AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i211_transcription_translation_synecho_reg_300.orf -o211_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 RCY30174 31 Synechocystis #2 RCY42399 64 Synechocystis #3 RCY23794 104 Synechocystis #4 RCY53156 108 Synechocystis #5 RCY31741 108 Synechocystis #6 RCY09512 82 Synechocystis #7 RCY38222 137 Synechocystis #8 RCY33689 119 Synechocystis #9 RCY05922 107 Synechocystis #10 RCY14231 101 Synechocystis #11 RCY17023 68 Synechocystis #12 RCY34894 39 Synechocystis #13 RCY03648 59 Synechocystis #14 RCY03870 91 Synechocystis #15 RCY00359 106 Synechocystis #16 RCY25341 23 Synechocystis #17 RCY37057 40 Synechocystis #18 RCY34487 29 Synechocystis #19 RCY46798 32 Synechocystis #20 RCY53151 73 Synechocystis #21 RCY50421 39 Synechocystis #22 RCY31267 300 Synechocystis Motif number 1 CTGAGATAGCGTCGGTCAAGCTATTTACACG 4 65 1 GTCGTCAAGC 0.982685 -44 GCATAGGTTGGCCAATGGAGCAACCTATATT 8 30 1 GCCATGGAGC 0.979916 -90 AAAAAAGACGGTCAAGGAAGCAGCTTTGTAA 9 77 0 GTCAGGAAGC 0.988529 -31 TATCACCTTTGCCCCGCAAGCAATGCTAGAC 15 15 1 GCCCGCAAGC 0.962581 -92 GCCGAAGGTGGTCTCTCAAGCAAAGCTTGAT 22 103 1 GTCCTCAAGC 0.982658 -198 GATGGAGCGTTTCAATCAAGCTTTGCTTGAG 22 117 0 TTCATCAAGC 0.892108 -184 ATTCAGTTACGTCGATGGAGCGTTTCAATCA 22 130 0 GTCATGGAGC 0.988529 -171 GTTATTCACTGGCTATGAAGCTGTTGACCAA 22 163 1 GGCATGAAGC 0.96983 -138 GTCGCTTTATGTCCGGGGAGCCTTTCTGCTT 22 212 1 GTCGGGGAGC 0.979503 -89 *** ******* Masking position 9 Map Score: 10.9635 Number of sites scoring better than the average of aligned sites = 238 Number in coding regions = 213 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 2 TCTTCCCCCCATCCCTGTCCTGTTTATTG 5 6 1 CCCCATCCTC 0.989938 -103 GAAAAAAGCGCCATCGTCAATCACAACAAATATA 8 55 0 CCACGTCATC 0.949683 -65 AGCTTACAAAGCTGCTTCCTTGACCGTCTTTTTT 9 74 1 GCTCTTCCTC 0.821113 -34 CAATGGTAACCAAAATCCTTCCCCATAGCCTGG 10 10 1 CCAAATCCTC 0.939391 -92 TCATTGTTTTGCTTCATCCCTCGCACTTTTACTC 10 66 1 GCTCATCCTC 0.962454 -36 GCTGAAGGCCCCAAGCCTTTACTAAGTGAAAA 11 9 1 CCCAAGCCTC 0.96579 -60 TGACCAATCACCCTGAGCCGCGACTAAA 14 5 0 CCCGAGCCCC 0.851613 -87 CATCAATCCACCTGAATCATCATCCCTTAGGAGA 14 51 1 CCTAATCACC 0.767596 -41 GCTCGAGTTCCCTTCGTCCATCTACTCTCTGACC 15 59 1 CCTCGTCCTA 0.88894 -48 AATTTTGTTCCTTCAGCAGTGACGGATAAAAAA 21 17 0 CCTCAGCATC 0.978054 -23 TGAGAGACCACCTTCGGCCCTAGCGGTAGGGAGA 22 87 0 CCTCGGCCTC 0.990285 -214 AAAGCGACGACCAGCGGCAATAACCTTTGGTCAA 22 186 0 CCACGGCATC 0.956252 -115 *** ***** * * Masking position 8 Map Score: 8.51198 Number of sites scoring better than the average of aligned sites = 1457 Number in coding regions = 1337 Number in noncoding regions = 120 Number of orfs with sites within 600 bp upstream = 129 Fraction of orfs with sites within 600 bp upstream = 0.0207196 Motif number 3 CGGGACATAATTATTTGCCTTGCTAATTTG 2 17 0 TTATTTGCCT 0.912348 -48 GACAGTTAAATTTTTTGCTAACAGCTTTTT 4 11 1 TTTTTTGCTA 0.649837 -98 AGGGACATTCTTTTTTGCCTTTTTGGGCCC 5 83 0 TTTTTTGCCT 0.970079 -26 GTTGATTTTCCTCTAAATAAGT 6 71 0 TGATTTTCCT 0.827615 -12 GAAGCATTAATTTTTTACCTTTGCCACCGT 7 22 0 TTTTTTACCT 0.783571 -116 GCCTGATTTTCTTTGGCAACACT 7 125 0 TGATTTTCTT 0.720857 -13 AACCTATATTTGTTGTGATTGACGATGGCG 8 51 1 TGTTGTGATT 0.722056 -69 TTGACCGTCTTTTTTTGATTAATTT 9 93 1 TTTTTTGATT 0.776381 -15 GTTAATTCATTGTTTTGCTTCATCCCTCGC 10 60 1 TGTTTTGCTT 0.946724 -42 CTATTTTTGTTTTTATTCGTTGGAACT 19 8 1 TGTTTTTATT 0.615591 -25 AATTTTGTTCCTTCAGCAGTGA 21 28 0 TTTTGTTCCT 0.915082 -12 GTCATCCCCCTTTTGTGCCTATGTAGGACT 22 54 1 TTTTGTGCCT 0.959688 -247 GCCCAGCTTTGTTCCTAAAATACCGA 22 285 0 CTTTGTTCCT 0.629579 -16 ********** Masking position 6 Map Score: 7.87857 Number of sites scoring better than the average of aligned sites = 1240 Number in coding regions = 1019 Number in noncoding regions = 221 Number of orfs with sites within 600 bp upstream = 246 Fraction of orfs with sites within 600 bp upstream = 0.0395117 Motif number 4 TAGAGGGGTACGGGTAAATCCAAAT 1 17 0 GGGGTAGGGT 0.974124 -15 TAATTTTTTAGGAGTTCAGTTACCATGCGAC 3 64 1 GGAGTTAGTT 0.75596 -41 TTTGCCTTTTTGGGCCCAGTTTTTCTGGTAG 5 69 0 TGGGCCAGTT 0.881675 -40 ATAAATTTATGGAGTAGGGTTTAAGACAGAC 6 37 0 GGAGTAGGTT 0.854899 -46 TAATTTGACGGTGGCAAAGGTAAAAAATTAA 7 15 1 GTGGCAAGGT 0.751112 -123 TTCCCCTCAGTGGGGAGAGTTAATTTAATAT 7 49 1 TGGGGAAGTT 0.918588 -89 AATGTCAAGACGAGCATAGGTTGGCCAATGG 8 17 1 CGAGCAAGGT 0.846732 -103 CCTATTTTTACGGGCAGAGTTGCATCAATCA 9 16 1 CGGGCAAGTT 0.963377 -92 TCCCAGGCTATGGGGAAGGATTTTGGTTACC 10 15 0 TGGGGAGGAT 0.812501 -87 TGGATGTTAATGGGTTTGGTTAACGTTG 12 8 0 TGGGTTGGTT 0.939298 -32 CATTGCTTGCGGGGCAAAGGTGATAGCCA 15 9 0 GGGGCAAGGT 0.980228 -98 TCGAGCACATCGGGTTAGGGTCTAGCATTGC 15 34 0 CGGGTTGGGT 0.93665 -73 ACAGGGTCTCTGGGCTTGGTCAGAGAGTAGA 15 79 0 TGGGCTGGTC 0.783213 -28 CGAATACCCATGGGTTTAGATAACAGTTAAT 20 40 0 TGGGTTAGAT 0.800933 -34 ****** **** Masking position 4 Map Score: 9.26315 Number of sites scoring better than the average of aligned sites = 2974 Number in coding regions = 2692 Number in noncoding regions = 282 Number of orfs with sites within 600 bp upstream = 313 Fraction of orfs with sites within 600 bp upstream = 0.050273 Motif number 5 TCGGTCAAGCTATTTACACGGAGATATAAGG 4 76 1 TATTTAACGG 0.959444 -33 TTATTGAACTTATTTAGAGGAAAATCAAC 6 64 1 TATTTAAGGA 0.937673 -19 TTATTAATTTGACGGTGGCAAAGGT 7 5 1 TAATTTACGG 0.864777 -133 TATTCCGCTTTATTTTTAGGAGGTCATTAAC 8 96 1 TATTTTAGGA 0.951432 -24 TCGCCCCTATTTTTACGGGCAGAGTTGC 9 8 1 TATTTTACGG 0.968558 -100 GGTATTTACAGGGTCTCTGGGCT 15 94 0 TATTTAAGGG 0.968821 -13 TCCGATTTTTTTAGGAAAACGCC 16 6 1 TTTTTTAGGA 0.802647 -18 ****** **** Masking position 8 Map Score: 3.80483 Number of sites scoring better than the average of aligned sites = 77 Number in coding regions = 53 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 6 GACAGTTAAATTTTTTGCTAACAGCTTTT 4 8 1 AAATTTTGCT 0.785328 -101 AGGACGCGCCATAATGATTGCTTGAAAGCTTC 5 39 0 ATATGATGCT 0.95239 -70 GCAAAGGTAAAAAATTAATGCTTCCCCTCAGT 7 28 1 AAATTATGCT 0.951565 -110 GTGTTTAATAAGACTGATTGATGCAACTCTGC 9 29 0 AGATGATGAT 0.868637 -79 TTAACTTTACAGAATTAATCCT 13 48 1 AGATTATCCT 0.897417 -12 GGATTGATGGAGACTTATTGCTGACCAATCAC 14 28 0 AGATTATGCT 0.983622 -64 GGATACTGAATGCTTAGGCTTTTA 22 3 1 ATATGATGCT 0.95239 -298 AGCGGTAGGGAGAGTTAGTCCTACATAGGCAC 22 68 0 AGATTATCCT 0.955213 -233 *** *** **** Masking position 3 Map Score: 5.03336 Number of sites scoring better than the average of aligned sites = 78 Number in coding regions = 57 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 7 CAGTTAAATTTTTTGCTAACAGCTTTTTTG 4 13 1 TTTTGCTAAC 0.788849 -96 AGGTTGCTCCATTGGCCAACCTATGCTCGT 8 26 0 ATTGGCCAAC 0.909598 -94 GGGGAAGGATTTTGGTTACCATTG 10 5 0 TTTGGTTACC 0.929225 -97 TGTTAATGGGTTTGGTTAACGTTG 12 5 0 TTTGGTTAAC 0.972854 -35 GCTCAGGGTGATTGGTCAGCAATAAGTCTC 14 21 1 ATTGGTCAGC 0.924051 -71 ATTAACGCCTATTCGTTAACACACT 17 26 1 ATTCGTTAAC 0.863442 -15 GGCAATAACCTTTGGTCAACAGCTTCATAG 22 175 0 TTTGGTCAAC 0.97603 -126 ********** Masking position 8 Map Score: 3.10356 Number of sites scoring better than the average of aligned sites = 427 Number in coding regions = 376 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 8 TGATTGCTTGAAAGCTTCAATAAACAGGACAGGGA 5 22 0 AAATAATAAC 0.984049 -87 GTGTCATGGCAAATATTAAATTAACTCTCCCCACT 7 57 0 AAATAATAAC 0.984038 -81 GGATGAAGCAAAACAATGAATTAACCTATTATCGC 10 50 0 AAATAATAAC 0.984049 -52 GACCACCACTGAATACTGAATTAACTGTTATCTAA 20 21 1 GAATAATAAC 0.96525 -53 TACCTAAATAAAAGTGTAAATAAACAAGCAGAAAG 22 233 0 AAATAATAAC 0.98405 -68 *** * *** *** Masking position 7 Map Score: 2.50503 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 30 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 9 AAAATTAACAACAGGGGGTTACTCTAAGGCAA 3 39 0 ACAGGGGTAC 0.868142 -66 TATCTCAGTCAGAGGAAATTACGATTTGCTCA 4 41 0 AGAGGAATAC 0.724528 -68 ACGGAGATATAAGGGAGGTCGCGTCA 4 93 1 AAGGGGGTGC 0.960035 -16 GACAGACCGGAATGGTAATCACTAGGAGAACT 6 12 0 AATGGAATAC 0.804727 -71 AATTAAGTTCACAGGAGATGGAATTTTCACTT 11 34 0 ACAGGGATGA 0.7403 -35 CATTAACATCCAAGGAAATTACT 12 27 1 CAAGGAATAC 0.812045 -13 AGTCGCGGCTCAGGGTGATTGGTCAGCAATAA 14 14 1 CAGGGGATGG 0.756724 -78 CTTGCGGGGCAAAGGTGATAGCCA 15 3 0 AAAGGGATGC 0.986993 -104 GGCGTTAATGAATGGCGATAGCGT 17 3 0 AATGGGATGC 0.965253 -38 ATAGGCACAAAAGGGGGATGACCGCAATTCCT 22 44 0 AAGGGGATAC 0.970508 -257 GCTGTTGACCAAAGGTTATTGCCGCTGGTCGT 22 182 1 AAAGGTATGC 0.894444 -119 ***** *** ** Masking position 9 Map Score: 4.49437 Number of sites scoring better than the average of aligned sites = 3564 Number in coding regions = 3267 Number in noncoding regions = 297 Number of orfs with sites within 600 bp upstream = 289 Fraction of orfs with sites within 600 bp upstream = 0.0464182 Motif number 10 ********** No masking Map Score: 5.70866e-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 11 CTTAGAGTAACCCCCTGTTGTTAATTTTTT 3 43 1 CCCCCTGTTG 0.810739 -62 TTTTTGCTAACAGCTTTTTTGAGCAAATCG 4 22 1 CAGCTTTTTT 0.843516 -87 ACATTCTTTTTTGCCTTTTTGGGCCCAGTT 5 79 0 TTGCCTTTTT 0.796258 -30 ATTGACGATGGCGCTTTTTTCGATACTTTA 8 68 1 GCGCTTTTTT 0.888756 -52 ATACTTTATTCCGCTTTATTTTTAGGAGGT 8 90 1 CCGCTTTATT 0.924923 -30 TCGCCCCTATTTTTACGGGCAGA 9 4 1 CCCCTATTTT 0.68854 -104 GCTTCCTTGACCGTCTTTTTTTGATTAATT 9 87 1 CCGTCTTTTT 0.833851 -21 TCCGATTTTTTTAGGAAAACG 16 2 1 CCGATTTTTT 0.812468 -22 GTTGCCTTTTTTATCCGTCAC 21 2 1 TTGCCTTTTT 0.796258 -38 TTGCGGTCATCCCCCTTTTGTGCCTATGTA 22 49 1 CCCCCTTTTG 0.925151 -252 CCGCTGGTCGTCGCTTTATGTCCGGGGAGC 22 203 1 TCGCTTTATG 0.630452 -98 GGGAGCCTTTCTGCTTGTTTATTTACACTT 22 227 1 CTGCTTGTTT 0.825185 -74 ********** Masking position 9 Map Score: 2.75993 Number of sites scoring better than the average of aligned sites = 1503 Number in coding regions = 1344 Number in noncoding regions = 159 Number of orfs with sites within 600 bp upstream = 165 Fraction of orfs with sites within 600 bp upstream = 0.0265018 Motif number 12 ********** No masking Map Score: 5.70866e-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 13 ********** No masking Map Score: 5.70866e-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 14 ********** No masking Map Score: 5.70866e-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