AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i255_heat_shock_synecho_reg_100.orf -o255_synecho_100.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 RCY18467 300 Synechocystis #2 RCY52233 205 Synechocystis #3 RCY00997 233 Synechocystis #4 RCY02791 295 Synechocystis #5 RCY10850 106 Synechocystis Motif number 1 AACTAATCTTTGACCCCCTGGAGAGGTGG 1 5 1 ATTTCCCCCT 0.925747 -296 TGGCAGAGTGGTCGAATGCGCCCGACTTGAAATCG 1 37 1 GCATGCCCGA 0.901821 -264 TCGAACCCACGTTGAGTTTCCCCAAACCCGATTTC 1 65 0 GTATCCCCAA 0.885777 -236 TTTAACATCTAGTCTTTAGCCCGCAATTTAGGAAA 1 274 1 ATTTCCCGCA 0.710195 -27 TGCGTGGCGTTAACTCCCCTTTTGACCAAT 2 6 1 GCTATCCCCT 0.90268 -200 AATGGCATACGGCTAGATGCCCCCATAGGTACGGA 2 38 1 GCAACCCCCA 0.981703 -168 CTGCACTTCCGAGAACTAAGCCCCTACCGTCACTA 2 76 1 GGATGCCCCT 0.94173 -130 TAAGAGTGTGAACGTGTCGGCCCCAGGCAATGGAT 2 111 1 ACTTGCCCCA 0.976609 -95 TTGGAACCATGGCTTTTCGGCCCATCGTTGTGTCT 2 145 1 GCTTGCCCAT 0.95325 -61 ACGAGGGACAGTGGAATGTCCCCCAAAATGACTGA 3 14 0 GGATCCCCCA 0.964581 -220 CCACTTGGCCATCCTTAGAGCCCATTTTATATTCC 3 121 0 ACTAGCCCAT 0.784171 -113 TGCAAATTTAGACCATTAAGCCCCACTTGGCCATC 3 143 0 GCATGCCCCA 0.988555 -91 GCCCTACGAAATTATTTTTCCCCCTTCGGCAATAA 4 15 0 ATTTCCCCCT 0.925747 -281 AAATAACATCGTCATAACTCCCGATCGGATTCGGA 4 211 1 GCTACCCGAT 0.661572 -85 CCAGATGGTTGCCCAGAAATCCCCACCTCCGCATC 5 11 0 GCAATCCCCA 0.90268 -96 TTACTGTAGCAAACTCTCGCCCCCAGATGGTTGCC 5 33 0 AATTCCCCCA 0.828361 -74 * * * * ****** Masking position 11 Map Score: 15.4337 Number of sites scoring better than the average of aligned sites = 3514 Number in coding regions = 3082 Number in noncoding regions = 432 Number of orfs with sites within 600 bp upstream = 402 Fraction of orfs with sites within 600 bp upstream = 0.0645679 Motif number 2 TTGGGGAAACTCAACGTGGGTTCGAATCCC 1 75 1 TCAACGTGGG 0.954851 -226 ACTCCCCTTTTGACCAATGGCATACGGCTA 2 23 1 TGACCAATGG 0.969705 -183 AATATAAGACACAACGATGGGCCGAAAAGC 2 156 0 ACAACGATGG 0.966005 -50 CGCCGAAAATAGAACGAGGGACAGTGGAAT 3 32 0 AGAACGAGGG 0.903565 -202 TACCTAGAAGTCACCAATTGTTTTTCGGGG 3 205 1 TCACCAATTG 0.907744 -29 TCACCGATGGTCACCATTGGCTAGGGAATA 4 122 0 TCACCATTGG 0.970413 -174 TTGTGAATAATCACCGATGGTCACCATTGG 4 132 0 TCACCGATGG 0.993023 -164 ********** Masking position 3 Map Score: 5.84511 Number of sites scoring better than the average of aligned sites = 543 Number in coding regions = 502 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 3 CGTTCTATTTTCGGCGTTTTCAGTCTTGCA 3 46 1 TCGGCGTTTT 0.989146 -188 CCTGGAGTGATCGGAGTTTTTGCAAGACTG 3 66 0 TCGGAGTTTT 0.990862 -168 ATGGTGACCATCGGTGATTATTCACAATGA 4 135 1 TCGGTGATTA 0.909231 -161 CCGATCGGATTCGGAGTTTTTTTCAGGTCG 4 231 1 TCGGAGTTTT 0.990862 -65 AATGCGTCGATGTTTTGCTTAACAAT 5 91 0 TCGATGTTTT 0.954081 -16 ********** Masking position 8 Map Score: 5.3631 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 37 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 4 CGACTTGAAATCGGGTTTGGGGAAACTCAA 1 59 1 TCGGGTTTGG 0.984347 -242 GATAGATAAATTGGGTTCAGAGTTAAAAGT 1 230 0 TTGGGTTCAG 0.916325 -71 ACGGTTGTTGTCGGGATAGATAAATTGGGT 1 244 0 TCGGGATAGA 0.862337 -57 CAATTGTTTTTCGGGGTCAGCAGTT 3 219 1 TCGGGGTCAG 0.985914 -15 ATCATACGAATCTGGGTAGGTCTTGCTATG 4 86 0 TCTGGGTAGG 0.944712 -210 TAACTCCCGATCGGATTCGGAGTTTTTTTC 4 225 1 TCGGATTCGG 0.969874 -71 TTTTTTCAGGTCGGGTTACGCTTAGATAAA 4 248 1 TCGGGTTACG 0.978322 -48 ********** Masking position 7 Map Score: 4.39566 Number of sites scoring better than the average of aligned sites = 424 Number in coding regions = 382 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 5 ATCTTTGACCCCCTGGAGAGGTGGCAGAGT 1 16 1 CCCTGGAGAG 0.971182 -285 TGCTGGTGTGCCCTGGATTATATCCCATCA 1 138 0 CCCTGGATTA 0.976665 -163 AAAATAATTACCCAGGATTTGCTTGGGCCG 1 169 0 CCCAGGATTT 0.947963 -132 CGGCCCCAGGCAATGGATTGGAACCATGGC 2 128 1 CAATGGATTG 0.889653 -78 TGGATTGGAACCATGGCTTTTCGGCCCATC 2 141 1 CCATGGCTTT 0.901218 -65 CATTCTTCGACCCTGGAGTGATCGGAGTTT 3 77 0 CCCTGGAGTG 0.99164 -157 ********** Masking position 5 Map Score: 3.0657 Number of sites scoring better than the average of aligned sites = 561 Number in coding regions = 507 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 6 CAGCAACGGCCCAAGCAAATCCTGGGTAAT 1 163 1 CCAAGCAAAT 0.973099 -138 ACGTGTCGGCCCCAGGCAATGGATTGGAAC 2 122 1 CCCAGGCAAT 0.961841 -84 CTTAAATTTTCCTAGAAAATACCTAGAAGT 3 186 1 CCTAGAAAAT 0.971022 -48 GTGCCGTTGCCCTACGAAATTATTTTTCCC 4 28 0 CCTACGAAAT 0.922387 -268 TCCTCCTCTTCCAAGAAAAGCCGTGCCGTT 4 50 0 CCAAGAAAAG 0.895297 -246 TAAACTATTCCCTAGCCAATGGTGACCATC 4 117 1 CCTAGCCAAT 0.977255 -179 ********** Masking position 4 Map Score: 2.27658 Number of sites scoring better than the average of aligned sites = 488 Number in coding regions = 416 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 7 AATCCTGGGTAATTATTTTATAATCTAATT 1 180 1 AATTATTTTA 0.947702 -121 TTTATAATCTAATTTTTTTAAGAATCCTTT 1 196 1 AATTTTTTTA 0.877672 -105 AGAAGTCACCAATTGTTTTTCGGGGTCAGC 3 210 1 AATTGTTTTT 0.938393 -24 TGCCCTACGAAATTATTTTTCCCCCTTCGG 4 21 0 AATTATTTTT 0.962573 -275 AAGCCTTGTCAATTATTGTTAAGCAAAACA 5 77 1 AATTATTGTT 0.92093 -30 ********** Masking position 6 Map Score: 1.1224 Number of sites scoring better than the average of aligned sites = 147 Number in coding regions = 111 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 8 TTCGACCACTCTGCCACCTCTCCAGGGGGTC 1 22 0 CTCCACCTCT 0.986453 -279 AGTCGGGCGCATTCGACCACTCTGCCACCTC 1 33 0 ATCGACCACT 0.959942 -268 CCTGGATTATATCCCATCAATTAAAAGTGAA 1 126 0 ATCCATCAAT 0.818731 -175 AACTAAGCCCCTACCGTCACTATAAGAGTGT 2 89 1 CTCCGTCACT 0.974952 -117 CTTGCAAAAACTCCGATCACTCCAGGGTCGA 3 70 1 CTCGATCACT 0.978337 -164 GCTATGACATCTTCCTCCTCTTCCAAGAAAA 4 61 0 CTCCTCCTCT 0.956771 -235 ** ******** Masking position 2 Map Score: 0.994359 Number of sites scoring better than the average of aligned sites = 494 Number in coding regions = 472 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 9 TGCGCCCGACTTGAAATCGGGTTTGGGGAAA 1 53 1 TTGAATCGGG 0.983585 -248 GTTAAAACGGTTGTTGTCGGGATAGATAAAT 1 249 0 TTGTGTCGGG 0.989498 -52 ATATTCTTACTTGTTAACGGGAGTTAATTAA 2 181 1 TTGTAACGGG 0.969801 -25 CAATTTATTGCCGAAGGGGGAAAAATAA 4 8 1 TTGCGAAGGG 0.92357 -288 AAAACTCCGAATCCGATCGGGAGTTATGACG 4 220 0 ATCCATCGGG 0.922787 -76 CGGAGTTTTTTTCAGGTCGGGTTACGCTTAG 4 242 1 TTCAGTCGGG 0.980098 -54 **** ****** Masking position 2 Map Score: 2.0126 Number of sites scoring better than the average of aligned sites = 369 Number in coding regions = 342 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 10 ********** No masking Map Score: 3.21409e-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: 3.21409e-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: 3.21409e-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