AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -irhaS_bsub_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 ybfI 230 similar to transcriptional regulator (AraC/XylS family) #2 ycnG 106 similar to 4-aminobutyrate aminotransferase #3 ycnH 68 similar to succinate-semialdehyde dehydrogenase #4 ycxE 122 similar to hypothetical proteins #5 glvA 300 6-phospho-alpha-glucosidase #6 yfiA 64 similar to hypothetical proteins #7 yfiB 105 similar to ABC transporter (ATP-binding protein) #8 yfiD 154 similar to hypothetical proteins #9 yfiF 93 similar to transcriptional regulator (AraC/XylS family) #10 yulE 25 similar to L-rhamnose isomerase #11 yulB 56 similar to transcriptional regulator (DeoR family) #12 yuxG 137 alternate gene name: yulA; similar to sorbitol-6-phosphate 2-dehydrogenase #13 tlpB 113 methyl-accepting chemotaxis protein #14 mcpA 125 methyl-accepting chemotaxis protein #15 tlpA 176 methyl-accepting chemotaxis protein #16 mcpB 157 methyl-accepting chemotaxis protein Motif number 1 ATTTTTATTAAAAAAGATAAAATTATTATTGA 1 65 1 AAAAAGTAAA 0.963453 -166 CTCTATTCCTAAACAGCAACATCATACAAGAA 1 151 1 AAACAGAAAT 0.738531 -80 TGATACCATCAAAAAGTTATAATTGGTACTTT 2 28 1 AAAAAGTAAA 0.963453 -79 ATGATTACTTAAAATGATAGCAGACCCGGCCA 3 26 0 AAAATGTACA 0.792875 -43 TAAGATTACAAAAAAGGTAAAAAAACCAAATC 5 131 1 AAAAAGTAAA 0.963453 -170 AAGTACTATAAAACTGTAACAAAAAAAGACCT 8 28 0 AAACTGAAAA 0.923438 -127 ACATTTTACGAAAATGAAATAAAAGTACTATA 8 50 0 AAAATGAAAA 0.968294 -105 TCATTTTCGTAAAATGTAACAAAATTACTTGA 8 65 1 AAAATGAAAA 0.968294 -90 CAAGGCGGACAAAAATAAAAAATCCCCCTGCC 9 35 0 AAAAATAAAA 0.725193 -59 TTTTTAACAAAAAAAGAAAGCAGCAGATATGC 12 26 0 AAAAAGAACA 0.944427 -112 TTTTTTTGTTAAAAAGCAAAAATAAACAAAAA 12 43 1 AAAAAGAAAA 0.983549 -95 ATTCAAAAACAAACAGAAATCATATATAATGA 12 77 1 AAACAGAACA 0.870326 -61 AGGTTTAATAAAAAAACTAAAAAAAACACCCA 13 40 0 AAAAAATAAA 0.672335 -74 ATATACAGCAAAAAAGAAGAAATTTAACAAAA 14 50 0 AAAAAGAGAA 0.947302 -76 GGGTAGCATAAAAAAGGAGAAATGAATG 14 108 1 AAAAAGAGAA 0.947302 -18 TTTATATGGTAAACAATAATAAAGTCCTAGTT 15 45 1 AAACAAAAAA 0.64761 -132 AATGGAGGAAAAAATGAAAAATAGTTCTAAAT 15 87 0 AAAATGAAAT 0.785105 -90 AATTACATTGAAAATGGAGGAAAAAATGAAAA 15 99 0 AAAATGAGAA 0.901795 -78 AATGAAAGTTAAAAAGGCAGAAGACAGCCAAA 16 56 1 AAAAAGCAAA 0.890251 -102 TTTAAAATAAAAAATGGAAGAAGTTCTTTTTG 16 84 0 AAAATGAAAA 0.968294 -74 CGGCTGCTTAAAAAAGTTTTAAAATAAAAAAT 16 101 0 AAAAAGTTAA 0.666118 -57 ****** ** ** Masking position 3 Map Score: 30.6809 Number of sites scoring better than the average of aligned sites = 1529 Number in coding regions = 1198 Number in noncoding regions = 331 Number of orfs with sites within 600 bp upstream = 335 Fraction of orfs with sites within 600 bp upstream = 0.0538066 Motif number 2 ACAAATAACGGTCTGCTTTCTCTATTCCTAAA 1 132 1 GTCGTTTCTC 0.73064 -99 GCATGATTTTGGGGGATTTCTTGTATGATGTT 1 168 0 GGGGTTTCTT 0.988358 -63 ATCCCCCTGTCGGTATTTTCTTATCATTCTGA 2 79 0 CGGATTTCTT 0.816045 -28 TAGCAGACCCGGCCATTTTCTTTCCAATGA 3 9 0 GGCATTTCTT 0.961078 -60 CGGATTTTCCGGCAGCTCTTTTTGTGTTCCGG 4 36 1 GGCGTCTTTT 0.803394 -87 TGTTGGGGAACCTTCTTTCAAAATGTA 4 106 0 GGGACTTCTT 0.912579 -17 CCCATAGAGCGGGAAATTTCTCATTTGCCTTA 5 172 0 GGGATTTCTC 0.933691 -129 TTCGAAAATGGGGGAATTTCAT 6 1 0 GGGATTTCAT 0.678742 -64 CCTCCTTTTCGGGAGGGTTTTCGTTTGCCGTC 7 18 1 GGGGGTTTTC 0.754412 -88 ACTTTACTATGGCGGTCTTTTTGACGGCAAAC 7 40 0 GGCGCTTTTT 0.931618 -66 AATAACGGCAGGGGGATTTTTTATTTTTGTCC 9 29 1 GGGGTTTTTT 0.969899 -65 GCAGCAGATATGCCGCTTTCTCGTTTCA 12 7 0 TGCGTTTCTC 0.856327 -131 GCGGCATATCTGCTGCTTTCTTTTTTTGTTAA 12 23 1 TGCGTTTCTT 0.907925 -115 TGTTGCGCTTGGGTGTTTTTTTTAGTTTTTTT 13 31 1 GGGGTTTTTT 0.969899 -83 GCTATCAAAGCGCTGTTTTTTTATATGGTAAA 15 26 1 CGCGTTTTTT 0.8527 -151 AGTTCTTTTTGGCTGTCTTCTGCCTTTTTAAC 16 63 0 GGCGCTTCTG 0.860379 -95 *** * ****** Masking position 9 Map Score: 16.9855 Number of sites scoring better than the average of aligned sites = 1264 Number in coding regions = 1018 Number in noncoding regions = 246 Number of orfs with sites within 600 bp upstream = 201 Fraction of orfs with sites within 600 bp upstream = 0.032284 Motif number 3 CTTTGCCCCTCCTATCTGTTCCAAACCATTATAACTGA 1 8 1 CCCCATCAAA 0.90746 -223 ACAACAATTCCAGCCAAAATAACAGCAAATACATTTTGAAA 4 77 1 CACCATGAAA 0.873 -46 ATGACGACCTCCTTGATAACGTTTACAATTCCATTTAT 5 273 0 CCCCTTTTAA 0.990874 -28 ATGAAATTCCCCCATTTTCGAATCTGTAATTGTATATAA 6 9 1 CCCCTTTTGA 0.969245 -56 ATCAGATCCCCCCATTTTCTTTCTATTATATACAATTA 6 37 0 CCCCATTTAA 0.988016 -28 GTCAAAAAGACCGCCATAGTAAAGTAAAGAAAGAGACAATC 7 47 1 CCCCTTTAAA 0.984108 -59 TTTATCCTCCTTGATAAATGTTATCACTTACTTAAT 8 129 0 CCCCTTGTAA 0.987612 -26 TTATTTTTGTCCGCCTTGTTATGATGAGAGAACCAACTTGT 9 49 1 CCCCTTTAGA 0.947298 -45 TACCCATTTCCAGCCGATATGAAGGGTAGCATAAAAAAGGA 14 85 1 CACCATGTAA 0.923385 -41 TTCATTTTTTCCTCCATTTTCAATGTAATTTAAAGGAAGAT 15 101 1 CCCCTTGAAT 0.895099 -76 AAAGGAAGATCCGCCGATATAATTTGTAAATTATTGAAAGA 15 132 1 CCCCATTTAT 0.939285 -45 GTTTAGCCCCCCTTGTTTTTTATAAGATATGCAAAGA 16 7 1 CCCCTTTTAA 0.990874 -151 AAAAGAACTTCTTCCATTTTTTATTTTAAAACTTTTTTAAG 16 86 1 CTCCTTTTAA 0.895341 -72 CTTTTTTAAGCAGCCGATATATACTGTATCAAACCTGAAGG 16 117 1 CACCATTTAA 0.942572 -41 ** ** * * * ** * Masking position 10 Map Score: 20.0403 Number of sites scoring better than the average of aligned sites = 171 Number in coding regions = 106 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 4 TAGCATGATTTTGGGGGATTTCTTGTATGA 1 172 0 TTGGGGGATT 0.826975 -59 ACCACACCGACAGGAGGCATCCC 1 218 1 CAGGAGGCAT 0.892612 -13 AAAATACCGACAGGGGGATATTCAC 2 92 1 CAGGGGGATA 0.836049 -15 AGATTCGAAAATGGGGGAATTTCAT 6 6 0 ATGGGGGAAT 0.930764 -59 TAGAAAGAAAATGGGGGGATCTGAT 6 50 1 ATGGGGGGAT 0.908016 -15 CCCTCCCGAAAAGGAGGGCAGTCT 7 5 0 AAGGAGGGCA 0.746696 -101 CCCTCCTTTTCGGGAGGGTTTTCGTTTGCC 7 17 1 CGGGAGGGTT 0.69483 -89 AAAAAGGGGTTTGGAGGCTTTTAC 7 92 1 TTGGAGGCTT 0.731737 -14 AACATTTATCAAGGAGGATAAA 8 143 1 AAGGAGGATA 0.876381 -12 GAAATAACGGCAGGGGGATTTTTTATTTTT 9 27 1 CAGGGGGATT 0.935752 -67 ACCAACTTGTTAGGAGGCGTTTAC 9 80 1 TAGGAGGCGT 0.695026 -14 ATAAAAGGGTATGGAGGAATATCAAAT 12 121 1 ATGGAGGAAT 0.932082 -17 ATTTATCTTAAAGGAGGAGTCAACGAGA 13 96 1 AAGGAGGAGT 0.919781 -18 TAGCATAAAAAAGGAGAAATGAATG 14 111 1 AAGGAGAAAT 0.516971 -15 TACATTGAAAATGGAGGAAAAAATGAAAAA 15 98 0 ATGGAGGAAA 0.827732 -79 TATAAAAAACAAGGGGGGCTAAAC 16 5 0 AAGGGGGGCT 0.891863 -153 ********** Masking position 6 Map Score: 14.3619 Number of sites scoring better than the average of aligned sites = 752 Number in coding regions = 405 Number in noncoding regions = 347 Number of orfs with sites within 600 bp upstream = 392 Fraction of orfs with sites within 600 bp upstream = 0.0629618 Motif number 5 AAGACCACCACACCGACAGGAGGCATCCC 1 212 1 CACCGACAGG 0.757755 -19 GATAAGAAAATACCGACAGGGGGATATTCA 2 86 1 TACCGACAGG 0.937497 -21 CTGCCGGAAAATCCGGCAGCTCTCAGGAGC 4 21 0 ATCCGGCAGC 0.870436 -102 CTGCCGGATTTTCCGGCAGCTCTTTTTGTG 4 32 1 TTCCGGCAGC 0.979485 -91 TTTGCTGTTATTTTGGCTGGAATTGTTGTG 4 76 0 TTTTGGCTGG 0.778427 -47 CTGCCCTCCTTTTCGGGAGGGTTTTCGTTT 7 14 1 TTTCGGGAGG 0.898284 -92 CCTGCCGTTATTTCGGCAAGGGGATTGCAG 9 11 0 TTTCGGCAAG 0.856292 -83 CTTGCCGAAATAACGGCAGGGGGATTTTTT 9 21 1 TAACGGCAGG 0.949126 -73 GAAAGCGGCATATCTGCTGCTTTCTTTTTT 12 19 1 TATCTGCTGC 0.708699 -119 CTACCCTTCATATCGGCTGGAAATGGGTAA 14 84 0 TATCGGCTGG 0.981476 -42 ATACAGTATATATCGGCTGCTTAAAAAAGT 16 116 0 TATCGGCTGC 0.968629 -42 ********** Masking position 4 Map Score: 8.1586 Number of sites scoring better than the average of aligned sites = 1359 Number in coding regions = 1265 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 6 TTTTATCTTTTTTAATAAAAATTTATTTTTC 1 56 0 TTTATAAAAA 0.86412 -175 TTCTCTTTGGTATGATGAAAAGTACCAATTA 2 47 0 TATATGAAAA 0.956633 -60 CATTTTAAGTAATCATGAAAAGAAAGGAATG 3 42 1 AATATGAAAA 0.818361 -27 CCCTTCCAATTCTTATGAAAAGGTTCTTTTG 5 64 0 TCTATGAAAA 0.904622 -237 TGTAATTGTATATAATAGAAAGAAAATGGGG 6 35 1 TATATAGAAA 0.715769 -30 TTTTGTTACATTTTACGAAAATGAAATAAAA 8 58 0 TTTACGAAAA 0.580766 -97 ATATATGCTATGATAAAAATATAAGACGG 11 9 1 TATATAAAAA 0.941059 -48 AGAAATCATATATAATGAAAACGGATACAAA 12 91 1 TATATGAAAA 0.956633 -47 GGATAAAAGGTTTAATAAAAAAACTAAAAAA 13 48 0 TTTATAAAAA 0.86412 -66 ATATGAAGGGTAGCATAAAAAAGGAGAAATG 14 101 1 TAGATAAAAA 0.750422 -25 AAATGGAGGAAAAAATGAAAAATAGTTCTAA 15 89 0 AAAATGAAAA 0.502353 -88 TCTTTGCATATCTTATAAAAAACAAGGGGGG 16 17 0 TCTATAAAAA 0.872855 -141 AAAAAAGTTTTAAAATAAAAAATGGAAGAAG 16 93 0 TAAATAAAAA 0.781531 -65 *** ******* Masking position 5 Map Score: 10.7244 Number of sites scoring better than the average of aligned sites = 659 Number in coding regions = 442 Number in noncoding regions = 217 Number of orfs with sites within 600 bp upstream = 229 Fraction of orfs with sites within 600 bp upstream = 0.0367812 Motif number 7 CTTTGCCCCTCCTATCTGTTCC 1 2 1 TTTGCCCTCC 0.849157 -229 GTGAATATCCCCCTGTCGGTATTTTC 2 91 0 TATCCCCTGT 0.720673 -16 TAAGTGAATATACGCCCTTCCAATTCTTATG 5 78 0 TACGCCCTCC 0.95822 -223 CTGCAATCCCCTTGCCGAAATAACG 9 5 1 AATCCCCTGC 0.980457 -89 AAAAATAAAAAATCCCCCTGCCGTTATTTCG 9 26 0 AATCCCCTGC 0.980457 -68 CGGTAACGCCCTTCCTCATATCGTA 11 42 0 AACGCCCTCC 0.97764 -15 TAAGCCTTAACACCCAAGCTTGTTGCGCT 13 9 1 AACACCCAGC 0.937648 -105 AACTAAAAAAAACACCCAAGCGCAACAAGCT 13 27 0 AACACCCAGC 0.937648 -87 TTTAACTTTCATTGCCCAAGCTCTTTGCATA 16 38 0 ATTGCCCAGC 0.916132 -120 ******* *** Masking position 6 Map Score: 6.71687 Number of sites scoring better than the average of aligned sites = 262 Number in coding regions = 226 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 8 TTTTAATAAAAATTTATTTTTCAAATATTT 1 48 0 AATTTATTTT 0.557017 -183 AAGTTATAATTGGTACTTTTCATCATACCA 2 41 1 TGGTACTTTT 0.925476 -66 TCTTATGAAAAGGTTCTTTTGTACGATTCG 5 55 0 AGGTTCTTTT 0.947865 -246 CTGAGAGATTTGGTTTTTTTACCTTTTTTG 5 139 0 TGGTTTTTTT 0.832207 -162 TACAGTTTTATAGTACTTTTATTTCATTTT 8 42 1 TAGTACTTTT 0.8862 -113 TGTTTACGTCAAGTAATTTTGTTACATTTT 8 75 0 AAGTAATTTT 0.752717 -80 GAATCGTTTTTGTTTATTTTTGCTTTTTAA 12 51 0 TGTTTATTTT 0.667247 -87 GTGTTTTTTTTAGTTTTTTTATTAAACCTT 13 43 1 TAGTTTTTTT 0.756698 -71 ATGGGAAATTAGTTACTTTTGTTAAATTTC 14 34 1 AGTTACTTTT 0.777974 -92 AAAATGGAAGAAGTTCTTTTTGGCTGTCTT 16 76 0 AAGTTCTTTT 0.919361 -82 ********** Masking position 4 Map Score: 4.36326 Number of sites scoring better than the average of aligned sites = 439 Number in coding regions = 305 Number in noncoding regions = 134 Number of orfs with sites within 600 bp upstream = 131 Fraction of orfs with sites within 600 bp upstream = 0.0210408 Motif number 9 TCCTGTCGGTGTGGTGGTCTTGGATTAAGT 1 203 0 GTGGTGGTCT 0.92149 -28 CGTAACACGTTTGGCGCACTTAGGTCATTT 5 224 0 TTGGCGCACT 0.935929 -77 TTACTTTACTATGGCGGTCTTTTTGACGGC 7 44 0 ATGGCGGTCT 0.97637 -62 TCCTAACAAGTTGGTTCTCTCATCATAACA 9 65 0 TTGGTTCTCT 0.927142 -29 ACGGCTCTCTCCCTTTATCA 10 16 0 ACGGCTCTCT 0.905744 -10 GAAGTTCTTTTTGGCTGTCTTCTGCCTTTT 16 67 0 TTGGCTGTCT 0.974133 -91 ********** Masking position 10 Map Score: 0.227374 Number of sites scoring better than the average of aligned sites = 119 Number in coding regions = 101 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 10 ********** No masking Map Score: 5.81467e-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 CTATCTGTTCCAAACCATTATAACTGAAATATT 1 22 1 CAACCTTTAA 0.808663 -209 ATAGAGAAAGCAGACCGTTATTTGTCTGCTTTC 1 124 0 CAACCTTTTT 0.979078 -107 ATTGAACATTCCTTTCTTTTCATGATTAC 3 50 0 CATCCTTTTT 0.906675 -19 TAAAAGCCTCCAAACCCCTTTTTACTCGATTGT 7 82 0 CAACCCTTTT 0.982611 -24 TTGTCCTGCACAGAGGTCTTTTTTTGTTACAGT 8 15 1 CAAGGCTTTT 0.820923 -140 GATATTCCTCCATACCCTTTTATTTGTATCCGT 12 111 0 CAACCTTTAT 0.953178 -27 ACAGCGCTATCAAAGCGCTGTTTTTTTATATGG 15 21 1 CAAGCCTTTT 0.959751 -156 ** *** ** *** Masking position 2 Map Score: 0.107197 Number of sites scoring better than the average of aligned sites = 155 Number in coding regions = 123 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 12 ********** No masking Map Score: 5.81467e-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 13 ********** No masking Map Score: 5.81467e-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 14 ********** No masking Map Score: 5.81467e-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