AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i255_synecho_ctra_100.orf -o255_synecho_ctra_100.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 RCY18467 300 Synechocystis #2 RCY52233 205 Synechocystis #3 RCY00997 233 Synechocystis #4 RCY02791 295 Synechocystis #5 RCY10850 106 Synechocystis #6 RCT00326 28 Chlamydia_trachomatis #7 RCT00843 196 Chlamydia_trachomatis #8 RCT00373 300 Chlamydia_trachomatis #9 RCT00374 86 Chlamydia_trachomatis #10 RCT00376 25 Chlamydia_trachomatis Motif number 1 AACTAATCTTTGACCCCCTGGAGAGGTGGCA 1 1 1 AACTACCCCG 0.990861 -300 AACCCAATTTATCTATCCCGACAACAACCGTTTTAACATCT 1 243 1 ATCTACACCT 0.940747 -58 CCGTTTTAACATCTAGTCTTTAGCCCGCAATTTAGGAAACA 1 270 1 ATCTACCCCT 0.993863 -31 CTATGGGGGCATCTAGCCGTATGCCATTGGTCAAAAGGGGA 2 25 0 ATCTACCCTT 0.988014 -181 CACTTCCGAGAACTAAGCCCCTACCGTCACTATAAGAGTGT 2 79 1 AACTACCCCT 0.99245 -127 GTATGATGTAAACTATTCCCTAGCCAATGGTGACCATCGGT 4 109 1 AACTACCCTT 0.985274 -187 TGTACACTTTATCTAAGCGTAACCCGACCTGAAAAAAACTC 4 244 0 ATCTACCCCG 0.99257 -52 AAAGAATCTGAACTAGTTAAAATCCAATAAGAACAAAAAAA 8 37 1 AACTATCCTG 0.860388 -264 ACAGAGATTGATCTAGAAACACTCCTATGCTAAGATGCTCT 8 80 1 ATCTAACCTT 0.902008 -221 ***** * ** * * Masking position 5 Map Score: 8.57938 Number of sites scoring better than the average of aligned sites = 93 Number in coding regions = 76 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 2 AATCTTTGACCCCCTGGAGAGGTGGCAGAG 1 15 1 CCCCTGGAGA 0.774138 -286 GGGATTCGAACCCACGTTGAGTTTCCCCAA 1 75 0 CCCACGTTGA 0.879802 -226 TAGCCGTATGCCATTGGTCAAAAGGGGAGT 2 23 0 CCATTGGTCA 0.927123 -183 GCTTTTCGGCCCATCGTTGTGTCTTATATT 2 156 1 CCATCGTTGT 0.899424 -50 ATTCCACTGTCCCTCGTTCTATTTTCGGCG 3 32 1 CCCTCGTTCT 0.932355 -202 TATTCCCTAGCCAATGGTGACCATCGGTGA 4 122 1 CCAATGGTGA 0.849955 -174 CCAATGGTGACCATCGGTGATTATTCACAA 4 132 1 CCATCGGTGA 0.961129 -164 CAATGATAATCCTCCGGTCTAGTTAACTGG 4 159 1 CCTCCGGTCT 0.96129 -137 GGTGTTACAATCCCCGGTCTCTTGTGCGTT 7 126 1 TCCCCGGTCT 0.852642 -71 AATAAAGAAGCCTCCGTTCTTTCCTACGAG 8 197 1 CCTCCGTTCT 0.901453 -104 AAAACCGTCTCCACTGGTCAAGAATTTTAG 9 30 0 CCACTGGTCA 0.96147 -57 ********** Masking position 2 Map Score: 7.84591 Number of sites scoring better than the average of aligned sites = 1444 Number in coding regions = 1314 Number in noncoding regions = 130 Number of orfs with sites within 600 bp upstream = 152 Fraction of orfs with sites within 600 bp upstream = 0.0244137 Motif number 3 CGTTCTATTTTCGGCGTTTTCAGTCTTGCA 3 46 1 TCGGCGTTTT 0.976063 -188 CCTGGAGTGATCGGAGTTTTTGCAAGACTG 3 66 0 TCGGAGTTTT 0.985819 -168 TGGTGACTTCTAGGTATTTTCTAGGAAAAT 3 191 0 TAGGTATTTT 0.813631 -43 CCGATCGGATTCGGAGTTTTTTTCAGGTCG 4 231 1 TCGGAGTTTT 0.985819 -65 AATGCGTCGATGTTTTGCTTAACAAT 5 91 0 TCGATGTTTT 0.949908 -16 CATCTTAGCATAGGAGTGTTTCTAGATCAA 8 87 0 TAGGAGTGTT 0.911944 -214 TAAATCCCTTTAGATGTTTTGAAAAGATAC 8 244 0 TAGATGTTTT 0.901782 -57 ********** Masking position 7 Map Score: 5.91323 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 61 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 4 GCGCATTCGACCACTCTGCCACCTCTCCAGGG 1 26 0 CCTCTGCCAC 0.951634 -275 TCTCCGCTTGCTTAACTTTCACTTTTAATTGA 1 109 1 CAACTTTCAC 0.857422 -192 GTACGGAAACCTGCACTTCCGAGAACTAAGCC 2 66 1 CCACTTCCGA 0.982158 -140 TGCCTGGGGCCGACACGTTCACACTCTTATAG 2 108 0 CCACGTTCAC 0.832768 -98 TGACATCTTCCTCCTCTTCCAAGAAAAGCCGT 4 56 0 CCTCTTCCAA 0.981415 -240 ATAACATCGTCATAACTCCCGATCGGATTCGG 4 213 1 CAACTCCCGA 0.783967 -83 GCCCAGAAATCCCCACCTCCGCATC 5 4 0 CCACCTCCGC 0.95351 -103 CTATGCTAAGATGCTCTTCCACACGAAACAAT 8 104 1 ACTCTTCCAC 0.880346 -197 TCCTGTTTTACAGAACTTCCAAAAATGCAAAT 8 168 1 CAACTTCCAA 0.956168 -133 CTCATACACACCTCTCTTCCAACGAGTTATCC 8 274 1 CCTCTTCCAA 0.981415 -27 * ********* Masking position 6 Map Score: 5.53415 Number of sites scoring better than the average of aligned sites = 924 Number in coding regions = 877 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 5 CCCACGTTGAGTTTCCCCAAACCCGATTTCA 1 64 0 GTTCCCCAAA 0.937163 -237 TGTTTCCTAAATTGCGGGCTAA 1 289 0 GTTCCTAAAT 0.863855 -12 ACAGTGGAATGTCCCCCAAAATGACTGAGTA 3 11 0 GTCCCCAAAA 0.945297 -223 AAGACTTAAATTTTCCTAGAAAATACCTAGA 3 182 1 TTTCCTAGAA 0.955469 -52 CCCCCAGATGGTTGCCCAGAAATCCCCACCT 5 18 0 GTGCCCAGAA 0.944244 -89 TGAAAAGTTGTTGTCCCAAAAGGAAAACACT 7 11 0 TTTCCCAAAA 0.972484 -186 TTCCAACGAGTTATCCTAAAA 8 290 1 TTTCCTAAAA 0.957075 -11 TTATCCTAGAAATTAGGTGTT 10 1 1 TTTCCTAGAA 0.956246 -25 ** ******** Masking position 10 Map Score: 4.33955 Number of sites scoring better than the average of aligned sites = 190 Number in coding regions = 137 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 6 ATCGGGTTTGGGGAAACTCAACGTGGGTTCGA 1 68 1 GGGAAACCAC 0.978084 -233 TCAAAAGGGGAGTTAACGCCACGCA 2 4 0 AGTTAACCAC 0.976841 -202 TAGTGCGGCCAGTTAACTAGACCGGAGGATTA 4 165 0 AGTTAACAAC 0.92004 -131 CTTTATCTAAGCGTAACCCGACCTGAAAAAAA 4 247 0 GCGTAACCAC 0.935329 -49 AGTTTGCTACAGTAAACACTACAGAAGCCTTG 5 53 1 AGTAAACCAC 0.982118 -54 GACGAAACACCACTAACAAAGAT 6 16 0 ACGAAACCAC 0.965501 -13 TTACCAAACAAGTAAACAAAACTCTTGAAAAG 7 35 0 AGTAAACAAC 0.937431 -162 ******* * ** Masking position 6 Map Score: 4.30793 Number of sites scoring better than the average of aligned sites = 90 Number in coding regions = 76 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 7 CTTTTAACTCTGAACCCAATTTATCTATCCCG 1 231 1 TGAACCATTT 0.852495 -70 TGCGTGGCGTTAACTCCCCTTTTGACCAATGG 2 11 1 TAACCCCTTT 0.97907 -195 AATTTTAATTAACTCCCGTTAACAAGTAAGA 2 185 0 TAACCCCTTA 0.961406 -21 TGGCCATCCTTAGAGCCCATTTTATATTCCCA 3 119 0 TAGACCCTTT 0.922697 -115 CCGGGGATTGTAACACCACTTTTATTTAGGCT 7 111 0 TAACCCATTT 0.957771 -86 CGTTATTAAATAAAACCAATTACGTATTAAGG 7 169 1 TAAACCATTA 0.935106 -28 TGTGTATGAGTAAATCCCTTTAGATGTTTTGA 8 252 0 TAAACCCTTA 0.957974 -49 **** *** *** Masking position 10 Map Score: 3.4915 Number of sites scoring better than the average of aligned sites = 79 Number in coding regions = 61 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 8 CACACCAGCAACGGCCCAAGCAAATCCTGG 1 158 1 ACGGCCCAAG 0.981285 -143 ATACGGCTAGATGCCCCCATAGGTACGGAA 2 44 1 ATGCCCCCAT 0.928463 -162 TGTGAACGTGTCGGCCCCAGGCAATGGATT 2 117 1 TCGGCCCCAG 0.995164 -89 TAGCAAACTCTCGCCCCCAGATGGTTGCCC 5 32 0 TCGCCCCCAG 0.995223 -75 ********** Masking position 9 Map Score: 0.595354 Number of sites scoring better than the average of aligned sites = 123 Number in coding regions = 110 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 9 AAACCCGATTTCAAGTCGGGCGCATTCGAC 1 47 0 TCAAGTCGGG 0.962684 -254 CGACTTGAAATCGGGTTTGGGGAAACTCAA 1 59 1 TCGGGTTTGG 0.906816 -242 ATGATAATCCTCCGGTCTAGTTAACTGGCC 4 161 1 TCCGGTCTAG 0.947023 -135 AAACTCCGAATCCGATCGGGAGTTATGACG 4 220 0 TCCGATCGGG 0.904156 -76 GGAGTTTTTTTCAGGTCGGGTTACGCTTAG 4 243 1 TCAGGTCGGG 0.990502 -53 ********** Masking position 6 Map Score: 0.327855 Number of sites scoring better than the average of aligned sites = 178 Number in coding regions = 163 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 10 CAAGCAAATCCTGGGTAATTATTTTATAATCTAAT 1 174 1 CTAATTTTTT 0.970409 -127 ATACCTAGAAGTCACCAATTGTTTTTCGGGGTCAG 3 204 1 GTAATTTTTT 0.826539 -30 TGCCGTTGCCCTACGAAATTATTTTTCCCCCTTCG 4 22 0 CTAATTTTTT 0.970409 -274 TCACCATTGGCTAGGGAATAGTTTACATCATACGA 4 107 0 CTAATATTTA 0.80755 -189 CTACAGAAGCCTTGTCAATTATTGTTAAGCAAAAC 5 71 1 CTAATTTTGT 0.884555 -36 CGAAACACCACTAACAAAGATTTTTT 6 2 0 CTAAGATTTT 0.956438 -27 GGGACAACAACTTTTCAAGAGTTTTGTTTACTTGT 7 25 1 CTAAGATTTT 0.956438 -172 CTAGATCAATCTCTGTGATTTTTTTGTTCTTATTG 8 61 0 CTGATTTTTT 0.884555 -240 ACCGTCTCCACTGGTCAAGAATTTTAGCGCTCGCA 9 22 0 CTAAGATTTT 0.956438 -65 ** **** **** Masking position 8 Map Score: 3.70067 Number of sites scoring better than the average of aligned sites = 98 Number in coding regions = 74 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 11 GATGGGATATAATCCAGGGCACACCAGCAA 1 139 1 AATCCAGGGC 0.986002 -162 GGCCCAAGCAAATCCTGGGTAATTATTTTA 1 170 1 AATCCTGGGT 0.962716 -131 CCATGGTTCCAATCCATTGCCTGGGGCCGA 2 127 0 AATCCATTGC 0.828659 -79 ATGGGCCGAAAAGCCATGGTTCCAATCCAT 2 140 0 AAGCCATGGT 0.932378 -66 AACTCCGATCACTCCAGGGTCGAAGAATGG 3 78 1 ACTCCAGGGT 0.968673 -156 GTGGTGTTACAATCCCCGGTCTCTTGTGCG 7 124 1 AATCCCCGGT 0.934546 -73 ********** Masking position 1 Map Score: 0.578157 Number of sites scoring better than the average of aligned sites = 359 Number in coding regions = 334 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 12 GTGGGTTCGAATCCCACCCTCTCCGCTTGCTTAA 1 90 1 ATCCCCCTCC 0.99123 -211 GTGGCGTTAACTCCCCTTTTGACCAATGGCATAC 2 14 1 CTCCCTTTCC 0.799736 -192 TAGACCATTAAGCCCCACTTGGCCATCCTTAGAG 3 136 0 AGCCCCTTCC 0.985081 -98 AAGATGTCATAGCAAGACCTACCCAGATTCGTAT 4 79 1 AGCAACCTCC 0.976557 -217 GTTAACTGGCCGCACTAACTTACCTGAATTGAAA 4 180 1 CGCACACTCC 0.941071 -116 TTGCCCAGAAATCCCCACCTCCGCATC 5 4 0 ATCCCCCTGC 0.949255 -103 TGTTTACTGTAGCAAACTCTCGCCCCCAGATGGT 5 37 0 AGCAATCTCC 0.919161 -70 AACAATATAAAGCACTTCCTTCCCTATGAGAATG 8 130 1 AGCACCCTCC 0.994544 -171 ***** *** ** Masking position 10 Map Score: 2.73975 Number of sites scoring better than the average of aligned sites = 527 Number in coding regions = 457 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 13 ********** No masking Map Score: 3.58357e-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: 3.58357e-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 15 ********** No masking Map Score: 3.58357e-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