AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i314_mjan_pyro_100.orf -o314_mjan_pyro_100.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.37 -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 = 0.37 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RMJ11898 300 M_jannaschii_chromosome #2 RMJ05555 123 M_jannaschii_chromosome #3 RMJ05273 101 M_jannaschii_chromosome #4 RPH00709 47 Pyrococcus_OT3 Motif number 1 AAAATAGTTATAGGAGTTTTAGTATA 1 6 0 TGGAGTTTTA 0.956152 -295 ATATCCGTATCCAAATTTTTACTGCATGATT 1 40 1 CAAATTTTTA 0.950654 -261 CTTAATCTTTTAAAGGTTTTAATAATCATGC 1 63 0 TAAGGTTTTA 0.890901 -238 TAGTTATGTATCGGATTTATATGACTATGCA 1 102 0 TGGATTTATA 0.882574 -199 AGATTTGGTTTTAAGTTTTTATAGTAAATAT 1 149 0 TAAGTTTTTA 0.974051 -152 AGAGTATTGTTTATATTTTTATAGTTTTAAG 1 178 0 TATATTTTTA 0.906536 -123 ATATTGATATTAGATTTTTTAATTTTGTTTA 1 208 0 TGATTTTTTA 0.958827 -93 GTTTAGTTTATTGGATTTTTAATATTGATAT 1 229 0 TGGATTTTTA 0.986016 -72 ATAAGATTTCTGGATTTTTTATTATTGTTAA 2 67 0 TGATTTTTTA 0.959761 -57 CCAATCACCCAAAATTTTTAACCAAAAATA 2 104 0 CAAATTTTTA 0.916625 -20 CTATTTTTAATCAGATTTTTAGTAAAAATTT 3 70 1 TAGATTTTTA 0.979909 -32 TTTTATCCCTCAAATTTTTACTAAAAATCT 3 82 0 TAAATTTTTA 0.948012 -20 ATAAATAGCATGGAGTTTTTATCCATTGCTG 4 26 1 TGAGTTTTTA 0.98172 -22 * ********* Masking position 11 Map Score: 25.2997 Number of sites scoring better than the average of aligned sites = 570 Number in coding regions = 400 Number in noncoding regions = 170 Number of orfs with sites within 600 bp upstream = 172 Fraction of orfs with sites within 600 bp upstream = 0.0276261 Motif number 2 TATACTAAAACTCCTATAACTATTTTTCTA 1 9 1 AACTCCATAC 0.896829 -292 AAAACCTTTAAAAGATTAAGAAAGGTTTTGCA 1 74 1 AAAGATAAAA 0.740873 -227 ATAGTCATATAAATCCGATACATAACTATTAA 1 105 1 AAATCCATCA 0.80332 -196 TCCGATACATAACTATTAACAAAAATCCCCAA 1 118 1 AACTATAAAA 0.922162 -183 ATTTACTATAAAAACTTAAAACCAAATCTTAA 1 151 1 AAAACTAAAC 0.83163 -150 ACTTAAAACCAAATCTTAAAACTATAAAAATA 1 164 1 AAATCTAAAC 0.980463 -137 AAAACTATAAAAATATAAACAATACTCTAAAC 1 181 1 AAATATAAAA 0.951456 -120 ATATAAACAATACTCTAAACAAAATTAAAAAA 1 193 1 TACTCTAAAA 0.89701 -108 CAAAATTAAAAAATCTAATATCAATATTAAAA 1 212 1 AAATCTATTC 0.908713 -89 TCAATATTAAAAATCCAATAAACTAAACTAAA 1 232 1 AAATCCATAA 0.959665 -69 AAATATAATCAAATCTCAAATAAACTATAAAA 1 261 1 AAATCTAATA 0.960472 -40 ATCTCAAATAAACTATAAAAAATGCTGAGTTG 1 273 1 AACTATAAAA 0.922162 -28 CCATCATTTGTAATCTTAACAATAATAAAAAA 2 52 1 TAATCTAAAA 0.935105 -72 AAAAATCCAGAAATCTTATTTAAAATATTTTT 2 79 1 AAATCTATTA 0.942755 -45 TTTTTACTAAAAATCTGATTAAAAATAGATTA 3 66 0 AAATCTATAA 0.982539 -36 ****** ** ** Masking position 8 Map Score: 19.6611 Number of sites scoring better than the average of aligned sites = 1279 Number in coding regions = 1036 Number in noncoding regions = 243 Number of orfs with sites within 600 bp upstream = 198 Fraction of orfs with sites within 600 bp upstream = 0.0318021 Motif number 3 ATATCCGTATCCAAATTTTTACTGCATGAT 1 40 1 CCAAATTTTT 0.986647 -261 TATGACTATGCAAAACCTTTCTTAATCTTT 1 84 0 CAAAACCTTT 0.881175 -217 AACAAAAATCCCCAATATTTACTATAAAAA 1 135 1 CCCAATATTT 0.924915 -166 AAACTTAAAACCAAATCTTAAAACTATAAA 1 162 1 CCAAATCTTA 0.922736 -139 AAATCTTATTTAAAATATTTTTGGTTAAAA 2 89 1 TAAAATATTT 0.868253 -35 CCAATCACCCAAAATTTTTAACCAAAAAT 2 105 0 CAAAATTTTT 0.925192 -19 CTATTTTTAATCAGATTTTTAGTAAAAATT 3 70 1 TCAGATTTTT 0.893755 -32 TTTTATCCCTCAAATTTTTACTAAAAATC 3 83 0 TCAAATTTTT 0.963378 -19 ********** Masking position 5 Map Score: 7.11463 Number of sites scoring better than the average of aligned sites = 845 Number in coding regions = 704 Number in noncoding regions = 141 Number of orfs with sites within 600 bp upstream = 122 Fraction of orfs with sites within 600 bp upstream = 0.0195952 Motif number 4 TATACTAAAACTCCTATAACTATTT 1 6 1 TAAAACTCCT 0.915473 -295 TAACTATTAACAAAAATCCCCAATATTTAC 1 127 1 CAAAAATCCC 0.932441 -174 AAAATATAAACAATACTCTAAACAAAATTA 1 190 1 CAATACTCTA 0.791173 -111 AAACAAAATTAAAAAATCTAATATCAATAT 1 209 1 AAAAAATCTA 0.966036 -92 ATATCAATATTAAAAATCCAATAAACTAAA 1 229 1 TAAAAATCCA 0.976499 -72 ATCAAATCTCAAATAAACTATAAAAAATGC 1 268 1 AAATAAACTA 0.526666 -33 AATAAACTATAAAAAATGCTGAGTTGATGA 1 279 1 AAAAAATGCT 0.759608 -22 TAACAATAATAAAAAATCCAGAAATCTTAT 2 68 1 AAAAAATCCA 0.98522 -56 AAATTTTTACTAAAAATCTGATTAAAAATA 3 71 0 TAAAAATCTG 0.845099 -31 AGCAATGGATAAAAACTCCATGCTATTTAT 4 26 0 AAAAACTCCA 0.979365 -22 ********** Masking position 5 Map Score: 9.01887 Number of sites scoring better than the average of aligned sites = 971 Number in coding regions = 876 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 5 ********** No masking Map Score: 1.4022e-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 6 ********** No masking Map Score: 1.4022e-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 7 ********** No masking Map Score: 1.4022e-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