AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i210_trans4_hpyl_reg_300.orf -o210_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 RHP00445 140 AE000511 #2 RHP00454 53 AE000511 #3 RHP00455 72 AE000511 #4 RHP00458 63 AE000511 #5 RHP00461 148 AE000511 #6 RHP00489 66 AE000511 #7 RHP00612 35 AE000511 #8 RHP00614 48 AE000511 #9 RHP00615 119 AE000511 #10 RHP00809 24 AE000511 #11 RHP00810 101 AE000511 #12 RHP00892 153 AE000511 #13 RHP00893 226 AE000511 #14 RHP00894 101 AE000511 Motif number 1 GTATAATGCTAGTTTTAAAAATGAAAGGGT 2 12 1 AGTTTTAAAA 0.96993 -42 TCAACAATAGGGGTTTAAAAT 2 43 1 GGGTTTAAAA 0.975499 -11 CTTGGAGTTAAGGTTTAAAATTTTAGCGTT 4 19 1 AGGTTTAAAA 0.972216 -45 CAATGCCACTATATTTAACACTTAGGATTT 5 14 0 ATATTTAACA 0.535362 -135 ATTGAAAGAAACTTTTAACAAACAATTCAA 5 115 1 ACTTTTAACA 0.877796 -34 AAATGGCATGGGTTTTAGCAAGGA 6 53 1 GGTTTTAGCA 0.969008 -14 AGGCGGGTTTTAGCAACGACTTTGG 7 6 1 GGTTTTAGCA 0.969008 -30 TCTTAGGGGCAGATTTAAAAA 9 2 0 AGATTTAAAA 0.888932 -118 GCGGTCATCTGGGTTTAAAAACAACCACAT 9 88 1 GGGTTTAAAA 0.975499 -32 TAAGGGTTTTAGTTTTAGCATGTTAGCATT 11 39 0 AGTTTTAGCA 0.964887 -63 GATTAAAAAAAGTTTTAGCATT 12 3 0 AGTTTTAGCA 0.964887 -151 TAATAACCTTAGGTTTAAAACTTGACTAAA 12 99 1 AGGTTTAAAA 0.972216 -55 ACTTGACTAAATTTTTAGAAAAAAGTAAAT 12 118 1 ATTTTTAGAA 0.753431 -36 TGCTCTTAAGGATTTTAAAAAAGTAGTTTT 13 132 1 GATTTTAAAA 0.822813 -95 TTAAAAAAGTAGTTTTATCAAAAATTTAGC 13 146 1 AGTTTTATCA 0.809564 -81 CCTTTTTTGAGAGTTTAAAATAAGCGTTAT 13 190 0 GAGTTTAAAA 0.83437 -37 GGGATATGGCGCGTTTAAAAGAAATTTTAT 14 23 0 GCGTTTAAAA 0.886263 -79 ********** Masking position 5 Map Score: 27.3435 Number of sites scoring better than the average of aligned sites = 595 Number in coding regions = 506 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 2 AATCTAAAATCAATGCCTTAATCTGGTAGGTG 1 10 1 TAATCCTTAT 0.749561 -131 TTTATATTATAATAAGCCTAAAAAGACAAACCA 1 41 0 ATAACCTAAA 0.923641 -100 CGTATGATACAAAAAAGCTTATTTTACGCTATA 1 81 1 AAAAGCTTAT 0.910946 -60 ATTTTAAACCCCTATTGTTGATACCC 2 38 0 TAAACCCTAT 0.688857 -16 ATTCCAAAAAATAAACCCTAATTCAGGA 3 6 0 AAAACCTAAT 0.960522 -67 AATTAAAACGACTAACGCTAAAATTTTAAACCT 4 29 0 ATAAGCTAAA 0.84941 -35 TAAAAATCCTAAGTGTTAAATATA 5 2 1 AAAACCTAAT 0.960522 -147 TAAAATCTATATTATAACTAAAAGGGGGTTTT 6 10 0 ATATACTAAA 0.350415 -57 TGATTAATCCTTAGTCTTTTGTCT 10 10 0 ATAACCTTAT 0.897994 -15 ACAAATTCCTTAAAAAGAGTGGTG 11 2 1 CAATCCTTAA 0.794796 -100 ATGCTAAAACTAAAACCCTTATAAGTTATGGAT 11 48 1 TAAACCTTAA 0.942793 -54 TAAGTTATGGATAAAAACTTAAAGAATAGGGTA 11 69 1 AAAAACTTAA 0.846171 -33 TTGGTATTTTCTTAATCCTAAAACAAATTTAAG 12 42 1 CTAACCTAAA 0.827306 -112 ATTCTATTTAATAATACCTTAAATTTGTTTTAG 12 59 0 AAATCCTTAA 0.935177 -95 AAAAGTAAATAAAAAGGCTAAAAGAA 12 138 1 AAAAGCTAAA 0.921645 -16 AAATTCAAAAAGAAATCCTAAGATTCCTTTCAT 13 12 0 AAAACCTAAA 0.974127 -215 AACAAACATGAAAAAGCCCTATAGAAACCGCCA 13 55 1 AAAACCCTAA 0.913159 -172 ACTACTTTTTTAAAATCCTTAAGAGCATCTTAA 13 126 0 TAAACCTTAG 0.739946 -101 TTTAGTTTAAAATAACGCTTATTTTAAACTCTC 13 179 1 ATAAGCTTAT 0.736511 -48 * *** ***** * Masking position 4 Map Score: 19.9105 Number of sites scoring better than the average of aligned sites = 1454 Number in coding regions = 1242 Number in noncoding regions = 212 Number of orfs with sites within 600 bp upstream = 166 Fraction of orfs with sites within 600 bp upstream = 0.0266624 Motif number 3 AATAAGCCTAAAAAGACAAACCACCTACCAGA 1 32 0 AAAAAAAACC 0.63671 -109 TATTATAATATAAAGTTTAAGCGTATGATACA 1 60 1 TAAATTAAGC 0.810682 -81 TGCTAGTTTTAAAAATGAAAGGGTATCAACAA 2 18 1 AAAATAAAGG 0.935492 -36 TGAAAGGGTATCAACAATAGGGGTTTAAAAT 2 33 1 TCAAATAGGG 0.859177 -21 ATCCAATTCCAAAAAATAAACCCTAATTCAGG 3 12 0 AAAAAAAACC 0.63671 -61 GTTAAGGTTTAAAATTTTAGCGTTAGTCGTTT 4 25 1 AAAATTAGCG 0.882293 -39 ATAACCCCCTAAAATTAAAACGACTAACGCTA 4 42 0 AAAATAAACG 0.88044 -22 CTTTTAACAAACAATTCAAGGGATTTGGCGAT 5 126 1 ACAATAAGGG 0.883307 -23 ATCTATATTATAACTAAAAGGGGGTTTT 6 7 0 TAACAAAGGG 0.724343 -60 TGGTTTGTCTTAAACTTTAACCT 8 2 0 TAAATTAACC 0.684983 -47 CAACAAACCTACACTAATAAGGCTAGGAGGAT 9 34 0 ACACATAAGG 0.758251 -86 AGACAAAAGACTAAGGATTAATCA 10 5 1 AAAAATAAGG 0.935492 -20 TTTTTATCCATAACTTATAAGGGTTTTAGTTT 11 54 0 TAACTTAAGG 0.831367 -48 GATAAAAACTTAAAGAATAGGGTAAAATAAAC 11 78 1 TAAAATAGGG 0.90557 -24 TAATCCTAAAACAAATTTAAGGTATTATTAAA 12 54 1 ACAATTAAGG 0.919658 -100 TAGAAAAAAGTAAATAAAAAGGCTAAAAGAA 12 133 1 TAAAAAAAGG 0.904043 -21 TAGTTTTATCAAAAATTTAGCGGGTTTAGTTT 13 155 1 AAAATTAGCG 0.882293 -72 CGACAGAACATCAATTTAAAGGAACTTAAGA 14 81 1 TCAATAAAGG 0.881467 -21 **** * ***** Masking position 9 Map Score: 17.6637 Number of sites scoring better than the average of aligned sites = 1340 Number in coding regions = 1101 Number in noncoding regions = 239 Number of orfs with sites within 600 bp upstream = 197 Fraction of orfs with sites within 600 bp upstream = 0.0316415 Motif number 4 AATCTAAAATCAATGCCTTAATCTG 1 5 1 TAAAACAATG 0.748814 -136 CATTATAGCGTAAAATAAGCTTTTTTGTATC 1 86 0 TAAAAAAGCT 0.952007 -55 CTAAAATAATTAAAATGACCGGTTAAAATGG 5 80 0 TAAAAGACCG 0.832564 -69 TTAGTATAATTGAAAGAAACTTTTAACAAAC 5 107 1 TGAAAAAACT 0.699823 -42 CATTTTTAGCTAAAATAAAATCTATATTATA 6 27 0 TAAAAAAAAT 0.657215 -40 TATGCGCATGTAAAAGTAGCGGTCATCTGGG 9 70 1 TAAAATAGCG 0.883966 -50 ACAAATTCCTTAAAAAGAGTGGTGGCTGAAT 11 11 1 TAAAAGAGTG 0.880418 -91 AAGAATAGGGTAAAATAAACGC 11 90 1 TAAAAAAACG 0.953319 -12 AAAATGTGATTAAAAAAAGTTTTAGCATT 12 9 0 TAAAAAAGTT 0.925336 -145 TTCTTAATCCTAAAACAAATTTAAGGTATTA 12 50 1 TAAAAAAATT 0.902297 -104 AAATTTTTGATAAAACTACTTTTTTAAAATC 13 142 0 TAAAATACTT 0.592454 -85 TTTGAGAGTTTAAAATAAGCGTTATTTTAAA 13 184 0 TAAAAAAGCG 0.964796 -43 ATGGCGCGTTTAAAAGAAATTTTATTATAGC 14 17 0 TAAAAAAATT 0.902297 -85 ***** ***** Masking position 5 Map Score: 11.5235 Number of sites scoring better than the average of aligned sites = 571 Number in coding regions = 493 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 5 ATCTGGTAGGTGGTTTGTCTTTTTAGGCTTATT 1 31 1 TGTTGTCTTT 0.749494 -110 TTTTGGAATTGGATTTAGCGCTTATCTCTTTAG 3 30 1 GGTTAGCGTT 0.976733 -43 ACAATTCAAGGGATTTGGCGATT 5 136 1 GGTTGGCGTT 0.991324 -13 TTTTAGCAACGACTTTGGCTATTTTTCC 7 18 1 GATTGGCTTT 0.946661 -18 ACAAACCAAAGAGTTTGTCTTGTTTGTTTTTGA 8 26 1 GATTGTCTGT 0.757881 -23 TTTTTCCATAGAGTTTGGCGGTTTCTATAGGGC 13 70 0 GATTGGCGTT 0.986235 -157 GTTTTATCAAAAATTTAGCGGGTTTAGTTTAAA 13 157 1 AATTAGCGGT 0.708553 -70 AAAGAAATTTTATTATAGCGAATTT 14 3 0 TATTAGCGAT 0.668129 -99 GTTTTGTGGGGGATATGGCGCGTTTAAAAGAAA 14 29 0 GGTTGGCGGT 0.987857 -73 TTTTCTATCATTCTCTAGCGTTTTGTGGGGGAT 14 48 0 TTTTAGCGTT 0.734853 -54 TTTAAATTGATGTTCTGTCGTTTTCTATCATTC 14 68 0 TGTTGTCGTT 0.923539 -34 ** * ***** ** Masking position 6 Map Score: 8.9887 Number of sites scoring better than the average of aligned sites = 611 Number in coding regions = 575 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 6 GTTGATACCCTTTCATTTTTAAAACTAGCA 2 18 0 TTTCATTTTT 0.82434 -36 CATTGTAGCATGACTTTATTAGGGTGGGTA 5 39 1 TGACTTTATT 0.622247 -110 AAAAATTTTACTCCATTTTAACCGGTCATT 5 68 1 CTCCATTTTA 0.68901 -81 CTAAAACCCATGCCATTTTTAGCTAAAATA 6 41 0 TGCCATTTTT 0.889099 -26 CTTTTTTTAATCACATTTTTCTTGGTATTT 12 21 1 TCACATTTTT 0.859518 -133 AAGGTTATTATTACATTATTCTATTTAATA 12 79 0 TTACATTATT 0.866621 -75 TAAAACTTGACTAAATTTTTAGAAAAAAGT 12 114 1 CTAAATTTTT 0.790479 -40 GCCTTTTTATTTACTTTTTTCTAAAAATTT 12 126 0 TTACTTTTTT 0.939172 -28 TTTGATAAAACTACTTTTTTAAAATCCTTA 13 138 0 CTACTTTTTT 0.93523 -89 ACTAAACCCGCTAAATTTTTGATAAAACTA 13 155 0 CTAAATTTTT 0.790479 -72 GTGCGTTTGATTCCTTTTTTGAGAGTTTAA 13 202 0 TTCCTTTTTT 0.916619 -25 ********** Masking position 6 Map Score: 5.56208 Number of sites scoring better than the average of aligned sites = 557 Number in coding regions = 452 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 7 AGGTGGTTTGTCTTTTTAGGCTTATTATAA 1 38 1 TCTTTTTAGG 0.971473 -103 AATTAGGGTTTATTTTTTGGAATTGGATTT 3 16 1 TATTTTTTGG 0.798715 -57 TTAGCGCTTATCTCTTTAGGCGAGGGGGTC 3 44 1 TCTCTTTAGG 0.960392 -29 TTAGTCGTTTTAATTTTAGGGGGTTAT 4 47 1 TAATTTTAGG 0.936681 -17 GCTAGGAGGATTTTCTTAGGGGCAGATTTA 9 15 0 TTTTCTTAGG 0.9391 -105 CAGCCACCACTCTTTTTAAGGAATTTGT 11 9 0 TCTTTTTAAG 0.748446 -93 TACCTTAAATTTGTTTTAGGATTAAGAAAA 12 48 0 TTGTTTTAGG 0.86952 -106 AATGTAATAATAACCTTAGGTTTAAAACTT 12 92 1 TAACCTTAGG 0.882343 -62 AATGAAAGGAATCTTAGGATTTCTTTTT 13 9 1 GAATCTTAGG 0.687164 -218 AGTTTGGCGGTTTCTATAGGGCTTTTTCAT 13 62 0 TTTCTATAGG 0.684519 -165 ********** Masking position 7 Map Score: 4.28993 Number of sites scoring better than the average of aligned sites = 530 Number in coding regions = 470 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 8 AAGCCTAAAAAGACAAACCACCTACCAGAT 1 31 0 AGACAAACCA 0.970871 -110 CAATTCCAAAAAATAAACCCTAATTCAGGA 3 11 0 AAATAAACCC 0.84494 -62 AAGAAACTTTTAACAAACAATTCAAGGGAT 5 120 1 TAACAAACAA 0.88511 -29 TTAAAGTTTAAGACAAACCAAAGAGTTTGT 8 14 1 AGACAAACCA 0.970871 -35 TCAAAAACAAACAAGACAAACTCT 8 35 0 AAACAAACAA 0.973759 -14 CGCATAAGTTCAACAAACCTACACTAATAA 9 46 0 CAACAAACCT 0.906602 -74 CTGGGTTTAAAAACAACCACATTGCAGGAA 9 96 1 AAACAACCAC 0.890963 -24 TTGAACATGGAAACAAACATGAAAAAGCCC 13 44 1 AAACAAACAT 0.952127 -183 ********** Masking position 5 Map Score: 5.1628 Number of sites scoring better than the average of aligned sites = 230 Number in coding regions = 183 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 9 AAGTTTAAGCGTATGATACAAAAAAGCTTA 1 72 1 GTATGATACA 0.809732 -69 AATAAAGTTCGCATTATAGCGTAAAATAAG 1 98 0 GCATTATAGC 0.980625 -43 TTTAAAACTAGCATTATACA 2 1 0 GCATTATACA 0.912506 -53 AAATATAGTGGCATTGTAGCATGACTTTAT 5 28 1 GCATTGTAGC 0.949139 -121 TTTAGTTTTAGCATGTTAGCATTCAGCCAC 11 32 0 GCATGTTAGC 0.938303 -70 AAAAGAAATTTTATTATAGCGAATTT 14 7 0 TTATTATAGC 0.691109 -95 AAACGCTAGAGAATGATAGAAAACGACAGA 14 58 1 GAATGATAGA 0.85118 -44 ********** Masking position 3 Map Score: 0.473319 Number of sites scoring better than the average of aligned sites = 303 Number in coding regions = 268 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 10 ********** No masking Map Score: -1.97998e-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 11 ********** No masking Map Score: -1.97998e-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 12 ********** No masking Map Score: -1.97998e-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