AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i321_mjan_pyro_100.orf -o321_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 RMJ00843 201 M_jannaschii_chromosome #2 RMJ04712 278 M_jannaschii_chromosome #3 RPH01107 45 Pyrococcus_OT3 #4 RPH01557 59 Pyrococcus_OT3 #5 RPH01559 70 Pyrococcus_OT3 #6 RPH01560 55 Pyrococcus_OT3 #7 RPH01561 233 Pyrococcus_OT3 Motif number 1 AATCATTATAAATTCCTAATAAGTTGGTGATG 1 14 0 AATCTAATAA 0.822749 -188 AGGAATTTATAATGATTAATAATGATAAATCT 1 29 1 AATTTAATAA 0.892507 -173 ATATGCTCTCAAATCTTTATTAAAGTGAGGTT 1 143 0 AAATTTATTA 0.91167 -59 TTGGCATCAAAATTCCTTATATGGTATAAAAA 2 43 0 AATCTTATAT 0.8693 -236 ATTCAATCATAAAATTTTATTTCTGTGAAAGT 2 85 1 AAATTTATTT 0.785834 -194 ATTTTCTCCAAAATTTTTATAAATCTTTTTTA 2 193 1 AAATTTATAA 0.978753 -86 ATAAGATATTAAATTTTTGTAAAAAGGAAAA 4 10 0 AAATTTGTAA 0.887745 -50 ACAAAAATTTAATATCTTATAAAGGTAATAAA 4 22 1 AATCTTATAA 0.949258 -38 TTTCTCCGCAAAAGATTTATAATTCCTGGAAC 5 31 1 AAATTTATAA 0.978754 -40 TCTTTATTGTAAAGGTTCATAAGCATCCATTT 7 71 0 AAATTCATAA 0.905724 -163 CAAATACTCCAATTATTTATAATTCATTGAAT 7 110 1 AATTTTATAA 0.970983 -124 GAGAAATCCGAAAAATTTATATAGTTTTTCCG 7 173 1 AAATTTATAT 0.942455 -61 *** ******* Masking position 2 Map Score: 14.2421 Number of sites scoring better than the average of aligned sites = 666 Number in coding regions = 424 Number in noncoding regions = 242 Number of orfs with sites within 600 bp upstream = 232 Fraction of orfs with sites within 600 bp upstream = 0.0372631 Motif number 2 AATAAGATTTATCATTATTAATCATTATAA 1 35 0 ATCATTATTA 0.860084 -167 ATAATGATAAATCTTATTTATAACTTTTGG 1 47 1 ATCTTATTTA 0.726149 -155 ATGCTCTCAAATCTTTATTAAAGTGAGGTT 1 143 0 ATCTTTATTA 0.974997 -59 TTGGATGTATAACTTTTTTG 1 192 1 AACTTTTTTG 0.826371 -10 GGGAAAACCCTATTGACAAAGGACT 2 6 1 AACCCTATTG 0.659382 -273 TGCCAAAGGCATCTTTATTCAATCATAAAA 2 69 1 ATCTTTATTC 0.91195 -210 ATTTTTATAAATCTTTTTTATAAATACTCT 2 205 1 ATCTTTTTTA 0.961415 -74 CTTCATAATTATCCCTATTAAAGCATATAT 2 247 0 ATCCCTATTA 0.910191 -32 TTTTCCTTTTTACAAAAATTTA 4 3 1 TTCCTTTTTA 0.86809 -57 TGTTTCTTTCTTTTTTAGTATTATTTT 6 8 1 TTCTTTTTTA 0.888884 -48 CCTGGATAGCATCTTTACTGGTTAAATGGA 7 48 1 ATCTTTACTG 0.851892 -186 TTTGAGCATGTTCTTTATTGTAAAGGTTCA 7 84 0 TTCTTTATTG 0.921309 -150 AATTCATTGAATCCTTATTTGGCCATAATC 7 130 1 ATCCTTATTT 0.851826 -104 ********** Masking position 9 Map Score: 11.3291 Number of sites scoring better than the average of aligned sites = 774 Number in coding regions = 680 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 3 GATAAATCTTATTTATAACTTTTGGTGATAATAGG 1 52 1 ATTAACTTTG 0.823438 -150 CAAAAAAGTTATACATCCAAGGGTTTTGCTC 1 181 0 ATTAAATCCG 0.961828 -21 TCAATCATAAAATTTTATTTCTGTGAAAGTCCTGT 2 87 1 ATTTATTCTG 0.883077 -192 CCTGTGATACCCTAACACCTCCTCGCTATGCCCGG 2 117 1 CTAAACTCCG 0.938952 -162 TAATTTGCTAATTTACACCTCCGGGCATAGCGAGG 2 137 0 ATTAACTCCG 0.993898 -142 TTATAAAGGTAATAAAAACTCTGGGAGTTACT 4 38 1 ATAAACTCTG 0.960272 -22 TCCGCAAAAGATTTATAATTCCTGGAACTATCAAC 5 35 1 ATTAATTCCG 0.988081 -36 AATTCCTGGAACTATCAACTCCACGTCAAA 5 51 1 ATATACTCCG 0.953491 -20 TATTATTTTTAAGTAGATTTCCATGAGCTATTCTT 6 29 1 AGTAATTCCG 0.945321 -27 TACTCCAATTATTTATAATTCATTGAATCCTTATT 7 114 1 ATTAATTCAG 0.914915 -120 * *** * **** * Masking position 7 Map Score: 8.45442 Number of sites scoring better than the average of aligned sites = 144 Number in coding regions = 113 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 4 GGTATCCCAATAGGGGTTTTCCCCATGGCAA 1 93 0 TAGGGGTTTC 0.973908 -109 GCAACCTCGCTCGGGTATCCCAATAGGGGTT 1 106 0 TCGGGTATCC 0.986173 -96 TTATACATCCAAGGGTTTTGCTCCTATTGAT 1 173 0 AAGGGTTTTC 0.961809 -29 CCTTTGTCAATAGGGTTTTCCC 2 2 0 TAGGGTTTTC 0.990299 -277 GAGGAGGTGTTAGGGTATCACAGGACTTTCA 2 110 0 TAGGGTATCC 0.98851 -169 TATAAATTTTTCGGATTTCTCATGCCTGCAT 7 163 0 TCGGATTTCC 0.953672 -71 ********* * Masking position 8 Map Score: 5.81544 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 12 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 5 ATTCCTAATAAGTTGGTGATGCTT 1 5 0 AGTTGGTGAT 0.952902 -197 TATTTATAACTTTTGGTGATAATAGGCTTA 1 61 1 TTTTGGTGAT 0.955939 -141 CAAGATAATAATTTGCTAATTTACACCTCC 2 150 0 ATTTGCTAAT 0.743954 -129 TTTATAAAAATTTTGGAGAAAATATTGTGT 2 186 0 TTTTGGAGAA 0.723973 -93 AAAGATTAAAAGTTGCAAATTAAATTAGTT 3 15 1 AGTTGCAAAT 0.671198 -31 ATTAAATTAGTTTTGGTGATTGA 3 33 1 TTTTGGTGAT 0.955939 -13 AAATGGAAGAATTTGCCAATTTATGGTC 7 9 0 ATTTGCCAAT 0.734052 -225 TTGAATCCTTATTTGGCCATAATCTCTATG 7 136 1 ATTTGGCCAT 0.906715 -98 TTTTCCGCCCATTTTGAAATGAAAAGACTG 7 198 1 ATTTTGAAAT 0.653605 -36 ********** Masking position 4 Map Score: 3.65369 Number of sites scoring better than the average of aligned sites = 793 Number in coding regions = 692 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 114 Fraction of orfs with sites within 600 bp upstream = 0.0183103 Motif number 6 CCCCATGGCAATATAAGCCTATTATCACCA 1 74 0 ATATAAGCCT 0.841435 -128 ATGATTGAATAAAGATGCCTTTGGCATCAA 2 65 0 AAAGATGCCT 0.971441 -214 CAAACCTCATATATATGCTTTAATAGGGAT 2 237 1 ATATATGCTT 0.962843 -42 TGATATTAGATGCTTCATAATTATC 2 264 0 TTAGATGCTT 0.949846 -15 TTTAACCAGTAAAGATGCTATCCAGGTAAG 7 44 0 AAAGATGCTA 0.910191 -190 TACTGGTTAAATGGATGCTTATGAACCTTT 7 63 1 ATGGATGCTT 0.964157 -171 ********** Masking position 5 Map Score: 1.98179 Number of sites scoring better than the average of aligned sites = 189 Number in coding regions = 162 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 7 GGGATACCCGAGCGAGGTTGCCAAGACAAC 1 116 1 AGCGAGGTTG 0.99573 -86 TCTTTATTAAAGTGAGGTTGTCTTGGCAAC 1 132 0 AGTGAGGTTG 0.988439 -70 CTCCGGGCATAGCGAGGAGGTGTTAGGGTA 2 124 0 AGCGAGGAGG 0.991084 -155 ********** Masking position 5 Map Score: 1.10309 Number of sites scoring better than the average of aligned sites = 5 Number in coding regions = 4 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 8 ********** No masking Map Score: -1.40444e-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: -1.40444e-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: -1.40444e-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