AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i326_not_clear1_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 HI0176 107 sfhB protein (sfhB) #2 HI0997 300 H. influenzae predicted coding region HI0997 #3 HI0998 180 ribosomal protein L34 (rpL34) #4 HI1002 130 thiophene and furan oxidation protein (thdF) #5 HI1004 272 peptidyl-prolyl cis-trans isomerse, putative #6 HI1005 87 conserved hypothetical protein #7 HI1006 69 lipoprotein signal peptidase (lspA) Motif number 1 TTTTTTCCTTAATTTTTACGAAAACCAATAA 1 13 1 AATTTTTCGA 0.857476 -95 CAACTTTTAAAATTTTTGAGAGCTATTT 1 90 1 AATTTTTAGA 0.922587 -18 TTTCAAATTGAATTTTGGCAGCTTCATTTTC 2 23 0 AATTTTGCAG 0.438116 -278 CTCTGTACGTAATTTTTCAAATTGAATTTTG 2 37 0 AATTTTTAAA 0.891241 -264 AACACCTAAAAATTTTTCATCATCTACCTCT 2 64 0 AATTTTTATC 0.676282 -237 AGTAGGATTAAATTTTTTAAATGATGATAAT 2 145 1 AATTTTTAAA 0.891241 -156 ATTTTTGTGCCACTTTTTGGAGCGTTATTCA 2 177 0 CACTTTTGGA 0.832704 -124 TCCAACTACCAATTTTTGTGCCACTTTTTGG 2 188 0 AATTTTTTGC 0.892465 -113 TGCCCATGGCCATTTTTTTTCTACTGATAAA 2 259 0 CATTTTTTTC 0.652722 -42 ATGGGCAGATCATTTTTTTAGTAAAACT 2 283 1 CATTTTTTAG 0.83018 -18 GTTAGGTTACAACTTTTCAGCC 3 2 0 AACTTTTAGC 0.917468 -179 GTTGTAACCTAACTTTTGAGGTATCTCTAAC 3 20 1 AACTTTTAGG 0.866278 -161 AAAATATATGCACTTTGCTAAAGTTAGAGAT 3 42 0 CACTTTGTAA 0.632085 -139 AAGAAACGGAAATTTTTAAAAAAAACTTCAA 3 84 0 AATTTTTAAA 0.891241 -97 ATATATTCTGCATTTTGTAGAGATAGAGTTT 4 67 1 CATTTTGAGA 0.832774 -64 AAAGTGCGGTCATTTTTTGGCAAAATTTAAA 5 18 1 CATTTTTGGC 0.873554 -255 ATGGAGTTTTCACTTTTTAAGATGCTAATTT 5 113 1 CACTTTTAAG 0.867515 -160 TTAAATTGTGCATTTTTTCAATTAACATTCT 5 195 0 CATTTTTCAA 0.858781 -78 AAATTTACCGCACTTTTGAGCAGAATTTATC 6 31 0 CACTTTTAGC 0.942335 -57 AATTTCACCGCACTTTTTTACTTTTGTGCGA 6 57 1 CACTTTTTAC 0.873047 -31 GAATGAGCGGAATTTTTTTAAAAGGGAAATA 7 47 1 AATTTTTTAA 0.833758 -23 ******* *** Masking position 6 Map Score: 23.1246 Number of sites scoring better than the average of aligned sites = 1177 Number in coding regions = 891 Number in noncoding regions = 286 Number of orfs with sites within 600 bp upstream = 241 Fraction of orfs with sites within 600 bp upstream = 0.0387086 Motif number 2 TTTATTGGTTTTCGTAAAAATTAAGGAAAAAACA 1 11 0 TGAAAAATAA 0.727829 -97 AAATAGCTCTCAAAAATTTTAAAAGTTGGCT 1 87 0 TCAAAATTTA 0.692196 -21 CAAAATTCAATTTGAAAAATTACGTACAGAGGTA 2 37 1 TGAAAATTCG 0.961819 -264 ATTATCATCATTTAAAAAATTTAATCCTACTTGC 2 142 0 TAAAAATTAA 0.760708 -159 ATATATGCACTTTGCTAAAGTTAGAGATACCTCA 3 36 0 TGTAAAGTAG 0.828087 -145 TTAATTGTATTTAGGTAAATTAAA 3 167 1 TGTAAATTAA 0.961727 -14 CGGTCATTTTTTGGCAAAATTTAAATCAAAAGCG 5 24 1 TGAAAATTAA 0.961728 -249 TAGATTATAATCGGGAAAATTTTATATTTATAAC 5 152 1 TGAAAATTTA 0.954846 -121 AATCTTTGAGTTTGTTAAATTGTGCATTTTTTCA 5 206 0 TGTAAATTTG 0.962547 -67 CAATCAAACCTAAGATAAATTTAGAAATCTTTGA 5 231 0 TGTAAATTAG 0.968294 -42 TAGGTTAAATTATAATTTGAGATA 6 1 1 TGTAAATTTA 0.954843 -87 AATTATAATTTGAGATAAATTCTGCTCAAAAGTG 6 18 1 TGTAAATTTG 0.962547 -70 TGCTCAAAAGTGCGGTAAATTTCACCGCACTTTT 6 40 1 TGTAAATTCA 0.953974 -48 TATTTCCCTTTTAAAAAAATTCCGCTCATTCTAG 7 44 0 TAAAAATTCG 0.761179 -26 * * ****** ** Masking position 7 Map Score: 17.7549 Number of sites scoring better than the average of aligned sites = 349 Number in coding regions = 273 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 3 AAGATACAATTGTCCGCTATTGTATAGAACA 1 46 1 TGTCGCTATT 0.909223 -62 TTAAAATTTTTGAGAGCTATTT 1 96 1 TGAAGCTATT 0.861326 -12 CATCTACCTCTGTACGTAATTTTTCAAATTG 2 44 0 TGTCGTAATT 0.785139 -257 TAGGTGTTATTGATCAGTATCTTTTAACACT 2 87 1 TGACAGTATC 0.643475 -214 TAACACTAAATCAGCGGAATCAATGGATATG 2 111 1 TCACGGAATC 0.89698 -190 TGAATAAAATAGAGCGCAATTCTAGTCATAA 3 133 0 AGACGCAATT 0.935748 -48 TGCCAAAAAATGACCGCACTTTACGCTTC 5 9 0 TGACGCACTT 0.985973 -264 GGTGTTTTGTTGATAGGAATTGCTATTAGCT 5 70 1 TGAAGGAATT 0.936093 -203 ACCGCACTTTTGAGCAGAATTTATCTCAAAT 6 25 0 TGACAGAATT 0.936093 -63 GCGGTGAAATTTACCGCACTTTTGAGCAGAA 6 37 0 TTACGCACTT 0.85997 -51 GCGGTAAATTTCACCGCACTTTTTTACTTTT 6 51 1 TCACGCACTT 0.943665 -37 TGTGCTAGAATGAGCGGAATTTTTTTAAAAG 7 40 1 TGACGGAATT 0.990604 -30 *** ******* Masking position 10 Map Score: 9.79067 Number of sites scoring better than the average of aligned sites = 721 Number in coding regions = 565 Number in noncoding regions = 156 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 4 CTACTGATAAAGAATACCCTACCCCCTGCCCAC 2 237 0 AAATACCACC 0.974299 -64 TTCTAGTCATAAAATACGCGTTCGTCAAATAAG 3 112 0 AAATACCTTC 0.960796 -69 CAAATAATAAAGAAAGCACATTCCGTGCCTTTC 4 28 0 AAAAGCCTTC 0.974707 -103 GTTTCTACTAAAAAAACTCTATCTCTACAAAAT 4 78 0 AAAAACCATC 0.990774 -53 ATTCCTATCAACAAAACACCACCAAATATTGCC 5 57 0 AAAAACCACC 0.983823 -216 TCTTAAAAAGTGAAAACTCCATCCTCACAAAGC 5 102 0 TAAAACCATC 0.950607 -171 GTTAATTGAAAAAATGCACAATTTAACAAACTC 5 200 1 AAATGCCATT 0.879916 -73 CCGATAAATGATAAAGCACGATCTCAT 7 5 0 AAAAGCCATC 0.99059 -65 * ***** * *** Masking position 4 Map Score: 8.41466 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 54 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 5 GCGGACAATTGTATCTTATTTATTGGTTTT 1 33 0 GTATCTTATT 0.962154 -75 TTATTGATCAGTATCTTTTAACACTAAATC 2 93 1 GTATCTTTTA 0.820011 -208 CCCCTGCCCACTTTCTTTTTCCCAAGCGGT 2 218 0 CTTTCTTTTT 0.962154 -83 AAAAATTTCCGTTTCTTATTTGACGAACGC 3 98 1 GTTTCTTATT 0.962154 -83 GAATTGCGCTCTATTTTATTCACTCTTAAT 3 142 1 CTATTTTATT 0.76731 -39 CATTCCGTGCCTTTCTTTTTGCCTGTTCGT 4 13 0 CTTTCTTTTT 0.962154 -118 AATGTGCTTTCTTTATTATTTGATCTTAAT 4 39 1 CTTTATTATT 0.76731 -92 TTTGATTGCTGTATCGTTTTTAGTTG 5 257 1 GTATCGTTTT 0.871008 -16 ********** Masking position 4 Map Score: 4.86079 Number of sites scoring better than the average of aligned sites = 123 Number in coding regions = 90 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 6 TGTTTTTTCCTTAATTTTTACGAAAACC 1 6 1 TTTTTAATTT 0.771294 -102 ATTGTATCTTATTTATTGGTTTTCGTAAAAATT 1 23 0 ATTTTGGTTT 0.96695 -85 AAGTTGGCTTATTGATTAATGTTCTATACAATA 1 63 0 ATTTTAATTT 0.949542 -45 ATGATGAAAAATTTTTAGGTGTTATTGATCAGT 2 72 1 ATTTAGGTTT 0.914607 -229 AAGTGCATATATTTTTTAATATTCGTTTGAAGT 3 58 1 ATTTTAATTT 0.949203 -123 TGCTTTCTTTATTATTTGATCTTAATATATTCT 4 43 1 ATTTTGATTT 0.967567 -88 AAGCGGCAATATTTGGTGGTGTTTTGTTGATAG 5 53 1 ATTGTGGTTT 0.943077 -220 CCTAAGATAAATTTAGAAATCTTTGAGTTTGTT 5 224 0 ATTGAAATTT 0.795967 -49 *** ***** ** Masking position 10 Map Score: 3.60547 Number of sites scoring better than the average of aligned sites = 180 Number in coding regions = 144 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 7 ATCCTACTTGCCATATCCATTGATTCCGCT 2 123 0 CCATATCCAT 0.883942 -178 TGCCCACTTTCTTTTTCCCAAGCGGTCCAA 2 214 0 CTTTTTCCCA 0.936104 -87 CCGTGCCTTTCTTTTTGCCTGTTCGTGA 4 9 0 CTTTTTGCCT 0.931583 -122 CAGGGATAAGCCTTATCCCTCTAAATTAAA 4 110 1 CCTTATCCCT 0.980093 -21 AATTAACATTCTATAACCCTTGTTATAAAT 5 177 0 CTATAACCCT 0.936104 -96 ACTATTTCCCTTTTAAAAAAA 7 59 0 CTATTTCCCT 0.98344 -11 ********** Masking position 4 Map Score: 2.20248 Number of sites scoring better than the average of aligned sites = 29 Number in coding regions = 19 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 8 ********** No masking Map Score: -1.54655e-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 9 ********** No masking Map Score: -1.54655e-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 10 ********** No masking Map Score: -1.54655e-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