AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i175_biotin_biosynthesis1_synecho_reg_300.orf -o175_synecho_300.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 RCY00022 120 Synechocystis #2 RCY52230 73 Synechocystis #3 RCY26391 300 Synechocystis #4 RCY23132 293 Synechocystis #5 RCY41564 233 Synechocystis Motif number 1 ATCATTTTTTTCCCCCGGCGATCGCCT 1 104 1 TCCCCCGGCG 0.987345 -17 CCTCTCCTGGCACCTCTGCCCA 2 3 1 TCTCCTGGCA 0.766321 -71 CAATTTTTTGTCCCGAGCTGGTCTT 3 6 0 TCCCGAGCTG 0.913601 -295 GACTGCTCTATCCCGCGTCGCTTCGAATAT 3 247 0 TCCCGCGTCG 0.989784 -54 CAAATGGTAATCCCGAGCCAAACCTAGGAA 4 38 1 TCCCGAGCCA 0.985226 -256 TTCAAATCCGCCTCCCGCCATTAAAAAAAA 4 213 1 CCTCCCGCCA 0.959237 -81 GAAAAAAATTCCCCCCGCCGGATAATGGTT 4 244 1 CCCCCCGCCG 0.997305 -50 TAAAACAAACCCCCCAACCATTATCCGGCG 4 259 0 CCCCCAACCA 0.88455 -35 TTTACCCCCATGTCATGGCAGATTA 5 6 1 CCCCATGTCA 0.925481 -228 AGTTTTTGCTCCCCATGTCGAATTTTTCCC 5 167 1 CCCCATGTCG 0.964759 -67 GTCGAATTTTTCCCGAGCCGTTGACCAAAA 5 183 1 TCCCGAGCCG 0.99325 -51 CCCTGTGTCGCAACCCGCAA 5 224 0 CCCTGTGTCG 0.878387 -10 ********** Masking position 2 Map Score: 18.8223 Number of sites scoring better than the average of aligned sites = 2016 Number in coding regions = 1860 Number in noncoding regions = 156 Number of orfs with sites within 600 bp upstream = 177 Fraction of orfs with sites within 600 bp upstream = 0.0284292 Motif number 2 TAACCGCCCATTTCAACGGTTTTCC 1 1 0 TTTCACGTCC 0.795608 -120 TCAGCCTCAGTTTAAGCCAGAAACCCAGGAAAAGA 1 67 0 TTTAGCCACC 0.730002 -54 CCTCTCCTGGCACCTCTGCCCACCGTGATAA 2 7 1 CTGGACCCCC 0.976848 -67 TGCCCTTTAATTTGATCCAGACCCCTAACCCCATA 2 44 1 TTTGTCCCCC 0.985823 -30 GCCGCCGAATTTTGCGACTCTCCCCGTATTTGATC 3 64 1 TTTGGACCCC 0.960335 -237 AAAATAAAGTTTGGCAAAAATTCCCCCGATCAGTT 3 209 1 TTGGAAACCC 0.89851 -92 TTACATCTTGCGACCTGAGCCCGACGAGCTAC 3 279 0 TTGCACCCCC 0.989663 -22 GGGATTACCATTTGAAAGGCTTCCCCGAATTTGAG 4 17 0 TTTGAAGCCC 0.966516 -277 AAAACTGTAGTTGGTAAGCATAACCCGAAGGTCGG 4 175 1 TTGGAAGACC 0.944365 -119 GGGAGGCGGATTTGAACCACCGACCTTCGGGTTAT 4 194 0 TTTGACCACC 0.982585 -100 AACCCTGGGTTTGCTTCCGGGCACCCGACTAAGGG 5 45 0 TTGCTCCACC 0.940922 -189 TCCGCTATGATTGGATCGAAAACCCTGGGTTTGCT 5 65 0 TTGGTCGCCC 0.984816 -169 **** *** *** Masking position 2 Map Score: 11.4389 Number of sites scoring better than the average of aligned sites = 1416 Number in coding regions = 1290 Number in noncoding regions = 126 Number of orfs with sites within 600 bp upstream = 132 Fraction of orfs with sites within 600 bp upstream = 0.0212014 Motif number 3 ATAATGTGGGGGCCTCTGCTTTAACCGCCCA 1 26 0 GGCCTTGCTT 0.782719 -95 TCTTTTCCTGGGTTTCTGGCTTAAACTGAGG 1 67 1 GGTTTTGGCT 0.867782 -54 GGCAATATGGGGTTAGGGGTCTGGATCAAAT 2 53 0 GGTTAGGGTC 0.888194 -21 AGTGGATTGTGGTTTTGGCTTAAGAGCAATT 3 31 0 GGTTTGGCTT 0.967154 -270 TTCATCCCATAGTCTATGCACTGAAGAGTAA 3 169 0 AGTCTTGCAC 0.557736 -132 GTAGCTCGTCGGGCTCAGGTCGCAAGATGTA 3 279 1 GGGCTAGGTC 0.762305 -22 AAGCATTCCTAGGTTTGGCTCGGGATTACCA 4 42 0 AGGTTGGCTC 0.894155 -252 TGACTCTGTCAGTTTGTGGTCTGGACTTTCT 4 137 0 AGTTTTGGTC 0.956002 -157 ACCGACCTTCGGGTTATGCTTACCAACTACA 4 180 0 GGGTTTGCTT 0.935843 -114 ATAACCCGAAGGTCGGTGGTTCAAATCCGCC 4 194 1 GGTCGTGGTT 0.927525 -100 GCCGGATAATGGTTGGGGGGTTTGTTTTATT 4 260 1 GGTTGGGGGT 0.771498 -34 TTCTCTTCCCAGTTTTTGCTCCCCATGTCGA 5 157 1 AGTTTTGCTC 0.942602 -77 AACTAATAAAGTTTTTTGGTCAACGGCTCGG 5 195 0 GTTTTTGGTC 0.788801 -39 AAACTTTATTAGTTGCGGGTTGCGACACAGG 5 212 1 AGTTGGGGTT 0.874451 -22 ***** ***** Masking position 8 Map Score: 7.80925 Number of sites scoring better than the average of aligned sites = 2392 Number in coding regions = 2110 Number in noncoding regions = 282 Number of orfs with sites within 600 bp upstream = 294 Fraction of orfs with sites within 600 bp upstream = 0.0472213 Motif number 4 CCCACATTATAACCAAGGGATCTTTTCCTGG 1 47 1 AACCAGGGAT 0.968353 -74 TTAAGCCAGAAACCCAGGAAAAGATCCCTTG 1 60 0 AACCAGGAAA 0.896926 -61 AAGAGTAAGAATTTTAGGGATTTTCGAAGTA 3 146 0 ATTTAGGGAT 0.81829 -155 TCAGTGCATAGACTATGGGATGAATCTGCCC 3 176 1 GACTTGGGAT 0.937793 -125 TATCATAACTGATCGGGGGAATTTTTGCCAA 3 219 0 GATCGGGGAA 0.940764 -82 TTATCTCTCAAATTCGGGGAAGCCTTTCAAA 4 11 1 AATTGGGGAA 0.901871 -283 TCCCGAGCCAAACCTAGGAATGCTTGGTGTT 4 48 1 AACCAGGAAT 0.906721 -246 AATGCTTGGTGTTTCTGGGAAGGTGTAGAGA 4 66 1 GTTTTGGGAA 0.641445 -228 CCGGGCACCCGACTAAGGGAAACACCAGTAA 5 33 0 GACTAGGGAA 0.976309 -201 CCCGGAAGCAAACCCAGGGTTTTCGATCCAA 5 59 1 AACCAGGGTT 0.527849 -175 **** ****** Masking position 7 Map Score: 5.98822 Number of sites scoring better than the average of aligned sites = 1667 Number in coding regions = 1430 Number in noncoding regions = 237 Number of orfs with sites within 600 bp upstream = 247 Fraction of orfs with sites within 600 bp upstream = 0.0396723 Motif number 5 CCACCGTGATAAAATGCCCTTTAATTTGAT 2 30 1 AAAATGCCCT 0.946253 -44 TCGGGACAAAAAATTGCTCTTAAGCCAAAA 3 20 1 AAATTGCTCT 0.96255 -281 CTATGGGATGAATCTGCCCTAAAAATAAAG 3 188 1 AATCTGCCCT 0.986026 -113 ACGAGCTACCAGACTGCTCTATCCCGCGTC 3 258 0 AGACTGCTCT 0.95878 -43 AAACACCAGTAATCTGCCATGACATGGGGG 5 15 0 AATCTGCCAT 0.950614 -219 GCGAGGAAAGAATCCGCTATGATTGGATCG 5 82 0 AATCCGCTAT 0.830637 -152 AACCTCCAATAAATTTCTCTTCCCAGTTTT 5 143 1 AAATTTCTCT 0.7693 -91 ********** Masking position 1 Map Score: 2.91219 Number of sites scoring better than the average of aligned sites = 741 Number in coding regions = 659 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 6 AAGCAGAGGCCCCCACATTATAACCAAGGG 1 36 1 CCCCACATTA 0.910155 -85 GGCACCTCTGCCCACCGTGATAAAATGCCC 2 19 1 CCCACCGTGA 0.949395 -55 TGTTAGGGTGTCTCCCATTAAGTCTCTACA 4 89 0 TCTCCCATTA 0.927418 -205 AAATCCGCCTCCCGCCATTAAAAAAAAAGA 4 216 1 CCCGCCATTA 0.991286 -78 AACAAACCCCCCAACCATTATCCGGCGGGG 4 256 0 CCAACCATTA 0.906325 -38 ACACCAGTAATCTGCCATGACATGGGGGTA 5 13 0 TCTGCCATGA 0.957401 -221 GAGGAAAGAATCCGCTATGATTGGATCGAA 5 80 0 TCCGCTATGA 0.896128 -154 ********** Masking position 10 Map Score: 2.32528 Number of sites scoring better than the average of aligned sites = 964 Number in coding regions = 876 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 7 GATCAAATACGGGGAGAGTCGCAAAATTCG 3 69 0 GGGGAGAGTC 0.972067 -232 AGTCTATGCACTGAAGAGTAAGAATTTTAG 3 160 0 CTGAAGAGTA 0.935312 -141 TTCTGGGAAGGTGTAGAGACTTAATGGGAG 4 78 1 GTGTAGAGAC 0.968825 -216 AAAGCTGAGGGTGAAGAGAAAGTCCAGACC 4 121 1 GTGAAGAGAA 0.986477 -173 AGCAAAAACTGGGAAGAGAAATTTATTGGA 5 147 0 GGGAAGAGAA 0.987461 -87 ********** Masking position 5 Map Score: 1.89019 Number of sites scoring better than the average of aligned sites = 87 Number in coding regions = 70 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 8 AGGCGATCGCCGGGGGAAAAAAAT 1 107 0 GATCGCCGGG 0.990733 -14 CCTCTCCTGGCACCTCTGCC 2 1 1 CCTCTCCTGG 0.919444 -73 TGGCACCTCTGCCCACCGTGATAAAATGCC 2 18 1 GCCCACCGTG 0.950191 -56 CAGTCTGGTAGCTCGTCGGGCTCAGGTCGC 3 272 1 GCTCGTCGGG 0.990701 -29 TTGAACCACCGACCTTCGGGTTATGCTTAC 4 188 0 GACCTTCGGG 0.962034 -106 AAAAAATTCCCCCCGCCGGATAATGGTTGG 4 246 1 CCCCGCCGGA 0.955883 -48 ********** Masking position 4 Map Score: 2.85764 Number of sites scoring better than the average of aligned sites = 936 Number in coding regions = 880 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 9 CGGTTAAAGCAGAGGCCCCCACATTATAAC 1 30 1 AGAGGCCCCC 0.96987 -91 ACACCTTCCCAGAAACACCAAGCATTCCTA 4 62 0 AGAAACACCA 0.970623 -232 AGACTTAATGGGAGACACCCTAACAGAAAA 4 94 1 GGAGACACCC 0.988321 -200 ATTGAATAAAACAAACCCCCCAACCATTAT 4 265 0 ACAAACCCCC 0.958025 -29 CCCGACTAAGGGAAACACCAGTAATCTGCC 5 27 0 GGAAACACCA 0.972726 -207 ********** Masking position 3 Map Score: 1.92243 Number of sites scoring better than the average of aligned sites = 128 Number in coding regions = 112 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 10 ********** No masking Map Score: -1.39023e-12 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: -1.39023e-12 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: -1.39023e-12 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