AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -ipdhR_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 HI1231 113 dihydrolipoamide dehydrogenase (lpdA) #2 HI1232 62 dihydrolipoamide acetyltransferase (aceF) #3 HI1233 299 pyruvate dehydrogenase, E1 component (aceE) Motif number 1 AAAGACCGTAAAAGTGCGGTCAATATTTTT 1 74 1 AAAGTGCGGT 0.999159 -40 TTGATGAAAACTGCGGTCAAAAAACAT 2 8 1 AAACTGCGGT 0.997863 -55 TGTTCCTTTTAAAGTGCGGTCATAAAACAC 2 39 0 AAAGTGCGGT 0.999159 -24 TAATTATTTGAAAGTGCGGTAATTTTTTTG 3 106 0 AAAGTGCGGT 0.999159 -194 ********** Masking position 5 Map Score: 14.118 Number of sites scoring better than the average of aligned sites = 1115 Number in coding regions = 700 Number in noncoding regions = 415 Number of orfs with sites within 600 bp upstream = 285 Fraction of orfs with sites within 600 bp upstream = 0.0457758 Motif number 2 AAAACTGCGGTCAAAAAACATTGTGTTTTATG 2 17 1 TCAAAAAATT 0.990708 -46 GAAAAAAATCTGAAAAAACTTTAAAACAAAGC 3 26 1 TGAAAAAATT 0.939361 -274 GAACAAAAAAACACAAAAAAATTACCGCACTT 3 93 1 ACACAAAAAT 0.811656 -207 TACCGCACTTTCAAATAATTATTTATGGCAAA 3 115 1 TCAAATAAAT 0.967036 -185 AATCATCATATCAAATCAGCTTTGCCATAAAT 3 135 0 TCAAATCATT 0.978782 -165 TGAATTTTCATCAAATCATCATATCAAATCAG 3 148 0 TCAAATCAAT 0.960315 -152 TATCTTTATCTCAAAAAATCTTCTAAAATTTA 3 181 1 TCAAAAAATT 0.990708 -119 TATTTGCTTTTCACAAACATTTAACAAATCTT 3 214 0 TCACAAACTT 0.924105 -86 TAATATTCACTCAAAACAGATTAAGGAAAACC 3 277 1 TCAAAACATT 0.988756 -23 ******** ** Masking position 5 Map Score: 12.1118 Number of sites scoring better than the average of aligned sites = 171 Number in coding regions = 137 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 3 CACCGATTAATGAAATCTTTGGTGGGCAGAA 1 32 1 TGAATCTTTG 0.925754 -82 TAAAAGTGCGGTCAATATTTTTAACGTTTTT 1 82 1 GTAATATTTT 0.933722 -32 CCCGATGGAATGCAATATTTTACTGGTTATT 3 57 1 TGAATATTTT 0.90071 -243 ATATTTTACTGGTTATTTTAGCGAACAAAAA 3 71 1 GGTATTTTAG 0.842851 -229 TTGAAAGTGCGGTAATTTTTTTGTGTTTTTT 3 98 0 GGAATTTTTT 0.95507 -202 AACAAATCTTGTAAATTTTAGAAGATTTTTT 3 193 0 GTAATTTTAG 0.944893 -107 ACAAGATTTGTTAAATGTTTGTGAAAAGCAA 3 212 1 TTAATGTTTG 0.863878 -88 ACACGAATACGGCAATATTTGCTTTTCACAA 3 230 0 GGAATATTTG 0.988298 -70 TCTGTTTTGAGTGAATATTAGTTTAGACAAG 3 266 0 GTAATATTAG 0.957534 -34 ** ******** Masking position 6 Map Score: 9.06045 Number of sites scoring better than the average of aligned sites = 522 Number in coding regions = 456 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 4 CCCACCAAAGATTTCATTAATCGGTGGGCT 1 28 0 ATTTCATTAA 0.850442 -86 TTGACCGCAGTTTTCATCAA 2 1 0 TTTTCATCAA 0.980384 -62 TTTTTTCAGATTTTTTTCAAAAAGGACTCA 3 14 0 TTTTTTTCAA 0.931984 -286 TCCATCGGGCTTTGTTTTAAAGTTTTTTCA 3 36 0 TTTGTTTTAA 0.853451 -264 TCAAATCAGCTTTGCCATAAATAATTATTT 3 127 0 TTTGCCATAA 0.857478 -173 AGATAGTGAATTTTCATCAAATCATCATAT 3 156 0 TTTTCATCAA 0.980384 -144 ATTCACTATCTTTATCTCAAAAAATCTTCT 3 175 1 TTTATCTCAA 0.883474 -125 AGGTTTTCCTTAATCTGTTTTGA 3 287 0 TTTTCCTTAA 0.98034 -13 ********** Masking position 9 Map Score: 7.07121 Number of sites scoring better than the average of aligned sites = 613 Number in coding regions = 497 Number in noncoding regions = 116 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 5 TCTGTAGGTGGGCTTTAAGCCCAC 1 5 1 TAGGTGGGCT 0.997107 -109 ATTTCATTAATCGGTGGGCTTAAAGCCCAC 1 18 0 TCGGTGGGCT 0.998046 -96 AATGAAATCTTTGGTGGGCAGAAACCCATC 1 40 1 TTGGTGGGCA 0.99491 -74 ********** Masking position 5 Map Score: 4.15984 Number of sites scoring better than the average of aligned sites = 22 Number in coding regions = 9 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 6 TTTTACGGTCTTTATAGGATGGGTTTCTGCC 1 56 0 TTTATAGATG 0.978524 -58 ATTTTTAACGTTTTTACGAGGTAAAA 1 98 1 TTTTTAGAGG 0.941462 -16 TTTCAGATTTTTTTCAAAAAGGACTCAGCA 3 10 0 TTTTCAAAAG 0.738471 -290 GTTTTAAAGTTTTTTCAGATTTTTTTCAAAA 3 22 0 TTTTTCGATT 0.646664 -278 CAAAGCTGATTTGATATGATGATTTGATGAA 3 143 1 TTGATAGATG 0.957029 -157 AGAAGATTTTTTGAGATAAAGATAGTGAATT 3 174 0 TTGAGAAAAG 0.793155 -126 TCTTGTAAATTTTAGAAGATTTTTTGAGATA 3 187 0 TTTAGAGATT 0.947459 -113 TCTTCTAAAATTTACAAGATTTGTTAAATGT 3 199 1 TTTACAGATT 0.92526 -101 TGAATATTAGTTTAGACAAGGCTAAACACGA 3 255 0 TTTAGAAAGG 0.923864 -45 ****** **** Masking position 9 Map Score: 2.82495 Number of sites scoring better than the average of aligned sites = 653 Number in coding regions = 564 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 7 CTGTAGGTGGGCTTTAAGCCCACCGATTAAT 1 12 1 GTTTAAGCCC 0.990681 -102 TTATAGGATGGGTTTCTGCCCACCAAAGATT 1 45 0 GTTTCTGCCC 0.995632 -69 AAAACACAATGTTTTTTGACCGCAGTTTTCA 2 15 0 GTTTTTGACC 0.989653 -48 AAAACATTGTGTTTTATGACCGCACTTTAAA 2 31 1 GTTTATGACC 0.994108 -32 * ********* Masking position 5 Map Score: 4.20017 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 18 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 8 ********** No masking Map Score: 6.56131e-13 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: 6.56131e-13 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: 6.56131e-13 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