AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i170_Urease_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 HI0535 74 urease accessory protein (ureH) #2 HI0536 102 urease accessory protein (ureG) #3 HI0537 107 urease accessory protein (ureF) #4 HI0538 127 urease accessory protein (ureE) #5 HI0540 75 urease, beta subunit (ureB) #6 HI0541 162 urease, gamma subunit (ureA) Motif number 1 ATTTCACCAATAATTGGGCAAATGTAATTCACC 1 18 0 TTGGGCAAAT 0.994734 -57 ATTGGTGAAATATCGGGGCTAATATAATTAGCC 1 40 1 TGGGGCTAAT 0.998268 -35 AGATTTTGTAGGGGCTAATTATATTAGCC 1 56 0 TGGGGCTAAT 0.998262 -19 AGATTTTACTTGTAGGGGCAAATCACATTTGCC 2 30 1 TGGGGCAAAT 0.998262 -73 TCAACGAATGTTCAAGGGCAAATGTGATTTGCC 2 46 0 TAGGGCAAAT 0.9868 -57 TTCGTTGATATATAGGGGCAAATGTAACTTGCC 2 71 1 TGGGGCAAAT 0.998262 -32 GGGTGTAGGGGCAAGTTACATTTGCC 2 87 0 TGGGGCAAGT 0.991743 -16 ATATTTTTATTTTGTGGGCTAAAGCCCACCCTA 5 14 0 TTGGGCTAAA 0.983521 -62 AAAAATATCAATGGTGGGCTAAAGCCCACCCTA 5 39 1 ATGGGCTAAA 0.893603 -37 TTTTTTTCTTTCAAGGGGCTTACAAAAAATTCT 6 63 1 TGGGGCTTAC 0.955632 -100 * ********* Masking position 9 Map Score: 27.2023 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 AGATTTTGTAGGGGCTAATTATAT 1 61 0 TTTGTAGGGG 0.996527 -14 TGAGATTTTACTTGTAGGGGCAAATCACAT 2 28 1 CTTGTAGGGG 0.99388 -75 CATTCGTTGATATATAGGGGCAAATGTAAC 2 69 1 TATATAGGGG 0.958827 -34 GGGTGTAGGGGCAAGTTACAT 2 92 0 GGTGTAGGGG 0.980393 -11 GACGAATTAGTGTAAAAGGGCGTGTACGAT 4 26 1 TGTAAAAGGG 0.798087 -102 AGAAAGTGGATTTATAGAGGAAAG 4 114 1 TTTATAGAGG 0.916643 -14 ATCTTTGTTCCTTGTAGGGTGGGCTTTAGC 5 56 0 CTTGTAGGGT 0.940937 -20 TTCTTAATAATTTGTAAGTGCGGTTTCTAT 6 22 1 TTTGTAAGTG 0.847091 -141 ATTTTTTTTCTTTCAAGGGGCTTACAAAAA 6 61 1 TTTCAAGGGG 0.954113 -102 ********** Masking position 6 Map Score: 11.635 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 77 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 3 ACCAAGTGCAACAACGCACCTAAATCCGTT 3 21 0 ACAACGCACC 0.966881 -87 TTGGAATGGTTAAATCCACCAATCGGTAAA 3 60 0 TAAATCCACC 0.979323 -48 CTTTCCTCTATAAATCCACTTTCTTCTCTT 4 108 0 TAAATCCACT 0.928161 -20 TTTGTGGGCTAAAGCCCACCCTACGG 5 7 0 AAAGCCCACC 0.994664 -69 ATGGTGGGCTAAAGCCCACCCTACAAGGAA 5 49 1 AAAGCCCACC 0.994664 -27 CCTTATATAGAAACCGCACTTACAAATTAT 6 28 0 AAACCGCACT 0.921005 -135 TGAAAGAAAAAAAATCCTCCTTATATAGAA 6 46 0 AAAATCCTCC 0.957631 -117 ********** Masking position 3 Map Score: 7.82219 Number of sites scoring better than the average of aligned sites = 242 Number in coding regions = 182 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 4 AGTAAAATCTCAATAAAAAATAACCGCAC 2 10 0 CAATAAAAAA 0.836684 -93 CTTACTTGATAAATAAGAAATCATTGTAGC 4 62 1 AAATAAGAAA 0.965788 -66 CTTCTCTTCGAAAGAAAAACTACAGCTACA 4 86 0 AAAGAAAAAC 0.941127 -42 TTTCTTTCGAAGAGAAGAAAGTGGATTTAT 4 99 1 AGAGAAGAAA 0.917918 -29 AAGTGGATTTATAGAGGAAAG 4 117 1 ATAGAGGAAA 0.916489 -11 TTAGCCCACAAAATAAAAATATCAATGGTG 5 25 1 AAATAAAAAT 0.819891 -51 AATCCTCCTTATATAGAAACCGCACTTACA 6 34 0 ATATAGAAAC 0.789443 -129 AAGCCCCTTGAAAGAAAAAAAATCCTCCTT 6 54 0 AAAGAAAAAA 0.965788 -109 AAAAAATCTAAAATAGGAAAAATATTTTGT 6 97 0 AAATAGGAAA 0.958822 -66 ********** Masking position 5 Map Score: 7.21361 Number of sites scoring better than the average of aligned sites = 561 Number in coding regions = 378 Number in noncoding regions = 183 Number of orfs with sites within 600 bp upstream = 160 Fraction of orfs with sites within 600 bp upstream = 0.0256987 Motif number 5 ACATTTGCCCAATTATTGGTGAAATATCGG 1 26 1 AATTATTGGT 0.939455 -49 GCCCTTTTACACTAATTCGTCTATGAAAAC 4 17 0 ACTAATTCGT 0.875685 -111 TTTCCTTCTTAATAATTTGTAAGTGCGGTT 6 17 1 AATAATTTGT 0.96245 -146 ATTTTGTCAGAATTTTTTGTAAGCCCCTTG 6 74 0 AATTTTTTGT 0.963754 -89 AAATAGGAAAAATATTTTGTCAGAATTTTT 6 87 0 AATATTTTGT 0.963705 -76 AAAGTCAGCGAATTTTACGTAAAAAATCTA 6 117 0 AATTTTACGT 0.876292 -46 ********** Masking position 6 Map Score: 3.46686 Number of sites scoring better than the average of aligned sites = 266 Number in coding regions = 225 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 6 ATAATTGGGCAAATGTAATTCACCCCTACG 1 12 0 AAATGTAATT 0.960978 -63 ATATCGGGGCTAATATAATTAGCCCCTACA 1 49 1 TAATATAATT 0.695879 -26 CCTACAAGTAAAATCTCAATAAAAAATAAC 2 16 0 AAATCTCAAT 0.93476 -87 GTTCAAGGGCAAATGTGATTTGCCCCTACA 2 40 0 AAATGTGATT 0.918936 -63 ATATAGGGGCAAATGTAACTTGCCCCTACA 2 80 1 AAATGTAACT 0.936543 -23 CACAAAATAAAAATATCAATGGTGGGCTAA 5 31 1 AAATATCAAT 0.902531 -45 TTTACGTAAAAAATCTAAAATAGGAAAAAT 6 104 0 AAATCTAAAA 0.78204 -59 ********** Masking position 3 Map Score: 1.41965 Number of sites scoring better than the average of aligned sites = 273 Number in coding regions = 215 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 7 AAATGTAATTCACCCCTACGA 1 2 0 CACCCCTACG 0.980957 -73 ATGGTTAAATCCACCAATCGGTAAAGTTGG 3 55 0 CCACCAATCG 0.953505 -53 CGAAGGTTTCCAAGCCATTGGAATGGTTAA 3 77 0 CAAGCCATTG 0.85566 -31 CAATGGCTTGGAAACCTTCGTCCAGCAACG 3 87 1 GAAACCTTCG 0.866207 -21 GGGCTAAAGCCCACCCTACGG 5 2 0 CCACCCTACG 0.993715 -74 TGGGCTTTAGCCCACCATTGATATTTTTAT 5 37 0 CCCACCATTG 0.907459 -39 GGGCTAAAGCCCACCCTACAAGGAACAAAG 5 54 1 CCACCCTACA 0.953506 -22 ********** Masking position 5 Map Score: 2.24407 Number of sites scoring better than the average of aligned sites = 238 Number in coding regions = 178 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 8 ********** No masking Map Score: 2.65333e-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: 2.65333e-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: 2.65333e-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