AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i270_synecho_ctra_300.orf -o270_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 RCY52916 300 Synechocystis #2 RCY27405 123 Synechocystis Motif number 1 TGTCGTGACAATTTACCAAAATGTTCCTAACTTTTGTAGGC 1 25 0 ATACCATTAC 0.922511 -276 TTCGGTCAATAATGACCGAGTTTCATTTTCCTATCCCTGTC 1 62 0 ATACCGTTCC 0.998317 -239 CTCGCCACTGAGTTGCCGCTCCTTTCCTCCCTGAACCGATG 1 130 1 ATGCCTCTCC 0.985546 -171 AGTTGATGCCGTTTACCGTGGTCTGGGTTCGCAATCACCCC 1 199 1 GTACCGTTCG 0.963028 -102 CTGGGTTCGCAATCACCCCGGCTTTGGTAGCAACACTAGTT 1 221 1 ATACCGCTGC 0.994495 -80 AGTTCATCCCATTGACCCCTTTCACTTTACCCAGGAAATAC 1 258 1 ATACCTTTCC 0.993859 -43 GCTTAACCGAACTAACCCCGACGGTTATCCCACTCAGGCAA 2 38 0 ATACCGCTCC 0.998933 -86 CGTAGGATCTAGTCAACAGGCCTCGATTTCCGTTAAC 2 97 1 ATAACGCTCC 0.990333 -27 * * *** * * * ** Masking position 18 Map Score: 8.79791 Number of sites scoring better than the average of aligned sites = 523 Number in coding regions = 472 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 2 ACTAAGGTCAGGCCCTTTCTTTTTCGGTCA 1 95 0 GGCCCTTTCT 0.978116 -206 GACCTTAGTAGCTCCTCGCCACTGAGTTGC 1 116 1 GCTCCTCGCC 0.987971 -185 CTGAGTTGCCGCTCCTTTCCTCCCTGAACC 1 137 1 GCTCCTTTCC 0.997535 -164 CATCCCATTGACCCCTTTCACTTTACCCAG 1 262 1 ACCCCTTTCA 0.967948 -39 GTTCGGTTAAGCACCTTTCCCCCAATCCAC 2 67 1 GCACCTTTCC 0.995649 -57 ********** Masking position 6 Map Score: 5.27258 Number of sites scoring better than the average of aligned sites = 298 Number in coding regions = 278 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 3 AAATGTCGGCGAAAGCCTACA 1 2 1 AATGTCGGCG 0.908815 -299 GGTAAATTGTCACGACAGGGATAGGAAAAT 1 49 1 CACGACAGGG 0.938281 -252 TAGGAAAATGAAACTCGGTCATTATTGACC 1 70 1 AAACTCGGTC 0.936462 -231 AGGAGCTACTAAGGTCAGGCCCTTTCTTTT 1 102 0 AAGGTCAGGC 0.961487 -199 AAAGGAGCGGCAACTCAGTGGCGAGGAGCT 1 125 0 CAACTCAGTG 0.936753 -176 TGTTGCTACCAAAGCCGGGGTGATTGCGAA 1 226 0 AAAGCCGGGG 0.97778 -75 GACGGTTATCCCACTCAGGCAATTCTTAAC 2 30 0 CCACTCAGGC 0.949761 -94 GAGTGGGATAACCGTCGGGGTTAGTTCGGT 2 44 1 ACCGTCGGGG 0.985249 -80 ********** Masking position 6 Map Score: 2.92809 Number of sites scoring better than the average of aligned sites = 1521 Number in coding regions = 1366 Number in noncoding regions = 155 Number of orfs with sites within 600 bp upstream = 178 Fraction of orfs with sites within 600 bp upstream = 0.0285898 Motif number 4 CCTCCCTGAACCGATGAACCTGCCAATCTA 1 155 1 CCGATGAACC 0.972811 -146 GATGAACCTGCCAATCTAGCAAGAATATTT 1 167 1 CCAATCTAGC 0.967469 -134 GTCTGGGTTCGCAATCACCCCGGCTTTGGT 1 219 1 GCAATCACCC 0.978871 -82 CTAGTTCATCCCATTGACCCCTTTCACTTT 1 256 1 CCATTGACCC 0.969794 -45 GACGGTTATCCCACTCAGGCAATTCTTAAC 2 30 0 CCACTCAGGC 0.962766 -94 CACCTTTCCCCCAATCCACCGTAGGATCTA 2 78 1 CCAATCCACC 0.988282 -46 ********** Masking position 5 Map Score: 2.87538 Number of sites scoring better than the average of aligned sites = 760 Number in coding regions = 673 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 5 TGTCGTGACAATTTACCAAAATGTTCCTAA 1 36 0 ATTTACCAAA 0.804043 -265 TTCGGTCAATAATGACCGAGTTTCATTTTC 1 73 0 AATGACCGAG 0.920787 -228 CTCGGTCATTATTGACCGAAAAAGAAAGGG 1 83 1 ATTGACCGAA 0.968215 -218 AGTTGATGCCGTTTACCGTGGTCTGGGTTC 1 199 1 GTTTACCGTG 0.979622 -102 ACCCCTTTCACTTTACCCAGGAAATACGGA 1 272 1 CTTTACCCAG 0.887988 -29 AGTTTACCGTCCGTATTTCCT 1 290 0 GTTTACCGTC 0.97059 -11 GCCTGAGTGGGATAACCGTCGGGGTTAGTT 2 40 1 GATAACCGTC 0.889004 -84 GGGAAAGGTGCTTAACCGAACTAACCCCGA 2 58 0 CTTAACCGAA 0.968216 -66 GTTAACGGAAATCGAGGCCT 2 114 0 GTTAACGGAA 0.894384 -10 ********** Masking position 5 Map Score: 7.10049 Number of sites scoring better than the average of aligned sites = 970 Number in coding regions = 841 Number in noncoding regions = 129 Number of orfs with sites within 600 bp upstream = 139 Fraction of orfs with sites within 600 bp upstream = 0.0223257 Motif number 6 ********** No masking Map Score: -5.51791e-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: -5.51791e-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: -5.51791e-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