AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -inarP_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 PH1509 300 440aa long hypothetical NADH oxidase #2 PH1670 300 102aa long hypothetical protein Motif number 1 AGGAGCATCTCTCCGATTATCTTTATCGCGCA 1 166 0 CTCCATATCT 0.987542 -135 CGGAGAGATGCTCCTGAACTCTAGACAAAAAA 1 183 1 CTCCGACTCT 0.942295 -118 TGAACGAATGCCCTCATTTTCTCCCCAACATT 1 240 1 CCCTATTTCT 0.950289 -61 CTCATTTTCTCCCCAACATTTTAATATCTCTT 1 252 1 CCCCAATTTT 0.801706 -49 TATCTCTTAACCCTTTCTCTCTTGGGTGGAGA 1 276 1 CCCTTTCTCT 0.957616 -25 GGAGATCCTTTTCTCTAGAGGTTTCT 2 5 1 ATCCTTCTCT 0.780739 -296 GAGGTTTCTCCCCTAATTATCTCGACTTTTGC 2 28 1 CCCTATATCT 0.977749 -273 TCGACTTTTGCCCCAAGAATCTTTGAGAGGAA 2 49 1 CCCCAAATCT 0.990687 -252 CAATTGTCAACTCCTTCAATCTTGTTCTCCTT 2 151 1 CTCCTAATCT 0.965988 -150 GCACTTTCCTCACCCAATATCTTTTCTACGAA 2 236 1 CACCATATCT 0.960148 -65 **** * ***** Masking position 10 Map Score: 11.3511 Number of sites scoring better than the average of aligned sites = 537 Number in coding regions = 495 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 2 TATTTCGATAAACCTCTCCTTATCGAATGCT 1 94 0 AACTCTCCTT 0.859482 -207 ACATTTTGTTGGCCTTTCCTTCCTTATTTCG 1 118 0 GGCTTTCCTT 0.957261 -183 GTTCCTTATTTGCCTCCCCTTTAACTGGAGG 2 89 1 TGCTCCCCTT 0.985138 -212 GGAGCTTTTATGCTTATCCTTATTCTATTTT 2 118 1 TGCTATCCTT 0.982662 -183 TTTTCCAATTGTCAACTCCTTCAATCTTGTT 2 146 1 GTCACTCCTT 0.914241 -155 TCCTTCAATCTTGTTCTCCTTGGAGTTTGGT 2 162 1 TTGTCTCCTT 0.976879 -139 TGTTCCATCTTTGGTTTCCTTAAGCACTTTC 2 213 1 TTGTTTCCTT 0.934533 -88 CTACGAAGATTTAATACCCTTCGATGAAAGG 2 271 0 TTATACCCTT 0.809417 -30 GTATTAAATCTTCGTAGCCTTGGCCA 2 285 1 TTCTAGCCTT 0.946785 -16 *** ******* Masking position 10 Map Score: 6.25563 Number of sites scoring better than the average of aligned sites = 697 Number in coding regions = 649 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 3 CCCTCATAGCGAGCTTCTCAGCTTTTCGGG 1 37 0 GAGCTTCTCA 0.903967 -264 TTATTTCGATAAACCTCTCCTTATCGAATG 1 96 0 AAACCTCTCC 0.946776 -205 TTTATCGCGCAAAGATCTCCAAATGTTGAC 1 147 0 AAAGATCTCC 0.93275 -154 TAGAGTTCAGGAGCATCTCTCCGATTATCT 1 176 0 GAGCATCTCT 0.911815 -125 GCATTCGTTCAAATTTTTCCTTCATATTTC 1 221 0 AAATTTTTCC 0.697848 -80 CTCTAGAGAAAAGGATCTCC 2 1 0 AAGGATCTCC 0.979466 -300 TTTTCTCTAGAGGTTTCTCCCCTAATTATC 2 19 1 AGGTTTCTCC 0.943792 -282 GGAACTTATAAAGTTCCTCTCAAAGATTCT 2 64 0 AAGTTCCTCT 0.88934 -237 ATAAGCATAAAAGCTCCTCCAGTTAAAGGG 2 105 0 AAGCTCCTCC 0.986407 -196 ********** Masking position 8 Map Score: 6.05225 Number of sites scoring better than the average of aligned sites = 1070 Number in coding regions = 1007 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 4 CGGGAGTCAATCCTCTTTAGTCAAAAAGAT 1 11 0 TCCTCTTTAG 0.782463 -290 AGCGAGCTTCTCAGCTTTTCGGGAGTCAAT 1 30 0 TCAGCTTTTC 0.749686 -271 GGCCTTTCCTTCCTTATTTCGATAAACCTC 1 109 0 TCCTTATTTC 0.953317 -192 CAACAAAATGTCAACATTTGGAGATCTTTG 1 138 1 TCAACATTTG 0.868837 -163 AAATTTTTCCTTCATATTTCAGTGAGTTTT 1 211 0 TTCATATTTC 0.701999 -90 GGAGATCCTTTTCTCTAGAGGTTTC 2 6 1 TCCTTTTCTC 0.825722 -295 CCTAATTATCTCGACTTTTGCCCCAAGAAT 2 39 1 TCGACTTTTG 0.872764 -262 CTTTATAAGTTCCTTATTTGCCTCCCCTTT 2 81 1 TCCTTATTTG 0.944818 -220 TTATCCTTATTCTATTTTTCCAATTGTCAA 2 131 1 TCTATTTTTC 0.804428 -170 GAATTATTGTTCCATCTTTGGTTTCCTTAA 2 206 1 TCCATCTTTG 0.95409 -95 TTTTCTACGAACCACCTTTCATCGAAGGGT 2 257 1 ACCACCTTTC 0.808661 -44 ********** Masking position 7 Map Score: 4.46464 Number of sites scoring better than the average of aligned sites = 923 Number in coding regions = 846 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 5 ATAAGGAAGGAAAGGCCAACAAAATGTCAA 1 122 1 AAAGGCCAAC 0.973011 -179 AAGGCCAACAAAATGTCAACATTTGGAGAT 1 133 1 AAATGTCAAC 0.990552 -168 TATGAAGGAAAAATTTGAACGAATGCCCTC 1 225 1 AAATTTGAAC 0.907787 -76 CTATTTTTCCAATTGTCAACTCCTTCAATC 2 142 1 AATTGTCAAC 0.976467 -159 ********** Masking position 8 Map Score: 0.554713 Number of sites scoring better than the average of aligned sites = 21 Number in coding regions = 15 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 6 ATCTTTTTGACTAAAGAGGATTGACT 1 7 1 TTGACTAAAG 0.462169 -294 CTAAAGAGGATTGACTCCCGAAAAGCTGAG 1 21 1 TTGACTCCCG 0.975439 -280 TTTGTTGGCCTTTCCTTCCTTATTTCGATA 1 115 0 TTTCCTTCCT 0.832109 -186 AATGCCCTCATTTTCTCCCCAACATTTTAA 1 246 1 TTTTCTCCCC 0.968601 -55 TTCTCTAGAGGTTTCTCCCCTAATTATCTC 2 21 1 GTTTCTCCCC 0.878159 -280 ATCTCGACTTTTGCCCCAAGAATCTTTGAG 2 46 1 TTGCCCCAAG 0.850169 -255 AGTTCCTTATTTGCCTCCCCTTTAACTGGA 2 88 1 TTGCCTCCCC 0.993178 -213 CCATCTTTGGTTTCCTTAAGCACTTTCCTC 2 217 1 TTTCCTTAAG 0.811837 -84 CCTTAAGCACTTTCCTCACCCAATATCTTT 2 230 1 TTTCCTCACC 0.982922 -71 ********** Masking position 2 Map Score: 5.17464 Number of sites scoring better than the average of aligned sites = 787 Number in coding regions = 738 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 7 ********** No masking Map Score: 1.30983e-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: 1.30983e-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: 1.30983e-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