AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00780_bsub_reg_300.orf -o00780_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 ylxS 300 alternate gene name: ymxA; similar to hypothetical proteins #2 nusA 34 nusA #3 truB 81 tRNA pseudouridine 55 synthase #4 rpsO 156 ribosomal protein S15 (BS18) #5 pnpA 172 polynucleotide phosphorylase (PNPase) #6 ylxY 117 alternate gene name: ymxI; similar to deacetylase #7 ymxG 39 similar to processing protease #8 yqhS 86 similar to 3-dehydroquinate dehydratase #9 yqhR 226 yqhR #10 yteI 185 similar to protease IV #11 bioW 251 6-carboxyhexanoate-CoA ligase #12 ytaP 217 ytaP Motif number 1 TTACCGAGGCAAAGAGTGGGGAAACCCGCTC 1 149 1 AAAGAGGGGG 0.985786 -152 GTTCAATACAAAAGAGCGGGTTTCCCCACTC 1 162 0 AAAGAGGGGT 0.885646 -139 CCCTGCTTCAAAAGAGCAGGGGCTAAAAAGT 1 225 0 AAAGAGAGGG 0.942438 -76 TCGACAGCACAAGGAGGAAGAAC 1 288 1 AAGGAGAAGA 0.927129 -13 CAAATGTTTTAAGGGGGGAGACCGTTAA 2 17 1 AAGGGGGAGA 0.960104 -18 AAAAAGAGAGGATAGGCGTAT 3 1 1 AAAAAGGAGG 0.959784 -81 TAAACGAAGAAAGAGGACAGACGATATACGC 3 26 0 AAGAGGCAGA 0.84837 -56 AACTCAAAAGAAGGAGTGAAAGGCAA 3 66 1 AAGGAGGAAA 0.704045 -16 TCGTAAAAAGCGGGAGGATTCCCGC 5 5 1 AAAAAGGGGA 0.97648 -168 TAATACGATAAAAAAGCGGGAATCCTCCCGC 5 20 0 AAAAAGGGGA 0.97648 -153 ATTTCACACAACGAAGAGAGGAGTTCGTAAT 5 149 1 ACGAAGGAGG 0.786349 -24 GAAAACATAAAAGGAGCCTGGGAGACCCGGC 6 13 1 AAGGAGCTGG 0.853341 -105 CTTCAAAATAAAGAAGCCGGGTCTCCCAGGC 6 28 0 AAGAAGCGGG 0.959101 -90 AGCTTTTCAAAAGCAGGCGGGTTCTACCTTG 6 57 1 AAGCAGCGGG 0.830236 -61 TCACATTATGAAGGAGAAGGACAAGGTAGAA 6 78 0 AAGGAGAGGA 0.958258 -40 AACCCTCGCGAAAAGGAGAGATTGT 8 72 1 AAAAGGGAGA 0.911303 -15 CGCAGCTGCCAAAAAGTGTGAGCTTTTTTAT 9 166 1 AAAAAGGTGA 0.864794 -61 AGAGTTTAGGAAAAAGGAGGAGAAAAA 10 169 1 AAAAAGAGGA 0.907415 -17 GTTATCAGTGAAAGGGCGAGAAATGATGCAA 11 195 1 AAAGGGGAGA 0.943011 -57 ****** **** Masking position 1 Map Score: 24.5374 Number of sites scoring better than the average of aligned sites = 1281 Number in coding regions = 908 Number in noncoding regions = 373 Number of orfs with sites within 600 bp upstream = 359 Fraction of orfs with sites within 600 bp upstream = 0.0576614 Motif number 2 TACCGAGGCAAAGAGTGGGGAAACCCGCTC 1 150 1 AAGAGTGGGG 0.886542 -151 TTCAATACAAAAGAGCGGGTTTCCCCACTC 1 162 0 AAGAGCGGGT 0.886542 -139 CCTGCTTCAAAAGAGCAGGGGCTAAAAAGT 1 225 0 AAGAGCAGGG 0.973175 -76 CGACAGCACAAGGAGGAAGAAC 1 289 1 AGGAGGAAGA 0.737533 -12 AAATGTTTTAAGGGGGGAGACCGTTAA 2 18 1 AGGGGGGAGA 0.663312 -17 AAAAAGAGAGGATAGGCGTAT 3 2 1 AAAAGAGAGG 0.912594 -80 AAAAAAACTCAAAAGAAGGAGTGAAAGGCA 3 61 1 AAAAGAAGGA 0.915214 -21 TCGTAAAAAGCGGGAGGATTCCCGC 5 6 1 AAAAGCGGGA 0.974448 -167 AATACGATAAAAAAGCGGGAATCCTCCCGC 5 20 0 AAAAGCGGGA 0.974448 -153 TCACACAACGAAGAGAGGAGTTCGTAATTG 5 152 1 AAGAGAGGAG 0.674678 -21 TTCAAAATAAAGAAGCCGGGTCTCCCAGGC 6 28 0 AGAAGCCGGG 0.799535 -90 GAAGCTTTTCAAAAGCAGGCGGGTTCTACC 6 55 1 AAAAGCAGGC 0.765742 -63 CACATTATGAAGGAGAAGGACAAGGTAGAA 6 78 0 AGGAGAAGGA 0.929618 -40 TCATAATGTGAGGTGAGGGGGGGACAGAAC 6 98 1 AGGTGAGGGG 0.751298 -20 ACCCTCGCGAAAAGGAGAGATTGT 8 73 1 AAAGGAGAGA 0.719941 -14 TGCATGTAGGAAAAGCAAGGCTATGGCAAT 9 109 0 AAAAGCAAGG 0.884282 -118 GAGTTTAGGAAAAAGGAGGAGAAAAA 10 170 1 AAAAGGAGGA 0.871147 -16 TTCTGTCAATAGAAGAAAGGATCGATTTAT 11 81 0 AGAAGAAAGG 0.782889 -171 TTATCAGTGAAAGGGCGAGAAATGATGCAA 11 196 1 AAGGGCGAGA 0.869553 -56 TACTAAATAGATGAGAGGGATACCC 12 6 0 ATGAGAGGGA 0.790094 -212 ********** Masking position 1 Map Score: 17.3399 Number of sites scoring better than the average of aligned sites = 2213 Number in coding regions = 1766 Number in noncoding regions = 447 Number of orfs with sites within 600 bp upstream = 426 Fraction of orfs with sites within 600 bp upstream = 0.0684227 Motif number 3 TAGTTTTATTGGAAATGCTAACGATTACCGAGGCAAA 1 125 1 GAAAGACGAA 0.950481 -176 GAGCAGGGGCTAAAAAGTAAACGATGAACATGTCGAG 1 206 0 TAAAGACGAA 0.980397 -95 AAGTAGTATGTAAAAGGATTTCAATGATTTGTTATAA 5 63 0 TAAAGTCAAA 0.94413 -110 CGCCTGCTTTTGAAAAGCTTCAAAATAAAGAAGCCGG 6 39 0 TAAAGCAAAA 0.69547 -79 TCCAGTATGATAAAATGTTCACGAGAAGTGAACATTT 8 24 1 TAAAGACGAA 0.980397 -63 GCCCAAAAAATGAAATGTCAATAAAAAAGCTCACACT 9 180 0 TAAAGATAAA 0.823699 -47 CACCTCCAGTTAAAGTGTGCCCAAAAAATGAAATGTC 9 198 0 TAAGGCCAAA 0.909357 -29 CTGTAAAAAGAAATCGAAAAAGACCGTTTT 11 4 1 TAAAGTCGAA 0.94049 -248 TGGCAGTTGGTTAAAAGGAAACAAAAAGACCGTTTTC 11 45 0 TAAAGACAAA 0.981644 -207 CCAATTATATTCAAAGGTTAACAATTAGAATATATTA 11 122 0 TAAAGACAAA 0.981643 -130 TCATATAAAAGTAAGCGGTTACAATAATTGTTTTCGA 12 73 1 GAAGGACAAA 0.887352 -145 * *** * **** * Masking position 4 Map Score: 10.1931 Number of sites scoring better than the average of aligned sites = 232 Number in coding regions = 185 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 4 GGCAAAGAGTGGGGAAACCCGCTCTTTTGTATT 1 156 1 GGGGACCGCT 0.996046 -145 ATGTTTTAAGGGGGGAGACCGTTAA 2 20 1 GGGGGCCGTT 0.906978 -15 AACGAAGAAAGAGGACAGACGATATACGCCTAT 3 22 0 GAGGAACGAT 0.667044 -60 AGCAACCGTCGGTGACTTCGGATTGCCAAGCAA 4 95 0 GGTGACGGAT 0.952855 -62 ACGGTTGCTAGGTAACTGGGGCTAAATATGATT 4 119 1 GGTAAGGGCT 0.825481 -38 TAAAAAGCGGGAGGATTCCCGCTTTTTTATCGT 5 14 1 GAGGACCGCT 0.982339 -159 AAAGGAGCCTGGGAGACCCGGCTTCTTTATTTT 6 22 1 GGGAGCGGCT 0.928819 -96 CAGATGAAGGCAGCTTGTCTTTGAA 7 3 1 GATGACAGCT 0.804053 -37 TCTATTGTACAGGAAACACCGCTAAACCTCTAG 9 59 1 AGGAACCGCT 0.799638 -168 TGACAGCAAAGGGGAAATGGGAT 10 1 0 GGGGAGGGAT 0.960641 -185 TAACAATTTAGGTGAGAAGCGCTACACGTTCTT 11 160 1 GGTGAGCGCT 0.969376 -92 GAAAAATAAAGGGGAACCCAGATCTGTCTCGTA 12 161 1 GGGGACAGAT 0.954902 -57 ***** ***** Masking position 13 Map Score: 9.79875 Number of sites scoring better than the average of aligned sites = 642 Number in coding regions = 568 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 5 ACAAAAGAGCGGGTTTCCCCACTCTTTGCC 1 156 0 GGGTTTCCCC 0.989194 -145 TTAACGGTCTCCCCCCTTAAAACA 2 21 0 CGGTCTCCCC 0.988734 -14 TAAAGAAGCCGGGTCTCCCAGGCTCCTTTT 6 21 0 GGGTCTCCCA 0.989352 -97 GTTCTGTCCCCCCCTCACCTCAC 6 105 0 CTGTCCCCCC 0.886413 -13 CTTTTCGCGAGGGTTTCTCATGTAAAAAAT 8 57 0 GGGTTTCTCA 0.885808 -30 GGGTATCCCTCTCATCTATT 12 1 1 GGGTATCCCT 0.957374 -217 AGACAGATCTGGGTTCCCCTTTATTTTTCC 12 160 0 GGGTTCCCCT 0.975725 -58 ********** Masking position 4 Map Score: 7.00602 Number of sites scoring better than the average of aligned sites = 100 Number in coding regions = 59 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 6 TTTTGTATTGAACAGGAGAATTTTGTCTCGACAT 1 180 1 AAAGAATTTT 0.957461 -121 CACGATTTTTAGTATGATAGTTTTCGTAGTCTTA 4 55 1 AGAGAATTTT 0.894717 -102 TTATCGTATTAAAGCGAAATTTCTTATAACAAAT 5 40 1 AAGGAATTCT 0.851493 -133 ATGTTCACGAGAAGTGAACATTTTTTACATGAGA 8 38 1 GAGGACTTTT 0.961633 -49 GCTGCCAAAAAGTGTGAGCTTTTTTATTGACATT 9 170 1 AGGGACTTTT 0.939987 -57 GCTTTCTCATGAAGTGAAACATTTTTCATATTGA 10 122 1 GAGGAAATTT 0.825701 -64 TGAATCGTATAATGAGAGAGTTTAGGAAAAAGGA 10 153 1 AAGGAATTTA 0.7948 -33 AAAGAAATCGAAAAAGACCGTTTTGTGTGAAAAC 11 17 1 AAAGACTTTT 0.66844 -235 AAAAGGAAACAAAAAGACCGTTTTCACACAAAAC 11 36 0 AAAGACTTTT 0.66844 -216 GTCAATAGAAGAAAGGATCGATTTATGGCAGTTG 11 73 0 GAAGACATTT 0.791887 -179 GAAATGATGCAAGAAGAAACTTTTTATAGTGTCA 11 214 1 AAAGAATTTT 0.957461 -38 ** * ** * **** Masking position 7 Map Score: 6.46676 Number of sites scoring better than the average of aligned sites = 266 Number in coding regions = 196 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 7 CCTAAGCAAGTGACAGAAACTCTAATATTACGATGG 1 41 0 TGACGAACTT 0.75783 -260 TGCTTAGGTATGAAGGTAAGCGTATATCCATTTGCA 1 69 1 TGAAGAAGTA 0.970278 -232 TGAATACAAATGTTTTAAGGGGGGAG 2 1 1 TGAAAAAGTT 0.862898 -34 TACAATAGAGTGAAAGGAAATGGTTAGCAATCCTAA 9 32 0 TGAAGAAGGA 0.987085 -195 GAGTAAAATTTGAAAATAACGGGTATAATGCATGTA 9 131 0 TGAAAAAGGT 0.936501 -96 AACTTAAATATGACAGCAAAGGGGAAATGGGAT 10 8 0 TGACGAAGGA 0.988082 -178 CTTAACGGGCTGCCGGCAAACGTGGTACACTTATGG 10 81 0 TGCCGAAGTT 0.834435 -105 TTTCTTCTATTGACAGAAACAGGAGAGAATAATATA 11 93 1 TGACGAAGGA 0.988082 -159 TGTTAACCTTTGAATATAATTGGTTAACAATTTAGG 11 136 1 TGAAAAAGGA 0.955721 -116 TATTATCATATAAAAGTAAGCGGTTACAATAATTGT 12 68 1 TAAAGAAGGA 0.869839 -150 **** * ** ** * Masking position 8 Map Score: 5.78765 Number of sites scoring better than the average of aligned sites = 424 Number in coding regions = 379 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 8 ATAACCATATTTTTATTGCAAATGGATATACG 1 89 0 TTTATTCAAA 0.85214 -212 TATGGTATAGTTTTATTGGAAATGCTAACGAT 1 118 1 TTTATTGAAA 0.683168 -183 TTTTGAGTTTTTTTCTTATAAACGAAGAAAGA 3 43 0 TTTCTTTAAA 0.942713 -39 CGCACGCAAATTTTATTCTAAAATATTTGCAT 4 18 1 TTTATTTAAA 0.875379 -139 TCGCGAGGGTTTCTCATGTAAAAAATGTTCAC 8 51 0 TTTCATTAAA 0.917876 -36 GCCAAAGGTATTTTATCACAAATACTGGATGG 10 50 0 TTTATCCAAA 0.862607 -136 AAAAAGACCGTTTTCACACAAAACGGTCTTTT 11 28 0 TTTCACCAAA 0.909461 -224 CGTGTAGCGCTTCTCACCTAAATTGTTAACCA 11 156 0 TTTCACTAAA 0.924144 -96 TAAATTGATATTATCATATAAAAGTAAGCGGT 12 60 1 TTTCATTAAA 0.91832 -158 GAACCCAGATCTGTCTCGTAAATGTGAAGTAA 12 174 1 CTTCTCTAAA 0.788123 -44 ** **** **** Masking position 4 Map Score: 4.38876 Number of sites scoring better than the average of aligned sites = 396 Number in coding regions = 306 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 9 GTTCTTCCTCCTTGTGCTGTC 1 290 0 TTCTTCCTCC 0.968384 -11 CCTGTTTCACCTCCAAATCATATT 4 143 0 TTTCACCTCC 0.932914 -14 ATTTGTTCCTCCTATTCAAAGA 7 28 0 TTGTTCCTCC 0.968384 -12 CTATGGCAATTTTTTCAGCCTGTCAATCTA 9 89 0 TTTTTCAGCC 0.915265 -138 CATATTTAAGTTTTTCTGCCATCCAGTATT 10 32 1 TTTTTCTGCC 0.915265 -154 TTTTTCTCCTCCTTTTTCCTAA 10 174 0 TTTCTCCTCC 0.982569 -12 ********** Masking position 2 Map Score: 2.00495 Number of sites scoring better than the average of aligned sites = 336 Number in coding regions = 267 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 10 TCATATTCGTCTCGTCACTCTGCATAAAAAC 1 255 0 CTCTCACTCT 0.959387 -46 TTGCCTTTCACTCCTTCTTTTGAG 3 68 0 CCTTCACTCC 0.987731 -14 GTTCTGTCCCCCCCTCACCTCACATTATGAA 6 97 0 CCCTCACCTC 0.941982 -21 CTAACCATTTCCTTTCACTCTATTGTACAGG 9 41 1 CCTTCACTCT 0.989807 -186 ATTTTTTCAGCCTGTCAATCTAGAGGTTTAG 9 80 0 CCTTCAATCT 0.93759 -147 CCCATCACCCTTCCTTATTCG 12 207 0 CCCTCACCCT 0.992163 -11 *** ******* Masking position 5 Map Score: 3.28984 Number of sites scoring better than the average of aligned sites = 103 Number in coding regions = 59 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 11 GGTATAATGCATGTAGGAAAAGCAAGGCTA 9 116 0 ATGTAGGAAA 0.91143 -111 TAATGAGAGAGTTTAGGAAAAAGGAGGAGA 10 162 1 GTTTAGGAAA 0.911416 -24 CCTCTCATCTATTTAGTAAAATATTAACTC 12 18 1 ATTTAGTAAA 0.963044 -200 ATTATGGAATATTTCGAAAACAATTATTGT 12 93 0 ATTTCGAAAA 0.782129 -125 TTTACTAAATATTTAGTAAATATTATGGAA 12 114 0 ATTTAGTAAA 0.963044 -104 TTTACTAAATATTTAGTAAATGATGTGATT 12 124 1 ATTTAGTAAA 0.963044 -94 ********** Masking position 4 Map Score: 2.83638 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 22 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 12 GTGACTTCGGATTGCCAAGCAATGGTTTTA 4 87 0 ATTGCCAAGC 0.933484 -70 ATTATCAACCTGCCTATTTC 9 1 1 ATTATCAACC 0.897662 -226 TTTCTTTAGGATTGCTAACCATTTCCTTTC 9 27 1 ATTGCTAACC 0.978621 -200 ATATATTCTAATTGTTAACCTTTGAATATA 11 124 1 ATTGTTAACC 0.97696 -128 TCTCACCTAAATTGTTAACCAATTATATTC 11 147 0 ATTGTTAACC 0.97696 -105 ********** Masking position 7 Map Score: 2.64574 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 23 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 13 CACTTTTTGCGCTTATGTATGCATAGAAGC 1 10 0 GCTTAGTATG 0.958337 -291 TCTGTCACTTGCTTAGGTATGAAGGTAAGCG 1 60 1 GCTTAGTATG 0.958337 -241 AAGAAATTTCGCTTTAATACGATAAAAAAGC 5 34 0 GCTTTATACG 0.910274 -139 TACTACTTTGACATTGATATGTTCAATTCAT 5 92 1 ACATTATATG 0.813193 -81 TGGCAGAAAAACTTAAATATGACAGCAAAGG 10 22 0 ACTTAATATG 0.946367 -164 GTAACCGCTTACTTTTATATGATAATATCAA 12 64 0 ACTTTATATG 0.946366 -154 ***** ***** Masking position 4 Map Score: 0.146612 Number of sites scoring better than the average of aligned sites = 87 Number in coding regions = 75 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 14 ********** No masking Map Score: -5.24137e-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 15 ********** No masking Map Score: -5.24137e-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