AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i021_Succinyl-CoA_Synthetase_aful_reg_300.orf -o021_aful_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 RAG47772 146 Archaeoglobus_fulgidus #2 RAG47799 135 Archaeoglobus_fulgidus #3 RAG46830 65 Archaeoglobus_fulgidus #4 RAG14228 300 Archaeoglobus_fulgidus Motif number 1 ATTTTCGGAATTTCTTTTCCAAAAAATTTAAATA 1 16 0 TTCTTTCCAA 0.970473 -131 CGGAAGTCCTTTTGGTTTCGTTGAAAATGGGGTG 1 118 1 TTGTTTCGGA 0.905853 -29 ACTCTCACCTCTCTGAGAACAGGCGT 2 3 1 TTCCCTCTGA 0.984317 -133 AAACTTAATTTACCACTTCGCAACATTAAAAC 3 44 1 TCCCTTCGAC 0.882132 -22 TTAAAGCAGATGTGATTTCTTGGATG 4 3 0 TTGTTTCTGA 0.934635 -298 GAACGCTGTCTATCTCCTCCAGAACCTTTCCCAG 4 57 0 TTCCCTCCAA 0.974734 -244 TAGACAGCGTTCTCATCTCCTCAATGCATAGAAA 4 79 1 TTCTCTCCAA 0.972684 -222 GTTTTTGTCGTATCCTTTCTATGCATTGAGGAGA 4 94 0 TTCTTTCTGC 0.974407 -207 TTACGATCGTTCTCTTTTCTCTGCTGTGTTTATG 4 134 0 TTCTTTCTGC 0.974407 -167 CAGAACCTTCTGCCCCCTCTACAACTTAATAGAA 4 214 1 TCCCCTCTAA 0.944207 -87 * ** ***** ** Masking position 8 Map Score: 7.77162 Number of sites scoring better than the average of aligned sites = 734 Number in coding regions = 671 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 2 TTTAACATTCTCAATTTTTCAATATAAAAAA 1 49 0 TCAATTTTCA 0.963675 -98 CCTTTTAAGTTCGATTTAACATTCTCAATTT 1 63 0 TCGATTTACA 0.993227 -84 ATATCGGTTCTCGATTTATAAGGATTCCGTT 2 104 0 TCGATTTAAA 0.984861 -32 ATCGATTTTCGATATCGGTTCT 2 124 0 TCGATTTTGA 0.963683 -12 GAAAGGCAGATCGATTTAGAACCTTAAAACC 3 12 1 TCGATTTAAA 0.984868 -54 AAACCTAAACTTAATTTACCACTTCGCAACA 3 38 1 TTAATTTACA 0.884607 -28 ******** ** Masking position 6 Map Score: 5.94959 Number of sites scoring better than the average of aligned sites = 22 Number in coding regions = 13 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 3 CAACCGCCGCTAAGGCTGATGACGCCTGTT 2 28 0 TAAGGCTGAT 0.993959 -108 ATTGAATCGGTATGGGTGATGGCGTCCACC 2 60 0 TATGGGTGAT 0.960465 -76 AGAAAGGCAGATCGATTTAGAA 3 3 1 AAAGGCAGAT 0.93695 -63 CAATTCCTTTTAAAGCAGATGTGATTTCTT 4 16 0 TAAAGCAGAT 0.932049 -285 AGAACGATCGTAACGCTGCTTAGAAAAACC 4 155 1 TAACGCTGCT 0.96918 -146 TGCTGCTATATCTGGCTGATATAGCCTTTT 4 257 0 TCTGGCTGAT 0.974927 -44 AATCGATGGCTATTGCTGCTATATCTGGCT 4 270 0 TATTGCTGCT 0.942178 -31 ********** Masking position 10 Map Score: 5.90936 Number of sites scoring better than the average of aligned sites = 305 Number in coding regions = 282 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 4 GAACTTAAAAGGTGGTTGGATGTGCAGGCAGA 1 82 1 GGGGTGGATG 0.99523 -65 GGTTGGATGTGCAGGCAGAATGGCGGAAGTCC 1 95 1 GCGGCGAATG 0.990914 -52 TCGTTGAAAATGGGGTGGTATG 1 135 1 TGGGTGTATG 0.964256 -12 CAGCCTTAGCGGCGGTTGAAGGTGGACGCCAT 2 40 1 GGGGTGAAGG 0.997403 -96 AAGTTGTAGAGGGGGCAGAAGGTTCTGCCTAT 4 209 0 GGGGCGAAGG 0.997593 -92 ** *** ***** Masking position 10 Map Score: 4.46973 Number of sites scoring better than the average of aligned sites = 107 Number in coding regions = 102 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 5 GTTAAATCGAACTTAAAAGGTGGTTGGATG 1 74 1 ACTTAAAAGG 0.924418 -73 TACCGGGCTAATTGAATCGGTATGGGTGAT 2 70 0 ATTGAATCGG 0.945584 -66 TTAGCCCGGTATTTAAACGGAATCCTTATA 2 89 1 ATTTAAACGG 0.988321 -47 TCGGTTCTCGATTTATAAGGATTCCGTTTA 2 102 0 ATTTATAAGG 0.926703 -34 ATCACATCTGCTTTAAAAGGAATTGAAGCT 4 21 1 CTTTAAAAGG 0.949977 -280 GTCTTTGAGTCTTGTAACGGTTTTTCTAAG 4 173 0 CTTGTAACGG 0.934759 -128 ********** Masking position 3 Map Score: 3.77451 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 83 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 6 AAAAAATTTTCGGAATTTCTTTTCCAAAAA 1 25 0 CGGAATTTCT 0.95579 -122 GGCAGAATGGCGGAAGTCCTTTTGGTTTCG 1 108 1 CGGAAGTCCT 0.853167 -39 AGGCTGATGACGCCTGTTCTCAGAGAGGTG 2 16 0 CGCCTGTTCT 0.982009 -120 CTAAATCGATCTGCCTTTCT 3 1 0 CTGCCTTTCT 0.923729 -65 AGCAGCGTTACGATCGTTCTCTTTTCTCTG 4 145 0 CGATCGTTCT 0.903564 -156 AGTCTTGTAACGGTTTTTCTAAGCAGCGTT 4 166 0 CGGTTTTTCT 0.97459 -135 TGGCTGATATAGCCTTTTCTCGTCGAATTC 4 245 0 AGCCTTTTCT 0.854246 -56 ********** Masking position 7 Map Score: 1.81496 Number of sites scoring better than the average of aligned sites = 444 Number in coding regions = 418 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 7 CAGGCGTCATCAGCCTTAGCGGCGGTTGAA 2 30 1 CAGCCTTAGC 0.97772 -106 TGGACGCCATCACCCATACCGATTCAATTA 2 62 1 CACCCATACC 0.973941 -74 ATAAATCGAGAACCGATATCGAAAATCGAT 2 116 1 AACCGATATC 0.896454 -20 AGGAGATAGACAGCGTTCTCATCTCCTCAA 4 73 1 CAGCGTTCTC 0.943506 -228 TTTTTCTAAGCAGCGTTACGATCGTTCTCT 4 153 0 CAGCGTTACG 0.965566 -148 TGCTTAGAAAAACCGTTACAAGACTCAAAG 4 171 1 AACCGTTACA 0.797136 -130 CCAGATATAGCAGCAATAGCCATCGATTAT 4 272 1 CAGCAATAGC 0.925126 -29 ********** Masking position 2 Map Score: 0.858894 Number of sites scoring better than the average of aligned sites = 537 Number in coding regions = 502 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 8 ********** No masking Map Score: -9.63906e-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 AATTTCTTTTCCAAAAAATTTAAATAGTAAC 1 11 0 CCAAAAATTT 0.85655 -136 CCTGCACATCCAACCACCTTTTAAGTTCGAT 1 79 0 CAACACCTTT 0.943577 -68 CATACCACCCCATTTTCAACGAAAC 1 132 0 CCACCCATTT 0.963673 -15 ACGCCATCACCCATACCGATTCAATTAGCCC 2 65 1 CCAACCGATT 0.963674 -71 TCTATCTCCTCCAGAACCTTTCCCAGAATTG 4 52 0 CCAAACCTTT 0.983526 -249 AAGGATACGACAAAAACGATTACCATAAACA 4 111 1 CAAAACGATT 0.915343 -190 *** ******* Masking position 3 Map Score: 0.273516 Number of sites scoring better than the average of aligned sites = 349 Number in coding regions = 305 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 10 ********** No masking Map Score: -9.63906e-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: -9.63906e-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: -9.63906e-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