AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i307_mixed21_mjan_reg_300.orf -o307_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 RMJ00828 300 M_jannaschii_chromosome #2 RMJ01433 174 M_jannaschii_chromosome #3 RMJ13076 300 M_jannaschii_chromosome #4 RMJ05639 152 M_jannaschii_chromosome Motif number 1 AATTTAAATTAATAAATATTATTACCTAAA 1 92 0 AATAAATATT 0.749165 -209 AAAATTTCGTTTTTAAAATTGTAATCTTTA 1 124 0 TTTTAAAATT 0.942905 -177 TTTAAAAATATTTAAAAATTTCGTTTTTAA 1 138 0 TTTAAAAATT 0.967321 -163 ATTTGAAAATTTTAAAAATATTTAAAAATT 1 148 0 TTTAAAAATA 0.970685 -153 AAATAATCTTTTTTAATATAAGTTTAAATA 1 174 1 TTTTAATATA 0.911548 -127 TTAATATAAGTTTAAATATTTAGAAGCATA 1 186 1 TTTAAATATT 0.942905 -115 ATTTAAGATTTTTTAGTATATAATTTTTCC 2 12 0 TTTTAGTATA 0.789595 -163 ACACTCTCTTTATAAAAATATACCTTATTT 2 118 1 TATAAAAATA 0.96002 -57 TTGCAAAACATTTTAGAATAAATAAGGTAT 2 137 0 TTTTAGAATA 0.870582 -38 AAAATAAGACTATAAAAATAAAAATAAAAA 3 173 1 TATAAAAATA 0.96002 -128 AAAAGAAAAGAATAAAAATAATAAGATATT 3 200 1 AATAAAAATA 0.855266 -101 ATATCACCATTATAAGTATTTTAAAGTAGT 3 272 0 TATAAGTATT 0.824046 -29 AATAGTTGGATTTAAAAATTTTACTATAAT 4 11 0 TTTAAAAATT 0.967321 -142 TCTAAAAATAATTTAAAATAGTTGGATTTA 4 27 0 ATTTAAAATA 0.810583 -126 ATATTAATACTCTAAAAATAATTTAAAATA 4 37 0 TCTAAAAATA 0.87367 -116 ATTTTTAGAGTATTAATATTATTTGGGAGT 4 48 1 TATTAATATT 0.876559 -105 GTTTTGAATTTATAAAAATTACTTTAGTGA 4 91 0 TATAAAAATT 0.958069 -62 ********** Masking position 5 Map Score: 25.9173 Number of sites scoring better than the average of aligned sites = 1585 Number in coding regions = 1024 Number in noncoding regions = 561 Number of orfs with sites within 600 bp upstream = 424 Fraction of orfs with sites within 600 bp upstream = 0.0681015 Motif number 2 CCTGCACCATTTTTATTTTAGGTAATAATA 1 76 1 TTTTATTTTA 0.944122 -225 TATTTAAAAATTTCGTTTTTAAAATTGTAA 1 130 0 TTTCGTTTTT 0.575848 -171 AAATAATCTTTTTTAATATAAGTTTAAATA 1 174 1 TTTTAATATA 0.765966 -127 ATAATTATAATTTCATTTTTTAGGTGATGA 1 213 1 TTTCATTTTT 0.878186 -88 ATTTAAGATTTTTTAGTATATAATTTTTCC 2 12 0 TTTTAGTATA 0.829085 -163 GGGGAGACACTCTCTTTATAAAAATATACC 2 112 1 TCTCTTTATA 0.666685 -63 ATATCACCACTTTTATTATAATCCTATATC 3 97 1 TTTTATTATA 0.958761 -204 ATTTTTATAGTCTTATTTTATATGGTTGTG 3 162 0 TCTTATTTTA 0.932885 -139 TTCTTTTCTTTTTTATTTTTATTTTTATAG 3 182 0 TTTTATTTTT 0.897576 -119 CATTATAATATCTTATTATTTTTATTCTTT 3 206 0 TCTTATTATT 0.908463 -95 AACTAATTCATCTCATTATAATATCTTATT 3 219 0 TCTCATTATA 0.94025 -82 GATTTAAAAATTTTACTATAAT 4 3 0 TTTTACTATA 0.829082 -150 ********** Masking position 7 Map Score: 10.3232 Number of sites scoring better than the average of aligned sites = 984 Number in coding regions = 599 Number in noncoding regions = 385 Number of orfs with sites within 600 bp upstream = 292 Fraction of orfs with sites within 600 bp upstream = 0.0469001 Motif number 3 GTGATGAGATTGGAGAAAGTTTTCTATCTA 1 236 1 TGGAGAAAGT 0.669149 -65 CATTTTAGAATAAATAAGGTATATTTTTAT 2 129 0 TAAATAAGGT 0.908741 -46 CTAATCAGGATAAAGTAGTTAT 3 3 0 TAAAGTAGTT 0.974392 -298 AAATTCATCTTAGATAAGTTAAAGAAAGCT 3 31 0 TAGATAAGTT 0.855094 -270 TGATATGGAATGAAGAAGGTTGTTATATCT 3 73 0 TGAAGAAGGT 0.954572 -228 TATAATGAGATGAATTAGTTAAAAACATTA 3 229 1 TGAATTAGTT 0.924632 -72 ATAAGTATTTTAAAGTAGTTAAATAATTAG 3 261 0 TAAAGTAGTT 0.974392 -40 AAAAATAATTTAAAATAGTTGGATTTAAAA 4 24 0 TAAAATAGTT 0.854788 -129 TCACTCTCACTAAAGTAATTTTTATAAATT 4 85 1 TAAAGTAATT 0.882251 -68 ********** Masking position 4 Map Score: 7.13694 Number of sites scoring better than the average of aligned sites = 581 Number in coding regions = 531 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 4 TTTTAGGTAATAATATTTATTAATTTAAATT 1 91 1 TAATTTTATT 0.907359 -210 TTTAAAATTGTAATCTTTATTAATTTAAATT 1 112 0 TAATTTTATT 0.907386 -189 TAAATATTTTTAAAATTTTCAAATAATCTTT 1 154 1 TAAATTTTCA 0.884854 -147 AATTTTCAAATAATCTTTTTTAATATAAGTT 1 167 1 TAATTTTTTT 0.970942 -134 TGAGATTGGAGAAAGTTTTCTATCTAACCAA 1 240 1 GAAATTTTCT 0.739104 -61 TACATATCAATAAAATTTTCTAAATCTTTGG 1 279 0 TAAATTTTCT 0.954213 -22 TTTTAGTATATAATTTTTCCT 2 1 0 TAATTTTCCT 0.825189 -174 ATAATCTATTTAAGATTTTTTAGTATATAAT 2 18 0 TAAGTTTTTT 0.886568 -157 TTATTTATTCTAAAATGTTTTGCAAAGAACT 2 142 1 TAAATGTTTT 0.784297 -33 TTATTATTTTTATTCTTTTCTTTTTTATTTT 3 193 0 TATTTTTTCT 0.715686 -108 ATAATTAGCTTAATGTTTTTAACTAATTCAT 3 238 0 TAATTTTTTA 0.926929 -63 ATTATAGTAAAATTTTTAAATCCAACTA 4 8 1 TAAATTTTTA 0.780561 -145 CCAACTATTTTAAATTATTTTTAGAGTATTA 4 32 1 TAAATATTTT 0.714156 -121 TTTAGAGTATTAATATTATTTGGGAGTATCC 4 51 1 TAATTTATTT 0.753602 -102 CTCACTAAAGTAATTTTTATAAATTCAAAAC 4 90 1 TAATTTTATA 0.788628 -63 **** ****** Masking position 2 Map Score: 14.5014 Number of sites scoring better than the average of aligned sites = 1451 Number in coding regions = 1042 Number in noncoding regions = 409 Number of orfs with sites within 600 bp upstream = 337 Fraction of orfs with sites within 600 bp upstream = 0.0541279 Motif number 5 CATTTTTTAGGTGATGAGATTGGAGAAAGT 1 226 1 GTGATGAGAT 0.874871 -75 GGTAGTAGGATTGGTTAGATAGAAAACTTT 1 251 0 TTGGTTAGAT 0.919532 -50 CAAAGAACTCTTGGTGAAATC 2 164 1 TTGGTGAAAT 0.838234 -11 AATGAAGAAGGTTGTTATATCTGATGAAGC 3 65 0 GTTGTTATAT 0.745762 -236 TATAATAAAAGTGGTGATATGGAATGAAGA 3 87 0 GTGGTGATAT 0.972415 -214 TATATAATTTATGGTTATGTCAATACTTAA 3 132 1 ATGGTTATGT 0.886759 -169 CTTATTTTATATGGTTGTGTTAAGTATTGA 3 151 0 ATGGTTGTGT 0.750337 -150 ATAAGATATTATAATGAGATGAATTAGTTA 3 220 1 ATAATGAGAT 0.605106 -81 GTATTTTAAAGTAGTTAAATAATTAGCTTA 3 257 0 GTAGTTAAAT 0.763274 -44 AATACTTATAATGGTGATATTTTATGCAA 3 282 1 ATGGTGATAT 0.964764 -19 ATAATTTAAAATAGTTGGATTTAAAAATTT 4 20 0 ATAGTTGGAT 0.739893 -133 ********** Masking position 5 Map Score: 4.40803 Number of sites scoring better than the average of aligned sites = 468 Number in coding regions = 373 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 118 Fraction of orfs with sites within 600 bp upstream = 0.0189528 Motif number 6 AAAAATGGTGCAGGGGAGGGGATTTGAACC 1 60 0 CAGGGGAGGG 0.993995 -241 GGCTAACCCACTGGGGAGCATAATCTATTT 2 38 0 CTGGGGAGCA 0.988141 -137 GGGTGTTAAACTGGGGAGACACTCTCTTTA 2 100 1 CTGGGGAGAC 0.98814 -75 TTTATATAATGTGGGGAGGGATATTATG 4 135 1 GTGGGGAGGG 0.993632 -18 ********** Masking position 7 Map Score: 2.27298 Number of sites scoring better than the average of aligned sites = 16 Number in coding regions = 14 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 7 ********** No masking Map Score: -2.81785e-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: -2.81785e-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: -2.81785e-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