AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i156_HYP_operon_pyro_reg_300.orf -o156_pyro_300.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 RPH00379 122 Pyrococcus_OT3 #2 RPH00253 247 Pyrococcus_OT3 #3 RPH00235 107 Pyrococcus_OT3 #4 RPH00234 91 Pyrococcus_OT3 Motif number 1 GTTCCCGAAAAAGCTTTTAAACAGTAAGATCG 1 51 1 AAGCTTAAAC 0.968802 -72 AGAAATCTTTGGGGTTAAAAACCCAACGACGA 1 80 0 GGGGTTAAAC 0.982928 -43 TTTAAACTAATGGTTTTAAAAACCGCTATAAA 2 68 0 TGGTTTAAAA 0.932103 -180 TTCCTTTTAGAGGGTTTTAAACTAATGGTTTT 2 83 0 AGGGTTAAAC 0.995408 -165 GATAAGGGGATAGGTTGAAAACTTTTGGTTTT 2 180 1 TAGGTTAAAC 0.986512 -68 TGAAAACTTTTGGTTTTAAAAATGTCTAAAAA 2 195 1 TGGTTTAAAA 0.932103 -53 AATATAAAAAAAGTTTTCAAACATTAAGTAGT 3 57 0 AAGTTTAAAC 0.985701 -51 ACCTAAGGTTAAAAATCTCCCTTCTG 4 5 1 AAGGTTAAAT 0.973646 -87 TCTAAAACCAAAAGTTGGAAACAGAAGGGAGA 4 26 0 AAAGTTAAAC 0.927153 -66 GAACCTTTATAGGTTTCTAAAACCAAAAGTTG 4 41 0 AGGTTTAAAA 0.96807 -51 GAAACCTATAAAGGTTCCAAATTCTGAAAAAT 4 56 1 AAGGTTAAAT 0.973647 -36 ****** **** Masking position 9 Map Score: 20.1593 Number of sites scoring better than the average of aligned sites = 191 Number in coding regions = 159 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 2 ATGCATCCCTTTAGGATGATTCCTT 1 6 1 TCCCTTTAGG 0.983271 -117 TTTAGGATGATTCCTTAAAGAACTAATAAA 1 20 1 TTCCTTAAAG 0.974448 -103 AAGATTTCTCTTCCATTTGGGGGATTATAA 1 103 1 TTCCATTTGG 0.972388 -20 AATAATTTTATCCGTTATAGGCCTGGAATT 2 33 1 TCCGTTATAG 0.954986 -215 AACGCTTCCTTTCCTTTTAGAGGGTTTTAA 2 95 0 TTCCTTTTAG 0.989914 -153 CCGACAACATTCCCTTTTGGGATAAGGGGA 2 160 1 TCCCTTTTGG 0.989506 -88 ATTACTTCACTTCCATAAAGTGGGGGATCA 3 86 1 TTCCATAAAG 0.933159 -22 TTTCCAACTTTTGGTTTTAGAAACCTATAA 4 37 1 TTGGTTTTAG 0.851784 -55 ********** Masking position 6 Map Score: 11.0431 Number of sites scoring better than the average of aligned sites = 381 Number in coding regions = 355 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 3 CTTTTTCGGGAACGTTTATTAGTTCTTTAA 1 34 0 AACGTTTATT 0.921849 -89 GTGTACCACCTTTGTTCATTAAAATA 2 7 1 CACCTTTGTT 0.938938 -241 CGGTTTTTAAAACCATTAGTTTAAAACCCT 2 75 1 AACCATTAGT 0.927864 -173 ATAGGTTGAAAACTTTTGGTTTTAAAAATG 2 189 1 AACTTTTGGT 0.983619 -59 AAAGTTTTCAAACATTAAGTAGTCAGAGCA 3 50 0 AACATTAAGT 0.831692 -58 AATGTTTGAAAACTTTTTTTATATTACTTC 3 64 1 AACTTTTTTT 0.859112 -44 GGAGATTTTTAACCTTAGGT 4 1 0 AACCTTAGGT 0.97592 -91 TTCTGTTTCCAACTTTTGGTTTTAGAAACC 4 32 1 AACTTTTGGT 0.983619 -60 CAGAATTTGGAACCTTTATAGGTTTCTAAA 4 52 0 AACCTTTATA 0.867586 -40 ********** Masking position 6 Map Score: 8.72501 Number of sites scoring better than the average of aligned sites = 292 Number in coding regions = 254 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 4 AGAGAAATCTTTGGGGTTAAAAACCCAACG 1 84 0 TTGGGGTTAA 0.919551 -39 ATCCCCCAAATGGAAGAGAAATCTTTGGGG 1 98 0 TGGAAGAGAA 0.97066 -25 CTCTTCCATTTGGGGGATTATAA 1 110 1 TGGGGGATTA 0.965917 -13 ATGCTTATCCTGGAGTAGAGTAGAAAATGC 2 129 1 TGGAGTAGAG 0.842571 -119 AACATTCCCTTTTGGGATAAGGGGATAGGT 2 165 1 TTTGGGATAA 0.777119 -83 CCCCACTTTATGGAAGTGAAGTAATATAAA 3 81 0 TGGAAGTGAA 0.923721 -27 TTCCATAAAGTGGGGGATCAAA 3 96 1 TGGGGGATCA 0.976746 -12 GAAAAATATCTGGGAGAGAGA 4 81 1 TGGGAGAGAG 0.979562 -11 ********** Masking position 1 Map Score: 4.91444 Number of sites scoring better than the average of aligned sites = 1075 Number in coding regions = 974 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 119 Fraction of orfs with sites within 600 bp upstream = 0.0191134 Motif number 5 TCCCCCAAATGGAAGAGAAATCTTTGGGGT 1 97 0 GGAAGAGAAA 0.988574 -26 CCCTCTAAAAGGAAAGGAAGCGTTTTTCAT 2 101 1 GGAAAGGAAG 0.965139 -147 CCCACTTTATGGAAGTGAAGTAATATAAAA 3 80 0 GGAAGTGAAG 0.981471 -28 AGTTGGAAACAGAAGGGAGATTTTTAACCT 4 16 0 AGAAGGGAGA 0.965139 -76 AAAAATATCTGGGAGAGAGA 4 82 1 GGGAGAGAGA 0.976785 -10 ********** Masking position 4 Map Score: 2.62048 Number of sites scoring better than the average of aligned sites = 462 Number in coding regions = 432 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 6 AGCTTTTTCGGGAACGTTTATTAGTTCTTT 1 36 0 GGAACGTTTA 0.804843 -87 TTACTGTTTAAAAGCTTTTTCGGGAACGTT 1 48 0 AAAGCTTTTT 0.90047 -75 TAAGATCGTCGTTGGGTTTTTAACCCCAAA 1 75 1 GTTGGGTTTT 0.715197 -48 TTCAGGGTTTATAGCGGTTTTTAAAACCAT 2 61 1 ATAGCGGTTT 0.841724 -187 CTTTCCTTTTAGAGGGTTTTAAACTAATGG 2 87 0 AGAGGGTTTT 0.95971 -161 AAAAGGAAAGGAAGCGTTTTTCATGCTTAT 2 107 1 GAAGCGTTTT 0.976033 -141 GAATGTTGTCGGAGCATTTTCTACTCTACT 2 142 0 GGAGCATTTT 0.953725 -106 TTAATGTTTGAAAACTTTTTTTATATTACT 3 62 1 AAAACTTTTT 0.516815 -46 GAAACAGAAGGGAGATTTTTAACCTTAGGT 4 11 0 GGAGATTTTT 0.871055 -81 ********** Masking position 8 Map Score: 4.52612 Number of sites scoring better than the average of aligned sites = 544 Number in coding regions = 486 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 7 ********** No masking Map Score: 1.81432e-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: 1.81432e-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: 1.81432e-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