AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00150_mjan_reg_100.orf -o00150_mjan_100.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 MJ0771 88 cobalamin biosynthesis precorrin-2 methyltransferase (cbiL) #2 MJ1027 125 formate hydrogenlyase, subunit 5 #3 MJ1028 60 DNA topoisomerase VI, subunit B (top6B) #4 MJ1029 47 dimethyladenosine transferase (ksgA) #5 MJ1522 146 cobalamin biosynthesis precorrin-6Y methylase (cbiE) #6 MJ1575 300 GMP synthase (guaA) #7 MJ1576 80 LemA protein #8 MJ1577 29 M. jannaschii predicted coding region MJ1577 #9 MJ1578 66 cobalamin biosynthesis precorrin-3 methylase (cbiF) Motif number 1 GTCACCAAAAATTTATTGTCAATTTAGCT 1 9 1 AAATTTATTT 0.580229 -80 TCTAAAAAAGTTTTTAATTGTAATTTTATAA 1 59 1 TTTTTAATTT 0.980338 -30 CTAATTATCATTATTAATTATGATAAATTAT 2 52 1 TTATTAATTT 0.977223 -74 TATTATCATGTTTATAATTGTTGG 2 112 1 TTTATAATTT 0.76282 -14 TTTTGTTACATTATTTATTTTACTGATATTT 3 39 1 TTATTTATTT 0.958254 -22 ATTTTTATTTTCTTTTCTCTT 4 1 1 ATTTTTATTT 0.891967 -47 GTTTCACTTTTTATTTATTCTAAAAAAGAGA 4 26 0 TTATTTATTT 0.95867 -22 TTTCAATTTTTAAATTTTTAATTCAAAA 5 8 1 TTTTAAATTT 0.964773 -139 TAACTTATATTTTTATATTCTTATTTTATAT 5 41 1 TTTTATATTT 0.933289 -106 TATATTCTTATTTTATATTCTTATTCTGATA 5 54 1 TTTTATATTT 0.933289 -93 TTACCTTATCTTTTTAATTTTATTGATATTT 5 88 1 TTTTTAATTT 0.980337 -59 TACTATTATGTTTTTAAATATCAATAAAATT 5 103 0 TTTTTAAATT 0.899885 -44 AACATAATAGTAATAAATTATTTGAATGTGA 5 122 1 TAATAAATTT 0.826791 -25 TTTTAAAATTTCTTTTATTATGATTATCCTC 6 31 0 TCTTTTATTT 0.740717 -270 ATAAAAGAAATTTTAAAATATAGTGTCTTTC 6 44 1 TTTTAAAATT 0.831955 -257 TCCATTATTAATATTAATTTTAACAACTTTG 6 74 0 ATATTAATTT 0.921449 -227 TGAAAGATACTAATAAAATATAAGGTGATAA 6 279 1 TAATAAAATT 0.463097 -22 ATATCAACTTATATAAATTTTATTATTAG 7 9 0 ATATAAATTT 0.890228 -72 ACAAAAAAGAATTTGAATTATTTGGATAGTT 7 51 0 ATTTGAATTT 0.703094 -30 TTATTAATTTTAATTTTTAGG 8 1 1 TTATTAATTT 0.978235 -29 TAAGTAAATTTTATTAATTTTGAAAGACCTA 9 17 1 TTATTAATTT 0.978235 -50 ********* * Masking position 9 Map Score: 34.4722 Number of sites scoring better than the average of aligned sites = 1484 Number in coding regions = 1011 Number in noncoding regions = 473 Number of orfs with sites within 600 bp upstream = 382 Fraction of orfs with sites within 600 bp upstream = 0.0613556 Motif number 2 TAAAATTACAATTAAAAACTTTTTTAGATAACT 1 54 0 ATTAAAAATT 0.907887 -35 ATTGTAATTTTATAAAATCGTAAG 1 75 1 TATAAAATAA 0.738807 -14 ATAGTTTTGTTTTAATAAAGTTATCGAG 2 6 0 TTTAATAATA 0.827046 -120 ATTTATCATAATTAATAATGATAATTAGCTTAA 2 47 0 ATTAATAATA 0.805566 -79 AGTTTAAAAATAGTTTAGTTAATTT 3 3 1 TTTAAAAATT 0.914718 -58 TTTTAGAATAAATAAAAAGTGAAACA 4 32 1 AATAAAAAAA 0.876975 -16 GAATTAAAAATTTAAAAATTGAAA 5 2 0 TTTAAAAAAA 0.952657 -145 TAAATTTTTAATTCAAAATTTAACTTATATTTT 5 21 1 ATTCAAAAAA 0.919178 -126 AAAATAAGAATATAAAAATATAAGTTAAATTTT 5 35 0 TATAAAAAAA 0.885837 -112 AGAATAAGAATATAAAATAAGAATATAAAAATA 5 48 0 TATAAAATAA 0.738813 -99 TATCAATAAAATTAAAAAGATAAGGTAAAGATA 5 83 0 ATTAAAAAAA 0.951357 -64 TTTATTGATATTTAAAAACATAATAGTAATAAA 5 106 1 TTTAAAAAAA 0.955131 -41 AGTTTCACATTCAAATAATTTATTACTATTA 5 126 0 ATTCAAATTT 0.677032 -21 GACACTATATTTTAAAATTTCTTTTATTATGAT 6 38 0 TTTAAAATTT 0.795977 -263 TAAAATTAATATTAATAATGGATATTTGAACGC 6 83 1 ATTAATAAAT 0.784837 -218 TAAAAGGTTCATCAAAAATCTAACACCTCCTCG 6 221 0 ATCAAAAAAA 0.629912 -80 TAAAAGGTTCTTTCAAAATGTTTTTGAAAGATA 6 255 1 TTTCAAAATT 0.862172 -46 CTAATAATAAAATTTATATAAGTTG 7 3 1 AATAATAATT 0.510276 -78 TATCCAAATAATTCAAATTCTTTTTTGTGGTGA 7 54 1 ATTCAAATTT 0.677028 -27 TCCCCTAAAAATTAAAATTAATAA 8 2 0 ATTAAAATTA 0.846314 -28 TTTTCATAAGTAAATTTTATTAAT 9 2 1 TTTCATAAAA 0.781845 -65 ATAGTAGGTCTTTCAAAATTAATAAAATTTACT 9 19 0 TTTCAAAAAT 0.866754 -48 AAAGACCTACTATAAAAACAAAAACAAGAGGAG 9 39 1 TATAAAAAAA 0.885838 -28 ******** ** Masking position 7 Map Score: 26.9101 Number of sites scoring better than the average of aligned sites = 3745 Number in coding regions = 2665 Number in noncoding regions = 1080 Number of orfs with sites within 600 bp upstream = 634 Fraction of orfs with sites within 600 bp upstream = 0.101831 Motif number 3 TTACTATATAAATTTAGCTAAATTGACAATAA 1 23 0 AATAGCTAAA 0.859361 -66 TTTATATAGTAAGTTATCTAAAAAAGTTTTTA 1 43 1 AATATCTAAA 0.970102 -46 TATTAAAACAAAACTATATAAAAGGTTAAGCT 2 22 1 AATATATAAA 0.952872 -104 ATGAATAGATAATTTATCATAATTAATAATGA 2 59 0 AATATCATAA 0.737478 -67 AACAAAATAGAAATTAACTAAACTATTTTTAA 3 14 0 AATAACTAAA 0.943539 -47 TAAAATAAATAATGTAACAAAATAGAAATTAA 3 29 0 AATAACAAAA 0.936307 -32 AAAAAAGAGAAAAGAAAATAAAAAT 4 4 0 AAAAAATAAA 0.627002 -44 TCTTTTTTAGAATAAATAAAAAGTGAAACA 4 28 1 AAAATAAAAA 0.741672 -20 TTTTGAATTAAAAATTTAAAAATTGAAA 5 7 0 AATTTAAAAA 0.619508 -140 ATATAAAATAAGAATATAAAAATATAAGTTAA 5 40 0 AGTATAAAAA 0.692831 -107 AGATAAGGTAAAGATATCAGAATAAGAATATA 5 67 0 AATATCAGAA 0.884558 -80 TATGTTTTTAAATATCAATAAAATTAAAAAGA 5 96 0 AATCAATAAA 0.585557 -51 TAATAGTAATAAATTATTTGAATGTGAAACT 5 126 1 AATATTTGAA 0.631707 -21 GTTTGATATCAACTTATATAAATTTTATTATT 7 13 0 AATATATAAA 0.952871 -68 CAAACATACTAAACTATCCAAATAATTCAAAT 7 40 1 AATATCCAAA 0.883464 -41 AGGTCTTTCAAAATTAATAAAATTTACTTATG 9 15 0 AATAATAAAA 0.743239 -52 ** ******** Masking position 11 Map Score: 12.3641 Number of sites scoring better than the average of aligned sites = 1524 Number in coding regions = 1132 Number in noncoding regions = 392 Number of orfs with sites within 600 bp upstream = 357 Fraction of orfs with sites within 600 bp upstream = 0.0573402 Motif number 4 TATATAAATTTAGCTAAATTGACAATAAAT 1 21 0 TAGCTAAATT 0.831764 -68 GATAACTTACTATATAAATTTAGCTAAATT 1 31 0 TATATAAATT 0.859784 -58 AAAACTTTTTTAGATAACTTACTATATAAA 1 43 0 TAGATAACTT 0.966376 -46 CTCGATAACTTTATTAAAACA 2 2 1 TCGATAACTT 0.884912 -124 CTTAACCTTTTATATAGTTTTGTTTTAATA 2 22 0 TATATAGTTT 0.84835 -104 AGGTAATGAATAGATAATTTATCATAATTA 2 66 0 TAGATAATTT 0.972154 -60 AAAAATAGTTTAGTTAATTTCTATTTTGTT 3 16 1 TAGTTAATTT 0.862071 -45 TAATAAAATTTATATAAGTTGATATCAAAC 7 15 1 TATATAAGTT 0.837547 -66 TTGAATTATTTGGATAGTTTAGTATGTTTG 7 40 0 TGGATAGTTT 0.819292 -41 ********** Masking position 5 Map Score: 5.37743 Number of sites scoring better than the average of aligned sites = 268 Number in coding regions = 233 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 5 TTTAACAACTTTGAAAGACACTATATTTTAA 6 56 0 TTGAAAGAAC 0.990675 -245 TAGGAGAGCGTTCAAATATCCATTATTAATA 6 92 0 TTCAAATACC 0.928717 -209 CAAAAACATTTTGAAAGAACCTTTTAGTAAA 6 250 0 TTGAAAGACC 0.99584 -51 CAAAATGTTTTTGAAAGATACTAATAAAATA 6 268 1 TTGAAAGAAC 0.990676 -33 TTTATTAATTTTGAAAGACCTACTATAAAAA 9 26 1 TTGAAAGACT 0.978666 -41 ******** ** Masking position 6 Map Score: 4.605 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 15 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 6 TATAAAAGGTTAAGCTAATTATCATTATTAA 2 38 1 TAAGCTAATA 0.958613 -88 TATGACTCACTAAGGTAATGAATAGATAATT 2 77 0 TAAGGTAATA 0.987976 -49 ATTAAAAAGATAAGGTAAAGATATCAGAATA 5 75 0 TAAGGTAAAA 0.961508 -72 CTGGAATAACTAAGGCATTAATGAACACCTC 6 127 0 TAAGGCATTA 0.918384 -174 TAATAAAATATAAGGTGATAAA 6 289 1 TAAGGTGATA 0.973682 -12 ********* * Masking position 3 Map Score: 1.24913 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 61 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 7 TCTCCTATAGGGAGGTGTTCATTAATGCCT 6 116 1 GGAGGTGTTC 0.991947 -185 GCTTACGCTCGGAGGTGCAACTCAGAAGGA 6 192 0 GGAGGTGCAA 0.98592 -109 GCGTAAGCGAGGAGGTGTTAGATTTTTGAT 6 214 1 GGAGGTGTTA 0.993238 -87 ********** Masking position 3 Map Score: 0.77236 Number of sites scoring better than the average of aligned sites = 19 Number in coding regions = 2 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 8 ********** No masking Map Score: -1.58208e-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: -1.58208e-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: -1.58208e-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