AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i012_mjan_pyro_300.orf -o012_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 RMJ06822 167 M_jannaschii_chromosome #2 RMJ10722 300 M_jannaschii_chromosome #3 RPH00972 82 Pyrococcus_OT3 #4 RPH01394 71 Pyrococcus_OT3 Motif number 1 AATATCATCATTTAGATTTTTAAATATAGT 1 11 1 TTTAGATTTT 0.926674 -157 CTTTCTAAGATTTATACTATATTTAAAAAT 1 26 0 TTTATACTAT 0.876771 -142 TATTATCTAATTTAAAGTATCTATTAGATA 1 66 0 TTTAAAGTAT 0.836833 -102 TCACAATGTTTTTATATTATCTAATTTAAA 1 80 0 TTTATATTAT 0.979426 -88 AACAATAAATATTATATTATGATGTACATA 1 112 0 ATTATATTAT 0.877694 -56 CAATTTCAATTTCAGATTTTAACAATAAAT 1 132 0 TTCAGATTTT 0.866507 -36 ATTTATGTGGTTTATTTTTTAT 2 3 0 TTTATTTTTT 0.949443 -298 TGAATTAATATCTATTTTATTTATGTGGTT 2 21 0 TCTATTTTAT 0.83081 -280 TAGTCGTAGTTTTATTTTTCGTAATATATT 2 94 1 TTTATTTTTC 0.718165 -207 CAGCCAACAATCCATAGTATGATTATTAAA 2 122 0 TCCATAGTAT 0.695723 -179 TGTTGGCTGGATTATATTAAATAAACAGTA 2 143 1 ATTATATTAA 0.532529 -158 TTTCATTAAGTTCATATTATTTTTAAGGCA 2 188 1 TTCATATTAT 0.961142 -113 AATGAAGTTCTTTATTTTTTAAGTAATGCC 2 214 0 TTTATTTTTT 0.949443 -87 CTCCCCCAATTTTATTTTTTTAGGATTATT 2 277 0 TTTATTTTTT 0.949443 -24 TCCTCACTTTTTTAAATTTTCAGAAAGGTT 3 40 0 TTTAAATTTT 0.9213 -43 CTTTTCACCATTCAAAGTTTCAAATAAGGT 4 12 1 TTCAAAGTTT 0.70161 -60 AAATAAGGTTTTTATATTAAACTGTAATTC 4 33 1 TTTATATTAA 0.884418 -39 ********** Masking position 4 Map Score: 20.2894 Number of sites scoring better than the average of aligned sites = 2232 Number in coding regions = 1614 Number in noncoding regions = 618 Number of orfs with sites within 600 bp upstream = 461 Fraction of orfs with sites within 600 bp upstream = 0.0740443 Motif number 2 ATTTATACTATATTTAAAAATCTAAATGATG 1 16 0 TATTTAAAAT 0.922692 -152 TTTTTATACCTTTCTAAGATTTATACTATAT 1 34 0 TTTCTAAATT 0.789505 -134 ATGATGTACATATATCACAATGTTTTTATAT 1 93 0 TATATCAAAT 0.61006 -75 TGTACATCATAATATAATATTTATTGTTAAA 1 114 1 AATATAAATT 0.469571 -54 TCAATTTCAGATTTTAACAATAAATATTATA 1 126 0 ATTTTAAAAT 0.862235 -42 AATTACCCCTTTAAAGCAATTTCAATTTCA 1 148 0 TTTAAAGAAT 0.734033 -20 ACGACTAAACTAATTAACATTACAATCCCTC 2 70 0 TAATTAAATT 0.753961 -231 CGTAGTTTTATTTTTCGTAATATATTTAATA 2 98 1 TTTTTCGAAT 0.863843 -203 TTTCGTAATATATTTAATAATCATACTATGG 2 110 1 TATTTAAAAT 0.926695 -191 AAGTAATGCCTTAAAAATAATATGAACTTAA 2 193 0 TTAAAAAAAT 0.521087 -108 GTTCTTTATTTTTTAAGTAATGCCTTAAAAA 2 207 0 TTTTAAGAAT 0.854594 -94 TCATAATAAATTTTTATTAATTGAAAGACGC 2 247 0 TTTTTATAAT 0.87283 -54 TAATAAAAATTTATTATGAATAATCCTAAAA 2 259 1 TTATTATAAT 0.691823 -42 CAATTTTATTTTTTTAGGATTATTCATAATA 2 270 0 TTTTTAGATT 0.947403 -31 TTCAGAAAGGTTAATAAGATTAAGGATGAAG 3 21 0 TTAATAAATT 0.769327 -62 TCATCCTCACTTTTTTAAATTTTCAGAAAGG 3 42 0 TTTTTTAATT 0.635162 -41 AGATCACCTAATTTTAGAATTACAGTTTAAT 4 48 0 ATTTTAGATT 0.801627 -24 ******* *** Masking position 9 Map Score: 9.66448 Number of sites scoring better than the average of aligned sites = 4085 Number in coding regions = 3029 Number in noncoding regions = 1056 Number of orfs with sites within 600 bp upstream = 583 Fraction of orfs with sites within 600 bp upstream = 0.0936396 Motif number 3 CATCATAATATAATATTTATTGTTAAAATCT 1 118 1 TAATATTATT 0.768397 -50 TAAATAAAATAGATATTAATTCATGCAACAG 2 28 1 AGATATTATT 0.947466 -273 AATCCCTCAGAAATATTCACTGTTGCATGAA 2 47 0 AAATATTACT 0.830437 -254 AGTATGGCAAAGAGATTGATTTCATTAAGTT 2 169 1 AGAGATTATT 0.914113 -132 TAAAAAATAAAGAACTTCATTTTGGCGTCTT 2 223 1 AGAACTTATT 0.958612 -78 TTCAATTAATAAAAATTTATTATGAATAATC 2 253 1 AAAAATTATT 0.958602 -48 TTTAAAACCCCATTGAGAGTTCAT 3 69 0 AAAACCCATT 0.780451 -14 GTTTAATATAAAAACCTTATTTGAAACTTTG 4 24 0 AAAACCTATT 0.930412 -48 ******* *** Masking position 3 Map Score: 1.42807 Number of sites scoring better than the average of aligned sites = 581 Number in coding regions = 454 Number in noncoding regions = 127 Number of orfs with sites within 600 bp upstream = 136 Fraction of orfs with sites within 600 bp upstream = 0.0218439 Motif number 4 AGATTTATACTATATTTAAAAATCTAAATG 1 19 0 TATATTTAAA 0.830454 -149 AGGTATAAAAACTATCTAATAGATACTTTA 1 54 1 ACTATCTAAT 0.928632 -114 ATGTTTTTATATTATCTAATTTAAAGTATC 1 75 0 ATTATCTAAT 0.869257 -93 ATCATAATATAATATTTATTGTTAAAATCT 1 119 1 AATATTTATT 0.784428 -49 TGAATTAATATCTATTTTATTTATGTGGTT 2 21 0 TCTATTTTAT 0.842341 -280 TTTTTCGTAATATATTTAATAATCATACTA 2 108 1 TATATTTAAT 0.95844 -193 TGCCATACTGTTTATTTAATATAATCCAGC 2 148 0 TTTATTTAAT 0.937194 -153 ********** Masking position 4 Map Score: 2.68558 Number of sites scoring better than the average of aligned sites = 513 Number in coding regions = 381 Number in noncoding regions = 132 Number of orfs with sites within 600 bp upstream = 135 Fraction of orfs with sites within 600 bp upstream = 0.0216833 Motif number 5 ********** No masking Map Score: -2.10731e-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 6 ********** No masking Map Score: -2.10731e-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 7 ********** No masking Map Score: -2.10731e-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