AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00030_mthe_reg_300.orf -o00030_mthe_300.ace -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -g0.50 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 MTH384 249 unknown #2 MTH387 24 conserved protein #3 MTH388 35 unknown #4 MTH393 41 NADH dehydrogenase (ubiquinone), subunit 1 related protein #5 MTH394 55 unknown #6 MTH397 40 formate hydrogenlyase, subunit 7 #7 MTH399 23 polyferredoxin #8 MTH400 33 polyferredoxin #9 MTH403 187 formylmethanofuran:tetrahydromethanopterin formyltransferase II #10 MTH610 84 glycerol 1-phosphate dehydrogenase #11 MTH784 83 ribose-phosphate pyrophosphokinase #12 MTH816 43 sporulation protein IVFB related protein #13 MTH817 56 conserved protein #14 MTH1544 219 ribokinase #15 MTH1545 63 conserved protein #16 MTH1837 128 unknown #17 MTH1840 158 cell division inhibitor Motif number 1 CTCCATAGGAACCTCCAGGACATGATGGGG 1 18 0 ACCTCCAGGA 0.972666 -232 TGAAGGGTCCCTCTACAGAAGATTTAGTAA 1 114 0 CTCTACAGAA 0.975922 -136 TGTAGAGGGACCCTTCAGATATCAGTAAAA 1 127 1 CCCTTCAGAT 0.795685 -123 CTGGAGGTTTCTCTACAGAAACTTTTTTTT 1 153 0 CTCTACAGAA 0.975922 -97 CTGTAGAGAAACCTCCAGATATTAGTAAAA 1 165 1 ACCTCCAGAT 0.958678 -85 CCTCTGAACACTCTCCTGAACTCATCCACC 9 21 0 CTCTCCTGAA 0.967747 -167 GAGGCAGAGGACCTCCTGGACGCAAGCATG 9 79 1 ACCTCCTGGA 0.912792 -109 ATTAGTGTTTATCTCCAGGGAAAAATATAT 10 13 0 ATCTCCAGGG 0.836938 -72 AATGGATATGATGTACAGAATGG 13 44 1 ATGTACAGAA 0.820384 -13 ATAAAGGATGCTCAACAGAACCAGGCCCAA 14 123 1 CTCAACAGAA 0.922681 -97 ATAAACCAACCCCAACAGAATTAACCCCAT 14 183 1 CCCAACAGAA 0.935513 -37 ATGATCACCTGAAAAATATGGGG 14 207 0 ATCACCTGAA 0.845656 -13 ATCGGATATCCTGTCCAGAACTAACAATAT 17 36 1 CTGTCCAGAA 0.948573 -123 TCCAATACCTCCAGATAATAATCAGT 17 143 0 ACCTCCAGAT 0.958678 -16 ********** Masking position 6 Map Score: 18.9346 Number of sites scoring better than the average of aligned sites = 815 Number in coding regions = 726 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 2 CCATAATTTTATTAAGAGGTCTTTTTTAGGTCTAACT 1 199 1 ATAACTTTTT 0.652619 -51 ACTCACCTTTTTTAAAAAGATTTATAT 1 233 1 TTAATTATAT 0.917622 -17 TCACCAGTAATCATCTATATATTC 2 3 0 ATAATTATAT 0.95582 -22 TTTAAGTAGGAGTAATAAAATAATTTTTGATTAGTGT 10 35 0 ATAATATTTT 0.740453 -50 GTTAACCCTCTAATGGAGTATATTTTAAGTAGGAG 10 60 0 TTAATTATTT 0.851608 -25 CCTTCCGGTAATTAACAATTTTTATATAGATAACTCT 11 48 0 ATAATTATAT 0.954599 -36 GGGTGCTATGAATAAATCATTTTTTATAGC 12 4 0 ATAATTTTAT 0.96894 -40 TTTGAGGCGGATTAAGGTGATTTTTATAAAATGTGGT 14 69 0 ATAATTTTAT 0.961439 -151 CCCCAACAGAATTAACCCCATATTTTTCAGGTGATCA 14 192 1 ATAATTTTTT 0.941373 -28 ATATTTTAGGTGGAATACTCTGTTTATGGAGGCATAG 16 12 0 TGAATTTTAT 0.690457 -117 ATATATAGGCTTTAAGCATTTATTAATTAAATGGGTA 16 45 1 TTAATTTAAT 0.600035 -84 TGACTAACTAATTAACAGTTTCTATTTGATTCCAGCA 16 82 1 ATAATTATTT 0.916473 -47 TCCAGCAAGTATTAAAGGAGTGATTAT 16 112 1 ATAATATTAT 0.846948 -17 CCTGTCCAGAACTAACAATATTTTTATACCGGACTTA 17 45 1 ATAATTTTAT 0.967786 -114 AGGCGACGTGTGTAACAATATTTATATCGGAATGACT 17 109 1 TTAATTATAT 0.917646 -50 * *** * ***** Masking position 5 Map Score: 16.2654 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 22 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 3 ATTCCCACCCCATCATGTCCTGG 1 3 1 TCCCACCCCT 0.894289 -247 TCCTATGGAGTCACATCCACTTACCGGTTTC 1 38 1 TCACATCCAT 0.973289 -212 CTCATCACCATTAACACCGGAA 4 30 0 TCATCACCAT 0.8234 -12 TCTGATTAAATCCCTTCCATTTTCATTCCAC 5 21 0 TCCCTTCCAT 0.827433 -35 ATGTTCTTTCTGACCTCCATGCTTGCGTCCA 9 95 0 TGACCTCCAG 0.861142 -93 GGATCCGACGTCCTCTCCCCGGATGTTCTTT 9 117 0 TCCTCTCCCG 0.895727 -71 CTGAATGTAAGCACATCCAGGGATTCAGCCG 9 150 0 GCACATCCAG 0.888144 -38 TGAGCATCACAACCATGCTGAATGTAA 9 171 0 TCACAACCAG 0.933306 -17 TGATTAGTGTTTATCTCCAGGGAAAAATATA 10 14 0 TTATCTCCAG 0.624446 -71 GAAAAATCACCTTCCGGTAATTAACAA 11 67 0 TCACCTTCCG 0.659753 -17 ATTCTGTACATCATATCCATTCGGTTTTTCA 13 34 0 TCATATCCAT 0.935398 -23 AAGTATAAAGTCCCACCCAATAAAGGATGCT 14 104 1 TCCCACCCAT 0.943687 -116 AATTAGTTAGTCATACCCATTTAATTAATAA 16 64 0 TCATACCCAT 0.900683 -65 ********* * Masking position 8 Map Score: 8.60698 Number of sites scoring better than the average of aligned sites = 1095 Number in coding regions = 1022 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 4 AGGTCTAACTCACCTTTTTTAAAAAGATTTA 1 226 1 CACTTTTTTA 0.895725 -24 CCTTTTTTAAAAAGATTTATAT 1 238 1 AAAATTTATA 0.832539 -12 TTAGTCTGACAAAATTTTATAATTAGAATTA 11 15 1 AAATTTTATA 0.888585 -69 CGGTAATTAACAATTTTTATATAGATAACTC 11 49 0 CAATTTTATA 0.972122 -35 ATGAATAAATCATTTTTTATAGC 12 3 0 CATTTTTATA 0.895861 -41 ATTTGAGGACCACATTTTATAAAAATCACCT 14 61 1 CACTTTTATA 0.959124 -159 CCAGAACTAACAATATTTTTATACCGGACTT 17 50 1 CAAATTTTTA 0.888349 -109 ACGTGTGTAACAATATTTATATCGGAATGAC 17 114 1 CAAATTTATA 0.956015 -45 *** ******* Masking position 2 Map Score: 6.08092 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 20 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 5 CGAAAACGACTATGAAAATCCTTAAAATTTA 1 83 1 TATAAAATCC 0.680628 -167 CCTCTTTTCTGATTAAATCCCTTCCATTTTC 5 28 0 GATAAATCCC 0.874268 -28 GGAGATGATAAAATTCCAGCTGCAGCA 8 7 1 GATAAATTCC 0.755294 -27 ATTCCAGCTGCAGCAAAACCC 8 23 1 CAGAAAACCC 0.927693 -11 TCCTCTGCCTCCTCAATAACCGTTATGATCG 9 59 0 CCTAATAACC 0.817217 -129 CCAGGATCAAAAAACTCGAGCGATG 13 5 1 GATAAAAAAC 0.757747 -52 AAACTCGAGCGATGAAAAACCGAATGGATAT 13 22 1 GATAAAAACC 0.977574 -35 GCATGAAAACCCGCTGAAAAAC 14 2 1 CATAAAACCC 0.973698 -218 ATGAAAACCCGCTGAAAAACCATTTATGGGA 14 13 1 GCTAAAAACC 0.937919 -207 AATCCAATCACATTATAAACCAACCCCAACA 14 169 1 CATATAAACC 0.948677 -51 CCAACCCCAACAGAATTAACCCCATATTTTT 14 188 1 CAGATTAACC 0.613828 -32 TTCAGGGTTTCATAATCAACCGGACCATATT 15 25 0 CATATCAACC 0.794029 -39 *** ******* Masking position 5 Map Score: 5.48502 Number of sites scoring better than the average of aligned sites = 398 Number in coding regions = 356 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 6 ATCCTTAAAATTTATTACTAAATCTTCTGT 1 100 1 TTTATTACTA 0.719164 -150 ACAGAAACTTTTTTTTACTGATATCTGAAG 1 139 0 TTTTTTACTG 0.784301 -111 AATTATGGCCTTTTTTACTAATATCTGGAG 1 177 0 TTTTTTACTA 0.87806 -73 GTTTATGATAATAGAATCATT 4 2 1 TTTATGATAA 0.571522 -40 AATCCCCTCTTTTCTGATTAAATCCCTTCC 5 34 0 TTTCTGATTA 0.792994 -22 CATTTGCTCTTTATTGATTGAAGTTCA 6 8 0 TTATTGATTG 0.675059 -33 AATAAAATAATTTTTGATTAGTGTTTATCT 10 29 0 TTTTTGATTA 0.948334 -56 AATCAAAAATTATTTTATTACTCCTACTTA 10 40 1 TATTTTATTA 0.602797 -45 CTGACAAAATTTTATAATTAGAATTAATAG 11 20 1 TTTATAATTA 0.804555 -64 TATATAAAAATTGTTAATTACCGGAAGGTG 11 57 1 TTGTTAATTA 0.667381 -27 GAATAAATCATTTTTTATAGC 12 2 0 TTTTTTATAG 0.595319 -42 CTTTAAGCATTTATTAATTAAATGGGTATG 16 54 1 TTATTAATTA 0.685934 -75 ACACGTCGCCTTTTTAATTACCCTACTTTA 17 90 0 TTTTTAATTA 0.918959 -69 ********** Masking position 7 Map Score: 2.70787 Number of sites scoring better than the average of aligned sites = 144 Number in coding regions = 80 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 7 TAATAGAATCATTCCGGTGTTAATGGTGATGAG 4 19 1 ATCCGTTTAA 0.906305 -23 TTATTTTATTACTCCTACTTAAAATATACTCCA 10 49 1 ATCCTCTAAA 0.958942 -36 GCATGAAAACCCGCTGAAAAACCATTTATG 14 8 1 ACCCGTAAAA 0.878424 -212 AAATCACCTTAATCCGCCTCAAAGTATAAAGTC 14 83 1 ATCCGCCAAA 0.969045 -137 ACTATGCCTCCATAAACAGAGTATTC 16 4 1 AGCCTCTAAA 0.877848 -125 TAAACAGAGTATTCCACCTAAAATATATAGGCT 16 23 1 ATCCACAAAA 0.852112 -106 AAGACATGTAAGTCCGGTATAAAAATATTGTTA 17 57 0 ATCCGTTAAA 0.981811 -102 ATAATCAGTCATTCCGATATAAATATTGTTACA 17 119 0 ATCCGTTAAA 0.98181 -40 * **** * **** Masking position 12 Map Score: 2.40049 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 29 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 8 ATAAAATTATGGCCTTTTTTACTAATATCT 1 181 0 GGCCTTTTTT 0.959079 -69 TTTATTAAGAGGTCTTTTTTAGGTCTAACT 1 206 1 GGTCTTTTTT 0.975583 -44 ATTACCGGAAGGTGATTTTTC 11 73 1 GGTGATTTTT 0.975583 -11 GGCGGATTAAGGTGATTTTTATAAAATGTG 14 71 0 GGTGATTTTT 0.975583 -149 ********** Masking position 6 Map Score: 1.11397 Number of sites scoring better than the average of aligned sites = 30 Number in coding regions = 15 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 9 TCATGTCCTGGAGGTTCCTATGGAGTCACAT 1 23 1 GAGGTTCCTT 0.958694 -227 CCGGTAAGTGGATGTGACTCCATAGGAACCT 1 34 0 GATGTGACTC 0.944124 -216 CTAATATCTGGAGGTTTCTCTACAGAAACTT 1 159 0 GAGGTTTCTT 0.936548 -91 ATTTTATTAAGAGGTCTTTTTTAGGTCTAAC 1 204 1 GAGGTCTTTT 0.806558 -46 AGAGTGTTCAGAGGTGACTACCCGATCATAA 9 37 1 GAGGTGACTC 0.975858 -151 CCTCTCCCCGGATGTTCTTTCTGACCTCCAT 9 106 0 GATGTTCTTC 0.870618 -82 TGAATCCCTGGATGTGCTTACATTCAGCATG 9 154 1 GATGTGCTTC 0.92968 -34 TAATTACCGGAAGGTGATTTTTC 11 71 1 AAGGTGATTT 0.803646 -13 GAGGCGGATTAAGGTGATTTTTATAAAATGT 14 72 0 AAGGTGATTT 0.803646 -148 CTATGGTGTTTCTGTGGTTTCAGGG 15 49 0 GGTGTTTCTT 0.567782 -15 ********* * Masking position 5 Map Score: 1.87423 Number of sites scoring better than the average of aligned sites = 640 Number in coding regions = 590 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 10 ********** No masking Map Score: 3.12882e-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 11 ********** No masking Map Score: 3.12882e-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 12 ********** No masking Map Score: 3.12882e-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