AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00650_aquae_reg_300.orf -o00650_aquae_300.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 purB 41 adenylosuccinate lyase #8 aq_598 99 putative protein #9 frdB2 39 fumarate reductase iron-sulfur subunit #10 gsa 24 glutamate-1-semialdehyde aminotransferase #11 topG1 276 reverse gyrase #12 aq_1163 36 putative protein #13 aq_1166 113 putative protein #14 forB2 23 ferredoxin oxidoreductase beta subunit #15 fdx3 74 ferredoxin #16 ilvH 27 acetolactate synthase Motif number 1 CTACAAGCTTACTTTTTAAAGGCTATTATA 2 18 0 ACTTTTTAAA 0.927921 -36 CTTGTAGAAATATTATTAATAAG 2 41 1 TATTATTAAT 0.733543 -13 CCACCGTAAGAATTTTTAAGTGTCAAGTTT 4 26 1 AATTTTTAAG 0.952194 -136 CTGGGGGATAAATTTTTCAAACGGAATT 5 9 0 AATTTTTCAA 0.803179 -27 GTATCAAAGAAATTATTAATCCGTAGAGCA 6 81 0 AATTATTAAT 0.903903 -215 TTCACTCATCTCTTTTTAATTTACCACCTA 6 141 0 TCTTTTTAAT 0.689575 -155 AAAGGGATAAAATTTTTAATCGTGGGAG 8 9 0 AATTTTTAAT 0.942837 -91 CCTTTCGGTTAATGTTTAAAGTCATAGAAA 8 34 1 AATGTTTAAA 0.803179 -66 TAGTGAATACTATTTTTAAAAAATCTATAA 8 76 1 TATTTTTAAA 0.891151 -24 GAAGGAATATAATTATTAAAGTAGACATGT 11 248 0 AATTATTAAA 0.941018 -29 TTCCTCATAAACTTTTTAAGCTTAAATTAT 13 73 1 ACTTTTTAAG 0.901633 -41 ACCCTTGTAAAATTATTAAGGAATTTTTAT 15 18 1 AATTATTAAG 0.919096 -57 ATTATTAAGGAATTTTTATATTTTAATTCA 15 29 1 AATTTTTATA 0.733567 -46 AATAAATTATTAAACAGGAGGATT 16 5 1 AATTATTAAA 0.941018 -23 ********** Masking position 6 Map Score: 14.7556 Number of sites scoring better than the average of aligned sites = 237 Number in coding regions = 183 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 2 GCACCGTTTTAATAGACGGAAATCCTGTGAG 3 64 1 AATGACGGAA 0.890233 -237 AAATAATAACCATCGAGGGAATTCCCGAAGA 3 133 1 CATGAGGGAA 0.921844 -168 AGCCCGGACAAATAGTGGAAGCCTATGCACT 3 220 1 AATGTGGAAG 0.968824 -81 CGAACCCTTCAAAAGAGGAAATAGTAAGTGT 3 265 1 AAAGAGGAAA 0.916091 -36 AACGAACAAAAATGGAGGTAAGAGT 4 147 1 AATGAGGTAA 0.906449 -15 TTTTTTCCTTAATCGTGGGAGGCACGATTAT 6 211 1 AATGTGGGAG 0.98022 -85 AGGATATCAGAAGGGAGGGAAAGGAAAGAAG 7 14 0 AAGGAGGGAA 0.936036 -28 TAAAATTTTTAATCGTGGGAG 8 1 0 AATGTGGGAG 0.98022 -99 AAGAAATGGAAAAAGAGGAAGGTATGT 11 7 0 AAAGAGGAAG 0.936108 -270 TCGAAGAAATAATAGAAGAAATGGAAAAAGA 11 22 0 AATGAAGAAA 0.774336 -255 TACCTTCTAAAGTTGTGGAAGTTTACGAGGA 11 208 0 AGTGTGGAAG 0.854062 -69 *** ******* Masking position 10 Map Score: 10.8432 Number of sites scoring better than the average of aligned sites = 425 Number in coding regions = 390 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 3 TTCAGTGTCCAGAAATTGGCACGAAAATTGCAATAAA 4 107 1 AGATGAAAAA 0.942268 -55 TAATTCTGTGAGAGCATCCTTACTAAAT 6 2 0 AGATCTTAAA 0.960969 -294 ATTAATCCGTAGAGCATCAAACCAAAATTGGGTTTAT 6 60 0 AGATCAAAAA 0.942268 -236 GCAGGTAGCTAGACGCTGTATCTTAAAATATTGTT 6 271 1 AGATGTTAAA 0.960969 -25 AATCTGGATAATAAATTCTAAAGCTATAAAAT 9 6 1 GGATATTAAA 0.855561 -34 ATTCACCGAAGGAATATAATTATTAAAGTAGACATGT 11 248 0 GGATATTAAA 0.855561 -29 TGAATATTATAGAAATTCAAATCAAAAAATTGTT 12 8 0 AGATCAAAAA 0.942268 -29 AAGTTTATGAGGAAGCTCAAAATTAAAACAACGGTTT 13 50 0 GGATCATAAA 0.962497 -64 AAGAATTTGTTACCTAAAGATATAATTT 13 96 0 AGATGATAAA 0.973006 -18 CCTCCAGAAAAGAGTTTGTGAATTAAAATATAAAAAT 15 40 0 AGATGATAAA 0.973006 -35 *** ** * **** Masking position 7 Map Score: 8.04243 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 32 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 4 AAATCCGAACCCTTCAAAAGAGGAAATAGT 3 260 1 CCTTCAAAAG 0.937819 -41 ATTCTAAGGAACTTGAAAAGAATCAGGTGT 4 77 0 ACTTGAAAAG 0.904412 -85 TGATACTACTACTTCTAGAGTTCAATATTA 6 105 1 ACTTCTAGAG 0.895439 -191 CGATTATATACCTTGTAAACAGGCAAATAA 6 235 1 CCTTGTAAAC 0.968336 -61 CTGGATAATAAATTCTAAAGCTATAAAATT 9 14 1 AATTCTAAAG 0.610787 -26 GAAGAGGAAGCCCTCAAGAGTCTTGAGCTT 11 54 0 CCCTCAAGAG 0.713464 -223 GTGACTACGTACTTGTACACGTTGGGTTTG 11 101 0 ACTTGTACAC 0.789774 -176 TCATGCCAGAACCTGTAAACGTAGGTGACT 11 125 0 ACCTGTAAAC 0.860552 -152 GCTGTTCCGTCCTCGTAAACTTCCACAACT 11 199 1 CCTCGTAAAC 0.852053 -78 CTTGGCTATACCTTCTAAAGTTGTGGAAGT 11 217 0 CCTTCTAAAG 0.974255 -60 AAAATAGACCCTTGTAAAATTATTAAGGA 15 10 1 CCTTGTAAAA 0.854232 -65 ********** Masking position 7 Map Score: 5.70977 Number of sites scoring better than the average of aligned sites = 662 Number in coding regions = 618 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 5 GTTGAGACTTACCGGGACGAA 3 2 1 TTGAGACTTA 0.815534 -299 AGGAACCGCATATTCCCTTACCGCATCCGA 3 34 0 TATTCCCTTA 0.725925 -267 GTGTGAAGACATGACACTTACTATTTCCTC 3 279 0 ATGACACTTA 0.82789 -22 AGTGACAAACTTGACACTTAAAAATTCTTA 4 32 0 TTGACACTTA 0.974265 -130 AGTGTCAAGTTTGTCACTAAGGTGTCATTT 4 44 1 TTGTCACTAA 0.847055 -118 GGTGTCATTTTTGACACCTGATTCTTTTCA 4 64 1 TTGACACCTG 0.847943 -98 CTTTATTGTATTTACACTTATCCTTGTTTT 6 185 1 TTTACACTTA 0.932926 -111 TTAAAAATAGTATTCACTAACCATTCTATC 8 65 0 TATTCACTAA 0.631311 -35 TACAAGTACGTAGTCACCTACGTTTACAGG 11 114 1 TAGTCACCTA 0.87818 -163 TTGGACGTTATATACACTTAAACCGTTGTT 13 31 1 TATACACTTA 0.921289 -83 AAAATAGACCCTTGTAAAATTATT 15 5 1 TAGACCCTTG 0.824337 -70 ********** Masking position 7 Map Score: 6.20816 Number of sites scoring better than the average of aligned sites = 106 Number in coding regions = 95 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 6 CTTATTAATAATATTTCTACAAGCTTACTT 2 34 0 ATATTTCTAC 0.755446 -20 TCGATGGTTATTATTTCTTTTCATTCCGCT 3 119 0 TTATTTCTTT 0.92734 -182 ATAGTAAGTGTCATGTCTTCACACCT 3 285 1 TCATGTCTTC 0.942688 -16 GGGAAAAATTTCTTTCCACCGTAAG 4 6 1 AAATTTCTTT 0.755935 -156 TACGGATTAATAATTTCTTTGATACTACTA 6 86 1 TAATTTCTTT 0.872455 -210 TCAACTTCACTCATCTCTTTTTAATTTACC 6 146 0 TCATCTCTTT 0.869454 -150 AACCATTCTATCATTTCTATGACTTTAAAC 8 47 0 TCATTTCTAT 0.90899 -53 TCCTCTTTTTCCATTTCTTCTATTATTTCT 11 19 1 CCATTTCTTC 0.899374 -258 ATTTCTTCTATTATTTCTTCGAAAAGCTCA 11 31 1 TTATTTCTTC 0.944835 -246 ATAGCCAAGCACATGTCTACTTTAATAATT 11 238 1 ACATGTCTAC 0.747897 -39 TAAGCTTAAATTATATCTTTAGGTAACAAA 13 89 1 TTATATCTTT 0.695784 -25 ********** Masking position 3 Map Score: 5.55158 Number of sites scoring better than the average of aligned sites = 349 Number in coding regions = 315 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 7 TCCAGAAATTGGCACGAAAATTGCAATAAA 4 114 1 GGCACGAAAA 0.832598 -48 AATACTTTTTGCTACGAATAAACCCAATTT 6 43 1 GCTACGAATA 0.92874 -253 AATCGTGCCTCCCACGATTAAGGAAAAAAC 6 210 0 CCCACGATTA 0.986295 -86 AATCGTGGGAGGCACGATTATATACCTTGT 6 221 1 GGCACGATTA 0.974103 -75 CTCCCACGATTAAAAATTTTAT 8 3 1 CCCACGATTA 0.986295 -97 TACGTAGTCACCTACGTTTACAGGTTCTGG 11 120 1 CCTACGTTTA 0.857126 -157 ********** Masking position 4 Map Score: 3.07675 Number of sites scoring better than the average of aligned sites = 62 Number in coding regions = 56 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 8 CTTTTCATTCCGCTTCCTTGACTGGGTACT 3 103 0 CGCTTCCTTG 0.89115 -198 GTTATTATTTCTTTTCATTCCGCTTCCTTG 3 113 0 CTTTTCATTC 0.817997 -188 TGACAAAGCTCTCTTTATTGTATTTACACT 6 173 1 CTCTTTATTG 0.765088 -123 TCCCTTCTTTCCTTTCCCTCC 7 2 1 CCCTTCTTTC 0.949751 -40 TCTTTCCTTTCCCTCCCTTCTGATATCCTA 7 16 1 CCCTCCCTTC 0.918773 -26 ACATACCTTCCTCTTTTTCCATTTCTTCTA 11 11 1 CTCTTTTTCC 0.862959 -266 TGAGGGCTTCCTCTTCATCCAGCTTTTGTA 11 68 1 CTCTTCATCC 0.975278 -209 TACCTCTTCCTCCAGAAAAGAGT 15 62 0 CTCTTCCTCC 0.984135 -13 ********** Masking position 4 Map Score: 2.22382 Number of sites scoring better than the average of aligned sites = 568 Number in coding regions = 521 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 9 TATTCCCTTACCGCATCCGAACTTCGTCCCG 3 23 0 CCGATCCGAA 0.963177 -278 TAAAACGGTGCAGGAACCGCATATTCCCTTA 3 44 0 CAGAACCGCA 0.988989 -257 TCCGGGCTGGCAGTATCCGCACTGGGGAACC 3 197 0 CAGATCCGCA 0.984297 -104 TGACTTTAAACATTAACCGAAAGGGATAAAA 8 27 0 CATAACCGAA 0.973633 -73 CCATTCACCGAAGGAATATAAT 11 265 0 CATCACCGAA 0.943293 -12 *** ******* Masking position 11 Map Score: 0.923351 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 10 AATAGACGGAAATCCTGTGAGGAGCTGTCAGTA 3 74 1 AACTTGAGGA 0.98336 -227 TCTGGACACTGAAATTCTAAGGAACTTGAAAAG 4 87 0 GATTTAAGGA 0.955604 -75 ATTTTGGTTTGATGCTCTACGGATTAATAATTT 6 69 1 GACTTACGGA 0.900676 -227 TATTTTTAAAAAATCTATAAGGAG 8 86 1 AACTTAAGGA 0.983684 -14 AAAGTTGTGGAAGTTTACGAGGACGGAACAGCC 11 198 0 AATTCGAGGA 0.908222 -79 TAAGCTTAAAAAGTTTATGAGGAAGCTCAAAAT 13 64 0 AATTTGAGGA 0.973861 -50 AAAAACTTTAAGGAGGTGTTGAT 14 2 1 AACTTAAGGA 0.983685 -22 GACCCTTGTAAAATTATTAAGGAATTTTTATAT 15 17 1 AATATAAGGA 0.871989 -58 ** ** ****** Masking position 2 Map Score: 5.9362 Number of sites scoring better than the average of aligned sites = 128 Number in coding regions = 111 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 11 ********** No masking Map Score: -7.64954e-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 12 AACGCTATTTTAACATTTTCAGG 1 11 0 AACGCTTTAA 0.89938 -13 ATTCCCGAAGAACACCCTGTTAAAAGGGCATGG 3 153 1 AACACCTTAA 0.972283 -148 AACAATATTTTAAGATACAGCGT 6 283 0 AACAATTTAA 0.960088 -13 AACAATTTTTTGATTTGAATTTC 12 1 1 AACAATTTGA 0.880977 -36 TCAAAATTAAAACAACGGTTTAAGTGTATATAA 13 38 0 AACAACTTAA 0.96672 -76 ATCAACACCTCCTTAAAGTTTTT 14 8 0 AACACCTTAA 0.972283 -16 ATTAAAATATAAAAATTCCTTAATAATTTTACA 15 23 0 AAAAATTTAA 0.757293 -52 ****** **** Masking position 2 Map Score: 1.69359 Number of sites scoring better than the average of aligned sites = 30 Number in coding regions = 19 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 13 ********** No masking Map Score: -7.64954e-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 14 ********** No masking Map Score: -7.64954e-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 15 ********** No masking Map Score: -7.64954e-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