AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00760_mjan_reg_300.orf -o00760_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 MJ0493 119 nicotinate-nucleotide pyrophosphorylase (nadC) #2 MJ0535 300 acetylpolyamine aminohydrolase (aphA) #3 MJ1352 300 NH(3)-dependent NAD+ synthetase (nadE) Motif number 1 TATTTAGAAATTTTTATACTACACATATTTTTT 1 29 1 TTTTTATACA 0.864944 -91 TAATAAAAACTTTTGTTAAAAAATATGTGTAGT 1 46 0 TTTTTAAAAA 0.742861 -74 GTTTTTAATTTTTTAATTTAATAAAACTTAAAT 1 78 0 TTTTTTAATA 0.963344 -42 TACAACAATGTTCTTCTTAAACAGACTATCAGA 2 39 0 TTCTTTAACA 0.970058 -262 ACACCTCCCGTTTCCATACAACAATGTTCTTCT 2 55 0 TTTCTAAACA 0.94105 -246 TACAATACTGTTCTCCTTAAACAATTTTAGAGA 2 107 0 TTCTTTAACA 0.970058 -194 CTATGATGGGTTTCCATACAATACTGTTCTCCT 2 123 0 TTTCTAAATA 0.922487 -178 TACAATATTGTTCTTCTTAAACACGAAATATAG 2 192 0 TTCTTTAACA 0.970058 -109 AAAAAAGAGTTTTTGATACAATATTGTTCTTCT 2 208 0 TTTTTAAATA 0.951535 -93 AAAATAGGTTTTTAGTTTAATATTTCTCTTTT 2 279 0 TTTTTTAATA 0.966893 -22 CATCATCTGGATTTATTTCAATAAATGGTTCAT 3 15 0 ATTTTTAATA 0.772649 -286 GGAAATATGATTCCTATTATATAAACAATTCTA 3 276 0 TTCCTTTATA 0.751514 -25 **** ** **** Masking position 11 Map Score: 15.4501 Number of sites scoring better than the average of aligned sites = 485 Number in coding regions = 390 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 2 AATTTCTAAATACAACACACTATTTATTGA 1 7 0 TAAACCTATT 0.981688 -113 ACATATTTTTTAACAAAAGTTTTTATTATTTAAG 1 51 1 TACAAATTTT 0.735114 -69 GAATATCCCCCATTATTAAGTTTTTAA 1 103 0 TACCCCTATT 0.8278 -17 CCCGTTTCCATACAACAATGTTCTTCTTAAACAG 2 48 0 TAAACATTCT 0.759299 -253 ACGATTTTTGTCCAACCCTATATTTCGTGTTTAA 2 175 1 TCAACCTATT 0.97447 -126 CAATATTGTATCAAAAACTCTTTTTTATCCACTC 2 215 1 TCAAACTTTT 0.94216 -86 TCTTTTGGGATATAAAAAATTATTTAGGATATTT 2 251 0 TAAAAATATT 0.865831 -50 AATATTAAACTAAAAACCTATTTT 2 287 1 TAAAACTTTT 0.958103 -14 ATGGCATAAATACAACTCCTTTTTTAATGTCTTC 3 131 0 TAAACCTTTT 0.981664 -170 ACACAACTCATCTAACGCAGTATTGGTTAATACG 3 190 0 TCAACCTATT 0.97446 -111 ** *** * **** Masking position 11 Map Score: 8.01201 Number of sites scoring better than the average of aligned sites = 307 Number in coding regions = 252 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 3 AAATATGTGTAGTATAAAAATTTCTAAATA 1 29 0 AGTATAAAAA 0.912853 -91 AGAACATTGTTGTATGGAAACGGGAGGTGT 2 58 1 TGTATGGAAA 0.974281 -243 AGAACAGTATTGTATGGAAACCCATCATAG 2 126 1 TGTATGGAAA 0.974281 -175 AATATAGGGTTGGACAAAAATCGTGGAAAA 2 169 0 TGGACAAAAA 0.927904 -132 AGAACAATATTGTATCAAAAACTCTTTTTT 2 211 1 TGTATCAAAA 0.961391 -90 TATTTTAGAGTGGATAAAAAAGAGTTTTTG 2 226 0 TGGATAAAAA 0.972369 -75 ********** Masking position 4 Map Score: 4.03409 Number of sites scoring better than the average of aligned sites = 175 Number in coding regions = 149 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 4 CAATAAATAGTGTGTTGTATTTAGAAATTT 1 12 1 TGTGTTGTAT 0.942313 -108 TTAAAAAATATGTGTAGTATAAAAATTTCT 1 34 0 TGTGTAGTAT 0.772275 -86 TATGGAAACGGGAGGTGTGAGGGCGGCTCC 2 70 1 GGAGGTGTGA 0.947021 -231 GAAAAAGAGAGGAGGTGACTATGATGGGTT 2 144 0 GGAGGTGACT 0.869593 -157 CATTAAAAAAGGAGTTGTATTTATGCCATT 3 136 1 GGAGTTGTAT 0.978422 -165 CTGCGTTAGATGAGTTGTGTAAAATTCCAG 3 204 1 TGAGTTGTGT 0.983345 -97 TTCCAGAGCTTAAGGTGTGTGCTGTAAAGA 3 228 1 TAAGGTGTGT 0.902424 -73 ********** Masking position 4 Map Score: 3.2721 Number of sites scoring better than the average of aligned sites = 114 Number in coding regions = 96 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 5 GTTTTTATTATTTAAGTTTTATTAAATTAA 1 69 1 TTTAAGTTTT 0.907137 -51 GTTTTTAATTTTTTAATTTAATAAAACTTA 1 81 0 TTTTAATTTA 0.919942 -39 ATCCCCCATTATTAAGTTTTTAATTTTTTA 1 96 0 ATTAAGTTTT 0.907138 -24 AAAATAGGTTTTTAGTTTAATATTTCTCT 2 282 0 TTTTAGTTTA 0.971434 -19 GAGAATGGTGATTTAGTTAAGGTGATTTCA 3 65 1 ATTTAGTTAA 0.893499 -236 GATTGAACGAATTTAATTTATAGAATTGTT 3 256 1 ATTTAATTTA 0.919942 -45 ********** Masking position 5 Map Score: 2.74319 Number of sites scoring better than the average of aligned sites = 285 Number in coding regions = 224 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 6 TAGTCTGTTTAAGAAGAACATTGTTGTATG 2 44 1 AAGAAGAACA 0.983534 -257 AAAATTGTTTAAGGAGAACAGTATTGTATG 2 112 1 AAGGAGAACA 0.992625 -189 AATCGTGGAAAAAGAGAGGAGGTGACTATG 2 151 0 AAAGAGAGGA 0.950281 -150 TTTCGTGTTTAAGAAGAACAATATTGTATC 2 197 1 AAGAAGAACA 0.983534 -104 AGGTGATTTCAAGGAGAGGAGAGATAACTG 3 84 1 AAGGAGAGGA 0.990074 -217 ********** Masking position 5 Map Score: 6.78989 Number of sites scoring better than the average of aligned sites = 78 Number in coding regions = 74 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 7 GTGTGTTGTATTTAGAAATTTTTATACTAC 1 21 1 TTTAGAAATT 0.931867 -99 TTTTATTAAATTAAAAAATTAAAAACTTAA 1 85 1 TTAAAAAATT 0.757617 -35 CTTAAACAATTTTAGAGATTAGGGGGGAGC 2 95 0 TTTAGAGATT 0.97589 -206 ATTCTCAATTTTTAATGATTTGGCATCATC 3 41 0 TTTAATGATT 0.902442 -260 AGGTGTGTGCTGTAAAGATTGAACGAATTT 3 240 1 TGTAAAGATT 0.93202 -61 ACGAATTTAATTTATAGAATTGTTTATATA 3 262 1 TTTATAGAAT 0.785439 -39 ********** Masking position 4 Map Score: 0.669276 Number of sites scoring better than the average of aligned sites = 518 Number in coding regions = 428 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 8 ********** No masking Map Score: 1.43773e-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: 1.43773e-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 10 ********** No masking Map Score: 1.43773e-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