AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_aquae.txt -z/home/amcguire/genomes/aquae.fna -inarP_aquae_opreg_300.orf -g0.435 -x5 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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 dmsB2 232 dimethylsulfoxide reductase chain B #2 rpmJ 60 ribosomal protein L36 #3 secY 44 preprotein translocase SecY #4 nirB 120 nitrite reductase (NAD(P)H) large subunit #5 fhp 133 flavohemoprotein #6 aq_811 66 putative protein #7 lysR2 50 transcriptional regulator (LysR family) #8 fdoG 212 formate dehydrogenase alpha subunit #9 aq_1188 48 putative protein #10 fdx3 74 ferredoxin #11 dmsA 23 DMSO reductase chain A #12 aq_1809 21 putative protein #13 trxA2 168 thioredoxin #14 aq_1912 300 putative protein #15 rplI 70 ribosomal protein L09 Motif number 1 AAAGTCTTCATTCAGCTCCTCATCCTTCTTAC 1 28 1 TTACTCCTCA 0.920869 -205 TACCAGTAAATTTTACTTCTCCTTACCTCGGG 1 88 0 TTTCTTCTCC 0.915393 -145 CGGCATTGACTTTTCCCCCTTAATACTTATCC 1 180 1 TTTCCCCTTA 0.950267 -53 CTTTCACTCCTCCTGAGGAAACT 4 108 0 TTCCTCCTCC 0.95577 -13 GCGTGCCAAATTCTCCCCGTTCTGTTTTAACA 5 77 0 TTTCCCGTTC 0.911653 -57 CTTTTCACCTCCTTCACTCAAACTA 5 119 0 TTACTCCTTC 0.980776 -15 TTTAGCCCCTCCTGTTTAAAAT 6 55 0 TTACCCCTCC 0.989539 -12 AGTTTTTAGTTTATTCCCCTTTCAAATCATGA 8 174 0 TTTCCCCTTT 0.964762 -39 TCTTAAGTCCTTGTCCCCCTTTTAAAAATAAA 13 24 0 TTTCCCCTTT 0.964762 -145 TCTTCATCCTCTCCTTTTTCCTCG 14 3 1 TTACCTCTCC 0.935784 -298 AAGGTTTAAATTATACTACTTCCTTTAGACAT 15 32 0 TTTCTACTTC 0.841185 -39 CCTTTACCTCCTTTGCGAAGGTTT 15 57 0 TTACTCCTTT 0.935043 -14 ** * ******* Masking position 10 Map Score: 14.52 Number of sites scoring better than the average of aligned sites = 483 Number in coding regions = 429 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 2 TATGTACCAGTAAATTTTACTTCTCCTTACC 1 93 0 TAATTTTACT 0.802039 -140 GTTAAAAGATTTTAATATAATAAAGT 3 29 0 AAATTTTAAT 0.862681 -16 ACGTATAACTTTCATTTTACAACCTCTGTAA 4 27 1 TTATTTTACA 0.682138 -94 CGTTTTTTGCAAGAGTTTCCTCAGGAGGAGT 4 95 1 AAAGTTTCCT 0.594678 -26 ACAATCAGAGAAAAGTTTCCAAGAACTGTTA 5 51 1 AAAGTTTCCA 0.757576 -83 TAAGTTAGTGAATATTTTAAATAGAGAACTA 6 23 1 AAATTTTAAA 0.930463 -44 AATAGAGAACTACATTTTAAACAGGAGGGGC 6 42 1 TAATTTTAAA 0.913094 -25 TTTTTCGAACATTTTCATTGAATAATTA 8 8 1 AAATTTTCAT 0.860222 -205 TTTTCAAAACAATATTTTAAAAATAGGCATA 8 120 0 AAATTTTAAA 0.930463 -93 AAAAAAAGACAAAATTTTCAAAACAATATTT 8 134 0 AAATTTTCAA 0.929119 -79 CAAATCATGAAAAAATTTAAAAAAAAGACAA 8 153 0 AAAATTTAAA 0.715181 -60 AAATTCCTTAATAATTTTACAAGGGTCTATT 10 13 0 ATATTTTACA 0.732131 -62 AAGGAATTTTTATATTTTAATTCACAAACTC 10 35 1 TAATTTTAAT 0.831442 -40 ATAAAATGTCTTAATTTTCAAAAATGATAAA 13 89 0 TTATTTTCAA 0.719059 -80 CAGGCGTGATTAGATTTTCGAGAGATATAAA 14 124 0 TAATTTTCGA 0.659658 -177 AAGGAAGTAGTATAATTTAAACCTTCGCAAA 15 39 1 TAAATTTAAA 0.663296 -32 ** ******** Masking position 6 Map Score: 12.2458 Number of sites scoring better than the average of aligned sites = 186 Number in coding regions = 135 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 3 AAAGTAAGAAGGATGAGGAGCTGAATGAAG 1 33 0 GGATGAGGAG 0.728699 -200 CTTGGTTTCCCGAGGTAAGGAGAAGTAAAA 1 80 1 CGAGGTAAGG 0.868016 -153 TAAGTATTAAGGGGGAAAAGTCAATGCCGT 1 179 0 GGGGGAAAAG 0.93897 -54 AGTATCCTCAGGAGGATAGAGAGTATAAGG 1 210 0 GGAGGATAGA 0.9047 -23 CCGCTATTGTGGAGGTTCGGT 2 50 1 GGAGGTTCGG 0.729935 -11 AAGTTCTCTCGGAGGTAGAAGA 3 3 0 GGAGGTAGAA 0.953772 -42 AGTTTCCTCAGGAGGAGTGAAAG 4 108 1 GGAGGAGTGA 0.8158 -13 TTTGAGTGAAGGAGGTGAAAAG 5 122 1 GGAGGTGAAA 0.959108 -12 ACTCTTTTCTGGAGGAAGAGGTA 10 62 1 GGAGGAAGAG 0.977581 -13 TAAAAACTCTGGAGGTGGGAT 12 11 1 GGAGGTGGGA 0.946091 -11 ATTTTTAAAAGGGGGACAAGGACTTAAGAC 13 27 1 GGGGGACAAG 0.803398 -142 ACGCCGAGTCCGAGGAAAAAGGAGAGGATG 14 15 0 CGAGGAAAAA 0.855779 -286 TAAAGCTACTGGAAGAAAAAAAGGCGAGGG 14 185 1 GGAAGAAAAA 0.685085 -116 CCTTCGCAAAGGAGGTAAAGG 15 60 1 GGAGGTAAAG 0.975756 -11 ********** Masking position 5 Map Score: 12.4937 Number of sites scoring better than the average of aligned sites = 1239 Number in coding regions = 1068 Number in noncoding regions = 171 Number of orfs with sites within 600 bp upstream = 187 Fraction of orfs with sites within 600 bp upstream = 0.0300353 Motif number 4 AGTGAATATTTTAAATAGAGAACTACATTTTA 6 29 1 TTAAATAAAA 0.957055 -38 CATTGAATAATTAAATAAATAAGTTATGTGAT 8 26 1 TTAAATAAAA 0.956493 -187 AAACAATATTTTAAAAATAGGCATATGAACAT 8 113 0 TTAAAAAAGC 0.734008 -100 ATGAAAAAATTTAAAAAAAAGACAAAATTTTC 8 146 0 TTAAAAAAGA 0.921941 -67 ACTTTTTAAATATACAATTCACGTCAA 9 6 1 TTAAATAAAA 0.956493 -43 GTTTGTGAATTAAAATATAAAAATTCCTTAAT 10 32 0 TAAAATAAAA 0.778481 -43 TGTCCCCCTTTTAAAAATAAAGGATAATTCTC 13 13 0 TTAAAAAAAG 0.865187 -156 AAATGGTAAATTAAACATATAAAAATTAGTTT 13 59 0 TTAAACAAAA 0.908899 -110 GATATAAAACTCAAAAAGAAAAACGTTCCGAG 14 100 0 TCAAAAAAAA 0.865188 -201 TTTATTCCAGTTAAAAAGAGAAGAGCGTTTGC 14 157 0 TTAAAAAAAA 0.964872 -144 ******* * ** Masking position 7 Map Score: 7.64458 Number of sites scoring better than the average of aligned sites = 56 Number in coding regions = 45 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 5 TGAAAAAGGCAAGGACTTAGGTTATACTAAGA 2 14 1 AAGGACTAGT 0.897469 -47 CAACCTCTGTAAGGACTTACAAAACATAACTA 4 46 1 AAGGACTAAA 0.965825 -75 AAAAGTTTCCAAGAACTGTTAAAACAGAACGG 5 61 1 AAGAACTTAA 0.917401 -73 GGAATAAACTAAAAACTAAGAATGCTTAAAGG 8 189 1 AAAAACTAAA 0.817673 -24 TAAAAACTCTGGAGGTGGGAT 12 2 1 AAAAACTTGA 0.877326 -20 AAAGGGGGACAAGGACTTAAGACTTAAACTAA 13 34 1 AAGGACTAGA 0.982309 -135 GACTATTAAGAAATACTTATGAATGCATAAAA 13 114 0 AAATACTAGA 0.860122 -55 CAAAGGGTTAAAGGACTATTAAGAAATACTTA 13 127 0 AAGGACTTAA 0.958227 -42 GAATATTAAGAAGTACTGTGGATCGGGATTTA 14 269 0 AAGTACTTGA 0.938381 -32 ******* * ** Masking position 7 Map Score: 6.31585 Number of sites scoring better than the average of aligned sites = 150 Number in coding regions = 139 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 6 CCGGAACTTTTTGGCACGTTTTTTGCAAGAGTT 4 79 1 TGGACGTTTT 0.989863 -42 TACAATTTTGTAGCTACATTTTTGTT 5 4 0 TGCACATTTT 0.910627 -130 GGAGACGCTTTGCGTACAATTTTGTAGCTACAT 5 18 0 TCGACATTTT 0.969859 -116 CGGGGAGAATTTGGCACGCTTTTTGCAATTAGT 5 90 1 TGGACGTTTT 0.989863 -44 TTTTTCGAACATTTTCATTGAATAAT 8 4 1 TCGACATTTC 0.895248 -209 AAAATAGGCATATGAACATTTTTTTATTGTGTA 8 99 0 TTGACATTTT 0.954133 -114 TCGGCGTCGATCTGAAAGGTTTTCCGAAATTAT 14 38 1 TTGAAGTTTT 0.786532 -263 CTAGGCATTCTCGGAACGTTTTTCTTTTTGAGT 14 91 1 TGGACGTTTT 0.989863 -210 * ** *** **** Masking position 6 Map Score: 6.89743 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 19 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 7 CTTAGGTTATACTAAGATATTCCGCTATTG 2 29 1 ACTAAGATAT 0.913021 -32 TAAAATATTCACTAACTTATAATTATTACC 6 12 0 ACTAACTTAT 0.914994 -55 TCTTTTGTGAACTACCATATGGAAAAGAG 7 32 1 ACTACCATAT 0.983453 -19 AATTTTTTATACTACGTTATCTTGACGTGA 9 29 0 ACTACGTTAT 0.943275 -20 AAAGACGGGCTACCATATTCCTT 11 6 0 GCTACCATAT 0.95601 -18 GCGAGGGATTACTACCAGATTACACTTCTA 14 208 1 ACTACCAGAT 0.95601 -93 ********** Masking position 4 Map Score: 3.55364 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 = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 8 GAGTGCGTGAATGAAAGTAAGAAGGATGAGGAGCTG 1 40 0 AAAGGAAGGA 0.967519 -193 AAGGATAAGTATTAAGGGGGAAAAGTCAATGCCGTT 1 178 0 AAAGAAAAGT 0.871885 -55 AAAAATTTAAAAAAAAGACAAAATTTTCAAAACAAT 8 138 0 AAAGAAATTT 0.627666 -75 ACTAAAAACTAAGAATGCTTAAAGGAG 8 196 1 AAAGAAAGGA 0.979406 -17 CTTAATTTTCAAAAATGATAAAATGGTAAATTAAAC 13 75 0 AAAGAAATGG 0.938777 -94 AGAAATACTTATGAATGCATAAAATGTCTTAATTTT 13 102 0 AAAGAAAATG 0.791591 -67 AAGATACAGGACAAAGGGTTAAAGGACTATTAAGAA 13 134 0 AAAGAAAGGA 0.979406 -35 GAGTCCGAGGAAAAAGGAGAGGATGAAGA 14 4 0 AAAGGGATGA 0.686782 -297 TTCGAGAGATATAAAACTCAAAAAGAAAAACGTTCC 14 103 0 AAACAAAAGA 0.684638 -198 CGCCGAGCTCAGGAAAGCTAGAAGTGTAATCTGGTA 14 220 0 AAAGGAAGTG 0.858876 -81 CTTATTATAAACTAATGTCTAAAGGAAGTAGTATAA 15 18 1 AAAGAAAGGA 0.979406 -53 * ** * ****** Masking position 5 Map Score: 4.49922 Number of sites scoring better than the average of aligned sites = 523 Number in coding regions = 478 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 9 CTCGGGTCTTGGTTTCCCGAGGTAAGGAGA 1 73 1 GGTTTCCCGA 0.980575 -160 GCCGTTAATCGGTTTTACGACTTTCCTTAT 1 154 0 GGTTTTACGA 0.942826 -79 GTTATACTAAGATATTCCGCTATTGTGGAG 2 34 1 GATATTCCGC 0.926101 -27 CGATCTGAAAGGTTTTCCGAAATTATCAAG 14 45 1 GGTTTTCCGA 0.988513 -256 TGTGGATCGGGATTTACCGCAGTGGACACC 14 255 0 GATTTACCGC 0.942255 -46 ********** Masking position 5 Map Score: 1.12583 Number of sites scoring better than the average of aligned sites = 94 Number in coding regions = 89 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 10 AAAACTCGTTAAAGTCTTCATTCAGCTCCTC 1 18 1 AAGTCTTCAT 0.930746 -215 AAAATATAAAAATTCCTTAATAATTTTACAA 10 22 0 AATCCTTAAT 0.845581 -53 AAAATTAGTTTAAGTCTTAAGTCCTTGTCCC 13 39 0 TAGTCTTAAG 0.896754 -130 GAATGCATAAAATGTCTTAATTTTCAAAAAT 13 95 0 AAGTCTTAAT 0.973514 -74 CATTCATAAGTATTTCTTAATAGTCCTTTAA 13 121 1 TATTCTTAAT 0.931821 -48 GCATTTAACAAAAGTCTTGATAATTTCGGAA 14 59 0 AAGTCTTGAT 0.930746 -242 CGATCCACAGTACTTCTTAATATTCTCACTG 14 276 1 TATTCTTAAT 0.931821 -25 ** ******** Masking position 2 Map Score: 1.64096 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 38 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 11 TCAGGAGGATAGAGAGTATAAGGATAAGTA 1 203 0 AGAGAGTATA 0.840262 -30 GTTAAAAGATTTTAATATAATAAA 3 31 0 AAAGATTTTA 0.647077 -14 AACAGAACGGGGAGAATTTGGCACGCTTTT 5 83 1 GGAGAATTTG 0.790858 -51 AGAGATGATAAGAGAATATAAGCT 7 5 0 AGAGAATATA 0.864449 -46 ATTTGAATATAAGGAATTTATTAACATGCA 8 58 1 AAGGAATTTA 0.862792 -155 TAAAATTATTAAGGAATTTTTATATTTTAA 10 25 1 AAGGAATTTT 0.608046 -50 TTCCTCCAGAAAAGAGTTTGTGAATTAAAA 10 49 0 AAAGAGTTTG 0.903645 -26 AAGGAATATGGTAGCCCGTC 11 1 1 AAGGAATATG 0.785673 -23 GAGAATGCCTAGAGCATTTAACAAAAGTCT 14 73 0 AGAGCATTTA 0.858274 -228 TAAAAAGAGAAGAGCGTTTGCCACAGGCGT 14 148 0 AGAGCGTTTG 0.865427 -153 ********** Masking position 7 Map Score: 0.542098 Number of sites scoring better than the average of aligned sites = 456 Number in coding regions = 426 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 12 ********** No masking Map Score: -5.2337e-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 13 ********** No masking Map Score: -5.2337e-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: -5.2337e-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