AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i248_cell_division_synecho_reg_300.orf -o248_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 RCY22631 194 Synechocystis #2 RCY51824 142 Synechocystis #3 RCY05216 230 Synechocystis #4 RCY35933 256 Synechocystis #5 RCY04292 53 Synechocystis #6 RCY31157 272 Synechocystis #7 RCY24367 125 Synechocystis #8 RCY12587 220 Synechocystis #9 RCY33712 164 Synechocystis #10 RCY53924 189 Synechocystis #11 RCY50562 300 Synechocystis Motif number 1 GCAGGTAGAGGGCGTTGGCAAGGGTACTTTG 1 48 0 GGCTTGGCAA 0.959632 -147 GCAGTTTCCGGCCAATGGCGATCGCCAAGCG 1 91 1 GCCATGGCGA 0.966831 -104 TCCCAATCCTGACAGTGGCAAGGCCCAGCGG 1 145 0 GACGTGGCAA 0.908935 -50 CCGCATAGTTGCCCAGGGAAAAATC 2 5 0 GCCAGGGAAA 0.9825 -138 AGCTGAATTTGGCAGTGGAATGGTTCAACGC 3 15 1 GGCGTGGAAT 0.660026 -216 GGGGTAATTAGGCTTGGGCGCTGACCACGGC 3 105 0 GGCTGGGCGC 0.775656 -126 CTTAATCACAAGCTAGGGAAACCTAATCAGC 3 191 1 AGCAGGGAAA 0.892027 -40 GAAGGTTAAAACCTGGGGAAATACATCGCCG 4 35 1 ACCGGGGAAA 0.891068 -222 AACTTCAGGGGACAAGGGAAACGGCGATGTA 4 56 0 GACAGGGAAA 0.917881 -201 TTTTTGGCCTGCCATTGGCAATTTGGGCAAA 6 64 0 GCCTTGGCAA 0.963449 -209 CATAGTCATATCTATGGGCAACCT 6 259 1 TCTTGGGCAA 0.496702 -14 TGTATCCATGGGTGATGGCGAGAGAAAAAGT 7 78 0 GGTATGGCGA 0.801577 -48 TACAGCAACAACCAAGGGCAACAAAGCAACC 7 105 1 ACCAGGGCAA 0.962295 -21 TTTGGGCAGGGCAACAAGCGGGTT 8 4 1 GGGAGGGCAA 0.907112 -217 ACAATTTATGGCTGGTGGAAATAAAATTCAG 8 89 1 GCTGTGGAAA 0.734415 -132 TGGCCATGGCGTATTAAAGAAG 9 2 1 GGCATGGCGT 0.758733 -163 AAAAAGCCTAGCCAAGGGAAAAGTTTGGGGT 9 76 1 GCCAGGGAAA 0.9825 -89 AGGGGCTAAAAACCAGGGCAATTTTTCCTTT 10 50 0 AACAGGGCAA 0.835555 -140 ACACCGGGGAGGCAGGGGCTAAAAACCAGGG 10 63 0 GGCGGGGCTA 0.910053 -127 CTGCCTCCCCGGTGTGGGAAAAACCGATAAA 10 79 1 GGTTGGGAAA 0.785091 -111 GGGATTTCCATCCCAGGGCGATCGCCTAGAA 10 138 1 TCCAGGGCGA 0.87657 -52 ATCTCCTCTCGCCTGGGGCAAACCCAGGACT 11 241 1 GCCGGGGCAA 0.992892 -60 *** ******* Masking position 7 Map Score: 29.1244 Number of sites scoring better than the average of aligned sites = 5410 Number in coding regions = 4946 Number in noncoding regions = 464 Number of orfs with sites within 600 bp upstream = 454 Fraction of orfs with sites within 600 bp upstream = 0.07292 Motif number 2 GCCGGAAACTGCCCAGGGACTAATGCAGGTAGA 1 70 0 GCCAGGGCTA 0.991866 -125 AATGGCGATCGCCAAGCGTCGTATATTAGGCAT 1 104 1 GCAAGCGCGA 0.977546 -91 CAGTGGCAAGGCCCAGCGGCTCAATATATGCCT 1 131 0 GCCAGCGCTA 0.995244 -64 AGAAAGGGAGGAGAAGGGGCTCCGTATTCTAAG 2 74 0 GAAAGGGCTC 0.922012 -69 TGCCCGCCGTGGTCAGCGCCCAAGCCTAATTAC 3 100 1 GGCAGCGCCA 0.966179 -131 CTTGTTACGTGATCAGCGCCTACCCGATACCAA 4 164 0 GACAGCGCTC 0.982212 -93 GGCAATTTGGGCAAAGGGTGCAAATTTTTAGGA 6 46 0 GCAAGGGGCA 0.811879 -227 AGGATATGGGCCAAAGCGTCCACATGCTCTACC 6 132 1 CCAAGCGCCC 0.933919 -141 CAATAATGACGAACAGCGTCGCCGAAAACGTTA 6 199 0 GACAGCGCGC 0.968994 -74 CCCTTTTAAGCCCCAGCGGCTTAGGCCACTAAC 7 47 1 CCCAGCGCTA 0.980341 -79 GGTGCTCAGGGTCTAATGTTGCTAGT 9 149 0 GCCAGGGCTA 0.991866 -16 ** ***** ** * Masking position 5 Map Score: 13.1344 Number of sites scoring better than the average of aligned sites = 292 Number in coding regions = 263 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 3 TTCCGGCCAATGGCGATCGCCAAGCGTCGT 1 96 1 TGGCGATCGC 0.995193 -99 TTTAACCTTCTGGGGATAGTTGCCGAGAGG 4 15 0 TGGGGATAGT 0.838014 -242 TATTTTATGGAGGCGATCGTTGCATCCTAA 6 22 1 AGGCGATCGT 0.967347 -251 CCATGGGTGATGGCGAGAGAAAAAGTTAGT 7 74 0 TGGCGAGAGA 0.908001 -52 ATTCAGACAGTAGCGATAGCGACTTCTATC 8 114 1 TAGCGATAGC 0.927512 -107 TGGCCATGGCGTATTAAAGA 9 1 1 TGGCCATGGC 0.895212 -164 TGTGACTGTATGGCGATCGCCGTAATATTC 9 42 1 TGGCGATCGC 0.995193 -123 CCAAAATTCTAGGCGATCGCCCTGGGATGG 10 145 0 AGGCGATCGC 0.990876 -45 GGTTTGCCCCAGGCGAGAGGAGATTAGTTC 11 235 0 AGGCGAGAGG 0.884705 -66 ********** Masking position 6 Map Score: 9.768 Number of sites scoring better than the average of aligned sites = 7187 Number in coding regions = 6555 Number in noncoding regions = 632 Number of orfs with sites within 600 bp upstream = 424 Fraction of orfs with sites within 600 bp upstream = 0.0681015 Motif number 4 AGGGACTAATGCAGGTAGAGGGCGTTGGCAAGG 1 56 0 GCAGGAGGGC 0.982923 -139 TAGTCCCTGGGCAGTTTCCGGCCAATGGCGATC 1 81 1 GCAGTTGGCC 0.912658 -114 GTCAGGATTGGGAGGGCCTGGATTACCCCGTCC 1 163 1 GGAGGCGGAT 0.897729 -32 GGAGGTTGGGGACGGGGTAATCC 1 182 0 GGAGGTGGAC 0.955118 -13 GGGCAACTATGCGGTCATCAGATATTTAAATCA 2 22 1 GCGGTAAGAT 0.593441 -121 GGGGTCAAGGGGAGTGGTGAGGA 2 130 0 GGGGTAGGGA 0.797929 -13 ATTGTTGAGGGGGGTAATTAGGCTTGGGCGCTG 3 113 0 GGGGTAAGGC 0.907359 -118 CTATCAGAGGGGGGGATCAGCGTACAGCATTGT 3 141 0 GGGGGTGCGT 0.793703 -90 AATAAAGTCGGGAGTTTTTGGCCTGCCATTGGC 6 76 0 GGAGTTGGCC 0.930347 -197 TGACTGTTGAGCAGGATATGGGCCAAAGCGTCC 6 120 1 GCAGGTGGGC 0.973532 -153 CATTATTGGGGCAGGAATAAGACTAGGTGGATT 6 224 1 GCAGGAAGAC 0.849541 -49 GGGCTTAAAAGGGGTGACTGGGTTTAGTGTAAT 7 27 0 GGGGTAGGGT 0.950051 -99 GGAAAAGTTTGGGGTTAACGGGCTGAAATTAAG 9 92 1 GGGGTAGGGC 0.978334 -73 CCCACACCGGGGAGGCAGGGGCTAAAAACCAGG 10 64 0 GGAGGAGGCT 0.947489 -126 CCCCCTCAGTGCGGGGCTAGCCCAATGGTCATA 11 132 1 GCGGGCGCCC 0.803335 -169 TTTAATCCTGGCAGGTCAAAGATAGTCCTGGGT 11 262 0 GCAGGCAGAT 0.598108 -39 ***** * **** Masking position 4 Map Score: 14.1897 Number of sites scoring better than the average of aligned sites = 3930 Number in coding regions = 3587 Number in noncoding regions = 343 Number of orfs with sites within 600 bp upstream = 268 Fraction of orfs with sites within 600 bp upstream = 0.0430453 Motif number 5 GATTTTTCCCTGGGCAACTATG 2 3 1 TTTTTCCCTG 0.820978 -140 ATCTGCCTGCTTTTTGACTGCGTTGAACCA 3 35 0 TTTTTGACTG 0.917219 -196 GGGACTTATGTTTTGGTTGGGTCATAGTAA 4 97 1 TTTTGGTTGG 0.771178 -160 AGTCGGGAGTTTTTGGCCTGCCATTGGCAA 6 74 0 TTTTGGCCTG 0.981377 -199 TTTGGGCAGGGCAACAAGCG 8 1 1 TTTGGGCAGG 0.778791 -220 GTATCACAATTTATGGCTGGTGGAAATAAA 8 84 1 TTATGGCTGG 0.793163 -137 TGTTGCCCTATTTTTGATTGAATTAGCTAT 8 175 1 TTTTTGATTG 0.825433 -46 AAGTACAGGTTTTGTGACTGTATGGCGATC 9 30 1 TTTGTGACTG 0.809615 -135 TTGGCTAGGCTTTTTGCCGGAATATTACGG 9 61 0 TTTTTGCCGG 0.981377 -104 TCGCCTAGAATTTTGGCCGGCTTCGTATTT 10 159 1 TTTTGGCCGG 0.986057 -31 AGATTTGTTAATTTTGCTTGGCTAGTCAAA 11 72 0 ATTTTGCTTG 0.680442 -229 ********** Masking position 2 Map Score: 7.09122 Number of sites scoring better than the average of aligned sites = 1299 Number in coding regions = 1180 Number in noncoding regions = 119 Number of orfs with sites within 600 bp upstream = 123 Fraction of orfs with sites within 600 bp upstream = 0.0197559 Motif number 6 AGGCCCTCCCAATCCTGACAGTGGCAAGGCC 1 151 0 AATCCGACAG 0.948646 -44 TCCACTGCCAAATTCAGCTAATT 3 3 0 AATTCGCTAA 0.811158 -228 GCAGGCAGATAATCCGCCCAACTCTTAATCT 3 55 1 AATCCCCCAA 0.983249 -176 GAATTGAATCCTCCCAACTGCTGATTA 3 214 0 AATCCCCCAA 0.983249 -17 ACCAAAACATAAGTCCCCCAAAGTCTGAACT 4 83 0 AAGTCCCCAA 0.848029 -174 TGACTATGCTAATCCACCTAGTCTTATTCCT 6 236 0 AATCCCCTAG 0.931494 -37 GTGGAAATAAAATTCAGACAGTAGCGATAGC 8 103 1 AATTCGACAG 0.820653 -118 GAAAAATACGAAGCCGGCCAAAATTCTAGGC 10 161 0 AAGCCGCCAA 0.964117 -29 AAAATTAACAAATCTTGACAAACACGATAAG 11 87 1 AATCTGACAA 0.608821 -214 TTTGTTGATGAATCCCCCTCAGTGCGGGGCT 11 119 1 AATCCCCTCA 0.732482 -182 TTTGGCTTTTAATCCTGGCAGGTCAAAGATA 11 271 0 AATCCGGCAG 0.91551 -30 ***** ***** Masking position 2 Map Score: 7.16202 Number of sites scoring better than the average of aligned sites = 1372 Number in coding regions = 1208 Number in noncoding regions = 164 Number of orfs with sites within 600 bp upstream = 162 Fraction of orfs with sites within 600 bp upstream = 0.0260199 Motif number 7 CAGATAATCCGCCCAACTCTTAATCTTAGAGG 3 60 1 GCCCAACTTA 0.967806 -171 CCCATATCCTGCTCAACAGTCAGGAGAGCATC 6 110 0 GCTCAACTCA 0.973847 -163 GCGTCCACATGCTCTACCTTTAACATTGTCCT 6 147 1 GCTCTACTTA 0.900725 -126 CGTTTATGTTGCCCTATTTTTGATTGAATTAG 8 169 1 GCCCTATTTG 0.758332 -52 TACGGCGATCGCCATACAGTCACAAAACCTGT 9 34 0 GCCATACTCA 0.842604 -131 GATAAACTAGGCACAATGGTCATTTGAAAACA 10 104 1 GCACAATTCA 0.902828 -86 TGCGGGGCTAGCCCAATGGTCATATACTTGGA 11 141 1 GCCCAATTCA 0.979792 -160 GACTGTTTTTGCTCAATGATCACCGAATTAAC 11 184 1 GCTCAATTCA 0.959144 -117 ******* *** Masking position 6 Map Score: 3.03915 Number of sites scoring better than the average of aligned sites = 207 Number in coding regions = 183 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 8 CGTGATCAGCGCCTACCCGATACCAATGAT 4 160 0 GCCTACCCGA 0.715659 -97 AATTGCCAATGGCAGGCCAAAAACTCCCGA 6 72 1 GGCAGGCCAA 0.985984 -201 TTTGGGCAGGGCAACAAGCGGGTT 8 5 1 GGCAGGGCAA 0.920905 -216 CCGGCAAAAAGCCTAGCCAAGGGAAAAGTT 9 71 1 GCCTAGCCAA 0.977037 -94 ATAATAATTTGACTAGCCAAGCAAAATTAA 11 65 1 GACTAGCCAA 0.914597 -236 CTCAGTGCGGGGCTAGCCCAATGGTCATAT 11 136 1 GGCTAGCCCA 0.975124 -165 AGTCTTTGACGCCAATCCAAGTATATGACC 11 158 0 GCCAATCCAA 0.871786 -143 TCTCGCCTGGGGCAAACCCAGGACTATCTT 11 247 1 GGCAAACCCA 0.862341 -54 TTTTAATCCTGGCAGGTCAAAGATAGTCCT 11 266 0 GGCAGGTCAA 0.887078 -35 ********** Masking position 10 Map Score: 4.78542 Number of sites scoring better than the average of aligned sites = 604 Number in coding regions = 555 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 9 CCCTTGCCAACGCCCTCTACCTGCATTAGT 1 55 1 CGCCCTCTAC 0.957636 -140 GCCTAATTACCCCCCTCAACAATGCTGTAC 3 123 1 CCCCCTCAAC 0.977401 -108 ACGCTGATCCCCCCCTCTGATAGACTTTTG 3 151 1 CCCCCTCTGA 0.982701 -80 TTTCCCTCTCGGCAACTATCCCC 4 4 1 CCCTCTCGGC 0.968382 -253 TCTAGGCGATCGCCCTGGGATGGAAATCCC 10 138 0 CGCCCTGGGA 0.913269 -52 GTTGATGAATCCCCCTCAGTGCGGGGCTAG 11 122 1 CCCCCTCAGT 0.969893 -179 ********** Masking position 6 Map Score: 1.42098 Number of sites scoring better than the average of aligned sites = 385 Number in coding regions = 351 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 10 CGATCGCCATTGGCCGGAAACTGCCCAGGG 1 85 0 TGGCCGGAAA 0.928835 -110 TATTTGAAACTCTCCGTAATTTTAATGATA 4 199 0 TCTCCGTAAT 0.877285 -58 TTTGCACCCTTTGCCCAAATTGCCAATGGC 6 55 1 TTGCCCAAAT 0.824867 -218 ACGAACAGCGTCGCCGAAAACGTTAAACTT 6 194 0 TCGCCGAAAA 0.961063 -79 TGTATGGCGATCGCCGTAATATTCCGGCAA 9 48 1 TCGCCGTAAT 0.978842 -117 GCTAGGCTTTTTGCCGGAATATTACGGCGA 9 58 0 TTGCCGGAAT 0.963403 -107 ********** Masking position 8 Map Score: 0.284301 Number of sites scoring better than the average of aligned sites = 366 Number in coding regions = 331 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 11 TCCTCCCTTTCTAAGCTAAAGGAGACGGCTTT 2 95 1 CTAAGTAAGG 0.958148 -48 CAAAGATCCTCTAAGATTAAGAGTTGGGCGGA 3 67 0 CTAAGTAAGA 0.965053 -164 TTTTCTCCTACAAGGATTAAGAATTGGAAATT 5 20 0 CAAGGTAAGA 0.958696 -34 AACTCCAGGACAATGTTAAAGGTAGAGCATGT 6 153 0 CAATGTAAGG 0.928485 -120 TAGTCAAAGATAAATAATGAGTATGT 8 205 0 CAAAGTAATA 0.888528 -16 GATTAAAAGCCAAAGTTCAAGAC 11 288 1 CAAAGTAAGA 0.980961 -13 ***** * **** Masking position 7 Map Score: 0.672545 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 38 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 12 ********** No masking Map Score: 2.09143e-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: 2.09143e-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: 2.09143e-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