AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00271_bsub_reg_300.orf -o00271_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 metS 300 methionyl-tRNA synthetase #2 yjcI 300 similar to cystathionine gamma-synthase #3 metC 300 cobalamin-independent methionine synthase #4 ykrB 300 similar to formylmethionine deformylase #5 yloB 115 similar to calcium-transporting ATPase #6 yloC 82 similar to hypothetical proteins #7 yloD 233 similar to guanylate kinase #8 yloI 80 similar to pantothenate metabolism flavoprotein #9 def 26 polypeptide deformylase #10 metB 300 homoserine O-succinyltransferase #11 yrhA 64 similar to cysteine synthase #12 yrrT 192 yrrT #13 metK 300 S-adenosylmethionine synthetase Motif number 1 GCTCCCGCCCAAAGGACGAGAGCGGCGATAA 1 250 0 AAAGGCGAGA 0.867813 -51 TCTTATCGTGAGAGGTGGAGGGACTGGCCCT 2 124 1 AGAGGGGAGG 0.992732 -177 TTTTACATATAAAGGAGGAGAAACA 3 286 1 AAAGGGGAGA 0.987387 -15 TGGCGTAATTAAAAGAGGAGGTTATGTAATA 4 13 1 AAAAGGGAGG 0.913237 -288 TGGATATGGTTACGGCGGAGGCTGCTGCAGT 4 48 1 TACGGGGAGG 0.973525 -253 AGCTGCTTATTTAGGTGGAGGCTGTTGCTAA 4 171 1 TTAGGGGAGG 0.959632 -130 ATAATTATCGAATGCAGGAAGAATGAGAGGG 5 15 0 AATGCGGAAG 0.70752 -101 AAATCATCCGATTGGCGGAGATGATATTGCC 7 117 0 ATTGGGGAGA 0.899921 -117 TGTAAAGTGCAGAGGGGGAGAATTCA 8 65 1 AGAGGGGAGA 0.982901 -16 CTATACGTGTTGAGGGGGAAACAACAGAAAA 10 209 0 TGAGGGGAAA 0.760646 -92 ACGGGGAAATAATGGAGGTGGCACG 10 286 1 AATGGGGTGG 0.887434 -15 TTTAGAGAAAAACGGAGGAGAACGTTCTCCC 11 15 0 AACGGGGAGA 0.967789 -50 CAACCTCTATTAAGGAGGAGGACATAT 11 48 1 TAAGGGGAGG 0.98967 -17 ATGACTTGTGAAAGCTGGAGGGTCAAGAC 12 9 0 AAAGCGGAGG 0.979871 -184 CGGGAGGCCTTGTGCAGGAGGAAGCAAATC 13 281 1 TGTGCGGAGG 0.894991 -20 ***** ***** Masking position 8 Map Score: 20.9517 Number of sites scoring better than the average of aligned sites = 621 Number in coding regions = 440 Number in noncoding regions = 181 Number of orfs with sites within 600 bp upstream = 179 Fraction of orfs with sites within 600 bp upstream = 0.0287504 Motif number 2 GTCTTGATTTAAAAGGATTTTTAGTAGGATAATAG 1 18 0 AAAGGTTTTT 0.921348 -283 ATGAAAATAAAAAAAGTCTGTTCGTGTCGAATTTT 1 94 0 AAAAGTGTTT 0.93576 -207 TTTATTTTCATTAAAGATTTTTAATTTTAATTATT 1 118 1 TAAAGTTTTT 0.561544 -183 CTTCTTATGAAGAAGGGGTTTTTATTTTGAAAAGG 2 261 1 AAAGGTTTTT 0.921348 -40 ACTCTCGATAAGAGAAAATGTTATTAATTTT 3 7 0 AAGAATGTTT 0.760558 -294 CCCATGAGAGAAAGAGGCTTTTCTACGTAAAACAC 3 189 0 AAGAGTTTTA 0.830045 -112 CTCTCATGGGAAAGAGGCTTTTTGTTGTGAGAAAA 3 214 1 AAGAGTTTTT 0.957516 -87 TCCGCGGGTGAAAGAGAGTGTTTTACATATAAAGG 3 266 1 AAGAGTGTTA 0.88711 -35 CAAAGATGTAAGAGGGAATTGTAATGTTTTATAGA 10 120 0 AAGGGTTGTT 0.872338 -181 CTGTGAAACCAAAAGGCGTGTCAGTGCGTTTTATT 10 167 1 AAAGGTGTCT 0.805303 -134 CGTTTTATTTAAAGAGTTTTCTGTTGTTTCCCCCT 10 193 1 AAGAGTTCTT 0.741253 -108 CTCCTCCTTAATAGAGGTTGTTTTTAGAGAAAAAC 11 33 0 AAGAGTGTTT 0.973237 -32 CATAAAATACACAAAGTGTTTTAGTACCTGCTTTT 12 84 1 AAAAGTTTTT 0.900438 -109 ATGTGGTATTATAGGAACTGTTCCATCATTAATCC 12 125 1 AAGGATGTTA 0.471322 -68 GCTGGGCTTCATAGGGCCTGTCCCTCCGCCAGCTC 13 15 0 AAGGGTGTCT 0.911743 -286 TCCATCGAGGAAAGGGTTTGGTCTTTGTGCCTTTC 13 145 0 AAGGGTGGTT 0.916703 -156 TCCTCGATGGAAAAGGTTTTTTTATTTCATAAATA 13 169 1 AAAGGTTTTT 0.921348 -132 TACAGTTATATTAGAGAATGTTAATTGGCATATTT 13 199 0 TAGAGTGTTT 0.837471 -102 * **** **** * Masking position 9 Map Score: 16.2009 Number of sites scoring better than the average of aligned sites = 675 Number in coding regions = 516 Number in noncoding regions = 159 Number of orfs with sites within 600 bp upstream = 162 Fraction of orfs with sites within 600 bp upstream = 0.0260199 Motif number 3 TTAGAAACCTCAGCAACCGGCTTGTTTTGCATT 2 154 1 CAGCACCGGT 0.983624 -147 TTGCTGGATTTAGCACCTTGGCGCTTTGCAAAT 2 184 0 TAGCACTTGG 0.910566 -117 TTGACCCCAACAGCAACCGACCGTAATACCATT 3 61 1 CAGCACCGAG 0.8809 -240 CTGATGGAATTAGCACCGTGCCTTATGAGACAT 3 130 0 TAGCACGTGT 0.952143 -171 GAAAACCTCTTAGCAGCCTGTATCCGCGGGTGA 3 244 1 TAGCACCTGT 0.99171 -57 CCGCGGTCTCTTGCATCCTGAATCATCCGTTTG 7 176 0 TTGCACCTGT 0.944201 -58 TAGCACAAGTAGCAACCTATATCATGTAGGTT 8 10 1 TAGCACCTAT 0.971373 -71 CGGAAAAAAATAACAACCTACATGATATAGGTT 8 24 0 TAACACCTAT 0.747762 -57 CTATGAAGCCCAGCAACCGGTTTCTCTGTTATT 13 36 1 CAGCACCGGT 0.983841 -265 TGCAACAGGTTAGCACCTTGGTTGTCTCACTCA 13 82 0 TAGCACTTGT 0.959471 -219 ***** **** * Masking position 5 Map Score: 8.88283 Number of sites scoring better than the average of aligned sites = 234 Number in coding regions = 208 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 4 TTTCTTCGTGTGCCGAACCGTTTAAAGAGAGAAATTTCT 2 21 0 TCCAGTAGAG 0.674315 -280 AACAAGCCGGTTGCTGAGGTTTCTAAGGGCCAGTCCCTC 2 141 0 TGCATTAGGG 0.718376 -160 TGAAGAAGGGGTTTTTATTTTGAAAAGGGAAGGTGTCAG 2 268 1 GTTATGAGGG 0.708086 -33 AATAACATTTTCTCTTATCGAGAGTTGGGCGAGGGATTG 3 17 1 TTCAGGTGGG 0.918997 -284 GTGCGCCCCATTTCACAATGGTATTACGGTCGGTTGCTG 3 71 0 TTCAGTACGG 0.835094 -230 CATCAGATTGTGTCTGAGAGATGAGAGAGGCAGTGTTTT 3 157 1 TTCAGTAGAG 0.938499 -144 GAAAAGCCTCTTTCTCTCATGGGAAAGAGGCTTTTTGTT 3 201 1 TTCTTGAGAG 0.810394 -100 TAGAGTGATATCTCTATAAGAGAGCAGGGGAGTGGACGA 5 82 1 TTCTGGAGGG 0.98419 -34 CATATGATATAATCTTAGGGGTAATAGCGTGTCTATTGC 6 14 1 ATCAGTAGCG 0.563314 -69 TCTATTGCCCTTTTATTATGAGAACAGGGAAGAATTGGG 6 45 1 TTTTGGAGGG 0.930987 -38 TTCCGTGCGGTTTTGTAAAGTGCAGAGGGGGAGAATTCA 8 52 1 TTTAGGAGGG 0.966367 -29 GATCTCACGTCTTGGAGGGTAACAAA 9 1 1 GTCATTAGGG 0.845131 -26 GTAAAATGATTTTCAAAGATGTAAGAGGGAATTGTAATG 10 129 0 TTCATTAGGG 0.949496 -172 ATTTTCAATCTATCTATACGTGTTGAGGGGGAAACAACA 10 214 0 TTCTGGAGGG 0.98419 -87 AGGTTGTATGATTCCTTGAGCGATAAGAGTGAAAGGCAC 13 115 1 ATCTGGAGAG 0.733877 -186 TAAAAAAACCTTTTCCATCGAGGAAAGGGTTTGGTCTTT 13 154 0 TTTAGGAGGG 0.966367 -147 * ** * * * **** Masking position 19 Map Score: 8.83669 Number of sites scoring better than the average of aligned sites = 319 Number in coding regions = 258 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 5 GCGCCAAGGTGCTAAATCCAGCAAGCGTTT 2 193 1 GCTAAATCCA 0.831336 -108 CTCCGCCGTAACCATATCCATACATATTAC 4 38 0 ACCATATCCA 0.901926 -263 ATCCGCAGCCACCATATCCGTAACCACCAT 4 80 0 ACCATATCCG 0.959229 -221 TGCGGCCGTAGCCATATCCGCAGCCACCAT 4 95 0 GCCATATCCG 0.990372 -206 AAATTGACCAGCCATATACGGCTGGTCATT 4 214 1 GCCATATACG 0.959228 -87 AGATGATATTGCCAAATCCGATATTAATCA 7 100 0 GCCAAATCCG 0.982184 -134 GCTAATTGACGCTACATACGGACGAAGAAC 7 212 1 GCTACATACG 0.816891 -22 CGTGCCACCTCCATTATTTCCCC 10 288 0 GCCACCTCCA 0.898514 -13 ********** Masking position 4 Map Score: 6.79854 Number of sites scoring better than the average of aligned sites = 312 Number in coding regions = 279 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 6 AAACCCCTTCTTCATAAGAAGAAGGGGTTT 2 252 0 TTCATAAGAA 0.738394 -49 AGACTGATGTCTCATAAGGCACGGTGCTAA 3 124 1 CTCATAAGGC 0.963853 -177 ATTCATATGATATAATCTTAG 6 2 1 TTCATATGAT 0.574275 -81 CTTCCCTGTTCTCATAATAAAAGGGCAATA 6 47 0 CTCATAATAA 0.614523 -36 CAATTAAGAACTCATAAGAAACCTAACGAT 10 39 1 CTCATAAGAA 0.873388 -262 TCATTATCAATTCATATGGCTCGTTTTTTA 10 81 1 TTCATATGGC 0.942599 -220 AAGCTTATACTTCATATGACTTGTGAAAGC 12 25 0 TTCATATGAC 0.744691 -168 TTTATGCCATCTCATATTGCGCATTGACCG 12 60 0 CTCATATTGC 0.840139 -133 GTTGCTGGGCTTCATAGGGCCTGTCCCTCC 13 23 0 TTCATAGGGC 0.90292 -278 ********** Masking position 5 Map Score: 3.44415 Number of sites scoring better than the average of aligned sites = 202 Number in coding regions = 168 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 7 TAATCAAATGAAATAAAAAACTTTGGTTCGA 1 55 0 AATAAAAAAC 0.951266 -246 TCTTTAATGAAAATAAAAAAAGTCTGTTCGT 1 104 0 AATAAAAAAA 0.862937 -197 AATTGCGCTAATATAAAACAATCAGAAAATT 2 81 1 AATAAAACAA 0.894169 -220 TATCTTCCAAGCATAAAAAACGCTTGCTGGA 2 209 0 GATAAAAAAC 0.916054 -92 TCCCTTTTCAAAATAAAAACCCCTTCTTCAT 2 267 0 AATAAAAACC 0.78614 -34 AGGCTTTTCTACGTAAAACACTGCCTCTCTC 3 179 0 AGTAAAACAC 0.900778 -122 CCTCCTTTATATGTAAAACACTCTCTTTCAC 3 273 0 AGTAAAACAC 0.900777 -28 TTAACAGAATGAATAAAACAACGATTAGCGC 4 130 0 GATAAAACAA 0.825279 -171 TAGAATGATAAGATAAAAAACGAGCCATATG 10 93 0 AATAAAAAAC 0.951266 -208 AAAACTCTTTAAATAAAACGCACTGACACGC 10 182 0 AATAAAACGC 0.831453 -119 ATATGAGATGGCATAAAATACACAAAGTGTT 12 73 1 GATAAAATAC 0.693764 -120 CATATTTATGAAATAAAAAAACCTTTTCCAT 13 175 0 AATAAAAAAA 0.862937 -126 * ********* Masking position 6 Map Score: 10.1161 Number of sites scoring better than the average of aligned sites = 241 Number in coding regions = 167 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 8 TTAGAAATTTCTCTCTTTAAACGGTTCGGC 2 19 1 CTCTCTTTAA 0.819755 -282 CCCTCCACCTCTCACGATAAGAAATATCGA 2 116 0 CTCACGATAA 0.590479 -185 CCTCGCCCAACTCTCGATAAGAGAAAATGT 3 21 0 CTCTCGATAA 0.911087 -280 ATTCTTCCTGCATTCGATAATTATAGCATG 5 22 1 CATTCGATAA 0.899428 -94 CGTCCCATTTCATGCTATAATTATCGAATG 5 32 0 CATGCTATAA 0.859937 -84 ATAGAGATATCACTCTATAAGCATGCTTAT 5 69 0 CACTCTATAA 0.972483 -47 ATAGAGTGATATCTCTATAAGAGAGCAGGG 5 81 1 ATCTCTATAA 0.718053 -35 GGGCAATAGACACGCTATTACCCCTAAGAT 6 25 0 CACGCTATTA 0.611056 -58 TTTATCTTATCATTCTATAAAACATTACAA 10 107 1 CATTCTATAA 0.941166 -194 AACAACAGAAAACTCTTTAAATAAAACGCA 10 191 0 AACTCTTTAA 0.549216 -110 TGCCAATTAACATTCTCTAATATAACTGTA 13 204 1 CATTCTCTAA 0.769381 -97 TATAACTGTACATTGTATAAGAGGGAGCGA 13 224 1 CATTGTATAA 0.629795 -77 ********** Masking position 10 Map Score: 3.5178 Number of sites scoring better than the average of aligned sites = 251 Number in coding regions = 169 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 9 TCGTTGTTTTATTCATTCTGTTAATCATTGT 4 137 1 ATTCATCTGT 0.854958 -164 GGCTGGTCAATTTCATGCTGTGTGGTTAGCA 4 196 0 TTTCAGCTGT 0.951943 -105 ACTCGTCCCATTTCATGCTATAATTATCGAA 5 34 0 TTTCAGCTAT 0.959829 -82 CTTATAGAGATATCACTCTATAAGCATGCTT 5 71 0 TATCATCTAT 0.939198 -45 TTTTTTATCTTATCATTCTATAAAACATTAC 10 104 1 TATCATCTAT 0.939198 -197 TCACGCCAATTTTCAATCTATCTATACGTGT 10 230 0 TTTCATCTAT 0.966465 -71 ***** ***** Masking position 5 Map Score: 1.19306 Number of sites scoring better than the average of aligned sites = 101 Number in coding regions = 79 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 10 TTGGAAGATAAGAAGAAGCGTTAAACCCCTT 2 230 1 AGAAGAAGGT 0.911711 -71 CTTCTTCATAAGAAGAAGGGGTTTAACGCTT 2 245 0 AGAAGAAGGG 0.987595 -56 CTTCTTCTTATGAAGAAGGGGTTTTTATTTT 2 258 1 TGAAGAAGGG 0.971936 -43 GAATGCAGGAAGAATGAGAGGGTGTA 5 6 0 AGAATGAGGG 0.922243 -110 GGGGGAACGTAGAAGATGACGATTAAACTGA 7 72 1 AGAAGATGCG 0.869419 -162 CCTGCTTTTCAGAATATGTGGTATTATAGGA 12 110 1 AGAATATGGG 0.943721 -83 AACTGTACATTGTATAAGAGGGAGCGAGTTC 13 227 1 TGTATAAGGG 0.77685 -74 ******** ** Masking position 4 Map Score: 1.15831 Number of sites scoring better than the average of aligned sites = 448 Number in coding regions = 396 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 11 AATATTCATATATGATTTGCACTTATCGCCG 1 228 1 TTGATTTGCA 0.916749 -73 TGAAATAAACTGTGAATTGCGCTAATATAAA 2 67 1 TTGAATTGCG 0.975641 -234 ATCGAAATCATCCGATTGGCGGAGATGATAT 7 121 0 TCGATTGGCG 0.965434 -113 GAATCATCCGTTTGATTGGCGCAGACTCCGG 7 159 0 TTGATTGGCG 0.984138 -75 ATGTTTACATTTTGAATTGCGATTTAAA 10 8 0 TTGAATTGCG 0.975675 -293 * ********* Masking position 5 Map Score: 0.563228 Number of sites scoring better than the average of aligned sites = 81 Number in coding regions = 71 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 12 ********** No masking Map Score: 1.61536e-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: 1.61536e-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 ********** No masking Map Score: 1.61536e-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