AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i307_aful_mthe_100.orf -o307_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 RAG30868 101 Archaeoglobus_fulgidus #2 RAG45953 33 Archaeoglobus_fulgidus #3 RAG50460 57 Archaeoglobus_fulgidus #4 RAG30980 17 Archaeoglobus_fulgidus #5 RAG03171 83 Archaeoglobus_fulgidus #6 RTH00085 42 M.thermo #7 RTH01194 65 M.thermo #8 RTH01780 17 M.thermo #9 RTH01772 74 M.thermo #10 RTH01242 170 M.thermo #11 RTH00244 62 M.thermo #12 RTH00523 88 M.thermo Motif number 1 GTTGAAATAGAGTTCCCTTACAAACGTTTTTGTACTTGA 1 20 0 AGCCCACTTT 0.998176 -82 GTGTAATAAAAGTATCCAAACCTGCATTTTTCGAGTTGA 1 54 0 AGTCCACTTT 0.986105 -48 TTAAGTTTATATTCCCCCGACCAACTTTTTTC 2 12 1 ATCCCACTTT 0.986103 -22 TTACCTTCTCAGCCCCTTTACCCCTGTTTCGGAGGCCCC 9 18 0 AGCCTACTTT 0.996239 -57 GGTAAGATAAAGCCCCCCGTCTTAACTTTTTTT 9 52 1 AGCCCTCTTT 0.991268 -23 TTCCATTAAACGGACCTTCACTGACATTTCATTGATGTG 10 28 1 CGCCTACTTT 0.987881 -143 CAGATGTAGTAGCACCTAAACCGCTATTTTTCAGGGATA 10 97 1 AGCCTACTTT 0.996239 -74 ** *** ** *** Masking position 17 Map Score: 12.127 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 24 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 2 TTTGAAGGCTAAAAGGAGAGGAGGA 6 5 0 AAAAGAGAGG 0.973898 -38 TTAGCCTTCAAAAAACAGGGAGGCATAAC 6 24 1 AAAACAGGGA 0.971482 -19 TTATCCATCAATAAAGAGAGGTTAGAAAA 7 47 1 ATAAGAGAGG 0.95139 -19 AAGAACAGGGGCCTCCGAAAC 9 1 1 AAGACAGGGG 0.991963 -74 CAGGGGCCTCCGAAACAGGGGTAAAGGGGCT 9 16 1 CGAACAGGGG 0.954575 -59 AAAAAAAGTTAAGACGGGGGGCTTTATCTTA 9 54 0 AAGAGGGGGG 0.954579 -21 GTTTAATGGAAAAATCAAAGGTGTTGTT 10 8 0 AAAACAAAGG 0.868872 -163 CGTATCCCTGAAAAATAGCGGTTTAGGTGCT 10 107 0 AAAATAGCGG 0.808811 -64 CTCAGTCAGTATATTCAGGGGGTTTAGTATC 11 32 0 ATATCAGGGG 0.92925 -31 TACAATAGTTATAACCGGAGATACATAAATT 12 26 1 ATAACGGAGA 0.74534 -63 ACACTCCAGAAGGAGCAGGGTCACAGGTGGT 12 61 1 AGGACAGGGT 0.872638 -28 **** ****** Masking position 10 Map Score: 7.54441 Number of sites scoring better than the average of aligned sites = 833 Number in coding regions = 770 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 3 GGTTTTATTTCAAGTACAAAAA 1 2 1 GTTTATTTCA 0.901197 -100 TTGAAATAGAGTTCCCTTACAAACGTTTTTG 1 27 0 GTTCCTTACA 0.960078 -75 GGTTTGGATACTTTTATTACACCTGAAATCA 1 71 1 CTTTATTACA 0.918009 -31 GGTGGGAGTTTGATTTCAGGTGTAATAA 1 84 0 GTTTATTTCA 0.901197 -18 AGCTTCGATGAAATTTGAAATTA 3 45 0 CTTCATGAAA 0.913791 -13 ATATTTAAATCTTTCCTTTAATATTTCTTCG 5 30 1 CTTTCTTTAA 0.843652 -54 GTGAAGGTCCGTTTAATGGAAAAATCAAAGG 10 18 0 GTTTATGGAA 0.743533 -153 TTAAACGGACCTTCACTGACATTTCATTGAT 10 33 1 CTTCCTGACA 0.964345 -138 CTGTCAGTCACATCAATGAAATGTCAGTGAA 10 44 0 CATCATGAAA 0.72453 -127 CACTTAAAAAGTTTACTGTCAGTCACATCAA 10 59 0 GTTTCTGTCA 0.942616 -112 CATCTGGTGTGATCACTTAAAAAGTTTACTG 10 72 0 GATCCTTAAA 0.758294 -99 **** ****** Masking position 11 Map Score: 7.56152 Number of sites scoring better than the average of aligned sites = 386 Number in coding regions = 348 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 4 AGCTTCGATGAAATTTGAAATT 3 46 0 CTTCGATGAA 0.963674 -12 TTTAATATTTCTTCGAAACAAATTTCTATC 5 46 1 CTTCGAAACA 0.973378 -38 TCCTTTTAGCCTTCAAAAAACAGGGAGGCA 6 19 1 CTTCAAAAAA 0.936141 -24 ATAAATTATCCATCAATAAAGAGAGGTTAG 7 42 1 CATCAATAAA 0.936141 -24 GAACAGGGGCCTCCGAAACAGGGGTAAAGG 9 13 1 CTCCGAAACA 0.930405 -62 CTGTCAGTCACATCAATGAAATGTCAGTGA 10 45 0 CATCAATGAA 0.907957 -126 TCACCTTTCCAACGATACAATAGTTATAA 12 10 1 CAACGATACA 0.9002 -79 ********** Masking position 6 Map Score: 4.51734 Number of sites scoring better than the average of aligned sites = 159 Number in coding regions = 144 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 5 CCTTCATGGACTCACCT 8 7 0 CCTTCATGAC 0.958357 -11 CTTTATCTTACCTTCTCAGCCCCTTTACCCC 9 33 0 CCTTCTCGCC 0.992449 -42 ATTAAACGGACCTTCACTGACATTTCATTGA 10 32 1 CCTTCACGAC 0.991742 -139 GATGAACCTCCTCAGTCAGTATATTCA 11 46 0 CCTCCTCGTC 0.994111 -17 CACCTGTGACCCTGCTCCTTCTGGAGTGTAA 12 59 0 CCTGCTCTTC 0.934171 -30 TTAATTAACCACCTGTGACCCTGCTCCTT 12 70 0 CCACCTGGAC 0.944286 -19 ******* *** Masking position 5 Map Score: 2.89209 Number of sites scoring better than the average of aligned sites = 419 Number in coding regions = 401 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 6 GGTTTTATTTCAAGTACAAAA 1 1 1 GGTTTTTTTC 0.954373 -101 GAAAAATGCAGGTTTGGATACTTTTATTACA 1 61 1 GGTTTGATAC 0.883012 -41 GGTGGGAGTTTGATTTCAGGTGTAATA 1 85 0 AGTTTGTTTC 0.965083 -17 ATTAAGTTTATATTCCCCCGACCAA 2 5 1 AGTTTAATTC 0.947001 -29 TCACTTAAAAAGTTTACTGTCAGTCACATCA 10 60 0 AGTTTATGTC 0.924186 -111 GAAAAATAGCGGTTTAGGTGCTACTACATCT 10 98 0 GGTTTAGTGC 0.918974 -73 ATATTCAGGGGGTTTAGTATCGTGTGGATAT 11 22 0 GGTTTATATC 0.944398 -41 ****** **** Masking position 5 Map Score: 1.19136 Number of sites scoring better than the average of aligned sites = 116 Number in coding regions = 98 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 7 TCAGGTGTAATAAAAGTATCCAAACCTGCAT 1 66 0 TAAAATATCC 0.961154 -36 GTCACTAATTTTATCCTTAATATTTA 5 6 1 TAATTTATCC 0.961178 -78 CCTTAATATTTAAATCTTTCCTTTAATATTT 5 25 1 TAAATTTTCC 0.859334 -59 CTTCGAAACAAATTTCTATCCACCCACAAAT 5 56 1 AATTTTATCC 0.929932 -28 TCATGATTACATAAATTATCCATCAATAAAG 7 32 1 ATAAATATCC 0.859308 -34 GCTCAGAATTAATATCCACACGATACT 11 7 1 AATTATATCC 0.929927 -56 ***** ***** Masking position 7 Map Score: 0.150485 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 40 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 8 ACATAAAAATTAAATAATTTCAAATTTCAT 3 31 1 TAAATAATTT 0.894393 -27 GTCACTAATTTTATCCTTAAT 5 2 1 TCACTAATTT 0.954026 -82 CCCCCCGTCTTAACTTTTTTT 9 64 1 TAACTTTTTT 0.907563 -11 TCTCCGGTTATAACTATTGTATCGTTGGAA 12 17 0 TAACTATTGT 0.934613 -72 TTCTGGAGTGTAACTAATTTATGTATCTCC 12 42 0 TAACTAATTT 0.978233 -47 ********** Masking position 5 Map Score: 1.75628 Number of sites scoring better than the average of aligned sites = 14 Number in coding regions = 7 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 9 ********** No masking Map Score: 1.65857e-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 10 ********** No masking Map Score: 1.65857e-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 11 ********** No masking Map Score: 1.65857e-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