AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -iglpR_pyro_opreg_300.orf -g0.419 -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 = 0.419 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 PH1361 274 537aa long hypothetical proline permease #2 PH1363 211 493aa long hypothetical protein #3 PH1497 109 197aa long hypothetical protein Motif number 1 ATAGTTTTCACCCCCTAATTTATGATATTTT 1 9 1 CCCCCTAATT 0.99369 -266 TTCATATAAATACCCCCTAAATCTTTATATACT 1 43 1 TCCCCTAATC 0.990755 -232 ATCTAAGTCACCTCCAATAAATTTCAAAATGTA 1 90 0 CTCCATAATT 0.854465 -185 GCCCAAGCTGCTCCACTAAAACCCATCTAAGTC 1 114 0 CCCACAAACC 0.865656 -161 CCCGTAATTTTGTCCCAAAACCCATAAACTATC 1 186 0 TTCCCAAACC 0.930709 -89 ATAGTACTCCTTCCCCGTAATTTTGTCCCAAAA 1 199 0 TCCCCTAATT 0.985338 -76 CCCTCCAAAAATTGAAACAAATT 2 199 0 CCTCCAAATT 0.954914 -13 CCATCCCTCCCTTTAGTCATCGTTCATC 3 6 1 CTCCCTTATC 0.937808 -104 AATACTTTTCTTCACCATAAGTCTTTTAAATCT 3 61 0 TCACCTAATC 0.922882 -49 CTTTCCTAAATTTTCAGGCGATT 3 97 0 CTTCCAAATT 0.900384 -13 * **** *** ** Masking position 10 Map Score: 8.39641 Number of sites scoring better than the average of aligned sites = 588 Number in coding regions = 520 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 2 GCAGCGTGGCCCAAGCTGCTCCACTAAAAC 1 125 0 CCAAGCTGCT 0.996583 -150 GCAGCTTGGGCCACGCTGCTAGTTCCAACG 1 136 1 CCACGCTGCT 0.994511 -139 GGGCAAAGAGCCAAGCTGAAAACGTCTTTG 2 85 1 CCAAGCTGAA 0.991072 -127 TCTCAATTAACCAAGCTCGACAGATGAACG 3 31 0 CCAAGCTCGA 0.98004 -79 ********** Masking position 7 Map Score: 3.8639 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 16 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 3 ATAGTTTTCACCCCCTAATTTATGAT 1 6 1 TTTCACCCCT 0.841014 -269 GTTCCAACGATTCTTGCTTTTGTAGTAATGA 1 157 1 TTCTTGCTTT 0.763398 -118 TACATAGTACTCCTTCCCCGTAATTTTGTCC 1 204 0 TCCTTCCCCT 0.990376 -71 CAACCTTTATTTTCTCACTCTTTTCTATCGG 2 51 0 TTTCTCACTT 0.896834 -161 TCAGCTTGGCTCTTTGCCCTTGCAACCTTTA 2 73 0 TCTTTGCCCT 0.980051 -139 GCTGAAAACGTCTTTGATTTTGCAATTGCTT 2 99 1 TCTTTGATTT 0.714785 -113 CTTCCGGCCTTCTTTAACCTTTTTTTGCTAA 2 127 1 TCTTTAACCT 0.862894 -85 CCATCCCTCCCTTTAGTCATCGTT 3 4 1 TCCCTCCCTT 0.977376 -106 TAAAATACTTTTCTTCACCATAAGTCTTTTA 3 66 0 TTCTTCACCT 0.963845 -44 ********* * Masking position 1 Map Score: 3.49396 Number of sites scoring better than the average of aligned sites = 1601 Number in coding regions = 1492 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 4 TTTTTTTCATATAAATACCCCCTAAATCTTTAT 1 38 1 ATAAAACCCT 0.964147 -237 ACTAAAACCCATCTAAGTCACCTCCAATAAATT 1 100 0 ATCTAGCCCT 0.90766 -175 CCTTATGCAGTTTAACAACATCT 2 1 0 TTTAAACTCT 0.960259 -211 CGGAACTTTTTTAAAGAGCTCCTTATGCAGTTT 2 21 0 TTAAAACCCT 0.98408 -191 TTGAAACAAATTCAACATTACCTATGTAAAGTC 2 178 0 TTCAAATCCT 0.925387 -34 ACCATAAGTCTTTTAAATCTTCTCAATTAACCA 3 48 0 TTTTAACTCT 0.948867 -62 AAGAAAAGTATTTTAAATCGCCTGAAAATTTAG 3 82 1 TTTTAACCCT 0.985512 -28 ***** * * *** Masking position 5 Map Score: 2.74494 Number of sites scoring better than the average of aligned sites = 215 Number in coding regions = 188 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 5 ATTTATGATATTTTTTTCATATAAATACCC 1 28 1 TTTTTTTCAT 0.692036 -247 TAAAATATCCTCATCTACATAGTACTCCTT 1 220 0 TCATCTACAT 0.85119 -55 CTTGGTAAGCTCTTCATCATATGCTAAAAT 1 244 0 TCTTCATCAT 0.960804 -31 ATTTTCTCACTCTTTTCTATCGGAACTTTT 2 44 0 TCTTTTCTAT 0.885382 -168 TCAGCTTGGCTCTTTGCCCTTGCAACCTTT 2 74 0 TCTTTGCCCT 0.93824 -138 CTTCCGGCCTTCTTTAACCTTTTTTTGCTA 2 127 1 TCTTTAACCT 0.897448 -85 GTCTTTTAAATCTTCTCAATTAACCAAGCT 3 44 0 TCTTCTCAAT 0.924542 -66 AAAATACTTTTCTTCACCATAAGTCTTTTA 3 66 0 TCTTCACCAT 0.986403 -44 ********** Masking position 4 Map Score: 3.12904 Number of sites scoring better than the average of aligned sites = 1108 Number in coding regions = 1030 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 6 CTATCATTACTACAAAAGCAAGAATCGTTG 1 161 0 TACAAAAGCA 0.953882 -114 GTTGTTAAACTGCATAAGGAGCTCTTTAAA 2 15 1 TGCATAAGGA 0.896879 -197 AAATAAAGGTTGCAAGGGCAAAGAGCCAAG 2 70 1 TGCAAGGGCA 0.978523 -142 CGGAAGCAATTGCAAAATCAAAGACGTTTT 2 103 0 TGCAAAATCA 0.97923 -109 ACATTACCTATGTAAAGTCATAATTTATAA 2 167 0 TGTAAAGTCA 0.909376 -45 ********** Masking position 4 Map Score: 0.428309 Number of sites scoring better than the average of aligned sites = 219 Number in coding regions = 213 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 7 ********** No masking Map Score: 1.21035e-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 8 ********** No masking Map Score: 1.21035e-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 9 ********** No masking Map Score: 1.21035e-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