AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00053_mjan_reg_300.orf -o00053_mjan_300.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 MJ0102 300 Phenylacrylic acid decarboxylase #2 MJ1656 300 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase (hpcE) Motif number 1 TGAAAGATTTTGTTTAACTTTTTCTAAAAGTTTCGTTTG 1 139 1 TACTCTAAAA 0.993646 -162 TCTAAAAAAATAAATATAACAACCTAAAATAAAATAATA 1 200 0 TAACCTAAAA 0.969837 -101 TTAAAAATAGTTAATCCATAAATCTAAAAAAATAAATAT 1 222 0 TCATCTAAAA 0.969837 -79 TATAGCCTCATCTCTAAAAGTGTCTAAAATAATACACAA 2 48 0 TAATCTAAAA 0.993537 -253 GTTTTGATATTGAAGAACTATCTCTTAATATTGATTTTG 2 94 1 TACTCTTAAT 0.954597 -207 AATGGAGCTGTTAAAAAAGAGATTTTAAAGTTCCCAAAA 2 143 1 TAATTTTAAA 0.851549 -158 CCTCTAAAATTATAAAACAATCTCTTAAATAATAAGTTA 2 204 0 TACTCTTAAA 0.986655 -97 TAAATAATCATCAACATAGTCCTCTAAAATTATAAAACA 2 224 0 TAATCTAAAA 0.993556 -77 CCTACTGAATTCATCACCCTCATCTAAATAATCATCAAC 2 248 0 TACTCTAAAT 0.978918 -53 CTCCCTAAATGCATCTAAAACTCCCCTACT 2 281 0 TAATCTAAAA 0.993556 -20 * * * ******* Masking position 15 Map Score: 15.0681 Number of sites scoring better than the average of aligned sites = 182 Number in coding regions = 149 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 2 TGAAAACTCTTTTAGTTTTCATTTAACCGAAGCGT 1 84 1 TTTTTATTTA 0.954645 -217 TCTGAAAGATTTTGTTTAACTTTTTCTAAAAGTTT 1 137 1 TTTTATTTTT 0.93759 -164 CGGCACCATTTTATTATTTTATTTTAGGTTGTTAT 1 189 1 TTATTATTTT 0.908456 -112 TTTTAGGTTGTTATATTTATTTTTTTAGATTTATG 1 210 1 TTTTTTTTTT 0.898553 -91 ATTAACTATTTTTAAATAGTATTTATTTTTTAAAT 1 246 1 TTATAATTTA 0.908453 -55 TTAAAAACTGTTAAGTTAAGATTTAAAAAATAAAT 1 266 0 TTTTAATTTA 0.972733 -35 CCATTGTTATATAGATTAGGATTTTTCTC 2 5 0 ATTTAATTTT 0.884971 -296 TGGACTTTTATTTGTGTATTATTTTAGACACTTTT 2 37 1 TTGTAATTTT 0.93398 -264 GGCTATAAGCTTTGGTTTTGATATTGAAGAACTAT 2 80 1 TTTTTATATT 0.819367 -221 TAATGAATCATTAACTTATTATTTAAGAGATTGTT 2 193 1 TTTTAATTTA 0.972748 -108 ATTTAAGAGATTGTTTTATAATTTTAGAGGACTAT 2 213 1 TTTTAATTTT 0.983753 -88 ** *** ***** Masking position 7 Map Score: 12.5894 Number of sites scoring better than the average of aligned sites = 815 Number in coding regions = 550 Number in noncoding regions = 265 Number of orfs with sites within 600 bp upstream = 239 Fraction of orfs with sites within 600 bp upstream = 0.0383874 Motif number 3 CAATGCATCCTATTTTGATGAAATGGAAAGC 1 38 1 TATTTGATGA 0.978578 -263 AAATCTGAAAGATTTTGTTTAACTTTTTCTA 1 134 1 GATTTGTTTA 0.843217 -167 CTTTGGTTTTGATATTGAAGAACTATCTCTT 2 89 1 GATTTGAAGA 0.976366 -212 TCTTAATATTGATTTTGAGGAGGAATTAATG 2 116 1 GATTTGAGGA 0.983931 -185 CCCAAAAACAGAGGTTGATAATGAATCATTA 2 175 1 GAGTTGATAA 0.945748 -126 TTTAGAGGACTATGTTGATGATTATTTAGAT 2 235 1 TATTTGATGA 0.978578 -66 TTATTTAGATGAGGGTGATGAATTCAGTAGG 2 256 1 GAGGTGATGA 0.971967 -45 *** ******* Masking position 2 Map Score: 6.21235 Number of sites scoring better than the average of aligned sites = 553 Number in coding regions = 520 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 4 TACGCTCGGCAATGCCTCTTA 1 2 0 AATGCCTCTT 0.95525 -299 GTAGCGAGGCAATGCATCCTATTTTGATGA 1 29 1 AATGCATCCT 0.978892 -272 GTAGCTTTCCATTTCATCAAAATAGGATGC 1 42 0 ATTTCATCAA 0.81855 -259 AAATTCACCATTAAAAACTGT 1 290 0 AATTCACCAT 0.914602 -11 ACCAAAGCTTATAGCCTCATCTCTAAAAGT 2 66 0 ATAGCCTCAT 0.818371 -235 CAGCTCCATTAATTCCTCCTCAAAATCAAT 2 123 0 AATTCCTCCT 0.953929 -178 AGAGGTTGATAATGAATCATTAACTTATTA 2 184 1 AATGAATCAT 0.934026 -117 ACCCTCATCTAAATAATCATCAACATAGTC 2 242 0 AAATAATCAT 0.711634 -59 TCCCCTACTGAATTCATCACCCTCATCTAA 2 260 0 AATTCATCAC 0.931695 -41 CTCCCTAAATGCATCTAAAACTCCCCT 2 284 0 AATGCATCTA 0.904527 -17 ********** Masking position 1 Map Score: 7.86627 Number of sites scoring better than the average of aligned sites = 798 Number in coding regions = 730 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 5 GGCATTGCCGAGCGTAGCGAGGCAATGCAT 1 16 1 AGCGTAGCGA 0.964858 -285 ATAGCTGGAAAGCGTAGCTTTCCATTTCAT 1 55 0 AGCGTAGCTT 0.984073 -246 TTTTCATTTAACCGAAGCGTTAGCTTCGGG 1 99 1 ACCGAAGCGT 0.992864 -202 GATTTTGTAGCCCGAAGCTAACGCTTCGGT 1 109 0 CCCGAAGCTA 0.970511 -192 GAGGGATACAAACGAAACTTTTAGAAAAAG 1 156 0 AACGAAACTT 0.867357 -145 CAATATCAAAACCAAAGCTTATAGCCTCAT 2 76 0 ACCAAAGCTT 0.962935 -225 ********** Masking position 6 Map Score: 4.3485 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 12 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 6 CAGCTATGAAAACTCTTTTAGTTTTCATTT 1 78 1 AACTCTTTTA 0.945847 -223 GGATACAAACGAAACTTTTAGAAAAAGTTA 1 153 0 GAAACTTTTA 0.458316 -148 AGGTTGTTATATTTATTTTTTTAGATTTAT 1 214 1 ATTTATTTTT 0.734852 -87 TTTATGGATTAACTATTTTTAAATAGTATT 1 239 1 AACTATTTTT 0.924662 -62 TTTAAATAGTATTTATTTTTTAAATCTTAA 1 256 1 ATTTATTTTT 0.734852 -45 ATCTTAACTTAACAGTTTTTAATGGTGAAT 1 279 1 AACAGTTTTT 0.897531 -22 TATTATTTTAGACACTTTTAGAGATGAGGC 2 53 1 GACACTTTTA 0.867084 -248 GAACTTTAAAATCTCTTTTTTAACAGCTCC 2 146 0 ATCTCTTTTT 0.945848 -155 CATTATCAACCTCTGTTTTTGGGAACTTTA 2 168 0 CTCTGTTTTT 0.803605 -133 TTATTTAAGAGATTGTTTTATAATTTTAGA 2 211 1 GATTGTTTTA 0.782367 -90 ********** Masking position 6 Map Score: 3.2298 Number of sites scoring better than the average of aligned sites = 1599 Number in coding regions = 1379 Number in noncoding regions = 220 Number of orfs with sites within 600 bp upstream = 187 Fraction of orfs with sites within 600 bp upstream = 0.0300353 Motif number 7 ********** No masking Map Score: 1.30983e-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 8 ********** No masking Map Score: 1.30983e-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 9 ********** No masking Map Score: 1.30983e-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