AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00900_mjan_reg_300.orf -o00900_mjan_300.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.31 -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 = 0.31 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 MJ0861 131 conserved hypothetical protein #2 MJ0862 176 carotenoid biosynthetic gene ERWCRTS isolog #3 MJ0863 70 heterodisulfide reductase, subunit B2 (hdrB2) #4 MJ0864 160 heterodisulfide reductase, subunit C2 (hdrC2) Motif number 1 GGATAACAGTATTAACAATACTGTT 1 6 0 ATTAACAATA 0.892466 -126 AACATCTAAGATAAAAATAAAAATCATAAA 1 38 0 ATAAAAATAA 0.899357 -94 TGTAAATTTATTTAAAATAATTAAATATTT 1 72 1 TTTAAAATAA 0.918771 -60 AATTTTAATGTTTATAAATATTTAATTATT 1 87 0 TTTATAAATA 0.898435 -45 ATTTATAAACATTAAAATTATAAAAAATTA 1 98 1 ATTAAAATTA 0.987521 -34 ATTAAAATTATAAAAAATTAAAGGATGTGA 1 108 1 TAAAAAATTA 0.725575 -24 ATAAAAAATATTTAAATATAAAATGCTAAT 2 14 0 TTTAAATATA 0.697166 -163 ATTATGAATAATAAAAAATATTTAAATATA 2 24 0 ATAAAAAATA 0.965827 -153 AAGAAATAAAATAAAAATTATGAATAATAA 2 40 0 ATAAAAATTA 0.962638 -137 TATCAAAAATATTAAAAAAAGAAATAAAAT 2 58 0 ATTAAAAAAA 0.967849 -119 AAATAGACACATTATAAAAAAGTTAGTATT 2 93 0 ATTATAAAAA 0.881853 -84 TTAATAACAAATTAAAAATAGACACATTAT 2 108 0 ATTAAAAATA 0.988611 -69 TTAATTTGTTATTAAAATTTCACAAAGTTA 2 123 1 ATTAAAATTT 0.934667 -54 CACCAAATACTATATAAATATTTGCTATAT 2 152 0 TATATAAATA 0.687848 -25 ATCCAATAAAATTAGAATTAAAAT 3 5 1 AATAAAATTA 0.951701 -66 TAAAATTAGAATTAAAATTAAACAATAAAA 3 17 1 ATTAAAATTA 0.987521 -54 AAATTAAACAATAAAAAATTAAAGGAAATA 3 31 1 ATAAAAAATT 0.836318 -40 AAGAAGTTAAATAAAATAACCCCCTCATG 4 10 1 AATAAAATAA 0.872351 -151 TTAAAGAGAAATTAAAAACATGAGGGGGTT 4 28 0 ATTAAAAACA 0.916735 -133 ATAAATAAATTTTAAAATTTAATTTAAAGA 4 51 0 TTTAAAATTT 0.854991 -110 AAAATACCTCATTATAAATAAATTTTAAAA 4 64 0 ATTATAAATA 0.95566 -97 ********** Masking position 4 Map Score: 38.1191 Number of sites scoring better than the average of aligned sites = 2646 Number in coding regions = 1772 Number in noncoding regions = 874 Number of orfs with sites within 600 bp upstream = 545 Fraction of orfs with sites within 600 bp upstream = 0.0875361 Motif number 2 TCTAAGATAAAAATAAAAATCATAAATGGG 1 34 0 AAATAAAAAT 0.96657 -98 TAATTATTTTAAATAAATTTACAGCCTAAC 1 65 0 AAATAAATTT 0.936542 -67 TATTTAAAATAATTAAATATTTATAAACAT 1 80 1 AATTAAATAT 0.950007 -52 TATTTATAAACATTAAAATTATAAAAAATT 1 97 1 CATTAAAATT 0.770555 -35 CATTAAAATTATAAAAAATTAAAGGATGTG 1 107 1 ATAAAAAATT 0.686508 -25 AATAAAAAATATTTAAATATAAAATGCTAA 2 15 0 ATTTAAATAT 0.798375 -162 AATTATGAATAATAAAAAATATTTAAATAT 2 25 0 AATAAAAAAT 0.929733 -152 AAAAGAAATAAAATAAAAATTATGAATAAT 2 42 0 AAATAAAAAT 0.96657 -135 AAAATATTAAAAAAAGAAATAAAATAAAAA 2 53 0 AAAAAGAAAT 0.842195 -124 TTTAATAACAAATTAAAAATAGACACATTA 2 109 0 AATTAAAAAT 0.968833 -68 TTTAATTTGTTATTAAAATTTCACAAAGTT 2 122 1 TATTAAAATT 0.693476 -55 ACCAAATACTATATAAATATTTGCTATATA 2 151 0 ATATAAATAT 0.782205 -26 ATCCAATAAAATTAGAATTAAAATTAAAC 3 10 1 AATTAGAATT 0.921572 -61 AAAATTAAACAATAAAAAATTAAAGGAAAT 3 30 1 AATAAAAAAT 0.929733 -41 TAAAGGAAATAATAAGATTTTTGGTGATAA 3 50 1 AATAAGATTT 0.760061 -21 AAGAAGTTAAATAAAATAACCCCCTCAT 4 9 1 AAATAAAATA 0.659085 -152 AATTTAATTTAAAGAGAAATTAAAAACATG 4 36 0 AAAGAGAAAT 0.661195 -125 TTTCTCTTTAAATTAAATTTTAAAATTTAT 4 47 1 AATTAAATTT 0.938608 -114 ACCTCATTATAAATAAATTTTAAAATTTAA 4 59 0 AAATAAATTT 0.936542 -102 ********** Masking position 5 Map Score: 32.1834 Number of sites scoring better than the average of aligned sites = 1852 Number in coding regions = 1222 Number in noncoding regions = 630 Number of orfs with sites within 600 bp upstream = 444 Fraction of orfs with sites within 600 bp upstream = 0.0713138 Motif number 3 AATTAAATATTTATAAACATTAAAATTATA 1 90 1 TTATAAACAT 0.75017 -42 AACATTAAAATTATAAAAAATTAAAGGATG 1 105 1 TTATAAAAAA 0.949418 -27 AGTATTGACTTTATCAAAAATATTAAAAAA 2 69 0 TTATCAAAAA 0.932388 -108 AATAGACACATTATAAAAAAGTTAGTATTG 2 92 0 TTATAAAAAA 0.949418 -85 TGTGAAATTTTAATAACAAATTAAAAATAG 2 117 0 TAATAACAAA 0.873902 -60 TGTTATTAAAATTTCACAAAGTTATATAGC 2 129 1 ATTTCACAAA 0.867818 -48 TCACAAAGTTATATAGCAAATATTTATATA 2 142 1 ATATAGCAAA 0.794046 -35 AATTTCACCAAATACTATATA 2 166 0 ATTTCACCAA 0.898147 -11 TTAGAATTAAAATTAAACAATAAAAAATTA 3 22 1 AATTAAACAA 0.600108 -49 CTTATCACCAAAAATCTTATT 3 60 0 TTATCACCAA 0.971528 -11 AAATACCTCATTATAAATAAATTTTAAAAT 4 63 0 TTATAAATAA 0.79723 -98 CTAACTATATATATAACCAAAACCCTACCT 4 124 1 ATATAACCAA 0.9679 -37 ********** Masking position 9 Map Score: 13.4437 Number of sites scoring better than the average of aligned sites = 1153 Number in coding regions = 914 Number in noncoding regions = 239 Number of orfs with sites within 600 bp upstream = 236 Fraction of orfs with sites within 600 bp upstream = 0.0379056 Motif number 4 TATAATTTTAATGTTTATAAATATTTAATT 1 90 0 ATGTTTATAA 0.953118 -42 CTTTTTTATAATGTGTCTATTTTTAATTTG 2 101 1 ATGTGTCTAT 0.963639 -76 TAACCCCCTCATGTTTTTAATTTCTCTTTA 4 27 1 ATGTTTTTAA 0.953122 -134 GGTATTTTACAAGTGTCTAATACTAACATT 4 86 1 AAGTGTCTAA 0.983834 -75 CTAACATTCGAAGTTTCTAACTATATATAT 4 108 1 AAGTTTCTAA 0.982571 -53 ********** Masking position 6 Map Score: 4.48218 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 40 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 5 ********** No masking Map Score: -3.74156e-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: -3.74156e-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: -3.74156e-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