AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i007_Pyrimidine_Nucleotides_Biosynthesis_synecho_reg_300.orf -o007_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 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 ACAGTCCAGCTCGCCGGAGTTGGGTTAACCTGA 1 68 0 TCGCCAGTGG 0.984334 -233 AGTCCATTGATTCCCGGTGATGGCAAGTTTGTT 1 130 0 TTCCCTGTGG 0.991979 -171 GGGGAGCATTTCCCCCCTGGTTGCTAATTTTCC 1 182 1 TCCCCTGTTG 0.986106 -119 CTGGGTAAATGTCCCCAAGCTGGACTGAAACCG 3 48 1 GTCCCAGTGG 0.937525 -60 ATCCCCAAATTCCCAAAAGATTGTCTTCCCAGA 3 85 0 TCCCAAGTTG 0.77508 -23 GATGGGGGTATTGACCATGGTGGCTTACCAGGG 4 36 1 TTGACTGTGG 0.934911 -102 TACCAGGGCTTTGCCAGAGTTGTTTCTAGAGTG 4 61 1 TTGCCAGTGT 0.948209 -77 ACGACTTTTTTTCACATTGCTGGTGAGCGGGGA 5 75 1 TTCACTGTGG 0.934911 -226 CTTAAAATTATTGCCGATGATTGACCTAACTGG 5 116 1 TTGCCTGTTG 0.983165 -185 CAATCTTTTTTTGCAACTGGTGTGGGGAATTTT 5 198 1 TTGCATGTGT 0.835707 -103 GCTGGCCCATGCCCCACTGATTTTTATGATAAA 6 23 1 GCCCCTGTTT 0.879455 -70 TATTATCTGCTCTCCATTGAGGGGCAGGGGGGG 7 96 1 TCTCCTGGGG 0.83372 -189 AGTGTTAATCTTTCCTCTGGTTTGACCCCGCCA 7 194 1 TTTCCTGTTT 0.825488 -91 GGCTGCCATTTCGCCCCTGGTTTATTGGCGGGG 7 219 0 TCGCCTGTTT 0.961736 -66 ***** ** *** Masking position 9 Map Score: 17.0643 Number of sites scoring better than the average of aligned sites = 2571 Number in coding regions = 2320 Number in noncoding regions = 251 Number of orfs with sites within 600 bp upstream = 267 Fraction of orfs with sites within 600 bp upstream = 0.0428847 Motif number 2 GGGTTAGGATTGGGGAGAAGGGGAGCATTTCC 1 163 1 TGGGGAGAGG 0.975021 -138 ATTAGCAACCAGGGGGGAAATGCTCCCCTTCT 1 178 0 AGGGGGGATG 0.997393 -123 AGAGATAAACAGGGGACATAGGAAATAGCTTG 1 232 0 AGGGGACTGG 0.895165 -69 TAAACAGGTCATGGGGGCTGGGTTTGTTACCA 2 32 0 ATGGGGGTGG 0.969725 -61 AATATTTTGGATGGGGGTATTGACCATGGTGG 4 27 1 ATGGGGGATG 0.991962 -111 TTGCAACTGGTGTGGGGAATTTTGCCTAGTCA 5 208 1 TGTGGGGATT 0.758935 -93 ATTACTAATTAGTGGACTAAGGGGACATCGAT 5 257 1 AGTGGACAGG 0.924768 -44 CATAAAAATCAGTGGGGCATGGGCCAGCGCTT 6 19 0 AGTGGGGAGG 0.993054 -74 GGAGTTTGTTATGGTGGTATTGGTTTTGTTGT 7 22 0 ATGGTGGATG 0.898529 -263 ATTGAGGGGCAGGGGGGGAATGTCTAACTTTA 7 111 1 AGGGGGGATG 0.997393 -174 CCAATAAACCAGGGGCGAAATGGCAGCCGGCA 7 224 1 AGGGGCGATG 0.982331 -61 TTTTTGGCTTTTTGGGCAACTGTGTA 7 269 1 TTTGGGCATG 0.830865 -16 ******* * ** Masking position 4 Map Score: 18.1515 Number of sites scoring better than the average of aligned sites = 2137 Number in coding regions = 1852 Number in noncoding regions = 285 Number of orfs with sites within 600 bp upstream = 255 Fraction of orfs with sites within 600 bp upstream = 0.0409573 Motif number 3 TCCCGGTGATGGCAAGTTTGTTGAATTTTC 1 122 0 GGCAAGTTTG 0.985765 -179 GAAGAGTGATGCGAATTTTGGTAACAAACC 2 14 1 GCGAATTTTG 0.89216 -79 GCATTGGCAATTTGCAATTTTTAAC 3 6 1 GGCAATTTGC 0.978745 -102 ACAATCTTTTGGGAATTTGGGGAT 3 94 1 GGGAATTTGG 0.986511 -14 ACCCCGATAAGGCAAGTTGGTAAAAAACGG 4 117 0 GGCAAGTTGG 0.988907 -21 TTTGACTCAACGGAATTTTCTGCGTGATAG 5 159 1 CGGAATTTTC 0.810191 -142 AACTGGTGTGGGGAATTTTGCCTAGTCAAG 5 212 1 GGGAATTTTG 0.982762 -89 GATGAGCTTTGGCAAGATGGCTGGGAATTG 7 147 1 GGCAAGATGG 0.933577 -138 AATGGCAGCCGGCAAATTTCAGACTTATTT 7 242 1 GGCAAATTTC 0.899824 -43 ********** Masking position 5 Map Score: 11.7459 Number of sites scoring better than the average of aligned sites = 714 Number in coding regions = 623 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 4 TGACAGTCCAGCTCGCCGGAGTTGGGTTAAC 1 72 0 GCTCGCGGAG 0.914293 -229 CCATACTCTGCCTTGTGGAAGTTATCTTCCC 1 279 1 CCTTGGGAAG 0.864304 -22 CCATTGCTGGAGCCAAGGATCA 2 81 0 CATTGTGGAG 0.980152 -12 TACCAACTTGCCTTATCGGGGTT 4 125 1 CCTTACGGGG 0.958824 -13 CTTTTTTTCACATTGCTGGTGAGCGGGGACA 5 79 1 CATTGTGGTG 0.89842 -222 CGATGATTGACCTAACTGGGGTTGGAGCTTT 5 130 1 CCTAATGGGG 0.924703 -171 CCTAGATGAAGCGCTGGCCCA 6 1 1 CCTAGTGAAG 0.914808 -92 ACGGCGATCGCCTAGATGGAGTTTGTTATGG 7 40 0 CCTAGTGGAG 0.985993 -245 CCCCCCTGCCCCTCAATGGAGAGCAGATAAT 7 97 0 CCTCATGGAG 0.948229 -188 AATTGCTTAGCATTGTCGGAGAAGTGTTAAT 7 172 1 CATTGCGGAG 0.981631 -113 GCCCCTGGTTTATTGGCGGGGTCAAACCAGA 7 209 0 TATTGCGGGG 0.769001 -76 ***** ***** Masking position 3 Map Score: 11.4031 Number of sites scoring better than the average of aligned sites = 1263 Number in coding regions = 1172 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 5 GAAGGTAGTTGAGCTAAGGCCGACAAAATGG 1 39 0 GAGCAAGGCC 0.955996 -262 CATCACCGGGAATCAATGGACTGGGTTAGGA 1 141 1 AATCATGGAC 0.780801 -160 GGGAGAAGGGGAGCATTTCCCCCCTGGTTGC 1 175 1 GAGCTTTCCC 0.956538 -126 CCGCAAGCCCAAGCTATTTCCTATGTCCCCT 1 223 1 AAGCATTTCC 0.866943 -78 GATAATTATTGATCCTTGGCTCCAGCAATGG 2 72 1 GATCTTGGCT 0.816945 -21 TCTAGAGTGTGATCACTTGCCATGGGTTACT 4 85 1 GATCCTTGCC 0.957018 -53 ACTGGGGTTGGAGCTTTTGACTCAACGGAAT 5 144 1 GAGCTTTGAC 0.918445 -157 ACTTTTTGGCGATCGATGTCCCCTTAGTCCA 5 269 0 GATCATGTCC 0.92533 -32 CCTAGATGAAGCGCTGGCCCATGCCCCAC 6 9 1 AAGCCTGGCC 0.976931 -84 TTAGGACGATGAGCTTTGGCAAGATGGCTGG 7 140 1 GAGCTTGGCA 0.923935 -145 CGACAATGCTAAGCAATTCCCAGCCATCTTG 7 159 0 AAGCATTCCC 0.909702 -126 **** ****** Masking position 2 Map Score: 6.8152 Number of sites scoring better than the average of aligned sites = 1910 Number in coding regions = 1749 Number in noncoding regions = 161 Number of orfs with sites within 600 bp upstream = 170 Fraction of orfs with sites within 600 bp upstream = 0.0273049 Motif number 6 GGGAATCAATGGACTGGGTTAGGATTGGGG 1 148 1 GGACTGGGTT 0.936905 -153 CAGGTCATGGGGGCTGGGTTTGTTACCAAA 2 30 0 GGGCTGGGTT 0.977751 -63 CCCCTAACTCTGTCTGGGTAAATGTCCCCA 3 35 1 TGTCTGGGTA 0.926965 -73 CAACTTGCCTTATCGGGGTT 4 128 1 TATCGGGGTT 0.864752 -10 CATTGCTGGTGAGCGGGGACAGAAAGACTT 5 89 1 GAGCGGGGAC 0.919615 -212 GTGGGTTTCCGGACGGCGATCGCCTAGATG 7 53 0 GGACGGCGAT 0.796715 -232 TTTGGCAAGATGGCTGGGAATTGCTTAGCA 7 154 1 TGGCTGGGAA 0.955111 -131 TGCTTAGCATTGTCGGAGAAGTGTTAATCT 7 175 1 TGTCGGAGAA 0.693273 -110 CCTGGTTTATTGGCGGGGTCAAACCAGAGG 7 207 0 TGGCGGGGTC 0.982331 -78 ********** Masking position 4 Map Score: 4.91064 Number of sites scoring better than the average of aligned sites = 2022 Number in coding regions = 1861 Number in noncoding regions = 161 Number of orfs with sites within 600 bp upstream = 184 Fraction of orfs with sites within 600 bp upstream = 0.0295535 Motif number 7 GGCTGTATTTAGCTGTTACCTCAAAGTCAC 1 11 0 AGCTGTTACC 0.881139 -290 CTAATTTTCCGGCTTTAACCGCAAGCCCAA 1 205 1 GGCTTTAACC 0.938479 -96 TGGGGGCTGGGTTTGTTACCAAAATTCGCA 2 23 0 GTTTGTTACC 0.928396 -70 GCAATTTGCAATTTTTAACCCCTAACTCTG 3 17 1 ATTTTTAACC 0.634987 -91 CCAGCTTGGGGACATTTACCCAGACAGAGT 3 41 0 GACATTTACC 0.854844 -67 CCCCAAGCTGGACTGAAACCGCTAATCTGG 3 60 1 GACTGAAACC 0.780589 -48 TTTGGATGGGGGTATTGACCATGGTGGCTT 4 32 1 GGTATTGACC 0.770367 -106 GGTAAAAAACGGCAGTAACCCATGGCAAGT 4 99 0 GGCAGTAACC 0.953424 -39 GGTTACTGCCGTTTTTTACCAACTTGCCTT 4 109 1 GTTTTTTACC 0.889661 -29 AGACTTCATTGATTGTAGCCTCGATAACAA 5 17 1 GATTGTAGCC 0.769049 -284 ********** Masking position 9 Map Score: 2.96152 Number of sites scoring better than the average of aligned sites = 1377 Number in coding regions = 1247 Number in noncoding regions = 130 Number of orfs with sites within 600 bp upstream = 148 Fraction of orfs with sites within 600 bp upstream = 0.0237713 Motif number 8 GTAGTTGAGCTAAGGCCGACAAAATGGCTGT 1 35 0 TAAGCCGACA 0.856488 -266 GCTTGCGGTTAAAGCCGGAAAATTAGCAACC 1 200 0 AAAGCGGAAA 0.936181 -101 GCGGGGACAGAAAGACTTAAAATTATTGCCG 5 101 1 AAAGCTTAAA 0.838809 -200 AGTTGCAAAAAAAGATTGAAAAAGCCACTAT 5 185 0 AAAGTTGAAA 0.953314 -116 ATTAGTAATGAAAGCTTGACTAGGCAAAATT 5 225 0 AAAGTTGACT 0.805609 -76 TCATCGTCCTAAAGTTAGACATTCCCCCCCT 7 121 0 AAAGTAGACA 0.919592 -164 AAACCAGAGGAAAGATTAACACTTCTCCGAC 7 186 0 AAAGTTAACA 0.857408 -99 AAGCCAAAAATAAGTCTGAAATTTGCCGGCT 7 248 0 TAAGCTGAAA 0.926889 -37 AGTTGCCCAAAAAGCCAAAAATAAGTCTGAA 7 259 0 AAAGCAAAAA 0.799675 -26 **** ****** Masking position 3 Map Score: 1.53186 Number of sites scoring better than the average of aligned sites = 325 Number in coding regions = 250 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 9 TAAGCACAATTGTAAAGAAAATTCAACAAAC 1 106 1 TGTAAAGAAA 0.966666 -195 TGGGAAGATAACTTCCACAAG 1 290 0 TGGGAAGAAA 0.986021 -11 ACCGCTAATCTGGGAAGACAATCTTTTGGGA 3 77 1 TGGGAAGAAA 0.986021 -31 TCACCAGCAATGTGAAAAAAAGTCGTGGTCA 5 70 0 TGTGAAAAAA 0.926039 -231 TTGGTTTTGTTGTAAAGAGGAATA 7 4 0 TGTAAAGAGA 0.928895 -281 ******** ** Masking position 6 Map Score: 1.34419 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 26 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 10 ********** 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 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