AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00900_pyro_reg_100.orf -o00900_pyro_100.ace -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -g0.42 -x5 -e 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 = 0.42 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 PH1070 300 320aa long hypothetical protein #2 PH1071 65 450aa long hypothetical protein #3 PH1072 57 342aa long hypothetical geranylgeranyl pyrophosphate synthetase Motif number 1 AGTACTAACTTTTTACAAAAATTAAATAAAAA 1 21 1 TTTCAAAAAT 0.969634 -280 TTACAAAAATTAAATAAAAACTCTCAAACCTT 1 33 1 TAAAAAAACT 0.925663 -268 CTCTCAAACCTTTTCCAAAAATATATCCTCCT 1 53 1 TTTCAAAAAT 0.969634 -248 TTGAAATTTTTAAATAAAATATTGAGGAGGAT 1 77 0 TAAAAAATAT 0.833072 -224 TTTATTTAAAAATTTCAAAAATTTTCGTAACA 1 91 1 AATCAAAAAT 0.983048 -210 GTAACAATTTAATAACAAAACTTTAACATAAG 1 117 1 AATCAAAACT 0.973345 -184 CTAAAACCTCTATTCTAAAAATTAAGCCTAGA 1 191 1 TATTAAAAAT 0.898077 -110 ACAAAGCCAAAAATCCAAAAATAATCCCAAAT 1 222 1 AAACAAAAAT 0.984911 -79 ATCCAAAAATAATCCCAAATATCTTGCACCGA 1 234 1 AATCAAATAT 0.93604 -67 TTGATAGTAATTATTCAAAAATTTTTCGGTGC 1 259 0 TTACAAAAAT 0.969356 -42 CACATCTTTTTAAATCAAAACTCAAACAACAA 2 22 1 TAACAAAACT 0.980496 -44 TCCAACCAGGAAAAGAAAAAATTAAGCCCCTT 3 27 0 AAAAAAAAAT 0.941793 -31 *** ******* Masking position 7 Map Score: 20.7737 Number of sites scoring better than the average of aligned sites = 255 Number in coding regions = 173 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 2 AATTTTTGTAAAAAGTTAGTACTTTTCTTGG 1 13 0 AAAAGTTATA 0.874311 -288 ACTTTTTACAAAAATTAAATAAAAACTCTCA 1 28 1 AAAATTAATA 0.929407 -273 ACCTTTTCCAAAAATATATCCTCCTCAATAT 1 60 1 AAAATATACC 0.892712 -241 AATTTTCGTAACAATTTAATAACAAAACTTT 1 110 1 ACAATTTATA 0.756776 -191 TTTAATAACAAAACTTTAACATAAGGAAAAT 1 124 1 AAACTTTACA 0.959783 -177 TAACTAAGTCAAACTCTAATCCCTCTAAAAC 1 167 1 AAACTCTATC 0.957115 -134 ATCCCTCTAAAACCTCTATTCTAAAAATTAA 1 185 1 AACCTCTATC 0.79302 -116 CTCTATTCTAAAAATTAAGCCTAGACAAAGC 1 198 1 AAAATTAACC 0.971204 -103 CCAAAAATCCAAAAATAATCCCAAATATCTT 1 228 1 AAAAATAACC 0.825958 -73 AATTACTATCAAAAGCTAATAAGTGGTTAGA 1 279 1 AAAAGCTATA 0.866763 -22 TTTTAAATCAAAACTCAAACAACAATTCAGT 2 29 1 AAACTCAACA 0.941901 -37 AGGAAAAGAAAAAATTAAGCCCCTTATGAGC 3 21 0 AAAATTAACC 0.971204 -37 ******** ** Masking position 8 Map Score: 11.7539 Number of sites scoring better than the average of aligned sites = 393 Number in coding regions = 321 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 3 GAAAAGTACTAACTTTTTACAAAAATTAAA 1 17 1 AACTTTTTAC 0.978231 -284 AAAACTCTCAAACCTTTTCCAAAAATATAT 1 49 1 AACCTTTTCC 0.916258 -252 AAAATTTTTGAAATTTTTAAATAAAATATT 1 86 0 AAATTTTTAA 0.916599 -215 AATTGTTACGAAAATTTTTGAAATTTTTAA 1 96 0 AAAATTTTTG 0.671881 -205 TTTTGTTATTAAATTGTTACGAAAATTTTT 1 107 0 AAATTGTTAC 0.900486 -194 TTTAATAACAAAACTTTAACATAAGGAAAA 1 124 1 AAACTTTAAC 0.74406 -177 TGTCTAGGCTTAATTTTTAGAATAGAGGTT 1 195 0 TAATTTTTAG 0.860024 -106 AATTATTCAAAAATTTTTCGGTGCAAGATA 1 253 0 AAATTTTTCG 0.933432 -48 AACTTTTCTCCCACATCTTT 2 1 1 AACTTTTCTC 0.830965 -65 TTTCTCCCACATCTTTTTAAATCAAAACTC 2 15 1 ATCTTTTTAA 0.566339 -51 ATAAGGGGCTTAATTTTTTCTTTTCCTGGT 3 25 1 TAATTTTTTC 0.862144 -33 ********** Masking position 5 Map Score: 6.68748 Number of sites scoring better than the average of aligned sites = 510 Number in coding regions = 353 Number in noncoding regions = 157 Number of orfs with sites within 600 bp upstream = 161 Fraction of orfs with sites within 600 bp upstream = 0.0258593 Motif number 4 AGCCAAGAAAAGTACTAACTTT 1 3 1 CCAAGAAAAG 0.976845 -298 AGGATATATTTTTGGAAAAGGTTTGAGAGT 1 52 0 TTTGGAAAAG 0.900061 -249 AAAATTAAGCCTAGACAAAGCCAAAAATCC 1 208 1 CTAGACAAAG 0.943643 -93 TGAATAATTACTATCAAAAGCTAATAAGTG 1 274 1 CTATCAAAAG 0.933202 -27 ACACCTCCAACCAGGAAAAGAAAAAATTAA 3 34 0 CCAGGAAAAG 0.994022 -24 ********** Masking position 7 Map Score: 1.10079 Number of sites scoring better than the average of aligned sites = 471 Number in coding regions = 430 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 5 TAAATAAAAACTCTCAAACCTTTTCCAAAA 1 43 1 CTCTCAAACC 0.991544 -258 ACTCTAATCCCTCTAAAACCTCTATTCTAA 1 179 1 CTCTAAAACC 0.986981 -122 AACTTTTCTCCCACATCTTTTTAAATC 2 8 1 CTCCCACATC 0.982424 -58 TAAATCAAAACTCAAACAACAATTCAGTTC 2 32 1 CTCAAACAAC 0.960601 -34 ********** Masking position 6 Map Score: 1.43571 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 51 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 6 ********** No masking Map Score: -7.64954e-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 7 ********** No masking Map Score: -7.64954e-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 8 ********** No masking Map Score: -7.64954e-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