AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -irpoH_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 HI0071 63 heat shock protein (grpE) #2 HI0104 216 heat shock protein (htpG) #3 HI0462 192 ATP-dependent proteinase (lon) #4 HI0496 218 heat shock protein (hslV) #5 HI0531 231 ribosomal protein S21 (rpS21) #6 HI0532 133 DNA primase (dnaG) #7 HI0533 69 RNA polymerase sigma-70 factor (rpoD) #8 HI0542 162 chaperonin (groES) #9 HI0543 22 heat shock protein (groEL) #10 HI0714 122 ATP-dependent Clp protease, proteolytic subunit (clpP) #11 HI0859 127 ATP-dependent Clp protease, ATPase subunit (clpB) #12 HI1237 265 heat shock protein 70 (dnaK) #13 HI1238 50 heat shock protein (dnaJ) #14 HI1334 126 cell division protein (ftsJ) #15 HI1335 90 cell division protein (ftsH) Motif number 1 ACTTTAAATGAAATAAAAAATTTCTTATCCCCC 2 91 0 AAAAAAATTT 0.956283 -126 TATAAGAATAAAAAGAAAGATTTCAAGAGGAAT 2 169 0 AAAAAAGTTT 0.645643 -48 AAAGATAAAAATTGAACGTCACAG 2 203 0 AAGAAAATTG 0.945965 -14 ATGGCTAAAATAATGAAAAATTTTATTAAATTT 3 27 0 TAAAAAATTT 0.837374 -166 GGTTTTAAACAAAAAAGAATTTTGGCAAATGAA 3 66 0 AAAAGAATTT 0.785764 -127 AAAAGGAATTCAAGGAAAAGATTATAACAAAAT 3 114 0 CAAAAAAATT 0.721901 -79 TATTGAATATAAGCTAAAAAATGTATGATCTGA 4 45 0 AAGAAAAATG 0.914132 -174 TCTTCACTCATAAATAAAAAATGTGAAGTTGAT 4 108 0 TAAAAAAATG 0.64625 -111 GTCCTTTATAAAGTGAAAAGTTGTTCGTTATAT 4 190 0 AAGAAAATTG 0.945965 -29 ACCTGTGTGTAAATGACAAATTTAATAAAGGAC 5 148 0 AAAACAATTT 0.665884 -84 TGCTTTGGCAAAAATAAAATTTTAAATTGCAAT 5 180 1 AAAAAAATTT 0.956232 -52 TGTGATTGAGAAGATAAGATTTTTTATGAACTT 7 26 0 AAGAAGATTT 0.714225 -44 AAATCTAAAATAGGAAAAATATTTTGTCAGAAT 8 60 1 TAGAAAAATT 0.811143 -103 AGCCCCTTGAAAGAAAAAAAATCCTCCTTATAT 8 101 1 AAGAAAAATC 0.671765 -62 TTTTATCTATCAATAAAAATTTGATGATAGGTT 11 11 0 CAAAAAATTG 0.713517 -117 TTGATAGATAAAATCAAAATATTTCATTTTTTC 11 31 1 AAAAAAAATT 0.930079 -97 AATAAATTTCAAGAGAAAAAATGAAATATTTTG 11 45 0 AAGAAAAATG 0.914132 -83 TCCTATTTTAAAGTAAAAATTTTCGCCAAATTT 12 20 1 AAGAAAATTT 0.967748 -246 CTTCAAGGGGAAAACAAAATTTTCAGGCAAGAA 12 68 0 AAAAAAATTT 0.956279 -198 GCACTTTAAGAAATAAAAAATTTTTAAAATTTT 12 146 1 AAAAAAATTT 0.956283 -120 TTCGCATTTCAAGAGAAAATTTTAAAAATTTTT 12 161 0 AAGAAAATTT 0.967748 -105 TTTGTACTCCTAGTAAAAATTTTAAAATTCGGG 12 243 0 TAGAAAATTT 0.875977 -23 ACGACTACAAAAAATAGAAGATT 14 114 1 AAAAGAAATT 0.690435 -13 TACCTTTCCTAAGTTAAAAAATTTCGTCACAAG 15 50 0 AAGAAAAATT 0.948042 -41 *** **** *** Masking position 12 Map Score: 36.2634 Number of sites scoring better than the average of aligned sites = 450 Number in coding regions = 342 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 2 AGGAATTTAAACCGCACTTTAAATGAAATA 2 109 0 ACCGCACTTT 0.997829 -108 GTGTTTTTTTACCGCACTTTTCCTCTTAAA 2 140 1 ACCGCACTTT 0.997829 -77 TTTTGTTTAAAACCCACTTTATAACTCAGA 3 85 1 AACCCACTTT 0.930082 -108 GCCAAAAACGACCGCACTTTCACACCACGA 6 98 1 ACCGCACTTT 0.997829 -36 TTATATAGAAACCGCACTTACAAATTATTA 8 128 1 ACCGCACTTA 0.984781 -35 AAAAAGAGCGACCGCACTTTTATTCAATCA 10 26 0 ACCGCACTTT 0.997829 -97 AACGGAAATTACCGCACTTTAAGAAATAAA 12 133 1 ACCGCACTTT 0.997829 -133 TTCACCGCTCTTCTTAGCATAAA 13 4 1 ACCGCTCTTC 0.968057 -47 GGCGTGTTTCCACGCCCTTTGTTTATGCTA 13 25 0 CACGCCCTTT 0.955296 -26 GGCGTGGAAACACGCCCTTTTG 13 39 1 CACGCCCTTT 0.955296 -12 GAGAAAATCAACCGCTCTTTTTTATTAGGA 14 17 0 ACCGCTCTTT 0.993165 -110 ********** Masking position 8 Map Score: 31.1303 Number of sites scoring better than the average of aligned sites = 1480 Number in coding regions = 978 Number in noncoding regions = 502 Number of orfs with sites within 600 bp upstream = 323 Fraction of orfs with sites within 600 bp upstream = 0.0518792 Motif number 3 CGCACTTTAAATGAAATAAAAAATTTCTTATC 2 95 0 ATAATAAAAA 0.896793 -122 GTCACAGATATAAGAATAAAAAGAAAGATTTC 2 178 0 TAAATAAAAA 0.930767 -39 ATAATGGCTAAAATAATGAAAAATTTTATTAA 3 31 0 AAAATGAAAA 0.935871 -162 GGAAAAAGGAATTCAAGGAAAAGATTATAACA 3 118 0 ATAAGGAAAA 0.83915 -75 ATTCTTCACTCATAAATAAAAAATGTGAAGTT 4 111 0 CAAATAAAAA 0.837657 -108 TCTGTCCTTTATAAAGTGAAAAGTTGTTCGTT 4 194 0 ATAGTGAAAA 0.892627 -25 TCTAATCTATTTTTAGGGAAAAAGTAAAGGAT 5 111 0 TTAGGGAAAA 0.821366 -121 ATAATAAATTAAGGAATGAAAAT 8 2 0 AAAATGAAAA 0.935871 -161 AAAAAATCTAAAATAGGAAAAATATTTTGTCA 8 57 1 AAAGGAAAAA 0.867615 -106 TGTAAGCCCCTTGAAAGAAAAAAAATCCTCCT 8 97 1 TTAAGAAAAA 0.827764 -66 TTATTAAATAAGGGAAAAGAAA 9 7 1 AAAGGGAAAA 0.876758 -16 GTAAATAACCCACAAATAAAAATGCGATCGCT 10 62 0 CAAATAAAAA 0.837657 -61 TAATTAGCAGTTTTAATGAAAAAGGTAAGAAA 10 101 1 TTAATGAAAA 0.901145 -22 TGATTTTATCTATCAATAAAAATTTGATGATA 11 15 0 TAAATAAAAA 0.930766 -113 CTTTCCTATTTTAAAGTAAAAATTTTCGCCAA 12 17 1 TTAGTAAAAA 0.884506 -249 ACCGCACTTTAAGAAATAAAAAATTTTTAAAA 12 143 1 AAAATAAAAA 0.930767 -123 TTTGTACTCCTAGTAAAAATTTTAAAATT 12 247 0 TCAGTAAAAA 0.789185 -19 AAGGATTCCTAATAAAAAAGAGCGGTTG 14 7 1 TCAATAAAAA 0.809427 -120 AGCTAATTGAAATCAGTAAAAAACATTGAGAA 14 42 0 AAAGTAAAAA 0.922174 -85 TACACATCATTAGCAATGAAAAGCTATCAAAG 15 14 0 TAAATGAAAA 0.935871 -77 ** ******** Masking position 5 Map Score: 24.2311 Number of sites scoring better than the average of aligned sites = 688 Number in coding regions = 424 Number in noncoding regions = 264 Number of orfs with sites within 600 bp upstream = 230 Fraction of orfs with sites within 600 bp upstream = 0.0369419 Motif number 4 TTTATAGCGATCAAGGGGGATAAGAAATTT 2 77 1 TCAAGGGGGA 0.968273 -140 CAAGAGGAATTTAAGAGGAAAAGTGCGGTA 2 149 0 TTAAGAGGAA 0.948932 -68 AAGAAAGATTTCAAGAGGAATTTAAGAGGA 2 160 0 TCAAGAGGAA 0.984766 -57 AAAAAGGAATTCAAGGAAAAGATTATAACA 3 118 0 TCAAGGAAAA 0.871439 -75 TTGATTAAATTCAAGAGGGAAATTTATATT 4 151 0 TCAAGAGGGA 0.970268 -68 ACCACAAATATTAAGGTGAATTGGCATTCT 5 81 1 TTAAGGTGAA 0.659922 -151 CTGACTCGAGTTAAGACAAACCGTGAATCC 6 24 1 TTAAGACAAA 0.692219 -110 CTCAATCACATCAAGCAAAACGAGTATAAA 7 49 1 TCAAGCAAAA 0.779871 -21 TTACAAATTATTAAGAAGGAAATTAATC 8 145 1 TTAAGAAGGA 0.725784 -18 TGAATAAATTTCAAGAGAAAAAATGAAATA 11 50 0 TCAAGAGAAA 0.96253 -78 ATGATGAACTTCAAGGGGAAAACAAAATTT 12 79 0 TCAAGGGGAA 0.983728 -187 CTTTCGCATTTCAAGAGAAAATTTTAAAAA 12 166 0 TCAAGAGAAA 0.96253 -100 TCTGTCAAATTCAAGCCGAAGCTAATTGAA 14 63 0 TCAAGCCGAA 0.905873 -64 ********** Masking position 4 Map Score: 18.3002 Number of sites scoring better than the average of aligned sites = 194 Number in coding regions = 170 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 5 CACAAGGAATTTAAACCGCACTTTAAATGAA 2 112 0 TAAACCGCAC 0.981662 -105 CCTTGTGTTTTTTTACCGCACTTTTCCTCTT 2 136 1 TTTACCGCAC 0.925824 -81 ACGCTGATTTAAAAACCGCTCAGATCATACA 4 26 1 AAAACCGCTC 0.981662 -193 TTCAACTGGTTAAAACCGCTTAAACAGGGTA 5 50 0 TAAACCGCTT 0.733539 -182 CTACGCCAAAAACGACCGCACTTTCACACCA 6 94 1 ACGACCGCAC 0.988085 -40 CTCCTTATATAGAAACCGCACTTACAAATTA 8 124 1 AAAACCGCAC 0.990296 -39 TATTAAAAAGAGCGACCGCACTTTTATTCAA 10 29 0 ACGACCGCAC 0.988085 -94 CAAGAACGGAAATTACCGCACTTTAAGAAAT 12 129 1 ATTACCGCAC 0.959668 -137 CATTGAGAAAATCAACCGCTCTTTTTTATTA 14 20 0 ACAACCGCTC 0.984767 -107 * ********* Masking position 5 Map Score: 12.9109 Number of sites scoring better than the average of aligned sites = 710 Number in coding regions = 479 Number in noncoding regions = 231 Number of orfs with sites within 600 bp upstream = 181 Fraction of orfs with sites within 600 bp upstream = 0.0290716 Motif number 6 GCAATGGTTTTAAAGGAACGATATAA 1 48 1 TAAAGGACGA 0.969481 -16 ATATAAGAATAAAAAGAAAGATTTCAAGAGG 2 172 0 AAAAAGAAGA 0.926408 -45 TTACCCAAATTATCGGAACGAAATTATAAGA 3 162 1 TATCGGACGA 0.819004 -31 GGAACGAAATTATAAGAGAGACCAATT 3 176 1 TATAAGAAGA 0.895816 -17 TTTCACTTTATAAAGGACAGAACA 4 205 1 TAAAGGAAGA 0.978077 -14 AGGGAAAAAGTAAAGGATAGAATGCCAATTC 5 98 0 TAAAGGAAGA 0.978077 -134 AAAAATCTAAAATAGGAAAAATATTTTGTCA 8 58 1 AATAGGAAAA 0.726957 -105 CGCTTTTATTAAAAAGAGCGACCGCACTTTT 10 35 0 AAAAAGACGA 0.899629 -88 GTTTTAATGAAAAAGGTAAGAAA 10 110 1 AAAAGGTAGA 0.862595 -13 TTTACTTTAAAATAGGAAAGAAATAA 12 6 0 AATAGGAAGA 0.968228 -260 ******* *** Masking position 2 Map Score: 8.44639 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 27 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 7 TCGCAATGATATTAACTTACAA 1 3 0 ATTAACTTAC 0.624058 -61 TTTCATTACTATTAAATTACTATCTAGTAT 2 19 1 ATTAAATTAC 0.919222 -198 CCTTGATCGCTATAAATTTATGTATATAAT 2 63 0 TATAAATTTA 0.645623 -154 TAAATGAAATAAAAAATTTCTTATCCCCCT 2 90 0 AAAAAATTTC 0.746173 -127 TAAAGTGCGGTTTAAATTCCTTGTGTTTTT 2 118 1 TTTAAATTCC 0.691457 -99 GAAAAATTTTATTAAATTTCACAAAATATT 3 16 0 ATTAAATTTC 0.939996 -177 AAATCTACAATATAAATTTCCCTCTTGAAT 4 143 1 TATAAATTTC 0.82094 -76 CGACAAATTGATTAAATTCAAGAGGGAAAT 4 158 0 ATTAAATTCA 0.752653 -61 CATTTTAGGTAATAAATTAAGAAAATCA 5 9 0 AATAAATTAA 0.818906 -223 TGCGTCCTTTATTAAATTTGTCATTTACAC 5 145 1 ATTAAATTTG 0.694769 -87 TTAAATTGCAATTAAATTAAACTCATTGAG 5 201 1 ATTAAATTAA 0.818906 -31 ACTTTCGTATAATAAATTAAGGAATGAAAA 8 12 0 AATAAATTAA 0.818906 -151 AGCTCGGTTGAATAAATTTCAAGAGAAAAA 11 58 0 AATAAATTTC 0.939996 -70 TTCCTAAGTTAAAAAATTTCGTCACAAGAT 15 48 0 AAAAAATTTC 0.746173 -43 ********** Masking position 5 Map Score: 9.0587 Number of sites scoring better than the average of aligned sites = 302 Number in coding regions = 234 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 8 ATGGTTTTAAAGGAACGATATAA 1 51 1 AGGAACGATA 0.95763 -13 CCCAAATTATCGGAACGAAATTATAAGAGA 3 165 1 CGGAACGAAA 0.899856 -28 AGCGTTTGTGAGGAAAGGCA 4 1 0 AGGAAAGGCA 0.919641 -218 TAATAAATTAAGGAATGAAAAT 8 3 0 AGGAATGAAA 0.915574 -160 AATCTAAAATAGGAAAAATATTTTGTCAGA 8 61 1 AGGAAAAATA 0.705361 -102 TTAATGAAAAAGGTAAGAAA 10 113 1 AGGTAAGAAA 0.891712 -10 ACTTTAAAATAGGAAAGAAATAA 12 4 0 AGGAAAGAAA 0.981216 -262 CAAAATTTTCAGGCAAGAAAAAGGGATTTG 12 57 0 AGGCAAGAAA 0.92427 -209 TTTGAAAAACAAGAACGGAAATTACCGCAC 12 120 1 AAGAACGGAA 0.728278 -146 TTTTTAACTTAGGAAAGGTAGGTTAGACTT 15 63 1 AGGAAAGGTA 0.951243 -28 ********** Masking position 5 Map Score: 7.52692 Number of sites scoring better than the average of aligned sites = 107 Number in coding regions = 66 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 9 TCTAGTATCTAAAACAGAATTCATTATATAC 2 41 1 AAAAAGAATT 0.950257 -176 CTTTAAATGAAATAAAAAATTTCTTATCCCC 2 92 0 AATAAAAATT 0.863799 -125 TAAGAATAAAAAGAAAGATTTCAAGAGGAAT 2 169 0 AAGAAGATTT 0.756722 -48 GGTTTTAAACAAAAAAGAATTTTGGCAAATG 3 68 0 AAAAAGAATT 0.950289 -125 TGGGGTAGGGAAAAAGGAATTCAAGGAAAAG 3 127 0 AAAAGGAATT 0.913913 -66 ATAAATCTACAATATAAATTTCCCTCTTGAA 4 141 1 AATAAAATTT 0.748491 -78 TTTTTCCCTAAAAATAGATTAGAATTGCGTC 5 120 1 AAAAAGATTA 0.690591 -112 TGCTTTGGCAAAAATAAAATTTTAAATTGCA 5 180 1 AAAAAAAATT 0.938136 -52 CAAATTATTAAGAAGGAAATTAATC 8 148 1 AGAAGAAATT 0.516552 -15 TTTATCTATCAATAAAAATTTGATGATAGGT 11 12 0 AATAAAATTT 0.748591 -116 TTCAAGAGAAAAAATGAAATATTTTGATTTT 11 40 0 AAAAGAAATA 0.676924 -88 TCAGGCAAGAAAAAGGGATTTGTGATAAATT 12 48 0 AAAAGGATTT 0.832894 -218 CTTCAAGGGGAAAACAAAATTTTCAGGCAAG 12 70 0 AAAAAAAATT 0.93813 -196 CACTTTAAGAAATAAAAAATTTTTAAAATTT 12 147 1 AATAAAAATT 0.863799 -119 TTCGCATTTCAAGAGAAAATTTTAAAAATTT 12 163 0 AAGAAAAATT 0.840203 -103 ACGACTACAAAAAATAGAAGATT 14 114 1 AAAAAGAAGA 0.376127 -13 **** ****** Masking position 4 Map Score: 12.7632 Number of sites scoring better than the average of aligned sites = 462 Number in coding regions = 338 Number in noncoding regions = 124 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 10 AACTCAATATTTTGTGAAATTTAATAA 3 8 1 TATTTTGTGA 0.957803 -185 TTATAACTCAGATTTTGTTATAATCTTTTC 3 103 1 GATTTTGTTA 0.863507 -90 AAGTTGATCATATTTTGAGATGGCAAACGA 4 86 0 TATTTTGAGA 0.781574 -133 TGATTTTCTTAATTTATTACC 5 2 1 GATTTTCTTA 0.836265 -230 TTTATAGTATTTTCTGACTCGAGTTAA 6 8 1 TATTTTCTGA 0.948254 -126 TAAAAAATCTTATCTTCTCAATCACATCAA 7 33 1 TATCTTCTCA 0.872115 -37 ATAGGAAAAATATTTTGTCAGAATTTTTTG 8 69 1 TATTTTGTCA 0.945299 -94 AAGAGCGGTTGATTTTCTCAATGTTTTTTA 14 28 1 GATTTTCTCA 0.92005 -99 TGATGTGTAGTATCTTGTGACGAAATTTTT 15 37 1 TATCTTGTGA 0.917321 -54 ********** Masking position 5 Map Score: 6.4482 Number of sites scoring better than the average of aligned sites = 123 Number in coding regions = 93 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 11 TTTGGGTAAATATTGGGGTAGGGAAAAAGG 3 141 0 TATTGGGGTA 0.935972 -52 TCGTTCCGATAATTTGGGTAAATATTGGGG 3 153 0 AATTTGGGTA 0.934141 -40 ATCGCGCAACATTTTAGGTAATAAATTAAG 5 18 0 ATTTTAGGTA 0.851349 -214 GTGCGGTCGTTTTTGGCGTAGATTTTTGTT 6 85 0 TTTTGGCGTA 0.902736 -49 AAGTCAGCGAATTTTACGTAAAAAATCTAA 8 38 1 ATTTTACGTA 0.746931 -125 GCCGAAATCAAATTGAGGAAAGTGT 11 113 1 AATTGAGGAA 0.742675 -15 TTTGTGATAAATTTGGCGAAAATTTTTACT 12 31 0 ATTTGGCGAA 0.848282 -235 AAATTTTAAAATTCGGGGTAGGGCTTTTAG 12 230 0 ATTCGGGGTA 0.889156 -36 GTTTCGCCTATATTTGGGTACAATCTGTCA 14 86 0 TATTTGGGTA 0.881521 -41 ********** Masking position 3 Map Score: 2.24324 Number of sites scoring better than the average of aligned sites = 284 Number in coding regions = 247 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 12 ********** No masking Map Score: 3.21409e-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: 3.21409e-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: 3.21409e-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