AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i007_synecho_ctra_300.orf -o007_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 RCY26871 300 Synechocystis #2 RCY34492 92 Synechocystis #3 RCY01518 107 Synechocystis #4 RCY43032 137 Synechocystis #5 RCY10747 300 Synechocystis #6 RCY33781 92 Synechocystis #7 RCY31630 284 Synechocystis Motif number 1 AGCTAAGGCCGACAAAATGGCTGTATTTAG 1 29 0 GACAAAATGG 0.868015 -272 ACCCAACTCCGGCGAGCTGGACTGTCAACT 1 76 1 GGCGAGCTGG 0.973684 -225 TCCCGGTGATGGCAAGTTTGTTGAATTTTC 1 122 0 GGCAAGTTTG 0.96448 -179 GGTTAGGATTGGGGAGAAGGGGAGCATTTC 1 164 1 GGGGAGAAGG 0.828607 -137 AGCAACCAGGGGGGAAATGCTCCCCTTCTC 1 177 0 GGGGAAATGC 0.93051 -124 GCATTGGCAATTTGCAATTTTTAAC 3 6 1 GGCAATTTGC 0.94495 -102 ACAATCTTTTGGGAATTTGGGGAT 3 94 1 GGGAATTTGG 0.920932 -14 ACCCCGATAAGGCAAGTTGGTAAAAAACGG 4 117 0 GGCAAGTTGG 0.991936 -21 AGCTTGACTAGGCAAAATTCCCCACACCAG 5 214 0 GGCAAAATTC 0.911906 -87 GATGAGCTTTGGCAAGATGGCTGGGAATTG 7 147 1 GGCAAGATGG 0.993205 -138 ATAAACCAGGGGCGAAATGGCAGCCGGCAA 7 227 1 GGCGAAATGG 0.986912 -58 AATGGCAGCCGGCAAATTTCAGACTTATTT 7 242 1 GGCAAATTTC 0.897024 -43 ********** Masking position 5 Map Score: 17.1983 Number of sites scoring better than the average of aligned sites = 995 Number in coding regions = 883 Number in noncoding regions = 112 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 2 CTCCCCTTCTCCCCAATCCTAACCCAGTCC 1 158 0 CCCCAATCCT 0.926748 -143 GGGAGCATTTCCCCCCTGGTTGCTAATTTT 1 183 1 CCCCCCTGGT 0.994869 -118 ACAAACCCAGCCCCCATGACCTGTTTACCC 2 37 1 CCCCCATGAC 0.965095 -56 GACCTGTTTACCCCCGTGGATAATTATTGA 2 54 1 CCCCCGTGGA 0.966524 -39 ATGGTCAATACCCCCATCCAAAATATTGAT 4 24 0 CCCCCATCCA 0.947544 -114 CCCTGGTAAGCCACCATGGTCAATACCCCC 4 39 0 CCACCATGGT 0.968693 -99 CTGGCCCATGCCCCACTGATTTTTATGATA 6 24 1 CCCCACTGAT 0.951066 -69 CCCCCCTGCCCCTCAATGGAGAGCAGATAA 7 98 0 CCTCAATGGA 0.771782 -187 TTAGACATTCCCCCCCTGCCCCTCAATGGA 7 108 0 CCCCCCTGCC 0.988846 -177 AACACTTCTCCGACAATGCTAAGCAATTCC 7 170 0 CGACAATGCT 0.686232 -115 GCTGCCATTTCGCCCCTGGTTTATTGGCGG 7 221 0 CGCCCCTGGT 0.978818 -64 ********** Masking position 7 Map Score: 13.9093 Number of sites scoring better than the average of aligned sites = 1807 Number in coding regions = 1607 Number in noncoding regions = 200 Number of orfs with sites within 600 bp upstream = 190 Fraction of orfs with sites within 600 bp upstream = 0.0305172 Motif number 3 TTCAGGTTAACCCAACTCCGGCGAGCTGGACT 1 67 1 CCCAACTCGC 0.992446 -234 TCTCCCCAATCCTAACCCAGTCCATTGATTCC 1 149 0 CCTAACCCGC 0.97648 -152 GTAGCAGGCACCATACTCTGCCTTGTGGAAGT 1 269 1 CCATACTCGC 0.98379 -32 AATTTTGGTAACAAACCCAGCCCCCATGACCT 2 27 1 ACAAACCCGC 0.964193 -66 ATTTTTAACCCCTAACTCTGTCTGGGTAAATG 3 27 1 CCTAACTCGC 0.983139 -81 ACACTCTAGAAACAACTCTGGCAAAGCCCTGG 4 63 0 AACAACTCGC 0.940545 -75 TACCACCATAACAAACTCCATCTAGGCGATCG 7 35 1 ACAAACTCAC 0.767666 -250 CAATGCTAAGCAATTCCCAGCCATCTTGCCAA 7 155 0 CAATTCCCGC 0.893052 -130 GAAAGATTAACACTTCTCCGACAATGCTAAGC 7 176 0 CACTTCTCGC 0.919971 -109 TGGCAGCCGGCAAATTTCAGACTTATTTTTGG 7 244 1 CAAATTTCGC 0.69352 -41 ******** * * Masking position 8 Map Score: 9.17299 Number of sites scoring better than the average of aligned sites = 954 Number in coding regions = 848 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 132 Fraction of orfs with sites within 600 bp upstream = 0.0212014 Motif number 4 TGAGGTAACAGCTAAATACAGCCATTTTGTCGGC 1 18 1 GCTAATACCA 0.926828 -283 TTGGGCTTGCGGTTAAAGCCGGAAAATTAGCAAC 1 201 0 GGTAAAGGAA 0.826745 -100 CAGAGTTAGGGGTTAAAAATTGCAAATTGCCAAT 3 13 0 GGTAAAAGCA 0.986921 -95 ACTCTGTCTGGGTAAATGTCCCCAAGCTGGACTG 3 41 1 GGTAATGCCA 0.977445 -67 AAGCCACCATGGTCAATACCCCCATCCAAAATAT 4 28 0 GGTAATACCA 0.987102 -110 AAGGCAAGTTGGTAAAAAACGGCAGTAACCCATG 4 105 0 GGTAAAAGCA 0.986922 -33 AATTCCGTTGAGTCAAAAGCTCCAACCCCAGTTA 5 142 0 AGTAAAACCA 0.965614 -159 GAATATTTATAGTTAAAACTACCATAAATATTTT 6 53 0 AGTAAAACCA 0.965613 -40 *** **** *** Masking position 6 Map Score: 6.51079 Number of sites scoring better than the average of aligned sites = 299 Number in coding regions = 273 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 5 CCTGAAGGTAGTTGAGCTAAGGCCGACAAAATGG 1 39 0 GTGAGCTGCC 0.987602 -262 TTGGGGAGAAGGGGAGCATTTCCCCCCTGGTTGC 1 172 1 GGGAGCATCC 0.916255 -129 GTGAAAAAAAGTCGTGGTCAGACCACAATTAAGC 5 56 0 GCGTGGTGCC 0.955128 -245 TCACATTGCTGGTGAGCGGGGACAGAAAGACTTA 5 86 1 GTGAGCGGCA 0.943285 -215 TAAAATTATTGCCGATGATTGACCTAACTGGGGT 5 118 1 GCGATGAGCC 0.967129 -183 TTAACTTTTTGGCGATCGATGTCCCCTTAGTCCA 5 269 0 GCGATCGGCC 0.983093 -32 ATAAAAATCAGTGGGGCATGGGCCAGCGCTTCAT 6 16 0 GGGGGCAGCC 0.988913 -77 ACTCCATCTAGGCGATCGCCGTCCGGAAACCCAC 7 49 1 GCGATCGGCC 0.981657 -236 TTGAGGGGCAGGGGGGGAATGTCTAACTTTAGGA 7 112 1 GGGGGGAGCT 0.835956 -173 ACTTTAGGACGATGAGCTTTGGCAAGATGGCTGG 7 137 1 GTGAGCTGCA 0.932308 -148 CTGGTTTATTGGCGGGGTCAAACCAGAGGAAAGA 7 202 0 GCGGGGTACC 0.880783 -83 * ****** * ** Masking position 13 Map Score: 8.55811 Number of sites scoring better than the average of aligned sites = 886 Number in coding regions = 810 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 6 GTTAACCCAACTCCGGCGAGCTGGACTGTC 1 72 1 CTCCGGCGAG 0.917788 -229 AACTTGCCATCACCGGGAATCAATGGACTG 1 134 1 CACCGGGAAT 0.980348 -167 TGATCCTTGGCTCCAGCAATGG 2 81 1 CTCCAGCAAT 0.978384 -12 GCATTGGCAATTTGCAATTTT 3 2 1 CATTGGCAAT 0.84792 -106 CTAGAAACAACTCTGGCAAAGCCCTGGTAA 4 60 0 CTCTGGCAAA 0.862334 -78 TGTCCCCGCTCACCAGCAATGTGAAAAAAA 5 80 0 CACCAGCAAT 0.973502 -221 TTAGGTCAATCATCGGCAATAATTTTAAGT 5 115 0 CATCGGCAAT 0.969927 -186 TATGTTTCGGCTCCTGGAATATTTATAGTT 6 73 0 CTCCTGGAAT 0.87281 -20 ATTAACACTTCTCCGACAATGCTAAGCAAT 7 173 0 CTCCGACAAT 0.957505 -112 TCTGGTTTGACCCCGCCAATAAACCAGGGG 7 209 1 CCCCGCCAAT 0.92431 -76 ********** Masking position 9 Map Score: 10.0838 Number of sites scoring better than the average of aligned sites = 1696 Number in coding regions = 1538 Number in noncoding regions = 158 Number of orfs with sites within 600 bp upstream = 159 Fraction of orfs with sites within 600 bp upstream = 0.0255381 Motif number 7 CCAGGGGGGAAATGCTCCCCTTCTCCCCAA 1 172 0 AATGCTCCCC 0.95936 -129 AAGGATCAATAATTATCCACGGGGGTAAAC 2 59 0 AATTATCCAC 0.588144 -34 TGTCTGGGTAAATGTCCCCAAGCTGGACTG 3 45 1 AATGTCCCCA 0.768307 -63 ATCCCCAAATTCCCAAAAGATTGTCTT 3 91 0 AATTCCCAAA 0.782997 -17 CACCATGGTCAATACCCCCATCCAAAATAT 4 28 0 AATACCCCCA 0.894888 -110 GACTAGGCAAAATTCCCCACACCAGTTGCA 5 209 0 AATTCCCCAC 0.986662 -92 AGCGCTGGCCCATGCCCCACTGATTTTTAT 6 20 1 CATGCCCCAC 0.963284 -73 TAAAGTTAGACATTCCCCCCCTGCCCCTCA 7 113 0 CATTCCCCCC 0.98425 -172 AATGCTAAGCAATTCCCAGCCATCTTGCCA 7 156 0 AATTCCCAGC 0.852088 -129 GCCGGCTGCCATTTCGCCCCTGGTTTATTG 7 225 0 ATTTCGCCCC 0.771935 -60 ********** Masking position 3 Map Score: 5.15434 Number of sites scoring better than the average of aligned sites = 2805 Number in coding regions = 2458 Number in noncoding regions = 347 Number of orfs with sites within 600 bp upstream = 295 Fraction of orfs with sites within 600 bp upstream = 0.0473819 Motif number 8 ACTCTGGCAAAGCCCTGGTAAGCCACCATGGTCAA 4 46 0 ACCTGTAAGA 0.799567 -92 GTTGGTAAAAAACGGCAGTAACCCATGGCAAGTGA 4 97 0 ACGCGTAACA 0.962929 -41 AACCCCGATAAGGCAAGTTGGTAAA 4 123 0 ACCCATAAGA 0.983731 -15 CATTGATTGTAGCCTCGATAACAAAAAAATGGGGC 5 23 1 ACCCATAACA 0.986825 -278 AGATTGAAAAAGCCACTATCACGCAGAAAATTCCG 5 169 0 ACCCATCACA 0.973413 -132 GGGGACATCGATCGCCAAAAAGTTAACGGAATCG 5 277 1 ACGCAAAAGA 0.907816 -24 ACAAAACCAATACCACCATAACAAACTCCATCTAG 7 25 1 TCCCATAACA 0.921923 -260 CCGTCCGGAAACCCACTTTCACAGAATTCTATTAT 7 67 1 ACCCTTCACA 0.940925 -218 GCCAAAGCTCATCGTCCTAAAGTTAGACATTCCCC 7 125 0 ACGCTAAAGA 0.810752 -160 * ** * ***** * Masking position 11 Map Score: 3.18455 Number of sites scoring better than the average of aligned sites = 191 Number in coding regions = 163 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 9 CAAGTTTGTTGAATTTTCTTTACAATTGTG 1 110 0 GAATTTTCTT 0.867336 -191 AAATTCGCATCACTCTTCTTA 2 2 0 CACTCTTCTT 0.896304 -91 TCTGGGAAGACAATCTTTTGGGAATTTGGG 3 85 1 CAATCTTTTG 0.95384 -23 GACCAAGCATCAATATTTTGGATGGGGGTA 4 16 1 CAATATTTTG 0.833515 -122 AATTAAGCCCCATTTTTTTGTTATCGAGGC 5 34 0 CATTTTTTTG 0.809383 -267 GTCTGACCACGACTTTTTTTCACATTGCTG 5 67 1 GACTTTTTTT 0.817797 -234 TGACTCAACGGAATTTTCTGCGTGATAGTG 5 161 1 GAATTTTCTG 0.912049 -140 GTGGCTTTTTCAATCTTTTTTTGCAACTGG 5 188 1 CAATCTTTTT 0.929093 -113 ********** Masking position 2 Map Score: 2.08945 Number of sites scoring better than the average of aligned sites = 554 Number in coding regions = 484 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 10 GTCCAGCTCGCCGGAGTTGGGTTAACCTGA 1 68 0 CCGGAGTTGG 0.965336 -233 CCATTGATTCCCGGTGATGGCAAGTTTGTT 1 130 0 CCGGTGATGG 0.989198 -171 TTTCACATTGCTGGTGAGCGGGGACAGAAA 5 84 1 CTGGTGAGCG 0.974924 -217 ATTGACCTAACTGGGGTTGGAGCTTTTGAC 5 135 1 CTGGGGTTGG 0.97158 -166 TTTTTTGCAACTGGTGTGGGGAATTTTGCC 5 204 1 CTGGTGTGGG 0.975135 -97 CGTTAACTTTTTGGCGATCGATGTCCCCTT 5 275 0 TTGGCGATCG 0.906093 -26 GGGTTTCCGGACGGCGATCGCCTAGATGGA 7 51 0 ACGGCGATCG 0.92096 -234 ********** Masking position 6 Map Score: 4.38676 Number of sites scoring better than the average of aligned sites = 1812 Number in coding regions = 1663 Number in noncoding regions = 149 Number of orfs with sites within 600 bp upstream = 173 Fraction of orfs with sites within 600 bp upstream = 0.0277867 Motif number 11 ********** No masking Map Score: 1.97774e-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 12 ********** No masking Map Score: 1.97774e-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: 1.97774e-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