AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00071_synecho_reg_100.orf -o00071_synecho_100.ace -a/home/amcguire/alignace/lib/ORF_synecho.txt -z/skink1/amcguire/genomes/synecho.fna -g0.48 -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 = 0.48 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 slr1609 300 patA; long-chain-fatty-acid CoA ligase. [EC:6.2.1.3] #2 slr0092 117 hisB; hypothetical protein. Motif number 1 ATTTCTCCCGTGGGTGGGTTAAGGCTAAGA 1 46 0 TGGGTGGGTT 0.848683 -255 ACCCACCCACGGGAGAAATTGAGTCAAGCA 1 57 1 GGGAGAAATT 0.953804 -244 CAAAGGCGGTGGGGTAAATAAAATGCTTGA 1 80 0 GGGGTAAATA 0.859279 -221 TCCCCTAATCGGGGGAAGTGCCTCGAGCTC 1 112 0 GGGGGAAGTG 0.952331 -189 TCCCCCGATTAGGGGAGGCTGGGAAGGGTC 1 126 1 AGGGGAGGCT 0.919157 -175 CTAAGGCCTATGGGTAAACTTTTAGTCAGG 1 172 0 TGGGTAAACT 0.936013 -129 TGGGGGGCCAGGGGGGCTTTTCAAACACGA 1 203 0 GGGGGGCTTT 0.976778 -98 CCCAAGTTTGGGGGGAAACTAAGTCAAAGT 1 229 1 GGGGGAAACT 0.994317 -72 CCCCAATACTGGGGGACTTTGACTTAGTTT 1 244 0 GGGGGACTTT 0.990048 -57 CCCCCAGTATTGGGGGATTTAGGGGGCAGA 1 259 1 TGGGGGATTT 0.938706 -42 GGGGATTTAGGGGGCAGAATCAGACTTTAT 1 271 1 GGGGCAGAAT 0.924311 -30 CAGGTCACAGGAGGGACACTTGT 2 4 0 GAGGGACACT 0.883485 -114 TTGCTCCAGGGCGGCAGTTTCAGGTCACAG 2 24 0 GCGGCAGTTT 0.850473 -94 ATAGCCGGTTTGGATAAACTTTTCCTGGCT 2 54 0 TGGATAAACT 0.610929 -64 GGGTAAGGCTGGGGCAGTTTGATCAACTCC 2 84 0 GGGGCAGTTT 0.984386 -34 ********** Masking position 3 Map Score: 18.5429 Number of sites scoring better than the average of aligned sites = 7206 Number in coding regions = 6232 Number in noncoding regions = 974 Number of orfs with sites within 600 bp upstream = 652 Fraction of orfs with sites within 600 bp upstream = 0.104722 Motif number 2 AAGGCTAAGAGGGAAAACCCTAGCTTTGGT 1 26 0 GGGAAAACCC 0.94823 -275 TCCCGTGGGTGGGTTAAGGCTAAGAGGGAA 1 41 0 GGGTTAAGGC 0.958641 -260 GCCTCGAGCTCTGCAAAGGCGGTGGGGTAA 1 93 0 CTGCAAAGGC 0.879767 -208 CCCCTAATCGGGGGAAGTGCCTCGAGCTCT 1 111 0 GGGGAAGTGC 0.890513 -190 CCTATCTCTTGAGAAAGACCCTTCCCAGCC 1 142 0 GAGAAAGACC 0.860789 -159 TCTTTCTCAAGAGATAGGCCTGACTAAAAG 1 154 1 GAGATAGGCC 0.973727 -147 TTTCAAACACGATCTAAGGCCTATGGGTAA 1 185 0 GATCTAAGGC 0.848589 -116 TAGATCGTGTTTGAAAAGCCCCCCTGGCCC 1 199 1 TTGAAAAGCC 0.803469 -102 TGCCGCCCTGGAGCAAAGCCAGGAAAAGTT 2 38 1 GAGCAAAGCC 0.989401 -80 AAGTTAGTTAGGGGTAAGGCTGGGGCAGTT 2 95 0 GGGGTAAGGC 0.985727 -23 ********** Masking position 6 Map Score: 7.90642 Number of sites scoring better than the average of aligned sites = 3100 Number in coding regions = 2800 Number in noncoding regions = 300 Number of orfs with sites within 600 bp upstream = 319 Fraction of orfs with sites within 600 bp upstream = 0.0512367 Motif number 3 CAAGCTTACTCGCCAACCAAAGCT 1 5 1 CTTACTCGCC 0.895285 -296 TAGGGTTTTCCCTCTTAGCCTTAACCCACC 1 34 1 CCTCTTAGCC 0.973229 -267 ATTTTATTTACCCCACCGCCTTTGCAGAGC 1 86 1 CCCCACCGCC 0.994319 -215 GAGAAAGACCCTTCCCAGCCTCCCCTAATC 1 132 0 CTTCCCAGCC 0.994489 -169 TTTGAAAAGCCCCCCTGGCCCCCCAAGTTT 1 208 1 CCCCCTGGCC 0.995452 -93 GACTTAGTTTCCCCCCAAACTTGGGGGGCC 1 224 0 CCCCCCAAAC 0.922426 -77 GTTTGATCAACTCCATAGCCGGTTTGGATA 2 68 0 CTCCATAGCC 0.987532 -50 TTGATCAAACTGCCCCAGCCTTACCCCTAA 2 88 1 TGCCCCAGCC 0.967989 -30 ********** Masking position 10 Map Score: 11.1048 Number of sites scoring better than the average of aligned sites = 2491 Number in coding regions = 2276 Number in noncoding regions = 215 Number of orfs with sites within 600 bp upstream = 211 Fraction of orfs with sites within 600 bp upstream = 0.0338901 Motif number 4 TTTATAAAGTCTGATTCTGCCCCCTAAATC 1 274 0 CTGATTCTGC 0.985 -27 CTCCTGTGACCTGAAACTGCCGCCCTGGAG 2 21 1 CTGAAACTGC 0.995126 -97 TATGGAGTTGATCAAACTGCCCCAGCCTTA 2 81 1 ATCAAACTGC 0.976006 -37 ********** Masking position 4 Map Score: 0.229824 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 31 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 5 TCCCTCTTAGCCTTAACCCACCCACGGGAG 1 42 1 CCTTAACCCA 0.96399 -259 TAAATAAAATGCTTGACTCAATTTCTCCCG 1 66 0 GCTTGACTCA 0.989238 -235 CAAGAGATAGGCCTGACTAAAAGTTTACCC 1 161 1 GCCTGACTAA 0.984651 -140 TACTGGGGGACTTTGACTTAGTTTCCCCCC 1 238 0 CTTTGACTTA 0.903906 -63 CCAGCCTTACCCCTAACTAACTTACT 2 102 1 CCCTAACTAA 0.976455 -16 ********** Masking position 6 Map Score: 1.78332 Number of sites scoring better than the average of aligned sites = 253 Number in coding regions = 204 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 6 ********** No masking Map Score: -3.6705e-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 7 ********** No masking Map Score: -3.6705e-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: -3.6705e-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