AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i150_ATP_synthase_1_hpyl_reg_300.orf -o150_hpyl_300.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -g0.39 -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 = 0.39 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RHP00251 121 AE000511 #2 RHP00253 58 AE000511 #3 RHP00255 91 AE000511 #4 RHP00256 76 AE000511 #5 RHP00533 22 AE000511 #6 RHP00535 20 AE000511 #7 RHP00538 110 AE000511 #8 RHP00542 23 AE000511 #9 RHP00543 39 AE000511 #10 RHP00544 243 AE000511 Motif number 1 GACAAATCGTTAAAAAACTCGTTAAAAAGCTTGGTT 1 28 1 TAAAAAAGAA 0.90439 -94 CAATTAAGTTTTAAAAACTCATTAAACCAAGCTTTT 1 52 0 TTAAAAAAAA 0.987028 -70 TCTAAGCATGTTAAACTACCATTAAATTTTTTGTAA 2 23 1 TTAAACTAAA 0.897976 -36 ACATGCTAGCTAAAAAATCTAAATTATTGTAACAAA 3 14 0 TAAAAAAATA 0.795185 -78 ATGGATATTGTTAAAAAGTAAGCTAAGGAGTGTTT 3 67 1 TTAAAAAATA 0.929906 -25 CTAATTTTGATTAAATTGAAGCGATAAAAAAG 4 7 0 TTAAATTGAA 0.86511 -70 TTCAATTTAATCAAAATTAGATTACAATATTATAGT 4 23 1 TCAAAATAAA 0.898968 -54 TATTTAAGCTTTAAATAACTATAATATTGTAATCTA 4 40 0 TTAAATAAAA 0.953438 -37 AAAAAATCGCTTAAAATTTGAGAATATTCAAGCG 7 9 0 TTAAAATAAA 0.981072 -102 TATTTCTTTCCTAAAATCCTACAAAATATTTGAAAC 7 81 0 CTAAAATAAA 0.875507 -30 TTGAATTAAAAACAAGGAATAAC 8 6 1 TTAAAAAGAA 0.97 -18 AAAAACTACATTATAAATAAAAAAAATGAAGAAATT 10 71 0 TTATAAAAAA 0.929931 -173 CAACAAAAAATAAAAAAGGCAAAAAATACCCTTCGC 10 109 0 TAAAAAAAAA 0.957231 -135 AATAGGGATTTTAAATACAAACAACAAAAAATAAAA 10 130 0 TTAAATAAAA 0.957226 -114 TTTTTATATTTTATAATAGAATGAGATCAATTTAAC 10 197 0 TTATAATAAA 0.899952 -47 ******* * * * Masking position 5 Map Score: 18.3895 Number of sites scoring better than the average of aligned sites = 674 Number in coding regions = 478 Number in noncoding regions = 196 Number of orfs with sites within 600 bp upstream = 171 Fraction of orfs with sites within 600 bp upstream = 0.0274655 Motif number 2 TTTTTAGCCTTACAAAAAATTTAATGGTAG 2 38 0 TACAAAAAAT 0.984419 -21 TAACATGCTAGCTAAAAAATCTAAATTATT 3 22 0 GCTAAAAAAT 0.880448 -70 AAATTGAAGCGATAAAAAAG 4 1 0 GATAAAAAAG 0.867961 -76 ACTCTATCTTAACAAAAAATCGCTTAAAAT 7 28 0 AACAAAAAAT 0.964895 -83 TTAATGTTTTTATAACAAATGCGAGTTTCA 7 57 1 TATAACAAAT 0.870239 -54 CCTAAAATCCTACAAAATATTTGAAACTCG 7 78 0 TACAAAATAT 0.898889 -33 ACATTATAAATAAAAAAAATGAAGAAATTG 10 70 0 TAAAAAAAAT 0.907186 -174 AAATAAAAAAGGCAAAAAATACCCTTCGCA 10 108 0 GGCAAAAAAT 0.935356 -136 AAATACAAACAACAAAAAATAAAAAAGGCA 10 124 0 AACAAAAAAT 0.964895 -120 TATTATAAAATATAAAAAATCAAATCTTAA 10 215 1 TATAAAAAAT 0.969841 -29 ********** Masking position 5 Map Score: 11.7557 Number of sites scoring better than the average of aligned sites = 297 Number in coding regions = 248 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 3 TTTCAATAAGGCTTAGAGAAACTTTTTC 1 104 1 GCTTAGAGAA 0.974602 -18 AGTTTAACATGCTTAGAGATAAAACGAGC 2 10 0 GCTTAGAGAT 0.98879 -49 ATTCATTAAGGCATGGATATTGTTAAAAAG 3 55 1 GCATGGATAT 0.905406 -37 GTTATTTAAAGCTTAAATAAGGGTCTAGCG 4 57 1 GCTTAAATAA 0.899958 -20 CGCTTGAATATTCTCAAATTT 7 2 1 GCTTGAATAT 0.957123 -109 TTTGTGGTGTGCTTTGAGATGATATTGTGA 9 13 1 GCTTTGAGAT 0.984015 -27 GATTTTCCTTTAAGATTTGATTTTTT 10 228 0 CCTTTAAGAT 0.851412 -16 ********** Masking position 7 Map Score: 6.30798 Number of sites scoring better than the average of aligned sites = 129 Number in coding regions = 114 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 4 AAAACAAGACAAATCGTTAAAAAACTCGTT 1 21 1 AAATCGTTAA 0.943114 -101 ATCGTTAAAAAACTCGTTAAAAAGCTTGGT 1 33 1 AACTCGTTAA 0.980027 -89 AAGTTTTAAAAACTCATTAAACCAAGCTTT 1 53 0 AACTCATTAA 0.978473 -69 CTTATTGAAAATTTCCTTAATTGTAGCAAT 1 84 0 ATTTCCTTAA 0.898387 -38 GCATGTTAGCAATTCATTAAGGCATGGATA 3 44 1 AATTCATTAA 0.938871 -48 AAACACTCCTTAGCTTACTTTTT 3 79 0 CACTCCTTAG 0.914893 -13 TATTTATCTCCTTAGATTGA 6 6 0 ATCTCCTTAG 0.936775 -15 ATTTGTTATAAAAACATTAACTCTATCTTA 7 47 0 AAAACATTAA 0.733505 -64 ********** Masking position 9 Map Score: 5.81669 Number of sites scoring better than the average of aligned sites = 392 Number in coding regions = 330 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 5 AAACTCGTTAAAAAGCTTGGTTTAATGAGT 1 42 1 AAAAGCTTGG 0.877552 -80 AATGAGTTTTTAAAACTTAATTGCTACAAT 1 65 1 TAAAACTTAA 0.913382 -57 AAATTTTCAATAAGGCTTAGAGAAACTTTT 1 100 1 TAAGGCTTAG 0.96758 -22 AAATTTTTTGTAAGGCTAAAAAC 2 46 1 TAAGGCTAAA 0.827877 -13 AGCAATTCATTAAGGCATGGATATTGTTAA 3 51 1 TAAGGCATGG 0.90259 -41 TATAGTTATTTAAAGCTTAAATAAGGGTCT 4 53 1 TAAAGCTTAA 0.910707 -24 AAAAATCGCTTAAAATTTGAGAATATTCAA 7 14 0 TAAAATTTGA 0.818959 -97 TATGGTTCTCTAAAACTTGTGCTTTTGGGA 10 13 1 TAAAACTTGT 0.852494 -231 GATTTTCCTTTAAGATTTGATTTTTTATAT 10 224 0 TAAGATTTGA 0.857174 -20 ********** Masking position 3 Map Score: 5.15485 Number of sites scoring better than the average of aligned sites = 860 Number in coding regions = 762 Number in noncoding regions = 98 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 6 GCCTTATTGAAAATTTCCTTAATTGTAGCAA 1 85 0 AAATTTCTTA 0.854262 -37 CTAGCTAAAAAATCTAAATTATTGTAACAAA 3 14 0 AATCTAATTA 0.955926 -78 AATTTAATCAAAATTAGATTACAATATTATA 4 26 1 AAATTAATTA 0.958663 -51 AAATTATATTAATCAAGGAGC 5 1 1 AAATTAATTA 0.958663 -22 AAAAACATTAACTCTATCTTAACAAAAAATC 7 37 0 ACTCTACTTA 0.889675 -74 CTTCGCATAAAAACTACATTATAAATAAAAA 10 84 0 AAACTAATTA 0.965797 -160 GAATGAGATCAATTTAACTTAAGCAGGTTTT 10 184 0 AATTTACTTA 0.955926 -60 ****** **** Masking position 1 Map Score: 5.36945 Number of sites scoring better than the average of aligned sites = 60 Number in coding regions = 38 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 7 ********** No masking Map Score: -3.31523e-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: -3.31523e-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 9 ********** No masking Map Score: -3.31523e-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