AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i094_Ribose_Transport_bbur_reg_100.orf -o094_borburg_100.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 RBB00366 86 3615 #2 RBB00362 41 3615 #3 RBB00361 300 3615 #4 RBB00360 40 3615 #5 RBB00359 24 3615 #6 RBB00358 67 3615 #7 RBB00356 82 3615 #8 RBB00355 70 3615 #9 RBB00352 51 3615 #10 RBB00351 23 3615 #11 RBB00808 108 3615 #12 RBB00084 242 3615 Motif number 1 CAATTTATATATTTTATTTTTAAGTATAAAA 1 20 1 ATTTTATTTT 0.961003 -67 AACCAATGTGTTTTTTATACTTAAAAATAAA 1 32 0 TTTTTTATAT 0.785438 -55 GCACTTCTCCATTTCAATTATTCAAACAAAA 1 61 0 ATTTCAATTT 0.791113 -26 GTGAAAAATCTTTTTAATTCTTTAAAGATGT 3 20 1 TTTTTAATTT 0.971932 -281 TTTAAAGGGTTTTTTAATTGTTGTAATTTGA 3 51 1 TTTTTAATTT 0.971932 -250 TACTACTGTGTTTTTATTAATGCTAGAAGTA 3 150 1 TTTTTATTAT 0.886085 -151 ATAAAATAAAATTTTAATAATCCCTTTTAAA 3 185 0 ATTTTAATAT 0.901678 -116 CAAGTAGTATTCTTTATTTATAAAATAAAAT 3 204 0 TCTTTATTTT 0.936851 -97 TAAAGTTAATATTTTAATTTTTAAAAAATTT 3 244 1 ATTTTAATTT 0.969524 -57 TTTTAAGGTGTCTTTTTTTGTTTATATGCC 4 21 1 TCTTTTTTTT 0.843944 -20 ATTTGCTACCATTTTATTAATAGTTTCAAGA 6 29 1 ATTTTATTAT 0.877051 -39 CTTTGATATATTTTTAATTTT 7 1 0 TTTTTAATTT 0.971932 -82 ACAGTGTTAGTCTTAATTTTTGAGTGCATGC 8 15 1 TCTTAATTTT 0.851622 -56 AATTTAATACTAATGGGAGCT 9 1 1 AATTTAATAT 0.666072 -51 TTAAAGCCTCACTTTAATTCTAACAACAGGT 11 87 0 ACTTTAATTT 0.946226 -22 CTTTTGTAATAATTTATTTATTCTTTTATTT 12 19 1 AATTTATTTT 0.841968 -224 ATTTATTTATTCTTTTATTTTAACATTAATT 12 30 1 TCTTTTATTT 0.874711 -213 TTATTAAGGTTTTTATATTTTAAGCATTTTT 12 69 1 TTTTATATTT 0.830032 -174 ATTTTAAGCATTTTTATTTATTAGCAATTAA 12 85 1 TTTTTATTTT 0.964058 -158 ATTTATTAGCAATTAATTTTTATAGATAATT 12 100 1 AATTAATTTT 0.673338 -143 TTTATAGATAATTTATTTTGTTTATTAAAAT 12 118 1 ATTTATTTTT 0.776557 -125 TTCAATAGCATTTTAAATTTTAATAAACAAA 12 134 0 TTTTAAATTT 0.930539 -109 AAAGCTTAAAATTTATATTTTCAATAGCATT 12 153 0 ATTTATATTT 0.81774 -90 ********* * Masking position 4 Map Score: 33.7009 Number of sites scoring better than the average of aligned sites = 3021 Number in coding regions = 1930 Number in noncoding regions = 1091 Number of orfs with sites within 600 bp upstream = 191 Fraction of orfs with sites within 600 bp upstream = 0.0306778 Motif number 2 CACATTGGTTTTGTTTGAATAATTGAAATGGAG 1 53 1 TTTTTAAAAT 0.955718 -34 ATCTTTTTAATTCTTTAAAGATGTTTTAAAGGG 3 27 1 TTTTTAAATG 0.837817 -274 GGTTTTTTAATTGTTGTAATTTGAATTTAAATT 3 58 1 TTTTGAATTG 0.743258 -243 AATTTAAACCCTTTTGCAAGATTAATTTAAATT 3 81 0 CTTTGAAATT 0.940585 -220 TTAATAATCCCTTTTAAAAAAATACTTCTAGCA 3 170 0 CTTTAAAAAT 0.869844 -131 TTAAAAGGGATTATTAAAATTTTATTTTATAAA 3 186 1 TTTTAAATTT 0.759579 -115 GTAGTATTCTTTATTTATAAAATAAAATTTTAA 3 199 0 TTTTTTAAAT 0.840207 -102 AGAATACTACTTGTTAGTAAAATAAAGTTAATA 3 222 1 TTTTATAAAT 0.785664 -79 AAATTCTAAATTTTTTAAAAATTAAAATATTAA 3 249 0 TTTTTAAATT 0.929388 -52 CTCCTTATATTTTTTTTAAAAATTCTAAATTTT 3 268 0 TTTTTAAAAT 0.942915 -33 CGCTCTCCTTTTCTTGAAACTATTAATAAAATG 6 38 0 TTTTGAATAT 0.923642 -30 TTTTATTATAAGAAGGGTAAATT 10 3 1 TTTTAAAAAG 0.85166 -21 CCCTCCTGACCTGTTGTTAGAATTAAAGTGAGG 11 79 1 CTTTGTAAAT 0.865458 -30 AATACTCTCTTTTGTAATAATTTATTTATTC 12 9 1 CTTTGAAAAT 0.962681 -234 ATTTATTCTTTTATTTTAACATTAATTTGCTCT 12 34 1 TTTTTAAATT 0.92963 -209 ATTTAAAATGCTATTGAAAATATAAATTTTAAG 12 147 1 CTTTGAATAT 0.89887 -96 ** *** ** *** Masking position 5 Map Score: 18.2208 Number of sites scoring better than the average of aligned sites = 1579 Number in coding regions = 1086 Number in noncoding regions = 493 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 3 AATTAATCCTCTCCTTATATTTTTTTTA 3 283 0 CTCTCCTTAT 0.989704 -18 AAAGACACCTTTTTAAGGTGTCT 4 4 1 GACACCTTTT 0.832193 -37 TTAATATTAACCCACCTTTCAG 5 3 0 CCCACCTTTC 0.904556 -22 TTATCAACGCTCTCCTTTTCTTGAAACTA 6 49 0 CTCTCCTTTT 0.984999 -19 TAAAAGACTCCTTTTTTAAGACATA 7 68 0 GACTCCTTTT 0.946923 -15 ATTAACTCCTTATATATTTTCAT 8 58 0 AACTCCTTAT 0.944089 -13 ATAATCTCCTTATGGTAGTAACG 9 39 0 ATCTCCTTAT 0.956497 -13 AATTTACCCTTCTTATAATAAAA 10 8 0 CCCTTCTTAT 0.91025 -16 GGGTTCGAATCCCTCCTGACCTGTTGTTAG 11 69 1 CCCTCCTGAC 0.912355 -40 CATTAATTTGCTCTCTTTATTAAGGTTTTT 12 53 1 CTCTCTTTAT 0.893601 -190 ********** Masking position 7 Map Score: 9.11942 Number of sites scoring better than the average of aligned sites = 161 Number in coding regions = 70 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 4 TTAAAACATCTTTAAAGAATTAAAAAGATTT 3 25 0 TTTAAAGATT 0.932976 -276 TTAAAGATGTTTTAAAGGGTTTTTTAATTGT 3 41 1 TTTAAAGGTT 0.976301 -260 AATATCCAAATTTAAACCCTTTTGCAAGATT 3 91 0 TTTAAACCTT 0.842131 -210 AAAGACACCTTTTTAAGGTGTCTTTTTTTGT 4 11 1 TTTTAAGGGT 0.961253 -30 AAGACTCCTTTTTTAAGACATAACAAGCCGC 7 59 0 TTTTAAGAAT 0.754502 -24 TAATGGGAGCTTTGAAGGCGTTACTACCATA 9 21 1 TTTGAAGGGT 0.900707 -31 TTTAAAGCCTCACTTTAATTC 11 98 0 TTTAAAGCTC 0.895738 -11 TTGCTCTCTTTATTAAGGTTTTTATATTTTA 12 60 1 TATTAAGGTT 0.877173 -183 GGTTTTTATATTTTAAGCATTTTTATTTATT 12 76 1 TTTTAAGCTT 0.980678 -167 AAAATATAAATTTTAAGCTTTATTATATTTC 12 163 1 TTTTAAGCTT 0.980678 -80 ******** ** Masking position 6 Map Score: 8.02863 Number of sites scoring better than the average of aligned sites = 490 Number in coding regions = 335 Number in noncoding regions = 155 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 5 TAAAATATATAAATTGATTCTTTAT 1 5 0 AATTGATTCT 0.643447 -82 TCAATTTATATATTTTATTTTTAAGTATAAA 1 19 1 TATTTATTTT 0.921851 -68 TAATTGTTGTAATTTGAATTTAAATTAATCT 3 65 1 AATTGAATTT 0.839044 -236 ACCCTTTTGCAAGATTAATTTAAATTCAAAT 3 76 0 AAATTAATTT 0.914185 -225 TGATGTAGGAAAAATTATTTTTCCTACTACT 3 126 1 AAATTATTTT 0.718696 -175 GGATTATTAAAATTTTATTTTATAAATAAAG 3 193 1 AATTTATTTT 0.934989 -108 TTAAAATATTAACTTTATTTTACTAACAAGT 3 230 0 AATTTATTTT 0.96406 -71 ATAAAGTTAATATTTTAATTTTTAAAAAATT 3 243 1 TATTTAATTT 0.909569 -58 ACTTTGATATATTTTTAATTTT 7 2 0 ATTTTAATTT 0.772089 -81 CTTTTATTTTAACATTAATTTGCTCTCTTTA 12 41 1 AAATTAATTT 0.914185 -202 ATTATCTATAAAAATTAATTGCTAATAAATA 12 99 0 AAATTAATTG 0.681324 -144 TTTTTATAGATAATTTATTTTGTTTATTAAA 12 116 1 TATTTATTTT 0.913572 -127 ATAAAGCTTAAAATTTATATTTTCAATAGCA 12 155 0 AATTTATATT 0.628774 -88 ** ******** Masking position 7 Map Score: 15.394 Number of sites scoring better than the average of aligned sites = 1069 Number in coding regions = 675 Number in noncoding regions = 394 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 6 GGAAAAATAATTTTTCCTACATCACCATAA 3 120 0 TTTTTCCTAC 0.984184 -181 GGAAAAATTATTTTTCCTACTACTGTGTTT 3 133 1 TTTTTCCTAC 0.984184 -168 ATAAGTGATATATTTGCTACCATTTTATTA 6 18 1 TATTTGCTAC 0.958701 -50 AATAGGTCAGTAGTTCCAACGGTAGAACGA 11 16 1 TAGTTCCAAC 0.935259 -93 ********** Masking position 5 Map Score: 0.51486 Number of sites scoring better than the average of aligned sites = 11 Number in coding regions = 6 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 7 ATTATTTTTCCTACTACTGTGTTTTTATTA 3 139 1 CTACTACTGT 0.96009 -162 AAAATTAAGACTAACACTGTCATG 8 5 0 CTAACACTGT 0.987356 -66 TGAGTGCATGCTATCACTGTGAAATGAAAA 8 35 1 CTATCACTGT 0.977918 -36 ACGACAGTCTCCAAAACTGTATGCTGGGGG 11 42 1 CCAAAACTGT 0.943782 -67 ********** Masking position 6 Map Score: 0.279446 Number of sites scoring better than the average of aligned sites = 2 Number in coding regions = 0 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 8 CTTTACAAACAAAGCTATATTTAAGTAGT 2 9 0 AAAGTATATT 0.808318 -33 CTTTGTTTGTAAAGGGGAAATAGTTT 2 26 1 AAAGGGAAAT 0.591196 -16 TTAAAGAATTAAAAAGATTTTTCACAAATCA 3 14 0 AAAAGATTTT 0.736474 -287 TTAATTCTTTAAAGATGTTTTAAAGGGTTTT 3 33 1 AAAGTGTTTT 0.951166 -268 AAGATGTTTTAAAGGGTTTTTTAATTGTTGT 3 44 1 AAAGGTTTTT 0.807955 -257 TGATGTAGGAAAAATTATTTTTCCTACTACT 3 126 1 AAAATATTTT 0.631828 -175 TATTTTTTTAAAAGGGATTATTAAAATTTTA 3 179 1 AAAGGATTAT 0.953001 -122 TTAGTAAAATAAAGTTAATATTTTAATTTTT 3 235 1 AAAGTAATAT 0.784558 -66 GACACCTTAAAAAGGTGTCTTT 4 2 0 AAAGTGTCTT 0.804202 -39 CTGAAAGGTGGGTTAATATTAAAT 5 4 1 AAAGTGGGTT 0.611883 -21 AAAATATATCAAAGTTGTTATTCCGCATGTC 7 18 1 AAAGTGTTAT 0.944385 -65 TTACTACCATAAGGAGATTAT 9 41 1 AAGGGATTAT 0.761811 -11 AATTATTACAAAAGAGAGTATT 12 2 0 AAAGGAGTAT 0.88614 -241 **** ****** Masking position 2 Map Score: 5.10201 Number of sites scoring better than the average of aligned sites = 897 Number in coding regions = 639 Number in noncoding regions = 258 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 9 ********** No masking Map Score: 2.12695e-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 10 ********** No masking Map Score: 2.12695e-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: 2.12695e-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