AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00760_mjan_reg_100.orf -o00760_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 MJ0493 119 nicotinate-nucleotide pyrophosphorylase (nadC) #2 MJ0535 300 acetylpolyamine aminohydrolase (aphA) #3 MJ1352 300 NH(3)-dependent NAD+ synthetase (nadE) Motif number 1 AAATAGTGTGTTGTATTTAGAAATTTTTATACTACACA 1 16 1 TTTAAATTTT 0.988758 -104 TAATAAAAACTTTTGTTAAAAAATATGTGTAGTATAAA 1 41 0 TTTAAATTGT 0.943098 -79 AACAAAAGTTTTTATTATTTAAGTTTTATTAAATTAAA 1 62 1 TTTTAATTTA 0.735073 -58 TCCCCCATTATTAAGTTTTTAATTTTTTAATTTAATAA 1 87 0 TTTTAATTTT 0.956173 -33 ATGTAACCGATATTATCGATAAACGTTTA 2 2 0 TATAAACTTT 0.933093 -299 GGCTCCCCCCTAATCTCTAAAATTGTTTAAGGAGAACA 2 94 1 TATAAATTTT 0.986676 -207 AAGAACAATATTGTATCAAAAACTCTTTTTTATCCACT 2 210 1 TTTAAATTTT 0.988765 -91 CACTCTAAAATATCCTAAATAATTTTTTATATCCCAAA 2 244 1 TATAAATTTT 0.986678 -57 AGAGAAATATTAAACTAAAAACCTATTTT 2 282 1 TATAACTTTT 0.933099 -19 TCATCTGGATTTATTTCAATAAATGGTTCATTAAT 3 8 0 TTTAAATGTT 0.943098 -293 TGAACGAATTTAATTTATAGAATTGTTTATATAATAGG 3 259 1 TATAAATTTT 0.986677 -42 ** * * ** * *** Masking position 11 Map Score: 13.9522 Number of sites scoring better than the average of aligned sites = 278 Number in coding regions = 216 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 2 TAAAAATTTCTAAATACAACACACTATTTATTGA 1 9 0 TAAAAACATA 0.951671 -111 AAAACTTAAATAATAAAAACTTTTGTTAAAAAATAT 1 53 0 TAAAAACTGT 0.959496 -67 ATAGTCTGTTTAAGAAGAACATTGTTGTATGGAAAC 2 43 1 TAAAAACATT 0.992043 -258 TAAAATTGTTTAAGGAGAACAGTATTGTATGGAAAC 2 111 1 TAAAAACATT 0.991991 -190 ATTTCGTGTTTAAGAAGAACAATATTGTATCAAAAA 2 196 1 TAAAAACATT 0.991991 -105 AACAATATTGTATCAAAAACTCTTTTTTATCCACTC 2 213 1 TATAAACTTT 0.940873 -88 GAAATCACCTTAACTAAATCACCATTCTCAATTTTT 3 58 0 TAAAATCATT 0.951672 -243 TGGAATGGCATAAATACAACTCCTTTTTTAATGTCT 3 133 0 TAAAAACTTT 0.989965 -168 CCTAACGTATTAACCAATACTGCGTTAGATGAGTTG 3 185 1 TAAATACTTT 0.941069 -116 *** * **** ** Masking position 6 Map Score: 13.2641 Number of sites scoring better than the average of aligned sites = 77 Number in coding regions = 62 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 3 TCAATAAATAGTGTGTTGTATTTA 1 2 1 CAATAAAAGT 0.917569 -118 CTCCCGTTTCCATACAACAATGTTCTTCTTAAA 2 51 0 CATACAAAGT 0.988278 -250 GATGGGTTTCCATACAATACTGTTCTCCTTAAA 2 119 0 CATACAAAGT 0.988278 -182 AAGAGTTTTTGATACAATATTGTTCTTCTTAAA 2 204 0 GATACAAAGT 0.97266 -97 TTTTAGAGTGGATAAAAAAGAGTTTTTGATACA 2 221 0 GATAAAAAGT 0.96717 -80 GATGCCAAATCATTAAAAATTGAGAATGGTGAT 3 44 1 CATTAAAAGA 0.95889 -257 TAACTGAAGACATTAAAAAAGGAGTTGTATTTA 3 126 1 CATTAAAAGA 0.95889 -175 ******* * ** Masking position 7 Map Score: 5.87754 Number of sites scoring better than the average of aligned sites = 73 Number in coding regions = 59 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 4 TTGTATGGAAACGGGAGGTGTGAGGGCGGC 2 67 1 ACGGGAGGTG 0.9893 -234 GTGGAAAAAGAGAGGAGGTGACTATGATGG 2 147 0 AGAGGAGGTG 0.995663 -154 GGTGATTTCAAGGAGAGGAGAGATAACTGC 3 85 1 AGGAGAGGAG 0.949902 -216 AGACATTAAAAAAGGAGTTGTATTTATGCC 3 133 1 AAAGGAGTTG 0.962473 -168 ATACTGCGTTAGATGAGTTGTGTAAAATTC 3 201 1 AGATGAGTTG 0.962474 -100 ********** Masking position 6 Map Score: 2.98955 Number of sites scoring better than the average of aligned sites = 112 Number in coding regions = 95 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 5 AAATACAACACACTATTTATTGA 1 4 0 CACTATTTAT 0.815576 -116 GTGTTGTATTTAGAAATTTTTATACTACAC 1 23 1 TAGAAATTTT 0.655692 -97 TCTCTTTTTCCACGATTTTTGTCCAACCCT 2 164 1 CACGATTTTT 0.950823 -137 TCTTCTTAAACACGAAATATAGGGTTGGAC 2 184 0 CACGAAATAT 0.856732 -117 AAAAATTATTTAGGATATTTTAGAGTGGAT 2 241 0 TAGGATATTT 0.846615 -60 TTGGCATCATCTGGATTTATTTCAATAAAT 3 22 0 CTGGATTTAT 0.951244 -279 AATCACCATTCTCAATTTTTAATGATTTGG 3 48 0 CTCAATTTTT 0.751279 -253 AAAAAAGGAGTTGTATTTATGCCATTCCAC 3 140 1 TTGTATTTAT 0.655691 -161 ACCTTAAGCTCTGGAATTTTACACAACTCA 3 214 0 CTGGAATTTT 0.930198 -87 TAGGAAATATGATTCCTATT 3 291 0 TAGGAAATAT 0.79036 -10 ********** Masking position 5 Map Score: 3.17143 Number of sites scoring better than the average of aligned sites = 833 Number in coding regions = 742 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 6 ATTTAAGTTTTATTAAATTAAAAAATTAAA 1 78 1 TATTAAATTA 0.616541 -42 ACAATGTTCTTCTTAAACAGACTATCAGAT 2 38 0 TCTTAAACAG 0.920226 -263 ATACTGTTCTCCTTAAACAATTTTAGAGAT 2 106 0 CCTTAAACAA 0.968674 -195 ATATTGTTCTTCTTAAACACGAAATATAGG 2 191 0 TCTTAAACAC 0.955014 -110 AAAAGAGAAATATTAAACTAAAAACCTATT 2 279 1 TATTAAACTA 0.925287 -22 TAACTGAAGACATTAAAAAAGGAGTTGTAT 3 126 1 CATTAAAAAA 0.716573 -175 AATCCTAACGTATTAACCAATACTGCGTTA 3 182 1 TATTAACCAA 0.859552 -119 ACAGCACACACCTTAAGCTCTGGAATTTTA 3 223 0 CCTTAAGCTC 0.799645 -78 ********** Masking position 5 Map Score: 1.51675 Number of sites scoring better than the average of aligned sites = 222 Number in coding regions = 187 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 7 GAACATTGTTGTATGGAAACGGGAGGTGTG 2 59 1 GTATGGAAAC 0.974106 -242 GAACAGTATTGTATGGAAACCCATCATAGT 2 127 1 GTATGGAAAC 0.974106 -174 ********** Masking position 4 Map Score: 0.183064 Number of sites scoring better than the average of aligned sites = 8 Number in coding regions = 3 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 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