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_300.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 0.999288 -40 TTGATGAAAACTGCGGTCAAAAAACAT 2 8 1 AAACTGCGGT 0.998233 -55 TGTTCCTTTTAAAGTGCGGTCATAAAACAC 2 39 0 AAAGTGCGGT 0.999288 -24 TAATTATTTGAAAGTGCGGTAATTTTTTTG 3 106 0 AAAGTGCGGT 0.999288 -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 0.991208 -46 GAAAAAAATCTGAAAAAACTTTAAAACAAAGC 3 26 1 TGAAAAAATT 0.942465 -274 GAACAAAAAAACACAAAAAAATTACCGCACTT 3 93 1 ACACAAAAAT 0.820045 -207 TACCGCACTTTCAAATAATTATTTATGGCAAA 3 115 1 TCAAATAAAT 0.968771 -185 AATCATCATATCAAATCAGCTTTGCCATAAAT 3 135 0 TCAAATCATT 0.979911 -165 TGAATTTTCATCAAATCATCATATCAAATCAG 3 148 0 TCAAATCAAT 0.962389 -152 TATCTTTATCTCAAAAAATCTTCTAAAATTTA 3 181 1 TCAAAAAATT 0.991208 -119 TATTTGCTTTTCACAAACATTTAACAAATCTT 3 214 0 TCACAAACTT 0.92793 -86 TAATATTCACTCAAAACAGATTAAGGAAAACC 3 277 1 TCAAAACATT 0.989361 -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 TTCTGCCCACCAAAGATTTCATTAATCGGTG 1 32 0 CAAAGATTCA 0.936937 -82 AAAAACGTTAAAAATATTGACCGCACTTTTA 1 82 0 AAAATATTAC 0.943778 -32 AATAACCAGTAAAATATTGCATTCCATCGGG 3 57 0 AAAATATTCA 0.915319 -243 TTTTTGTTCGCTAAAATAACCAGTAAAATAT 3 71 0 CTAAAATACC 0.864695 -229 AAAAAACACAAAAAAATTACCGCACTTTCAA 3 98 1 AAAAAATTCC 0.962018 -202 AAAAAATCTTCTAAAATTTACAAGATTTGTT 3 193 1 CTAAAATTAC 0.95316 -107 TTGCTTTTCACAAACATTTAACAAATCTTGT 3 212 0 CAAACATTAA 0.883204 -88 TTGTGAAAAGCAAATATTGCCGTATTCGTGT 3 230 1 CAAATATTCC 0.99016 -70 CTTGTCTAAACTAATATTCACTCAAAACAGA 3 266 1 CTAATATTAC 0.964116 -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 AGCCCACCGATTAATGAAATCTTTGGTGGG 1 28 1 TTAATGAAAT 0.82871 -86 TTGATGAAAACTGCGGTCAA 2 1 1 TTGATGAAAA 0.977066 -62 TGAGTCCTTTTTGAAAAAAATCTGAAAAAA 3 14 1 TTGAAAAAAA 0.921039 -286 TGAAAAAACTTTAAAACAAAGCCCGATGGA 3 36 1 TTAAAACAAA 0.832076 -264 AAATAATTATTTATGGCAAAGCTGATTTGA 3 127 1 TTATGGCAAA 0.836574 -173 ATATGATGATTTGATGAAAATTCACTATCT 3 156 1 TTGATGAAAA 0.977066 -144 AGAAGATTTTTTGAGATAAAGATAGTGAAT 3 175 0 TTGAGATAAA 0.865984 -125 TCAAAACAGATTAAGGAAAACCT 3 287 1 TTAAGGAAAA 0.976975 -13 ********** Masking position 8 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 0.997126 -109 ATTTCATTAATCGGTGGGCTTAAAGCCCAC 1 18 0 TCGGTGGGCT 0.998059 -96 AATGAAATCTTTGGTGGGCAGAAACCCATC 1 40 1 TTGGTGGGCA 0.994944 -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 CATCCTATAAAGACCGTAAAAGTGCGGTCAA 1 66 1 AGACGTAAAA 0.971539 -48 TACCTCGTAAAAACGTTAAAAATATTGACCG 1 90 0 AAACTTAAAA 0.985954 -24 TTTTATGACCGCACTTTAAAAGGAACAAAAA 2 42 1 GCACTTAAAA 0.920396 -21 AAATCTGAAAAAACTTTAAAACAAAGCCCGA 3 31 1 AAACTTAAAA 0.985954 -269 TCGCTAAAATAACCAGTAAAATATTGCATTC 3 64 0 AACCGTAAAA 0.965165 -236 GCGAACAAAAAAACACAAAAAAATTACCGCA 3 91 1 AAACCAAAAA 0.910378 -209 **** ****** Masking position 8 Map Score: 3.50501 Number of sites scoring better than the average of aligned sites = 147 Number in coding regions = 110 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 7 GGCAGAAACCCATCCTATAAAGACCGTAAAA 1 56 1 CATCTATAAA 0.978807 -58 TTTTACCTCGTAAAAACGTTAAAAAT 1 98 0 CCTCTAAAAA 0.942206 -16 TGCTGAGTCCTTTTTGAAAAAAATCTGAAA 3 10 1 CTTTTGAAAA 0.741084 -290 TTTTGAAAAAAATCTGAAAAAACTTTAAAAC 3 22 1 AATCGAAAAA 0.649762 -278 TTCATCAAATCATCATATCAAATCAGCTTTG 3 143 0 CATCTATCAA 0.957584 -157 AATTCACTATCTTTATCTCAAAAAATCTTCT 3 174 1 CTTTTCTCAA 0.795375 -126 TATCTCAAAAAATCTTCTAAAATTTACAAGA 3 187 1 AATCTCTAAA 0.948131 -113 ACATTTAACAAATCTTGTAAATTTTAGAAGA 3 199 0 AATCTGTAAA 0.926194 -101 TCGTGTTTAGCCTTGTCTAAACTAATATTCA 3 255 1 CCTTTCTAAA 0.924814 -45 **** ****** Masking position 3 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 8 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 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 Motif number 11 ********** 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