AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i170_Urease_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 HI0535 74 urease accessory protein (ureH) #2 HI0536 102 urease accessory protein (ureG) #3 HI0540 75 urease, beta subunit (ureB) #4 HI0541 162 urease, gamma subunit (ureA) Motif number 1 ATTTCACCAATAATTGGGCAAATGTAATTCACC 1 18 0 TTGGGCAAAT 0.996877 -57 ATTGGTGAAATATCGGGGCTAATATAATTAGCC 1 40 1 TGGGGCTAAT 0.998974 -35 AGATTTTGTAGGGGCTAATTATATTAGCC 1 56 0 TGGGGCTAAT 0.998965 -19 AGATTTTACTTGTAGGGGCAAATCACATTTGCC 2 30 1 TGGGGCAAAT 0.998965 -73 TCAACGAATGTTCAAGGGCAAATGTGATTTGCC 2 46 0 TAGGGCAAAT 0.992146 -57 TTCGTTGATATATAGGGGCAAATGTAACTTGCC 2 71 1 TGGGGCAAAT 0.998965 -32 GGGTGTAGGGGCAAGTTACATTTGCC 2 87 0 TGGGGCAAGT 0.995091 -16 ATATTTTTATTTTGTGGGCTAAAGCCCACCCTA 3 14 0 TTGGGCTAAA 0.990181 -62 AAAAATATCAATGGTGGGCTAAAGCCCACCCTA 3 39 1 ATGGGCTAAA 0.934178 -37 TTTTTTTCTTTCAAGGGGCTTACAAAAAATTCT 4 63 1 TGGGGCTTAC 0.973259 -100 * ********* Masking position 9 Map Score: 31.84 Number of sites scoring better than the average of aligned sites = 75 Number in coding regions = 55 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 2 ATATAATTAGCCCCTACAAAATCT 1 61 1 CCCCTACAAA 0.996996 -14 ATGTGATTTGCCCCTACAAGTAAAATCTCA 2 28 0 CCCCTACAAG 0.997511 -75 ATCACATTTGCCCTTGAACATTCGTTGATA 2 51 1 CCCTTGAACA 0.930969 -52 GTTACATTTGCCCCTATATATCAACGAATG 2 69 0 CCCCTATATA 0.926834 -34 ATGTAACTTGCCCCTACACCC 2 92 1 CCCCTACACC 0.990159 -11 GCTAAAGCCCACCCTACAAGGAACAAAGAT 3 56 1 ACCCTACAAG 0.978146 -20 ATAGAAACCGCACTTACAAATTATTAAGAA 4 22 0 CACTTACAAA 0.935433 -141 TTTTGTAAGCCCCTTGAAAGAAAAAAAATC 4 60 0 CCCTTGAAAG 0.960319 -103 ********** Masking position 8 Map Score: 12.2836 Number of sites scoring better than the average of aligned sites = 126 Number in coding regions = 91 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 3 TCGTAGGGGTGAATTACATTTGCCC 1 3 1 GTAGGGGATT 0.99853 -72 AGATTTTGTAGGGGCTAATTATATTAGCCC 1 55 0 GTAGGGTATT 0.990575 -20 GATTTTACTTGTAGGGGCAAATCACATTTGCCC 2 31 1 GTAGGGAATC 0.98602 -72 TCGTTGATATATAGGGGCAAATGTAACTTGCCC 2 72 1 ATAGGGAATG 0.932834 -31 GGGTGTAGGGGCAAGTTACATTTGCCC 2 86 0 GTAGGGAATT 0.996248 -17 CCGTAGGGTGGGCTTTAGCCCACAA 3 3 1 GTAGGGGGTT 0.998219 -73 TTTGTTCCTTGTAGGGTGGGCTTTAGCCCACCA 3 50 0 GTAGGGGGTT 0.998219 -26 TTAATAATTTGTAAGTGCGGTTTCTATATAAGG 4 25 1 GTAAGTGGTT 0.915377 -138 CGGTTTCTATATAAGGAGGATTTTTTTTCTTTC 4 42 1 ATAAGGGATT 0.963425 -121 ****** ** ** Masking position 3 Map Score: 21.1864 Number of sites scoring better than the average of aligned sites = 92 Number in coding regions = 42 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 4 CCAATTATTGGTGAAATATCGGGGCTAATA 1 34 1 GTGAAATATC 0.964633 -41 AAATCTCAATAAAAAATAACCGCAC 2 6 0 AAAAAATAAC 0.891865 -97 GCCCCTACAAGTAAAATCTCAATAAAAAAT 2 19 0 GTAAAATCTC 0.964633 -84 GCCCACAAAATAAAAATATCAATGGTGGGC 3 28 1 TAAAAATATC 0.957504 -48 CCCTTGAAAGAAAAAAAATCCTCCTTATAT 4 50 0 AAAAAAAATC 0.945325 -113 TCTAAAATAGGAAAAATATTTTGTCAGAAT 4 91 0 GAAAAATATT 0.938327 -72 CGAATTTTACGTAAAAAATCTAAAATAGGA 4 109 0 GTAAAAAATC 0.975181 -54 ********** Masking position 5 Map Score: 6.42748 Number of sites scoring better than the average of aligned sites = 566 Number in coding regions = 471 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 5 GTGCGGTTATTTTTTATTGA 2 1 1 GTGCGGTTAT 0.978192 -102 CCGTAGGGTGGGCTTTAGCCCACAAAA 3 8 1 GTGGGCTTTA 0.995018 -68 TCCTTGTAGGGTGGGCTTTAGCCCACCATT 3 48 0 GTGGGCTTTA 0.995018 -28 TAATTTGTAAGTGCGGTTTCTATATAAGGA 4 29 1 GTGCGGTTTC 0.994078 -134 ********** Masking position 7 Map Score: 4.02838 Number of sites scoring better than the average of aligned sites = 75 Number in coding regions = 41 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 6 CGTAGGGGTGAATTACATTTGCCCAATTAT 1 12 1 AATTACATTT 0.980804 -63 TGTAGGGGCTAATTATATTAGCCCCGATAT 1 49 0 AATTATATTA 0.89191 -26 TGTAGGGGCAAATCACATTTGCCCTTGAAC 2 40 1 AATCACATTT 0.980753 -63 TGTAGGGGCAAGTTACATTTGCCCCTATAT 2 80 0 AGTTACATTT 0.980753 -23 ********** Masking position 5 Map Score: 2.58014 Number of sites scoring better than the average of aligned sites = 66 Number in coding regions = 54 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 7 ACATTTGCCCAATTATTGGTGAAATATCGGGG 1 26 1 AATTATTGGA 0.968174 -49 CGCACTTACAAATTATTAAGAAGGAAATTAAT 4 12 0 AATTATTAAA 0.928265 -151 ATTTTGTCAGAATTTTTTGTAAGCCCCTTGAA 4 72 0 AATTTTTGAA 0.979222 -91 AAAGTCAGCGAATTTTACGTAAAAAATCTAAA 4 115 0 AATTTTAGAA 0.970493 -48 TTCCTTAATTTATTATACGAAAGTCAGCGAAT 4 134 0 TATTATAGAA 0.934686 -29 ******* * ** Masking position 6 Map Score: 0.287448 Number of sites scoring better than the average of aligned sites = 150 Number in coding regions = 107 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 8 ********** No masking Map Score: -5.80213e-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: -5.80213e-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: -5.80213e-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