AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -ifruR_mjan_opreg_300.orf -g0.314 -x5 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 = 0.314 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 MJ0107 167 dihydropteroate synthase #2 MJ0542 127 phosphoenolpyruvate synthase #3 MJ0543 132 ubiquinol-cytochrome C reductase complex, subunitVI requiring protein #4 MJ0544 103 dolichyl-phosphate mannose synthase #5 MJ0547 165 cell division inhibitor minD #6 MJ0548 111 conserved hypothetical protein #7 MJ0641 166 phosphoglycerate kinase (pgk) #8 MJ0720 194 3-isopropylmalate dehydrogenase 1 (leuB1) #9 MJ1596 226 3-isopropylmalate dehydrogenase 2 (leuB2) Motif number 1 TAATTAAATTAAAACATAATTTATACTTAGCT 1 15 0 AAAATAATTT 0.679484 -153 TAGATGCCCTTAAGCATAAATTTTCTTTAAAA 1 100 1 TAAATAAATT 0.59286 -68 TCGTAGAAATAAATTTTTTAAAGAAAATTTAT 1 115 0 AAATTTTAAA 0.844218 -53 CGAAAGTCCTAAATCTTATATTGACTATGAAA 1 144 1 AAATTATATT 0.732888 -24 AAATGTTATAAAAAATTAAAAAAAGTTTCATA 2 12 0 AAATTAAAAA 0.95724 -116 ATTTGAATGATAATATTATAAATAAAATAGTA 2 60 0 TAATTATAAA 0.781232 -68 TATTTTAAAATAAATTTAAATATTTGAATGAT 2 81 0 TAATTAAATA 0.919492 -47 AAAATAACAGTAAGCTTTAAATATTAAGTTAA 3 12 1 TAATTTAAAT 0.565164 -121 ATTGTGATGCTAATATTTTTAACTTAATATTT 3 30 0 TAATTTTTAA 0.567336 -103 GCATCACAATAAATTTTATATATTGGGAATTG 3 52 1 AAATTATATA 0.919542 -81 TTATTACCATAAAATTTTAAAATTTTGTTAAA 4 47 1 AAATTTAAAA 0.931359 -57 TCTAAAATCTTTATATTACCTATTTA 5 150 0 AAATTTATAT 0.663566 -16 TTATTATCGTTAATCTTATATATTAGTTATTA 6 52 0 TAATTATATA 0.820439 -60 ATTATTAAGTTAATTTTAATAACTGAT 7 6 0 TAATTAATAA 0.843933 -161 AAATATAAAGAAATCTTAAATAATTATTAAGT 7 28 0 AAATTAAATA 0.966265 -139 GTTTTTGCAGAAAGAATAAATATAAAGAAATC 7 45 0 AAAATAAATA 0.938217 -122 CTTTCTGCAAAAACCTTAAAAACTTTAAAATG 7 63 1 AAATTAAAAA 0.95724 -104 AAAAACTTTAAAATGATAATTAGGAAATATCT 7 80 1 AAAATAATTA 0.89028 -87 AAAACTTCTAAAAACATAAAAATCTTAGAGGG 7 145 1 AAAATAAAAA 0.922368 -22 AAAATGATTTTAAAATTAAAAATAAAACTTTT 8 20 1 TAATTAAAAA 0.899407 -175 AAAACAACACAAAATATAAATACTTATAATGC 8 64 0 AAAATAAATA 0.935129 -131 ACCATATCAAAAATGATTAAAATACTCAACAA 8 96 0 AAAATTAAAA 0.878067 -99 AGTCACCAACAAAACATTTTTATGTGAAAGTA 8 131 1 AAAATTTTTA 0.68679 -64 TTTTTATGTGAAAGTATTTTTATTAATATTGC 8 147 1 AAAATTTTTA 0.682579 -48 TTATCACCAAAAAGATTAATTATAGCAATATT 8 171 0 AAATTAATTA 0.945473 -24 TATTTCTATTAAACGTTAATAAGAGGGATAAA 9 12 0 AAATTAATAA 0.931359 -215 ATAGAAATAGAAACAATAAATATACCGTATTA 9 35 1 AAAATAAATA 0.938217 -192 AAGATATTTTTAAGTATTAATACGGTATATTT 9 52 0 TAAATTAATA 0.785964 -175 ATTTATTAATAAACTTTAATTAATTTTGAAGA 9 96 0 AAATTAATTA 0.945431 -131 ATTTATTGTCAAATATTTATTAATAAACTTTA 9 110 0 AAATTTATTA 0.908578 -117 ATTTGACAATAAATATTTAAATGCCTTCCTTT 9 128 1 AAATTTAAAT 0.764936 -99 GACAGCACCAAAAACTTTTTTATATAGTGTCT 9 204 0 AAATTTTTTA 0.807753 -23 *** ******* Masking position 7 Map Score: 42.1243 Number of sites scoring better than the average of aligned sites = 3655 Number in coding regions = 2358 Number in noncoding regions = 1297 Number of orfs with sites within 600 bp upstream = 675 Fraction of orfs with sites within 600 bp upstream = 0.108416 Motif number 2 TTATGTTTTAATTTAATTACATTTATAGTTTTCAT 1 28 1 ATTTATATTA 0.710255 -140 TCTAAATGCCTTTTAATATATAATACTGCGAAAGT 1 69 0 TTTTAATATA 0.675617 -99 GCATAAATTTTCTTTAAAAAATTTATTTCTACGAA 1 113 1 TCTTAAATTA 0.905777 -55 TTTTTTTAATTTTTTATAACATTTTCACTTGTAAT 2 20 1 TTTTAAATTT 0.920327 -108 TAACTCTACTATTTTATTTATAATATTATCATTCA 2 54 1 ATTTATTATA 0.342132 -74 TATAGCTTTTATTTTAAAATAAATTTAAATATTTG 2 87 0 ATTTAAAATT 0.930831 -41 ATGCTAATATTTTTAACTTAATATTTAAAGCTTAC 3 21 0 TTTTATTTTT 0.342189 -112 GCTAGTAAATTTTTAACAAAATTTTAAAATTTTAT 4 55 0 TTTTAAATTT 0.920327 -49 GACACGCTTATCTTCAAAAACATTACATCATTAAT 5 63 0 TCTTAAAATA 0.905777 -103 TATATATTTAACTTAACTATAACTTTAGTGTTGTA 5 117 1 ACTTATAATT 0.738581 -49 AAATATTACTATTTAATAACTAATATATAAGATTA 6 39 1 ATTTAAAATA 0.920294 -73 ATTAAAATTAACTTAATAATTATTTAAGATTTCTT 7 18 1 ACTTAAAATT 0.930061 -149 TTTTAAGGTTTTTGCAGAAAGAATAAATATAAAGA 7 49 0 TTTGAAAATA 0.611206 -118 AACCTTAAAAACTTTAAAATGATAATTAGGAAATA 7 74 1 ACTTAAAAAA 0.388394 -93 ATTATCGTCATTTGTAGAAACTTTTCTTAGATATT 7 105 0 TTTGAAATTT 0.649129 -62 GATTTTTATGTTTTTAGAAGTTTTAATAGATTATC 7 134 0 TTTTAAATTA 0.907541 -33 TTTATTTTTAATTTTAAAATCATTTTGGTGATTAA 8 11 0 ATTTAAAATT 0.931411 -184 TTTTAATCATTTTTGATATGGTTTAAGTCACCAAC 8 106 1 TTTTAATTTA 0.675637 -89 AAATACTTTCACATAAAAATGTTTTGTTGGTGACT 8 131 0 ACATAAATTT 0.579567 -64 CCGTATTAATACTTAAAAATATCTTTAAACTATAC 9 59 1 ACTTAAATTT 0.930136 -168 AACTATACTGTCTTCAAAATTAATTAAAGTTTATT 9 86 1 TCTTAAAATT 0.918657 -141 ATTAATAAATATTTGACAATAAATATTTAAATGCC 9 118 1 ATTTAAAATA 0.920288 -109 GCTACTGGTTACTTCAAAATGTTTTTGAAAGACAC 9 175 1 ACTTAAATTT 0.930136 -52 GAAAGACACTATATAAAAAAGTTTTTGGTGCTGTC 9 201 1 ATATAAATTT 0.584637 -26 **** * ** * ** Masking position 6 Map Score: 21.3234 Number of sites scoring better than the average of aligned sites = 1347 Number in coding regions = 969 Number in noncoding regions = 378 Number of orfs with sites within 600 bp upstream = 336 Fraction of orfs with sites within 600 bp upstream = 0.0539672 Motif number 3 GTATAAATTATGTTTTAATTTAATTACATTT 1 21 1 TGTTTTATTT 0.971795 -147 TTACATTTATAGTTTTCATTTTAAGACTTTC 1 44 1 AGTTTTATTT 0.953084 -124 TTATGAAACTTTTTTTAATTTTTTATAACAT 2 11 1 TTTTTTATTT 0.841474 -117 GATTATATATAGCTTTTATTTTAAAATAAAT 2 98 0 AGCTTTATTT 0.792774 -30 GGACTATGTGTGTTTTCAATTCCCAATATAT 3 69 0 TGTTTTAATT 0.860618 -64 CTATTTTGGCTGTTTCGTTTTATAGATAAAG 3 104 0 TGTTTCTTTT 0.886322 -29 TAGGAATTGGTGTTTTTAGTT 4 1 0 TGTTTTAGTT 0.960833 -103 CCCTCTAAGATTTTTATGTTTTTAGAAGTT 7 147 0 ATTTTTTGTT 0.567816 -20 TTCCCTTAAAAGTTTTATTTTTAATTTTAAA 8 28 0 AGTTTTTTTT 0.922944 -167 TATTTTGTGTTGTTTTTTGTTGAGTATTTTA 8 80 1 TGTTTTTGTT 0.935334 -115 GTATATTTATTGTTTCTATTTCTATTAAACG 9 29 0 TGTTTCATTT 0.929695 -198 ****** **** Masking position 5 Map Score: 10.1515 Number of sites scoring better than the average of aligned sites = 427 Number in coding regions = 341 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 4 ATATATAAAATTTATTGTGATGCTAATATTT 3 44 0 TTTATTGTGT 0.959844 -89 ATTTTAAAATTTTATGGTAATAAGAAAAAGT 4 39 0 TTTATGGTAT 0.864926 -65 GCATCCAATTTATATTGTGATTACCT 4 88 1 TATATTGTGT 0.912268 -16 TTTTAAAATCATTTTGGTGATTAA 8 4 0 ATTTTGGTGT 0.930291 -191 TAAGTATTTATATTTTGTGTTGTTTTTTGTT 8 70 1 TATTTTGTGT 0.931224 -125 ATAATTAATCTTTTTGGTGATAAGT 8 180 1 TTTTTGGTGT 0.984682 -15 TATAAAAAAGTTTTTGGTGCTGTCT 9 212 1 TTTTTGGTGT 0.984682 -15 ********* * Masking position 5 Map Score: 6.15764 Number of sites scoring better than the average of aligned sites = 161 Number in coding regions = 110 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 5 GCTATATATAATCCCCTATATA 2 116 1 ATCCCTATAT 0.966247 -12 TGTGTTTTCAATTCCCAATATATAAAATTTA 3 61 0 ATTCCAATAT 0.911603 -72 ATCATCACCTATTTTGGCTGTTTC 3 119 0 ATCCCTATTT 0.973874 -14 TAAAAACACCAATTCCTATTTTTCTACTTTT 4 14 1 AATCCTATTT 0.86501 -90 AAATCTTTATATTACCTATTTACAACACTAA 5 141 0 ATTCCTATTT 0.96862 -25 TTTCTTAGATATTTCCTAATTATCATTTTAA 7 87 0 ATTCCTAATT 0.930611 -80 TTAATCACCAAAATGATTTTAAAA 8 4 1 ATCCCAAAAT 0.844178 -191 *** ******* Masking position 8 Map Score: 4.7758 Number of sites scoring better than the average of aligned sites = 104 Number in coding regions = 84 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 6 ATAGTAGAGTTATTACAAGTGAAAATGTTA 2 36 0 TATTACAAGT 0.79741 -92 TTATTTATAATATTATCATTCAAATATTTA 2 67 1 TATTATCATT 0.842476 -61 ATCATTCAAATATTTAAATTTATTTTAAAA 2 81 1 TATTTAAATT 0.733071 -47 TACTTTTTCTTATTACCATAAAATTTTAAA 4 38 1 TATTACCATA 0.561592 -66 AACTAACAAATATTACTATTTAATAACTAA 6 32 1 TATTACTATT 0.957706 -80 TATTAGTTAGTATTATTATTATCGTTAATC 6 69 0 TATTATTATT 0.916102 -43 TACTAACTAATATTATTAGTCTAAGGGGTG 6 87 1 TATTATTAGT 0.80802 -25 ATCAGTTATTAAAATTAACTTAATAA 7 7 1 TATTAAAATT 0.883946 -160 GCATTATAAGTATTTATATTTTGTGTTGTT 8 64 1 TATTTATATT 0.861985 -131 AAAGTATTTTTATTAATATTGCTATAATTA 8 157 1 TATTAATATT 0.946095 -38 TTATTGTTTCTATTTCTATTAAACGTTAAT 9 24 0 TATTTCTATT 0.889522 -203 AAATATACCGTATTAATACTTAAAAATATC 9 52 1 TATTAATACT 0.785822 -175 ********** Masking position 8 Map Score: 9.86499 Number of sites scoring better than the average of aligned sites = 321 Number in coding regions = 204 Number in noncoding regions = 117 Number of orfs with sites within 600 bp upstream = 132 Fraction of orfs with sites within 600 bp upstream = 0.0212014 Motif number 7 ATATATAATACTGCGAAAGTCTTAAAATGA 1 59 0 CTGCGAAAGT 0.988794 -109 AAATTTATTTCTACGAAAGTCCTAAATCTT 1 131 1 CTACGAAAGT 0.982771 -37 CTTATATTGACTATGAAAGT 1 158 1 CTATGAAAGT 0.973599 -10 AAACATTTTTATGTGAAAGTATTTTTATTA 8 142 1 ATGTGAAAGT 0.934883 -53 ********** Masking position 6 Map Score: 2.11804 Number of sites scoring better than the average of aligned sites = 60 Number in coding regions = 11 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 8 CAGTATTATATATTAAAAGGCATTTAGATGCCCTT 1 76 1 TATAAGATTT 0.637731 -92 AGAAAATTTATGCTTAAGGGCATCTAAATGCCTTT 1 91 0 TGTTAGATCT 0.970927 -77 TAATATTTAAAGCTTACTGTTATTTTG 3 3 0 AGTTAGATTT 0.923999 -130 TAACAACATTTGCTTATTGAACTTTAGGACTATG 5 10 0 TGTTAGCTTT 0.888404 -156 ATTAATTAATTGAATAAGGTTATCTAACAACATTT 5 34 0 TGATAGATCT 0.913348 -132 AGAAAGAATAAATATAAAGAAATCTTAAATAATTA 7 34 0 AAATAGATCT 0.737342 -133 AAGTTTTAATAGATTATCGTCATTTGTAGAAACTT 7 117 0 AGTTAGATTT 0.958581 -50 CCAAAAAGATTAATTATAGCAATATTAATAAAAAT 8 162 0 TATTAGATAT 0.733671 -33 AAGACAGTATAGTTTAAAGATATTTTTAAGTATTA 9 65 0 AGTTAGATTT 0.965072 -162 ** *** * **** Masking position 6 Map Score: 1.42006 Number of sites scoring better than the average of aligned sites = 139 Number in coding regions = 121 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 9 ATTTTCAAACTAACAAATATTACTATTTAA 6 25 1 TAACAAATAT 0.91916 -87 TACTATTTAATAACTAATATATAAGATTAA 6 45 1 TAACTAATAT 0.96307 -67 ATAATAATACTAACTAATATTATTAGTCTA 6 80 1 TAACTAATAT 0.96307 -32 GAAAGTATTTTTATTAATATTGCTATAATT 8 156 1 TTATTAATAT 0.811474 -39 AATATTGCTATAATTAATCTTTTTGGTGAT 8 171 1 TAATTAATCT 0.887401 -24 TAATAAACTTTAATTAATTTTGAAGACAGT 9 92 0 TAATTAATTT 0.834344 -135 TAAAGTTTATTAATAAATATTTGACAATAA 9 110 1 TAATAAATAT 0.903917 -117 ********** Masking position 6 Map Score: 5.15851 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 62 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 10 ********** No masking Map Score: -1.94446e-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 11 ********** No masking Map Score: -1.94446e-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 12 ********** No masking Map Score: -1.94446e-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