AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -ilexA_hinf_opreg_100.orf -g0.38 -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 = 0.38 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 HI0070 143 DNA repair protein (recN) #2 HI0249 153 excinuclease ABC, subunit A (uvrA) #3 HI0313 62 Holliday junction DNA helicase (ruvA) #4 HI0314 46 crossover junction endodeoxyribonuclease (ruvC) #5 HI0315 159 conserved hypothetical protein #6 HI0600 300 recA protein (recA) #7 HI0749 248 lexA repressor (lexA) #8 HI1188 300 DNA helicase II (uvrD) #9 HI1247 300 excinuclease ABC, subunit B (uvrB) #10 HI1593 34 H. influenzae predicted coding region HI1593 #11 HI1596 58 leucine responsive regulatory protein (lrp) #12 HI1597 84 DNA repair protein (radA) #13 HI1598 300 conserved hypothetical protein Motif number 1 AGCAAAATCCTTTAACTGTATATTTAATATGATAT 1 119 0 TTTAAAATTT 0.804657 -25 AAAAAAACCTCATTTTTTATCTAAAAA 2 3 1 AAAAAATTTT 0.816326 -151 TTTCAGGCAAAATAACCGCACTTTTTTAGATAAAA 2 25 0 AATAAATTTT 0.892446 -129 ATCTATATATTTTAACTGGATATTTGCACAGATAT 2 71 1 TTTAAAATTT 0.804657 -83 AAAAGTATGAAATAAATGTAAATTTTGCGATCATT 2 119 0 AATAAAATTT 0.919372 -35 ATGGGTAATTTAATTACCCATTTTTTATAGAAATT 4 22 1 TAATTATTTT 0.494962 -25 TTGATCTTGATTTAATTAAACGTTTTGACCTAGGC 5 110 0 TTTAAAGTTT 0.445632 -50 TGATTTCATTTATATCATGAAATTTTTACTACACC 6 42 1 TATATAATTT 0.826308 -259 ACACCTAAATATAAATGTCAGATTTGTGAGCCAGA 6 72 1 ATAAAAATTT 0.763916 -229 TTAGATAAAAATAAATTTTAAATTTACGATCTGGC 6 101 0 ATAAAAATTT 0.756893 -200 GTTTATATATTAATATACTATATTTAAAACTTTTA 6 143 1 TAATAAATTT 0.732024 -158 GGGGAAGGCTTAAAATAAAAGTTTTAAATATAGTA 6 158 0 TAAAAATTTT 0.852168 -143 TTACTGAAATATATACCCCATATTTTTTTATTAAT 6 200 1 ATATAAATTT 0.553563 -101 TTTTTTTATTAATATAAATATTTTTCTTGACCTGT 6 222 1 AATATATTTT 0.785462 -79 GGATGTGTTAAAATATTTGAGTTTTTGGACGATAA 7 102 0 AAATAATTTT 0.639897 -147 CGATCTCAACTAATTTAGAAAATTTGGCGACAAAA 7 136 1 TAATTAATTT 0.567107 -113 TAAATCTGTGTATTAAGTCACATTTTGTCGCCAAA 7 158 0 TATTAAATTT 0.804657 -91 CTCTCATTCCTAAAATGCAAGGTTTCTCATTTTTC 8 66 0 TAAAAAGTTT 0.608681 -235 TTATACTATTTATAAACAAACTTTTAATTCGTTTA 8 102 0 TATAAATTTT 0.886606 -199 ATGGGACTATAATAACTGTAAATTTAAACAGATTA 8 266 1 AATAAAATTT 0.919372 -35 ACTTATTGATTTTAAATTAAAATTTAATTTTAGGC 9 109 0 TTTAAAATTT 0.804657 -192 ATTTAAAATCAATAAGTTAAGTTTTGTCTAGTAAA 9 127 1 AATAAATTTT 0.892446 -174 AATTCATTAAAAAAACTTTAAATTTTTACTAGACA 9 151 0 AAAAAAATTT 0.885792 -150 TTGATCAGGCAAAAATCTAAGTTTTACACAGACTT 9 212 0 AAAAAATTTT 0.800358 -89 GAATAATGCCTATTTTAGCATATTTACTGTGTAAA 9 248 0 TATTTAATTT 0.645451 -53 GTGCGGTCGGTTTTTTGATAGTTTTGAATAATGCC 9 273 0 TTTTTATTTT 0.336521 -28 GAGTAAGATGAAAATATTCATATTTTCATCTTACT 13 16 1 AAAATAATTT 0.772628 -285 ATCTTACTTATTTTAATTGACATTTCACAATTATT 13 43 1 TTTTAAATTT 0.612032 -258 AAGCCAGATTAAAATGTGAATATTTACTAATCTAA 13 84 0 AAAATAATTT 0.772628 -217 TTCATCGGATAATATTGATAATTTTAAATAACAAA 13 117 0 AATATATTTT 0.767069 -184 TTGTGATTAAAATATTGCGACTTTTAAATAAAAAA 13 176 0 AATATATTTT 0.785283 -125 ATTAAATAGCTATAAATGAATTTTTATTTATTGTG 13 206 0 TATAAATTTT 0.886601 -95 ATACAATAGAAATAAATCAAGATTTTTGTGGTGTT 13 252 0 AATAAAATTT 0.919453 -49 ***** * **** Masking position 10 Map Score: 37.1578 Number of sites scoring better than the average of aligned sites = 924 Number in coding regions = 620 Number in noncoding regions = 304 Number of orfs with sites within 600 bp upstream = 228 Fraction of orfs with sites within 600 bp upstream = 0.0366206 Motif number 2 GTAGCAAATTAGGTTGGTTAAAATCATTTTGATT 1 9 1 TGTGTAAAAT 0.71503 -135 AAAATCATTTTGATTATGGTAAAAATTTTCGATTGA 1 30 1 TTTGTAAAAT 0.969151 -114 TCGATTGAAATAGATTTGACAAAATACTGTAAAAAA 1 58 1 TTTGCAAATA 0.744015 -86 TTAAGTCAGTTATATCATATTAAATATACAGTTAAA 1 108 1 TTATTAAATA 0.558265 -36 ATAACCGCACTTTTTTAGATAAAAAATGAGGTTTTT 2 13 0 TTAGTAAAAA 0.542206 -141 TTAAAATATATAGATCTTTTAAAAAATTTCAGGCAA 2 50 0 TTTTTAAAAA 0.850367 -104 AATTCTTCCGAATGATAAAAAAATTAACGCAT 3 41 0 TATGTAAAAA 0.774744 -22 TAAATCAAGATCAATAAGATCAAAACAGAAGGAAAT 5 131 1 TTAGTAAAAC 0.691681 -29 GTACTTCTACTGACTCTTTTAAAATAAT 6 3 0 TTTTTAAATA 0.699273 -298 CATTTATATTTAGGTGTAGTAAAAATTTCATGATAT 6 53 0 TTTATAAAAT 0.856072 -248 TATAAACCAATCGTTTAGATAAAAATAAATTTTAAA 6 114 0 TTAGTAAAAT 0.94649 -187 AGAAAAATATTTATATTAATAAAAAAATATGGGGTA 6 213 0 TATATAAAAA 0.394365 -88 TAAAATCCTGTTTGAATGTTCAAATTTTTGTGATTA 6 272 0 TATGTAAATT 0.63639 -29 GGGCTAAAAATAGTTCTATTCACAAACTGCTTTTTA 7 56 0 TTTATACAAA 0.495753 -193 CAATACCAGTTATCTGTGTTTAAAAACAGGA 7 228 1 TTTGTAAAAA 0.961754 -21 GCAAGGTTTCTCATTTTTCCAAAAATACCCATGATG 8 49 0 TTTTCAAAAT 0.665288 -252 TACCCTACTTTTGATATACTCACAAATCTTATTGTT 8 219 1 TTTATACAAA 0.495818 -82 AAACTATCTTTAATCTGTTTAAATTTACAGTTATT 8 276 0 TTTGTAAATT 0.92782 -25 ATCTTGATTATAGATTAGCCTAAAATTAAATTTTAA 9 92 1 TTAGCAAAAT 0.832626 -209 AAAACTTAACTTATTGATTTTAAATTAAAATTTAAT 9 116 0 TTATTAAATT 0.619341 -185 TAAGTTAAGTTTTGTCTAGTAAAAATTTAAAGTTTT 9 139 1 TTTATAAAAT 0.856068 -162 CTGTGTAAAATTGATCAGGCAAAAATCTAAGTTTTA 9 221 0 TTAGCAAAAT 0.832626 -80 TTTTACACAGTAAATATGCTAAAATAGGCATTATTC 9 247 1 TTTGTAAATA 0.911772 -54 TTTACTCAAGTTTCTTTGCTAACAAAAGATGAA 10 12 1 TTTGTACAAA 0.836713 -23 ATGCTGAGTAAGATGAAAATATTCATATTT 13 5 1 TTAGTAAAAT 0.946494 -296 TCAATTAAAATAAGTAAGATGAAAATATGAATATTT 13 27 0 TTAGTAAAAT 0.946465 -274 TTAATCTGGCTTTGTTATTTAAAATTATCAATATTA 13 107 1 TTATTAAATT 0.615843 -194 GAATTTTTATTTATTGTGATTAAAATATTGCGACTT 13 188 0 TTTGTAAAAT 0.969147 -113 * * ** * ***** Masking position 12 Map Score: 26.6734 Number of sites scoring better than the average of aligned sites = 959 Number in coding regions = 732 Number in noncoding regions = 227 Number of orfs with sites within 600 bp upstream = 203 Fraction of orfs with sites within 600 bp upstream = 0.0326052 Motif number 3 ATTAGGTTGGTTAAAATCATTTTGATTATG 1 18 1 TTAAAATCAT 0.630206 -126 AACTGTATATTTAATATGATATAACTGACT 1 111 0 TTAATATGAT 0.470973 -33 TATAGATCTTTTAAAAAATTTCAGGCAAAA 2 48 0 TTAAAAAATT 0.604341 -106 AAATATCCAGTTAAAATATATAGATCTTTT 2 66 0 TTAAAATATA 0.935406 -88 TGCACAGATATTAAAATATGCGATAATGAT 2 95 1 TTAAAATATG 0.881495 -59 AACGCATAGAATAAAATAAAACTGGACGAA 3 18 0 ATAAAATAAA 0.333247 -45 ACTGACTCTTTTAAAATAAT 6 1 0 TTAAAATAAT 0.886075 -300 GATCGTAAATTTAAAATTTATTTTTATCTA 6 105 1 TTAAAATTTA 0.746093 -196 ATATAGTATATTAATATATAAACCAATCGT 6 136 0 TTAATATATA 0.727777 -165 AAATAAAAGTTTTAAATATAGTATATTAAT 6 151 0 TTTAAATATA 0.569281 -150 TGGGGAAGGCTTAAAATAAAAGTTTTAAAT 6 164 0 TTAAAATAAA 0.909087 -137 TATTTTTTTATTAATATAAATATTTTTCTT 6 220 1 TTAATATAAA 0.629407 -81 ATCGGATGTGTTAAAATATTTGAGTTTTTG 7 110 0 TTAAAATATT 0.918154 -139 ATACACAGATTTAAAAAATAACAGTTGCAA 7 180 1 TTAAAAAATA 0.663513 -69 AATATTATTCTTAAAATGTTCTACCCTACT 8 198 1 TTAAAATGTT 0.874158 -103 CCGCAAAATTTTAAAAAGTTAATCCACAAA 9 35 0 TTAAAAAGTT 0.486077 -266 TGATTTTAAATTAAAATTTAATTTTAGGCT 9 108 0 TTAAAATTTA 0.746093 -193 AAATTTTAATTTAAAATCAATAAGTTAAGT 9 119 1 TTAAAATCAA 0.687475 -182 CATCGCCTACTGAAAATGAAAGGAAAATTC 11 17 1 TGAAAATGAA 0.571071 -42 CTGAGTAAGATGAAAATATTCATATTTTCA 13 14 1 TGAAAATATT 0.706036 -287 ATAAGTAAGATGAAAATATGAATATTTTCA 13 24 0 TGAAAATATG 0.614281 -277 GAAATGTCAATTAAAATAAGTAAGATGAAA 13 39 0 TTAAAATAAG 0.837609 -262 CAAAGCCAGATTAAAATGTGAATATTTACT 13 91 0 TTAAAATGTG 0.821621 -210 GCTTTGTTATTTAAAATTATCAATATTATC 13 115 1 TTAAAATTAT 0.612078 -186 TATTGCGACTTTTAAATAAAAAAATAATCC 13 169 0 TTTAAATAAA 0.477321 -132 TTTATTGTGATTAAAATATTGCGACTTTTA 13 185 0 TTAAAATATT 0.918154 -116 TTATAGCTATTTAATATGTAAAGTAAAACA 13 226 1 TTAATATGTA 0.623759 -75 ********** Masking position 6 Map Score: 25.0025 Number of sites scoring better than the average of aligned sites = 472 Number in coding regions = 306 Number in noncoding regions = 166 Number of orfs with sites within 600 bp upstream = 156 Fraction of orfs with sites within 600 bp upstream = 0.0250562 Motif number 4 TATTTAATATGATATAACTGACTTAATTTA 1 104 0 GATATAACTG 0.914744 -40 TCAAAAGTATGAAATAAATGTAAATTTTGC 2 126 0 GAAATAAATG 0.972083 -28 TGATGCAATAAATGGGTAATTTAA 4 5 1 GCAATAAATG 0.971577 -42 AAAATTTCATGATATAAATGAAATCAGAAG 6 38 0 GATATAAATG 0.97192 -263 ACTACACCTAAATATAAATGTCAGATTTGT 6 69 1 AATATAAATG 0.795665 -232 ATCTAAATTAGCAATAATTGTGAAATGTCA 13 60 0 GCAATAATTG 0.876496 -241 ATATTAAATAGCTATAAATGAATTTTTATT 13 213 0 GCTATAAATG 0.971571 -88 CAATACAATAGAAATAAATCAAGATTTTTG 13 259 0 GAAATAAATC 0.850922 -42 ********** Masking position 6 Map Score: 7.14822 Number of sites scoring better than the average of aligned sites = 45 Number in coding regions = 37 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 5 TGTAGCTTTTCCCAAAAGAGAACCGCTATCACCATA 5 28 0 CCCAAGGACC 0.998722 -132 TACATCCACTCCCAACGGGGTAACACTTTTACTAAC 5 60 1 CCCAAGGACC 0.998722 -100 ATCAAACTACCCCAACGGAGTAGCACTGAGATCAGC 12 22 0 CCCAAGGACC 0.998722 -63 TTTGATGTTCCCCAAAGGGGAACCACTATAACTATA 12 52 1 CCCAAGGACC 0.998722 -33 ***** * * * * * Masking position 5 Map Score: 5.45899 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 TGACAAAATACTGTAAAAAATCCTTTACTG 1 74 1 CTGTAAAAAA 0.743359 -70 AAATCCTTTACTGTAAATTAAGTCAGTTAT 1 91 1 CTGTAAATTA 0.656996 -53 AAAAAGCAGTTTGTGAATAGAACTATTTTT 7 57 1 TTGTGAATAG 0.690057 -192 TTTTTTAAATCTGTGTATTAAGTCACATTT 7 168 0 CTGTGTATTA 0.915377 -81 TGTATACAGATTGTGTAAAGTTGCAACTGT 7 200 0 TTGTGTAAAG 0.737188 -49 TTTACACAATCTGTATACAATACCAGTTAT 7 211 1 CTGTATACAA 0.487899 -38 TACCAGTTATCTGTGTTTAAAAACAGGA 7 231 1 CTGTGTTTAA 0.651165 -18 TCCACAGGCTCTGTGGATAG 9 1 0 CTGTGGATAG 0.931586 -300 TCCACAGAGCCTGTGGATAACTTTGTGGAT 9 14 1 CTGTGGATAA 0.953582 -287 GTGGATAACTTTGTGGATTAACTTTTTAAA 9 26 1 TTGTGGATTA 0.752364 -275 ATCGCTAAGTCTGTGTAAAACTTAGATTTT 9 206 1 CTGTGTAAAA 0.942296 -95 AGCATATTTACTGTGTAAAATTGATCAGGC 9 237 0 CTGTGTAAAA 0.942296 -64 AAGGAAAATTCTGTAGAATAGTTGTTCCTT 11 36 1 CTGTAGAATA 0.72395 -23 TTAGCAATAATTGTGAAATGTCAATTAAAA 13 53 0 TTGTGAAATG 0.522978 -248 ********** Masking position 4 Map Score: 7.89696 Number of sites scoring better than the average of aligned sites = 208 Number in coding regions = 181 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 7 CTTTTACTAACCTAGGCTATACCTAGCCTA 5 85 1 CCTAGGCTAT 0.993116 -75 AACGTTTTGACCTAGGCTAGGTATAGCCTA 5 97 0 CCTAGGCTAG 0.988321 -63 AAACAACATTCCTATGCTATTATTGTCATC 8 23 1 CCTATGCTAT 0.973198 -278 CTGAGATCAGCCTAGGGTATAC 12 3 0 CCTAGGGTAT 0.981758 -82 ********** Masking position 4 Map Score: 2.73785 Number of sites scoring better than the average of aligned sites = 3 Number in coding regions = 0 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 8 TCACAGCTAATTATGGTGATAGCGGTTCTC 5 17 1 TTATGGTGAT 0.939641 -143 AATGTTCAAATTTTTGTGATTATATCTGTA 6 264 0 TTTTTGTGAT 0.948774 -37 TCCTATGCTATTATTGTCATCATGGGTATT 8 32 1 TTATTGTCAT 0.887937 -269 TTAATTATAGTTATAGTGGTTCCCCTTTGG 12 63 0 TTATAGTGGT 0.89699 -22 GAATTTTTATTTATTGTGATTAAAATATTG 13 194 0 TTATTGTGAT 0.971876 -107 TAAATCAAGATTTTTGTGGTGTTTTACTTT 13 245 0 TTTTTGTGGT 0.938857 -56 ********** Masking position 4 Map Score: 2.1335 Number of sites scoring better than the average of aligned sites = 79 Number in coding regions = 59 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 9 TTTTCGATTGAAATAGATTTGACAAAATAC 1 55 1 AAATAGATTT 0.923986 -89 GTTTAGATAAAAATAAATTTTAAATTTACG 6 108 0 AAATAAATTT 0.596254 -193 TTCTATTCACAAACTGCTTTTTAAACGTCT 7 49 0 AAACTGCTTT 0.813021 -200 GTGACTTAATACACAGATTTAAAAAATAAC 7 172 1 ACACAGATTT 0.868138 -77 AATAGTATAAAAATAGCTTTCAAAGCATAT 8 127 1 AAATAGCTTT 0.937556 -174 CTGTAAATTTAAACAGATTAAAGATAGTTT 8 281 1 AAACAGATTA 0.816264 -20 CGAAAAACATAAACAGATTTCATCGGATAA 13 140 0 AAACAGATTT 0.960253 -161 TTTACATATTAAATAGCTATAAATGAATTT 13 218 0 AAATAGCTAT 0.733003 -83 ********** Masking position 3 Map Score: 2.44233 Number of sites scoring better than the average of aligned sites = 143 Number in coding regions = 111 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 10 AATTTCAGGCAAAATAACCGCACTTTTTTAG 2 31 0 AAAATACCGC 0.967509 -123 AAAATATGCGATAATGATCGCAAAATTTACA 2 107 1 ATAATATCGC 0.949842 -47 GAATGATAAAAAAATTAACGCATAGAATAAA 3 33 0 AAAATAACGC 0.882283 -30 GTATAATCACAGCTAATTATGGT 5 3 1 ATAATACAGC 0.93514 -157 ACAGATTTAAAAAATAACAGTTGCAACTTTA 7 184 1 AAAATACAGT 0.677049 -65 ACCCATGATGACAATAATAGCATAGGAATGT 8 28 0 ACAATATAGC 0.874984 -273 TATAAATAGTATAAAAATAGCTTTCAAAGCA 8 123 1 ATAAAATAGC 0.681489 -178 AAAAATCATCGCCTACTGAAAA 11 2 1 AAAATATCGC 0.961026 -57 ***** ***** Masking position 7 Map Score: 2.10153 Number of sites scoring better than the average of aligned sites = 351 Number in coding regions = 250 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 11 ATTTTTACCATAATCAAAATGATTTTAACC 1 26 0 TAATCAAAAT 0.762506 -118 ACGTTTAATTAAATCAAGATCAATAAGATC 5 122 1 AAATCAAGAT 0.90871 -38 GTCAGATTTGTGAGCCAGATCGTAAATTTA 6 88 1 TGAGCCAGAT 0.819574 -213 GGCTAATCTATAATCAAGATCGAATAATCC 9 82 0 TAATCAAGAT 0.908711 -219 TATTGATTTTAAATTAAAATTTAATTTTAG 9 111 0 AAATTAAAAT 0.578085 -190 AGCGATGTCAAGAGGAAGATGTCACAAATT 9 182 0 AGAGGAAGAT 0.822605 -119 ACTGAAAATGAAAGGAAAATTCTGTAGAAT 11 25 1 AAAGGAAAAT 0.645149 -34 ATGCTGAGTAAGATGAAAATATTC 13 5 1 TGAGTAAGAT 0.848333 -296 TCAATTAAAATAAGTAAGATGAAAATATGA 13 33 0 TAAGTAAGAT 0.87178 -268 TTTAAATAACAAAGCCAGATTAAAATGTGA 13 100 0 AAAGCCAGAT 0.846664 -201 TTATTTATTGTGATTAAAATATTGCGACTT 13 188 0 TGATTAAAAT 0.529892 -113 CAATAGAAATAAATCAAGATTTTTGTGGTG 13 254 0 AAATCAAGAT 0.90871 -47 ********** Masking position 7 Map Score: 5.56551 Number of sites scoring better than the average of aligned sites = 330 Number in coding regions = 281 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 12 ********** No masking Map Score: -4.47399e-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: -4.47399e-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 14 ********** No masking Map Score: -4.47399e-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