AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -idnaA_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 PH0543 58 318aa long hypothetical protein #2 PH1408 233 226aa long hypothetical protein #3 PH1409 250 721aa long hypothetical protein #4 PH1410 117 332aa long hypothetical dipeptide transport system permease protein dppB #5 PH1414 26 129aa long hypothetical protein #6 PH1415 93 343aa long hypothetical 5' nuclease Motif number 1 ACTTTCTTCACTTCATGTATTTAAGGTTTCTTTGAGTTG 1 15 0 CTTTTATTTT 0.959479 -44 ATTTACTCCCTCTAAACTTTCTTCACTTCA 1 39 0 TTTTCCTTTT 0.939359 -20 GGCGTACATCTCTCTTTCCTCGAGGATTTTAAGAATCTC 2 27 0 TCTTCCTTTT 0.927239 -207 TAGGGGTTTTCCTAGTGCTTGCCAAATTTCATAGGCGTA 2 60 0 CCTTCTTTTT 0.967086 -174 TGATGAACGGCTTGATACTTTAGGGGTTTTCCTAGTGCT 2 80 0 CTTTCTTTTT 0.972764 -154 TCCTCTTCCCCTTTCTATATGCCTCCTTTATGAGGCCTA 2 142 0 CTTTTATTTT 0.959479 -92 TTTCAATAAGCCTTCTACCTCTCTCAGTCAGCTTGTAAT 2 184 0 CCTTCCTGTC 0.8471 -50 CTCTAATTCCCTTATTTTTTGAGATGTTTAACCTAGTGT 3 86 1 CTTTTTTTTT 0.968586 -165 TAATCTTTCTTCTCTCTTTTCTTTATTGCCCTTA 4 6 1 TTTTTCTTTT 0.930422 -112 CTTGTACATTCTTGTTCTATAACATCGTTTGAGAATTAT 4 78 0 CTTTTATGTT 0.929763 -40 ATATCCTCTTCTTTTTTCAATTTTTG 5 5 1 CCTTTTTTTT 0.96207 -22 CATCATCAGACTTGATATCTCTGAAAGTTTATAACAAT 6 10 0 CTTTTCTGTT 0.971318 -84 *** * *** *** Masking position 10 Map Score: 12.6646 Number of sites scoring better than the average of aligned sites = 402 Number in coding regions = 347 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 2 ATGAAGTGAAGAAAGTTTAGAGGGAGTAAA 1 38 1 GAAAGTTTAG 0.873242 -21 GCCTCATAAAGGAGGCATATAGAAAGGGGA 2 145 1 GGAGGCATAT 0.868221 -89 GAGAGAGGTAGAAGGCTTATTGAAAATCTT 2 198 1 GAAGGCTTAT 0.977378 -36 AATAAAATTATGAAGTTCATTTACACTAGG 3 117 0 TGAAGTTCAT 0.799627 -134 ACCAAGATCGAAAAGCTTATTAGCGAGGTG 3 189 1 AAAAGCTTAT 0.811374 -62 ACATCACCAGGGAAGGTTATCCAAAGAGAT 3 228 0 GGAAGGTTAT 0.977381 -23 TGATATCTCTGAAAGTTTATAACAAT 6 7 0 GAAAGTTTAT 0.970613 -87 CAGGTGAGGGGAAGGTTCATCATCAGACTT 6 36 0 GAAGGTTCAT 0.952977 -58 CCCCTCACCTGAAAGGTGATGAGCACACCG 6 55 1 GAAAGGTGAT 0.957608 -39 ACCGGTAGGCTGAGGGTGATAAT 6 81 1 TGAGGGTGAT 0.839257 -13 ********** Masking position 3 Map Score: 7.70912 Number of sites scoring better than the average of aligned sites = 517 Number in coding regions = 465 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 3 ACTAAGCTTGAGATTCTTAAAATCCTCGAGG 2 18 1 AGATTTTAAA 0.780559 -216 TTCCTTTATATGCTGATGAACGGCTTGATAC 2 101 0 TGCTGTGAAC 0.968501 -133 TTCACCTTGAAGATGCTTAAAAATCAGTGGT 3 20 1 AGATGTTAAA 0.947545 -231 TTATTTTTTGAGATGTTTAACCTAGTGTAAA 3 97 1 AGATGTTAAC 0.972596 -154 AAGATCGAAAAGCTTATTAGCGAGGTGCCTG 3 192 1 AGCTTTTAGC 0.739041 -59 TAACCTTCCCTGGTGATGTAAG 3 239 1 TGGTGTGTAA 0.7823 -12 ATAAAAATTTTGGTGTTTAAATAAGGGCAAT 4 35 0 TGGTGTTAAA 0.946541 -83 ATATCAAGTCTGATGATGAACCTTCCCCTCA 6 31 1 TGATGTGAAC 0.973744 -63 CTCACCTGAAAGGTGATGAGCACACCGGTAG 6 58 1 AGGTGTGAGC 0.964249 -36 ***** ***** Masking position 7 Map Score: 5.95714 Number of sites scoring better than the average of aligned sites = 251 Number in coding regions = 230 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 4 GAAGAAAGTTTAGAGGGAGTAAAT 1 45 1 TAGAGGGAGT 0.935602 -14 TCCTCGAGGAAAGAGAGATGTACGCCTATG 2 40 1 AAGAGAGATG 0.962561 -194 AGGAGGCATATAGAAAGGGGAAGAGGATAT 2 154 1 TAGAAAGGGG 0.952458 -80 TACAAGCTGACTGAGAGAGGTAGAAGGCTT 2 186 1 CTGAGAGAGG 0.897065 -48 AAATCTTGAGTAGAGGGTGGTGA 2 221 1 TAGAGGGTGG 0.96852 -13 ATAAGGGAATTAGAGAGATGTTTTTGAATG 3 71 0 TAGAGAGATG 0.985961 -180 AAAAGCTTATTAGCGAGGTGCCTGGTTATA 3 199 1 TAGCGAGGTG 0.902833 -52 CAATAAAGAAAAGAGAGAAGAAAGATTA 4 9 0 AAGAGAGAAG 0.910517 -109 AACAAGAATGTACAAGGAGGGGCAAAT 4 101 1 TACAAGGAGG 0.809163 -17 ********** Masking position 7 Map Score: 6.44384 Number of sites scoring better than the average of aligned sites = 607 Number in coding regions = 553 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 5 ATTTACTCCCTCTAAACTTTCTTC 1 45 0 TATCCCTCTA 0.741785 -14 CTAACTCTTGTAATTCCTTTATATGCTGATG 2 114 0 TATTCCTTTA 0.935889 -120 CCTTTCTATATGCCTCCTTTATGAGGCCTAA 2 141 0 TGCTCCTTTA 0.858801 -93 CAGCTTGTAATATATCCTCTTCCCCTTTCTA 2 164 0 TAATCCTCTT 0.887854 -70 GCTTATTGTTTCACCTTGAAGATGCTT 3 7 1 TGTTCACCTT 0.872481 -244 AAATCAGTGGTGTATCATTTTGATCATAAAA 3 40 1 TGATCATTTT 0.788302 -211 AACATCTCTCTAATTCCCTTATTTTTTGAGA 3 79 1 TATTCCCTTA 0.951807 -172 TGTTATAATTTGGATCTTCTATTTTCCACAA 3 153 1 TGATCTTCTA 0.742766 -98 TTTTCGATCTTGGTTCACTTTGTGGAAAATA 3 172 0 TGTTCACTTT 0.879751 -79 GGTGCCTGGTTATATCTCTTTGGATAACCTT 3 215 1 TAATCTCTTT 0.722125 -36 CTCTTTTCTTTATTGCCCTTATTTAAACACC 4 24 1 TATGCCCTTA 0.804772 -94 ** ******** Masking position 10 Map Score: 2.66631 Number of sites scoring better than the average of aligned sites = 1053 Number in coding regions = 988 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 6 ********** No masking Map Score: -1.00654e-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 7 ********** No masking Map Score: -1.00654e-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: -1.00654e-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