AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i003_synecho_ctra_300.orf -o003_synecho_ctra_300.ace -a/home/amcguire/genomes/ORF_synecho.txt -z/home/amcguire/genomes/synecho.fna -g0.46 -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 = 0.46 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RCY53439 283 Synechocystis #2 RCY05376 78 Synechocystis #3 RCY50998 180 Synechocystis #4 RCY13509 16 Synechocystis #5 RCY34085 102 Synechocystis #6 RCY46344 300 Synechocystis Motif number 1 TAGCAAAAGTTTTCCCATGGCAATGTCAACTCC 1 15 0 TCCCATGCAA 0.869029 -269 CCAGGTTCTAGGCCCGATCGCCACCGAAAACCA 1 134 1 GCCGATCCCA 0.969907 -150 CAATTTTTCTGGGCTCATGGCCCAGGGGGGATC 1 183 0 GCTCATGCCC 0.894836 -101 TCTTCCGGGTTGGCCCACTACCGATAAGATGGG 1 225 1 TCCCACTCCG 0.909942 -59 TGCTGAACCCGCTCCGACTCCCATTTAACGCTT 3 52 1 GCCGACTCCA 0.984512 -129 GCTCTGATCCCCACTGGATTAGG 5 1 1 GCTGATCCCA 0.969362 -102 TTATTAGGCTGTGCTGACGTCCAAAGGGTCAGA 5 35 1 GCTGACGCCA 0.995439 -68 AAGCCCAGAATAACCCACGGCAAATCTGCGCTA 6 130 0 TCCCACGCAA 0.953623 -171 TCTACCCCAATACCTGAAGCCCAGAATAACCCA 6 146 0 TCTGAAGCCA 0.940077 -155 AATACGGGGATTGTTGACGACCATGGCCTTGCC 6 178 1 TTTGACGCCA 0.912148 -123 TTTCTGGGTCTAACTGACGGCAAGGCCATGGTC 6 196 0 TCTGACGCAA 0.969541 -105 CTGGGGATTCGCCCTCACCTCCAGTATAAATTC 6 262 1 GCTCACCCCA 0.984167 -39 CCAGTATAAATTCCTGACTGCCGATCGCC 6 282 1 TCTGACTCCG 0.939934 -19 * ****** *** Masking position 7 Map Score: 16.9357 Number of sites scoring better than the average of aligned sites = 1154 Number in coding regions = 1052 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 2 CAGCACTTTGGCCAGGTTCTAGGCCCGATCGCCACC 1 123 1 GCCAGAGCCC 0.97993 -161 GCCACCGAAAACCAGTTTAAAGCCCATTGGGATCCC 1 153 1 ACCAGACCCA 0.91249 -131 GGGCTCATGGCCCAGGGGGGATCCCAATGGGCTTTA 1 170 0 CCCAGACCCA 0.981265 -114 GGGCCATGAGCCCAGAAAAATTGGCCAATTCTTCTT 1 193 1 CCCAGTGGCC 0.992265 -91 GTTGTTCATTCCCCAAACAATCCGCCAAATCCT 1 261 1 CCCCATCGCC 0.867202 -23 TAATTGCTGAACCCGCTCCGACTCCCATTTAACGCT 3 48 1 ACCCGATCCC 0.85403 -133 TGTCTCCCCCAGATGGGTTGTCCGTAGGTCGCC 3 158 0 CCCAGTGTCC 0.952034 -23 TGGACGTCAGCACAGCCTAATAACCCTAATCCAGTG 5 22 0 CACAGTACCC 0.827641 -81 GGATTCGAACCCCCGTTGAGTTGCCCCAAAACAGAT 6 12 1 CCCCGTGCCC 0.996214 -289 CTCAAGAATTCCCTGGAGAGGTGGCAGAGCGGTTGA 6 64 0 CCCTGGGGCA 0.831314 -237 CAATTTTCCGCCCCCATCTTAGCGCAGATTTGCCGT 6 111 1 CCCCCACGCA 0.755577 -190 CGTCAACAATCCCCGTATTCTACCCCAATACCTGAA 6 161 0 CCCCGTCCCC 0.994763 -140 TTCTGGGTCTAACTGACGGCAAGGCCATGGTCGTCA 6 192 0 AACTGAGGCC 0.553867 -109 GTCAGTTAGACCCAGAAACGACACCACGAATCTAGT 6 211 1 CCCAGAACCA 0.934588 -90 TCTGAGGTGTGCCTGGGGATTCGCCCTCACCTCCAG 6 250 1 GCCTGTGCCC 0.956725 -51 ***** * **** Masking position 3 Map Score: 15.6754 Number of sites scoring better than the average of aligned sites = 4031 Number in coding regions = 3743 Number in noncoding regions = 288 Number of orfs with sites within 600 bp upstream = 313 Fraction of orfs with sites within 600 bp upstream = 0.050273 Motif number 3 TTTTTAGCAAAAGTTTTCCCATGGCAATGT 1 22 0 AAGTTTTCCC 0.645598 -262 GGGAATAACCTGGTTTGCCAAAGTTTTTCA 1 73 0 TGGTTTGCCA 0.79572 -211 AAGCCCATTGGGATCCCCCCTGGGCCATGA 1 172 1 GGATCCCCCC 0.857563 -112 CCCGGAAGAAGAATTGGCCAATTTTTCTGG 1 204 0 GAATTGGCCA 0.908102 -80 TTCTTCTTCCGGGTTGGCCCACTACCGATA 1 221 1 GGGTTGGCCC 0.992355 -63 AGGATTTGGCGGATTGTTTGG 1 273 0 GGATTTGGCG 0.878348 -11 TCCCCCAGATGGGTTGTCCGTAGGTCGCCG 3 157 0 GGGTTGTCCG 0.967491 -24 AACCCCCGTTGAGTTGCCCCAAAACAGATT 6 19 1 GAGTTGCCCC 0.954477 -282 AACAGATTTCGAGTCTGCCGCATTCAACCG 6 41 1 GAGTCTGCCG 0.94312 -260 ATCTTAGCGCAGATTTGCCGTGGGTTATTC 6 126 1 AGATTTGCCG 0.914442 -175 GTGTGCCTGGGGATTCGCCCTCACCTCCAG 6 256 1 GGATTCGCCC 0.980961 -45 ********** Masking position 4 Map Score: 8.2873 Number of sites scoring better than the average of aligned sites = 2821 Number in coding regions = 2604 Number in noncoding regions = 217 Number of orfs with sites within 600 bp upstream = 231 Fraction of orfs with sites within 600 bp upstream = 0.0371025 Motif number 4 TGGGAAAACTTTTGCTAAAAATCTAGGACA 1 31 1 TTTGCTAAAA 0.948885 -253 CCTAGCTATCATTGCTAAAACACT 2 65 1 ATTGCTAAAA 0.983927 -14 TCAACACTAAATTGCTAAACACCAAACCTT 3 13 0 ATTGCTAAAC 0.985104 -168 TGAGTGGCTAATTGCTGAACCCGCTCCGAC 3 40 1 ATTGCTGAAC 0.986186 -141 GGGGCGGAAAATTGCAGAAATCCTTCTCAA 6 95 0 ATTGCAGAAA 0.952604 -206 ********** Masking position 3 Map Score: 5.16224 Number of sites scoring better than the average of aligned sites = 105 Number in coding regions = 90 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 5 AGATTTTTAGCAAAAGTTTTCCCATGGCAA 1 25 0 CAAAAGTTTT 0.866655 -259 ACCTGGTTTGCCAAAGTTTTTCAAAAATTT 1 66 0 CCAAAGTTTT 0.976753 -218 TAGAACCTGGCCAAAGTGCTGGACCTTAAC 1 114 0 CCAAAGTGCT 0.990393 -170 AGGGGGGATCCCAATGGGCTTTAAACTGGT 1 163 0 CCAATGGGCT 0.954722 -121 GTGCTGACGTCCAAAGGGTCAGATTATTTG 5 45 1 CCAAAGGGTC 0.974158 -58 CTTACTATTCCCAAACTGTTTAAATTAGCG 5 78 0 CCAAACTGTT 0.966117 -25 ********** Masking position 4 Map Score: 3.46866 Number of sites scoring better than the average of aligned sites = 418 Number in coding regions = 372 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 6 CCAGGTTATTCCCAGCAACGCTTAGTTAAGGTCC 1 90 1 CCCAACCTTA 0.990194 -194 TCCGGGTTGGCCCACTACCGATAAGATGGGAGGG 1 228 1 CCTACCATAA 0.90102 -56 CAGCAATTAGCCACTCAACACTAAATTGCTAAAC 3 23 0 CCCAACCTAA 0.992452 -158 GCTCCGACTCCCATTTAACGCTTACTTCTCACCC 3 62 1 CCTAACCTTA 0.97529 -119 TTAACGCTTACTTCTCACCCCTAACTCCTGCTGT 3 76 1 CTCACCCTAA 0.958828 -105 GTCAGCACAGCCTAATAACCCTAATCCAGTGGGG 5 19 0 CCTAACCTAA 0.980914 -84 CTGCAATTTTCCGCCCCCATCTTAGCGCAGATTT 6 108 1 CCCCCACTTA 0.906801 -193 GGGCGAATCCCCAGGCACACCTCAGAGAGACTAG 6 242 0 CCCACACTCA 0.955531 -59 ** **** **** Masking position 14 Map Score: 5.46834 Number of sites scoring better than the average of aligned sites = 353 Number in coding regions = 306 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 7 ********** No masking Map Score: -3.13817e-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 8 ********** No masking Map Score: -3.13817e-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 9 ********** No masking Map Score: -3.13817e-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