AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -ilexA_rpxx_opreg_300.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 RP084 300 unknown #3 RP183 300 unknown #4 RP203 80 EXCINUCLEASE ABC SUBUNIT B (uvrB) #5 RP385 300 HOLLIDAY JUNCTION DNA HELICASE RUVA (ruvA) #6 RP386 56 HOLLIDAY JUNCTION DNA HELICASE RUVB (ruvB) #7 RP446 300 GLYCOSYL TRANSFERASE (lgtD) #8 RP761 300 RECA PROTEIN (recA) #9 RP823 300 CELL DIVISION PROTEIN FTSK HOMOLOG (ftsK) #10 RP835 106 EXCINUCLEASE ABC SUBUNIT A (uvrA) Motif number 1 TATGCTCAAAATAAATATTACCACTGACAC 2 16 0 ATAAATATTA 0.772994 -285 TCTTGTTGTGTTATTTATTGCTTTCTTTCA 2 94 0 TTATTTATTG 0.935729 -207 TGAAAGTTTAATAATTCTTGTTGTGTTATT 2 109 0 ATAATTCTTG 0.764417 -192 TGTTTTCTTGATAAATTTTAATAAATATTA 2 239 1 ATAAATTTTA 0.633527 -62 ATAAATTTTAATAAATATTATATGATTCGC 2 249 1 ATAAATATTA 0.772994 -52 CCAATATCATTTTTATTTTGTTAAGTTGAC 3 38 0 TTTTATTTTG 0.674424 -263 TCTATTTTGCTTATTTCTTGTATCCAATAT 3 61 0 TTATTTCTTG 0.893723 -240 GGTGAACGCGTTAATTCTTGCTAATACAGC 3 149 0 TTAATTCTTG 0.907976 -152 ACCTCAAATCTTAAATCTTAGTTACCTAAA 3 176 1 TTAAATCTTA 0.856781 -125 GTTATATTTTTTATTTTTTGTAAGATCTTA 4 14 1 TTATTTTTTG 0.88082 -67 TTGTAAGATCTTATATATTATCTTAAACTA 4 31 1 TTATATATTA 0.8977 -50 CAAATTTACTATAATTTTTGTTACCATGTG 5 26 1 ATAATTTTTG 0.740376 -275 TATAAAATATTTATTTTTTTCTGTTTTATA 5 101 1 TTATTTTTTT 0.531995 -200 TTTTTCTGTTTTATATATTGTAGTAACAAT 5 116 1 TTATATATTG 0.925415 -185 CATATAAGCAATTATTATTGTTACTACAAT 5 132 0 ATTATTATTG 0.648806 -169 GGATAGGCCGATTATTATTCACTATATCTT 5 206 1 ATTATTATTC 0.464378 -95 ATAATTTATTTCTTGTTATTCTTAC 5 286 0 TTATTTCTTG 0.893723 -15 GGTACCTTTTTTATTTATTCTTATTTTCAT 7 150 1 TTATTTATTC 0.872327 -151 ATTAAAAGTCTTAAATATTAGATTTATTCC 7 181 0 TTAAATATTA 0.911671 -120 TAATTTTTGCTTTAATATTATCTATTAAAA 7 204 0 TTTAATATTA 0.773044 -97 ATATAATTTTTTAATTTTTGCTTTAATATT 7 215 0 TTAATTTTTG 0.896604 -86 AATTAAAAAATTATATTTTAAATCTGAAAA 7 229 1 TTATATTTTA 0.816974 -72 CATCTTATATTTAATTATTTTAAGCATTTG 8 43 0 TTAATTATTT 0.724319 -258 ATTAGTTATGTTATTTATTAATTGATTTTT 8 171 0 TTATTTATTA 0.911948 -130 GCGTATAAGATTAAATCTTCATTTCTTTAC 8 210 0 TTAAATCTTC 0.797836 -91 AAATCAAATTTTATTTATTGTGCGTATAAG 8 231 0 TTATTTATTG 0.935729 -70 TTTCTCAAACTTATATCTTAATTGATAAGT 8 264 1 TTATATCTTA 0.836026 -37 CGAACTATGTTTAAATTTTCGTATAGATTC 9 11 1 TTAAATTTTC 0.776204 -290 TTTATTTTAATTAAATATTTGACTATAATG 9 78 0 TTAAATATTT 0.69122 -223 GCAAAACTTTTTTTATTTTAATTAAATATT 9 89 0 TTTTATTTTA 0.595741 -212 TAAAAAATGCTTTTTTATTCAAGATTTTAT 9 159 0 TTTTTTATTC 0.692018 -142 TAAAAAAGCATTTTTTATTCATACTTTTTA 9 172 1 TTTTTTATTC 0.692018 -129 CAATAAAGAAATAATTATTACTGCTATAAA 9 217 0 ATAATTATTA 0.79986 -84 TGCTTTTAATATTAATCTAAATTA 9 287 0 TTTAATATTA 0.773044 -14 ACTACCTATTTTAAATATTATTATTGCAAT 10 16 1 TTAAATATTA 0.911671 -91 GCTCTTTTATTTTATTATTGCAATAATAAT 10 32 0 TTTATTATTG 0.84889 -75 AAATTTTGAGATATTTTTTAAAAAATCTGT 10 72 0 ATATTTTTTA 0.633576 -35 ********** Masking position 6 Map Score: 36.2963 Number of sites scoring better than the average of aligned sites = 1832 Number in coding regions = 1133 Number in noncoding regions = 699 Number of orfs with sites within 600 bp upstream = 274 Fraction of orfs with sites within 600 bp upstream = 0.044009 Motif number 2 ACTGAGCTATATAAGGATCTTGTATAACTTCTTTA 1 4 0 ATAATTTATT 0.637996 -142 AGTTTCTTCAAAAAGCTTATGTTCTAAAAAATTGCCTGTTTT 1 63 0 AAAATTTAAT 0.976959 -83 TCATACTCACAAAAAGATTTTAAGTAGCACATTTTAACTTGC 2 145 1 AAAATTTACT 0.897463 -156 ATTTATCAAGAAAACATTATTGTTAAAATAATTGTTACATAG 2 213 0 AAAATTAAAT 0.895559 -88 GAAATAAGCAAAATAGATATGTTCTATTGCTTATTATAATCA 3 74 1 AAATTTTACT 0.625986 -227 GAAGAATATTATAAGTTTTTGAGATTTTAAATTGAATCCTTG 3 217 1 ATAATTTTAT 0.746064 -84 TACCATGTGGATAAAACTATGTGGTAACAAATTAGGATTTGA 5 47 1 ATAATTTAAT 0.958827 -254 TTTGACATGAAAAATTTTATAAAATATTTATTTTTTTCTGTT 5 84 1 AAAATTTAAT 0.976268 -217 AAAATATAGCATAAAACTATTTTTTAGCTATTATATTCGATT 6 18 1 ATAATTTAAT 0.958827 -39 ATGTTAGTATAAATAGTTATCGTTTATGTAATCTTAAGATTC 7 69 1 AAATTTTAAT 0.890203 -232 CAATGGTAATAAAACTATTTATACTATAAATTCTAATTTTTC 7 254 0 AAAATTTAAT 0.976943 -47 TTATTTAAATAAAACTATCTTTTGCAAATAATATAATTAATA 8 116 1 AAAATTCAAT 0.834643 -185 TTACTATGTAAAAATTAGTTATGTTATTTATTAATTGATTTT 8 172 0 AAAAGTTAAT 0.810011 -129 ATCTTAATTGATAAGTTTATAATATAGAAATTT 8 278 1 ATAATTTAAT 0.958825 -23 AATTAAAATAAAAAAAGTTTTGCTTAGTCAATTATTCTAATA 9 96 1 AAAATTTAAT 0.97696 -205 TCTTGAATAAAAAAGCATTTTTTATTCATACTTTTTAAATAT 9 165 1 AAAATTTTAT 0.842508 -136 ATAAGACTCAATAATCTTGTCAATAAAGAAATAATTATTACT 9 225 0 ATAATTAAAT 0.821571 -76 TGCTTTTAATATTAATCTAAATTATGCATTTAGTATCTAA 9 271 0 ATATTTTAAT 0.816616 -30 TTATTGCAATAATAATATTTAAAATAGGTAGTAATCT 10 6 0 AATATTTAAT 0.742022 -101 AAAATATCTCAAAATTTTGTAGTAAAGTGATT 10 85 1 AAAATTAAAT 0.89588 -22 **** * * ** * * Masking position 10 Map Score: 24.84 Number of sites scoring better than the average of aligned sites = 176 Number in coding regions = 92 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 3 ATGCTGAAAGTTTAATAATTCTTGTTGTGTTA 2 111 0 TTAATAATCT 0.704617 -190 CATTTTAACTTGCAAATATTATCTTAATCAAT 2 174 1 TGAAATATAT 0.869182 -127 CTTGATAAATTTTAATAAATATTATATGATTC 2 245 1 TTAATAATAT 0.811157 -56 TCTCAAAAACTTATAATATTCTTCAGCAGTGA 3 209 0 TTTAATATCT 0.574968 -92 AAACTCTAGTTTAAGATAATATATAAGATCTT 4 35 0 TTAGATATAT 0.783095 -46 TTTTACTTGCTTTCAAAACTCTAGTTTAAGAT 4 50 0 TTCAAAATCT 0.66722 -31 CATGAAAAATTTTATAAAATATTTATTTTTTT 5 89 1 TTATAAATAT 0.708957 -212 CTTCTTGAAAAGATATGCATATTCAA 7 5 1 TTAAAAGTAT 0.771403 -296 GATATGCATATTCAAATAATATTCAGTAACAT 7 22 1 TTAAATATAT 0.96378 -279 TAATTGTTTATTTAAATAGTCTACAGTGGTAC 7 123 1 TTAAATATCT 0.936618 -178 AAAGCAAAAATTAAAAAATTATATTTTAAATC 7 221 1 TTAAAAATAT 0.963777 -80 GATAGTTTTATTTAAATAATATGGTATCGCAA 8 103 0 TTAAATATAT 0.96378 -198 AACTATCTTTTGCAAATAATATAATTAATAGA 8 128 1 TGAAATATAT 0.869182 -173 AATTAACATATTTAAAAAGTATGAATAAAAAA 9 182 0 TTAAAAATAT 0.96378 -119 TACTACCTATTTTAAATATTATTATTGCAATA 10 15 1 TTAAATATAT 0.96378 -92 CTACAGATTTTTTAAAAAATATCTCAAAATTT 10 70 1 TTAAAAATAT 0.96378 -37 ** ***** *** Masking position 10 Map Score: 16.4467 Number of sites scoring better than the average of aligned sites = 309 Number in coding regions = 189 Number in noncoding regions = 120 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 4 TAAAAACCAAAAAACAGGCAATTTTTTAGAAC 1 53 1 AAAAGGCAAT 0.921997 -93 AAGAAACTCGAGAAGAAGCAATATTGCGTCTT 1 97 1 AAAAAGCAAT 0.985684 -49 TTCTAATGATAAAAGACGCAATATTGCTTCTT 1 109 0 AAAACGCAAT 0.956049 -37 TACACAAATGAAAGAAAGCAATAAATAACACA 2 86 1 AAGAAGCAAT 0.915681 -215 TTGGATACAAGAAATAAGCAAAATAGATATGT 3 64 1 GAAAAGCAAA 0.746157 -237 TAGATTGATTATAATAAGCAATAGAACATATC 3 89 0 AAAAAGCAAT 0.985684 -212 TATAAAACAGAAAAAAATAAATATTTTATAAA 5 99 0 AAAAATAAAT 0.854958 -202 AACAGTAAGAATAACAAGAAATAAATTAT 5 282 1 AAAAAGAAAT 0.925832 -19 TCCTATGAAAATAAGAATAAATAAAAAAGGTA 7 152 0 AAAAATAAAT 0.854958 -149 ATCGATATTAAAACTAAGCAAATGCTTAAAAT 8 25 1 AACAAGCAAA 0.760664 -276 AAAAGCAATGAGAAAAATCAATTAATAAATAA 8 159 1 AAAAATCAAT 0.970161 -142 AGTTTGAGAAAGAAAAATCAAATTTTATTTAT 8 243 0 AAAAATCAAA 0.904901 -58 AAGTGTAGAAAGAAGAATCTATACGAAAATTT 9 23 0 AAAAATCTAT 0.761906 -278 ATCTAAATCTATAAGACTCAATAATCTTGTCA 9 245 0 AAAACTCAAT 0.911284 -56 * ** ******* Masking position 6 Map Score: 14.0017 Number of sites scoring better than the average of aligned sites = 255 Number in coding regions = 183 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 5 TTTTTGGTTTTTATTTATAAACTGAGCTATA 1 35 0 TTATTTTAAA 0.658812 -111 TATTTTGAGCATACTTCAATATCACTGTTAA 2 33 1 ATACTTAATA 0.716016 -268 TATGTAACAATTATTTTAACAATAATGTTTT 2 214 1 TTATTTAACA 0.847228 -87 TTTTCTTGATAAATTTTAATAAATATTATAT 2 241 1 AAATTTAATA 0.601203 -60 TTACCAACACTAATTTTAATATGTAGTAACA 5 255 1 TAATTTAATA 0.848635 -46 TTACTGAATATTATTTGAATATGCATATCTT 7 20 0 TTATTTAATA 0.969974 -281 AGTTAATTGTTTATTTAAATAGTCTACAGTG 7 120 1 TTATTTAATA 0.969959 -181 TTATTTATTCTTATTTTCATAGGAATAAATC 7 160 1 TTATTTCATA 0.910762 -141 AAAGATAGTTTTATTTAAATAATATGGTATC 8 107 0 TTATTTAATA 0.969959 -194 ATTAATTATATTATTTGCAAAAGATAGTTTT 8 126 0 TTATTTCAAA 0.749178 -175 TTTTTTTATTTTAATTAAATATTTGACTATA 9 81 0 TTAATTAATA 0.77466 -220 GCTTAGTCAATTATTCTAATATAATGTTTGC 9 117 1 TTATTCAATA 0.82494 -184 AGTAATTAACATATTTAAAAAGTATGAATAA 9 186 0 ATATTTAAAA 0.717684 -115 AATATGTTAATTACTTTTATAGCAGTAATAA 9 202 1 TTACTTTATA 0.656967 -99 TTTTATTTTATTATTGCAATAATAATATTTA 10 27 0 TTATTGAATA 0.82494 -80 ****** **** Masking position 3 Map Score: 9.05297 Number of sites scoring better than the average of aligned sites = 571 Number in coding regions = 338 Number in noncoding regions = 233 Number of orfs with sites within 600 bp upstream = 137 Fraction of orfs with sites within 600 bp upstream = 0.0220045 Motif number 6 TAAAATGTGCTACTTAAAATCTTTTTGTGAGT 2 149 0 TATTAAAATT 0.648584 -152 TAATATTTGCAAGTTAAAATGTGCTACTTAAA 2 163 0 AATTAAAATT 0.945456 -138 ATATACTTGTAACTCAAAATTTGAGTGCTAGA 3 117 0 AATCAAAATT 0.832967 -184 AGGTAACTAAGATTTAAGATTTGAGGTGAACG 3 171 0 GATTAAGATT 0.74794 -130 AAATCTCAAAAACTTATAATATTCTTCAGCAG 3 212 0 AATTATAATT 0.778717 -89 TCAAGGATTCAATTTAAAATCTCAAAAACTTA 3 228 0 AATTAAAATT 0.945456 -73 TTATTAACTTAATTTAAGTTCTT 3 288 1 AATTAAGTTT 0.834951 -13 ATGTGGTAACAAATTAGGATTTGACATGAAAA 5 65 1 AATTAGGATT 0.838937 -236 TTAAATTAAAATATAGCATAAAAC 6 3 1 AATTAAAATT 0.944115 -54 AAAAATTAAAAAATTATATTTTAAATCTGAAA 7 226 1 AATTATATTT 0.408296 -75 TAAATCTGAAAAATTAGAATTTATAGTATAAA 7 247 1 AATTAGAATT 0.793216 -54 AAAATAATTAAATATAAGATGTAAATATATAG 8 52 1 AAATAAGATT 0.632664 -249 CATAGTAAAGAAATGAAGATTTAATCTTATAC 8 206 1 AATGAAGATT 0.747429 -95 TGAGAAAGAAAAATCAAATTTTATTTATTGTG 8 239 0 AATCAAATTT 0.571104 -62 ATAAACTTATCAATTAAGATATAAGTTTGAGA 8 266 0 CATTAAGATT 0.74794 -35 ** ******* * Masking position 6 Map Score: 9.29756 Number of sites scoring better than the average of aligned sites = 206 Number in coding regions = 125 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 7 TAATCAAATTTACTATAATTTTTGTTACCAT 5 22 1 TACTATATTT 0.807837 -279 TTCTTACTGTTACTACATATTAAAATTAGTG 5 262 0 TACTACAATT 0.971698 -39 TTTGCTTTAATATTATCTATTAAAAGTCTTA 7 198 0 TATTATCATT 0.710676 -103 AAACTATTTATACTATAAATTCTAATTTTTC 7 254 0 TACTATAATT 0.963857 -47 TGCTTAGTTTTAATATCGATTTATGCATATA 8 14 0 TAATATCATT 0.710676 -287 ACTATCTTACTACTATATATTTACATCTTAT 8 65 0 TACTATAATT 0.963857 -236 AGATTACTACCTATTTTAAATATTA 10 5 1 TACTACCATT 0.965893 -102 GAGCCTATAATACTACAGATTTTTTAAAAAA 10 58 1 TACTACAATT 0.971698 -49 AATCACTTTACTACAAAATTTTGAGATAT 10 88 0 TACTACAAAT 0.844049 -19 ******* *** Masking position 5 Map Score: 7.38795 Number of sites scoring better than the average of aligned sites = 77 Number in coding regions = 51 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 8 CTCAAAATAAATATTACCACTGACACTTAG 2 12 0 ATATTACCAC 0.871791 -289 ACTATAATTTTTGTTACCATGTGGATAAAA 5 33 1 TTGTTACCAT 0.922221 -268 AAATCCTAATTTGTTACCACATAGTTTTAT 5 57 0 TTGTTACCAC 0.981077 -244 GCAATTATTATTGTTACTACAATATATAAA 5 125 0 TTGTTACTAC 0.953095 -176 TTAGCAGCAATTATTACCGCGTTACCAACA 5 234 1 TTATTACCGC 0.948915 -67 GTTATTCTTACTGTTACTACATATTAAAAT 5 267 0 CTGTTACTAC 0.862186 -34 ATAAATAGTTTTATTACCATTGACATGTTA 7 274 1 TTATTACCAT 0.882295 -27 AAAGAAATAATTATTACTGCTATAAAAGTA 9 213 0 TTATTACTGC 0.878949 -88 ********** Masking position 6 Map Score: 6.49224 Number of sites scoring better than the average of aligned sites = 54 Number in coding regions = 42 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 9 AAATATTATCTTAATCAATTTTTGATCTAT 2 187 1 TTAATCAATT 0.83377 -114 ATAAAGAAGCATAGTCAACTTAACAAAATA 3 25 1 ATAGTCAACT 0.815795 -276 ATTGCTTATTATAATCAATCTAGCACTCAA 3 99 1 ATAATCAATC 0.791965 -202 ATTCAATGTGATAATCAAATTTACTATAAT 5 11 1 ATAATCAAAT 0.932467 -290 CTAACACCATATAAGCAATTATTATTGTTA 5 139 0 ATAAGCAATT 0.808272 -162 AAAGATATGCATATTCAAATAATATTCAGT 7 19 1 ATATTCAAAT 0.712178 -282 GACTATTTAAATAAACAATTAACTACAAAA 7 114 0 ATAAACAATT 0.739883 -187 AGCAATGAGAAAAATCAATTAATAAATAAC 8 162 1 AAAATCAATT 0.833769 -139 TTGAGAAAGAAAAATCAAATTTTATTTATT 8 242 0 AAAATCAAAT 0.774061 -59 TTAGTGCATTATAGTCAAATATTTAATTAA 9 72 1 ATAGTCAAAT 0.907673 -229 AAAGTTTTGCTTAGTCAATTATTCTAATAT 9 109 1 TTAGTCAATT 0.78124 -192 ********** Masking position 7 Map Score: 5.2468 Number of sites scoring better than the average of aligned sites = 123 Number in coding regions = 77 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 10 ********** No masking Map Score: 1.21746e-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: 1.21746e-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: 1.21746e-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