AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i294_mixed1_bbur_reg_300.orf -o294_borburg_300.ace -a/home/amcguire/genomes/ORF_borburg.txt -z/home/amcguire/genomes/borburg.fna -g0.28 -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 = 0.28 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: RBB00067 53 3615 RBB00551 17 3615 Input sequences: #1 RBB00672 83 3615 #2 RBB00671 73 3615 #3 RBB00612 34 3615 #4 RBB00610 214 3615 #5 RBB00759 18 3615 #6 RBB00609 56 3615 #7 RBB00602 37 3615 #8 RBB00601 162 3615 #9 RBB00185 199 3615 #10 RBB00102 89 3615 #11 RBB00071 51 3615 #12 RBB00070 73 3615 #13 RBB00068 158 3615 #14 RBB00862 79 3615 #15 RBB00061 179 3615 #16 RBB00863 63 3615 #17 RBB00059 23 3615 Motif number 1 TTTGCAAAATAAAATAATTTAATTGCT 1 6 1 AAATAAATAA 0.820696 -78 TATCACAAATACAATATTAATAATAAGGAATT 2 18 0 ACATATAATA 0.842466 -56 TCGACTTAAAATTATATCACAAATACAATATT 2 32 0 ATATATACAA 0.725681 -42 TATTAATAAAAAAATATTAAAAGCTAAATCAA 4 38 0 AAATATAAAA 0.983546 -177 TTATCAACAAATTATATTAATAAAAAAATATT 4 52 0 ATATATAATA 0.933013 -163 CTTTTATAAGAATATAATAAAACAATCCAATT 4 130 0 AAATAAAAAA 0.941803 -85 TACAAAATATAAGATAAAAAAAATTATAAAAC 6 29 0 AAATAAAAAA 0.941803 -28 ATCTTATATTATAATATTAAAAAGAAAATT 8 9 0 ATATATAAAA 0.968146 -154 AAATTAGGGCAAAATAACAATATTTCATTTAT 8 58 0 AAATAAAATA 0.881211 -105 AAATTGATAAATGATATAATTATATAAAGTGT 8 103 1 ATATATATTA 0.797605 -60 CATTTTAAACAATATATACAAACCCCCGTTAC 8 133 0 AAATATCAAA 0.826828 -30 ATTGTTATGCAAAAAATTAAAAGAATTTGTTG 9 51 0 AAAAATAAAA 0.941802 -149 ATTAAATTGTAATATATAATTAACAAGTTTGT 9 81 1 AAATATATTA 0.885684 -119 AGAAATTGCTATATTATTAAAAGTAAAAAATT 9 147 1 ATTTATAAAA 0.719962 -53 TATTAAAAGTAAAAAATTTAAAAAACATCAAC 9 161 1 AAAAATTAAA 0.74153 -39 TATTTAAAATACTATATAATTAATTATAATAA 10 29 1 ACATATATTA 0.601996 -61 TATATAATTAATTATAATAAAAAATATATGAA 10 41 1 ATATAAAAAA 0.891641 -49 TATAATAAAAAATATATGAATATTACATATTT 10 53 1 AAATATAATA 0.964793 -37 TTAATACCATAATAAATAAAAAGGATATTTA 11 10 0 AAAAATAAAA 0.941781 -42 CAATTTTATTAAAAGGTTTAACCT 12 3 1 ATTTATAAAA 0.719922 -71 TCACATTCATAAAATATCAAAAAC 13 3 0 AAATATAAAA 0.983548 -156 ATTATAAAATATCATATCAAAAAAACCAATAC 13 103 0 ATATATAAAA 0.96815 -56 TAAAATAAAAAAAATATTATAAAATATCATAT 13 118 0 AAATATATAA 0.944159 -41 CTAATTTGCTAAAATATTTAAAATAATTAAAA 14 12 0 AAATATTAAA 0.913767 -68 AAAGTTTTTCAAAAAATCAAAACTTTAAATCT 15 68 0 AAAAATAAAA 0.941803 -112 TTACTCTTCAAAAAAATAAAAACAAATATTTA 15 125 0 AAAAATAAAA 0.941797 -55 CCTTAACTATAAAAAATAAATATTTACTCTTC 15 148 0 AAAAATAATA 0.881199 -32 AATTATCTTAATAATATATATATTAACCAAG 16 10 0 ATATATTATA 0.711611 -54 ATATATTATTAAGATAATTTAATGTAGTTTAA 16 23 1 AAATAATTAA 0.447969 -41 ** **** **** Masking position 6 Map Score: 43.4888 Number of sites scoring better than the average of aligned sites = 2164 Number in coding regions = 1376 Number in noncoding regions = 788 Number of orfs with sites within 600 bp upstream = 156 Fraction of orfs with sites within 600 bp upstream = 0.0250562 Motif number 2 ATAATAAGGAATTATAAGAA 2 1 0 ATTATAAGAA 0.762314 -73 AAATACAATATTAATAATAAGGAATTATAA 2 14 0 TTAATAATAA 0.905971 -60 TCCAACTCTTTTAAAAATCATTCTT 4 6 0 TTAAAAATCA 0.827592 -209 ACAAATTATATTAATAAAAAAATATTAAAA 4 48 0 TTAATAAAAA 0.773422 -167 GATAATTTTATTAAAGAGAATTACGTTTAT 4 79 1 TTAAAGAGAA 0.848394 -136 GTCCACCTCATTAAAAATAAACGTAATTCT 4 95 0 TTAAAAATAA 0.967692 -120 TATCCCCCCTTTTATAAGAATATAATAAAA 4 140 0 TTTATAAGAA 0.889291 -75 GTTCCCCCTTAAAAAGAA 5 1 0 TTAAAAAGAA 0.973338 -18 AAAATATAAGATAAAAAAAATTATAAAACC 6 28 0 ATAAAAAAAA 0.8073 -29 TATTATAATATTAAAAAGAAAATT 8 5 0 TTAAAAAGAA 0.973338 -158 AAGATTTTATTTTAAAAGAATAATAAATGA 8 36 1 TTTAAAAGAA 0.960913 -127 TATGCAAAAAATTAAAAGAATTTGTTGTGA 9 48 0 ATTAAAAGAA 0.907535 -152 TAAACTTTTCATTAAAATAAGTTTGAAACA 9 115 0 ATTAAAATAA 0.889598 -85 TGCTATATTATTAAAAGTAAAAAATTTAAA 9 153 1 TTAAAAGTAA 0.705325 -47 AGTAAAAAATTTAAAAAACATCAACCCAAA 9 168 1 TTAAAAAACA 0.626957 -32 ATTTTACTTAAAAATAAGTATTTAAAA 10 8 1 TTAAAAATAA 0.967692 -82 AAAATAAGTATTTAAAATACTATATAATTA 10 21 1 TTTAAAATAC 0.617149 -69 TATATAATTAATTATAATAAAAAATATATG 10 41 1 ATTATAATAA 0.724747 -49 TATTTTTAAAATAAAAAAAATATTATAAAA 13 126 0 ATAAAAAAAA 0.8073 -33 TTTTTTTATTTTAAAAATAAAGGAGGTGTA 13 137 1 TTAAAAATAA 0.967692 -22 TGCTAAAATATTTAAAATAATTAAAAA 14 8 0 TTTAAAATAA 0.952786 -72 TCATTGAAATTTAATAAGAATGG 15 4 0 TTAATAAGAA 0.922628 -176 TCCTTAACTATAAAAAATAAATATTTACTC 15 151 0 TAAAAAATAA 0.617601 -29 TATATATATTATTAAGATAATTTAATGTAG 16 20 1 ATTAAGATAA 0.552608 -44 TTTAATGTAGTTTAAAAGTAGTTAGGAGAA 16 40 1 TTTAAAAGTA 0.590757 -24 ********** Masking position 4 Map Score: 36.2404 Number of sites scoring better than the average of aligned sites = 2066 Number in coding regions = 1337 Number in noncoding regions = 729 Number of orfs with sites within 600 bp upstream = 145 Fraction of orfs with sites within 600 bp upstream = 0.0232894 Motif number 3 TTATATTAATAAAAAAATATTAAAAGCTAAATCAATATCCAA 4 31 0 AAAATATAAT 0.838555 -184 AATTCTCTTTAATAAAATTATCAACAAATTATATTAATAAAA 4 59 0 AAAATAATTT 0.946303 -156 TATTCTTTTAAAATAAAATCTTATATTATAATATTAAAAAGA 8 16 0 AAAATAATAT 0.957314 -147 TTTTATTTTAAAAGAATAATAAATGAAATATTGTTATTTTGC 8 40 1 AAAAAAATAT 0.847778 -123 ATTTTTAGTCAAACAAGAAATTAGGGCAAAATAACAATATTT 8 65 0 AAAATAAAAT 0.970688 -98 TTTGACTAAAAATTGATAAATGATATAATTATATAAAGTGTA 8 94 1 AAGATAATTT 0.690873 -69 TTTAATTGTTATGCAAAAAATTAAAAGAATTTGTTGTGAAGT 9 45 0 ATAATAAATT 0.689907 -155 TTTGCATAACAATTAAATTGTAATATATAATTAACAAGTTTG 9 70 1 AAAATATAAT 0.840794 -130 AACTTATTTTAATGAAAAGTTTAGCAGAAATTGCTATATTAT 9 122 1 AAAATAAAAT 0.970585 -78 TTTTACTTAAAAATAAGTATTTAAAATACTATATAATTAATT 10 12 1 AAAATAACTT 0.842779 -78 TTATAAGGCTAAAAAACATTTTACATCATAATATCACATTCA 13 26 0 AAAATAATAT 0.957324 -133 ATATCATATCAAAAAAACCAATACAATATTTTATCTATTCTT 13 85 0 AAAAAAATTT 0.813995 -74 TTATTTTTAAAATAAAAAAAATATTATAAAATATCATATCAA 13 115 0 AAAAAAAAAT 0.891695 -44 TCAAAAACAATTTTTAACCTCAATCTAATTTGATTC 14 54 0 AAAATAAATT 0.962964 -26 ACAAAAGCACAATTAAACCCTCATTGAAATTTAATAAGAATG 15 12 0 AAAATAAATT 0.962964 -168 AAAAAATAAAAACAAATATTTAAGAACAAAATCACTCACATA 15 105 0 AAAATAAAAT 0.970684 -75 ** ** * * *** * Masking position 13 Map Score: 20.1261 Number of sites scoring better than the average of aligned sites = 594 Number in coding regions = 372 Number in noncoding regions = 222 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 4 AATGATTTTTAAAAGAGTTGGATATTGATTTA 4 14 1 AAAGAGTGGA 0.98878 -201 ATAATTTTATTAAAGAGAATTACGTTTATTTT 4 80 1 TAAGAGATTA 0.740875 -135 CGTTTATTTTTAATGAGGTGGACTTATTAATT 4 102 1 TAAGAGTGGA 0.975552 -113 CATGGTGAGTAAAAGAGAAGGACAATAGGAGG 4 188 1 AAAGAGAGGA 0.960779 -27 GAGAAGGACAATAGGAGGTTGAT 4 202 1 ATAGAGTTGA 0.919648 -13 CTTTTCATTAAAATAAGTTTGAAACAATACAA 9 109 0 AAAAAGTTGA 0.888568 -91 TCAACCCAAATAAGGAGCTTGA 9 188 1 TAAGAGTTGA 0.973534 -12 TAATAAATAAAAAGGATATTTA 11 1 0 AAAGATTTTA 0.667169 -51 TTTTAAAAATAAAGGAGGTGTATT 13 145 1 AAAGAGTGTA 0.961338 -14 AAGATGAATCAAATTAGATTGAGGTTAAAAAT 14 49 1 AAATAGTTGA 0.888568 -31 *** *** **** Masking position 6 Map Score: 8.28609 Number of sites scoring better than the average of aligned sites = 216 Number in coding regions = 147 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 5 ATATACCCTAAAATAATCCACATATAACTTAC 1 57 0 AAAAATCACA 0.829086 -27 TATTAATAATAAGGAATTATAAGAA 2 4 0 AAGAATATAA 0.790072 -70 TATTAATAAAAAAATATTAAAAGCTAAATCAA 4 38 0 AAATATAAAA 0.870578 -177 CTCTTTAATAAAATTATCAACAAATTATATTA 4 65 0 AAATATAACA 0.621629 -150 GAATATAATAAAACAATCCAATTAATAAGTCC 4 121 0 AAAAATCAAT 0.516972 -94 TATAAGATAAAAAAAATTATAAAACCTCCCCC 6 22 0 AAAAATATAA 0.936249 -35 ACAAAATACAAAATATAAGATA 6 45 0 ACAAATCAAA 0.613343 -12 TAAACTCTCCTAATATCGATTTT 7 25 0 AAATCTCTAA 0.444112 -13 TTTTATTTTAAAAGAATAATAAATGAAATATT 8 40 1 AAAAATATAA 0.936248 -123 TTGTTTGACTAAAAATTGATAAATGATATAAT 8 91 1 AAAATTATAA 0.7157 -72 AATAAAAACTGCTAAGCAAAATCAA 9 4 1 AAAACTCTAA 0.753438 -196 ATCAACGCTAAAACACTTCACAACAAATTCTT 9 31 1 AAAACTCACA 0.56663 -169 ATTGTTATGCAAAAAATTAAAAGAATTTGTTG 9 51 0 AAAAATAAAA 0.962587 -149 AATAAGTTTGAAACAATACAAACTTGTTAATT 9 98 0 AAAAATCAAA 0.952064 -102 ATTAAAAGTAAAAAATTTAAAAAACATCAACC 9 162 1 AAAATTAAAA 0.815164 -38 ACTTAAAAATAAGTATTTAAAATACTATATAA 10 16 1 AAGATTAAAA 0.530556 -74 AATACTATATAATTAATTATAATAAAAAATAT 10 36 1 AATAATATAA 0.625511 -54 TTACATATTTAAGGAATACTAAAAC 10 75 1 AAGAATCTAA 0.743938 -15 TTAATACCATAATAAATAAAAAGGATATTTA 11 10 0 AATAATAAAA 0.745306 -42 TCACATTCATAAAATATCAAAAAC 13 3 0 AAATATAAAA 0.870578 -156 TAAAATAAAAAAAATATTATAAAATATCATAT 13 118 0 AAATATATAA 0.793374 -41 AAAATATTTAAAATAATTAAAAA 14 2 0 AAAAATAAAA 0.962586 -78 AAAGTTTTTCAAAAAATCAAAACTTTAAATCT 15 68 0 AAAAATAAAA 0.962587 -112 TTACTCTTCAAAAAAATAAAAACAAATATTTA 15 125 0 AAAAATAAAA 0.962587 -55 CCTTAACTATAAAAAATAAATATTTACTCTTC 15 148 0 AAAAATAATA 0.612645 -32 *** *** **** Masking position 7 Map Score: 35.6565 Number of sites scoring better than the average of aligned sites = 2521 Number in coding regions = 1621 Number in noncoding regions = 900 Number of orfs with sites within 600 bp upstream = 132 Fraction of orfs with sites within 600 bp upstream = 0.0212014 Motif number 6 TTAAATTATTTTATTTTGCAAA 1 2 0 TTATTTTGCA 0.844134 -82 AGTTGGATATTGATTTAGCTTTTAATATTTT 4 29 1 TGATTTAGCT 0.953909 -186 TTTTATAATTTTTTTTATCTTATATTTTGTA 6 30 1 TTTTTTATCT 0.762434 -27 CTAATATCGATTTTTTAGCATCAAGCAA 7 8 0 TTTTTTAGCT 0.973499 -30 TGAAATATTGTTATTTTGCCCTAATTTCTTG 8 63 1 TTATTTTGCC 0.819885 -100 GTTTTAGCGTTGATTTTGCTTAGCAGTTTTT 9 14 0 TGATTTTGCT 0.933934 -186 TGTTGTGAAGTGTTTTAGCGTTGATTTTGCT 9 25 0 TGTTTTAGCT 0.968051 -175 AATTCTTTTAATTTTTTGCATAACAATTAAA 9 56 1 ATTTTTTGCT 0.779276 -144 ATGTAAAATGTTTTTTAGCCTTATAAAGGCA 13 42 1 TTTTTTAGCT 0.973499 -117 TTATTTTAAATATTTTAGCAAATTAGGTCAT 14 18 1 TATTTTAGCA 0.70674 -62 ********* * Masking position 6 Map Score: 7.46468 Number of sites scoring better than the average of aligned sites = 365 Number in coding regions = 254 Number in noncoding regions = 111 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 7 GCTATAGCAATTAAATTATTTTATTTTGCAAA 1 11 0 TAAATTATTT 0.601266 -73 TACAAGTATGATTAATTGCTATAGCAATTAAA 1 28 0 ATAATTGCTT 0.879829 -56 ATAATGTGCTCTTTATCAGCAA 3 1 1 AAATGTGCTT 0.562122 -34 TTTTATTAATATAATTTGTTGATAATTTTATT 4 59 1 AAATTTGTTA 0.588963 -156 GGGAGGTTTTATAATTTTTTTTATCTTATATT 6 24 1 AAATTTTTTT 0.705655 -33 ATAATAAATGAAATATTGTTATTTTGCCCTAA 8 55 1 AATATTGTTT 0.557625 -108 AAAAATTAAAAGAATTTGTTGTGAAGTGTTTT 9 40 0 AAATTTGTTT 0.939883 -160 TATATTACAATTTAATTGTTATGCAAAAAATT 9 65 0 TTAATTGTTT 0.821933 -135 AAAGTTTAGCAGAAATTGCTATATTATTAAAA 9 137 1 AAAATTGCTT 0.892738 -63 AAATATCCTTTTTATTTATTATGGTATTAAAA 11 12 1 TTATTTATTT 0.601322 -40 GATATTTTATAATATTTTTTTTATTTTAAAAA 13 122 1 ATATTTTTTT 0.679601 -37 TTTTTAATTATTTTAAATATTTTA 14 3 1 TTAATTATTT 0.570224 -77 GATTGAGGTTAAAAATTGTTTTTGA 14 65 1 AAAATTGTTT 0.932257 -15 TTTGTTCTTAAATATTTGTTTTTATTTTTTTG 15 117 1 ATATTTGTTT 0.932292 -63 ATAAAAAATAAATATTTACTCTTCAAAAAAAT 15 140 0 ATATTTACTT 0.705223 -40 * ******** * Masking position 7 Map Score: 6.71191 Number of sites scoring better than the average of aligned sites = 808 Number in coding regions = 517 Number in noncoding regions = 291 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 8 TATCAGCAAGGAGGAGTTTAT 3 24 1 GAGGAGTTTA 0.929671 -11 TCTTATAAAAGGGGGGATAATTTCCGCCGT 4 151 1 GGGGGGATAA 0.761698 -64 TATTTTTGGGGGAGGTTTTATAATTTTTTT 6 15 1 GGAGGTTTTA 0.902912 -42 ATCGATATTAGGAGAGTTTA 7 28 1 GGAGAGTTTA 0.952639 -10 TTATTTTAATGAAAAGTTTAGCAGAAATTG 9 125 1 GAAAAGTTTA 0.618605 -75 AATTTTATTAAAAGGTTTAACCTGTGCTAA 12 12 1 AAAGGTTTAA 0.523346 -62 AAATTTCAATGAGGGTTTAATTGTGCTTTT 15 22 1 GAGGGTTTAA 0.899476 -158 TTAAAAAGCTGAAGATTTAAAGTTTTGATT 15 56 1 GAAGATTTAA 0.920632 -124 TTATTTTTTTGAAGAGTAAATATTTATTTT 15 138 1 GAAGAGTAAA 0.79273 -42 TTATAGTTAAGGAGAGTTAATT 15 168 1 GGAGAGTTAA 0.967157 -12 ********** Masking position 10 Map Score: 4.36567 Number of sites scoring better than the average of aligned sites = 222 Number in coding regions = 161 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 9 ********** No masking Map Score: -7.01005e-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 10 ********** No masking Map Score: -7.01005e-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 11 ********** No masking Map Score: -7.01005e-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