AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i306_mixed20_synecho_reg_300.orf -o306_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 RCY48542 119 Synechocystis #2 RCY26871 300 Synechocystis #3 RCY34492 92 Synechocystis #4 RCY39948 129 Synechocystis #5 RCY09678 84 Synechocystis Motif number 1 TAGTCGAGAAAATCTTCCCATTTTCCCTAG 1 20 0 AATCTTCCCA 0.617252 -100 GGATGTAAATCTTGGCACCACTGACTACAA 1 50 0 CTTGGCACCA 0.932191 -70 CGAACCGTGTCTTGCTCCCAGGGATTAATC 1 79 1 CTTGCTCCCA 0.985282 -41 CAGGGATTAATCTCTCCCCAATGAAAATAA 1 97 1 TCTCTCCCCA 0.960219 -23 ATTCAACAAACTTGCCATCACCGGGAATCA 2 126 1 CTTGCCATCA 0.827343 -175 AAATGCTCCCCTTCTCCCCAATCCTAACCC 2 163 0 CTTCTCCCCA 0.991078 -138 AAGGGGAGCATTTCCCCCCTGGTTGCTAAT 2 180 1 TTTCCCCCCT 0.962661 -121 AGCTATTTCCTATGTCCCCTGTTTATCTCT 2 234 1 TATGTCCCCT 0.87171 -67 TTGTGGAAGTTATCTTCCCA 2 291 1 TATCTTCCCA 0.754561 -10 GGGGGCTGGGTTTGTTACCAAAATTCGCAT 3 22 0 TTTGTTACCA 0.726758 -71 GGTAACAAACCCAGCCCCCATGACCTGTTT 3 33 1 CCAGCCCCCA 0.92512 -60 CCATGACCTGTTTACCCCCGTGGATAATTA 3 50 1 TTTACCCCCG 0.783078 -43 ATTATTGATCCTTGGCTCCAGCAATGG 3 76 1 CTTGGCTCCA 0.844739 -17 GCAGTGACGGCTTGCCCCCGGTCCATGGCC 4 76 1 CTTGCCCCCG 0.989798 -54 GTCCATGGCCATTGTCCTCTGCTTCCCCCC 4 96 1 ATTGTCCTCT 0.531652 -34 TTGTCCTCTGCTTCCCCCCAGCCCTAAGTT 4 107 1 CTTCCCCCCA 0.995099 -23 AGAAAAATAAACTGCCCCCAAGTAACAGTA 5 56 0 ACTGCCCCCA 0.974426 -29 ********** Masking position 9 Map Score: 23.5033 Number of sites scoring better than the average of aligned sites = 5793 Number in coding regions = 5089 Number in noncoding regions = 704 Number of orfs with sites within 600 bp upstream = 609 Fraction of orfs with sites within 600 bp upstream = 0.0978156 Motif number 2 ACTACAATAGTCGAGAAAATCTTCCCATTTTCCCT 1 22 0 TGAAAACTCC 0.850757 -98 GTCAGTGGTGCCAAGATTTACATCCGAACCGTGTC 1 55 1 CAATTTCACC 0.795376 -65 TTGCTCCCAGGGATTAATCTCTCCCCAATGAAAAT 1 90 1 GAAATCCTCC 0.970456 -30 TTTGAGGTAACAGCTAAATACAGCCATTTTGTCGG 2 16 1 CGAAATCACC 0.880156 -285 TAGCAACCAGGGGGGAAATGCTCCCCTTCTCCCCA 2 173 0 GGAAATCTCC 0.936791 -128 GGTTAAAGCCGGAAAATTAGCAACCAGGGGGGAAA 2 190 0 GAATTACACC 0.942681 -111 ATTGTAGCAGGCACCATACTCTGCCTTGTGGAAGT 2 266 1 GAATACCTCC 0.981566 -35 TGGGAAGATAACTTCCACAAGGCAGA 2 285 0 GGGATACTCC 0.882605 -16 GCGAATTTTGGTAACAAACCCAGCCCCCATGACCT 3 24 1 GAAAACCACC 0.981563 -69 AACAGTAAGAAAATCAATCTCTACCGTCTTTGTTC 5 28 0 AAAATCCTCC 0.894593 -57 GAATATCTAAGAAAAATAAACTGCCCCCAAGTAAC 5 60 0 GAATAACTCC 0.971064 -25 * * **** ** ** Masking position 11 Map Score: 8.25902 Number of sites scoring better than the average of aligned sites = 991 Number in coding regions = 884 Number in noncoding regions = 107 Number of orfs with sites within 600 bp upstream = 114 Fraction of orfs with sites within 600 bp upstream = 0.0183103 Motif number 3 ATTAATCCCTGGGAGCAAGACACGGTTCGG 1 78 0 GGGAGCAAGA 0.863108 -42 GAAGGTAGTTGAGCTAAGGCCGACAAAATG 2 40 0 GAGCTAAGGC 0.786072 -261 GTTAGGATTGGGGAGAAGGGGAGCATTTCC 2 165 1 GGGAGAAGGG 0.979278 -136 TAGCAACCAGGGGGGAAATGCTCCCCTTCT 2 178 0 GGGGGAAATG 0.879104 -123 AGATAAACAGGGGACATAGGAAATAGCTTG 2 232 0 GGGACATAGG 0.760455 -69 CTACAATCCAGAGATAAACAGGGGACATAG 2 243 0 GAGATAAACA 0.769291 -58 ATTATCCACGGGGGTAAACAGGTCATGGGG 3 48 0 GGGGTAAACA 0.949353 -45 CCATTGCTGGAGCCAAGGATCAATAATTA 3 74 0 GAGCCAAGGA 0.895685 -19 CCATGGACCGGGGGCAAGCCGTCACTGCCT 4 74 0 GGGGCAAGCC 0.969352 -56 CTTAGGGCTGGGGGGAAGCAGAGGACAATG 4 105 0 GGGGGAAGCA 0.984061 -25 ********** Masking position 3 Map Score: 4.26809 Number of sites scoring better than the average of aligned sites = 4073 Number in coding regions = 3552 Number in noncoding regions = 521 Number of orfs with sites within 600 bp upstream = 464 Fraction of orfs with sites within 600 bp upstream = 0.0745262 Motif number 4 GGAAAATGCCTAGGGAAAATGGGAA 1 5 1 AATGCTAGGG 0.976044 -115 ACCGGGAATCAATGGACTGGGTTAGGATTGG 2 145 1 AATGGCTGGG 0.988604 -156 GGACATAGGAAATAGCTTGGGCTTGCGGTTA 2 220 0 AATAGTTGGG 0.953135 -81 ACGGGGGTAAACAGGTCATGGGGGCTGGGTT 3 40 0 ACAGGCATGG 0.87924 -53 AGCCATCTTCAATAGGCAGTGACGGCTTGCC 4 61 1 AATAGCAGTG 0.926059 -69 AGCAGAGGACAATGGCCATGGACCGGGGGCA 4 88 0 AATGGCATGG 0.98195 -42 AAAAACTTAGGGCTGGGGGGAA 4 118 0 AAAACTAGGG 0.895637 -12 ***** ***** Masking position 1 Map Score: 2.73007 Number of sites scoring better than the average of aligned sites = 1633 Number in coding regions = 1495 Number in noncoding regions = 138 Number of orfs with sites within 600 bp upstream = 164 Fraction of orfs with sites within 600 bp upstream = 0.0263412 Motif number 5 AGATTTACATCCGAACCGTGTCTTGCTCCCAG 1 68 1 CCAACCGGTC 0.969587 -52 TTCAGGTTAACCCAACTCCGGCGAGCTGGACT 2 67 1 CCAACTCGGC 0.996769 -234 TCTCCCCAATCCTAACCCAGTCCATTGATTCC 2 149 0 CCAACCCGTC 0.994004 -152 GGCTTTAACCGCAAGCCCAAGCTATTTCCTAT 2 215 1 GCAGCCCAGC 0.920043 -86 GTAGCAGGCACCATACTCTGCCTTGTGGAAGT 2 269 1 CCTACTCGCC 0.966646 -32 AATTTTGGTAACAAACCCAGCCCCCATGACCT 3 27 1 ACAACCCGCC 0.970822 -66 GTTTAAGTTTCCGAGGTTGGGCATAAATTTAG 4 21 0 CCAGGTTGGC 0.889311 -109 GAAACTTAAACCGAAGTCGAGCCATCTTCAAT 4 42 1 CCAAGTCAGC 0.961589 -88 ** ***** *** Masking position 2 Map Score: 4.74265 Number of sites scoring better than the average of aligned sites = 1394 Number in coding regions = 1275 Number in noncoding regions = 119 Number of orfs with sites within 600 bp upstream = 130 Fraction of orfs with sites within 600 bp upstream = 0.0208802 Motif number 6 TCTCTCCCCAATGAAAATAAAGT 1 107 1 ATGAAAATAA 0.960593 -13 CACAATTGTAAAGAAAATTCAACAAACTTGC 2 110 1 AAGAAAATCA 0.973068 -191 AAGTAACAGTAAGAAAATCAATCTCTACCGT 5 36 0 AAGAAAATAA 0.98402 -49 GAATATCTAAGAAAAATAAACTGCCCCCA 5 66 0 AAGAAAAAAA 0.960595 -19 ******** ** Masking position 6 Map Score: 0.839274 Number of sites scoring better than the average of aligned sites = 63 Number in coding regions = 51 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 7 ********** No masking Map Score: -2.95996e-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: -2.95996e-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 ********** No masking Map Score: -2.95996e-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