AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -inarP_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 CT134 300 hypothetical protein #2 CT135 58 hypothetical protein #3 CT483 300 hypothetical protein Motif number 1 TCGACTTAGGAGATTTTCTCTAAGTAGAGTACAATGC 1 24 1 AATTTTTAGG 0.884193 -277 CCAATAAGATAGATCTTGCTTATGCAGCCCAGTCCCG 1 141 0 AATCTTTAGG 0.980221 -160 GGCAGCCAGCATATCCTCTTTAATTGGAATGAAAACC 1 176 0 AATCCTTATG 0.960604 -125 AGGAGAGACCGAAGCTTCGATAGAAAGTAAGGAAATC 1 252 1 GAGCTTTAAG 0.965164 -49 TCGTTCCCCCAAATCTTTTTTAGACTGTTTTA 2 6 0 AATCTTTAAG 0.991396 -53 TAAACAGAGAAGATCCTTCTTAAAAAGGCCTACATCC 3 24 0 AATCCTTAAG 0.993576 -277 AGCTTTAGGAATCGTCTTTGTAAACAGAGAAGATCCT 3 44 0 ACGTCTTAAG 0.797261 -257 ATCTAGGGTGGTTTCTTGTTTATAACGAGAAAGCAAG 3 79 0 GTTCTTTAAG 0.919224 -222 AAACCACCCTAGATCCTTTGTACATCGAACGAAAAGA 3 102 1 AATCCTTAAG 0.993576 -199 TAGTAAAAAAAACTCTTAAATATAAAGAAAGGGGAAT 3 158 0 ACTCTTTAAG 0.980221 -143 TGAAATAAAAGGATCCTCTGTAGATGGGAGTAAAATA 3 272 0 GATCCTTAAG 0.989782 -29 * ***** ** * * Masking position 12 Map Score: 15.427 Number of sites scoring better than the average of aligned sites = 101 Number in coding regions = 101 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 TCTTCGACTTAGGAGATTTTCTCTAAGTAGA 1 21 1 AGAGATTTTC 0.884534 -280 AGCTTTTATCAGGATTTTTTTAAGTTCCTAG 1 72 1 AGATTTTTTT 0.946442 -229 AAGGGCAGCCAGCATATCCTCTTTAATTGGA 1 185 0 AGATATCCTC 0.92434 -116 CTCCCGCCGCAGGATTTCCTTACTTTCTATC 1 270 0 AGATTTCCTT 0.974233 -31 TTGTAAACAGAGAAGATCCTTCTTAAAAAGG 3 33 0 AGAGATCCTT 0.977116 -268 AAGGATCTAGGGTGGTTTCTTGTTTATAACG 3 89 0 GGGGTTTCTT 0.919519 -212 AAGTTTGTATAGAGTTTCTTTTCGTTCGATG 3 124 0 AGGTTTCTTT 0.963438 -177 TTTATATTTAAGAGTTTTTTTTACTAATGAA 3 169 1 AGGTTTTTTT 0.942941 -132 ATTTTACCTTGGTATTTTTTTTTATGGAATA 3 235 0 GGATTTTTTT 0.871528 -66 GGAGTAAAATAGGAGATATTTTACCTTGGTA 3 252 0 AGAGATATTT 0.831207 -49 TCCCATCTACAGAGGATCCTTTTATTTCAGG 3 280 1 AGGGATCCTT 0.975564 -21 ** ******** Masking position 7 Map Score: 11.71 Number of sites scoring better than the average of aligned sites = 415 Number in coding regions = 414 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 3 CCTCTTTAATTGGAATGAAAACCAATAAGA 1 169 0 TGGAATGAAA 0.986141 -132 AAAGATTTGGGGGAACGAAATAAAAAGAGG 2 25 1 GGGAACGAAA 0.989335 -34 CCTTTGTACATCGAACGAAAAGAAACTCTA 3 116 1 TCGAACGAAA 0.93116 -185 ATAAAGAAAGGGGAATAAAAAGTTTGTATA 3 144 0 GGGAATAAAA 0.986142 -157 CTCTGTAGATGGGAGTAAAATAGGAGATAT 3 264 0 GGGAGTAAAA 0.962989 -37 CCTGAAATAAAAGGATCCTCTG 3 289 0 TGAAATAAAA 0.875014 -12 ********** Masking position 4 Map Score: 5.55244 Number of sites scoring better than the average of aligned sites = 71 Number in coding regions = 71 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 TTAGAGAAAATCTCCTAAGTCGAAGACTGT 1 17 0 TCTCCTAAGT 0.983977 -284 GCAGCCAGCATATCCTCTTTAATTGGAATG 1 182 0 TATCCTCTTT 0.946606 -119 AGCTTCGGTCTCTCCTAATTAGAAATCGCT 1 238 0 TCTCCTAATT 0.986682 -63 TTAAGAAGGATCTTCTCTGTTTACAAAGAC 3 38 1 TCTTCTCTGT 0.936296 -263 GAGAAATGAGTCTCCTATTCCATAAAAAAA 3 220 1 TCTCCTATTC 0.980599 -81 AGGTAAAATATCTCCTATTTTACTCCCATC 3 257 1 TCTCCTATTT 0.992818 -44 ********** Masking position 6 Map Score: 7.21626 Number of sites scoring better than the average of aligned sites = 116 Number in coding regions = 116 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 5 TCTGAGTCGCAGCTTTTATCAGGATTTTTT 1 62 1 AGCTTTTATC 0.957203 -239 TTTCTTCGCAAGTTTTTATATTCTAAGAGC 1 103 1 AGTTTTTATA 0.953851 -198 CCGCTTTTTGAGCTCTTAGAATATAAAAAC 1 114 0 AGCTCTTAGA 0.967475 -187 AAAGAGGTAAAGCTTTTAAAG 2 48 1 AGCTTTTAAA 0.977111 -11 GGGAATAAAAAGTTTGTATAGAGTTTCTTT 3 134 0 AGTTTGTATA 0.883143 -167 TAGTAAAAAAAACTCTTAAATATAAAGAAA 3 165 0 AACTCTTAAA 0.845559 -136 ********** Masking position 4 Map Score: 1.78304 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 85 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 CTGCGACTCAGAAGCATTGTACTCTACTTAGAGAA 1 39 0 GCATGACTCT 0.993962 -262 CGCTATCCACGTATCATAGGTCTCTAAAGGGCAGC 1 207 0 GCATGTCTCT 0.997602 -94 ACTTTCTATCGAAGCTTCGGTCTCTCCTAATTAGA 1 245 0 GCTTGTCTCT 0.993963 -56 TGGAATAGGAGACTCATTTCTCTCTGTAGTCGGAG 3 207 0 GCATTTCTCT 0.99054 -94 * *** * ***** Masking position 7 Map Score: 0.917745 Number of sites scoring better than the average of aligned sites = 2 Number in coding regions = 2 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 GGGTGGACAGTCTTCGACTTAGGA 1 5 1 GGACAGTCTT 0.984064 -296 TAAAACAGTCTAAAAAAGATTT 2 3 1 AAACAGTCTA 0.912941 -56 CAAGCTTTAGGAATCGTCTTTGTAAACAGA 3 53 0 GAATCGTCTT 0.975535 -248 TTTTACTAATGAATAGTCTTCTCCGACTAC 3 187 1 GAATAGTCTT 0.985518 -114 ********** Masking position 7 Map Score: 0.505645 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 24 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 ********** No masking Map Score: -8.92852e-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 9 ********** No masking Map Score: -8.92852e-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 10 ********** No masking Map Score: -8.92852e-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