AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i017_Glycolysis___PPS_bbur_reg_300.orf -o017_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 Input sequences: #1 RBB00632 156 3615 #2 RBB00123 129 3615 #3 RBB00036 16 3615 #4 RBB00034 263 3615 Motif number 1 TACAAAATAATAATCACCCCTAAAAA 1 6 1 AATAATAATA 0.904036 -151 AAGTATAAATATTAACAAAGTTAATATCAAG 1 40 1 ATTAACAAAT 0.858938 -117 TATCAAGAATTAAAATAATAAAAATTGTTAA 1 64 1 TAAAATAATA 0.791656 -93 AAAAAAAACATTTAACAATTTTTATTATTTT 1 75 0 TTTAACAATT 0.920624 -82 TAAAACTTTTTTTAAAAAAAACATTTAACAA 1 88 0 TTTAAAAAAA 0.834236 -69 AGTTTTAAGCTATAATAAAATTGATTTAACA 1 112 1 TATAATAAAT 0.947683 -45 ATAAAATTGATTTAACAATATTAATAAGTTA 1 126 1 TTTAACAATT 0.920624 -31 AAAACTAGTATATAATAAGGAGA 2 3 0 TATAATAAGA 0.805602 -127 TAGTTTTGTTTATAAAAAAATGATATTTAAT 2 27 1 TATAAAAAAT 0.9038 -103 CAAAAAACATATTCATAAAGATTAGCAGACA 2 72 0 ATTCATAAAA 0.580391 -58 ATTTATTATATATCACAAAAAACATATTCAT 2 87 0 TATCACAAAA 0.914086 -43 TTTTGTGATATATAATAAATTGACCAGATTG 2 98 1 TATAATAAAT 0.947683 -32 ATCATAATAAAGAGGT 3 3 1 CATAATAAAA 0.762472 -14 TAAAACTGTTTAAAACAATTTGAAGCT 4 7 0 TAAAACAATT 0.834151 -257 GTTTTACACAAATAAAAAAGTTTAAAACAAT 4 32 1 AATAAAAAAT 0.816648 -232 TAAAAAAGTTTAAAACAATTAAGCTATAAAC 4 44 1 TAAAACAATA 0.859354 -220 CTACCCTTAAAATCAAAAACATACCATCATC 4 99 1 AATCAAAAAA 0.619324 -165 AGTGTAAAATTATAACAATAATTTTACACTA 4 182 1 TATAACAATA 0.969654 -82 AATTTTACACTATAACAATCAACCCATAACA 4 201 1 TATAACAATA 0.969654 -63 GTGCATAAGAATTAATAATGTTATGGGTTGA 4 219 0 ATTAATAATT 0.773726 -45 ********* * Masking position 5 Map Score: 25.1485 Number of sites scoring better than the average of aligned sites = 2372 Number in coding regions = 1394 Number in noncoding regions = 978 Number of orfs with sites within 600 bp upstream = 181 Fraction of orfs with sites within 600 bp upstream = 0.0290716 Motif number 2 TTTGTTAATATTTATACTTTACTTTTTAGG 1 29 0 TTTATACTTT 0.793473 -128 TAAAAAAAACATTTAACAATTTTTATTATT 1 77 0 ATTTAACAAT 0.818105 -80 TAAAAAAAGTTTTAAGCTATAATAAAATTG 1 105 1 TTTAAGCTAT 0.944389 -52 AATAAAATTGATTTAACAATATTAATAAGT 1 125 1 ATTTAACAAT 0.818105 -32 ATCATTTTTTTATAAACAAAACTAGTATAT 2 21 0 TATAAACAAA 0.594439 -109 TTCAAATTGTTTTAAACAGTTTTACACAAA 4 14 1 TTTAAACAGT 0.881279 -250 TTTAAACAGTTTTACACAAATAAAAAAGTT 4 24 1 TTTACACAAA 0.899457 -240 GCTTAATTGTTTTAAACTTTTTTATTTGTG 4 38 0 TTTAAACTTT 0.924001 -226 GTTTAAAACAATTAAGCTATAAACACGCTT 4 51 1 ATTAAGCTAT 0.857906 -213 TTGTTATAATTTTACACTATGTAAACAGCA 4 170 0 TTTACACTAT 0.97213 -94 TAACAATAATTTTACACTATAACAATCAAC 4 194 1 TTTACACTAT 0.97213 -70 ACTTTTTACTAAAGTATACTAT 4 252 0 TTTTTACTAA 0.661818 -12 ********** Masking position 3 Map Score: 10.3818 Number of sites scoring better than the average of aligned sites = 643 Number in coding regions = 392 Number in noncoding regions = 251 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 3 AAAGTAAAGTATAAATATTAACAAAGTTAA 1 34 1 ATAAATATTA 0.81739 -123 AAAGTTAATATCAAGAATTAAAATAATAAA 1 56 1 TCAAGAATTA 0.756951 -101 AATTAAAATAATAAAAATTGTTAAATGTTT 1 71 1 ATAAAAATTG 0.924295 -86 TTTTTTATAAACAAAACTAGTATATAATAA 2 16 0 ACAAAACTAG 0.791267 -114 AGATTAGCAGACAAAAATTAAGCTCAAATT 2 55 0 ACAAAAATTA 0.978393 -75 AAACATATTCATAAAGATTAGCAGACAAAA 2 69 0 ATAAAGATTA 0.869011 -61 AAACAGTTTTACACAAATAAAAAAGTTTAA 4 27 1 ACACAAATAA 0.810461 -237 CTTTCAATTAACAAAACTTACAAAATGCTG 4 145 1 ACAAAACTTA 0.951148 -119 GTGTAAAATTATAACAATAATTTTACACTA 4 183 1 ATAACAATAA 0.773497 -81 CTATAAGTGCATAAGAATTAATAATGTTAT 4 226 0 ATAAGAATTA 0.932793 -38 ********** Masking position 3 Map Score: 6.69343 Number of sites scoring better than the average of aligned sites = 1337 Number in coding regions = 853 Number in noncoding regions = 484 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 4 AATAATAATCACCCCTAAAAAGTAAAGTAT 1 16 1 ACCCCTAAAA 0.984883 -141 TTTAAAAAAAACATTTAACAATTTTTATTA 1 79 0 ACATTTAACA 0.908531 -78 ACAGTTTTACACAAATAAAAAAGTTTAAAA 4 29 1 ACAAATAAAA 0.781766 -235 CAATAAATCTACCCTTAAAATCAAAAACAT 4 91 1 ACCCTTAAAA 0.976809 -173 ACCATCATCCACCTCTCACAGCATCTTTCA 4 121 1 ACCTCTCACA 0.943264 -143 ATAACAATCAACCCATAACATTATTAATTC 4 212 1 ACCCATAACA 0.985126 -52 ********** Masking position 6 Map Score: 3.34954 Number of sites scoring better than the average of aligned sites = 101 Number in coding regions = 76 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 5 ACCCCTAAAAAGTAAAGTATAAATATTAAC 1 26 1 AGTAAAGTAT 0.986184 -131 AATATTAATAAGTTAAGTATTTAGG 1 142 1 AGTTAAGTAT 0.965817 -15 ACCAGATTGGACTAAATTCT 2 120 1 ACTAAATTCT 0.913304 -10 ACTTTTTACTAAAGTATACTATAAGTG 4 247 0 ACTAAAGTAT 0.986186 -17 ********** Masking position 5 Map Score: 1.42616 Number of sites scoring better than the average of aligned sites = 17 Number in coding regions = 10 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 6 ********** No masking Map Score: -1.01364e-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 7 ********** No masking Map Score: -1.01364e-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: -1.01364e-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