AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i224_Holliday_Junction_enzyme_bbur_reg_300.orf -o224_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 RBB00708 44 3615 #2 RBB00707 79 3615 #3 RBB00551 17 3615 #4 RBB00524 163 3615 #5 RBB00511 49 3615 #6 RBB00462 198 3615 #7 RBB00392 26 3615 Motif number 1 TTTTTATAGTTATAAAATAGTTTTTAAGGA 1 19 1 TATAAAATAG 0.717504 -26 TTAAATTATAAATTATATTACACAGAAACA 2 56 0 AATTATATTA 0.640259 -24 ATAATTAAATTATAAATTATAT 2 68 0 AATTAAATTA 0.893852 -12 AGTTAATTAAATTTAAAACATTAG 4 5 1 AATTAAATTT 0.882004 -159 GCTTTTTAATAATTAAATAGCGTTTAATTG 4 35 1 AATTAAATAG 0.930963 -129 AGACCATAAAAAAAATATTTTACGCAATTA 4 59 0 AAAAATATTT 0.738398 -105 AAGAATATAAAATAATAAAAAGACCATAAA 4 79 0 AATAATAAAA 0.864563 -85 AATATAATTCAATTAAAAAGAAAGAATATA 4 100 0 AATTAAAAAG 0.910669 -64 TTTTTAATTGAATTATATTTATTTTATAAT 4 111 1 AATTATATTT 0.541776 -53 TTACAATTGATATTATAAAATAAATATAAT 4 122 0 TATTATAAAA 0.653763 -42 AATAATATTGAATTACAATTGATATTATAA 4 134 0 AATTACAATT 0.743576 -30 ATGCTTCCTAAATAATATTGAATTACAATT 4 144 0 AATAATATTG 0.953358 -20 AACACTTAGCAAAAATAATGTCAACA 5 7 0 AAAAATAATG 0.793134 -43 TTATAAATATATTATGACATTTTA 6 5 1 AAATATATTA 0.532807 -194 ACAAATATAAAATTAAAATGTCATAATATA 6 18 0 AATTAAAATG 0.927419 -181 AATTGTTTAAAAAAACAAATATAAAATTAA 6 32 0 AAAAACAAAT 0.492055 -167 AATAATAAATTATTAAATTGTTTAAAAAAA 6 47 0 TATTAAATTG 0.815599 -152 GGTTATTTTTAATAATAAATTATTAAATTG 6 57 0 AATAATAAAT 0.891461 -142 TTTTCTTAAAAATAACAAAAGCAATTTATC 6 94 0 AATAACAAAA 0.747121 -105 TACGATAGATTATAATATTTTTTCTTAAAA 6 113 0 TATAATATTT 0.757088 -86 TATCCCAAATAATTATATATA 7 2 0 AATTATATAT 0.891487 -25 ********** Masking position 5 Map Score: 24.6282 Number of sites scoring better than the average of aligned sites = 3603 Number in coding regions = 2221 Number in noncoding regions = 1382 Number of orfs with sites within 600 bp upstream = 241 Fraction of orfs with sites within 600 bp upstream = 0.0387086 Motif number 2 TTTTATAACTATAAAAAACTAATAA 1 6 0 ATAAAAAACT 0.89891 -39 TTAAAAACTATTTTATAACTATAAAAAACT 1 16 0 TTTTATAACT 0.496246 -29 AAATATTCCTTAAAAACTATTTTATAAC 1 27 0 CTTAAAAACT 0.839013 -18 ACATTCAACAATTTAAAGCAAAAGCCTTAA 2 29 0 ATTTAAAGCA 0.74929 -51 GTGTAATATAATTTATAATTTAATTAT 2 63 1 ATTTATAATT 0.835192 -17 AGTTAATTAAATTTAAAACATTAGGCTTTT 4 11 1 ATTTAAAACA 0.95924 -153 TAAAAAGACCATAAAAAAAATATTTTACGC 4 64 0 ATAAAAAAAA 0.692087 -100 AAAAGAAAGAATATAAAATAATAAAAAGAC 4 85 0 ATATAAAATA 0.953148 -79 ATATAATTCAATTAAAAAGAAAGAATATAA 4 99 0 ATTAAAAAGA 0.80926 -65 ACAATTGATATTATAAAATAAATATAATTC 4 120 0 TTATAAAATA 0.80602 -44 ATGCTTCCTAAATAATATTGAATTACA 4 147 0 CTAAATAATA 0.720182 -17 AAAAAAACAAATATAAAATTAAAATGTCAT 6 24 0 ATATAAAATT 0.925653 -175 ATAATTTATTATTAAAAATAACCCGAAAAG 6 64 1 ATTAAAAATA 0.953148 -135 AATATTTTTTCTTAAAAATAACAAAAGCAA 6 100 0 CTTAAAAATA 0.903496 -99 TCTTGCCATAATTTAAAATAACTACTACGA 6 138 0 ATTTAAAATA 0.962784 -61 TATATATAATTATTTGGGATA 7 2 1 ATATATAATT 0.81317 -25 ********** Masking position 5 Map Score: 18.467 Number of sites scoring better than the average of aligned sites = 2713 Number in coding regions = 1718 Number in noncoding regions = 995 Number of orfs with sites within 600 bp upstream = 185 Fraction of orfs with sites within 600 bp upstream = 0.0297141 Motif number 3 AATTTAAAGCAAAAGCCTTAAGTAAAAAAA 2 20 0 AAAAGCCTTA 0.908052 -60 ATTGTTAAGAGGTTAAG 3 7 1 AAGAGGTTAA 0.970906 -11 TTAATTATTAAAAAGCCTAATGTTTTAAAT 4 21 0 AAAAGCCTAA 0.955522 -143 AAATAATAAAAAGACCATAAAAAAAATATT 4 70 0 AAGACCATAA 0.846239 -94 AAACCTTAAGTCAAGGTTAACACTTAGCAA 5 25 0 TCAAGGTTAA 0.754435 -25 AAACTAAACCTTAAGTCAAGGTTA 5 36 0 TAAACCTTAA 0.696391 -14 AAATAACCCGAAAAGGATAAATTGCTTTTG 6 79 1 AAAAGGATAA 0.918776 -120 AAATTATGGCAAGAGGTTTGTTAGAGCTTT 6 154 1 AAGAGGTTTG 0.895499 -45 AGAGGTTTGTTAGAGCTTTGCTATAATGGT 6 165 1 TAGAGCTTTG 0.82604 -34 ********** Masking position 4 Map Score: 3.51421 Number of sites scoring better than the average of aligned sites = 959 Number in coding regions = 665 Number in noncoding regions = 294 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 4 TTTTGCTTTAAATTGTTGAATGTTTCTGTGT 2 36 1 AATTGTTAAT 0.88918 -44 AACGCTATTTAATTATTAAAAAGCCTAATGT 4 28 0 AATTATTAAA 0.957025 -136 AATAGCGTTTAATTGCGTAAAATATTTTTTT 4 50 1 AATTGCGAAA 0.902284 -114 ACTTAGCAAAAATAATGTCAACA 5 3 0 AATAATGCAA 0.861689 -47 TTATAAATATATTATGACATTTTAATTTTA 6 10 1 TATTATGCAT 0.823293 -189 TAAATTATTAAATTGTTTAAAAAAACAAATA 6 41 0 AATTGTTAAA 0.956364 -158 TTTAATAATTTATTATTAAAAATAACCCGAA 6 60 1 TATTATTAAA 0.890709 -139 AGTTATTTTAAATTATGGCAAGAGGTTTGTT 6 145 1 AATTATGCAA 0.97204 -54 ******* *** Masking position 2 Map Score: 4.22311 Number of sites scoring better than the average of aligned sites = 405 Number in coding regions = 267 Number in noncoding regions = 138 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 5 ********** No masking Map Score: -8.36008e-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 6 ********** No masking Map Score: -8.36008e-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 7 ********** No masking Map Score: -8.36008e-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