AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i021_Succinyl-CoA_Synthetase_aful_reg_100.orf -o021_aful_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 RAG47772 146 Archaeoglobus_fulgidus #2 RAG46830 65 Archaeoglobus_fulgidus #3 RAG14228 300 Archaeoglobus_fulgidus Motif number 1 TCCTCCAGAACCTTTCCCAGAATTGAAGCTT 3 46 0 CCTTTCCCGA 0.92373 -255 GAGAACGCTGTCTATCTCCTCCAGAACCTTT 3 62 0 TCTATCTCTC 0.945761 -239 AGACAGCGTTCTCATCTCCTCAATGCATAGA 3 80 1 CTCATCTCTC 0.942152 -221 TTTGTCGTATCCTTTCTATGCATTGAGGAGA 3 94 0 CCTTTCTAGC 0.988064 -207 CGATCGTTCTCTTTTCTCTGCTGTGTTTATG 3 134 0 CTTTTCTCGC 0.996036 -167 CTTGTAACGGTTTTTCTAAGCAGCGTTACGA 3 162 0 TTTTTCTAGC 0.94924 -139 CTGATATAGCCTTTTCTCGTCGAATTCTATT 3 241 0 CTTTTCTCTC 0.991848 -60 ******** ** Masking position 5 Map Score: 5.68234 Number of sites scoring better than the average of aligned sites = 1077 Number in coding regions = 996 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 2 TTTAACATTCTCAATTTTTCAATATAAAAAATT 1 47 0 TCAATTTCAT 0.97935 -100 CCTTTTAAGTTCGATTTAACATTCTCAATTTTT 1 61 0 TCGATTTCAT 0.992926 -86 AGGTTCTAAATCGATCTGCCTTTCT 2 3 0 TCGATCTCTT 0.980887 -63 AAACCTAAACTTAATTTACCACTTCGCAACATT 2 38 1 TTAATTTCAT 0.941264 -28 GTTCTGCCTATTGATTTGTCTTTGAGTCTTGTA 3 187 0 TTGATTTCTT 0.97935 -114 GCAATAGCCATCGATTATGCTTTATCC 3 284 1 TCGATTACTT 0.971931 -17 ******* ** * Masking position 5 Map Score: 4.61338 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 35 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 3 ATTGAAAAATTGAGAATGTTAAATCGAACT 1 57 1 TGAGAATGTT 0.908892 -90 AGAAAGGCAGATCGATTTAGAACCTT 2 7 1 GCAGATCGAT 0.902317 -59 GCAGATCGATTTAGAACCTTAAAACCTAAA 2 17 1 TTAGAACCTT 0.936458 -49 TCTATCTCCTCCAGAACCTTTCCCAGAATT 3 53 0 CCAGAACCTT 0.971709 -248 ATTGAGGAGATGAGAACGCTGTCTATCTCC 3 74 0 TGAGAACGCT 0.971937 -227 AGCAGAGAAAAGAGAACGATCGTAACGCTG 3 143 1 AGAGAACGAT 0.942188 -158 AAATCAATAGGCAGAACCTTCTGCCCCCTC 3 203 1 GCAGAACCTT 0.984426 -98 ********** Masking position 5 Map Score: 3.82654 Number of sites scoring better than the average of aligned sites = 482 Number in coding regions = 458 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 4 GCCATTCTGCCTGCACATCCAACCACCTTT 1 89 0 CTGCACATCC 0.953912 -58 AAAAGGACTTCCGCCATTCTGCCTGCACAT 1 101 0 CCGCCATTCT 0.978568 -46 CTAAATCGATCTGCCTTTCT 2 1 0 CTGCCTTTCT 0.988655 -65 AGAATTGAAGCTTCAATTCCTTTTAAAGCA 3 29 0 CTTCAATTCC 0.956982 -272 GGAATTGAAGCTTCAATTCTGGGAAAGGTT 3 39 1 CTTCAATTCT 0.964072 -262 GATGAGAACGCTGTCTATCTCCTCCAGAAC 3 66 0 CTGTCTATCT 0.878428 -235 ********** Masking position 8 Map Score: 3.06788 Number of sites scoring better than the average of aligned sites = 565 Number in coding regions = 532 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 5 TGTTAAATCGAACTTAAAAGGTGGTTGGAT 1 73 1 AACTTAAAAG 0.978334 -74 TCGATTTAGAACCTTAAAACCTAAACTTAA 2 22 1 ACCTTAAAAC 0.985733 -44 CCACTTCGCAACATTAAAAC 2 56 1 ACATTAAAAC 0.945557 -10 AATCACATCTGCTTTAAAAGGAATTGAAGC 3 20 1 GCTTTAAAAG 0.916307 -281 CCCCCTCTACAACTTAATAGAATTCGACGA 3 226 1 AACTTAATAG 0.932142 -75 ********** Masking position 5 Map Score: 1.94148 Number of sites scoring better than the average of aligned sites = 70 Number in coding regions = 57 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 6 AAAATTGAGAATGTTAAATCGAACTTAAAA 1 62 1 ATGTTAAATC 0.929992 -85 CGACGAGAAAAGGCTATATCAGCCAGATAT 3 250 1 AGGCTATATC 0.987378 -51 ATGGCTATTGCTGCTATATCTGGCTGATAT 3 265 0 CTGCTATATC 0.987378 -36 GCCATCGATTATGCTTTATCC 3 290 1 ATGCTTTATC 0.981406 -11 ********** Masking position 5 Map Score: 1.7569 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 19 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 7 TACTATTTAAATTTTTTGGAAAAGAAATTC 1 13 1 ATTTTTTGGA 0.979951 -134 CAATATAAAAAATTTTCGGAATTTCTTTTC 1 31 0 AATTTTCGGA 0.976237 -116 AGCAGATGTGATTTCTTGGATG 3 3 0 ATTTCTTGGA 0.986946 -298 TTGAAGCTTCAATTCTGGGAAAGGTTCTGG 3 43 1 AATTCTGGGA 0.984507 -258 ********** Masking position 6 Map Score: 2.91409 Number of sites scoring better than the average of aligned sites = 45 Number in coding regions = 42 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 8 ********** No masking Map Score: 6.63809e-14 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: 6.63809e-14 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: 6.63809e-14 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