AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i155_aful_mthe_300.orf -o155_aful_mthe_300.ace -a/home/amcguire/alignace/lib/ORF_aful.txt -z/skink1/amcguire/genomes/aful.fna -g0.49 -x5 -e 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 = 0.49 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RAG48483 139 Archaeoglobus_fulgidus #2 RAG50190 144 Archaeoglobus_fulgidus #3 RAG50188 135 Archaeoglobus_fulgidus #4 RAG48480 189 Archaeoglobus_fulgidus #5 RTH01517 171 M.thermo #6 RTH00578 116 M.thermo #7 RTH01585 51 M.thermo #8 RTH00323 300 M.thermo Motif number 1 TTAATTTATTAACTTTTTTCAACTAAAAATTG 1 26 1 AACTTTTTAA 0.872126 -114 TAAAAATTGCACAATTTTTCATGCATCTATTA 1 49 1 ACATTTTTAT 0.932923 -91 ATTAACTTTTACAATTTTTCATGTATGTAATT 1 77 1 ACATTTTTAT 0.932923 -63 CCAGCTTTAAATCATTTTATAAATAATTACAT 1 101 0 ATCTTTTAAA 0.708573 -39 TTAATTTCTTATTCTTTTTTAAATGCATTTAA 2 13 0 ATTTTTTTAA 0.879132 -132 CAGAAAAGTTAATATTTTTAATTTCTTATTCT 2 30 0 AATTTTTTAT 0.956908 -115 ACTTTTCTGCATTTTTTTTAATGGAAATCTTT 2 53 1 ATTTTTTTAT 0.944014 -92 TTTTAATGGAAATCTTTTTTATTAATTGAAAA 2 68 1 AATTTTTTAT 0.956908 -77 TTTAGGAAGTAAAGTTTTTTAATTGTAGATTT 3 94 1 AAATTTTTAA 0.905472 -42 AGATTTGTACAATTTTTTCGATGAGG 3 120 1 AATTTTTCAT 0.792193 -16 AGAGATAGTAAAATTTTTAAATGTTGAGGATA 4 22 0 AAATTTTAAT 0.912479 -168 TAAAATTTTTATTATTTTTAATACCACTCCCC 5 36 0 ATTTTTTTAT 0.944013 -136 ACAATTTCCGAAAATTTTATATGTGTGGTTAA 5 65 0 AAATTTTAAT 0.912479 -107 AAATTTTCGGAAATTGTTTCATAAGTAACCTT 5 80 1 AAATGTTTAT 0.725538 -92 ATAATAGATGATTATTTTTTAATATTTAACGT 8 99 0 ATTTTTTTAA 0.879132 -202 CCGCATGGCCATAATTTTAGATTATTGTGGAT 8 176 1 ATATTTTAAT 0.887848 -125 TAATCATTTAACCGTTTTAAATCCACAATAAT 8 196 0 ACCTTTTAAT 0.822987 -105 *** ***** ** Masking position 7 Map Score: 19.867 Number of sites scoring better than the average of aligned sites = 226 Number in coding regions = 119 Number in noncoding regions = 107 Number of orfs with sites within 600 bp upstream = 112 Fraction of orfs with sites within 600 bp upstream = 0.0179891 Motif number 2 CAAATTCATTTGAATTCCAGCTTTAAATCATTTT 1 115 0 TGATTAGTTT 0.968414 -25 AATTAATTCGGGATATCACAGTTGTT 3 3 1 TTATTGGTAT 0.814485 -133 GTTGCTTTTTTGGATTATGGGTTTAAAAACCTCA 3 34 1 TGATTGGTTT 0.982759 -102 GCAGACAAATTGGATTGCGATTTTTTAGGAAGTA 3 71 1 TGATTGATTT 0.968414 -65 GTAAAGTTTTTTAATTGTAGATTTGTACAATTTT 3 102 1 TTATTAGTTT 0.95688 -34 CCTTACCTCTTTAATTTCAGCTTTGGGAATCAGC 4 121 1 TTATTAGTTT 0.95688 -69 ATGCAGGGAATGGGTTCAGATTTTAATACCCCT 6 10 0 TGGTTGATTT 0.840339 -107 GGAAGGGATGCTAATTTAAGCTTTGATAAAAGTG 6 58 0 CTATTAGTTT 0.792081 -59 AGTTTGATGGTGATTTTCGAGCCAAAG 7 4 1 TTATGGATTT 0.777783 -48 TCATCTATTATGAATTATAATTTCCTGCCAGAAT 8 120 1 TGATTAATTC 0.722299 -181 ATAATTTTAGATTATTGTGGATTTAAAACGGTTA 8 186 1 ATATTGGTTT 0.826947 -115 AAAATTGGATTTTATTGTGATTTTCATGTAATTA 8 227 1 TTATTGATTT 0.95688 -74 ATGGTTCACATGCCTTTTAAATTTTAGGAACATT 8 263 1 TGCTTAATTT 0.738976 -38 ** *** ** *** Masking position 5 Map Score: 8.99261 Number of sites scoring better than the average of aligned sites = 190 Number in coding regions = 143 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 3 CATATTAATTTATTAACTTTTTTCAACTAA 1 22 1 TATTAACTTT 0.937352 -118 TTCATGCATCTATTAACTTTTACAATTTTT 1 66 1 TATTAACTTT 0.937352 -74 AAATTAAAAATATTAACTTTTCTGCATTTT 2 38 1 TATTAACTTT 0.937352 -107 TTAAAAATTTTACTATCTCTTTAGAAATTC 4 34 1 TACTATCTCT 0.899569 -156 GCGCCGCATTCCTTACCTCTTTAATTTCAG 4 111 1 CCTTACCTCT 0.879707 -79 CTTAGAATTCCACTATCTTTGGCTCGAAAA 7 24 0 CACTATCTTT 0.789934 -28 GGAAGGCTGCCCTTAACTCTGTAATGGCGT 8 34 1 CCTTAACTCT 0.952382 -267 TGGTTTGTACTCTGATCTCTAAGAACAACC 8 70 0 TCTGATCTCT 0.77932 -231 CCTGCCAGAATATTAACTCTGGATCTATTA 8 143 1 TATTAACTCT 0.967102 -158 ********** Masking position 5 Map Score: 7.29711 Number of sites scoring better than the average of aligned sites = 127 Number in coding regions = 111 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 4 TTTTCAACTAAAAATTGCACAATTTTTCAT 1 41 1 AAAATTGCAC 0.953104 -99 ACATACATGAAAAATTGTAAAAGTTAATAG 1 75 0 AAAATTGTAA 0.833884 -65 TTCCATTAAAAAAAATGCAGAAAAGTTAAT 2 49 0 AAAAATGCAG 0.894691 -96 TGCTAAGGATAAAAATGGAGGGTCTGTGAT 2 100 1 AAAAATGGAG 0.894691 -45 CAGACGCAGACAAATTGGATTGCGATTTTT 3 66 1 CAAATTGGAT 0.556146 -70 GTAAAGTTTTTTAATTGTAGATTTGTACAA 3 102 1 TTAATTGTAG 0.590754 -34 CCTCATCGAAAAAATTGTACAAATCTACAA 3 116 0 AAAATTGTAC 0.970103 -20 TCAACATTTAAAAATTTTACTATCTCTTTA 4 27 1 AAAATTTTAC 0.854694 -163 ACAATTTCCGAAAATTTTATATGTGTGGTT 5 67 0 AAAATTTTAT 0.696333 -105 GGATCGTACTATAATTGTACTTGGTATATG 5 132 0 ATAATTGTAC 0.931338 -40 GTGGGTTAATAAAAATGCAGGGAATGGGTT 6 28 0 AAAAATGCAG 0.894691 -89 CCGCATGGCCATAATTTTAGATTATTGTGG 8 176 1 ATAATTTTAG 0.709951 -125 TTAAATGATTAAAATTGGATTTTATTGTGA 8 217 1 AAAATTGGAT 0.888196 -84 TATTACATATATAAATGTTCCTAAAATTTA 8 280 0 ATAAATGTTC 0.358016 -21 ********** Masking position 4 Map Score: 8.21256 Number of sites scoring better than the average of aligned sites = 261 Number in coding regions = 200 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 5 GATTTAAAGCTGGAATTCAAATGAATTTGG 1 120 1 TGGAATCAAA 0.717261 -20 GAATTTCTAAAGAGATAGTAAAATTTTTAAA 4 33 0 AGAGATGTAA 0.752435 -157 GAGAATCCAGAGGAGTTCAACCTCTACGTAG 4 66 0 AGGAGTCAAC 0.809572 -124 GAAATAATTTAGGGATACTACATCGCTGATT 4 148 0 AGGGATCTAC 0.970656 -42 GTGGAAGGGGAGTGGTATTAAAAATAATAAA 5 30 1 AGTGGTTTAA 0.789642 -142 TATATGGTTTAGGAGTGGTAAGTATAAAGGT 5 107 0 AGGAGTGTAA 0.926384 -65 AGGGGTATTAAAATCTGAACC 6 1 1 AGGGGTTTAA 0.950158 -116 TCAGTATGGAAGGGATGCTAATTTAAGCTTT 6 68 0 AGGGATCTAA 0.987168 -49 CCAAAGATAGTGGAATTCTAAGGTGATGGT 7 32 1 TGGAATCTAA 0.901244 -20 GCTTCAATCCAGTGATCCTAACTGGAAGGCT 8 11 1 AGTGATCTAA 0.938074 -290 ****** **** Masking position 6 Map Score: 4.66563 Number of sites scoring better than the average of aligned sites = 195 Number in coding regions = 174 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 6 AATTAATTCGGGATATCACAGT 3 2 1 ATAATTCGGG 0.735869 -134 TTGGATTGCGATTTTTTAGGAAGTAAAGTTT 3 80 1 ATTTTTAGGA 0.965941 -56 AAAATTTTTAAATGTTGAGGATAAAATTAGG 4 14 0 AAGTTGAGGA 0.787942 -176 TAGTAGTGAAATAATTTAGGGATACTACATC 4 155 0 ATATTTAGGG 0.926402 -35 CACACATATAAAATTTTCGGAAATTGTTTCA 5 70 1 AATTTTCGGA 0.862585 -102 TACTTGGTATATGGTTTAGGAGTGGTAAGTA 5 114 0 ATGTTTAGGA 0.95021 -58 AAAAATAATCATCTATTATGAATTATAATTT 8 112 1 ATTATTATGA 0.528739 -189 TTAACTCTGGATCTATTAGGGCCGCATGGCC 8 155 1 ATTATTAGGG 0.901415 -146 ATAATTTTAGATTATTGTGGATTTAAAACGG 8 186 1 ATATTGTGGA 0.576677 -115 CATGCCTTTTAAATTTTAGGAACATTTATAT 8 271 1 AATTTTAGGA 0.927756 -30 ** ******** Masking position 6 Map Score: 2.28735 Number of sites scoring better than the average of aligned sites = 198 Number in coding regions = 159 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 7 ********** No masking Map Score: -1.72419e-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: -1.72419e-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: -1.72419e-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