AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i062_Glutamate_Synthase_1_mjan_reg_300.orf -o062_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 RMJ15209 60 M_jannaschii_chromosome #2 RMJ14537 177 M_jannaschii_chromosome #3 RMJ11064 57 M_jannaschii_chromosome #4 RMJ06935 293 M_jannaschii_chromosome Motif number 1 ACAAAGATTAAAAGATTAAA 1 1 1 ACAAAGATTA 0.803034 -60 AGATTAAAAGATTAAAAATAAAAACATGAG 1 15 1 ATTAAAAATA 0.920452 -46 AAATATTTAAACTAAAATTAAAAA 2 5 0 ACTAAAATTA 0.923243 -173 AAATAGAATAACTAAAATAAAATATTTAAA 2 24 0 ACTAAAATAA 0.904253 -154 ATATTACAATATATAAAATAATTTAATTTT 2 55 0 ATATAAAATA 0.956917 -123 TTGAAGTTATATTTAAATAATTATGGTCTG 2 101 0 ATTTAAATAA 0.948487 -77 TTCAACCAATATTTAGAAAACCCAAAAAAC 2 126 1 ATTTAGAAAA 0.711761 -52 CTCCGTAGAGATATAAAAGAGATAGTTTTT 2 150 0 ATATAAAAGA 0.895001 -28 GATTCCTATTATATAAACAATTCTATAAA 3 10 0 ATATAAACAA 0.908051 -48 TAAAAAATGAATATAAATTAGCAATATTAG 4 26 0 ATATAAATTA 0.973184 -268 AACTTCATAGACATAAAAAAGTGAGAACTT 4 63 0 ACATAAAAAA 0.917317 -231 ATGAAGTTCTATAAAAACTTTTCTATAATC 4 85 1 ATAAAAACTT 0.589459 -209 TTCTAAACATATTTAAATTAATTGATTATA 4 108 0 ATTTAAATTA 0.95911 -186 ATTTATAAACATAAAAATTAAAAAATAGGA 4 138 1 ATAAAAATTA 0.966944 -156 AAAAAATAGGATAAAAATTTACAGTTTTTA 4 157 1 ATAAAAATTT 0.805557 -137 TGCGAACCCAATATAAATAATACAAGGGAG 4 210 1 ATATAAATAA 0.966075 -84 CGAAGCATGCACAAAAATAAAAATTTAAAA 4 259 1 ACAAAAATAA 0.935947 -35 AAAAATAAAAATTTAAAAGAATTAGGTGAA 4 271 1 ATTTAAAAGA 0.846379 -23 ********** Masking position 5 Map Score: 25.8225 Number of sites scoring better than the average of aligned sites = 2358 Number in coding regions = 1644 Number in noncoding regions = 714 Number of orfs with sites within 600 bp upstream = 498 Fraction of orfs with sites within 600 bp upstream = 0.0799872 Motif number 2 ATTTTAGTTTAAATATTTTATTTTAGTTAT 2 17 1 AAATATTTTA 0.918295 -161 TTTAATTTTAAAATAGAATAACTAAAATAA 2 34 0 AAATAGAATA 0.900633 -144 ACAATATATAAAATAATTTAATTTTAAAAT 2 50 0 AAATAATTTA 0.836841 -128 ATAATTATTTAAATATAACTTCAACCAATA 2 107 1 AAATATAACT 0.712504 -71 GATATAAAAGAGATAGTTTTTTGGGTTTTC 2 141 0 AGATAGTTTT 0.621223 -37 TAACATTAGGAAATATGATTCCTATTATAT 3 26 0 AAATATGATT 0.945598 -32 TATTAGAACAAAATATGATAG 4 2 0 AAATATGATA 0.964673 -292 CAATTAATTTAAATATGTTTAGAAATTTAT 4 114 1 AAATATGTTT 0.832596 -180 AAAAATTAAAAAATAGGATAAAAATTTACA 4 150 1 AAATAGGATA 0.964097 -144 AACCCAATATAAATAATACAAGGGAGCAGG 4 214 1 AAATAATACA 0.763653 -80 ********** Masking position 5 Map Score: 7.26448 Number of sites scoring better than the average of aligned sites = 869 Number in coding regions = 625 Number in noncoding regions = 244 Number of orfs with sites within 600 bp upstream = 219 Fraction of orfs with sites within 600 bp upstream = 0.0351751 Motif number 3 ACAAAGATTAAAAGATTAAAAATAAA 1 7 1 ATTAAAAGAT 0.900526 -54 AAGATTAAAAATAAAAACATGAGGAAGTGA 1 22 1 ATAAAAACAT 0.94337 -39 GAATAACTAAAATAAAATATTTAAACTAAA 2 19 0 AATAAAATAT 0.773084 -159 ATTACAATATATAAAATAATTTAATTTTAA 2 53 0 ATAAAATAAT 0.707937 -125 GATTTGGAATATTACAATATATAAAATAAT 2 63 0 ATTACAATAT 0.894964 -115 GACCATAATTATTTAAATATAACTTCAACC 2 103 1 ATTTAAATAT 0.844528 -75 TAGCAATATTAGAACAAAATATGATAG 4 8 0 AGAACAAAAT 0.694247 -286 AACTTTAATTAGTAAAAAATGAATATAAAT 4 38 0 AGTAAAAAAT 0.886651 -256 CTTCATAGACATAAAAAAGTGAGAACTTTA 4 61 0 ATAAAAAAGT 0.82341 -233 ATGAAGTTCTATAAAAACTTTTCTATAATC 4 85 1 ATAAAAACTT 0.842502 -209 TAATCAATTAATTTAAATATGTTTAGAAAT 4 110 1 ATTTAAATAT 0.844528 -184 AAACATAAAAATTAAAAAATAGGATAAAAA 4 144 1 ATTAAAAAAT 0.960942 -150 AAAAAATAGGATAAAAATTTACAGTTTTTA 4 157 1 ATAAAAATTT 0.904244 -137 ATGCACAAAAATAAAAATTTAAAAGAATTA 4 265 1 ATAAAAATTT 0.904244 -29 ********** Masking position 6 Map Score: 15.2371 Number of sites scoring better than the average of aligned sites = 1726 Number in coding regions = 1219 Number in noncoding regions = 507 Number of orfs with sites within 600 bp upstream = 418 Fraction of orfs with sites within 600 bp upstream = 0.0671378 Motif number 4 AGTTATTCTATTTTAAAATTAAATTATTTT 2 41 1 TTTTAAAATT 0.761499 -137 TTTATAGAATTGTTTATATAA 3 2 1 TTATAGAATT 0.964165 -56 TTATAGAACTTCATAGACATAAAAAAGTGA 4 69 0 TCATAGACAT 0.912238 -225 AGAAAAGTTTTTATAGAACTTCATAGACAT 4 79 0 TTATAGAACT 0.957653 -215 AATTAATTGATTATAGAAAAGTTTTTATAG 4 93 0 TTATAGAAAA 0.912077 -201 ATTTAAATATGTTTAGAAATTTATAAACAT 4 120 1 GTTTAGAAAT 0.870394 -174 GTTTAGAAATTTATAAACATAAAAATTAAA 4 130 1 TTATAAACAT 0.902106 -164 ********** Masking position 5 Map Score: 1.58703 Number of sites scoring better than the average of aligned sites = 375 Number in coding regions = 302 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 5 TAAAATATTTAAACTAAAATTAAAAA 2 7 0 AAACTAAAAT 0.779711 -171 AATATAACTTCAACCAATATTTAGAAAACC 2 118 1 CAACCAATAT 0.966184 -60 ATATTTAGAAAACCCAAAAAACTATCTCTT 2 134 1 AACCCAAAAA 0.966717 -44 ACTCTCACCCCATAACATTAGGAAA 3 43 0 CACCCCATAA 0.952917 -15 CCACCCTGCGAACCCAATATAAATAATACA 4 204 1 AACCCAATAT 0.983508 -90 ********** Masking position 7 Map Score: 0.53096 Number of sites scoring better than the average of aligned sites = 187 Number in coding regions = 163 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 6 AAAAATAAAAACATGAGGAAGTGAAATCAT 1 28 1 ACATGAGGAA 0.972347 -33 AATTGTTTATATAATAGGAATCATATTTCC 3 18 1 ATAATAGGAA 0.952312 -40 TCACCCCATAACATTAGGAAATATGATTCC 3 34 0 ACATTAGGAA 0.98735 -24 AAATGAATATAAATTAGCAATATTAGAACA 4 22 0 AAATTAGCAA 0.934776 -272 TAAAAATTAAAAAATAGGATAAAAATTTAC 4 149 1 AAAATAGGAT 0.914555 -145 ********** Masking position 6 Map Score: 2.17882 Number of sites scoring better than the average of aligned sites = 162 Number in coding regions = 143 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 7 ********** No masking Map Score: -5.51791e-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: -5.51791e-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: -5.51791e-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