AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i165_aful_mthe_300.orf -o165_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 RAG48157 58 Archaeoglobus_fulgidus #2 RAG04564 122 Archaeoglobus_fulgidus #3 RTH00379 300 M.thermo #4 RTH01993 21 M.thermo Motif number 1 ATAAGGTTTTTCCCTAAAATATTAGGAAAAA 1 14 0 TCCTAAAATA 0.904997 -45 ATGTAAAAACACCGTTAAATTTAAATACAGC 2 28 0 ACCTTAAATT 0.986124 -95 AAAACTCATTAGCTTTAAATTATTTTTGAAC 2 93 0 AGCTTAAATT 0.921305 -30 AATCACTTCAACCTTTATATTATATGAATGT 3 28 0 ACCTTATATT 0.986094 -273 ATCTTCGGTTTCCCTTATATTGTGGTAATAT 3 66 1 TCCTTATATT 0.986126 -235 GAGGATTATTACCATTATACACCCTGAGACC 3 130 0 ACCTTATACA 0.936254 -171 ATATATAGATTCCATAAAATTAAAAACATCA 3 237 1 TCCTAAAATT 0.962961 -64 TGAATTCCTCCATTATCCTGA 4 3 0 TCCTTATCCT 0.914394 -19 *** ******* Masking position 7 Map Score: 8.83668 Number of sites scoring better than the average of aligned sites = 78 Number in coding regions = 51 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 2 CCCTAAAATATTAGGAAAAATTG 1 3 0 TTAGAAAAAT 0.972616 -56 TTTTACATGATTAAAAATAATCGAATTAGGC 2 51 1 TTAAAATAAT 0.973144 -72 TTAACACCGTTCAAAAATAATTTAAAGCTAA 2 85 1 TCAAAATAAT 0.960605 -38 AAACCGAAGATTAGTAATAATCACTTCAACC 3 46 0 TTAGAATAAT 0.9879 -255 TCCCCACCATTTATTAAAAAGGTCCATGTCT 3 176 1 TTATAAAAAG 0.829072 -125 TCATTATAAATCATTAATAATTGTCAATCGG 3 265 1 TCATAATAAT 0.960605 -36 CAATCGGGATTTAGTAATACTG 3 289 1 TTAGAATACT 0.961718 -12 **** ****** Masking position 6 Map Score: 6.24573 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 14 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 3 ACCTTGCCAAAAAGACACTATTT 1 46 1 AAACACTATT 0.920648 -13 CGTTAAATTTAAATACAGCGTTTGGTTTGAAA 2 15 0 AAACAGCGTT 0.969398 -108 TTAATCATGTAAAAACACCGTTAAATTTAAAT 2 33 0 AAACACCGTT 0.993966 -90 AATTAGGCAACTTAACACCGTTCAAAAATAAT 2 74 1 CTACACCGTT 0.971583 -49 CGGCAATGGTCATCCCTCCGCTCAGGGTGCGA 3 96 0 CACCTCCGCT 0.899002 -205 TATCTGGCACATCCCCACCATTTATTAAAAAG 3 165 1 ATCCACCATT 0.973896 -136 CCATAAAATTAAAAACATCATTATAAATCATT 3 248 1 AAACATCATT 0.93086 -53 TGAATTCCTCCATTATCCTGA 4 8 0 AACCTCCATT 0.973864 -14 ** ******** Masking position 12 Map Score: 5.71085 Number of sites scoring better than the average of aligned sites = 283 Number in coding regions = 257 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 4 AAATAGTGTCTTTTTGGCAAGGTCATAA 1 41 0 AAGTGTTGGC 0.957566 -18 TTATTTTTGAACGGTGTTAAGTTGCCTAATTCGATT 2 69 0 AGGTGTTGCC 0.998431 -54 CCCTCCGCTCAGGGTGCGATATTACCACAATATAAG 3 79 0 AGGTGTTACC 0.99537 -222 CCCTGAGCGGAGGGATGACCATTGCCGGGGGTCTCA 3 101 1 AGGATTTGCC 0.981393 -200 TGCCAGATAGGCGGAGGATTATTACCATTATACACC 3 138 0 GGGAGTTACC 0.976802 -163 TTTTTAATAAATGGTGGGGATGTGCCAGATAGGCGG 3 160 0 AGGTGGTGCC 0.995719 -141 * **** ***** Masking position 13 Map Score: 4.1941 Number of sites scoring better than the average of aligned sites = 89 Number in coding regions = 85 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 5 GACCTTGCCAAAAAGACACTATTT 1 45 1 AAAAACACAT 0.840023 -14 CCGTTAAATTTAAATACAGCGTTTGGTTTGAA 2 16 0 TAAAACAGGT 0.968259 -107 TTTAATCATGTAAAAACACCGTTAAATTTAAA 2 34 0 TAAAACACGT 0.990776 -89 GGACTCTTAAAAACTCATTAGCTTTAAAT 2 104 0 TAAAACTCTT 0.878471 -19 TTATTACCATTATACACCCTGAGACCCCCGGC 3 124 0 TATAACCCGA 0.840343 -177 GCTGAACACATAAAGACATGGACCTTTTTAAT 3 188 0 TAAAACATGA 0.950094 -113 GGAATCTATATATAAACTTTGTGCATTGTCGC 3 218 0 TATAACTTGT 0.892261 -83 TCCATAAAATTAAAAACATCATTATAAATCAT 3 247 1 TAAAACATAT 0.934153 -54 **** **** ** Masking position 6 Map Score: 3.4572 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 66 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 6 GGCAATGGTCATCCCTCCGCTCAGGGTGCG 3 97 0 ATCCCTCCGC 0.995937 -204 TAATGGTAATAATCCTCCGCCTATCTGGCA 3 144 1 AATCCTCCGC 0.99399 -157 TGAATTCCTCCATTATCCTGA 4 9 0 ATTCCTCCAT 0.975119 -13 ********** Masking position 1 Map Score: 0.591129 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 18 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 7 ********** No masking Map Score: 1.44541e-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 8 ********** No masking Map Score: 1.44541e-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: 1.44541e-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