AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -ilexA_rpxx_opreg_100.orf -g0.290 -x5 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 = 0.29 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 RP083 145 unknown #2 RP183 300 unknown #3 RP203 80 EXCINUCLEASE ABC SUBUNIT B (uvrB) #4 RP385 300 HOLLIDAY JUNCTION DNA HELICASE RUVA (ruvA) #5 RP386 56 HOLLIDAY JUNCTION DNA HELICASE RUVB (ruvB) #6 RP446 300 GLYCOSYL TRANSFERASE (lgtD) #7 RP761 300 RECA PROTEIN (recA) #8 RP823 300 CELL DIVISION PROTEIN FTSK HOMOLOG (ftsK) #9 RP835 106 EXCINUCLEASE ABC SUBUNIT A (uvrA) Motif number 1 TAAAGAAGTTATACAAGATCCTTAT 1 3 1 AAGAATTATA 0.753434 -143 GTTTATAAATAAAAACCAAAAAACAGGCAATTT 1 44 1 AAAAACAAAA 0.779328 -102 GAAACTCGAGAAGAAGCAATATTGCGTCTTTTA 1 99 1 AAGAACAATT 0.663394 -47 TCAACTTAACAAAATAAAAATGATATTGGATAC 2 39 1 AAAATAAAAA 0.564153 -262 GGATACAAGAAATAAGCAAAATAGATATGTTCT 2 66 1 AATAACAAAA 0.885114 -235 GATTGATTATAATAAGCAATAGAACATATCTAT 2 86 0 AATAACAATA 0.819335 -215 TTAAAATCTCAAAAACTTATAATATTCTTCAGC 2 214 0 AAAAATTATT 0.527599 -87 AAATTAAGTTAATAACTAAATATACATATAGGC 2 270 0 AATAATAAAT 0.919128 -31 AAGAACTTAAATTAAGTTAATAA 2 288 0 AAGAATTAAT 0.753434 -13 AAGATCTTACAAAAAATAAAAAATATAACATT 3 10 0 AAAAATAAAA 0.898482 -71 TATTTTTTGTAAGATCTTATATATTATCTTAAA 3 25 1 AAGATTTATA 0.607381 -56 TTTGACATGAAAAATTTTATAAAATATTTATTT 4 84 1 AAAATTTATA 0.489961 -217 ATAAAACAGAAAAAAATAAATATTTTATAAAAT 4 97 0 AAAAATAAAT 0.838964 -204 TTGTTACTACAATATATAAAACAGAAAAAAATA 4 112 0 AATATTAAAA 0.907208 -189 TAAGAATAACAAGAAATAAATTAT 4 287 1 AAGAATAAAA 0.934444 -14 AATCGAATATAATAGCTAAAAAATAGTTTTATG 5 27 0 AATAGTAAAA 0.739439 -30 AGACTATTTAAATAAACAATTAACTACAAAACC 6 112 0 AATAACAATA 0.819335 -189 TGAAAATAAGAATAAATAAAAAAGGTACCACTG 6 146 0 AATAATAAAA 0.950757 -155 TAAGACTTTTAATAGATAATATTAAAGCAAAAA 6 198 1 AATAGTAATT 0.494382 -103 ATATTAAAGCAAAAATTAAAAAATTATATTTTA 6 216 1 AAAAATAAAA 0.898482 -85 AAATGCTTAAAATAATTAAATATAAGATGTAAA 7 44 1 AATAATAAAT 0.919128 -257 AATTAAATATAAGATGTAAATATATAGTAGTAA 7 57 1 AAGATTAAAT 0.80948 -244 ATCTTTTGCAAATAATATAATTAATAGAAAAGC 7 132 1 AATAAATAAA 0.670055 -169 AAGCAATGAGAAAAATCAATTAATAAATAACAT 7 161 1 AAAAACAATA 0.675205 -140 TCAATTAATAAATAACATAACTAATTTTTACAT 7 176 1 AATAAATAAA 0.670055 -125 TAAAGAAATGAAGATTTAATCTTATACGCACAA 7 211 1 AAGATTAATT 0.525594 -90 TTATACGCACAATAAATAAAATTTGATTTTTCT 7 232 1 AATAATAAAT 0.919107 -69 AATCTATACGAAAATTTAAACATAGTTCG 8 7 0 AAAATTAAAT 0.725098 -294 ATAATGCACTAATAAATTAAGTAAACTGTAAGT 8 51 0 AATAATTAAA 0.875489 -250 ATTATAGTCAAATATTTAATTAAAATAAAAAAA 8 79 1 AATATTAATA 0.851939 -222 ATTTAATTAAAATAAAAAAAGTTTTGCTTAGTC 8 92 1 AATAAAAAAT 0.766491 -209 TTTTTTATTCAAGATTTTATTGAAAATAGACGC 8 146 0 AAGATTTATA 0.607416 -155 AAAAAGTATGAATAAAAAATGCTTTTTTATTCA 8 168 0 AATAAAAATT 0.658963 -133 ATACTTTTTAAATATGTTAATTACTTTTATAGC 8 192 1 AATATTTAAA 0.780728 -109 CTTGTCAATAAAGAAATAATTATTACTGCTATA 8 219 0 AAGAATAATT 0.831616 -82 AATTTAGATTAATATTAAAAGCA 8 288 1 AATATAAAAA 0.738476 -13 TTGCAATAATAATATTTAAAATAGGTAGTAATC 9 12 0 AATATTAAAA 0.90715 -95 TTATTATTGCAATAATAAAATAAAAGAGCCTAT 9 33 1 AATAAAAAAA 0.84794 -74 ***** **** * Masking position 9 Map Score: 39.8786 Number of sites scoring better than the average of aligned sites = 2120 Number in coding regions = 1401 Number in noncoding regions = 719 Number of orfs with sites within 600 bp upstream = 277 Fraction of orfs with sites within 600 bp upstream = 0.0444908 Motif number 2 TTGTGTGTCTAGTTGTTCTAATGATAAAAGA 1 125 0 TATTTTCTAA 0.682074 -21 CAATATCATTTTTATTTTGTTAAGTTGACTAT 2 35 0 TTATTTGTTA 0.588946 -266 CTATTTTGCTTATTTCTTGTATCCAATATCAT 2 58 0 TATTTTGTAT 0.723932 -243 GTGAACGCGTTAATTCTTGCTAATACAGCATA 2 146 0 TATTTTGCTA 0.953877 -155 TTATATTTTTTATTTTTTGTAAGATCTTATAT 3 15 1 TATTTTGTAA 0.928168 -66 AAATTTACTATAATTTTTGTTACCATGTGGAT 4 27 1 TATTTTGTTA 0.964609 -274 AAATATTTATTTTTTTCTGTTTTATATATTGT 4 105 1 TTTTCTGTTT 0.706309 -196 ATATAAGCAATTATTATTGTTACTACAATATA 4 129 0 TTTTTTGTTA 0.952439 -172 AACGCGGTAATAATTGCTGCTAAGATATAGTG 4 225 0 TATTCTGCTA 0.924459 -76 TTTCTTGTTATTCTTACTGTTACTACATATTA 4 271 0 TTTTCTGTTA 0.922181 -30 ATAATTTATTTCTTGTTATTCTTACTGT 4 283 0 TATTTTGTTA 0.964609 -18 GTACCTTTTTTATTTATTCTTATTTTCATAGG 6 151 1 TATTTTCTTA 0.819017 -150 TATAATTTTTTAATTTTTGCTTTAATATTATC 6 212 0 TATTTTGCTT 0.807585 -89 ATCTTATATTTAATTATTTTAAGCATTTGCTT 7 40 0 TATTTTTTAA 0.721274 -261 TTCGTATAGATTCTTCTTTCTACACTTACAGT 8 28 1 TTTTTTTCTA 0.752675 -273 AGCAAAACTTTTTTTATTTTAATTAAATATTT 8 88 0 TTTTTTTTAA 0.655337 -213 TTAAATATGTTAATTACTTTTATAGCAGTAAT 8 199 1 TATTCTTTTA 0.763593 -102 AAAGAAATAATTATTACTGCTATAAAAGTAAT 8 211 0 TTTTCTGCTA 0.899918 -90 CTCTTTTATTTTATTATTGCAATAATAATATT 9 29 0 TTTTTTGCAA 0.878106 -78 ** ** ****** Masking position 5 Map Score: 20.4488 Number of sites scoring better than the average of aligned sites = 561 Number in coding regions = 382 Number in noncoding regions = 179 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 3 GTATCCAATATCATTTTTATTTTGTTAAGTTG 2 40 0 TCTTTTATTT 0.39429 -261 CCTCAAATCTTAAATCTTAGTTACCTAAATCC 2 177 1 TAATTTAGTT 0.735319 -124 ATAAGTTTTTGAGATTTTAAATTGAATCCTTG 2 227 1 GAATTTAAAT 0.6038 -74 AATGTTATATTTTTTATTTTTTGTAAGAT 3 8 1 TATTTTATTT 0.635499 -73 TGTAAGATCTTATATATTATCTTAAACTAGAG 3 32 1 TAATTTATCT 0.542395 -49 TTACTGTTACTACATATTAAAATTAGTGTTGG 4 258 0 TAATTTAAAA 0.885407 -43 AGTTTTATGCTATATTTTAATTTAA 5 4 0 TAATTTAATT 0.922502 -53 AACTATTTTTTAGCTATTATATTCGATTTTAA 5 32 1 TACTTTATAT 0.643276 -25 GCTATTATATTCGATTTTAAATA 5 44 1 TCATTTAAAT 0.872307 -13 TTAAAAGTCTTAAATATTAGATTTATTCCTAT 6 178 0 TAATTTAGAT 0.810252 -123 GCTTTAATATTATCTATTAAAAGTCTTAAATA 6 194 0 TACTTTAAAA 0.614633 -107 ATTAAAAAATTATATTTTAAATCTGAAAAATT 6 230 1 TAATTTAAAT 0.948177 -71 ATTTATACTATAAATTCTAATTTTTCAGATTT 6 248 0 TAATCTAATT 0.65594 -53 TATGCATAAATCGATATTAAAACTAAGCAAAT 7 16 1 TCATTTAAAA 0.742589 -285 ACTATATATTTACATCTTATATTTAATTATTT 7 53 0 TAATTTATAT 0.897288 -248 TTAGTTATGTTATTTATTAATTGATTTTTCTC 7 168 0 TATTTTAATT 0.785014 -133 TTCTCAAACTTATATCTTAATTGATAAGTTTA 7 265 1 TAATTTAATT 0.922502 -36 AAATTTCTATATTATAAACTTATCAAT 7 284 0 TCATTTATAA 0.579374 -17 CAAAACTTTTTTTATTTTAATTAAATATTTGA 8 86 0 TTATTTAATT 0.600281 -215 TTTTTATTCATACTTTTTAAATATGTTAATTA 8 183 1 TATTTTAAAT 0.848774 -118 CTTATAGATTTAGATACTAAATGCATAATTTA 8 262 1 TAATCTAAAT 0.74557 -39 ATAATTTAGATTAATATTAAAAGCA 8 286 1 TTATTTAAAA 0.493617 -15 CTACCTATTTTAAATATTATTATTGCAATAAT 9 17 1 TAATTTATTA 0.705895 -90 AATTTTGAGATATTTTTTAAAAAATCTGTAGT 9 69 0 TATTTTAAAA 0.703281 -38 ** ** ****** Masking position 5 Map Score: 18.0459 Number of sites scoring better than the average of aligned sites = 816 Number in coding regions = 458 Number in noncoding regions = 358 Number of orfs with sites within 600 bp upstream = 180 Fraction of orfs with sites within 600 bp upstream = 0.028911 Motif number 4 TTGTTACCACATAGTTTTATCCACATGGTA 4 47 0 ATAGTTTTAT 0.969009 -254 TAGCTAAAAAATAGTTTTATGCTATATTTT 5 18 0 ATAGTTTTAT 0.969009 -39 GTCTTAAATATTAGATTTATTCCTATGAAA 6 174 0 TTAGATTTAT 0.934654 -127 TATAGTATAAATAGTTTTATTACCATTGAC 6 268 1 ATAGTTTTAT 0.969009 -33 TAGTTTTAATATCGATTTATGCATATATAA 7 11 0 ATCGATTTAT 0.818239 -290 AAGCATTTGCTTAGTTTTAATATCGATTTA 7 22 0 TTAGTTTTAA 0.773274 -279 TTTGCAAAAGATAGTTTTATTTAAATAATA 7 114 0 ATAGTTTTAT 0.969009 -187 AATATGTTAATTACTTTTATAGCAGTAATA 8 202 1 TTACTTTTAT 0.736937 -99 ATTGAGTCTTATAGATTTAGATACTAAATG 8 255 1 ATAGATTTAG 0.834321 -46 AATGCATAATTTAGATTAATATTAAAAGCA 8 281 1 TTAGATTAAT 0.675253 -20 ********** Masking position 6 Map Score: 10.0477 Number of sites scoring better than the average of aligned sites = 147 Number in coding regions = 96 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 5 TGCTTATTTCTTGTATCCAATATCATTTTTATTTTGTTAAG 2 43 0 TACCAACTTA 0.76724 -258 TAATTCTTGCTAATACAGCATATACTTGTAACTCAAAATTT 2 127 0 TAAGAAATTA 0.889627 -174 GGATTCAATTTAAAATCTCAAAAACTTATAATATTCTTCAG 2 215 0 TACTAAATTA 0.788642 -86 AGATTTTAAATTGAATCCTTGAAATTTTGTAAGCCTATATG 2 238 1 TACCTAATTA 0.530636 -63 TTATATATTATCTTAAACTAGAGTTTTGAAAGCAAGTAAAA 3 41 1 TAACAATTTA 0.950561 -40 ATTTTTCATGTCAAATCCTAATTTGTTACCACATAGTTTTA 4 58 0 TACCATTTTA 0.542856 -243 CTACAATATATAAAACAGAAAAAAATAAATATTTTATAAAA 4 98 0 TAAGAAATAA 0.606499 -203 GCTTATATGGTGTTAGCCCAAACTATTCCTAATGATGGACA 4 153 1 TACCAATTTA 0.945959 -148 CTATCATTTATGTTACTGAATATTATTTGAATATGCATATC 6 22 0 TATGAATTTA 0.85815 -279 AACAATTAACTACAAAACCAGAATCTTAAGATTACATAAAC 6 90 0 TAACAATTTA 0.950604 -211 ATAAAAAAGGTACCACTGTAGACTATTTAAATAAACAATTA 6 123 0 TATGAATTTA 0.85815 -178 GGAATAAATCTAATATTTAAGACTTTTAATAGATAATATTA 6 181 1 TATTAATTTA 0.75484 -120 TAATAGATAATATTAAAGCAAAAATTAAAAAATTATATTTT 6 207 1 TAAGAAATAA 0.606461 -94 AAAATTATATTTTAAATCTGAAAAATTAGAATTTATAGTAT 6 235 1 TATCGAATTA 0.555299 -66 GTGTGGAAATTGCGATACCATATTATTTAAATAAAACTATC 7 94 1 TAACAATTTA 0.950605 -207 AAACTATCTTTTGCAAATAATATAATTAATAGAAAAGCAAT 7 127 1 TAATAAATTA 0.793488 -174 AAATTTCTATATTATAAACTTATCAATTAAGATAT 7 276 0 TAATAAATTA 0.804012 -25 AAAAATGCTTTTTTATTCAAGATTTTATTGAAAATAGACGC 8 146 0 TATCAATTAA 0.713814 -155 TCTAAATCTATAAGACTCAATAATCTTGTCAATAAAGAAAT 8 235 0 TATCAATTTA 0.928794 -66 TAAAAGAGCCTATAATACTACAGATTTTTTAAAAAATATCT 9 53 1 TAACAAATTA 0.94558 -54 * * ** * * * ** * Masking position 16 Map Score: 15.0455 Number of sites scoring better than the average of aligned sites = 316 Number in coding regions = 207 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 6 TGCTAGATTGATTATAATAAGCAATAGAAC 2 94 0 ATTATAATAA 0.890153 -207 GGTAACAAAAATTATAGTAAATTTGATTAT 4 21 0 ATTATAGTAA 0.918005 -280 TGTTTTATATATTGTAGTAACAATAATAAT 4 122 1 ATTGTAGTAA 0.954158 -179 TCCTATGAAAATAAGAATAAATAAAAAAGG 6 154 0 ATAAGAATAA 0.74953 -147 TCTTATTTTCATAGGAATAAATCTAATATT 6 168 1 ATAGGAATAA 0.84764 -133 TAACATGTCAATGGTAATAAAACTATTTAT 6 274 0 ATGGTAATAA 0.778759 -27 ATGTAAATATATAGTAGTAAGATAGTGTGG 7 70 1 ATAGTAGTAA 0.915202 -231 TTATTAGTGCATTATAGTCAAATATTTAAT 8 69 1 ATTATAGTCA 0.638449 -232 CAAATATTTAATTAAAATAAAAAAAGTTTT 8 87 1 ATTAAAATAA 0.592206 -214 CAAACATTATATTAGAATAATTGACTAAGC 8 117 0 ATTAGAATAA 0.852285 -184 AATTACTTTTATAGCAGTAATAATTATTTC 8 210 1 ATAGCAGTAA 0.840685 -91 AAATATTATTATTGCAATAATAAAATAAAA 9 28 1 ATTGCAATAA 0.880441 -79 ATCTCAAAATTTTGTAGTAAAGTGATT 9 90 1 TTTGTAGTAA 0.688946 -17 ********** Masking position 6 Map Score: 7.91305 Number of sites scoring better than the average of aligned sites = 353 Number in coding regions = 227 Number in noncoding regions = 126 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 7 TGTTTTTTGGTTTTTATTTATAAACTGAGC 1 39 0 TTTTTATTTA 0.96745 -107 TCCAATATCATTTTTATTTTGTTAAGTTGA 2 39 0 TTTTTATTTT 0.913548 -262 AATGTTATATTTTTTATTTTTTGTAAGATC 3 11 1 TTTTTATTTT 0.913548 -70 GATAGGCCGATTATTATTCACTATATCTTA 4 207 1 TTATTATTCA 0.658061 -94 TTATGCTATATTTTAATTTAA 5 2 0 TTTTAATTTA 0.774906 -55 TGTAGTTAATTGTTTATTTAAATAGTCTAC 6 117 1 TGTTTATTTA 0.836127 -184 AGTGGTACCTTTTTTATTTATTCTTATTTT 6 147 1 TTTTTATTTA 0.96745 -154 GCAAAAGATAGTTTTATTTAAATAATATGG 7 111 0 GTTTTATTTA 0.848421 -190 GAAAAATCAAATTTTATTTATTGTGCGTAT 7 234 0 ATTTTATTTA 0.790641 -67 AGCAAAACTTTTTTTATTTTAATTAAATAT 8 90 0 TTTTTATTTT 0.913548 -211 AAAAAATGCTTTTTTATTCAAGATTTTATT 8 158 0 TTTTTATTCA 0.943233 -143 AAAAAAGCATTTTTTATTCATACTTTTTAA 8 173 1 TTTTTATTCA 0.943233 -128 ********** Masking position 6 Map Score: 18.0632 Number of sites scoring better than the average of aligned sites = 269 Number in coding regions = 168 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 8 AGTTTCTTCAAAAAGCTTATGTTCTAAAAA 1 75 0 AAAAGCTTAT 0.633772 -71 TTGTAAGCCTATATGTATATTTAGTTATTA 2 264 1 ATATGTATAT 0.656692 -37 TAACAATAATAATTGCTTATATGGTGTTAG 4 139 1 AATTGCTTAT 0.863692 -162 TCTTGAAAAGATATGCATATTCAAATAATA 6 13 1 ATATGCATAT 0.496949 -288 TTTTGTAGTTAATTGTTTATTTAAATAGTC 6 114 1 AATTGTTTAT 0.66471 -187 TTATATATGCATAAATCGATATTA 7 5 1 ATATGCATAA 0.674069 -296 AAAACTAAGCAAATGCTTAAAATAATTAAA 7 34 1 AAATGCTTAA 0.907298 -267 ATCTTAATTGATAAGTTTATAATATAGAAA 7 278 1 ATAAGTTTAT 0.53402 -23 TATGAATAAAAAATGCTTTTTTATTCAAGA 8 165 0 AAATGCTTTT 0.57308 -136 TTTAGATACTAAATGCATAATTTAGATTAA 8 270 1 AAATGCATAA 0.846647 -31 ********** Masking position 8 Map Score: 3.39758 Number of sites scoring better than the average of aligned sites = 306 Number in coding regions = 201 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 9 ********** No masking Map Score: 3.83936e-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 TAGCACTCAAATTTTGAGTTACAAGTATATG 2 119 1 ATTTTGAGTA 0.965702 -182 TCAAAACTCTAGTTTAAGATAATATATAAGA 3 39 0 AGTTTAAGTA 0.923993 -42 CATTAGGAATAGTTTGGGCTAACACCATATA 4 156 0 AGTTTGGGTA 0.966192 -145 TTAAGATATAAGTTTGAGAAAGAAAAATCAA 7 254 0 AGTTTGAGAA 0.950695 -47 TTACTACAAAATTTTGAGATATTTTTTAAAA 9 79 0 ATTTTGAGTA 0.965702 -28 ******** ** Masking position 5 Map Score: 0.0199013 Number of sites scoring better than the average of aligned sites = 49 Number in coding regions = 33 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 11 ********** No masking Map Score: 3.83936e-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 12 ********** No masking Map Score: 3.83936e-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 13 ********** No masking Map Score: 3.83936e-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