AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00020_ecoli_reg_100.orf -o00020_ecoli_100.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.51 -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 = 0.51 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 lpdA 300 lipoamide dehydrogenase (NADH); component of 2-oxodehydrogenase and pyruvate complexes; L-protein of glycine cleavage complex #2 acnB 300 aconitate hydrase B #3 prpC 41 putative citrate synthase; propionate metabolism? #4 citC 291 citrate lyase synthetase (citrate (pro-3S)-lyase ligase #5 gltA_sdhC 600 gltA: citrate synthase, sdhC: succinate dehydrogenase, cytochrome b556 #6 BIME45 63 BIME #7 sucC 85 succinyl-CoA synthetase, beta subunit #8 icdA 201 isocitrate dehydrogenase, specific for NADP+ #9 acnA 300 aconitate hydrase 1 #10 fumC 142 fumarase C= fumarate hydratase Class II; isozyme #11 fumA 198 fumarase A = fumarate hydratase Class I; aerobic isozyme #12 mdh 300 malate dehydrogenase #13 pckA 300 phosphoenolpyruvate carboxykinase #14 fumB 77 fumarase B= fumarate hydratase Class I; anaerobic isozyme #15 dcuB 300 anaerobic dicarboxylate transport #16 frdA 294 fumarate reductase, anaerobic, flavoprotein subunit Motif number 1 GCGAATAGACAAATCGGTTGCCGTTTGTTGTTT 1 51 1 ATCGGTGCCG 0.841312 -250 CATACCCGTCGTCTTTCAGGCCGCAGCGGCGTT 1 248 0 GTTTCGGCCG 0.837635 -53 GGTGATAATCACCTTTCTCAACGAATCCCAAGA 2 54 0 ATTTCCAACG 0.571316 -247 AGCGTGAAGAGAATCGCCTGCCGCACTATGACA 2 257 1 GTCGCTGCCG 0.974082 -44 AAATAAATCAAAATTTCACGCCGAAATACTCCT 4 213 1 ATTTCCGCCG 0.946733 -79 TGGAAGCAGTGTTTTGCATGACGCGCAGTTATA 5 30 0 GTTGCTGACG 0.961468 -571 CCCGTTTTTTATTTGGCTCGCCGCTCTGTGAAA 5 503 0 ATGGCCGCCG 0.971561 -98 AATAACGCGCATCTTTCATGACGGCAAACAATA 8 49 1 ATTTCTGACG 0.928915 -153 TAAAGCATCCGTATCGCAGGACGCAAACGCATA 8 129 1 GTCGCGGACG 0.863946 -73 GATAACACAAACATCGCGTAACGATTTGATAAC 9 220 0 ATCGCTAACG 0.835377 -81 AGTGAGCTAAAAGTTGCTTAACGAAAGCAAAAC 10 86 1 ATTGCTAACG 0.873588 -57 TTTTAAGCAGAATTTGCATGCCGTGACGCAGGC 12 14 0 ATTGCTGCCG 0.989266 -287 ATAAACGCTAAACTTGCGTGACTACACATTCTT 12 185 1 ATTGCTGACT 0.703697 -116 ATGCACTTTGCGTGCCGCCCGTGACTA 14 5 1 ATTGCTGCCG 0.989266 -73 TGTTATTCGAAAATGGCGTGCCGCGTAGTCACG 14 30 0 ATGGCTGCCG 0.980961 -48 CCTGCGTAAAATTTGTCTCGCCGTCGCGTTGCG 16 21 0 ATGTCCGCCG 0.90856 -274 * **** ***** Masking position 4 Map Score: 17.9418 Number of sites scoring better than the average of aligned sites = 1003 Number in coding regions = 947 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 2 GACAAATCGGTTGCCGTTTGTTGTTTAAAAAT 1 58 1 TTGCCGTGTT 0.601196 -243 ACCCTAACCACCACCGGGTCGTTCTATCCGTC 1 113 0 CCACCGGCGT 0.940015 -188 GTCTTTCAGGCCGCAGCGGCGTTAGCTTCACG 1 239 0 CCGCAGCCGT 0.946131 -62 AAAATTTAAACTACCGCCTCTTTATACTCGGA 2 16 0 CTACCGCCTT 0.921718 -285 AACTGCTGTCTCACAGGAGCGTGAAGAGAATC 2 240 1 TCACAGGCGT 0.755978 -61 TGGCTCGGGATTGCAGGGTGTTCCGGAGACCT 5 93 1 TTGCAGGGTT 0.412144 -508 ACAGCCTATACTGCCGCCAGGTCTCCGGAACA 5 111 0 CTGCCGCGGT 0.967447 -490 TTTATTTGGCTCGCCGCTCTGTGAAAGAGGGG 5 497 0 TCGCCGCTGT 0.878472 -104 TTGCGTAAGACTGCCGGAACTTAAATTTGCCT 5 557 0 CTGCCGGCTT 0.851 -44 GTTTGCTCGTCTGCCACCACGTTGCATATGCG 8 156 0 CTGCCACCGT 0.82786 -46 GACAACCCCGCCGCAGCGGGGTCAAGGATCAG 9 144 0 CCGCAGCGGT 0.947553 -157 GTCATTTGCTTTGCCACAAGGTTTCTCCTCTT 9 173 1 TTGCCACGGT 0.66815 -128 GTTCTCTCACTTACTGCCTGGTTTGGTTATGC 11 176 0 TTACTGCGGT 0.695312 -23 GGGTATATTGTCACCACCTGTTGGAATGTTGC 12 92 1 TCACCACGTT 0.508332 -209 TGTTGCTCCGCTGCCGCGACCTTAATCCACAA 12 245 0 CTGCCGCCCT 0.811963 -56 TTCACTGCTCCTTAGCCAATATG 13 288 0 TCACTGCCTT 0.768452 -13 GTGCATAAATTTGCCGCTGCTTTAATCAGCCA 15 137 1 TTGCCGCCTT 0.933157 -164 CAGCCAATATTCACTGTGAGGTATTTGCTAAA 15 163 1 TCACTGTGGT 0.453068 -138 GCTGAATAGATCACAGTCACGTTCTGTTTTGT 15 244 0 TCACAGTCGT 0.661382 -57 AAAATTTGTCTCGCCGTCGCGTTGCGAGTAGA 16 15 0 TCGCCGTCGT 0.921318 -280 TAGTCACTGCCCACCGCTGTTTGATTCCTGCG 16 48 0 CCACCGCTTT 0.725127 -247 GAACGCTATTCCACTGCTCCTTTATAGGTACA 16 202 0 CCACTGCCTT 0.831143 -93 TGTTTTTATCCCACAGCCACGTACTTCAGGGT 16 258 0 CCACAGCCGT 0.943367 -37 ******* *** Masking position 12 Map Score: 16.3795 Number of sites scoring better than the average of aligned sites = 5601 Number in coding regions = 5325 Number in noncoding regions = 276 Number of orfs with sites within 600 bp upstream = 256 Fraction of orfs with sites within 600 bp upstream = 0.0411179 Motif number 3 GCGCTTGCTACCTTGCTGCACCCAGAAATC 1 165 0 CCTTGCTGCA 0.742295 -136 GTGAAGCTAACGCCGCTGCGGCCTGAAAGA 1 240 1 CGCCGCTGCG 0.92115 -61 CTGCTATTCTGCCCGTTGCGGTACTGGGCA 2 199 1 GCCCGTTGCG 0.943532 -102 GAAGAGAATCGCCTGCCGCACTATGACAAT 2 262 1 GCCTGCCGCA 0.942326 -39 TTTTTATTTGGCTCGCCGCTCTGTGAAAGA 5 501 0 GCTCGCCGCT 0.727084 -100 ATATGCGTTTGCGTCCTGCGATACGGATGC 8 133 0 GCGTCCTGCG 0.832031 -69 TGATCCTTGACCCCGCTGCGGCGGGGTTGT 9 145 1 CCCCGCTGCG 0.984867 -156 TATGTTGCTCCGCTGCCGCGACCTTAATCC 12 249 0 CGCTGCCGCG 0.940319 -52 AATCTATGAGCCTTGTCGCGGTTAACACCC 13 230 1 CCTTGTCGCG 0.90902 -71 ATGCACTTTGCGTGCCGCCCGTGACTACG 14 10 1 GCGTGCCGCC 0.859017 -68 TTCGAAAATGGCGTGCCGCGTAGTCACGGG 14 28 0 GCGTGCCGCG 0.979189 -50 AAATTTGTCTCGCCGTCGCGTTGCGAGTAG 16 16 0 CGCCGTCGCG 0.918081 -279 GATAATTTAGCCCTCTTGCGCACTAAAAAA 16 128 1 CCCTCTTGCG 0.788481 -167 ********** Masking position 9 Map Score: 11.4247 Number of sites scoring better than the average of aligned sites = 2705 Number in coding regions = 2581 Number in noncoding regions = 124 Number of orfs with sites within 600 bp upstream = 122 Fraction of orfs with sites within 600 bp upstream = 0.0195952 Motif number 4 TTTACAAAATTGTTAACAATTTTTAAACAAC 1 77 0 TGTTACAATT 0.822204 -224 GGTGTTAATCTGTTTACAAAAAAGCAACATA 2 157 0 TGTTACAAAA 0.916137 -144 CAGTATAGGCTGTTCACAAAATCATTACAAT 5 130 1 TGTTACAAAA 0.916137 -471 GTTTCTCCTCTTTTATCAATTTGGGTTGTTA 9 193 1 TTTTTCAATT 0.656294 -108 CAATTTGGGTTGTTATCAAATCGTTACGCGA 9 209 1 TGTTTCAAAT 0.960499 -92 ACCAAACATTTGTTATCAAATGGTAAATAAT 10 54 1 TGTTTCAAAT 0.960499 -89 CTACACACTTTTTTAACAAAAACTGAGACTA 11 99 0 TTTTACAAAA 0.706773 -100 GTAAATTAATTGTTATCAAATTGATGTTGTT 12 47 1 TGTTTCAAAT 0.960499 -254 GTGTGGAAAATGTTCTCAAAAGGTTAAATCT 13 111 0 TGTTTCAAAA 0.941206 -190 TCACGGAGTTTTTTGTCAAATATGAATTTCT 13 188 1 TTTTTCAAAT 0.803238 -113 **** ****** Masking position 4 Map Score: 9.24191 Number of sites scoring better than the average of aligned sites = 56 Number in coding regions = 40 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 5 CCCGAGCCTCTTTGACGGATGTAATTAAAATGTTG 4 30 1 TTTAATTAAT 0.959001 -262 GTTTAAGTGATTTAATTGATTTAATGAATAAAATT 4 101 0 TTTAATTAAT 0.957186 -191 TTTTAAGTTTTTTAATTAATGTAATTACGAAATGA 4 143 0 TTTAATTAAT 0.958933 -149 GTTAGTGGTTTTTTATTTATTTAATGATTTTAAGT 4 170 0 TTTAATTAAT 0.958675 -122 TTTATTTAATTTTTAATCATCTAATTTGACAATCA 5 222 1 TTTAATTAAT 0.958675 -379 CAAGTTTAGCGTTTATGCATTTAATTGCCGTAATC 12 166 0 GTTAATTAAT 0.958194 -135 ACATATCTTAGTTTATCAATATAATAAGGAGTTTA 12 274 1 GTTAATTAAT 0.958206 -27 CGATCTGATGGTTTAGTAATTAAATTAATCATCTT 16 89 1 GTTAATAAAT 0.803982 -206 *** * ** **** Masking position 9 Map Score: 5.41975 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 18 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 6 CAATTTTGTAAAATACCGACGGATAGAACG 1 96 1 AAATACCGAC 0.944746 -205 TCAAAATTTAAACTACCGCCTCTTTATACT 2 20 0 AACTACCGCC 0.959617 -281 TGTTCAGGATAAAACCCGACAAACTATATG 5 168 0 AAAACCCGAC 0.964139 -433 ATCTTAGGTGAAATACCGACTTCATAACTT 5 306 0 AAATACCGAC 0.944746 -295 ATCGACAGAGAAAACGCGCCCATCCAGGAC 9 78 0 AAAACGCGCC 0.914347 -223 TGCCATGTAAAAAAACCGCCCCGAAGGGCG 10 18 0 AAAAACCGCC 0.978715 -125 AGGGCAACGGAACACCCGCCCAGAGCATAA 11 152 1 AACACCCGCC 0.973935 -47 ********** Masking position 2 Map Score: 5.66813 Number of sites scoring better than the average of aligned sites = 246 Number in coding regions = 186 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 7 TCATGCAAAACACTGCTTCCAGATGCGAAA 5 42 1 CACTGCTTCC 0.929121 -559 GATCATTACTCACTGATCCTTGACCCCGCT 9 132 1 CACTGATCCT 0.972863 -169 GGTTGCGAAGCCCTGATTCTCTTCAGGGTG 9 262 0 CCCTGATTCT 0.909444 -39 GACCTGCTCCTCACCTGATTA 10 132 0 ACCTGCTCCT 0.931541 -11 TTCACTGCTCCTTAGCCAATAT 13 289 0 CACTGCTCCT 0.990663 -12 AACGCTATTCCACTGCTCCTTTATAGGTAC 16 203 0 CACTGCTCCT 0.990663 -92 ********** Masking position 4 Map Score: 4.3084 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 48 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 8 TCAAAATCCTGCTATTCTGCCCGTTGCGGT 2 191 1 GCTATTCTGC 0.914644 -110 TCTGCCCGTTGCGGTACTGGGCATTTACCC 2 206 1 GCGGTACTGG 0.764352 -95 TTGTGAACAGCCTATACTGCCGCCAGGTCT 5 119 0 CCTATACTGC 0.620639 -482 GCCGGAGAAGGCGATAATGCCTTATCCGGT 6 37 0 GCGATAATGC 0.943628 -27 GCGTTATTAGGCTATAATGCGGCAATTCAT 8 27 0 GCTATAATGC 0.923454 -175 ACAAAAAATTGCTCTAAAGCATCCGTATCG 8 115 1 GCTCTAAAGC 0.627198 -87 CTACTGGTTTGCTCGTCTGCCACCACGTTG 8 164 0 GCTCGTCTGC 0.694056 -38 TCTCCTTCGAGCGCTACTGGTTTGCTCGTC 8 177 0 GCGCTACTGG 0.934104 -25 CTCTGTCGATGCTCTTCTGGGCCGAACTCC 9 98 1 GCTCTTCTGG 0.867684 -203 TTGGAATGTTGCGCTAATGCATAAGCGACT 12 112 1 GCGCTAATGC 0.957354 -189 CGCAAGTTTAGCGTTTATGCATTTAATTGC 12 173 0 GCGTTTATGC 0.689886 -128 CGAAACGGTTGCTATTATCGCAGAAATAGC 13 149 0 GCTATTATCG 0.409059 -152 GTGAACCCTCGCGATAATCCTATTTAAATT 15 279 0 GCGATAATCC 0.766501 -22 ********** Masking position 2 Map Score: 4.57187 Number of sites scoring better than the average of aligned sites = 1512 Number in coding regions = 1406 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 114 Fraction of orfs with sites within 600 bp upstream = 0.0183103 Motif number 9 TAATCTGTTTACAAAAAAGCAACATAAAAAAGT 2 150 0 ACAAAAAAAC 0.968912 -151 TAAATAAATAAAAAACCACTAACTCTATGTGAA 4 182 1 AAAAACAAAC 0.742621 -110 GAGCGGCGAGCCAAATAAAAAACGGGTAAAGCC 5 510 1 CCAAATAAAC 0.816064 -91 CAAGCCAATTACAAATCATTAACAAAAAATTGC 8 94 1 ACAAATAAAC 0.943515 -108 TTATCTCAACACAAAATAATAACCGTTAAGGGT 9 12 1 ACAAAAAAAC 0.968912 -289 TGAGAACAAAAAATAGACCGATAAATAT 15 6 1 ACAAAAAGAC 0.892217 -295 ATAACAGCAAACAAAACATTAACATCTGCGCAG 15 46 1 ACAAAAAAAC 0.968912 -255 TCTGCGCAGTACAAACTATAAACCCATCGCCAG 15 70 1 ACAAACAAAC 0.962739 -231 ****** * *** Masking position 8 Map Score: 3.28016 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 18 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 10 CGGATAGAACGACCCGGTGGTGGTTAGGGT 1 115 1 GACCCGGTGG 0.535073 -186 TACCTTGCTGCACCCAGAAATCCATAGGGT 1 157 0 CACCCAGAAA 0.639533 -144 GTAGGGTAAATGCCCAGTACCGCAACGGGC 2 209 0 TGCCCAGTAC 0.731956 -92 CCTTGCGGGTTGTCCCGAGCCTCTTTGACG 4 17 1 TGTCCCGAGC 0.605666 -275 TGTCGGGTTTTATCCTGAACAGTGATCCAG 5 177 1 TATCCTGAAC 0.428911 -424 TACCTGCAAGCGCCCAGAGCTCTGTACCCA 5 461 1 CGCCCAGAGC 0.955997 -140 TGACCGACAATGCCCGGAAGCGATACGAAA 7 14 1 TGCCCGGAAG 0.912947 -72 AGAGGAGTTCGGCCCAGAAGAGCATCGACA 9 101 0 GGCCCAGAAG 0.947793 -200 AGTGAGTAATGATCCAGAGGAGTTCGGCCC 9 116 0 GATCCAGAGG 0.664531 -185 CTTTAATATTCACCCTGAAGAGAATCAGGG 9 252 1 CACCCTGAAG 0.892866 -49 GTAAAAAAACCGCCCCGAAGGGCGGCTCTG 10 12 0 CGCCCCGAAG 0.943585 -131 ACGGAACACCCGCCCAGAGCATAACCAAAC 11 158 1 CGCCCAGAGC 0.955997 -41 TTCAGGTACTTACCCTGAAGTACGTGGCTG 16 247 1 TACCCTGAAG 0.839387 -48 ********** Masking position 5 Map Score: 3.38725 Number of sites scoring better than the average of aligned sites = 1350 Number in coding regions = 1280 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 11 GCTTTTTTCTGGTAATCTCATGAATG 1 7 1 TTCTGGTAAT 0.669809 -294 CTCCTGGGGATTCTGGCGCTTGCTACCTTG 1 180 0 TTCTGGCGCT 0.89127 -121 ATATATTTATCTCCGGCGGTCATACCCGTC 1 271 0 CTCCGGCGGT 0.968559 -30 CAAATTTAAGTTCCGGCAGTCTTACGCAAT 5 560 1 TTCCGGCAGT 0.948942 -41 TTATCGCCTTCTCCGGCAATTGAA 6 50 1 CTCCGGCAAT 0.976881 -14 GGCGCGTTTTCTCTGTCGATGCTCTTCTGG 9 88 1 CTCTGTCGAT 0.770765 -213 AGGTTCCTGATTACGGCAATTAAATGCATA 12 158 1 TTACGGCAAT 0.762897 -143 GACTTTACTATTCAGGCAATACATATTGGC 13 267 1 TTCAGGCAAT 0.862812 -34 GAGAAAGACTCTCTGGCGATGGGTTTATAG 15 85 0 CTCTGGCGAT 0.971669 -216 ********** Masking position 2 Map Score: 2.62886 Number of sites scoring better than the average of aligned sites = 1231 Number in coding regions = 1095 Number in noncoding regions = 136 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 12 TTAATGAATAAAATTTGCCACGATCATAAT 4 86 0 AAATTTGCCA 0.905061 -206 TTTAATCATCTAATTTGACAATCATTCAAC 5 233 1 TAATTTGACA 0.647548 -368 GCCGGAACTTAAATTTGCCTTCGCACATCA 5 547 0 AAATTTGCCT 0.790484 -54 TTCAATTGCCGGAGAAGGCGA 6 53 0 TCAATTGCCG 0.806788 -11 TCAGAGATTATGAATTGCCGCATTATAGCC 8 18 1 TGAATTGCCG 0.806788 -184 GTTTATGCATTTAATTGCCGTAATCAGGAA 12 161 0 TTAATTGCCG 0.83244 -140 CTTAATCCACAAAATTGCCGTTTACAATGA 12 227 0 AAAATTGCCG 0.952079 -74 GGAGAAATTCATATTTGACAAAAAACTCCG 13 191 0 ATATTTGACA 0.496147 -110 CACAGTGCATAAATTTGCCGCTGCTTTAAT 15 133 1 AAATTTGCCG 0.966763 -168 GATAAGTCTGAAATTTGACGAGATCGATTT 16 156 0 AAATTTGACG 0.891389 -139 ********** Masking position 5 Map Score: 2.12182 Number of sites scoring better than the average of aligned sites = 639 Number in coding regions = 568 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 13 GCACCCAGAAATCCATAGGGTATGTGAAGTA 1 147 0 ATCATAGGGT 0.811221 -154 AACTTCGTTAATTCGCATGGTGATAATCACC 2 74 0 ATTGCATGGT 0.669388 -227 CAACGGGCAGAATAGCAGGATTTTGACGAGG 2 186 0 AATGCAGGAT 0.669388 -115 TGAGACAGCAGTTTGTAGGGTAAATGCCCAG 2 222 0 GTTGTAGGGT 0.938386 -79 CATTGTTATCATTTGTAGGGTCGAGATTGT 3 10 0 ATTGTAGGGT 0.955338 -32 GGTGGCTCGGGATTGCAGGGTGTTCCGGAGA 5 91 1 GATGCAGGGT 0.942858 -510 CCTACATATAGTTTGTCGGGTTTTATCCTGA 5 164 1 GTTGTCGGGT 0.760547 -437 CATGACGGCAAACAATAGGGTAGTATTGACA 8 65 1 AACATAGGGT 0.811223 -137 GCTCCTCCTTAATGACAGGGTTGCGAAGCCC 9 279 0 AATACAGGGT 0.867354 -22 GTTTTGGCTGAACGGTAGGGTATATTGTCAC 12 75 1 AACGTAGGGT 0.938386 -226 *** ******* Masking position 11 Map Score: 1.47168 Number of sites scoring better than the average of aligned sites = 305 Number in coding regions = 262 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 14 ********** No masking Map Score: 6.16994e-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 AACCGATTTGTCTATTCGCTAATAACCTCAA 1 39 0 TCTATTCGTA 0.820411 -262 TCTATGTATTTTGATTCAACATTTTAATTAC 4 50 0 TTGATTCACA 0.932739 -242 CGTGGCAAATTTTATTCATTAAATCAATTAA 4 94 1 TTTATTCATA 0.758023 -198 TGCTAAGTACTTGATTCGCCATTTATTCGTC 5 416 1 TTGATTCGCA 0.94365 -185 TGATTCGCCATTTATTCGTCATCAATGGATC 5 427 1 TTTATTCGCA 0.932739 -174 CGGTAAAGTATCGATTCACCACGCTAACTTT 13 14 0 TCGATTCACA 0.94365 -287 GTGACTGTGATCTATTCAGCAAAAATTTAAA 15 256 1 TCTATTCACA 0.932739 -45 ******** ** Masking position 4 Map Score: 0.670663 Number of sites scoring better than the average of aligned sites = 128 Number in coding regions = 102 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912