AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i268_hypothetical13_mjan_reg_300.orf -o268_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 RMJ07298 86 M_jannaschii_chromosome #2 RMJ05688 127 M_jannaschii_chromosome #3 RMJ01733 162 M_jannaschii_chromosome #4 RMJ10835 26 M_jannaschii_chromosome #5 RMJ06373 34 M_jannaschii_chromosome #6 RMJ08937 116 M_jannaschii_chromosome Motif number 1 CCACAACCCTTAAATTGATGTATGTAATGTTTA 1 18 1 TAAATGTGAT 0.877753 -69 ATGTAATGTTTAAAGTTATAAATCATAACTCAC 1 39 1 TAAATTTAAT 0.971763 -48 CTCTCCTCTTTAAATTTGATTAGTGAGTTATGA 1 61 0 TAAATTATAG 0.806495 -26 CTCTTTTTAATAAAAAGATAAATATATTCCAAT 2 14 1 TAAAAGTAAT 0.929855 -114 TAAAAAGTATTAAATTGGAATATATTTATCTTT 2 27 0 TAAATGAAAT 0.964826 -101 TACTTTTTAATAAACTTAATAATAACTAAGTTT 2 51 1 TAAATTATAT 0.968472 -77 TAATAATAACTAAGTTTATATAATAAACTGTTT 2 67 1 TAAGTTTAAA 0.564566 -61 GTTTATATAATAAACTGTTTCTTAATTATGGAT 2 80 1 TAAATGTTTT 0.929854 -48 GTTATCCCTATAAAAATTAATTTAATCCATAAT 2 104 0 TAAAATAATT 0.851086 -24 AAAGTTTAGTTAAAAATTAAAATTAATTAAAAC 3 13 0 TAAAATAAAT 0.929827 -150 AATTTTTAACTAAACTTTTTTATGGTGGGCAGA 3 28 1 TAAATTTTAT 0.971763 -135 AAATAAACAGTAAATTTCATTTTGGGGAAGGAA 3 87 1 TAAATTATTT 0.929802 -76 AAAGAAACAGTAAAATTTTTCATTCAAATAGTT 3 126 1 TAAATTTTAT 0.971763 -37 GAATTAATTTTAAGGTGGTAATTT 6 2 0 TAAGTGTATT 0.755729 -115 TTTTATTTTGTAAATTTGAAAATATACAAATAT 6 35 0 TAAATTAAAT 0.968472 -82 AAAAGTCATATAAATAGTTTTTTATTTTGTAAA 6 54 0 TAAAAGTTTT 0.850764 -63 TGTGGAACCTTAAAAATAATAAAAAAGTCATAT 6 76 0 TAAAATATAA 0.68141 -41 **** ** ** ** Masking position 3 Map Score: 23.0375 Number of sites scoring better than the average of aligned sites = 1699 Number in coding regions = 1151 Number in noncoding regions = 548 Number of orfs with sites within 600 bp upstream = 408 Fraction of orfs with sites within 600 bp upstream = 0.0655316 Motif number 2 TAATGTTTAAAGTTATAAATCATAACTCAC 1 42 1 AGTTATAAAT 0.617574 -45 AATATATTTATCTTTTTATTAAAAAGAGAT 2 12 0 TCTTTTTATT 0.841787 -116 CCAATTTAATACTTTTTAATAAACTTAATA 2 42 1 ACTTTTTAAT 0.976216 -86 ATATAAACTTAGTTATTATTAAGTTTATTA 2 58 0 AGTTATTATT 0.879319 -70 TATATAATAAACTGTTTCTTAATTATGGAT 2 83 1 ACTGTTTCTT 0.94656 -45 CAGTTTTAATTAATTTTAATT 3 2 1 AGTTTTAATT 0.919019 -161 AGTTTTAATTAATTTTAATTTTTAACTAAA 3 12 1 AATTTTAATT 0.747016 -151 TTTTAACTAAACTTTTTTATGGTGGGCAGA 3 31 1 ACTTTTTTAT 0.960321 -132 AATGAAATTTACTGTTTATTTTTGGTTTCA 3 78 0 ACTGTTTATT 0.961355 -85 GAAAAATTTTACTGTTTCTTTCCAAACTTC 3 117 0 ACTGTTTCTT 0.94656 -46 GAAACAGTAAAATTTTTCATTCAAATAGTT 3 129 1 AATTTTTCAT 0.851962 -34 TCATTCAAATAGTTTGTTTTCTGCAATA 3 145 1 AGTTTGTTTT 0.77044 -18 TCATATAAATAGTTTTTTATTTTGTAAATT 6 52 0 AGTTTTTTAT 0.945858 -65 TATTTATATGACTTTTTTATTATTTTTAAG 6 71 1 ACTTTTTTAT 0.960321 -46 ********** Masking position 3 Map Score: 17.3981 Number of sites scoring better than the average of aligned sites = 892 Number in coding regions = 675 Number in noncoding regions = 217 Number of orfs with sites within 600 bp upstream = 205 Fraction of orfs with sites within 600 bp upstream = 0.0329264 Motif number 3 AGTTTCACCACAACCCTTAAATTGA 1 3 1 TTTCACCACC 0.995482 -84 ATACAACCATTTTCATCTCTGCCCACCATAAAA 3 45 0 TTTCACCGCC 0.983203 -118 TTATTTTTGGTTTCAATACAACCATTTTCATCT 3 60 0 TTTCATCACC 0.986746 -103 CTTTCCAAACTTCCTTCCCCAAAATGAAATTTA 3 97 0 TTCCTCCAAA 0.8999 -66 AATTTTACTGTTTCTTTCCAAACTTCCTTCCCC 3 110 0 TTTCTTCAAC 0.966936 -53 CAACTTTACATTTCTAAACCAACA 5 2 0 TTTCTACAAC 0.966936 -33 ATTTGTATATTTTCAAATTTACAAAATAAAAAA 6 37 1 TTTCAATACA 0.763386 -80 CATTTCACCTCAAAAATTTGTGGAA 6 102 0 TTTCACCAAA 0.981555 -15 ***** * * *** Masking position 2 Map Score: 6.50242 Number of sites scoring better than the average of aligned sites = 253 Number in coding regions = 235 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 4 TTTTCATCTCTGCCCACCATAAAAAAGTTT 3 39 0 TGCCCACCAT 0.945812 -124 CAAACTTCCTTCCCCAAAATGAAATTTACT 3 95 0 TCCCCAAAAT 0.982697 -68 TACTGTTTCTTTCCAAACTTCCTTCCCCAA 3 108 0 TTCCAAACTT 0.90288 -55 AACTTATCCCCCCAACTTATTTTATT 4 9 0 CCCCCAACTT 0.996168 -18 CTAAATCCCCCAACTTTACATTTCTA 5 19 0 CCCCCAACTT 0.996168 -16 TTTTTAAGGTTCCACAAATTTTTGAGGTGA 6 93 1 TCCACAAATT 0.942506 -24 ********** Masking position 6 Map Score: 5.36944 Number of sites scoring better than the average of aligned sites = 240 Number in coding regions = 204 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 5 AATCTCTTTTTAATAAAAAGATAA 2 5 1 TCTTTTTAAT 0.725283 -123 TTGGAATATATTTATCTTTTTATTAAAAAG 2 16 0 TTTATCTTTT 0.738365 -112 AATAACTAAGTTTATATAATAAACTGTTTC 2 71 1 TTTATATAAT 0.909509 -57 CCTATAAAAATTAATTTAATCCATAATTAA 2 101 0 TTAATTTAAT 0.717572 -27 CAGTTTTAATTAATTTTAATTTTT 3 5 1 TTTAATTAAT 0.56277 -158 TGAAATTTACTGTTTATTTTTGGTTTCAAT 3 76 0 TGTTTATTTT 0.689608 -87 TCCCCCCAACTTATTTTATT 4 1 0 TTATTTTATT 0.758518 -26 TTAATTCATATTTGTATATTTTCAAATTTA 6 28 1 TTTGTATATT 0.835797 -89 TATAAATAGTTTTTTATTTTGTAAATTTGA 6 49 0 TTTTTATTTT 0.904841 -68 TTATATGACTTTTTTATTATTTTTAAGGTT 6 74 1 TTTTTATTAT 0.904767 -43 ********** Masking position 7 Map Score: 1.02701 Number of sites scoring better than the average of aligned sites = 3237 Number in coding regions = 2224 Number in noncoding regions = 1013 Number of orfs with sites within 600 bp upstream = 565 Fraction of orfs with sites within 600 bp upstream = 0.0907485 Motif number 6 ********** No masking Map Score: 1.3033e-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: 1.3033e-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: 1.3033e-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