AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i079_mjan_pyro_300.orf -o079_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 RMJ01130 162 M_jannaschii_chromosome #2 RMJ14570 123 M_jannaschii_chromosome #3 RMJ05488 49 M_jannaschii_chromosome #4 RMJ00515 41 M_jannaschii_chromosome #5 RMJ05845 54 M_jannaschii_chromosome #6 RMJ03243 87 M_jannaschii_chromosome Motif number 1 TTCAATTTTGATGAAACTTTTTCTAAAAGT 1 22 1 ATGAAACTTT 0.861823 -141 GAGGTTTTAAAAGAAACTTTTAGAAAAAGT 1 37 0 AAGAAACTTT 0.895684 -126 GGATTATCCTAATAAATTATAGTAATCTTT 1 94 0 AATAAATTAT 0.931617 -69 ATCCTGCCTTATTAAAAAATAGCAAGTTAC 1 120 1 ATTAAAAAAT 0.917788 -43 ATATTCAATAAATAAACTATCCGACGATAA 2 59 0 AATAAACTAT 0.968546 -65 AATCCATACATTAAAAAATCCATTGAGGA 3 10 1 ATTAAAAAAT 0.917788 -40 CTGAAATAAAAATTAAATCTTCCT 3 36 0 AATAAAAATT 0.917788 -14 AATAAAATTTTTATTGTTAA 4 1 1 AATAAAATTT 0.969148 -41 TTTTATTGTTAATAAAATTTTGCTGGTGAA 4 19 1 AATAAAATTT 0.969148 -23 AAAATCCCTCAAAAAAATAT 5 1 0 AAAAAAATAT 0.858873 -54 AATCAAACAAATTAAATTAACTTCCAGCTC 5 33 0 ATTAAATTAA 0.689889 -22 TAGTGAAAACATTAAAATAACTATCTAAGT 6 58 1 ATTAAAATAA 0.875623 -30 ********** Masking position 5 Map Score: 16.1549 Number of sites scoring better than the average of aligned sites = 1208 Number in coding regions = 821 Number in noncoding regions = 387 Number of orfs with sites within 600 bp upstream = 337 Fraction of orfs with sites within 600 bp upstream = 0.0541279 Motif number 2 AAAGCTTTTTAATTTGGAACGCTATAAAAAGATT 1 67 1 AATTAAGCTA 0.924284 -96 AGATTACTATAATTTATTAGGATAATCCTGCCTT 1 96 1 AATTTAGATA 0.781803 -67 GCCTTATTAAAAAATAGCAAGTTACTAAAGAATT 1 125 1 AAATCAGTTA 0.829655 -38 GTTACTAAAGAATTTCTAAAGTGATATA 1 145 1 AATTAAGTGA 0.974299 -18 AATAAAATTTTTATTGTTAATAAAATTTT 4 6 1 AATTATGTTA 0.982645 -36 TTGTTAATAAAATTTTGCTGGTGAAATT 4 24 1 AATTCTGTGA 0.969163 -18 GCTGGAAGTTAATTTAATTTGTTTGATTGA 5 35 1 AATTTTGTTT 0.795201 -20 ACCCTACATCCAATTACATAGTGAAAACATTAAA 6 40 1 CATTATGTGA 0.916054 -48 GGTATCACCAACTTAGATAGTTATTTTAATGTT 6 65 0 AATTATGTTA 0.982639 -23 ** ** ** **** Masking position 5 Map Score: 4.92975 Number of sites scoring better than the average of aligned sites = 235 Number in coding regions = 179 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 3 TTTGATGAAACTTTTTCTAAAAGTTTCTTTT 1 28 1 CTTTTTCTAA 0.949583 -135 CTAAAAGTTTCTTTTAAAACCTCAAAGCTTT 1 44 1 CTTTTAAAAC 0.950922 -119 TTATAGTAATCTTTTTATAGCGTTCCAAATT 1 77 0 CTTTTTATAC 0.971206 -86 ATAATCCTGCCTTATTAAAAAATAGCAAGTT 1 117 1 CTTATTAAAA 0.787219 -46 TTCTTAGTTGCTTTAACTAAAGTCCAACATT 2 11 1 CTTTAACTAA 0.863747 -113 TAACTTCCAGCTCTTAAAATCCCTCAAAAAA 5 15 0 CTCTTAAAAC 0.86068 -40 AAACCACAACCTTTATATACACCCTACATCC 6 20 1 CTTTATATAA 0.924624 -68 ********* * Masking position 9 Map Score: 1.86641 Number of sites scoring better than the average of aligned sites = 791 Number in coding regions = 662 Number in noncoding regions = 129 Number of orfs with sites within 600 bp upstream = 118 Fraction of orfs with sites within 600 bp upstream = 0.0189528 Motif number 4 TAAGATATATATTCAATTTTG 1 2 1 AAGATATATA 0.686555 -161 AATTTTGATGAAACTTTTTCTAAAAGTTTC 1 25 1 AAACTTTTTC 0.863985 -138 TAAAACCTCAAAGCTTTTTAATTTGGAACG 1 58 1 AAGCTTTTTA 0.969636 -105 AAATTATAGTAATCTTTTTATAGCGTTCCA 1 81 0 AATCTTTTTA 0.967298 -82 ACTAAAGTCCAACATTTATGCCATGTTTTT 2 26 1 AACATTTATG 0.856732 -98 TTATTTATTGAATATGTTTATAAGACTGGA 2 74 1 AATATGTTTA 0.913432 -50 AATAAAATTTTTATTGTTAATAA 4 4 1 AAAATTTTTA 0.928514 -38 AAGTTAATTTAATTTGTTTGATTGA 5 40 1 AATTTGTTTG 0.645098 -15 ACCAAACCACAACCTTTATATACACCCTAC 6 17 1 AACCTTTATA 0.943666 -71 ********** Masking position 5 Map Score: 2.73027 Number of sites scoring better than the average of aligned sites = 1197 Number in coding regions = 863 Number in noncoding regions = 334 Number of orfs with sites within 600 bp upstream = 298 Fraction of orfs with sites within 600 bp upstream = 0.0478638 Motif number 5 TTAGAAAAAGTTTCATCAAAATTGAATATA 1 18 0 TTTCATCAAA 0.923285 -145 TCTTAGTTGCTTTAACTAAAGTCCAACATT 2 12 1 TTTAACTAAA 0.725879 -112 TAAAATATAATCAGCTCTTCCTTCT 2 109 0 TATAATCAGC 0.863865 -15 AATTTCACCAGCAAAATTTTAT 4 30 0 TTTCACCAGC 0.987578 -12 TCTCTCACCAAACCACAACCTT 6 3 1 TCTCACCAAA 0.971552 -85 GGTATCACCAACTTAGATAGTT 6 76 0 TATCACCAAC 0.985328 -12 ********** Masking position 5 Map Score: 3.05471 Number of sites scoring better than the average of aligned sites = 408 Number in coding regions = 314 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 6 ********** No masking Map Score: -5.94424e-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: -5.94424e-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 8 ********** No masking Map Score: -5.94424e-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