AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i224_Holliday_Junction_enzyme_synecho_reg_300.orf -o224_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 RCY09374 77 Synechocystis #2 RCY24913 188 Synechocystis #3 RCY27579 201 Synechocystis #4 RCY35636 89 Synechocystis #5 RCY46112 116 Synechocystis #6 RCY22383 35 Synechocystis #7 RCY11108 217 Synechocystis #8 RCY05884 180 Synechocystis #9 RCY44898 206 Synechocystis #10 RCY15128 40 Synechocystis #11 RCY23001 94 Synechocystis #12 RCY43048 300 Synechocystis Motif number 1 CCCTTTTCCTGGCGATCGTCGTTGGCATAG 2 111 1 GGCGATCGTC 0.627536 -78 AATGCTTTAACGCCTTGGGTAAATGGGGGA 3 33 1 CGCCTTGGGT 0.799202 -169 ACAACCCGGCGGCGATCGCCAATGTAGGAT 3 128 1 GGCGATCGCC 0.499846 -74 GCCAAATTTCCCCAATGGGCGGATTACTTA 5 21 1 CCCAATGGGC 0.906345 -96 CCCCCCGATCGGCGATCGCCAAATGCCCCT 5 85 1 GGCGATCGCC 0.499846 -32 GGTGGGCTTGGGCTAAATGGGCT 6 23 0 GGGCTTGGGC 0.905196 -13 GTGTGAACCGGATTGGCAAGGTTTTTT 7 8 1 CCGGATTGGC 0.726777 -210 GTAGTGCAACGGCGATCGCCTCTCCGCTAA 7 172 1 GGCGATCGCC 0.499846 -46 AAGCATGACTCCCATTGGGCCAGATCTCCC 8 82 0 CCCATTGGGC 0.978074 -99 GGGCTTAGTTCCCATTGGTCAAGCATCTTG 8 124 0 CCCATTGGTC 0.931699 -57 GGGAACTAAGCCCGATCGCCTGGATTGATT 8 141 1 CCCGATCGCC 0.649872 -40 AGGATTAAACCGCCTTGGCCGAGGAATTT 11 10 0 CGCCTTGGCC 0.970488 -85 ATGCCTAAGTCCCATTGGTCATTGGCAGTA 12 182 0 CCCATTGGTC 0.931699 -119 ATGGGACTTAGGCATTTGGCTCCAATGCCT 12 197 1 GGCATTTGGC 0.843763 -104 AACCACTCCAGGCGTTGGGCTGGGTAAGAT 12 234 0 GGCGTTGGGC 0.792503 -67 ********** Masking position 6 Map Score: 22.0972 Number of sites scoring better than the average of aligned sites = 8919 Number in coding regions = 8155 Number in noncoding regions = 764 Number of orfs with sites within 600 bp upstream = 494 Fraction of orfs with sites within 600 bp upstream = 0.0793447 Motif number 2 ACAACCTGGCCCTGAAGAAATTGAATCATAACTATTT 1 17 0 CCAGATTGAC 0.984786 -61 GGCCCGACTCCCGGAAAAATTTAATCCCTTTTCCTGG 2 86 1 CCAATTTAAC 0.932914 -103 AACAAATGATCCACCAACCATCGATGCTTCTGGCATT 2 156 1 CCAAATCGAC 0.988942 -33 AACCTTAAAAAATCAACCCCTGAATGCTT 3 3 1 CCAAATCAAC 0.982419 -199 AGCAAAAAAGCCTCCAGCCCTCGATAATCCGCTAACC 3 79 0 CCAGCTCGAA 0.886461 -123 AAAATAAAGTCCTACAGGCTTTAACCCTTAACAATTA 4 20 0 CCAGTTTAAC 0.941551 -70 TGCCAGTTTTCCTAGAAAGATTAAGTAATCCGCCCAT 5 35 0 CCAAATTAAA 0.918439 -82 ACTGTCAAAGCCCCAAGCCATCGACAACAGTGCCCAA 7 97 0 CCAGATCGAA 0.970944 -121 AATCAGGCAACCCTCAAAAATCAATCCAGGCGATCGG 8 152 0 CCAAATCAAC 0.982416 -29 GGCCCCAAAGCCATTGAAAAACTACACAAA 9 187 0 CCAGATTGAA 0.954292 -20 TTTTCCTAAACCAGGAAGGATTAAACCGCCTTGGCCG 11 19 0 CCAAATTAAC 0.972154 -76 TAGAATCGCCCCTTTAATTTTCGATGCCACTGCATTT 12 268 1 CCAATTCGAC 0.972387 -33 ** ** ***** * Masking position 6 Map Score: 17.5722 Number of sites scoring better than the average of aligned sites = 159 Number in coding regions = 140 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 3 AAAATTTAATCCCTTTTCCTGGCGATCGTCGTTGG 2 101 1 CCTTCCGGCA 0.979652 -88 ATAAACTGAACCCCCCGATCGGCGATCGCCAAATG 5 75 1 CCCCATGGCA 0.948944 -42 TCGCCAAATGCCCCTGGCTAGGTTAAG 5 100 1 CCCTCTGGTA 0.994879 -17 GATCGCCTCTCCGCTAACTGGGTTACAAACATTAC 7 185 1 CCCTCTGGTA 0.994878 -33 GTTAACTTTGCCTTTACCTGGGAATTGCGGGGAAG 8 30 1 CCTTCTGGAT 0.861588 -151 AGGAAATTAACCGTTAAATGGGTTACGATCAAAGC 9 34 0 CCTTATGGTA 0.968749 -173 GAGAGCAGTTCCTCCACCTGGGCCAGAGGAAATTA 9 60 0 CCCCCTGGCA 0.990787 -147 AGAATTTTAGCTTTTTGCTTGGTGACCCTTTCCTC 9 124 1 CTTTCTGGTA 0.94 -83 TGCTTGGTGACCCTTTCCTCGGTGACCTAAACTGC 9 139 1 CCTTCTGGTA 0.994454 -68 TCTTGTTCTGCCTTTGTCTGGGCTACCATTTGGTG 12 116 1 CCTTCTGGCA 0.995687 -185 ** ** ** *** * Masking position 1 Map Score: 16.0418 Number of sites scoring better than the average of aligned sites = 385 Number in coding regions = 358 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 4 TTCAATTTCTTCAGGGCCAGGTTGTTACAGTCACA 1 29 1 TCGGGGGTTT 0.989553 -49 GTTAAAGCATTCAGGGGTTGATTTTTTAAGGTT 3 9 0 TCGGGGATTT 0.968792 -193 GAAAGGCTCAGCTTGAGTCGGTTCTAGTCAGTATC 3 163 0 GCTGAGGTTT 0.969263 -39 CGCCAAATGCCCCTGGCTAGGTTAAG 5 101 1 CCTGGGGTTA 0.951317 -16 GTGTGAACCGGATTGGCAAGGTTTTTTTTGATAGC 7 11 1 GATGGGGTTT 0.969263 -207 CCTGGGAATTGCGGGGAAGGGTTATGCTGACTTTG 8 46 1 GCGGGGGTTT 0.997591 -135 AAGCCCGATCGCCTGGATTGATTTTTGAGGGTTGC 8 148 1 GCTGGGATTT 0.990603 -33 CAGGCGTTGGGCTGGGTAAGATTGTGTTTAGGCAT 12 221 0 GCGGGGATTT 0.992686 -80 CCAGCCCAACGCCTGGAGTGGTTGAATTAGAATCG 12 241 1 GCTGGGGTTA 0.990258 -60 ** *** **** * Masking position 12 Map Score: 12.8659 Number of sites scoring better than the average of aligned sites = 274 Number in coding regions = 241 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 5 TCTGCCTTAGGGCCCGACTCCCGGAAAAATTT 2 76 1 GGCCACTCCC 0.979197 -113 CGATGCTTCTGGCATTTTTCCC 2 177 1 GGCATTTCCC 0.98404 -12 CCTGAAATTAGGTACTTCTCCCCCATTTACCC 3 49 0 GGTATCTCCC 0.968534 -153 AGTCGGTTCTAGTCAGTATCCCCCCATCCTAC 3 151 0 AGTCTATCCC 0.766098 -51 CTTCAATTCAGCCAAATTTCCCCAATGGGCGG 5 11 1 GCCATTTCCC 0.978264 -106 GTTTATTACTGCCAGTTTTCCTAGAAAGATTA 5 49 0 GCCATTTCCT 0.853124 -68 CGACTTTGCTGGCCCCCATCCCATTAAAAGCT 7 139 1 GGCCCATCCC 0.93042 -79 CTCCCATTGGGCCAGATCTCCCCCAAAGTCAG 8 72 0 GCCATCTCCC 0.979837 -109 GCATTACCCAAGCATGACTCCCATTGGGCCAG 8 89 0 AGCAACTCCC 0.895988 -92 CAGGCGATCGGGCTTAGTTCCCATTGGTCAAG 8 131 0 GGCTGTTCCC 0.92472 -50 TTACGATCAAAGCTGTTTTCCCTTTAGGTTTC 9 15 0 AGCTTTTCCC 0.913146 -192 CCCATTTAACGGTTAATTTCCTCTGGCCCAGG 9 47 1 GGTTTTTCCT 0.657611 -160 CAGTAATATCGCTCAAAATCCCAACAGAGTAA 12 155 0 GCTCAATCCC 0.749235 -146 **** ****** Masking position 9 Map Score: 11.122 Number of sites scoring better than the average of aligned sites = 1863 Number in coding regions = 1688 Number in noncoding regions = 175 Number of orfs with sites within 600 bp upstream = 186 Fraction of orfs with sites within 600 bp upstream = 0.0298747 Motif number 6 AAAAAATCAACCCCTGAATGCTTTAACGCCT 3 17 1 CCCCTGAAGC 0.838615 -185 GTACTTCTCCCCCATTTACCCAAGGCGTTAA 3 39 0 CCCATTTACC 0.986168 -163 AACTAGTTAGCCCATTTAGCCCAAGCCCACC 6 15 1 CCCATTTACC 0.986168 -21 TGGCCCCCATCCCATTAAAAGCTGGTAGTGC 7 148 1 CCCATTAAAG 0.914427 -70 ATGTTTGTAACCCAGTTAGCGGAGAGGCGAT 7 186 0 CCCAGTTACG 0.965677 -32 CCCCGCAATTCCCAGGTAAAGGCAAAGTTAA 8 31 0 CCCAGGTAAG 0.841472 -150 TTGATCGTAACCCATTTAACGGTTAATTTCC 9 37 1 CCCATTTACG 0.982923 -170 ATAGGAATCTCCCCTTAAACCTGATTGAGC 10 10 0 CCCCTTAACC 0.970388 -31 AAAAAATTTCCCCGTGAATCCACTGTGGAGT 12 30 1 CCCGTGAACC 0.936255 -271 ******** ** Masking position 8 Map Score: 8.09906 Number of sites scoring better than the average of aligned sites = 443 Number in coding regions = 396 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 7 AGGGCCAGGTTGTTACAGTCACAAAAAATAT 1 41 1 TGTTACAGCA 0.959029 -37 TAATCTCTTTTGCTTCAGACTGTTTTGGCAC 2 31 1 TGCTTCAGCT 0.894471 -158 CAACCATCGATGCTTCTGGCATTTTTCCC 2 170 1 TGCTTCTGCA 0.955457 -19 AAAAATAAAGTCCTACAGGCTTTAACCCTTA 4 27 0 TCCTACAGCT 0.868007 -63 GGACTTTATTTTTTACTGTCTCTGTCTTTTA 4 45 1 TTTTACTGCT 0.81777 -45 GGGTTCAGTTTATTACTGCCAGTTTTCCTAG 5 57 0 TATTACTGCA 0.926977 -60 GCAAAGTCGTTGCTACTGTCAAAGCCCCAAG 7 117 0 TGCTACTGCA 0.983442 -101 TTTTGAGCGATATTACTGCCAATGACCAATG 12 169 1 TATTACTGCA 0.926977 -132 ******** ** Masking position 4 Map Score: 4.733 Number of sites scoring better than the average of aligned sites = 106 Number in coding regions = 96 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 8 AAAGATTGAACTGTGCCAAAACAGTCTGAA 2 44 0 CTGTGCCAAA 0.889638 -145 CTTGGGCTAAATGGGCTAACTAGTTCCAT 6 10 0 ATGGGCTAAC 0.853965 -26 TAGTTATGGTCTGGGCAAACCTTGGGCACT 7 76 1 CTGGGCAAAC 0.969184 -142 TCTCCGCTAACTGGGTTACAAACATTACCA 7 192 1 CTGGGTTACA 0.919072 -26 ATGACTCCCATTGGGCCAGATCTCCCCCAA 8 78 0 TTGGGCCAGA 0.93623 -103 GTTCCTCCACCTGGGCCAGAGGAAATTAAC 9 58 0 CTGGGCCAGA 0.991266 -149 CTGCCTTTGTCTGGGCTACCATTTGGTGCG 12 123 1 CTGGGCTACC 0.979866 -178 AGGCGTTGGGCTGGGTAAGATTGTGTTTAG 12 225 0 CTGGGTAAGA 0.920285 -76 ********** Masking position 8 Map Score: 5.15364 Number of sites scoring better than the average of aligned sites = 963 Number in coding regions = 887 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 9 GGGCCCGACTCCCGGAAAAATTTAATCCCT 2 85 1 CCCGGAAAAA 0.74434 -104 AACGACGATCGCCAGGAAAAGGGATTAAAT 2 104 0 GCCAGGAAAA 0.930223 -85 TTCGGAACATCCCAGCAAAAAAGCCTCCAG 3 99 0 CCCAGCAAAA 0.956573 -103 GGCGCAGGGAAAAGGAAAGGCTC 3 189 0 GCAGGGAAAA 0.910095 -13 TGGGATGGGGGCCAGCAAAGTCGTTGCTAC 7 132 0 GCCAGCAAAG 0.95646 -86 CCCGCAATTCCCAGGTAAAGGCAAAGTTAA 8 31 0 CCAGGTAAAG 0.749837 -150 CCTGGGAATTGCGGGGAAGGGTTATGCTGA 8 46 1 GCGGGGAAGG 0.853274 -135 TTTGCATTACCCAAGCATGACTCCCATTGG 8 94 0 CCAAGCATGA 0.561886 -87 CTTGGGTAATGCAAACAAGATGCTTGACCA 8 109 1 GCAAACAAGA 0.523986 -72 GAAAGGGTCACCAAGCAAAAAGCTAAAATT 9 126 0 CCAAGCAAAA 0.942575 -81 GTTTAGGTCACCGAGGAAAGGGTCACCAAG 9 141 0 CCGAGGAAAG 0.915017 -66 TTTTTCCTAAACCAGGAAGGATTAAACCGC 11 27 0 ACCAGGAAGG 0.676618 -68 AAATGGTAGCCCAGACAAAGGCAGAACAAG 12 117 0 CCAGACAAAG 0.745144 -184 ********** Masking position 7 Map Score: 5.03324 Number of sites scoring better than the average of aligned sites = 2672 Number in coding regions = 2368 Number in noncoding regions = 304 Number of orfs with sites within 600 bp upstream = 294 Fraction of orfs with sites within 600 bp upstream = 0.0472213 Motif number 10 ATGATTCAATTTCTTCAGGGCCAGGTTGTTA 1 25 1 TTTTCAGGGC 0.798515 -53 TTCCTGGCGATCGTCGTTGGCATAGCTCGAT 2 116 1 TCTCGTTGGC 0.799363 -73 GGTTAGCGGATTATCGAGGGCTGGAGGCTTT 3 79 1 TTTCGAGGGC 0.989761 -123 CCATCCTACATTGGCGATCGCCGCCGGGTTG 3 129 0 TTGCGATCGC 0.946757 -73 CCAGGGGCATTTGGCGATCGCCGATCGGGGG 5 86 0 TTGCGATCGC 0.946757 -31 GGCAAGGTTTTTTTTGATAGCCTGGACTCAG 7 25 1 TTTTGATAGC 0.810531 -193 TTGGGCACTGTTGTCGATGGCTTGGGGCTTT 7 97 1 TTTCGATGGC 0.992688 -121 CCTGGATTGATTTTTGAGGGTTGCCTGATTT 8 159 1 TTTTGAGGGT 0.704405 -22 TTTGTGTAGTTTTTCAATGGCTTTGGGGCC 9 187 1 TTTCAATGGC 0.93012 -20 GCCCCTTTAATTTTCGATGCCACTGCATTTA 12 275 1 TTTCGATGCC 0.946181 -26 ** ******** Masking position 1 Map Score: 6.91305 Number of sites scoring better than the average of aligned sites = 1418 Number in coding regions = 1266 Number in noncoding regions = 152 Number of orfs with sites within 600 bp upstream = 159 Fraction of orfs with sites within 600 bp upstream = 0.0255381 Motif number 11 ATCGAGCTATGCCAACGACGATCGCCAGGA 2 117 0 GCCAACGACG 0.88678 -72 AAAGCCCCAAGCCATCGACAACAGTGCCCA 7 98 0 GCCATCGACA 0.982476 -120 GATGGCTTGGGGCTTTGACAGTAGCAACGA 7 112 1 GGCTTTGACA 0.906003 -106 GGCCCCAAAGCCATTGAAAAACTACACAA 9 188 0 GCCATTGAAA 0.957409 -19 AGTCCCATTGGTCATTGGCAGTAATATCGC 12 175 0 GTCATTGGCA 0.887174 -126 ATTGTGTTTAGGCATTGGAGCCAAATGCCT 12 206 0 GGCATTGGAG 0.910544 -95 TAAATGCAGTGGCATCGAAAATTAAAGGGG 12 276 0 GGCATCGAAA 0.96447 -25 ********** Masking position 7 Map Score: 1.35495 Number of sites scoring better than the average of aligned sites = 694 Number in coding regions = 664 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 12 TTACAGTCACAAAAAATATTCAGAACCGTTG 1 53 1 AAAAAATTTC 0.905007 -25 GAAAAGGGATTAAATTTTTCCGGGAGTCGGG 2 88 0 TAAATTTTCC 0.814769 -101 TTTAACCCTTAACAATTATCCAAAAAT 4 7 0 AACAATTTCC 0.867025 -83 CTCTGTCTTTTAAAATTTTTCGCATTTCGAC 4 64 1 TAAAATTTTC 0.889716 -26 AGTTAACAACTAAAAATGTCCACTTC 8 6 0 TAAAAATTCC 0.960835 -175 AGCAAAAAGCTAAAATTCTCCCGTTTCAGCA 9 112 0 TAAAATTTCC 0.960835 -95 CTGGTTTAGGAAAAAATGTTGAAGTGATACT 11 42 1 AAAAAATTTG 0.61321 -53 TTCAAAAGTGAAAAAATTTCCCCGTGAATCC 12 20 1 AAAAAATTCC 0.960206 -281 ******* *** Masking position 4 Map Score: 2.32443 Number of sites scoring better than the average of aligned sites = 572 Number in coding regions = 447 Number in noncoding regions = 125 Number of orfs with sites within 600 bp upstream = 134 Fraction of orfs with sites within 600 bp upstream = 0.0215226 Motif number 13 TTCAGACTGTTTTGGCACAGTTCAATCTTTA 2 44 1 TTTGGACAGT 0.783208 -145 ATTTTTGGATAATTGTTAAGGGT 4 3 1 TTTTGATAAT 0.754999 -87 TCTTTTAAAATTTTTCGCATTTCGACCATCC 4 69 1 TTTTTGCATT 0.854091 -21 TGGACTCAGTTGTTGTGCAGTTGAGGAAATA 7 47 1 TGTTGGCAGT 0.927557 -171 AAAATCCTGTCTTTTAGCAGTTTAGGTCACC 9 159 0 CTTTTGCAGT 0.783209 -48 AAAGACAGGATTTTGTGTAGTTTTTCAATGG 9 176 1 TTTTGGTAGT 0.945425 -31 ATTTTTTCACTTTTGAACAATCCATT 12 6 0 TTTTGACAAT 0.916117 -295 GCAAAAGTACTTTTTCGTAATCACTCCACAG 12 52 0 TTTTTGTAAT 0.754999 -249 GAAAAAGTACTTTTGCGCATTGTACTCACCA 12 67 1 TTTTGGCATT 0.954014 -234 TCTGTTGGGATTTTGAGCGATATTACTGCCA 12 159 1 TTTTGGCGAT 0.889775 -142 ***** ***** Masking position 3 Map Score: 1.71891 Number of sites scoring better than the average of aligned sites = 1009 Number in coding regions = 881 Number in noncoding regions = 128 Number of orfs with sites within 600 bp upstream = 134 Fraction of orfs with sites within 600 bp upstream = 0.0215226 Motif number 14 AATCCGCCCATTGGGGAAATTTGGCTGAATT 5 15 0 TTGGGGAATT 0.886712 -102 GAAGTGGACATTTTTAGTTGTT 8 2 1 AAGTGGAATT 0.941624 -179 AACTTGCTGAAACGGGAGAATTTTAGCTTTT 9 108 1 AACGGGAAAT 0.855167 -99 AATCAGGTTTAAGGGGAGATTCCTATGGGAT 10 15 1 AAGGGGAATT 0.990508 -26 CAGTGGATTCACGGGGAAATTTTTTCACTTT 12 24 0 ACGGGGAATT 0.979176 -277 TCGAAAATTAAAGGGGCGATTCTAATTCAAC 12 261 0 AAGGGGCATT 0.974393 -40 ******* *** Masking position 9 Map Score: 1.66359 Number of sites scoring better than the average of aligned sites = 413 Number in coding regions = 355 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 15 ATTTTTCCGGGAGTCGGGCCCTAAGGCAGA 2 76 0 GAGTCGGGCC 0.862818 -113 CAGCAAAAAAGCCTCCAGCCCTCGATAATC 3 87 0 GCCTCCAGCC 0.909663 -115 CTTCAATTCAGCCAAATTTCCCC 5 4 1 CAATTCAGCC 0.865502 -113 CACAACAACTGAGTCCAGGCTATCAAAAAA 7 34 0 GAGTCCAGGC 0.981534 -184 CCTCAAAAATCAATCCAGGCGATCGGGCTT 8 148 0 CAATCCAGGC 0.984882 -33 CAGAACAAGACAATCAGGGCTGTCAAGCTG 12 96 0 CAATCAGGGC 0.871524 -205 CTAATTCAACCACTCCAGGCGTTGGGCTGG 12 241 0 CACTCCAGGC 0.985846 -60 ********** Masking position 4 Map Score: 1.46587 Number of sites scoring better than the average of aligned sites = 344 Number in coding regions = 310 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405