AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i254_soj_hinf_reg_100.orf -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -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 HI0486 139 glucose-inhibited division protein (gidB) #2 HI0582 300 glucose inhibited division protein (gidA) Motif number 1 TCAAATTACTAAAAACATTAAGGAAATTTA 1 73 1 AAAAACATTA 0.779322 -67 AATTTTTCAAAGAGATAATAAAT 1 127 1 AGAGATAATA 0.912507 -13 TGTAAAATGGAAAGTTATTAACAACTTTAT 2 13 0 AAAGTTATTA 0.882193 -288 CATTTTCTTTAAAAATCTTGTGTGTAAAAT 2 35 0 AAAAATCTTG 0.969118 -266 CAAGATTTTTAAAGAAAATGATCGCATTTT 2 45 1 AAAGAAAATG 0.805538 -256 TATAGGATCCAAAAATCTTGTGAAAATGCG 2 67 0 AAAAATCTTG 0.969118 -234 CACAACCAAAAAAGATCTTAATAATAACAA 2 131 1 AAAGATCTTA 0.858045 -170 TTTTATATATAAAGATCTTATTATTGTTAT 2 154 0 AAAGATCTTA 0.858045 -147 ATATATAAAAAGAGATCTTATTTACTAATA 2 174 1 AGAGATCTTA 0.975823 -127 TGATCCTTTGAAAGATCAGGTTTGTATTAG 2 198 0 AAAGATCAGG 0.927567 -103 ********** Masking position 3 Map Score: 13.0653 Number of sites scoring better than the average of aligned sites = 442 Number in coding regions = 381 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 2 ATGTTTTTAGTAATTTGATGAATTATTTAC 1 61 0 TAATTTGATG 0.832524 -79 AATCTTGTGAAAATGCGATCATTTTCTTTA 2 54 0 AAATGCGATC 0.908896 -247 GAAACAGGTGTTATAGGATCCAAAAATCTT 2 78 0 TTATAGGATC 0.953468 -223 GTGAGTAACCTTATTCGATCCTTATGGAAA 2 104 0 TTATTCGATC 0.966622 -197 TTATTGTTATTATTAAGATCTTTTTTGGTT 2 134 0 TATTAAGATC 0.953509 -167 ATAATAACAATAATAAGATCTTTATATATA 2 151 1 TAATAAGATC 0.982468 -150 TTGTATTAGTAAATAAGATCTCTTTTTATA 2 177 0 AAATAAGATC 0.953521 -124 ATAACGCCAATTTTTTGATCAGAATAAATA 2 272 1 TTTTTTGATC 0.872675 -29 ********** Masking position 8 Map Score: 6.43147 Number of sites scoring better than the average of aligned sites = 234 Number in coding regions = 203 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 3 CAATGTCCAGTTTTACACCATAAATTGAAT 1 26 0 TTTTACACCA 0.720642 -114 ATTTGATGAATTATTTACCGAATCAATGTC 1 49 0 TTATTTACCG 0.798526 -91 ATTCATCAAATTACTAAAAACATTAAGGAA 1 68 1 TTACTAAAAA 0.78547 -72 TTACGCTATTTTACTTAAAAGTGCGGTAAA 1 99 0 TTACTTAAAA 0.89547 -41 AATAGCGTAATTTTTCAAAGAGATAATAAA 1 119 1 TTTTTCAAAG 0.705539 -21 AAATGGAAAGTTATTAACAACTTTATTT 2 9 0 TTATTAACAA 0.883306 -292 ACTTTCCATTTTACACACAAGATTTTTAAA 2 28 1 TTACACACAA 0.932784 -273 TGCGATCATTTTCTTTAAAAATCTTGTGTG 2 41 0 TTCTTTAAAA 0.687689 -260 AAATGATCGCATTTTCACAAGATTTTTGGA 2 60 1 ATTTTCACAA 0.686634 -241 TCGAATAAGGTTACTCACAACCAAAAAAGA 2 116 1 TTACTCACAA 0.975014 -185 AATAAGATCTTTATATATAAAAAGAGATCT 2 162 1 TTATATATAA 0.395087 -139 AAAAGAGATCTTATTTACTAATACAAACCT 2 181 1 TTATTTACTA 0.807043 -120 ********** Masking position 7 Map Score: 5.66751 Number of sites scoring better than the average of aligned sites = 1186 Number in coding regions = 972 Number in noncoding regions = 214 Number of orfs with sites within 600 bp upstream = 179 Fraction of orfs with sites within 600 bp upstream = 0.0287504 Motif number 4 ATTATGCGGAGGTGCATTCAATTTATGGTGTAAA 1 10 1 ATGTTAATTT 0.965604 -130 TTTTACTTAAAAGTGCGGTAAATTTCCTTAATGTT 1 86 0 ATGGTAATTT 0.971661 -54 CTTTTAAGTAAAATAGCGTAATTTTTCAAAGAGAT 1 108 1 ATAGTATTTT 0.910003 -32 AATCTTGTGAAAATGCGATCATTTTCTTTAAAAAT 2 49 0 ATGATATTTT 0.96664 -252 TTATATATAAAGATCTTATTATTGTTATTATTAAG 2 147 0 ATCATATTGT 0.845828 -154 AAGGATCAATAGATCCATTCTTTTTTTGTCAGGTG 2 220 1 ATCTTTTTTT 0.838489 -81 TTTTTTTGTCAGGTGTTTTAAATTTCTGTAGAATA 2 240 1 ATGTTAATTT 0.965969 -61 CTGATCAAAAAATTGGCGTTATTCTACAGAAATTT 2 259 0 ATGGTATTCT 0.973696 -42 ATCTATCTCTATTTATTCTGATCAAAAAA 2 282 0 ATCTTATTCT 0.949598 -19 * ** ** ***** Masking position 9 Map Score: 5.51728 Number of sites scoring better than the average of aligned sites = 631 Number in coding regions = 429 Number in noncoding regions = 202 Number of orfs with sites within 600 bp upstream = 162 Fraction of orfs with sites within 600 bp upstream = 0.0260199 Motif number 5 ********** No masking Map Score: 5.92755e-14 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 ********** No masking Map Score: 5.92755e-14 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 7 ********** No masking Map Score: 5.92755e-14 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