AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i228_mjan_pyro_300.orf -o228_mjan_pyro_300.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 RMJ12346 274 M_jannaschii_chromosome #2 RMJ16681 161 M_jannaschii_chromosome #3 RMJ07132 119 M_jannaschii_chromosome #4 RMJ02735 111 M_jannaschii_chromosome #5 RPH01639 300 Pyrococcus_OT3 Motif number 1 ACTTTAATTTTTATTTTAGTTTTATTTTCAAAA 1 9 1 TTTTATTTTT 0.986855 -266 TGACATTAAAATTTATGCCATTTTTGAAAATAAAA 1 30 0 ATTTATCTTT 0.805672 -245 TGGCATAAATTTTAATGTCAATTTTCTTTTTTTAA 1 45 1 TTTAATTTTT 0.972413 -230 ATTTTCTTTTTTTAATATAGAATTTTCGCAGTTTA 1 65 1 TTTAATTTTT 0.972413 -210 ATAAATACTGTTTTATATAATCTTTATTTTCAAAT 1 168 1 TTTTATTTTT 0.986855 -107 GAGCTTTTGATTTTATCTTTTTTTTGAGATTTTCA 1 241 0 TTTTATTTTT 0.986855 -34 CTTTTTTATTTTTTATCTACTGTTATCGCTATATT 2 28 1 TTTTATTTTA 0.923777 -134 TTTAAATGTATTTTATGTTCGTTTTACAAAACATC 2 61 1 TTTTATTTTT 0.986856 -101 TTTGGTTCATATTTATCATGGATTTTTGGGACTGC 2 115 1 ATTTATATTT 0.876054 -47 TATTTTATCTTTTTATAATAATTTTCTCACTGGAG 3 80 0 TTTTATATTT 0.952802 -40 TTGCCATTTATATAATCATATATTTAAT 4 4 0 TATAATATTT 0.604023 -108 TATATTATTTTTTAATTTGCCATTTATATAATCAT 4 20 0 TTTAATTTTT 0.972413 -92 TGTTATGTTATATTATATATTATTTTTTAATTTGC 4 35 0 TATTATTTTT 0.923772 -77 ACATTAAAAAATTTATGTTATGTTATATTATATAT 4 50 0 ATTTATTTTA 0.809277 -62 ACATAAATTTTTTAATGTATAAGTTATGTGGGGAA 4 67 1 TTTAATTGTT 0.817189 -45 CGAAAAGTTTATATATCTCTATTTTCAAAAAACAG 5 48 0 ATATATTTTT 0.69223 -253 ****** * *** Masking position 6 Map Score: 26.0078 Number of sites scoring better than the average of aligned sites = 903 Number in coding regions = 629 Number in noncoding regions = 274 Number of orfs with sites within 600 bp upstream = 242 Fraction of orfs with sites within 600 bp upstream = 0.0388693 Motif number 2 TTAGTTTTATTTTCAAAAATGGCATAAATT 1 26 1 TTTCAAAAAT 0.897178 -249 GGCATCATATTTCCTCATAAAGATTTTTCC 1 131 1 TTCCTCATAA 0.509943 -144 TAATCTTTATTTTCAAATATTCATGTCTCT 1 185 1 TTTCAAATAT 0.753394 -90 AATATTCATGTCTCTAAAATAAATTAAGAA 1 200 1 TCTCTAAAAT 0.851133 -75 TGATTGAAAATCTCAAAAAAAAGATAAAAT 1 237 1 TCTCAAAAAA 0.947511 -38 ATTCCCTAAAAATTTTTCTTTT 2 3 1 TCCCTAAAAA 0.878326 -159 CCTATTGCAGTCCCAAAAATCCATGATAAA 2 126 0 TCCCAAAAAT 0.973663 -36 CTCCCCACAAAAACATCCTATT 2 150 0 CCCCACAAAA 0.971558 -12 TGTATAATTATTTCACAAATATGAACAAAA 3 14 1 TTTCACAAAT 0.904449 -106 ATGTTGGATTCCCCACATAACTTATACATT 4 80 0 CCCCACATAA 0.922839 -32 ATTGCAAATACCCCACAAATAACAAAATCT 5 18 0 CCCCACAAAT 0.977531 -283 ATATCTCTATTTTCAAAAAACAGATTGCAA 5 41 0 TTTCAAAAAA 0.87262 -260 TTCAGCTAAGCCCCAGAAATTTCACGCTGT 5 146 0 CCCCAGAAAT 0.893204 -155 TGAAATAATTACTCACAAATTAAGTATAAG 5 187 1 ACTCACAAAT 0.778237 -114 AATTAAAGACCTTCAAAAATTTTATTTGGG 5 272 1 CTTCAAAAAT 0.904449 -29 ATTCTCTCCCCCAAATAAAATTTTTGAA 5 283 0 CCCCAAATAA 0.91684 -18 ********** Masking position 7 Map Score: 23.1403 Number of sites scoring better than the average of aligned sites = 662 Number in coding regions = 562 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 3 AAAATAAAACTAAAATAAAAATTAAAGT 1 9 0 TAAAATAAAA 0.800761 -266 TATGCCATTTTTGAAAATAAAACTAAAATA 1 22 0 TTGAAAATAA 0.881279 -253 AAATTCTATATTAAAAAAAGAAAATTGACA 1 60 0 TTAAAAAAAG 0.718992 -215 AATACCTCCATAGAATATATATAAACTGCG 1 91 0 TAGAATATAT 0.792579 -184 GATTTTTCCATAAAGTATAAATACTGTTTT 1 152 1 TAAAGTATAA 0.816828 -123 ACATGAATATTTGAAAATAAAGATTATATA 1 181 0 TTGAAAATAA 0.881279 -94 TTCATGTCTCTAAAATAAATTAAGAATGTA 1 204 1 TAAAATAAAT 0.615525 -71 TAACAGTAGATAAAAAATAAAAAAGAAAAA 2 23 0 TAAAAAATAA 0.902703 -139 TAAAATACATTTAAATATAGCGATAACAGT 2 46 0 TTAAATATAG 0.884092 -116 ATTAAATATATGATTATATAA 4 2 1 TTAAATATAT 0.786972 -110 AATGGCAAATTAAAAAATAATATATAATAT 4 31 1 TAAAAAATAA 0.902703 -81 AAAAATAATATATAATATAACATAACATAA 4 43 1 TATAATATAA 0.59742 -69 AATCTGTTTTTTGAAAATAGAGATATATAA 5 45 1 TTGAAAATAG 0.85929 -256 TACTCACAAATTAAGTATAAGTAAAACTAT 5 196 1 TTAAGTATAA 0.79675 -105 AGTTCATTCATAGAGAAAAGGAATTAAAGA 5 251 1 TAGAGAAAAG 0.527979 -50 ********** Masking position 4 Map Score: 13.9762 Number of sites scoring better than the average of aligned sites = 1280 Number in coding regions = 889 Number in noncoding regions = 391 Number of orfs with sites within 600 bp upstream = 338 Fraction of orfs with sites within 600 bp upstream = 0.0542885 Motif number 4 TTCATATTTGTGAAATAATTATACACAA 3 8 0 TGAAAAATTA 0.975418 -112 TGAACAAAACCGAAAGGTTTATATAGAACTT 3 35 1 CGAAAGTTTA 0.888392 -85 TTATCTCCAGTGAGAAAATTATTATAAAAAG 3 76 1 TGAGAAATTA 0.957535 -44 ACTTATACATTAAAAAATTTATGTTATGTTA 4 60 0 TAAAAATTTA 0.81193 -52 GCTCAAATTCCGAAAAGTTTATATATCTCTA 5 62 0 CGAAAGTTTA 0.888392 -239 ATTATCAATGTGAATAAATTACCAGAAGGCT 5 90 0 TGAATAATTA 0.875483 -211 TTCACGCTGTTAAGACAATTAGTTAACCATG 5 125 0 TAAGAAATTA 0.837432 -176 TGAGGCAACTTGAAATAATTACTCACAAATT 5 177 1 TGAAAAATTA 0.975418 -124 ***** ***** Masking position 3 Map Score: 4.95841 Number of sites scoring better than the average of aligned sites = 351 Number in coding regions = 323 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 5 CCATAGAATATATATAAACTGCGAAAATTC 1 84 0 TATATAAACT 0.964833 -191 TGCCTTTAGGAATAAATACCTCCATAGAAT 1 105 0 AATAAATACC 0.634797 -170 TTCCATAAAGTATAAATACTGTTTTATATA 1 157 1 TATAAATACT 0.732859 -118 AATACTGTTTTATATAATCTTTATTTTCAA 1 171 1 TATATAATCT 0.896731 -104 ATCCATGATAAATATGAACCAAATTCTAAA 2 108 0 AATATGAACC 0.894832 -54 TTATTTCACAAATATGAACAAAACCGAAAG 3 21 1 AATATGAACA 0.790629 -99 GTTGAAGTTCTATATAAACCTTTCGGTTTT 3 40 0 TATATAAACC 0.970741 -80 ATTTGCCATTTATATAATCATATATTTAAT 4 11 0 TATATAATCA 0.823134 -101 AAAATAGAGATATATAAACTTTTCGGAATT 5 58 1 TATATAAACT 0.964833 -243 ********** Masking position 4 Map Score: 6.50179 Number of sites scoring better than the average of aligned sites = 483 Number in coding regions = 302 Number in noncoding regions = 181 Number of orfs with sites within 600 bp upstream = 186 Fraction of orfs with sites within 600 bp upstream = 0.0298747 Motif number 6 AAATAAAACTAAAATAAAAATTAAAGT 1 8 0 AAAATAAAAA 0.698984 -267 TCTATATTAAAAAAAGAAAATTGACATTAA 1 56 0 AAAAAGAAAA 0.976276 -219 AAATCTCAAAAAAAAGATAAAATCAAAAGC 1 244 1 AAAAAGATAA 0.937753 -31 ATAAAAAATAAAAAAGAAAAATTTTTAGGG 2 14 0 AAAAAGAAAA 0.976276 -148 GATGTTTTGTAAAACGAACATAAAATACAT 2 66 0 AAAACGAACA 0.894965 -96 TTATTTCACAAATATGAACAAAACCGAAAG 3 21 1 AATATGAACA 0.787739 -99 AAATTATTATAAAAAGATAAAATAAACGGA 3 91 1 AAAAAGATAA 0.937753 -29 ATACCCCACAAATAACAAAATCTGGAGGTG 5 11 0 AATAACAAAA 0.743339 -290 ********** Masking position 4 Map Score: 6.03545 Number of sites scoring better than the average of aligned sites = 476 Number in coding regions = 377 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 7 TTTTTTTAATATAGAATTTTCGCAGTTTAT 1 71 1 ATAGAATTTT 0.958276 -204 AACCTAATAGATAGGATGTTTTGTAAAACG 2 80 0 ATAGGATGTT 0.982135 -82 TGGGACTGCAATAGGATGTTTTTGTGGGGA 2 141 1 ATAGGATGTT 0.982135 -21 TCTCCCCCAAATAAAATTTTTGAAGGTCTT 5 277 0 ATAAAATTTT 0.852338 -24 ********** Masking position 6 Map Score: 0.978174 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 37 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 8 ********** No masking Map Score: -3.39396e-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: -3.39396e-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: -3.39396e-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