AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i047_Polysaccharide_Biosynthesis_1_hinf_reg_300.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 HI0058 70 3-deoxy-D-manno-octulosonate cytidylyltransferase (kdsB) #2 HI0059 72 conserved hypothetical protein #3 HI0060 40 ABC transporter, ATP-binding protein (msbA) #4 HI0061 258 recombination protein (rec2) #5 HI1279 104 acylneuraminate cytidylyltransferase (neuA) Motif number 1 TTTATTCCTTATTCTTTAATATTTCAGCTTT 1 48 0 ATTCTTTATA 0.819299 -23 AGAAAATCCTTTCTAATAAGTGCGG 2 58 0 AATCCTTCTA 0.933578 -15 CAATGCGTGCAATTTTTACTATTAGATAGCG 3 17 1 AATTTTTCTA 0.984179 -24 TTAGGAACCCAATTTTTGCGGGCGGTATAAA 4 94 1 AATTTTTCGG 0.966643 -165 CGTAAAAATAAATTTTTCAGGAAAATTTACT 4 149 0 AATTTTTAGG 0.925189 -110 CTGAAAAATTTATTTTTACGATATGGATCGC 4 160 1 TATTTTTCGA 0.904609 -99 CGGTTGCTTCAAATTTTGCGATCCATATCGT 4 177 0 AAATTTTCGA 0.904609 -82 GGCTGGAATTAATCTTTTATAAAA 4 245 1 AATCTTTATA 0.966399 -14 AGCAAAAACTAATCTTTAATATGGCACCACA 5 37 0 AATCTTTATA 0.966396 -68 ATTAAAGATTAGTTTTTGCTAAAACAAGGGA 5 48 1 AGTTTTTCTA 0.935627 -57 ******* *** Masking position 6 Map Score: 10.1924 Number of sites scoring better than the average of aligned sites = 525 Number in coding regions = 416 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 2 TATTCTTTAATATTTCAGCTTTATCGGCAA 1 40 0 TATTTCAGCT 0.942871 -31 TAATTCTGTATGTATTAGGAGTGAGAG 4 8 0 TGTATTAGGA 0.948468 -251 CCTGTCTTGTTATTTTAGTTTGTTCCTGAC 4 57 1 TATTTTAGTT 0.860596 -202 TCCTGACTGCTATTTTAGGAACCCAATTTT 4 80 1 TATTTTAGGA 0.982569 -179 AGAAGTTGTTTGTTTTAGCAAGTAAATTTT 4 129 1 TGTTTTAGCA 0.988603 -130 TAAAAATAAATTTTTCAGGAAAATTTACTT 4 148 0 TTTTTCAGGA 0.93756 -111 ATCTTTCCCTTGTTTTAGCAAAAACTAATC 5 54 0 TGTTTTAGCA 0.988603 -51 ********** Masking position 7 Map Score: 8.39396 Number of sites scoring better than the average of aligned sites = 195 Number in coding regions = 169 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 3 AAGGATTAATCCCCAGTTGTTTTGATTGCT 1 6 1 TTATCCCTTT 0.989408 -65 AATTTATTCCTTATTCTTTAATATTTC 1 54 0 TTTTTCCTTT 0.990179 -17 CTCGCGTTATTTTATCCGCACTTATTAGAAAGGAT 2 43 1 TTTTCCGTTT 0.959022 -30 GTTATTTTAGTTTGTTCCTGACTGCTATTTTAGGA 4 65 1 TTTTTCCCTC 0.954281 -194 TTATAAAAGATTAATTCCAGCCTCTCTAAGCCTAG 4 232 0 TTATTCCCTT 0.981168 -27 TTTATTTCCTCTTTGTTAAACAAAAA 5 2 1 TTATTCCTTT 0.98725 -103 TATTCTAGAATCTTTCCCTTGTTTTAGCAAAAACT 5 58 0 TCTTCCCTTT 0.974002 -47 *** **** ** * Masking position 5 Map Score: 5.27377 Number of sites scoring better than the average of aligned sites = 129 Number in coding regions = 108 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 4 AGCAATCAAAACAACTGGGGATTAATCCTT 1 11 0 ACAACTGGGG 0.983585 -60 CGCGAGTTTTTCAACTCGCGTTTTCGATAA 2 19 0 TCAACTCGCG 0.964545 -54 CGCGAGTTGAAAAACTCGCGTTATTTTATC 2 29 1 AAAACTCGCG 0.992538 -44 TACCGCCCGCAAAAATTGGGTTCCTAAAAT 4 91 0 AAAAATTGGG 0.88296 -168 ATATTTAAATAAAACTAGCCTAGGCTTAGA 4 213 1 AAAACTAGCC 0.95173 -46 AGTTTTTGCTAAAACAAGGGAAAGATTCTA 5 58 1 AAAACAAGGG 0.954984 -47 ********** Masking position 4 Map Score: 2.72901 Number of sites scoring better than the average of aligned sites = 124 Number in coding regions = 110 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 5 AGTTTTTCAACTCGCGTTTTCGATAATCAA 2 15 0 CTCGCGTTTT 0.987119 -58 AGTTGAAAAACTCGCGTTATTTTATCCGCA 2 33 1 CTCGCGTTAT 0.992652 -40 GTAAAAATTGCACGCATTGTACCTT 3 6 0 CACGCATTGT 0.97656 -35 TCGTGAAATCCACGCTTAATTCTGTATGTA 4 24 0 CACGCTTAAT 0.951497 -235 ********** Masking position 7 Map Score: 1.54511 Number of sites scoring better than the average of aligned sites = 17 Number in coding regions = 15 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 6 ********** No masking Map Score: -1.0847e-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 7 ********** No masking Map Score: -1.0847e-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 8 ********** No masking Map Score: -1.0847e-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