AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00650_aquae_reg_100.orf -o00650_aquae_100.ace -a/home/amcguire/genomes/ORF_aquae.txt -z/home/amcguire/genomes/aquae.fna -g0.44 -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 = 0.44 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 fabZ 23 (3R)-hydroxymyristoyl-(acyl carrier protein) dehydratase #2 aq_194 53 putative protein #3 aldH2 300 aldehyde dehydrogenase #4 dhsU 161 flavocytochrome C sulfide dehydrogenase #5 frdB1 35 fumarate reductase iron-sulfur subunit #6 frdA 295 fumarate reductase flavoprotein subunit #7 frdB2 39 fumarate reductase iron-sulfur subunit #8 gsa 24 glutamate-1-semialdehyde aminotransferase #9 aq_1166 113 putative protein #10 forB2 23 ferredoxin oxidoreductase beta subunit #11 fdx3 74 ferredoxin #12 ilvH 27 acetolactate synthase Motif number 1 CCCTCGATGGTTATTATTTCTTTTCATTCCGC 3 120 0 TATATTTCTT 0.89585 -181 GGGAAAAATTTCTTTCCACCGTAA 4 3 1 GAAATTTCTT 0.962215 -159 AACTTGACACTTAAAAATTCTTACGGTGGAAA 4 23 0 TAAAATTCTT 0.981799 -139 TTAGTCTGGGGGATAAATTTTTCAAACGGAAT 5 12 0 GAAAATTTTT 0.84064 -24 CTCTACGGATTAATAATTTCTTTGATACTACT 6 83 1 TAAATTTCTT 0.986702 -213 TTTTATAGCTTTAGAATTTATTATCCAGATT 7 10 0 TAAATTTATT 0.935985 -30 ACTCAAAATTTTATAGCTTTAGAA 7 26 0 TAAATTTTAT 0.707891 -14 TTGAGCTTCCTCATAAACTTTTTAAGCTTAAA 9 67 1 TAAAACTTTT 0.84064 -47 TATCTTTAGGTAACAAATTCTT 9 102 1 TAAAATTCTT 0.981799 -12 AATTAAAATATAAAAATTCCTTAATAATTTTA 11 25 0 TAAATTCCTT 0.926895 -50 ATATTTTAATTCACAAACTCTTTTCTGGAGGA 11 46 1 TAAAACTCTT 0.949227 -29 TCCTCCTGTTTAATAATTTATT 12 1 0 TAAATTTATT 0.935983 -27 * * ******** Masking position 6 Map Score: 12.9459 Number of sites scoring better than the average of aligned sites = 267 Number in coding regions = 235 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 2 GTTGAGACTTACCGGGACGAA 3 2 1 TTGAGACTTA 0.932946 -299 GTGTGAAGACATGACACTTACTATTTCCTC 3 279 0 ATGACACTTA 0.968529 -22 AGTGACAAACTTGACACTTAAAAATTCTTA 4 32 0 TTGACACTTA 0.988244 -130 GGTGTCAAAAATGACACCTTAGTGACAAAC 4 52 0 ATGACACCTT 0.811296 -110 GGTGTCATTTTTGACACCTGATTCTTTTCA 4 64 1 TTGACACCTG 0.969727 -98 CTTTATTGTATTTACACTTATCCTTGTTTT 6 185 1 TTTACACTTA 0.950563 -111 TTGGACGTTATATACACTTAAACCGTTGTT 9 31 1 TATACACTTA 0.875607 -83 AAAATAGACCCTTGTAAAATTATT 11 5 1 TAGACCCTTG 0.846164 -70 ********** Masking position 4 Map Score: 6.24766 Number of sites scoring better than the average of aligned sites = 56 Number in coding regions = 49 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 3 ATATTCCCTTACCGCATCCGAACTTCGTCC 3 25 0 ACCGCATCCG 0.890221 -276 TAAGGGAATATGCGGTTCCTGCACCGTTTT 3 44 1 TGCGGTTCCT 0.98636 -257 TTCTTTTCATTCCGCTTCCTTGACTGGGTA 3 105 0 TCCGCTTCCT 0.991068 -196 GGATTGAACTTCAGGTTCCCCAGTGCGGAT 3 184 1 TCAGGTTCCC 0.92372 -117 GGTTCCCCAGTGCGGATACTGCCAGCCCGG 3 197 1 TGCGGATACT 0.788086 -104 CTGATTCTTTTCAAGTTCCTTAGAATTTCA 4 81 1 TCAAGTTCCT 0.835831 -81 TAATTCTGTGAGAGCATCCTTACTAAAT 6 9 0 AGAGCATCCT 0.926175 -287 GTTTTAATTTTGAGCTTCCTCATAAACTTT 9 58 1 TGAGCTTCCT 0.978537 -56 TACCTCTTCCTCCAGAAAAGA 11 64 0 ACCTCTTCCT 0.866657 -11 ********** Masking position 7 Map Score: 6.0505 Number of sites scoring better than the average of aligned sites = 438 Number in coding regions = 412 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 4 CTTTTATAATAGCCTTTAAAAAGTAAGCTTGTA 2 14 1 ACCTTTAAAG 0.990429 -40 CGGTTCCTGCACCGTTTTAATAGACGGAAATCC 3 56 1 ACGTTTAAAG 0.959562 -245 ATAGACGGAAATCCTGTGAGGAGCTGTCAGTAC 3 75 1 ACCTGTAGAG 0.988014 -226 CCCGAAGAACACCCTGTTAAAAGGGCATGGATT 3 156 1 ACCTGTAAAG 0.992062 -145 TAAAAATCCGAACCCTTCAAAAGAGGAAATAGT 3 257 1 ACCCTTAAAG 0.969553 -44 ACGATTATATACCTTGTAAACAGGCAAATAAAG 6 234 1 ACTTGTAAAG 0.95082 -62 AAAAACTTTAAGGAGGTGTTGAT 10 3 1 AACTTTAGAG 0.900202 -21 * ***** ** ** Masking position 9 Map Score: 5.81158 Number of sites scoring better than the average of aligned sites = 67 Number in coding regions = 57 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 5 CCTGAAAATGTTAAAATAGCG 1 2 1 CTGAAAATGT 0.967159 -22 TTTCTGGACACTGAAATTCTAAGGAACTTG 4 92 0 CTGAAATTCT 0.915901 -70 TTTCAGTGTCCAGAAATTGGCACGAAAATT 4 106 1 CAGAAATTGG 0.842694 -56 GACGCTGTATCTTAAAATATTGTT 6 282 1 CTTAAAATAT 0.891778 -14 TCTTTACGACCTTAAATTGGACGTTATATA 9 15 1 CTTAAATTGG 0.955284 -99 ATAATTTAAGCTTAAAAAGTTTATGAGGAA 9 73 0 CTTAAAAAGT 0.835061 -41 ACTTTTTAAGCTTAAATTATATCTTTAGGT 9 83 1 CTTAAATTAT 0.914743 -31 ********** Masking position 5 Map Score: 1.77427 Number of sites scoring better than the average of aligned sites = 36 Number in coding regions = 31 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 6 GGAAGCGGAATGAAAAGAAATAATAACCAT 3 116 1 TGAAAAGAAA 0.925287 -185 CCTTCAAAAGAGGAAATAGTAAGTGTCATG 3 270 1 AGGAAATAGT 0.80026 -31 ATTCTTACGGTGGAAAGAAATTTTTCCC 4 9 0 TGGAAAGAAA 0.937326 -153 CTAAGGAACTTGAAAAGAATCAGGTGTCAA 4 74 0 TGAAAAGAAT 0.941609 -88 ACAAAAATGGAGGTAAGAGT 4 152 1 AGGTAAGAGT 0.865095 -10 GGTGGTAAATTAAAAAGAGATGAGTGAAGT 6 143 1 TAAAAAGAGA 0.768399 -153 CTCTTCCTCCAGAAAAGAGTTTGTGAATTA 11 52 0 AGAAAAGAGT 0.962375 -23 ********** Masking position 5 Map Score: 1.49217 Number of sites scoring better than the average of aligned sites = 679 Number in coding regions = 641 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 7 AACGCTATTTTAACATTTTCAGG 1 11 0 GCTATTTTAA 0.980485 -13 CTTTTTAAAGGCTATTATAAAAGTGT 2 7 0 GCTATTATAA 0.938541 -47 TTCAATCCATGCCCTTTTAACAGGGTGTTC 3 162 0 GCCCTTTTAA 0.929954 -139 ACTTGTTATTTTAAATTTAACTTA 8 11 0 GTTATTTTAA 0.957079 -14 CACTTAAACCGTTGTTTTAATTTTGAGCTT 9 45 1 GTTGTTTTAA 0.928979 -69 ********** Masking position 5 Map Score: 1.22745 Number of sites scoring better than the average of aligned sites = 30 Number in coding regions = 27 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 8 GCAATAAATACAACGAACAAAAATGGAGGTA 4 136 1 CACGAACAAA 0.956186 -26 ATACTTTTTGCTACGAATAAACCCAATTTTG 6 44 1 CACGAATAAA 0.979776 -252 GTTTGATGCTCTACGGATTAATAATTTCTTT 6 75 1 CACGGATTAA 0.973331 -221 ATCGTGCCTCCCACGATTAAGGAAAAAACAA 6 208 0 CACGATTAAG 0.938388 -88 AAAATTAAAACAACGGTTTAAGTGTATATAA 9 38 0 CACGGTTTAA 0.962223 -76 * ********* Masking position 3 Map Score: 0.0208573 Number of sites scoring better than the average of aligned sites = 19 Number in coding regions = 15 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 9 ********** No masking Map Score: 1.56563e-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: 1.56563e-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: 1.56563e-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