AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i156_HYP_operon_pyro_reg_100.orf -o156_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 RPH00379 122 Pyrococcus_OT3 #2 RPH00253 247 Pyrococcus_OT3 #3 RPH00235 107 Pyrococcus_OT3 #4 RPH00234 91 Pyrococcus_OT3 Motif number 1 CGATCTTACTGTTTAAAAGCTTTTTCGGGA 1 53 0 GTTTAAAAGC 0.950718 -70 AATCTTTGGGGTTAAAAACCCAACGACGAT 1 79 0 GTTAAAAACC 0.994258 -44 AACTAATGGTTTTAAAAACCGCTATAAACC 2 66 0 TTTAAAAACC 0.986655 -182 AAAACCATTAGTTTAAAACCCTCTAAAAGG 2 83 1 GTTTAAAACC 0.992437 -165 AAGGGGATAGGTTGAAAACTTTTGGTTTTA 2 183 1 GTTGAAAACT 0.976301 -65 TTTTAGACATTTTTAAAACCAAAAGTTTTC 2 196 0 TTTTAAAACC 0.982682 -52 CTACTTAATGTTTGAAAACTTTTTTTATAT 3 58 1 TTTGAAAACT 0.946181 -50 ACCTAAGGTTAAAAATCTCCCTTCTGT 4 8 1 GTTAAAAATC 0.944393 -84 AAAACCAAAAGTTGGAAACAGAAGGGAGAT 4 25 0 GTTGGAAACA 0.909465 -67 AACTTTTGGTTTTAGAAACCTATAAAGGTT 4 42 1 TTTAGAAACC 0.969503 -50 ********** Masking position 6 Map Score: 20.2058 Number of sites scoring better than the average of aligned sites = 94 Number in coding regions = 71 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 2 ATGCATCCCTTTAGGATGATTCCTT 1 6 1 TCCCTTTAGG 0.983851 -117 TTTAGGATGATTCCTTAAAGAACTAATAAA 1 20 1 TTCCTTAAAG 0.975327 -103 AAGATTTCTCTTCCATTTGGGGGATTATAA 1 103 1 TTCCATTTGG 0.973336 -20 AATAATTTTATCCGTTATAGGCCTGGAATT 2 33 1 TCCGTTATAG 0.956505 -215 AACGCTTCCTTTCCTTTTAGAGGGTTTTAA 2 95 0 TTCCTTTTAG 0.990266 -153 CCGACAACATTCCCTTTTGGGATAAGGGGA 2 160 1 TCCCTTTTGG 0.989872 -88 ATTACTTCACTTCCATAAAGTGGGGGATCA 3 86 1 TTCCATAAAG 0.935364 -22 TTTCCAACTTTTGGTTTTAGAAACCTATAA 4 37 1 TTGGTTTTAG 0.85626 -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 TTAAAGAACTAATAAACGTTCCCGAAAAAG 1 34 1 AATAAACGTT 0.921849 -89 TATTTTAATGAACAAAGGTGGTACAC 2 7 0 AACAAAGGTG 0.938938 -241 AGGGTTTTAAACTAATGGTTTTAAAAACCG 2 75 0 ACTAATGGTT 0.927864 -173 CATTTTTAAAACCAAAAGTTTTCAACCTAT 2 189 0 ACCAAAAGTT 0.983619 -59 TGCTCTGACTACTTAATGTTTGAAAACTTT 3 50 1 ACTTAATGTT 0.831692 -58 GAAGTAATATAAAAAAAGTTTTCAAACATT 3 64 0 AAAAAAAGTT 0.859112 -44 ACCTAAGGTTAAAAATCTCC 4 1 1 ACCTAAGGTT 0.97592 -91 GGTTTCTAAAACCAAAAGTTGGAAACAGAA 4 32 0 ACCAAAAGTT 0.983619 -60 TTTAGAAACCTATAAAGGTTCCAAATTCTG 4 52 1 TATAAAGGTT 0.867586 -40 ********** Masking position 5 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 CGTTGGGTTTTTAACCCCAAAGATTTCTCT 1 84 1 TTAACCCCAA 0.925534 -39 CCCCAAAGATTTCTCTTCCATTTGGGGGAT 1 98 1 TTCTCTTCCA 0.972953 -25 TTATAATCCCCCAAATGGAAGAG 1 110 0 TAATCCCCCA 0.96857 -13 GCATTTTCTACTCTACTCCAGGATAAGCAT 2 129 0 CTCTACTCCA 0.853365 -119 ACCTATCCCCTTATCCCAAAAGGGAATGTT 2 165 0 TTATCCCAAA 0.791289 -83 TTTATATTACTTCACTTCCATAAAGTGGGG 3 81 1 TTCACTTCCA 0.929416 -27 TTTGATCCCCCACTTTATGGAA 3 96 0 TGATCCCCCA 0.978575 -12 TCTCTCTCCCAGATATTTTTC 4 81 0 CTCTCTCCCA 0.981173 -11 ********** Masking position 10 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 0.98866 -26 CCCTCTAAAAGGAAAGGAAGCGTTTTTCAT 2 101 1 GGAAAGGAAG 0.965393 -147 CCCACTTTATGGAAGTGAAGTAATATAAAA 3 80 0 GGAAGTGAAG 0.981608 -28 AGTTGGAAACAGAAGGGAGATTTTTAACCT 4 16 0 AGAAGGGAGA 0.965393 -76 AAAAATATCTGGGAGAGAGA 4 82 1 GGGAGAGAGA 0.976957 -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 AAACGTTCCCGAAAAAGCTTTTAAACAGTA 1 47 1 GAAAAAGCTT 0.960242 -76 CCAAATGGAAGAGAAATCTTTGGGGTTAAA 1 93 0 GAGAAATCTT 0.887678 -30 CTATAACGGATAAAATTATTTTAATGAACA 2 23 0 TAAAATTATT 0.755736 -225 GAGTAGAGTAGAAAATGCTCCGACAACATT 2 141 1 GAAAATGCTC 0.858716 -107 GGGATAGGTTGAAAACTTTTGGTTTTAAAA 2 186 1 GAAAACTTTT 0.861571 -62 CTTTTGGTTTTAAAAATGTCTAAAAATATT 2 201 1 TAAAAATGTC 0.908237 -47 TAAAAATGTCTAAAAATATTGGTAAGCACT 2 211 1 TAAAAATATT 0.907569 -37 CTTAATGTTTGAAAACTTTTTTTATATTAC 3 61 1 GAAAACTTTT 0.861571 -47 ACCTAAGGTTAAAAATCTCCCTTCTGTTT 4 10 1 TAAAAATCTC 0.948977 -82 TTTAGAAACCTATAAAGGTTCCAAATTCTG 4 52 1 TATAAAGGTT 0.483026 -40 TCCAAATTCTGAAAAATATCTGGGAGAGAG 4 71 1 GAAAAATATC 0.932218 -21 ********** Masking position 5 Map Score: 8.18467 Number of sites scoring better than the average of aligned sites = 549 Number in coding regions = 409 Number in noncoding regions = 140 Number of orfs with sites within 600 bp upstream = 144 Fraction of orfs with sites within 600 bp upstream = 0.0231288 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