AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i221_aful_mthe_100.orf -o221_aful_mthe_100.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 0.879259 -92 ACTCGGGTCACGGCGTCCCGAACGCCGCAGGAT 2 18 0 CGCGTCCCAC 0.984245 -58 ACGCCGTGACCCGAGTTCAAATCTCGGCGGCCC 2 35 1 CGAGTTCATC 0.957459 -41 GTTCAAATCTCGGCGGCCCCATCTGCTTTAAGG 2 49 1 CGCGGCCCTC 0.997666 -27 GATATATTGACTGCAGCCCTGTTCCTTGTGGGC 3 63 0 CGCAGCCCTT 0.90876 -238 TCATCCTCATCGGAGTGCCTGTTTATCTTGGAT 3 93 0 CGAGTGCCTT 0.900161 -208 ACCTTGACCACAGGGTCCAGGTTGTTGCCCTGT 3 164 1 CGGGTCCATT 0.926127 -137 AGGCACTCTCCCCCGGCCCTCTCGATCTTATCC 3 216 0 CCCGGCCCTC 0.987219 -85 TTCTTAATGGCCGGGTTCTCTTCAACAATTTTT 3 258 0 CGGGTTCTTC 0.944308 -43 TGCTGACCATCCCCGTTCCAGTTGAAAAGTCCG 5 60 0 CCCGTTCCTT 0.9586 -112 CTCGGGTCTCCAGCGTTCCGGTGCTGACCATCC 5 81 0 CGCGTTCCTG 0.97632 -91 CGCTGGAGACCCGAGTTCAAATCTCGGCGGTCC 5 99 1 CGAGTTCATC 0.957459 -73 GTTCAAATCTCGGCGGTCCCATCAAATCGAATC 5 113 1 CGCGGTCCTC 0.996298 -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 GAAATCGTTTTTAGCCTTCCGCGGAAGGAAC 1 28 1 TTGCCTTCCG 0.967982 -195 TAATTTTTAATGTTCCTTCCGCGGAAGGCTA 1 39 0 TGTCCTTCCG 0.985583 -184 GAGGTTTGGATTTGACTTCCTCCTCTGCCAG 1 151 0 TTGACTTCCT 0.883888 -72 CTGGTGATCCTGCGGCGTTCGGGACGCCGTG 2 12 1 TGGGCGTTCG 0.883903 -64 TCCAGATTGCTGCGCCTTCCTGGGATG 3 7 0 TGGCCTTCCT 0.993843 -294 CGAGTCTCCTTGCAACGTCCTTCCAGATTGC 3 28 0 TGAACGTCCT 0.889881 -273 CTGTTCCTTGTGGGCCTTTCGAGTCTCCTTG 3 47 0 TGGCCTTTCG 0.980131 -254 GCACGAGAACTGTTTCATCCTCATCGGAGTG 3 109 0 TGTTCATCCT 0.914746 -192 ACTGAATCATTCTACTCTTTAGT 4 46 0 TGATCATTCT 0.678708 -13 TAGGGTAGCTTGGTCCATCCTCCCAGCCATT 5 18 1 TGTCCATCCT 0.975199 -154 ** ******** Masking position 8 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 0.940618 -159 CGGCGTTCGGGACGCCGTGACCCGAGTTCA 2 24 1 GACGCCGTGA 0.979278 -52 AGCAGATGGGGCCGCCGAGATTTGAACTCG 2 46 0 GCCGCCGAGA 0.998239 -30 ATTTGATGGGACCGCCGAGATTTGAACTCG 5 110 0 ACCGCCGAGA 0.988726 -62 CCATCAAATCGAATCCAAGAACCTCTATTT 5 131 1 GAATCCAAGA 0.887488 -41 ATGCCTCCAAGAAAAACATTAA 5 160 0 GCCTCCAAGA 0.991857 -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 0.890213 -83 CCTGGTGATCCTGCGGCGTT 2 1 1 CCTGGTGATC 0.916029 -75 GAGTTCAAATCTCGGCGGCCCCATCTGCTT 2 47 1 CTCGGCGGCC 0.930628 -29 CAGCCCTGTTCCTTGTGGGCCTTTCGAGTC 3 53 0 CCTTGTGGGC 0.85578 -248 ACAACCTGGACCCTGTGGTCAAGGTTTCCG 3 159 0 CCCTGTGGTC 0.985923 -142 CAGGTTGTTGCCCTGTCATTTTCACAGACA 3 181 1 CCCTGTCATT 0.872052 -120 CGATCTTATCCCTTGCTGTCTGTGAAAATG 3 197 0 CCTTGCTGTC 0.861449 -104 GGCACTCTCCCCCGGCCCTCTCGATCTTAT 3 218 0 CCCGGCCCTC 0.979141 -83 TTGAAGAGAACCCGGCCATTAAGAACATAA 3 266 1 CCCGGCCATT 0.965804 -35 GACCAAGCTACCCTACGGTCCC 5 3 0 CCCTACGGTC 0.939688 -169 GGTCCATCCTCCCAGCCATTGAAGAAGTTT 5 29 1 CCCAGCCATT 0.81435 -143 GAGTTCAAATCTCGGCGGTCCCATCAAATC 5 111 1 CTCGGCGGTC 0.984691 -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 TAGCTTCACCTCATATCGAAATCGTT 1 7 1 CACCTCATAT 0.992303 -216 TGGCGCCTCATTTTTTGCTGACT 1 210 0 CGCCTCATTT 0.946388 -13 CACCCCTTAAAGCAGATGGG 2 66 0 CACCCCTTAA 0.924922 -10 TAAAACACCTCATAATAAACTCTAG 6 37 0 CACCTCATAA 0.989008 -15 TCTATCACCTCAAATAAGTTTCAAT 7 13 0 CACCTCAAAT 0.975116 -15 ********** Masking position 6 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 AAGGACCTTTCCAGGCACGAGAACTGTTTCATCCTC 3 118 0 CCGCACGACG 0.987891 -183 AGGTTGTTGCCCTGTCATTTTCACAGACAGCAAGGG 3 182 1 CCGCATTACG 0.996317 -119 GGGGAGAGTGCCTGACACTCGGAAAAATTGTTGAAG 3 236 1 CCGCACTAAA 0.979679 -65 TGAAGAGAACCCGGCCATTAAGAACATAAAGATAAT 3 267 1 CCGCATTAAA 0.983094 -34 GTCCATCCTCCCAGCCATTGAAGAAGTTTCCGGACT 5 30 1 CCGCATTGAG 0.984357 -142 GAAGAAGTTTCCGGACTTTTCAACTGGAACGGGGAT 5 49 1 CCGCTTTACG 0.98524 -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 7 CCGCGGAAGGAACATTAAAAATTAACATGC 1 46 1 AACATTAAAA 0.953157 -177 GGCCATTAAGAACATAAAGATAATAGAATA 3 279 1 AACATAAAGA 0.969207 -22 TTTAGTTTATAAAATAAAAATATATAAAGT 4 22 0 AAAATAAAAA 0.928266 -37 TTTATTTTATAAACTAAAGAGTAGAATGAT 4 34 1 AAACTAAAGA 0.86288 -25 CTCCAAGAAAAACATTAAAATAGAGGTTCT 5 148 0 AACATTAAAA 0.953157 -24 ********** Masking position 5 Map Score: 1.55467 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 12 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 8 AACGGTCAAAACTACGCTGAGGTGTAGTTGA 1 101 1 ACTCGCTGAG 0.995064 -122 GCTCAGCAGTACATCGATGAGAGTAACGAGG 1 178 0 ACACGATGAG 0.992701 -45 ATAAACAGGCACTCCGATGAGGATGAAACAG 3 100 1 ACTCGATGAG 0.995848 -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 TACTGCTGAGCGAGTCAGCAAAAAATGAGG 1 198 1 CGAGTCAGCA 0.979048 -25 CGAACGCCGCAGGATCACCAGG 2 3 0 AGGATCACCA 0.932471 -73 GATTTGAACTCGGGTCACGGCGTCCCGAAC 2 28 0 CGGGTCACGG 0.964683 -48 GTGGGCCTTTCGAGTCTCCTTGCAACGTCC 3 39 0 CGAGTCTCCT 0.935719 -262 TGGAACGGGGATGGTCAGCACCGGAACGCT 5 73 1 ATGGTCAGCA 0.878476 -99 GATTTGAACTCGGGTCTCCAGCGTTCCGGT 5 92 0 CGGGTCTCCA 0.992907 -80 ********** Masking position 5 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 AGTAACGAGGTTTGGATTTGACTTCCTCCT 1 158 0 TTTGGATTTG 0.872484 -65 GCCTGTTTATCTTGGATATATTGACTGCAG 3 80 0 CTTGGATATA 0.89987 -221 TGGAAAGGTCCTTGGAAGCGGAAACCTTGA 3 141 1 CTTGGAAGCG 0.9801 -160 AATAGAGGTTCTTGGATTCGATTTGATGGG 5 130 0 CTTGGATTCG 0.987723 -42 TAATGTTTTTCTTGGAGGCAT 5 161 1 CTTGGAGGCA 0.970057 -11 ********** Masking position 6 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