AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i314_mjan_pyro_300.orf -o314_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 RMJ11898 300 M_jannaschii_chromosome #2 RMJ05555 123 M_jannaschii_chromosome #3 RMJ08568 143 M_jannaschii_chromosome #4 RMJ03695 30 M_jannaschii_chromosome #5 RMJ05273 101 M_jannaschii_chromosome #6 RPH00709 47 Pyrococcus_OT3 Motif number 1 TATACTAAAACTCCTATAACTAT 1 4 1 ACTAAAACTC 0.966921 -297 CATAACTATTAACAAAAATCCCCAATATTT 1 125 1 AACAAAAATC 0.895473 -176 AATATTTACTATAAAAACTTAAAACCAAAT 1 148 1 ATAAAAACTT 0.795725 -153 AAAACTTAAAACCAAATCTTAAAACTATAA 1 161 1 ACCAAATCTT 0.699386 -140 CTAAACAAAATTAAAAAATCTAATATCAAT 1 207 1 TTAAAAAATC 0.769319 -94 TAATATCAATATTAAAAATCCAATAAACTA 1 227 1 ATTAAAAATC 0.969707 -74 AATAAACTAAACTAAATATAATCAAATCTC 1 248 1 ACTAAATATA 0.815486 -53 ACTAAATATAATCAAATCTCAAATAAACTA 1 258 1 ATCAAATCTC 0.921051 -43 CAAATAAACTATAAAAAATGCTGAGTTGAT 1 277 1 ATAAAAAATG 0.8373 -24 CTTAACAATAATAAAAAATCCAGAAATCTT 2 66 1 ATAAAAAATC 0.977811 -58 AAAATTTTTAACCAAAAATATTTTAAATAA 2 94 0 ACCAAAAATA 0.96541 -30 TACGTTAGCAACCAAAAAGCTAAAAGCTAT 3 66 1 ACCAAAAAGC 0.907422 -78 ACTAAATTAGACAAAAAATCAAAATGG 3 127 1 ACAAAAAATC 0.984436 -17 CCAAAAATAAATAAAATATAAAA 4 4 0 ATAAAATATA 0.809126 -27 AGAACCACCAAAAATAAATAAAATAT 4 15 0 ACCAAAAATA 0.96541 -16 TAAAAATCTGATTAAAAATAGATTACAGTA 5 61 0 ATTAAAAATA 0.910903 -41 TCAAATTTTTACTAAAAATCTGATTAAAAA 5 73 0 ACTAAAAATC 0.978699 -29 ACAGCAATGGATAAAAACTCCATGCTATTT 6 28 0 ATAAAAACTC 0.96556 -20 ********** Masking position 5 Map Score: 28.8945 Number of sites scoring better than the average of aligned sites = 701 Number in coding regions = 564 Number in noncoding regions = 137 Number of orfs with sites within 600 bp upstream = 128 Fraction of orfs with sites within 600 bp upstream = 0.0205589 Motif number 2 ATCCGTATCCAAATTTTTACTGCATGATTA 1 42 1 AAATTTTTAC 0.935575 -259 TAATCTTTTAAAGGTTTTAATAATCATGCA 1 62 0 AAGGTTTTAA 0.958751 -239 AAGATTAAGAAAGGTTTTGCATAGTCATAT 1 85 1 AAGGTTTTGC 0.822133 -216 GTTTTAAGATTTGGTTTTAAGTTTTTATAG 1 156 0 TTGGTTTTAA 0.902516 -145 TTATATTTTTATAGTTTTAAGATTTGGTTT 1 169 0 ATAGTTTTAA 0.952528 -132 TTAACCAAAAATATTTTAAATAAGATTTCT 2 87 0 ATATTTTAAA 0.737451 -37 CAATCACCCAAAATTTTTAACCAAAAATAT 2 103 0 AAATTTTTAA 0.926125 -21 AATGACAGATTAGGTTTAACAGTATATAAA 3 33 1 TAGGTTTAAC 0.706133 -111 ATTAATATTTATGTTTTTAATAGCTTTTAG 3 85 0 ATGTTTTTAA 0.935575 -59 TTTGTCTAATTTAGTTTTACGCTTCAAATT 3 112 0 TTAGTTTTAC 0.902516 -32 CTACTGTAATCTATTTTTAATCAGATTTTT 5 60 1 CTATTTTTAA 0.745484 -42 TTTATCCCTCAAATTTTTACTAAAAATCTG 5 81 0 AAATTTTTAC 0.935575 -21 ********** Masking position 5 Map Score: 12.6226 Number of sites scoring better than the average of aligned sites = 804 Number in coding regions = 606 Number in noncoding regions = 198 Number of orfs with sites within 600 bp upstream = 186 Fraction of orfs with sites within 600 bp upstream = 0.0298747 Motif number 3 CTAAAACTCCTATAACTATTTTTCTATATCC 1 15 1 TATACTATTT 0.801759 -286 ATTTTTACTGCATGATTATTAAAACCTTTAA 1 54 1 CATATTATTA 0.968137 -247 AAATCCGATACATAACTATTAACAAAAATCC 1 115 1 CATACTATTA 0.970602 -186 ACTATAAAAATATAAACAATACTCTAAACAA 1 184 1 TATAACAATA 0.797282 -117 AAAAATCTAATATCAATATTAAAAATCCAAT 1 220 1 TATAATATTA 0.942042 -81 CTGGATTTTTTATTATTGTTAAGATTACAAA 2 58 0 TATATTGTTA 0.745746 -66 AATAATTTATCATTATCATTAATGACAGATT 3 13 1 CATATCATTA 0.961698 -131 TTTAACAGTATATAAACATTACGTTAGCAAC 3 47 1 TATAACATTA 0.962156 -97 CTATTAAAAACATAAATATTAATTTGAAGCG 3 92 1 CATAATATTA 0.975349 -52 *** ******* Masking position 5 Map Score: 8.33681 Number of sites scoring better than the average of aligned sites = 294 Number in coding regions = 207 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 4 TATACTAAAACTCCTATAACTATTTTTC 1 9 1 AACTCCTATA 0.913413 -292 ATAGTCATATAAATCCGATACATAACTATT 1 105 1 AAATCCGATA 0.977208 -196 ACTTAAAACCAAATCTTAAAACTATAAAAA 1 164 1 AAATCTTAAA 0.936845 -137 CAAAATTAAAAAATCTAATATCAATATTAA 1 212 1 AAATCTAATA 0.965845 -89 TCAATATTAAAAATCCAATAAACTAAACTA 1 232 1 AAATCCAATA 0.965178 -69 AAATATAATCAAATCTCAAATAAACTATAA 1 261 1 AAATCTCAAA 0.896921 -40 AAAAATCCAGAAATCTTATTTAAAATATTT 2 79 1 AAATCTTATT 0.936844 -45 TTTTTACTAAAAATCTGATTAAAAATAGAT 5 68 0 AAATCTGATT 0.941222 -34 ********** Masking position 8 Map Score: 8.75795 Number of sites scoring better than the average of aligned sites = 192 Number in coding regions = 156 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 5 ********** No masking Map Score: -4.38104e-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: -4.38104e-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: -4.38104e-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