AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i306_synecho_ctra_300.orf -o306_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 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 0.615331 -100 GGATGTAAATCTTGGCACCACTGACTACAA 1 50 0 CTTGGCACCA 0.931676 -70 CGAACCGTGTCTTGCTCCCAGGGATTAATC 1 79 1 CTTGCTCCCA 0.985164 -41 CAGGGATTAATCTCTCCCCAATGAAAATAA 1 97 1 TCTCTCCCCA 0.959908 -23 ATTCAACAAACTTGCCATCACCGGGAATCA 2 126 1 CTTGCCATCA 0.82618 -175 AAATGCTCCCCTTCTCCCCAATCCTAACCC 2 163 0 CTTCTCCCCA 0.991005 -138 AAGGGGAGCATTTCCCCCCTGGTTGCTAAT 2 180 1 TTTCCCCCCT 0.962367 -121 AGCTATTTCCTATGTCCCCTGTTTATCTCT 2 234 1 TATGTCCCCT 0.870799 -67 TTGTGGAAGTTATCTTCCCA 2 291 1 TATCTTCCCA 0.753053 -10 GGGGGCTGGGTTTGTTACCAAAATTCGCAT 3 22 0 TTTGTTACCA 0.725142 -71 GGTAACAAACCCAGCCCCCATGACCTGTTT 3 33 1 CCAGCCCCCA 0.924556 -60 CCATGACCTGTTTACCCCCGTGGATAATTA 3 50 1 TTTACCCCCG 0.781695 -43 ATTATTGATCCTTGGCTCCAGCAATGG 3 76 1 CTTGGCTCCA 0.84367 -17 GCAGTGACGGCTTGCCCCCGGTCCATGGCC 4 76 1 CTTGCCCCCG 0.989716 -54 GTCCATGGCCATTGTCCTCTGCTTCCCCCC 4 96 1 ATTGTCCTCT 0.529629 -34 TTGTCCTCTGCTTCCCCCCAGCCCTAAGTT 4 107 1 CTTCCCCCCA 0.995059 -23 AGAAAAATAAACTGCCCCCAAGTAACAGTA 5 56 0 ACTGCCCCCA 0.974223 -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 0.831765 -98 GTCAGTGGTGCCAAGATTTACATCCGAACCGTGTC 1 55 1 CAATTTCACC 0.769533 -65 TTGCTCCCAGGGATTAATCTCTCCCCAATGAAAAT 1 90 1 GAAATCCTCC 0.970653 -30 TTTGAGGTAACAGCTAAATACAGCCATTTTGTCGG 2 16 1 CGAAATCACC 0.863111 -285 TAGCAACCAGGGGGGAAATGCTCCCCTTCTCCCCA 2 173 0 GGAAATCTCC 0.938277 -128 GGTTAAAGCCGGAAAATTAGCAACCAGGGGGGAAA 2 190 0 GAATTACACC 0.93406 -111 ATTGTAGCAGGCACCATACTCTGCCTTGTGGAAGT 2 266 1 GAATACCTCC 0.978593 -35 TGGGAAGATAACTTCCACAAGGCAGA 2 285 0 GGGATACTCC 0.869017 -16 GCGAATTTTGGTAACAAACCCAGCCCCCATGACCT 3 24 1 GAAAACCACC 0.978591 -69 AACAGTAAGAAAATCAATCTCTACCGTCTTTGTTC 5 28 0 AAAATCCTCC 0.87932 -57 GAATATCTAAGAAAAATAAACTGCCCCCAAGTAAC 5 60 0 GAATAACTCC 0.966459 -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 CCGAACCGTGTCTTGCTCCCAGGGATTAAT 1 78 1 TCTTGCTCCC 0.873101 -42 CATTTTGTCGGCCTTAGCTCAACTACCTTC 2 40 1 GCCTTAGCTC 0.800387 -261 GGAAATGCTCCCCTTCTCCCCAATCCTAAC 2 165 0 CCCTTCTCCC 0.980977 -136 AGAAGGGGAGCATTTCCCCCCTGGTTGCTA 2 178 1 CATTTCCCCC 0.88808 -123 CAAGCTATTTCCTATGTCCCCTGTTTATCT 2 232 1 CCTATGTCCC 0.775996 -69 CTATGTCCCCTGTTTATCTCTGGATTGTAG 2 243 1 TGTTTATCTC 0.784421 -58 CCCCATGACCTGTTTACCCCCGTGGATAAT 3 48 1 TGTTTACCCC 0.95339 -45 TAATTATTGATCCTTGGCTCCAGCAATGG 3 74 1 TCCTTGGCTC 0.903565 -19 AGGCAGTGACGGCTTGCCCCCGGTCCATGG 4 74 1 GGCTTGCCCC 0.971842 -56 CATTGTCCTCTGCTTCCCCCCAGCCCTAAG 4 105 1 TGCTTCCCCC 0.985374 -25 ********** Masking position 8 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 0.979533 -115 ACCGGGAATCAATGGACTGGGTTAGGATTGG 2 145 1 AATGGCTGGG 0.990282 -156 GGACATAGGAAATAGCTTGGGCTTGCGGTTA 2 220 0 AATAGTTGGG 0.959822 -81 ACGGGGGTAAACAGGTCATGGGGGCTGGGTT 3 40 0 ACAGGCATGG 0.895306 -53 AGCCATCTTCAATAGGCAGTGACGGCTTGCC 4 61 1 AATAGCAGTG 0.93635 -69 AGCAGAGGACAATGGCCATGGACCGGGGGCA 4 88 0 AATGGCATGG 0.984592 -42 AAAAACTTAGGGCTGGGGGGAA 4 118 0 AAAACTAGGG 0.909751 -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 CTATTGTAGTCAGTGGTGCCAAGATTTACATCCGAACCG 1 47 1 CAGGTGATAC 0.937049 -73 GTAGTTGAGCTAAGGCCGACAAAATGGCTGTATTTAGCT 2 27 0 TAAGCGATCT 0.874794 -274 GGCCTTAGCTCAACTACCTTCAGGTTAACCCAACTCCGG 2 49 1 CAATCCATAC 0.959418 -252 CAGGTTAACCCAACTCCGGCGAGCTGGACTGTCAACTTA 2 69 1 CAATCGATAC 0.988816 -232 ATTTTCTTTACAATTGTGCTTAAGTTGACAGTCCAGCTC 2 89 0 CAATTGATAC 0.982282 -212 CCGGTGATGGCAAGTTTGTTGAATTTTCTTTACAATTGT 2 111 0 CAATTGATCT 0.951657 -190 GGCTTGCGGTTAAAGCCGGAAAATTAGCAACCAGGGGGG 2 193 0 TAAGCGATCA 0.734408 -108 TTGCTGGAGCCAAGGATCAATAATTATCCACGGGGGTAA 3 61 0 CAAGTCATCC 0.95387 -32 ACAAATCTGGCTAAATTTATGCCCAACCTC 4 2 1 CAATTGATAT 0.947836 -128 AATTTATGCCCAACCTCGGAAACTTAAACCGAAGTCGAG 4 24 1 CAACCGATAC 0.969995 -106 *** * ** * * ** Masking position 12 Map Score: 3.58666 Number of sites scoring better than the average of aligned sites = 1140 Number in coding regions = 1038 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 6 CTGGGAGCAAGACACGGTTCGGATGTAAATCT 1 68 0 GACCGGTTGG 0.967776 -52 AGTCCAGCTCGCCGGAGTTGGGTTAACCTGAA 2 67 0 GCCGAGTTGG 0.996572 -234 GGAATCAATGGACTGGGTTAGGATTGGGGAGA 2 149 1 GACGGGTTGG 0.993637 -152 ATAGGAAATAGCTTGGGCTTGCGGTTAAAGCC 2 215 0 GCTGGGCTGC 0.916027 -86 ACTTCCACAAGGCAGAGTATGGTGCCTGCTAC 2 269 0 GGCGAGTAGG 0.964667 -32 AGGTCATGGGGGCTGGGTTTGTTACCAAAATT 3 27 0 GGCGGGTTGT 0.969082 -66 CTAAATTTATGCCCAACCTCGGAAACTTAAAC 4 21 1 GCCAACCTGG 0.883304 -109 ATTGAAGATGGCTCGACTTCGGTTTAAGTTTC 4 42 0 GCTGACTTGG 0.959323 -88 *** ***** ** Masking position 11 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 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