AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i094_Ribose_Transport_bbur_reg_300.orf -o094_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 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 RBB00809 173 3615 #13 RBB00349 300 3615 #14 RBB00084 242 3615 Motif number 1 AATTTATATATTTTATTTTTAAGTATAAAA 1 21 1 TTTTATTTTT 0.951856 -66 TTAAAGGGTTTTTTAATTGTTGTAATTTGA 3 52 1 TTTTAATTGT 0.635595 -249 TGTAATTTGAATTTAAATTAATCTTGCAAA 3 72 1 ATTTAAATTA 0.618827 -229 ACTACTGTGTTTTTATTAATGCTAGAAGTA 3 151 1 TTTTATTAAT 0.870631 -150 TAATAATCCCTTTTAAAAAAATACTTCTAG 3 172 0 TTTTAAAAAA 0.599457 -129 TAAAATAAAATTTTAATAATCCCTTTTAAA 3 185 0 TTTTAATAAT 0.861568 -116 TAAAATTTTATTTTATAAATAAAGAATACT 3 200 1 TTTTATAAAT 0.616023 -101 AAAGTTAATATTTTAATTTTTAAAAAATTT 3 245 1 TTTTAATTTT 0.945495 -56 CTTATATTTTTTTTAAAAATTCTAAATTTT 3 268 0 TTTTAAAAAT 0.821691 -33 ATTTAATATTAACCCACCTT 5 15 0 ATTTAATATT 0.812874 -10 TTTGCTACCATTTTATTAATAGTTTCAAGA 6 30 1 TTTTATTAAT 0.870631 -38 TTTGATATATTTTTAATTTT 7 1 0 TTTTAATTTT 0.945495 -82 TTTTATTATAAGAAGGGTAA 10 1 1 TTTTATTATA 0.812711 -23 CAAGTACTAAATTTAATTTTC 12 2 0 ATTTAATTTT 0.865977 -172 GACGATTGCTTTTTAAATAGGTATTAAATT 13 15 1 TTTTAAATAG 0.757457 -286 TTAAATTAACATTTATTATAGGTCATTATA 13 38 1 ATTTATTATA 0.617665 -263 TTTACTATTTTTTTATATTGGAGTTTTATG 13 119 1 TTTTATATTG 0.869564 -182 TTATGCTAAATTTTAAATTTAGGCTTTAGT 13 144 1 TTTTAAATTT 0.930257 -157 AGTTTTGTTGTTTTAATATTTTTACATTGG 13 171 1 TTTTAATATT 0.921026 -130 TTGTCAAAATTTTTATAAATACTAACTTAA 13 224 0 TTTTATAAAT 0.616023 -77 TTTGACAACTTTTTAAATTGAGGTGTGCAT 13 246 1 TTTTAAATTG 0.853998 -55 GAGGTGTGCATTTTATTATGTGTAGTTTAT 13 265 1 TTTTATTATG 0.853566 -36 TTTTGTAATAATTTATTTATTCTTTTATTT 14 20 1 ATTTATTTAT 0.797074 -223 TTATTTATTCTTTTATTTTAACATTAATTT 14 32 1 TTTTATTTTA 0.865964 -211 TTATTAAGGTTTTTATATTTTAAGCATTTT 14 69 1 TTTTATATTT 0.938217 -174 TTTTAAGCATTTTTATTTATTAGCAATTAA 14 86 1 TTTTATTTAT 0.913404 -157 TTTATAGATAATTTATTTTGTTTATTAAAA 14 118 1 ATTTATTTTG 0.763564 -125 TTCAATAGCATTTTAAATTTTAATAAACAA 14 135 0 TTTTAAATTT 0.930257 -108 AAAGCTTAAAATTTATATTTTCAATAGCAT 14 154 0 ATTTATATTT 0.849729 -89 TATGTTTGATATTTATATTAGGATTAAAGC 14 220 1 ATTTATATTA 0.648803 -23 ********** Masking position 5 Map Score: 38.6917 Number of sites scoring better than the average of aligned sites = 3478 Number in coding regions = 2201 Number in noncoding regions = 1277 Number of orfs with sites within 600 bp upstream = 212 Fraction of orfs with sites within 600 bp upstream = 0.0340508 Motif number 2 TTATACTTAAAAATAAAATATATAAATTGATTCTT 1 14 0 AAAAAATAAA 0.948135 -73 ACAACAATTAAAAAACCCTTTAAAACATCTTTAAA 3 40 0 AAAACCTAAA 0.776607 -261 AGATTAATTTAAATTCAAATTACAACAATTAAAAA 3 61 0 AAATCATAAA 0.890652 -240 ATTTGAATTTAAATTAATCTTGCAAAAGGGTTTAA 3 76 1 AAATAATGAA 0.605947 -225 TAGCATTAATAAAAACACAGTAGTAGGAAAAATAA 3 140 0 AAAACATATA 0.740965 -161 CCCTTTTAAAAAAATACTTCTAGCATTAATAAAAA 3 160 0 AAATACTACA 0.684538 -141 TTATTTATAAAATAAAATTTTAATAATCCCTTTTA 3 187 0 AATAAATATA 0.680508 -114 TTTATTTTATAAATAAAGAATACTACTTGTTAGTA 3 206 1 AAAAAATATA 0.887302 -95 ACTTGTTAGTAAAATAAAGTTAATATTTTAATTTT 3 230 1 AAATAATATA 0.906093 -71 ATAAACAAAAAAAGACACCTTAAAAAGGTGTCTTT 4 11 0 AAAACATAAA 0.869229 -30 CCTTTTCTTGAAACTATTAATAAAATGGTAGCAAA 6 30 0 AAATATTAAA 0.833458 -38 AAAATTAAAAATATATCAAAGTTGTT 7 2 1 AAATAATAAT 0.509206 -81 ATGCACTCAAAAATTAAGACTAACACTGTCATG 8 9 0 AAATAATACA 0.805784 -62 ATCACTGTGAAATGAAAATATATAAGGAGTTAAT 8 47 1 AATAAATAAA 0.832019 -24 GAAAATTAAATTTAGTACTTGTTTTTT 12 3 1 AAATAATATA 0.906084 -171 ATAAGGGCACTAATTCCCTATAAAACTCTTTATTA 12 57 0 TAATCCTAAA 0.482002 -117 ACAAAACTCCTAACTACCAATAAAAGCCCTCAATC 12 146 0 TAATACTAAA 0.719217 -28 ATAGGTATTAAATTAACATTTATTATAGGTCATTA 13 31 1 AATAACTATA 0.493056 -270 AAAACGTTGAAAAATAATCTTATAATGACCTATAA 13 53 0 AAATAATAAA 0.957304 -248 ACTCCAATATAAAAAAATAGTAAAAATCATTTCAT 13 108 0 AAAAAATAAA 0.948179 -193 CCTAAATTTAAAATTTAGCATAAAACTCCAATATA 13 132 0 AAATTATAAA 0.557535 -169 CATTAACACCAATGTAAAAATATTAAAACAACAAA 13 174 0 AATTAATATA 0.723143 -127 TTTACAATATAAACTACACATAATAAAATGCACAC 13 268 0 AAATACTATA 0.834618 -33 TAAAAGAATAAATAAATTATTACAAAAGAGAGTAT 14 12 0 AATAATTAAA 0.52506 -231 TAAAGAGAGCAAATTAATGTTAAAATAAAAGAATA 14 37 0 AAATAATAAA 0.957303 -206 TGCTAATAAATAAAAATGCTTAAAATATAAAAACC 14 76 0 TAAAATTAAA 0.471474 -167 TAAACAAAATAAATTATCTATAAAAATTAATTGCT 14 107 0 AAATATTAAA 0.833458 -136 TTATTTTGTTTATTAAAATTTAAAATGCTATTGAA 14 130 1 TATAAATAAA 0.517146 -113 TAATGAAATATAATAAAGCTTAAAATTTATATTTT 14 163 0 TAAAAATAAA 0.799803 -80 *** *** ** ** Masking position 11 Map Score: 34.3106 Number of sites scoring better than the average of aligned sites = 2132 Number in coding regions = 1298 Number in noncoding regions = 834 Number of orfs with sites within 600 bp upstream = 154 Fraction of orfs with sites within 600 bp upstream = 0.024735 Motif number 3 AAAAAAAATATAAGGAGAGGATTAATT 3 284 1 TAAGGAGAGT 0.978927 -17 GACACCTTAAAAAGGTGTCTTT 4 1 0 AAAGGTGTCT 0.849139 -40 GACACCTTTTTAAGGTGTCTTTTTTTGTTTAT 4 14 1 TAAGGTGTCT 0.916169 -27 CTGAAAGGTGGGTTAATATTAAAT 5 4 1 AAAGGTGGGA 0.78244 -21 AGTTTCAAGAAAAGGAGAGCGTTGATAA 6 50 1 AAAGGAGAGT 0.95988 -18 ATGTCTTAAAAAAGGAGTCTTTTA 7 69 1 AAAGGAGTCT 0.892527 -14 TGAAAATATATAAGGAGTTAAT 8 59 1 TAAGGAGTTT 0.911148 -12 GTTACTACCATAAGGAGATTAT 9 40 1 TAAGGAGATT 0.911148 -12 TAACAACAGGTCAGGAGGGATTCGAACCCCCA 11 66 0 TCAGGAGGGT 0.848241 -43 TTGTTAGAATTAAAGTGAGGCTTTAAA 11 92 1 TAAAGTGAGT 0.881412 -17 ACTAAGATAATAAAGAGTTTTATAGGGAATTA 12 50 1 TAAAGAGTTA 0.394279 -124 ACCACCATGGTAAGGTGGGGGTCGTCGGTTCA 12 109 1 TAAGGTGGGT 0.962921 -65 CTTTTTAAATTGAGGTGTGCATTTTATTATGT 13 254 1 TGAGGTGTGT 0.821198 -47 AAATTATTACAAAAGAGAGTATT 14 2 0 AAAAGAGAGT 0.849578 -241 AAAACCTTAATAAAGAGAGCAAATTAATGTTA 14 50 0 TAAAGAGAGA 0.746751 -193 ********* * Masking position 3 Map Score: 13.5474 Number of sites scoring better than the average of aligned sites = 200 Number in coding regions = 111 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 4 AAAATATATAAATTGATTCTTTAT 1 4 0 AATGATTCTT 0.900442 -83 AACAAAACCAATGTGTTTTTTATACTTAAAA 1 37 0 ATTGTTTTTT 0.806797 -50 TAAAGAATTAAAAAGATTTTTCACAAATCAG 3 13 0 AAAGATTTTT 0.841809 -288 AGATGTTTTAAAGGGTTTTTTAATTGTTGTA 3 45 1 AAGGTTTTTT 0.927927 -256 GTAGTAGGAAAAATAATTTTTCCTACATCAC 3 125 0 AATAATTTTT 0.882234 -176 TTAATGCTAGAAGTATTTTTTTAAAAGGGAT 3 166 1 AATATTTTTT 0.870198 -135 ATTTTTTTAAAAGGGATTATTAAAATTTTAT 3 180 1 AAGGATTATT 0.749072 -121 TAAATTTAGTACTTGTTTTTTTCTAAACAAT 12 17 1 ACTGTTTTTT 0.860903 -157 GTCAGTTATGAAATGATTTTTACTATTTTTT 13 101 1 AATGATTTTT 0.973687 -200 ATTTATTAGCAATTAATTTTTATAGATAATT 14 100 1 AATAATTTTT 0.91053 -143 ** ******** Masking position 7 Map Score: 5.13758 Number of sites scoring better than the average of aligned sites = 531 Number in coding regions = 369 Number in noncoding regions = 162 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 5 TATATTTTATTTTTAAGTATAAAAAACACATTGGT 1 27 1 TTTATTAAAA 0.448194 -60 AAAACACATTGGTTTTGTTTGAATAATTGAAATGG 1 49 1 GTTTTTAATA 0.895339 -38 AGCTGATTTGTGAAAAATCTTTTTAA 3 2 1 GTGTTTAAAA 0.936516 -299 TGGATATTATGGTGATGTAGGAAAAATTATTTTTC 3 114 1 GTGTTGAAAA 0.91799 -187 AAGTTAATATTTTAATTTTTAAAAAATTTAGAATT 3 246 1 TTATTTAAAA 0.737042 -55 CCTCTCCTTATATTTTTTTTAAAAATTCTAAATTT 3 269 0 TTTTTTAAAA 0.935389 -32 ATGTGCGGCTTGTTATGTCTTAAAAAAGGAGTCTT 7 55 1 TTTTTTAAAA 0.936581 -28 TATCTTAGTTGATTGTTTAGAAAAAAACAAGTACT 12 24 0 GTTTTGAAAA 0.942098 -150 TTTAGACGATTGCTTTTTAAATAGGTATTAAAT 13 9 1 ATGTTTAATA 0.504307 -292 ATTTTTCAACGTTTTTGTGGTCATAATTGTCAGTT 13 73 1 GTTTTGCATA 0.407718 -228 AGGCTTTAGTTTTGTTGTTTTAATATTTTTACATT 13 164 1 TTGTTTAATA 0.803507 -137 TTTTTACATTGGTGTTAATGTAAAATGTGGTGATG 13 189 1 GTGTAGAAAA 0.694346 -112 GATGTTAAGTTAGTATTTATAAAAATTTTGACAAC 13 220 1 TGTTTTAAAA 0.613041 -81 ATTATGTGTAGTTTATATTGTAAAATACTCTT 13 279 1 GTTTTGAAAA 0.942087 -22 ATTTATTTATTCTTTTATTTTAACATTAATTTGCT 14 30 1 TTTTTTAACA 0.685412 -213 AAAATTAATTGCTAATAAATAAAAATGCTTAAAAT 14 85 0 GTATATAAAA 0.449552 -158 AAACAAAATAAATTATCTATAAAAATTAATTGCTA 14 106 0 ATTTTTAAAA 0.787538 -137 AGATAATTTATTTTGTTTATTAAAATTTAAAATGC 14 123 1 TTTTTTAAAA 0.932584 -120 TACAATATTCTATTCTAATGAAATATAATAAAGCT 14 178 0 TTTTAGAATA 0.477485 -65 * ** * * * **** Masking position 13 Map Score: 12.6747 Number of sites scoring better than the average of aligned sites = 1444 Number in coding regions = 962 Number in noncoding regions = 482 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 Motif number 6 TTATACTTAAAAATAAAATATATAAATTGA 1 19 0 AAATAAAATA 0.559867 -68 CAATTATTCAAACAAAACCAATGTGTTTTT 1 48 0 AACAAAACCA 0.907446 -39 CCCCTTTACAAACAAAGCTATATTTAAGTA 2 13 0 AACAAAGCTA 0.931977 -29 TAGAATTTTTAAAAAAAATATAAGGAGAGG 3 274 1 AAAAAAAATA 0.820661 -27 GGCATATAAACAAAAAAAGACACCTTAA 4 23 0 AACAAAAAAA 0.894819 -18 GATTGTTTAGAAAAAAACAAGTACTAAATT 12 19 0 AAAAAAACAA 0.825057 -155 CTAAACAATCAACTAAGATAATAAAGAGTT 12 39 1 AACTAAGATA 0.659688 -135 ATAACAAAACTCCTAACTACCA 12 162 0 AACAAAACTC 0.869198 -12 ATATTAAAACAACAAAACTAAAGCCTAAAT 13 160 0 AACAAAACTA 0.969571 -141 AATTTTAATAAACAAAATAAATTATCTATA 14 120 0 AACAAAATAA 0.721121 -123 ********** Masking position 5 Map Score: 4.61732 Number of sites scoring better than the average of aligned sites = 566 Number in coding regions = 356 Number in noncoding regions = 210 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 7 AAATATAAGGAGAGGATTAATT 3 289 1 AGAGGATTAA 0.637606 -12 GAAAGGTGGGTTAATATTAAAT 5 13 1 TTAATATTAA 0.460539 -12 CATGACAGTGTTAGTCTTAATTTTTGAGTG 8 11 1 TTAGTCTTAA 0.83282 -60 AAAGCTCCCATTAGTATTAAATT 9 4 0 TTAGTATTAA 0.874539 -48 TGACCTGTTGTTAGAATTAAAGTGAGGCTT 11 85 1 TTAGAATTAA 0.815124 -24 AGAATTAAAGTGAGGCTTTAAA 11 97 1 TGAGGCTTTA 0.902228 -12 AATTTTAAATTTAGGCTTTAGTTTTGTTGT 13 152 1 TTAGGCTTTA 0.949841 -149 TGATGTTAAGTTAGTATTTATAAAAATTTT 13 219 1 TTAGTATTTA 0.907421 -82 AATATAAATTTTAAGCTTTATTATATTTCA 14 165 1 TTAAGCTTTA 0.678557 -78 GATATTTATATTAGGATTAAAGCTTG 14 227 1 TTAGGATTAA 0.897848 -16 ********** Masking position 7 Map Score: 8.09556 Number of sites scoring better than the average of aligned sites = 218 Number in coding regions = 154 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 8 ********** No masking Map Score: 1.85695e-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 9 ********** No masking Map Score: 1.85695e-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: 1.85695e-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