AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00710_mjan_reg_100.orf -o00710_mjan_100.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.31 -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 = 0.31 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: MJ1425 25 malate dehydrogenase Input sequences: #1 MJ0002 300 M. jannaschii predicted coding region MJ0002 #2 MJ0107 167 dihydropteroate synthase #3 MJ0641 166 phosphoglycerate kinase (pgk) #4 MJ0679 39 transketolase'' #5 MJ0680 23 pentose-5-phosphate-3-epimerase #6 MJ0681 156 transketolase' #7 MJ0684 68 aspartate aminotransferase (aspB2) #8 MJ1235 284 ribulose bisphosphate carboxylase, large subunit (rbcL) #9 MJ1424 202 tRNA intron endonuclease (endA) #10 MJ1479 259 putative aminotransferase #11 MJ1603 300 ribose 5-phosphate isomerase Motif number 1 ATGGGAACGCTGAAATATTTCCAGTAGCAC 1 43 1 TGAAATATTT 0.803136 -258 TGATTGGATATATTATATTTAGTGCTACTG 1 64 0 TATTATATTT 0.905762 -237 GTTTAGTTAATTAAAGGTTTATTTGGATTG 1 107 0 TTAAAGGTTT 0.814651 -194 TAATTTTTTATATAATTTTTTATAATTGGT 1 210 0 TATAATTTTT 0.889503 -91 ATAGGACTTATGTAATTTTTTATATAATTT 1 222 0 TGTAATTTTT 0.88275 -79 TTAATTACATTTATAGTTTTCATTTTAAGA 2 40 1 TTATAGTTTT 0.868913 -128 TCATAGTCAATATAAGATTTAGGACTTTCG 2 144 0 TATAAGATTT 0.892775 -24 TTAATAATTATTTAAGATTTCTTTATATTT 3 30 1 TTTAAGATTT 0.945765 -137 TTTTAAAGTTTTTAAGGTTTTTGCAGAAAG 3 63 0 TTTAAGGTTT 0.906405 -104 CCTCTAAGATTTTTATGTTTTTAGAAGTTT 3 146 0 TTTTATGTTT 0.917898 -21 ATAATTAATTTATTATTTTTGTTT 4 5 0 TATTATTTTT 0.889502 -35 AATTTTATTTTTTGGTGATTTA 5 3 1 TTTTATTTTT 0.944011 -21 ATTTACTATCTATTATTTTTAGGTGTAAGT 6 20 1 TATTATTTTT 0.889502 -137 TATTTTTAGGTGTAAGTTTTAAATATGACT 6 33 1 TGTAAGTTTT 0.867049 -124 TGAGTAATGATATTATTTTTTAAATCTTAA 6 125 1 TATTATTTTT 0.889502 -32 GTTTCACCTTTTTAAGATTTAAAAAATAAT 6 136 0 TTTAAGATTT 0.945765 -21 ATTCTATTTGTTAAATTTTTTCAAAATATT 8 41 1 TTAAATTTTT 0.884418 -244 TTGATTTGATTTTAATATTTTGAAAAAATT 8 54 0 TTTAATATTT 0.952677 -231 ATTCATCCTTTTTTATATTTGGTTAAAATA 8 119 1 TTTTATATTT 0.952677 -166 TACCTTTAGTTTATATATTTAAATTAATTA 8 176 0 TTATATATTT 0.901342 -109 CACAATAAATTTTAAGATTTTATAAATAAT 9 179 1 TTTAAGATTT 0.945765 -24 TTCTATTTTTTTATATGTTTGAAGTGTTAT 10 146 0 TTATATGTTT 0.835365 -114 AAGAAAATAATATTATTTTTGTGTTTTATC 11 79 0 TATTATTTTT 0.889502 -222 TTCATTATATTTATATATTTAAATCTATAA 11 113 1 TTATATATTT 0.901342 -188 TTTTTGTAATTTATAGATTTAAATATATAA 11 123 0 TTATAGATTT 0.887822 -178 GTGAAAGTCCTGTAATATTTCAATAACAAC 11 256 1 TGTAATATTT 0.899893 -45 ********** Masking position 8 Map Score: 37.5618 Number of sites scoring better than the average of aligned sites = 1656 Number in coding regions = 1177 Number in noncoding regions = 479 Number of orfs with sites within 600 bp upstream = 365 Fraction of orfs with sites within 600 bp upstream = 0.0586251 Motif number 2 ATTTTATAATAGGACTTATGTAATTTTTTATA 1 228 0 AGACTTAGTA 0.929922 -73 TTTTCATTTTAAGACTTTCGCAGTATTATATA 2 56 1 AGACTTTGCA 0.996122 -112 TATAAGATTTAGGACTTTCGTAGAAATAAATT 2 132 0 AGACTTTGTA 0.98826 -36 TGGTTAAAATAAGCCTTTAGCATTATTTTACT 8 138 1 AGCCTTTGCA 0.992098 -147 TCAATATTATAGAACTTTCGCAGGAATAAATG 9 20 1 AAACTTTGCA 0.961802 -183 TATAAAACCAAAGACTTTTATATTCTTACCTT 10 63 0 AGACTTTATA 0.96502 -197 TTCTTAATACAGGACTTTCACAGTCTATATAT 11 165 1 AGACTTTACA 0.98826 -136 ATGTAAAAAGATGCCTTTGGCATCAAAATTCC 11 204 0 AGCCTTTGCA 0.992098 -97 GAAATATTACAGGACTTTCACAGAGGATAAGA 11 245 0 AGACTTTACA 0.98826 -56 * ****** *** Masking position 6 Map Score: 15.6203 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 34 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 3 TAGCACTAAATATAATATATCCAATCAATG 1 67 1 TATAATATAT 0.66795 -234 TCAAAATACCAATTATAAAAAATTATATAA 1 203 1 AATTATAAAA 0.716999 -98 AATTATAAAAAATTATATAAAAAATTACAT 1 213 1 AATTATATAA 0.755612 -88 ACATAAGTCCTATTATAAAATACTACCAAT 1 239 1 TATTATAAAA 0.872972 -62 AAACTATAAATGTAATTAAATTAAAACATA 2 29 0 TGTAATTAAA 0.802991 -139 ACTTTCGCAGTATTATATATTAAAAGGCAT 2 69 1 TATTATATAT 0.846584 -99 ATCAGTTATTAAAATTAACTTAA 3 4 1 AGTTATTAAA 0.803512 -163 TTAACTTAATAATTATTTAAGATTTCTTTA 3 25 1 AATTATTTAA 0.826163 -142 TTTCACCCAAAATAATTAATTTATTATTTT 4 16 0 AATAATTAAT 0.481154 -24 TAAAAGGAATTATTATTAATTAATAATACT 7 28 0 TATTATTAAT 0.874491 -41 TATTTAAATTAATTATTGAACAGTAAAATA 8 161 0 AATTATTGAA 0.686234 -124 TGGTATTAAGTATTATTAATTTTTTGTATG 8 239 0 TATTATTAAT 0.874491 -46 TTCACCTCAATATTATAGAACTTTCGCAGG 9 14 1 TATTATAGAA 0.796043 -189 ATATGGTTTATGTTATTTAACAAAATTAAT 9 131 0 TGTTATTTAA 0.931784 -72 ATAAACCATATGTTATTTATTTTATTATCC 9 150 1 TGTTATTTAT 0.898864 -53 AGTTATTATTTATAAAATCTTAA 9 190 0 TATTATTTAT 0.894538 -13 ATGTTTGAAGTGTTATATATCGAATACTTA 10 132 0 TGTTATATAT 0.852552 -128 GAAATAATTGTAATATAATCATCGAAAC 11 9 1 TGTAATATAA 0.764115 -292 CCATAATCCCTATAATTAAAATCAGACCAA 11 44 1 TATAATTAAA 0.795532 -257 AAAAAGTTTTTGTAATTTATAGATTTAAAT 11 129 0 TGTAATTTAT 0.764142 -172 GTATTAAGAATGTTATAAAAAGTTTTTGTA 11 145 0 TGTTATAAAA 0.877991 -156 GAGGATAAGATATTATTTAATGTAAAAAGA 11 225 0 TATTATTTAA 0.928755 -76 GCTTTGTGGTTGTTATTGAAATATTACAGG 11 264 0 TGTTATTGAA 0.862757 -37 ********** Masking position 6 Map Score: 23.3629 Number of sites scoring better than the average of aligned sites = 846 Number in coding regions = 637 Number in noncoding regions = 209 Number of orfs with sites within 600 bp upstream = 219 Fraction of orfs with sites within 600 bp upstream = 0.0351751 Motif number 4 CTATAAATGTAATTAAATTAAAACATAATT 2 26 0 AATTAAATTA 0.513966 -142 TGCCCTTAAGCATAAATTTTCTTTAAAAAA 2 104 1 CATAAATTTT 0.825568 -64 CTTTCGTAGAAATAAATTTTTTAAAGAAAA 2 120 0 AATAAATTTT 0.894607 -48 ATAATTATTAAGTTAATTTTAATAACTGAT 3 11 0 AGTTAATTTT 0.804013 -156 AAATTAACTTAATAATTATTTAAGATTTCT 3 22 1 AATAATTATT 0.396603 -145 TTGCAGAAAGAATAAATATAAAGAAATCTT 3 43 0 AATAAATATA 0.586152 -124 CACCCAAAATAATTAATTTATTATTTTTGT 4 13 0 AATTAATTTA 0.910803 -27 ATTTACTATCTATTATTTTTAGGTGTAAGT 6 20 1 TATTATTTTT 0.703708 -137 TATGACTAACAATTATTTTAGCATAACATC 6 56 1 AATTATTTTA 0.837176 -101 TGAGTAATGATATTATTTTTTAAATCTTAA 6 125 1 TATTATTTTT 0.703708 -32 CACTAAAAGGAATTATTATTAATTAATAAT 7 31 0 AATTATTATT 0.634823 -38 TTGAAAGGCACATAAAATTAA 8 2 0 CATAAAATTA 0.229599 -283 TAATATTTTGAAAAAATTTAACAAATAGAA 8 42 0 AAAAAATTTA 0.226087 -243 TTAATGAATTAATAAATTTTCATTCCGAAT 8 83 0 AATAAATTTT 0.894607 -202 TTTATTAATTCATTAATTTTACATTCATCC 8 97 1 CATTAATTTT 0.902818 -188 AAGCCTTTAGCATTATTTTACTGTTCAATA 8 148 1 CATTATTTTA 0.74213 -137 ACTGTTCAATAATTAATTTAAATATATAAA 8 167 1 AATTAATTTA 0.910803 -118 TATTAAGTATTATTAATTTTTTGTATGGTC 8 236 0 TATTAATTTT 0.825391 -49 TTAATGAATGAATTAATATAGAACTTCGCA 9 106 0 AATTAATATA 0.737117 -97 TTAATTCATTCATTAATTTTGTTAAATAAC 9 120 1 CATTAATTTT 0.902818 -83 TATTATCCACAATAAATTTTAAGATTTTAT 9 172 1 AATAAATTTT 0.894607 -31 AGTTATTATTTATAAAATCT 9 193 0 AGTTATTATT 0.364415 -10 TAAAAATTGCAGTTAATTTTGAAAAGCACG 10 34 0 AGTTAATTTT 0.804013 -226 AAGAAAATAATATTATTTTTGTGTTTTATC 11 79 0 TATTATTTTT 0.703708 -222 ********** Masking position 9 Map Score: 22.0003 Number of sites scoring better than the average of aligned sites = 1297 Number in coding regions = 899 Number in noncoding regions = 398 Number of orfs with sites within 600 bp upstream = 328 Fraction of orfs with sites within 600 bp upstream = 0.0526823 Motif number 5 CCATTAATAGAGCATCAAAATACCAATTATAAA 1 189 1 AGCATCAATC 0.9866 -112 TATGCTTAAGGGCATCTAAATGCCTTTTAATAT 2 85 0 GGCATCTATC 0.991544 -83 GATGCCCTTAAGCATAAATTTTCTTTAAAAAAT 2 102 1 AGCATAATTC 0.856185 -66 ATAAGCCTTTAGCATTATTTTACTGTTCAATAA 8 146 1 AGCATTATTC 0.856185 -139 GATGCCTAAAGGCATCATTATTCAATAAATCAT 9 49 0 GGCATCAATC 0.994719 -154 GATGCCTTTAGGCATCTAAATACCTTTTTAATA 9 66 1 GGCATCTATC 0.991544 -137 AGATGCCTTTGGCATCAAAATTCCAAACTCAAT 11 195 0 GGCATCAATC 0.994712 -106 TGATGCCAAAGGCATCTTTTTACATTAAATAAT 11 211 1 GGCATCTTTC 0.98651 -90 ******* ** * Masking position 4 Map Score: 11.2677 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 28 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 6 TTGGAGATATTAAAAATCCAATAGC 1 286 1 TAAAAATCAT 0.455036 -15 CTTAAGGGCATCTAAATGCCTTTTAATATATA 2 82 0 TCTAAATCTT 0.811942 -86 AAAATTAACTTAATAATTATTTAAGATTTCTT 3 21 1 TAATAATATT 0.592451 -146 GATTTCTTTATATTTATTCTTTCTGCAAAAAC 3 45 1 TATTTATCTT 0.879023 -122 TTGCTTTTTTTATTAATTCATTGAGTAATGAT 6 104 1 TATTAATCTT 0.972629 -53 TATTATTAATTAATAATACTTTTCGTGGTGGC 7 16 0 TAATAATCTT 0.953034 -53 TATTAATTAATAATAATTCCTTTTAGTGTTTA 7 33 1 TAATAATCTT 0.953037 -36 AATGAAAATTTATTAATTCATTAATTTTACAT 8 89 1 TATTAATCTT 0.972629 -196 TATTAAGTATTATTAATTTTTTGTATGGTCGT 8 234 0 TATTAATTTT 0.818011 -51 ATTTATTGAATAATGATGCCTTTAGGCATCTA 9 52 1 TAATGATCTT 0.776977 -151 CCTTTAGGCATCTAAATACCTTTTTAATATAA 9 70 1 TCTAAATCTT 0.811942 -133 CGAAGTTCTATATTAATTCATTCATTAATTTT 9 108 1 TATTAATCTT 0.972629 -95 TCTTTGGTTTTATAAGTGCCTTTTCTATAGTA 10 81 1 TATAAGTCTT 0.684521 -179 TTCTTCATTATATTTATATATTTAAATCTATA 11 110 1 TATTTATTTT 0.478978 -191 ******* * ** Masking position 7 Map Score: 11.2741 Number of sites scoring better than the average of aligned sites = 318 Number in coding regions = 245 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 7 AAATACCAATTATAAAAAATTATATAAAAA 1 206 1 TATAAAAAAT 0.884102 -95 TAAAAAATTATATAAAAAATTACATAAGTC 1 218 1 TATAAAAAAT 0.884102 -83 TCCTAAATCTTATATTGACTATGAAAGT 2 150 1 TATATTGACT 0.619241 -18 TTAAGTTAATTTTAATAACTGAT 3 4 0 TTTAATAACT 0.547916 -163 GACGATAATCTATTAAAACTTCTAAAAACA 3 131 1 TATTAAAACT 0.805494 -36 CATCACCATTTATAAACACTAAAAGGAATT 7 47 0 TATAAACACT 0.878393 -22 TTAATTTAAATATATAAACTAAAGGTAAAG 8 179 1 TATATAAACT 0.946206 -106 GAAACGACCATACAAAAAATTAATAATACT 8 231 1 TACAAAAAAT 0.688882 -54 ACCTTTTTAATATAAAAACTGCGAAGTTCT 9 87 1 TATAAAAACT 0.976785 -116 AGTTATTATTTATAAAATCTTAAAATTTAT 9 183 0 TATAAAATCT 0.805494 -20 AGATTTTATAAATAATAACT 9 193 1 AATAATAACT 0.547915 -10 ATCCCAGTAGTATATAAACTTTACTCTTAA 10 183 0 TATATAAACT 0.946206 -77 ATCTATAAATTACAAAAACTTTTTATAACA 11 135 1 TACAAAAACT 0.924318 -166 CCAAACTCAATATATAGACTGTGAAAGTCC 11 176 0 TATATAGACT 0.847492 -125 ********** Masking position 10 Map Score: 11.7026 Number of sites scoring better than the average of aligned sites = 793 Number in coding regions = 621 Number in noncoding regions = 172 Number of orfs with sites within 600 bp upstream = 179 Fraction of orfs with sites within 600 bp upstream = 0.0287504 Motif number 8 AAATACCAATTATAAAAAATTATATAAAAAA 1 206 1 TATAAAAAAT 0.895336 -95 TAAAAAATTATATAAAAAATTACATAAGTCC 1 218 1 TATAAAAAAT 0.895336 -83 TCTCCAAAATTATTAGAAATTCTAATTGGTA 1 262 0 TATTAGAAAT 0.769856 -39 ATTTTGGAGATATTAAAAATCCAATAGC 1 283 1 TATTAAAAAC 0.724683 -18 AAAGAATAAATATAAAGAAATCTTAAATAAT 3 36 0 TATAAAGAAT 0.681123 -131 TTAGGAAATATCTAAGAAAAGTTTCTACAAA 3 99 1 TCTAAGAAAG 0.815306 -68 TCAATGAATTAATAAAAAAAGCAAAAACAAA 6 97 0 AATAAAAAAG 0.634946 -60 ATTTTTTAAATCTTAAAAAGGTGAAACT 6 139 1 TCTTAAAAAG 0.918625 -18 TTTAACCAAATATAAAAAAGGATGAATGTAA 8 115 0 TATAAAAAAG 0.953112 -170 ACACTATTTATATTAGAAACGACCATACAAA 8 216 1 TATTAGAAAG 0.888254 -69 GCAGTTTTTATATTAAAAAGGTATTTAGATG 9 78 0 TATTAAAAAG 0.953112 -125 ATTTATAAAATCTTAAAATTTATTGTGGATA 9 175 0 TCTTAAAATT 0.43403 -28 AAAAACTTACTATAGAAAAGGCACTTATAAA 10 89 0 TATAGAAAAG 0.720505 -171 ACTTCAAACATATAAAAAAATAGAACTCTAT 10 151 1 TATAAAAAAT 0.895336 -109 TAAACTTTACTCTTAAAATAGAGTTCTATTT 10 168 0 TCTTAAAATG 0.645679 -92 GAAAGTCCTGTATTAAGAATGTTATAAAAAG 11 153 0 TATTAAGAAG 0.83541 -148 ********* * Masking position 8 Map Score: 13.4769 Number of sites scoring better than the average of aligned sites = 619 Number in coding regions = 477 Number in noncoding regions = 142 Number of orfs with sites within 600 bp upstream = 158 Fraction of orfs with sites within 600 bp upstream = 0.0253774 Motif number 9 TTGTTGACGCATTGATTGGATATATTATATT 1 75 0 ATTGATGGAT 0.890084 -226 ATTTTTTATAATTGGTATTTTGATGCTCTAT 1 195 0 ATTGGTTTTT 0.803007 -106 AGAAATTCTAATTGGTAGTATTTTATAATAG 1 248 0 ATTGGTGTAT 0.926684 -53 AAAAATCCATAATGATGTTATGCTAAAATAA 6 68 0 AATGATTTAT 0.863889 -89 TTCATTGAGTAATGATATTATTTTTTAAATC 6 120 1 AATGATTTAT 0.863889 -37 TTCATTCCGAATTGATTTGATTTTAATATTT 8 64 0 ATTGATTGAT 0.943073 -221 ACCATATGTTATTTATTTTATTATCCACAAT 9 154 1 ATTTATTTAT 0.663187 -49 TATAAAAGTCTTTGGTTTTATAAGTGCCTTT 10 73 1 TTTGGTTTAT 0.803007 -187 TTTATCCCGAATTGGTCTGATTTTAATTATA 11 54 0 ATTGGTTGAT 0.955213 -247 ****** **** Masking position 6 Map Score: 2.46947 Number of sites scoring better than the average of aligned sites = 154 Number in coding regions = 136 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 10 ATTGGTGAAAACCATTATCAACAAACCATG 1 16 1 ACCATTATCA 0.959062 -285 CTAAATATTCTCCATAATCAGTTCTCAATG 1 138 1 TCCATAATCA 0.959056 -163 AAACAAAAAATCCATAATGATGTTATGCTA 6 74 0 TCCATAATGA 0.924292 -83 TGTGTAATTTACCATTATCCCAGTAGTATA 10 199 0 ACCATTATCC 0.951034 -61 AAAATAGAGTTCCATTTTGAGATGAAAAC 10 241 1 TCCATTTTGA 0.751129 -19 CGAAACTCCAACCATAATCCCTATAATTAA 11 33 1 ACCATAATCC 0.951034 -268 ********** Masking position 5 Map Score: 1.59459 Number of sites scoring better than the average of aligned sites = 79 Number in coding regions = 71 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 11 TGATAATGGTTTTCACCAATCCCAG 1 6 0 TTTCACCAAT 0.866628 -295 TGAAAACCATTATCAACAAACCATGGGAAC 1 21 1 TATCAACAAA 0.894188 -280 GGATTTTTAATATCTCCAAAATTATTAGAA 1 275 0 TATCTCCAAA 0.94608 -26 AAAAAATTTATTTCTACGAAAGTCCTAAAT 2 128 1 TTTCTACGAA 0.77631 -40 ATATTTATTCTTTCTGCAAAAACCTTAAAA 3 54 1 TTTCTGCAAA 0.884282 -113 CTAAGAAAAGTTTCTACAAATGACGATAAT 3 110 1 TTTCTACAAA 0.923217 -57 GATTTTTCACCCAAAATAATTAAT 4 26 0 TTTCACCCAA 0.916307 -14 TTAAATCACCAAAAAATAAAATT 5 11 0 AATCACCAAA 0.773176 -13 AAAGGCTTATTTTAACCAAATATAAAAAAG 8 126 0 TTTAACCAAA 0.801597 -159 ********** Masking position 3 Map Score: 2.19313 Number of sites scoring better than the average of aligned sites = 400 Number in coding regions = 314 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 103 Fraction of orfs with sites within 600 bp upstream = 0.0165435 Motif number 12 ********** No masking Map Score: 4.23727e-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: 4.23727e-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: 4.23727e-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