AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i064_synecho_ctra_100.orf -o064_synecho_ctra_100.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 RCY10954 211 Synechocystis #2 RCY26047 35 Synechocystis #3 RCY44892 192 Synechocystis #4 RCY33884 213 Synechocystis #5 RCY44461 245 Synechocystis #6 RCY22265 286 Synechocystis #7 RCY39566 239 Synechocystis #8 RCY11341 81 Synechocystis #9 RCY10798 68 Synechocystis #10 RCY15876 126 Synechocystis #11 RCY45983 163 Synechocystis Motif number 1 GGCGATCGCCGTGGGGGGAAGCTCTCATCT 1 36 1 GTGGGGGGAA 0.969022 -176 CCCTCTCCGATTGGGGGCAAGGGCGGCGAA 2 12 0 TTGGGGGCAA 0.896755 -24 CTAGGAAAAAACAGGGGAAAGAATGCCCTT 3 76 0 ACAGGGGAAA 0.957108 -117 CGTCGCCTTTACAGCGGCAACGGTGTCGGG 3 107 1 ACAGCGGCAA 0.926101 -86 TATGGTCTGTAATGGGAGAAGCTTTAAACA 3 138 1 AATGGGAGAA 0.749925 -55 AATTACGATCAAAGGGGCAATAAATCCCTT 3 168 0 AAAGGGGCAA 0.924239 -25 CAACTAAGTTGCTGGGAAAATGTATTTGTC 4 39 1 GCTGGGAAAA 0.922382 -175 AAGGGACTTGGATGGGGAAATGGAACTTCA 4 73 1 GATGGGGAAA 0.948318 -141 GGCAGGGGAAATTAGTGAGTA 6 2 1 GCAGGGGAAA 0.982503 -285 ATACTGGAGTTTTGGGAAAACAGACTCTAA 6 179 1 TTTGGGAAAA 0.5758 -108 CAAGGCAAATTCAGGGGGAAAACTACCAGC 7 172 0 TCAGGGGGAA 0.975618 -68 GTATATCGTGATTGGGGCAAGGCAAATTCA 7 189 0 ATTGGGGCAA 0.944708 -51 GCAAATTTTGTCAGCGGCAATCAATAGCAA 9 29 1 TCAGCGGCAA 0.910489 -40 GTTCCTTGGGGTTGCGGGAAAACATTATAT 10 67 1 GTTGCGGGAA 0.936496 -60 CTTTGTTTCGGCAGGGGCAAGTTTAAACAT 10 102 0 GCAGGGGCAA 0.990724 -25 AGAGGACAGGGCGGGGAGAATGCAGTTGCT 11 40 1 GCGGGGAGAA 0.942671 -124 TGCTCAACTTCCTGCGGGAATACGGCCAGT 11 66 1 CCTGCGGGAA 0.858168 -98 TCAAAGGAAGGATGGGGGAATTCCGCCCCG 11 130 0 GATGGGGGAA 0.975925 -34 ********** Masking position 9 Map Score: 26.8618 Number of sites scoring better than the average of aligned sites = 3984 Number in coding regions = 3577 Number in noncoding regions = 407 Number of orfs with sites within 600 bp upstream = 410 Fraction of orfs with sites within 600 bp upstream = 0.0658529 Motif number 2 ATGAGAGCTTCCCCCCACGGCGATCGCCAGCGTTATGC 1 26 0 CCCCCAGCGC 0.906737 -186 AGGGCTTCTTTCACTCCCGCCGTTCGCCAATAAGATGG 1 70 1 TCCTCCGCGC 0.980037 -142 AATGTATTTGTCGGCCAAGGGACTTGGATGGGGAAATG 4 57 1 TCGCCAGTGA 0.775709 -157 ATAAAACATCCGAACCCGGCAATTTGTCCGTAGTATCC 4 128 0 CGACCCGTGC 0.747836 -86 CCGGGATCCTTCTGCCCAGAGATATTGCTAGTCCGTCC 5 125 1 TCGCCCGTTC 0.979675 -121 ATATTGCTAGTCCGTCCTGGGGAGCGGTCAACTTTGCG 5 146 1 TCGTCCGCGT 0.942147 -100 CCATTGATGATCGGACCTAACCCCCGTCTAGCCATTGT 5 185 0 TCGACCACGC 0.897803 -61 ATGGTCTAACTCTGTCCTACTTTGCGTCTTTTTTCCC 5 219 1 TCGTCCACGC 0.966558 -27 AGGGGCATAATGTGCCCAGGTTGTTTACTCACTAATTT 6 19 0 TGGCCCGTTC 0.904154 -268 CCAGATCTGATCAGCCCTGTAAACTGACCCAATCAAGC 6 134 1 TCGCCCGTGC 0.997382 -153 AATGGTTTTCTGTCCTGATCGTCGCCATTGAGTATA 7 214 0 TCGTCCGCGC 0.995641 -26 CTGCATTCTCCCCGCCCTGTCCTCTGGCTTTCATAAAC 11 27 0 CCGCCCGTGC 0.994827 -137 ATGGGGGAATTCCGCCCCGCAGAACGGCTTGACATTTA 11 111 0 TCGCCCGCGC 0.9916 -53 ** **** * ** * Masking position 6 Map Score: 18.5048 Number of sites scoring better than the average of aligned sites = 754 Number in coding regions = 690 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 3 CCCACGGCGATCGCCAGCGTTATGCACCGA 1 21 0 TCGCCAGCGT 0.592451 -191 TCTTTCACTCCCGCCGTTCGCCAATAAGAT 1 76 1 CCGCCGTTCG 0.806635 -136 GCCGCCCTTGCCCCCAATCGGAGAGGGATC 2 15 1 CCCCCAATCG 0.933303 -21 GGGATTTATTGCCCCTTTGATCGTAATTGC 3 170 1 GCCCCTTTGA 0.910904 -23 AAGTTCCATTTCCCCATCCAAGTCCCTTGG 4 71 0 TCCCCATCCA 0.905851 -143 GAACTTCACCGCCCCATTCGAGCTTAATCT 4 95 1 GCCCCATTCG 0.985128 -119 GGGATCAAGTTCGCCATTGGGCAATTTTGA 5 75 0 TCGCCATTGG 0.921275 -171 AACCCCCGTCTAGCCATTGTACGCAAAGTT 5 175 0 TAGCCATTGT 0.552024 -71 GGCACATTATGCCCCTTTCTCGGCCGGCCG 6 41 1 GCCCCTTTCT 0.924205 -246 CCTGTAAACTGACCCAATCAAGCGACCGCA 6 149 1 GACCCAATCA 0.708086 -138 ACAGCAAAGCCCCCCTTTGTTTGTATTTGG 7 43 0 CCCCCTTTGT 0.861311 -197 GGAAAACTACCAGCCAGTCACCGTTGGCAA 7 156 0 CAGCCAGTCA 0.603647 -84 AATTTGCCTTGCCCCAATCACGATATACTC 7 191 1 GCCCCAATCA 0.923733 -49 GTCCTGATCGTCGCCATTGAGTATATCGTG 7 209 0 TCGCCATTGA 0.879686 -31 TGACCCATTGGTAAGGGTTTT 10 2 1 GACCCATTGG 0.903478 -125 GTTTAAACTTGCCCCTGCCGAAACAAAGCC 10 104 1 GCCCCTGCCG 0.845718 -23 GGGCGGAATTCCCCCATCCTTCCTTTGATG 11 132 1 CCCCCATCCT 0.928119 -32 ********** Masking position 5 Map Score: 12.739 Number of sites scoring better than the average of aligned sites = 3410 Number in coding regions = 3051 Number in noncoding regions = 359 Number of orfs with sites within 600 bp upstream = 373 Fraction of orfs with sites within 600 bp upstream = 0.0599101 Motif number 4 TAAACAAGCAGCAAAGTCGCTGAGGTGCAAA 1 153 0 GCAAAGTGCT 0.94493 -59 ATATGCCATGGCCAAACTGCCAA 3 3 0 GCCAAACGCC 0.869006 -190 AATTCTAATATCAAAATTGCCCAATGGCGAA 5 65 1 TCAAAATGCC 0.954219 -181 GCCATTGTACGCAAAGTTGACCGCTCCCCAG 5 162 0 GCAAAGTGAC 0.792287 -84 GATGAGTCACTCAGAATAGCTTCTAGATTTG 6 79 1 TCAGAATGCT 0.914966 -208 ATGGCTTTTTTCAGAACAGCCTTAATCCATT 6 237 0 TCAGAACGCC 0.974776 -50 CGATAATACAGCAAAGCCCCCCTTTGTTTGT 7 49 0 GCAAAGCCCC 0.867614 -191 AACAAAAAGTTTAGAGTTGCCCAAAGTCTAG 7 119 0 TTAGAGTGCC 0.880832 -121 GACAGAATAAGCAGACCGGCCTTTGCT 8 7 0 GCAGACCGCC 0.976537 -75 TTGAGAATGTTTAAACTTGCCCCTGCCGAAA 10 96 1 TTAAACTGCC 0.660865 -31 ATTCCGCCCCGCAGAACGGCTTGACATTTAT 11 110 0 GCAGAACGCT 0.952267 -54 ATCAGAGTGGCTCATCAAAGGA 11 152 0 TCAGAGTGCT 0.944931 -12 ******* *** Masking position 5 Map Score: 8.9555 Number of sites scoring better than the average of aligned sites = 1003 Number in coding regions = 909 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 5 GAGATATGCCATGGCCAAACTGCCAA 3 7 0 ATGGCCAAAC 0.78669 -186 CCCTAAAAAATAGCCCAAACAAAGGGCATT 3 55 1 TAGCCCAAAC 0.975782 -138 TTGTCCGTAGTATCCCAAAGATTAAGCTCG 4 113 0 TATCCCAAAG 0.881515 -101 AATATCAAAATTGCCCAATGGCGAACTTGA 5 71 1 TTGCCCAATG 0.907194 -175 AGAGTCTGTTTTCCCAAAACTCCAGTATTG 6 177 0 TTCCCAAAAC 0.882569 -110 AAAGAGAAGATTGCCAAAAGTTAGAGTCTG 6 199 0 TTGCCAAAAG 0.969289 -88 AAGTTTAGAGTTGCCCAAAGTCTAGAAAAT 7 114 0 TTGCCCAAAG 0.984129 -126 CCAGTCACCGTTGGCAAAACCTTAACAAAA 7 143 0 TTGGCAAAAC 0.922526 -97 TGGGCAGAATTATCCAAAACCCTTACCAAT 10 17 0 TATCCAAAAC 0.824269 -110 ********** Masking position 7 Map Score: 6.95075 Number of sites scoring better than the average of aligned sites = 1006 Number in coding regions = 887 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 ATCTGTGGAGGGCTTCTTTCACTCCCGCCG 1 62 1 GGCTTCTTTC 0.94445 -150 CTTTCGCTAGGGCGTTGTTTGCACCTCAGC 1 136 1 GGCGTTGTTT 0.963685 -76 CCTTTGTTTGGGCTATTTTTTAGGGATGGA 3 50 0 GGCTATTTTT 0.846233 -143 CCGCTGTAAAGGCGACGTCTAGGAAAAAAC 3 94 0 GGCGACGTCT 0.864683 -99 ATGTTTTATTTGCTTCGTTTAATTCACATT 4 157 1 TGCTTCGTTT 0.888572 -57 TGTCCTACTTTGCGTCTTTTTTCCC 5 231 1 TGCGTCTTTT 0.839371 -15 GAGTGGCAATGGCTTTTTTCAGAACAGCCT 6 246 0 GGCTTTTTTC 0.896412 -41 TATACTCAATGGCGACGATCAGGACAGAAA 7 214 1 GGCGACGATC 0.780521 -26 GACGGCTTTGTTTCGGCAGGGGC 10 114 0 GGCTTTGTTT 0.95373 -13 ********** Masking position 3 Map Score: 4.32834 Number of sites scoring better than the average of aligned sites = 380 Number in coding regions = 342 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 7 ACGTCTAGGAAAAAACAGGGGAAAGAATGCC 3 79 0 AAAAACGGGG 0.974688 -114 AAAATCTTTGCTAAACCGGGGATCAAGTTCG 5 92 0 CTAAACGGGG 0.980227 -154 CGTACAATGGCTAGACGGGGGTTAGGTCCGA 5 182 1 CTAGACGGGG 0.957141 -64 CAAGCGACCGCAATACTGGAGTTTTGGGAAA 6 167 1 CAATACGGAG 0.96729 -120 GGGGCAAGGCAAATTCAGGGGGAAAACTACC 7 175 0 AAATTCGGGG 0.899781 -65 TCAATAGCAACAAATCTGGAGACTGAAACC 9 49 1 CAAATCGGAG 0.960005 -20 GCCCACCAAGGAAAACCGGAGAAATGTTCCT 10 42 1 GAAAACGGAG 0.940014 -85 ****** **** Masking position 3 Map Score: 3.74832 Number of sites scoring better than the average of aligned sites = 356 Number in coding regions = 285 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 8 GGTTCTCAAATCTCAAATAATGC 5 3 1 TTCTCAATCT 0.971045 -243 ACACACCAATTTCACTAATCTGTTGGCATTA 5 28 0 TTCACAATCT 0.988336 -218 TGCTCATTTTTTCAATAATCTGTTAGCCAGA 6 108 1 TTCAAAATCT 0.941986 -179 AGAGTCTGTTTTCCCAAAACTCCAGTATTGC 6 176 0 TTCCCAAACT 0.937916 -111 GCCACTCAATTTCACCAATCTTTTCCCC 6 269 1 TTCACAATCT 0.988336 -18 ***** ***** Masking position 7 Map Score: 2.26078 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 23 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 9 TCCCAAAGATTAAGCTCGAATGGGGCGGTG 4 101 0 TAAGCTCGAA 0.931367 -113 GGTTCTCAAATCTCAAATAATGCCAAC 5 8 1 AAATCTCAAA 0.713551 -238 AAAAATGAGCAAATCTAGAAGCTATTCTGA 6 89 0 AAATCTAGAA 0.951035 -198 GAGTTGCCCAAAGTCTAGAAAATTAAGTAT 7 107 0 AAGTCTAGAA 0.941528 -133 AGACCAAAAGCTAGAATTTAACAGAT 8 66 0 AAAGCTAGAA 0.968295 -16 CGGCCAGTGATAGGCTAGAAAGATAAATGT 11 88 1 TAGGCTAGAA 0.931367 -76 ********** Masking position 6 Map Score: 1.38434 Number of sites scoring better than the average of aligned sites = 100 Number in coding regions = 78 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 10 ********** No masking Map Score: 1.71484e-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 11 AGAATGCCCTTTGTTTGGGCTATTTTTTAG 3 57 0 TTGTTTGGGC 0.794758 -136 GGGGAAGGTTTTCTGTTGACTATTGAT 4 8 0 TTCTGTTGAC 0.806233 -206 GGGAAAATGTATTTGTCGGCCAAGGGACTT 4 52 1 ATTTGTCGGC 0.933586 -162 AATTTCACTAATCTGTTGGCATTATTTGAG 5 22 0 ATCTGTTGGC 0.976981 -224 AGTGAAATTGGTGTGTTGGCTGAATTCTAA 5 43 1 GTGTGTTGGC 0.935718 -203 TTTTTCAATAATCTGTTAGCCAGATCTGAT 6 115 1 ATCTGTTAGC 0.893134 -172 AACAGACTCTAACTTTTGGCAATCTTCTCT 6 197 1 AACTTTTGGC 0.686797 -90 AATAAGCAAATTTTGTCAGCGGCAATCAAT 9 24 1 TTTTGTCAGC 0.73461 -45 GACGGCTTTGTTTCGGCAGGGGCAAGT 10 110 0 TTGTTTCGGC 0.912129 -17 ********** Masking position 6 Map Score: 0.859544 Number of sites scoring better than the average of aligned sites = 614 Number in coding regions = 547 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 12 ********** No masking Map Score: 1.71484e-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 13 ********** No masking Map Score: 1.71484e-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 14 ********** No masking Map Score: 1.71484e-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