AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -ityrR_ctra_opreg_300.orf -g0.413 -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 = 0.413 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 aroA 169 Phosphoshikimate 1-carboxyl vinyltransferase #2 greA 113 Transcription Elongation Factor G #3 tyrB 187 Aromatic AA Aminotransferase #4 mrsA 245 Phosphoglucomutase #5 tyrP_1 51 Tyrosine Transport #6 tyrP_2 181 Tyrosine Transport Motif number 1 TGTTGAAAGATTTTATGTTTTTTT 1 1 0 TTTTTTTTTT 0.97509 -169 AAAAGGATTTTATTTTGTTGTTATAATTAATCTT 1 34 0 TATTTTGTAT 0.896031 -136 AAATAAGTTCTATTTTTTTGTTATGAAAAGGATT 1 59 0 TATTTTGTAT 0.896031 -111 CGGAAGAGTTTTTTGCATGATATTTAAGATCATA 1 99 0 TTTTCTATTT 0.898311 -71 AATCTCGATCTTTTATTTAATAATAAAATTTTTC 2 17 1 TTTTTTATAT 0.880596 -97 AATAATAAAATTTTTCTTGTTTTTTGTGATGTAA 2 35 1 TTTTCTTTTT 0.97268 -79 GTAATATTGCTCTTTTTTGTTATTCGGCGTATAT 2 65 1 TCTTTTTTTT 0.943919 -49 CACTGCTGCTTACTGTCTTTTTTTCCAGTAAGAT 3 144 0 TACTTTTTTT 0.747574 -44 AAATGATTTATTTTTTTTGTTTTT 4 1 0 TTTTTTTTTT 0.97509 -245 ATAATTATTTTCTTACTTCTTATTTAAAAAGTGA 4 43 1 TCTTCTTTTT 0.938684 -203 CCGTTTGAATTTTTGTTTGGTTATAAATAGTAAG 4 81 1 TTTTTTGTAT 0.943235 -165 CAGAGATAAATATTCCCTATTTTTATCAAAATCT 4 169 0 TATTCTTTTT 0.948628 -77 ATCTACAGTTTTTTCTCTCTTGATGAATAGCATA 5 12 1 TTTTTTTTAT 0.967451 -40 CTCCCCCTGTTTTTTCATGTTGATAGGGGAATCT 6 154 0 TTTTCTTTAT 0.96433 -28 **** * * ** ** Masking position 8 Map Score: 18.197 Number of sites scoring better than the average of aligned sites = 257 Number in coding regions = 257 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 2 CTTTTCATAACAAAAAAATAGAACTTATTTC 1 63 1 CAAAAAATAG 0.87595 -107 AAATATCATGCAAAAAACTCTTCCGAAGACT 1 108 1 CAAAAACTCT 0.972051 -62 AACAAAAATCTCGATCTTTTATT 2 3 1 CAAAAACTCG 0.989531 -111 TATTACATCACAAAAAACAAGAAAAATTTTA 2 40 0 CAAAAACAAG 0.94807 -74 TACCCCGAGGGAAGAAACTAGGTTATCATGT 3 86 1 GAAGAACTAG 0.861891 -102 CGATTTAGGACAACAAGCTGTCATCTTACTG 3 122 1 CAACAACTGT 0.937323 -66 TTTCCTCAAACATCAATCTGGGTATCAATAG 4 115 0 CATCAACTGG 0.837971 -131 CATCAAGAGAGAAAAAACTGTAGATT 5 6 0 GAAAAACTGT 0.952981 -46 GATCTGTTTACAAAAAGCTCGCATAAAGGAA 6 46 0 CAAAAACTCG 0.989546 -136 ACTATATGGAGAAAAACAACTAGCAAACAGT 6 94 0 GAAAAAAACT 0.554315 -88 CTATCAACATGAAAAAACAGGGGGAGGAGG 6 162 1 GAAAAACAGG 0.956472 -20 ****** **** Masking position 6 Map Score: 10.09 Number of sites scoring better than the average of aligned sites = 271 Number in coding regions = 270 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 3 AAAAAAACATAAAATCTTTCAACAAGATT 1 8 1 CAAAAATCTT 0.967907 -162 ATAACAACAAAATAAAATCCTTTTCATAACAA 1 44 1 AAAAAATCTT 0.981384 -126 AAATATCATGCAAAAAACTCTTCCGAAGACTA 1 108 1 CAAAAACTTT 0.77171 -62 TTTATTTAATAATAAAATTTTTCTTGTTTTTT 2 28 1 AAAAAATTTT 0.87387 -86 AATAAAACCTCTCTATAGCGCA 3 176 0 AAAAAACCCT 0.876034 -12 AAAACAAAAAAAATAAATCATTTAGTTTTCGA 4 12 1 AATAAATCTT 0.905596 -234 AATAAGAAGTAAGAAAATAATTATCGAAAACT 4 35 0 AAAAAATATT 0.879051 -211 CCCTATTTTTATCAAAATCTTTGCAATTCGCC 4 157 0 ATAAAATCTT 0.906923 -89 CTCTATCCCTAAGAATATCCTTTGGCTCAAAA 4 222 0 AAAATATCTT 0.842768 -24 ** ****** ** Masking position 7 Map Score: 6.14184 Number of sites scoring better than the average of aligned sites = 239 Number in coding regions = 239 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 4 GGTTCGATCCCGCTATGCTCCAATTTCTGT 3 11 0 CGCTATGCTC 0.867179 -177 ATAGCGGGATCGAACCGCTGACCTCAACAA 3 25 1 CGAACCGCTG 0.978734 -163 AACCGCTGACCTCAACAATGCCATTGTTGC 3 37 1 CTCAACAATG 0.807618 -151 GTTGGTAGAGCGCAACAATGGCATTGTTGA 3 48 0 CGCAACAATG 0.948331 -140 CTCTCTATAGCGCACTGCTGCTTACTGTCT 3 160 0 CGCACTGCTG 0.978734 -28 TGGCTCAAAACTAACTGATCCTTGATTTTC 4 202 0 CTAACTGATC 0.806264 -44 GTAAACAGATCGAAATGATGAAAGCGCGAC 6 66 1 CGAAATGATG 0.949143 -116 TTACGAAATACGATCCAATCTATACTATAT 6 118 0 CGATCCAATC 0.805063 -64 ********** Masking position 9 Map Score: 2.33714 Number of sites scoring better than the average of aligned sites = 144 Number in coding regions = 143 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 5 CTACATTAGCTATTCATTTTTAACCTTTTTA 1 137 1 TATTCATTTT 0.944011 -33 AAAAATAAATCATTTAGTTTTCGATAATTAT 4 20 1 CATTTATTTT 0.975031 -226 TTCAAACGGCCATTCACTTTTTAAATAAGAA 4 59 0 CATTCATTTT 0.988763 -187 AATCAAGGATCAGTTAGTTTTGAGCCAAAGG 4 205 1 CAGTTATTTT 0.946213 -41 CTCAAGCTCGCATTCAGATTTCCTTTATGCG 6 27 1 CATTCAATTT 0.963939 -155 ****** **** Masking position 6 Map Score: 1.83686 Number of sites scoring better than the average of aligned sites = 16 Number in coding regions = 16 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 6 TCTATTTTTTTGTTATGAAAAGGATTTTATTT 1 53 0 TGTTTGAAAG 0.921773 -117 ATGTCTATTTTCTAAAAAGGTTAAAAATG 1 151 0 TTTTTAAAAG 0.961786 -19 GACAGCTTGTTGTCCTAAATCGTGTAAACATG 3 112 0 TGTCTAAACG 0.906691 -76 TTCTTACTTCTTATTTAAAAAGTGAATGGCCG 4 52 1 TTATTAAAAG 0.871134 -194 ATTTTTGTTTGGTTATAAATAGTAAGCTATTG 4 89 1 GGTTTAAAAG 0.960966 -157 TTTGAGGAAAGGTCTTAAGAAGGCGAATTGCA 4 136 1 GGTCTAAGAG 0.842809 -110 GCAAAGATTTTGATAAAAATAGGGAATATTTA 4 165 1 TGATAAAAAG 0.715304 -81 TATGCGAGCTTTTTGTAAACAGATCGAAATGA 6 52 1 TTTTTAAAAG 0.962476 -130 TTGGATCGTATTTCGTAATGAGAAAGATTCCC 6 130 1 TTTCTAATAG 0.791434 -52 **** **** ** Masking position 8 Map Score: 2.10261 Number of sites scoring better than the average of aligned sites = 132 Number in coding regions = 132 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 7 GTGATGTAATATTGCTCTTTTTTGTTATTC 2 60 1 ATTGCTCTTT 0.876469 -54 GATGGCTCCCCTTTTTAGTCCGGA 2 100 0 GCTCCCCTTT 0.866902 -14 CAGCGGTTCGATCCCGCTATGCTCCAATTT 3 15 0 ATCCCGCTAT 0.947684 -173 CAATGCCATTGTTGCGCTCTACCAACTGAG 3 52 1 GTTGCGCTCT 0.961946 -136 AGTAAGCAGCAGTGCGCTATAGAGAGGTTT 3 164 1 AGTGCGCTAT 0.886191 -24 CTAGCAAACAGTCGCGCTTTCATCATTTCG 6 76 0 GTCGCGCTTT 0.967649 -106 AATGAGAAAGATTCCCCTATCAACATGAAA 6 146 1 ATTCCCCTAT 0.936451 -36 ********** Masking position 8 Map Score: 0.940493 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 72 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 8 GAAGACTACATTAGCTATTCATTTTTAACC 1 132 1 TTAGCTATTC 0.979585 -38 ATTGCTCTTTTTTGTTATTCGGCGTATATT 2 70 1 TTTGTTATTC 0.929455 -44 TTATAAATAGTAAGCTATTGATACCCAGAT 4 101 1 TAAGCTATTG 0.904859 -145 TATCAAAATCTTTGCAATTCGCCTTCTTAA 4 150 0 TTTGCAATTC 0.954334 -96 TACAGACGCTTATGCTATTCATCAAGAGAG 5 26 0 TATGCTATTC 0.979585 -26 ********** Masking position 7 Map Score: 2.6372 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 44 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 9 ********** No masking Map Score: 3.03645e-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: 3.03645e-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: 3.03645e-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