATCAAGAC 1 18 1 ACTAACTTTT 0.949539 -283 AATCAAATGAAATAAAAAACTTTGGTTCGAAAGTC 1 50 0 AATAACTTGG 0.722695 -251 AAAATTCGACACGAACAGACTTTTTTTATTTTCAT 1 94 1 ACGAACTTTT 0.939476 -207 TTCATAAATCAATTCCAGCCCTTTTAGGGTTAAGA 3 26 0 AATCACTTTT 0.842064 -60 TTCACAACGGAATGATAATCTTTTTCTCCCAAAAA 6 272 0 AATAACTTTT 0.95799 -29 AAGTCATATGAAGTATAAGCTTTTTTGCGGTCAAT 10 33 1 AAGAACTTTT 0.949549 -160 AAAAGCAGGTACTAAAACACTTTGTGTATTTTATG 10 84 0 ACTAACTTGT 0.901957 -109 TATTTACATGAAGCATAGCCGTTTTATCATTAGGA 13 37 1 AAGAACTTTT 0.949552 -134 GGTAAAGTTCAATTAGATGCAATTTTCGATCAGTT 13 123 1 AATAACATTT 0.782477 -48 *** * * * **** Masking position 7 Map Score: 1.56173 Number of sites scoring better than the average of aligned sites = 159 Number in coding regions = 117 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207