AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00040_mjan_reg_100.orf -o00040_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 Input sequences: #1 MJ0680 23 pentose-5-phosphate-3-epimerase #2 MJ0681 156 transketolase' #3 MJ1231 255 oxaloacetate decarboxylase alpha chain (oadA) #4 MJ1334 214 UDP-glucose pyrophosphorylase (gtaB) Motif number 1 TTACACCTAAAAATAATAGATAGTAAATAGAG 2 16 0 AAAAATAATA 0.657311 -141 TGTTAGTCATATTTAAAACTTACACCTAAAAA 2 35 0 ATTAAAATTA 0.9353 -122 TGTTATGCTAAAATAATTGTTAGTCATATTTA 2 52 0 AAAAATTTTA 0.656811 -105 ATCATTACTCAATGAATTAATAAAAAAAGCAA 2 104 0 AATAATTATA 0.928487 -53 CCTTTTTAAGATTTAAAAAATAATATCATTAC 2 128 0 ATTAAAAATA 0.941846 -29 TGTAGTATTGATTGAAATGATATATATGCTTT 3 23 0 ATTAAATATA 0.947764 -233 ATTGAGTTTAAATTAATTAATACAAAAATCTC 3 76 0 AATAATTATA 0.928487 -180 GATTAAGAAAATTTAAGATTTAGGAGATAAAA 3 107 0 ATTAAGATTA 0.861416 -149 AAATTTTCTTAATCAATTTTTGATGAGGGGTA 3 125 1 AATAATTTTG 0.896541 -131 GGTAACTATGATTGAAATTATAAGACTATGGC 3 153 1 ATTAAATATA 0.947764 -103 ATTTATTTTGATTTAAAAAAGGCACAGCCAAA 3 217 0 ATTAAAAAGG 0.722231 -39 TTTAAATCAAAATAAATATTTGTGAGGGATAG 3 232 1 AATAATATTG 0.88645 -24 ATTAAAATTTTATTTCCATTTT 4 1 1 ATTAAATTTA 0.941845 -214 TATATAATGCATTAAAAAATGGAAATAAAATT 4 16 0 ATTAAAATGG 0.69887 -199 AAAAAAAGCTATTGAAGTCATATATAATGCAT 4 36 0 ATTAAGTATA 0.886385 -179 ATTTTTATTAAATTAATTTATGTTACAATTAT 4 177 0 AATAATTATG 0.901656 -38 AAATTAATTTAATAAAAATTTACTAAAGGGAG 4 190 1 AATAAAATTA 0.928074 -25 *** **** *** Masking position 6 Map Score: 20.1395 Number of sites scoring better than the average of aligned sites = 2011 Number in coding regions = 1446 Number in noncoding regions = 565 Number of orfs with sites within 600 bp upstream = 426 Fraction of orfs with sites within 600 bp upstream = 0.0684227 Motif number 2 TTAAATCACCAAAAAATAAAATT 1 8 0 CACCAAAAAA 0.986604 -16 TTAAAACTTACACCTAAAAATAATAGATAG 2 25 0 CACCTAAAAA 0.963214 -132 AAAAAAGCAAAAACAAAAAATCCATAATGA 2 84 0 AAACAAAAAA 0.935657 -73 TCAATGAATTAATAAAAAAAGCAAAAACAA 2 98 0 AATAAAAAAA 0.681307 -59 TAGAACCTAAGTAAAGCATATAT 3 4 1 AACCTAAGTA 0.652471 -252 AGTTACCCCTCATCAAAAATTGATTAAGAA 3 130 0 CATCAAAAAT 0.875652 -126 GACTATGGCTAACCAAATAACGGAACTGCA 3 176 1 AACCAAATAA 0.962012 -80 AAAAAGGCACAGCCAAATAAAACGGCAATG 3 204 0 AGCCAAATAA 0.812991 -52 GCCTTTTTTAAATCAAAATAAATATTTGTG 3 226 1 AATCAAAATA 0.906069 -30 ATATATAATGCATTAAAAAATGGAAATAAA 4 19 0 CATTAAAAAA 0.71235 -196 TGCAAATGTGAAACTAAAATTCATTGAAGA 4 83 0 AAACTAAAAT 0.536679 -132 TCATAATCATCACCAAATTATTTATACCTA 4 132 1 CACCAAATTA 0.912508 -83 ********** Masking position 6 Map Score: 8.38198 Number of sites scoring better than the average of aligned sites = 1450 Number in coding regions = 1185 Number in noncoding regions = 265 Number of orfs with sites within 600 bp upstream = 232 Fraction of orfs with sites within 600 bp upstream = 0.0372631 Motif number 3 CATATTTAAAACTTACACCTAAAAATAATA 2 30 0 ACTTACACCT 0.97687 -127 AGTTTCACCTTTTTAAGATT 2 147 0 AGTTTCACCT 0.986869 -10 TTTCAATCATAGTTACCCCTCATCAAAAAT 3 140 0 AGTTACCCCT 0.991718 -116 AGCTATCCCTCACAAATATT 3 246 0 AGCTATCCCT 0.934833 -10 AATGAATTTTAGTTTCACATTTGCACTTTC 4 88 1 AGTTTCACAT 0.925544 -127 TCACCAAATTATTTATACCTACTATATTAA 4 141 1 ATTTATACCT 0.894402 -74 ********** Masking position 4 Map Score: 5.1977 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 39 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 4 AATTTTATTTTTTGGTGATTTAA 1 6 1 TATTTTTGAT 0.783663 -18 GTGTAAGTTTTAAATATGACTAACAATTATTTTA 2 42 1 TATATGTAAC 0.958214 -115 GACTAACAATTATTTTAGCATAACATCATTATGG 2 59 1 TATTAGTAAC 0.941406 -98 ATTGAAATGATATATATGCTTTACTTAGGTTCTA 3 11 0 TATATGTTAC 0.763407 -245 ATTTTTGTATTAATTAATTTAAACTCAATTTTAT 3 79 1 TATAATAAAC 0.675613 -177 TCCTAAATCTTAAATTTTCTTAATCAATTTTTGA 3 114 1 TATTTTTAAT 0.945563 -142 ATGACTTCAATAGCTTTTTTTAACTTTTCCTCAT 4 47 1 TATTTTTAAC 0.97062 -168 TTCCTCGAAATACTTTTTCATAATCATCACCAAA 4 115 1 TATTTTTAAT 0.945563 -100 ATTAATATAGTAGGTATAAATAATTTGGTGATGA 4 138 0 TATATATAAT 0.842546 -77 ATATTAATACTATATAATTGTAACATAAATTAAT 4 164 1 TATAATTAAC 0.942501 -51 AATTGTAACATAAATTAATTTAATAAAAATTTAC 4 179 1 TATTAATAAT 0.789437 -36 ** **** **** Masking position 2 Map Score: 7.16429 Number of sites scoring better than the average of aligned sites = 400 Number in coding regions = 292 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 126 Fraction of orfs with sites within 600 bp upstream = 0.0202377 Motif number 5 ACCTTTTTAAGATTTAAAAAATAATATCATT 2 130 0 GATTTAAAAA 0.969461 -27 ATCAAAAATTGATTAAGAAAATTTAAGATTT 3 118 0 GATTAGAAAA 0.990406 -138 TATTTATTTTGATTTAAAAAAGGCACAGCCA 3 219 0 GATTTAAAAA 0.969461 -37 CATTGAAGAAGATGAGGAAAAGTTAAAAAAA 4 61 0 GATGAGAAAA 0.978958 -154 ATTTGGTGATGATTATGAAAAAGTATTTCGA 4 119 0 GATTAGAAAA 0.990406 -96 ***** ***** Masking position 8 Map Score: 5.90854 Number of sites scoring better than the average of aligned sites = 109 Number in coding regions = 97 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 6 GTAAGTTTTAAATATGACTAACAATTATTT 2 44 1 AATATGACTA 0.924163 -113 TCAATACTACACTACGGCTATAAACAAGGA 3 44 1 ACTACGGCTA 0.986685 -212 AAATTATAAGACTATGGCTAACCAAATAAC 3 167 1 ACTATGGCTA 0.985643 -89 ACAGCCAAATAAAACGGCAATGCAGTTCCG 3 196 0 AAAACGGCAA 0.97096 -60 AATGCATTAAAAAATGGAAATAAAATTTTA 4 13 0 AAAATGGAAA 0.855808 -202 ********** Masking position 4 Map Score: 0.844173 Number of sites scoring better than the average of aligned sites = 119 Number in coding regions = 111 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 7 ********** No masking Map Score: -5.30475e-13 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 8 ********** No masking Map Score: -5.30475e-13 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 9 ********** No masking Map Score: -5.30475e-13 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