AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i221_aful_mthe_300.orf -o221_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 RAG50329 222 Archaeoglobus_fulgidus #2 RAG25938 75 Archaeoglobus_fulgidus #3 RTH00129 300 M.thermo #4 RTH02041 58 M.thermo #5 RTH01062 171 M.thermo #6 RTH01098 51 M.thermo #7 RTH00022 27 M.thermo Motif number 1 CCTCCTCTGCCAGCTTCCTTATCTTGCTCATAT 1 131 0 CGCTTCCTTC 0.866527 -92 ACTCGGGTCACGGCGTCCCGAACGCCGCAGGAT 2 18 0 CGCGTCCCAC 0.982362 -58 ACGCCGTGACCCGAGTTCAAATCTCGGCGGCCC 2 35 1 CGAGTTCATC 0.952528 -41 GTTCAAATCTCGGCGGCCCCATCTGCTTTAAGG 2 49 1 CGCGGCCCTC 0.997387 -27 GATATATTGACTGCAGCCCTGTTCCTTGTGGGC 3 63 0 CGCAGCCCTT 0.898811 -238 TCATCCTCATCGGAGTGCCTGTTTATCTTGGAT 3 93 0 CGAGTGCCTT 0.889358 -208 ACCTTGACCACAGGGTCCAGGTTGTTGCCCTGT 3 164 1 CGGGTCCATT 0.917882 -137 AGGCACTCTCCCCCGGCCCTCTCGATCTTATCC 3 216 0 CCCGGCCCTC 0.98593 -85 TTCTTAATGGCCGGGTTCTCTTCAACAATTTTT 3 258 0 CGGGTTCTTC 0.937951 -43 TGCTGACCATCCCCGTTCCAGTTGAAAAGTCCG 5 60 0 CCCGTTCCTT 0.953795 -112 CTCGGGTCTCCAGCGTTCCGGTGCTGACCATCC 5 81 0 CGCGTTCCTG 0.974701 -91 CGCTGGAGACCCGAGTTCAAATCTCGGCGGTCC 5 99 1 CGAGTTCATC 0.952528 -73 GTTCAAATCTCGGCGGTCCCATCAAATCGAATC 5 113 1 CGCGGTCCTC 0.99585 -59 * ******* ** Masking position 8 Map Score: 20.1357 Number of sites scoring better than the average of aligned sites = 331 Number in coding regions = 313 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 2 GTTCCTTCCGCGGAAGGCTAAAAACGATTTC 1 28 0 CGGAAGGCAA 0.963944 -195 TAGCCTTCCGCGGAAGGAACATTAAAAATTA 1 39 1 CGGAAGGACA 0.983727 -184 CTGGCAGAGGAGGAAGTCAAATCCAAACCTC 1 151 1 AGGAAGTCAA 0.870661 -72 CACGGCGTCCCGAACGCCGCAGGATCACCAG 2 12 0 CGAACGCCCA 0.870678 -64 CATCCCAGGAAGGCGCAGCAATCTGGA 3 7 1 AGGAAGGCCA 0.993043 -294 GCAATCTGGAAGGACGTTGCAAGGAGACTCG 3 28 1 AGGACGTTCA 0.877248 -273 CAAGGAGACTCGAAAGGCCCACAAGGAACAG 3 47 1 CGAAAGGCCA 0.977591 -254 CACTCCGATGAGGATGAAACAGTTCTCGTGC 3 109 1 AGGATGAACA 0.904655 -192 ACTAAAGAGTAGAATGATTCAGT 4 46 1 AGAATGATCA 0.651335 -13 AATGGCTGGGAGGATGGACCAAGCTACCCTA 5 18 0 AGGATGGACA 0.972047 -154 ******** ** Masking position 4 Map Score: 9.05615 Number of sites scoring better than the average of aligned sites = 294 Number in coding regions = 270 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 3 AAATTAACATGCGGCAAAGATTTAAATTAC 1 64 1 GCGGCAAAGA 0.937156 -159 CGGCGTTCGGGACGCCGTGACCCGAGTTCA 2 24 1 GACGCCGTGA 0.978017 -52 AGCAGATGGGGCCGCCGAGATTTGAACTCG 2 46 0 GCCGCCGAGA 0.99813 -30 ATTTGATGGGACCGCCGAGATTTGAACTCG 5 110 0 ACCGCCGAGA 0.988033 -62 CCATCAAATCGAATCCAAGAACCTCTATTT 5 131 1 GAATCCAAGA 0.881318 -41 ATGCCTCCAAGAAAAACATTAA 5 160 0 GCCTCCAAGA 0.991355 -12 ********** Masking position 10 Map Score: 5.73896 Number of sites scoring better than the average of aligned sites = 159 Number in coding regions = 147 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 4 TGACTTCCTCCTCTGCCAGCTTCCTTATCT 1 140 0 CTCTGCCAGC 0.902626 -83 CCTGGTGATCCTGCGGCGTT 2 1 1 CCTGGTGATC 0.92577 -75 GAGTTCAAATCTCGGCGGCCCCATCTGCTT 2 47 1 CTCGGCGGCC 0.938789 -29 CAGCCCTGTTCCTTGTGGGCCTTTCGAGTC 3 53 0 CCTTGTGGGC 0.87153 -248 ACAACCTGGACCCTGTGGTCAAGGTTTCCG 3 159 0 CCCTGTGGTC 0.987665 -142 CAGGTTGTTGCCCTGTCATTTTCACAGACA 3 181 1 CCCTGTCATT 0.886262 -120 CGATCTTATCCCTTGCTGTCTGTGAAAATG 3 197 0 CCTTGCTGTC 0.876669 -104 GGCACTCTCCCCCGGCCCTCTCGATCTTAT 3 218 0 CCCGGCCCTC 0.981704 -83 TTGAAGAGAACCCGGCCATTAAGAACATAA 3 266 1 CCCGGCCATT 0.969925 -35 GACCAAGCTACCCTACGGTCCC 5 3 0 CCCTACGGTC 0.946844 -169 GGTCCATCCTCCCAGCCATTGAAGAAGTTT 5 29 1 CCCAGCCATT 0.833742 -143 GAGTTCAAATCTCGGCGGTCCCATCAAATC 5 111 1 CTCGGCGGTC 0.986583 -61 ********** Masking position 1 Map Score: 14.119 Number of sites scoring better than the average of aligned sites = 861 Number in coding regions = 786 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 5 AACGATTTCGATATGAGGTGAAGCTA 1 7 0 ATATGAGGTG 0.993476 -216 AGTCAGCAAAAAATGAGGCGCCA 1 210 1 AAATGAGGCG 0.954232 -13 CCCATCTGCTTTAAGGGGTG 2 66 1 TTAAGGGGTG 0.935694 -10 CTAGAGTTTATTATGAGGTGTTTTA 6 37 1 TTATGAGGTG 0.990678 -15 ATTGAAACTTATTTGAGGTGATAGA 7 13 1 ATTTGAGGTG 0.978851 -15 ********** Masking position 5 Map Score: 3.89555 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 37 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 6 GCATGTTAATTTTTAATGTTCCTTCCGCGG 1 46 0 TTTTAATGTT 0.918065 -177 TCTGCCAGCTTCCTTATCTTGCTCATATCA 1 129 0 TCCTTATCTT 0.895346 -94 TCGGAGTGCCTGTTTATCTTGGATATATTG 3 87 0 TGTTTATCTT 0.912066 -214 TATTCTATTATCTTTATGTTCTTAATGGCC 3 279 0 TCTTTATGTT 0.975904 -22 ACTTTATATATTTTTATTTTATAAACTAAA 4 22 1 TTTTTATTTT 0.919559 -37 ATCATTCTACTCTTTAGTTTATAAAATAAA 4 34 0 TCTTTAGTTT 0.846882 -25 AGAACCTCTATTTTAATGTTTTTCTTGGAG 5 148 1 TTTTAATGTT 0.918065 -24 ********** Masking position 6 Map Score: 2.01117 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 78 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 7 AAGGACCTTTCCAGGCACGAGAACTGTTTCATCCTC 3 118 0 CCGCACGACG 0.989718 -183 AGGTTGTTGCCCTGTCATTTTCACAGACAGCAAGGG 3 182 1 CCGCATTACG 0.996883 -119 GGGGAGAGTGCCTGACACTCGGAAAAATTGTTGAAG 3 236 1 CCGCACTAAA 0.982759 -65 TGAAGAGAACCCGGCCATTAAGAACATAAAGATAAT 3 267 1 CCGCATTAAA 0.985665 -34 GTCCATCCTCCCAGCCATTGAAGAAGTTTCCGGACT 5 30 1 CCGCATTGAG 0.986738 -142 GAAGAAGTTTCCGGACTTTTCAACTGGAACGGGGAT 5 49 1 CCGCTTTACG 0.987488 -123 ** * **** ** * Masking position 6 Map Score: 2.27743 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 34 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 8 AACGGTCAAAACTACGCTGAGGTGTAGTTGA 1 101 1 ACTCGCTGAG 0.99498 -122 GCTCAGCAGTACATCGATGAGAGTAACGAGG 1 178 0 ACACGATGAG 0.992578 -45 ATAAACAGGCACTCCGATGAGGATGAAACAG 3 100 1 ACTCGATGAG 0.995778 -201 *** ******* Masking position 10 Map Score: 0.676585 Number of sites scoring better than the average of aligned sites = 20 Number in coding regions = 19 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 9 CCTCATTTTTTGCTGACTCGCTCAGCAGTA 1 198 0 TGCTGACTCG 0.977705 -25 CCTGGTGATCCTGCGGCGTTCG 2 3 1 TGGTGATCCT 0.928375 -73 GTTCGGGACGCCGTGACCCGAGTTCAAATC 2 28 1 CCGTGACCCG 0.962457 -48 GGACGTTGCAAGGAGACTCGAAAGGCCCAC 3 39 1 AGGAGACTCG 0.931798 -262 AGCGTTCCGGTGCTGACCATCCCCGTTCCA 5 73 0 TGCTGACCAT 0.871536 -99 ACCGGAACGCTGGAGACCCGAGTTCAAATC 5 92 1 TGGAGACCCG 0.992457 -80 ********** Masking position 6 Map Score: 1.16408 Number of sites scoring better than the average of aligned sites = 128 Number in coding regions = 112 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 10 AGGAGGAAGTCAAATCCAAACCTCGTTACT 1 158 1 CAAATCCAAA 0.863466 -65 CTGCAGTCAATATATCCAAGATAAACAGGC 3 80 1 TATATCCAAG 0.89255 -221 TCAAGGTTTCCGCTTCCAAGGACCTTTCCA 3 141 0 CGCTTCCAAG 0.978505 -160 CCCATCAAATCGAATCCAAGAACCTCTATT 5 130 1 CGAATCCAAG 0.98673 -42 ATGCCTCCAAGAAAAACATTA 5 161 0 TGCCTCCAAG 0.967684 -11 ********** Masking position 5 Map Score: 0.145179 Number of sites scoring better than the average of aligned sites = 165 Number in coding regions = 156 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 11 ********** No masking Map Score: 6.56131e-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 12 ********** No masking Map Score: 6.56131e-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 13 ********** No masking Map Score: 6.56131e-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