AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i308_mixed22_synecho_reg_300.orf -o308_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 RCY41704 31 Synechocystis #2 RCY18056 198 Synechocystis #3 RCY08755 34 Synechocystis #4 RCY48569 20 Synechocystis #5 RCY29363 49 Synechocystis #6 RCY51306 167 Synechocystis #7 RCY51398 55 Synechocystis #8 RCY29713 300 Synechocystis Motif number 1 CTAAGGCGATCGCCTTACCCCAGACTAACT 2 22 1 CGCCTTACCC 0.993987 -177 TACCATCTACGGCCAAACCCAACGGCTTAA 6 81 1 GGCCAAACCC 0.960257 -87 TCAAACTTTGAGCATTACCC 7 46 1 AGCATTACCC 0.989749 -10 AAAAATGGAAAGTCATACCCGCCAGCAAAA 8 30 0 AGTCATACCC 0.980295 -271 AGACTTACCCCGCAATACCCTGTCTGAATG 8 158 0 CGCAATACCC 0.990491 -143 CGATGTTTGGAGACTTACCCCGCAATACCC 8 168 0 AGACTTACCC 0.985377 -133 CTACTCCATAAAAAATACCCAGGCGAAGCT 8 210 1 AAAAATACCC 0.846419 -91 ********** Masking position 7 Map Score: 9.30975 Number of sites scoring better than the average of aligned sites = 321 Number in coding regions = 289 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 2 CCTTTGACCTAAGGCGATCGCCTTACCCCA 2 14 1 AAGGCGATCG 0.992373 -185 TTTTGCGTCAATGCCAGTCTTTTCCTGACA 2 81 1 ATGCCAGTCT 0.851778 -118 TGTATCTGATATGGCAGTATGATCGAAGAA 2 143 1 ATGGCAGTAT 0.785179 -56 ACAATGCAAAATGGGGATCTTCTTCGATCA 2 162 0 ATGGGGATCT 0.936899 -37 GTTTCGGTTAAGCCAATCTTTTGAGATTG 3 10 1 AAGCCAATCT 0.889795 -25 ATTAGGACTAAAGCCTATCGATACCATCTA 6 60 1 AAGCCTATCG 0.882184 -108 CGTTAGCAGGCGATCGCCGGGGAGAC 6 152 0 CAGGCGATCG 0.982439 -16 TCAAAGTTTGAAGGGGACAGAGAAACAGAT 7 27 0 AAGGGGACAG 0.808461 -29 TAAAGTACCTATGGCGGCAGGTGACGGTTG 8 115 0 ATGGCGGCAG 0.873365 -186 CCAGGCGAAGCTGGCGATCGAGTGTAAAAG 8 228 1 CTGGCGATCG 0.982432 -73 ********** Masking position 3 Map Score: 7.05612 Number of sites scoring better than the average of aligned sites = 8820 Number in coding regions = 8050 Number in noncoding regions = 770 Number of orfs with sites within 600 bp upstream = 517 Fraction of orfs with sites within 600 bp upstream = 0.0830389 Motif number 3 CAGTCTTTTCCTGACAATTTTGCGTTTTCTAAC 2 95 1 CTACAATTGC 0.927045 -104 TTTGCGTTTTCTAACAATTCGTCCAAATTCTGT 2 113 1 CTACAATTTC 0.95734 -86 CAGAGTTGAGATCAAAATCTTTTCAT 5 4 0 ATAAAATCTT 0.861533 -46 AACCCAACGGCTTAAAACCAGTCAAATTAAGCA 6 96 1 CTAAAACCTC 0.931284 -72 AATTCAGCAAATTAAAATCTGTTTCTCTGTCCC 7 11 1 ATAAAATCTT 0.861533 -45 CAGCAAAAAAATTACAATCGTTTATTT 8 5 0 ATACAATCTT 0.924478 -296 GTGACGGTTGCTGACATTCCATCCTACAACGCC 8 92 0 CTACATTCTC 0.972983 -209 ACCTCGGGGACTTACATTCAGACAGGGTATTGC 8 144 1 CTACATTCAC 0.882028 -157 GACTGAAAATCTTGCCGGTATCCCC 8 286 0 CTAAAATCGC 0.970454 -15 ** ****** ** Masking position 6 Map Score: 3.79681 Number of sites scoring better than the average of aligned sites = 309 Number in coding regions = 236 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 4 CTGGGGTAAGGCGATCGCCTTAGGTCAAAG 2 15 0 GCGATCGCCT 0.998385 -184 CGTCTCCCCGGCGATCGCCTGCTAACG 6 151 1 GCGATCGCCT 0.998385 -17 GGCGAAGCTGGCGATCGAGTGTAAAAGACT 8 231 1 GCGATCGAGT 0.991961 -70 ********** Masking position 4 Map Score: 3.85593 Number of sites scoring better than the average of aligned sites = 1415 Number in coding regions = 1285 Number in noncoding regions = 130 Number of orfs with sites within 600 bp upstream = 140 Fraction of orfs with sites within 600 bp upstream = 0.0224863 Motif number 5 AGTTTTAAGATTCTGTTTTAATAATTTTTA 1 11 1 TTCTGTTTTA 0.946751 -21 TTCGTCCAAATTCTGTATCTGATATGGCAG 2 130 1 TTCTGTATCT 0.950479 -69 AGGTCAGTTTTTATTGTTTTTA 5 38 0 GTCAGTTTTT 0.912505 -12 TAAATTCAACTTCTGTTTTTTGCCTCCATA 6 22 1 TTCTGTTTTT 0.983192 -146 GCAAATTAAAATCTGTTTCTCTGTCCCCTT 7 17 1 ATCTGTTTCT 0.961526 -39 ********** Masking position 6 Map Score: 1.43338 Number of sites scoring better than the average of aligned sites = 108 Number in coding regions = 82 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 6 AGATCAGTGATTTTTGCGTCAATGCCAGTC 2 70 1 TTTTTGCGTC 0.927186 -129 TTTCCTGACAATTTTGCGTTTTCTAACAAT 2 101 1 ATTTTGCGTT 0.953509 -98 GAAGATCCCCATTTTGCATTGTATTAGGAA 2 170 1 ATTTTGCATT 0.944394 -29 CAACTTCTGTTTTTTGCCTCCATAATCTAC 6 28 1 TTTTTGCCTC 0.89735 -140 GGCGGGTATGACTTTCCATTTTTAAATGCC 8 37 1 ACTTTCCATT 0.930743 -264 ATCTACTCAAACTTGGCATTTAAAAATGGA 8 51 0 ACTTGGCATT 0.836299 -250 ACGGTTGCTGACATTCCATCCTACAACGCC 8 92 0 ACATTCCATC 0.806296 -209 CGCCATAGGTACTTTACCTCGGGGACTTAC 8 129 1 ACTTTACCTC 0.846385 -172 TACCGGCAAGATTTTCAGTC 8 291 1 ATTTTCAGTC 0.708289 -10 ********** Masking position 4 Map Score: 2.45045 Number of sites scoring better than the average of aligned sites = 680 Number in coding regions = 536 Number in noncoding regions = 144 Number of orfs with sites within 600 bp upstream = 156 Fraction of orfs with sites within 600 bp upstream = 0.0250562 Motif number 7 ACGCAAAATTGTCAGGAAAAGACTGGCATT 2 90 0 GTCAGGAAAA 0.80762 -109 TGGACGAATTGTTAGAAAACGCAAAATTGT 2 108 0 GTTAGAAAAC 0.802771 -91 GCCAACAATCTCAAAAGATT 3 25 0 GCCAACAATC 0.898256 -10 AGATTATGGAGGCAAAAAACAGAAGTTGAA 6 26 0 GGCAAAAAAC 0.783931 -142 CCCGGCGATCGCCTGCTAACG 6 157 1 GCCTGCTAAC 0.816231 -11 AGTCATACCCGCCAGCAAAAAAATTACAAT 8 20 0 GCCAGCAAAA 0.955368 -281 AGGATGGAATGTCAGCAACCGTCACCTGCC 8 100 1 GTCAGCAACC 0.97163 -201 TGCGGGGTAAGTCTCCAAACATCGTGGGTT 8 174 1 GTCTCCAAAC 0.853462 -127 TATGGAGTAGGTTAACAACCCACGATGTTT 8 190 0 GTTAACAACC 0.818844 -111 ********** Masking position 8 Map Score: 1.32237 Number of sites scoring better than the average of aligned sites = 1379 Number in coding regions = 1229 Number in noncoding regions = 150 Number of orfs with sites within 600 bp upstream = 155 Fraction of orfs with sites within 600 bp upstream = 0.0248956 Motif number 8 ********** No masking Map Score: -1.82309e-13 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 9 ********** No masking Map Score: -1.82309e-13 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 10 ********** No masking Map Score: -1.82309e-13 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