AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i013_synecho_ctra_300.orf -o013_synecho_ctra_300.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 RCY22255 300 Synechocystis #2 RCY49058 126 Synechocystis #3 RCY53506 106 Synechocystis #4 RCY17695 300 Synechocystis #5 RCY44898 206 Synechocystis #6 RCY48136 300 Synechocystis #7 RCY07219 86 Synechocystis #8 RCY02847 174 Synechocystis #9 RCY27715 133 Synechocystis #10 RCT00174 300 Chlamydia_trachomatis #11 RCT00177 116 Chlamydia_trachomatis #12 RCT00178 24 Chlamydia_trachomatis #13 RCT00359 112 Chlamydia_trachomatis #14 RCT00361 28 Chlamydia_trachomatis #15 RCT00362 68 Chlamydia_trachomatis #16 RCT00363 300 Chlamydia_trachomatis Motif number 1 CTGCCTGCATCTTACAACGAAAAACCCCACCAG 2 77 0 CACACGAAAA 0.689912 -50 AGGTAAGGGCCCACCAAGAAGGGAAATCTGCC 2 105 0 CACCAGAAGG 0.678349 -22 AAAACTTTGCCAGAAAAAGAAAACTTTCGGGAA 3 35 1 CAAAAGAAAA 0.877948 -72 CCCGCAACACCAACCCCAGAAAATTCCCTCGGA 4 140 0 CCCCAGAAAA 0.894395 -161 GGACGAAACCTAAAGGGAAAACAGCTTTGAT 5 9 1 CAAAGGAAAA 0.872691 -198 TCCTCCACCTGGGCCAGAGGAAATTAACCGTTA 5 53 0 GCCAAGGAAA 0.723532 -154 CTAAAACTTGCTGAAACGGGAGAATTTTAGCTT 5 104 1 CAAAGGGAGA 0.862456 -103 CGAGGAAAGGGTCACCAAGCAAAAAGCTAAAAT 5 127 0 GACCAGCAAA 0.578669 -80 AGCAGTTTAGGTCACCGAGGAAAGGGTCACCAA 5 142 0 GACCAGGAAA 0.837034 -65 CCACTGAGCTACAAGGGCAAAAGGGATGGGC 6 9 1 CCAAGGCAAA 0.567849 -292 AAAAATCTGACCAACCCAGAAAAAAATATTTTG 6 163 0 CACCAGAAAA 0.938697 -138 GTAACCAATCCCGACACAGGAAGCGATTCCCAG 6 206 0 CACAAGGAAG 0.78108 -95 AATTCCTTTACCTAAACGGGAAACGACTCCAAG 7 22 1 CAAAGGGAAA 0.898832 -65 GTCAAGGCTTCAGACCTGGAAAAAAAC 8 5 0 CACCGGAAAA 0.935866 -170 CATCTGGAGTCGAAACAAGGAAAGACGCCCCAG 8 89 1 CAACAGGAAA 0.910074 -86 ACCCGACCATCCTAACAAGGAGATCGTTAACAA 10 180 0 CAACAGGAGA 0.877188 -121 TATCACATTTCCTCAAAAGGAGAATC 13 97 1 CCAAAGGAGA 0.78445 -16 GTTCTCTTCTCTTCAAGAGAAGAGGGCGTTTTT 16 186 1 CCAAAGAAGA 0.737389 -115 GCAAATCATACACACAGGGAAGAGAAAAGAAAT 16 238 0 CACAGGAAGA 0.904648 -63 GTTAAGAGAAGAAACAAGGAAAACAAATCTA 16 280 1 GACAGGAAAA 0.776738 -21 * *** ****** Masking position 11 Map Score: 16.529 Number of sites scoring better than the average of aligned sites = 1500 Number in coding regions = 1317 Number in noncoding regions = 183 Number of orfs with sites within 600 bp upstream = 195 Fraction of orfs with sites within 600 bp upstream = 0.0313203 Motif number 2 AGTTGACAATTTTCTTTAGATTCATGGTAG 1 158 0 TTTCTTTAGA 0.870315 -143 ATTGTACACGTTTTTTTCGAAAGAGTGGGA 1 190 0 TTTTTTTCGA 0.836316 -111 TTCAAACAAGTGTCTTAAGAAGACGGACTC 2 15 0 TGTCTTAAGA 0.945022 -112 TCTTTCTAATTGTCTTAAGATGTGAACGCA 4 241 1 TGTCTTAAGA 0.945022 -60 ATCTTAATACTTTTTTAAGATTTTCACAGA 9 41 1 TTTTTTAAGA 0.957034 -93 TATTTGATTATTTTTCACGAATGAAACGCG 10 102 0 TTTTTCACGA 0.793096 -199 GGCAAAGCCATGTTTTATGAGAGAGAAATC 11 21 1 TGTTTTATGA 0.767109 -96 AGAGTGTTAATTTTTTAAGAGAGAGCCCAC 11 82 0 TTTTTTAAGA 0.957034 -35 ATTCTTATTTTTTTTAAGAATCATGTTGG 15 10 1 TTTTTTAAGA 0.957034 -59 ATTTCAAGCTTTTCTTACGACGCTGATAGA 16 102 1 TTTCTTACGA 0.952184 -199 ********** Masking position 5 Map Score: 9.53651 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 29 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 3 ATTTTTAGCTTTTCCTCACACCTAATAATGA 1 252 0 TTTCCCACAC 0.948359 -49 GAAAGAAATTTTTCCTGAAAACTTTGCCAGA 3 18 1 TTTCCGAAAA 0.945708 -89 CCTGAAAACTTTGCCAGAAAAAGAAAACTTT 3 31 1 TTGCCGAAAA 0.848939 -76 CGCCAAGGCTTTTCCCGCAACACCAACCCCA 4 155 0 TTTCCGCAAC 0.936861 -146 CAGGAAGCGATTCCCAGCAAACCAGACAAAA 6 192 0 TTCCCGCAAA 0.82421 -109 GTTTTTCTAATTTCCTCACACCTGTCCTAAG 8 59 0 TTTCCCACAC 0.948359 -116 ATTTCCTCCGAAAATAAGCTAG 9 2 1 TTTCCCCGAA 0.839039 -132 TAAATTAGCCTTTCCGGACAAGGCCTCTGTG 9 65 0 TTTCCGACAA 0.969159 -69 CCGACCGGGATTTCCAGACCAGTTTGAACAG 9 99 0 TTTCCGACCA 0.888085 -35 TCGTATCACATTTCCTCAAAAGGAGAATC 13 94 1 TTTCCCAAAA 0.952045 -19 ***** ***** Masking position 2 Map Score: 6.68509 Number of sites scoring better than the average of aligned sites = 326 Number in coding regions = 253 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 4 ACAGACCAATGGCCTTGCTTAGCCTAGCATCTACCAT 1 128 1 GGTTGCCCAG 0.957121 -173 ACTGAGTATAGGACTTGGTTCCCGTAGTCATTATTAG 1 225 1 GGTTGGCGAG 0.98261 -76 AGGTAAGGGCCCACCAAGAAGGGAAATC 2 109 0 GGAGGGCCAG 0.968922 -18 AGCCATAACTGGGATGGGATGTGGAGGGGCATAGGAG 4 18 1 GGTGGGGGGG 0.990927 -283 GGAATTTTCTGGGGTTGGTGTTGCGGGAAAAGCCTTG 4 146 1 GGTTGGGCGG 0.994914 -155 GTCTTTTAGCAGTTTAGGTCACCGAGGAAAGGGTCAC 5 145 0 AGTAGGCGGG 0.826144 -62 AAGGGCAAAAGGGATGGGCCGAGCTGGATTTGAACCA 6 23 1 GGTGGGGCGG 0.99384 -278 TAAATCCGCTGGCTATGCCTACGCTGGTTCAAATCCA 6 47 0 GGATGCGCGG 0.959488 -254 TTCCTGTGTCGGGATTGGTTACCCTAGGATTGGCTCG 6 217 1 GGTTGGCCAG 0.988162 -84 CCACAGATGAAGCAATGGCGCTGGCGGATGGTA 8 152 1 AGATGGGGGG 0.912004 -23 ** **** ** ** Masking position 7 Map Score: 7.06002 Number of sites scoring better than the average of aligned sites = 1518 Number in coding regions = 1441 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 5 GTTGGTAAAGAAAAACCGCCTACAGCTTCT 1 60 0 AAAAACCGCC 0.946598 -241 GCTAGCCCGCAAAACAGACCAATGGCCTTG 1 115 1 AAAACAGACC 0.810164 -186 AATAACTCTTTAACCCCGCCTCTGGTGGGG 2 56 1 TAACCCCGCC 0.950107 -71 TTACAACGAAAAACCCCACCAGAGGCGGGG 2 69 0 AAACCCCACC 0.981846 -58 AATGGGTCTGAAACCCCGCCCTTGAGGACG 4 275 0 AAACCCCGCC 0.990677 -26 TGCCACTATTAAACCACGGCACCGAGCCAA 6 246 0 AAACCACGGC 0.887114 -55 AATTGCCATAAAAAAACACCTGGGGCGTCT 8 111 0 AAAAAACACC 0.821176 -64 CTAGTACACAGAACCCGACCATCCTAACAA 10 195 0 GAACCCGACC 0.813971 -106 TTTTCAATGAAAAAAACGCCCTCTTCTCTT 16 200 0 AAAAAACGCC 0.90022 -101 ********** Masking position 3 Map Score: 5.64301 Number of sites scoring better than the average of aligned sites = 642 Number in coding regions = 576 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 6 TGAAACCCCGCCCTTGAGGACGGCCTTGCGT 4 266 0 CCCTGAGGAC 0.850071 -35 AAGCTGTTTTCCCTTTAGGTTTCGTCC 5 7 0 CCCTTAGGTT 0.84001 -200 TTTCCTCTGGCCCAGGTGGAGGAACTGCTCT 5 63 1 CCCGGTGGAG 0.973044 -144 TGGGTCGATGCCCGAGTGGTTAATGGGGGCG 6 89 0 CCCAGTGGTT 0.949 -212 ATTATCCATTCCCCAGAGGTTTCC 7 73 1 CCCAGAGGTT 0.948992 -14 CCTTGACAATCCCCGTTGGTGATTTATACTT 8 31 1 CCCGTTGGTG 0.957071 -144 GGAAAGACGCCCCAGGTGTTTTTTTATGGCA 8 107 1 CCCGGTGTTT 0.876662 -68 GAAGCAATGGCGCTGGCGGATGGTA 8 160 1 CGCGGCGGAT 0.890906 -15 GTCTGGAAATCCCGGTCGGTCGGGCCATGGT 9 111 1 CCCGTCGGTC 0.927567 -23 ACGAATGAAACGCGGGAGGTGTCGAATATAG 10 85 0 CGCGGAGGTG 0.955197 -216 *** ******* Masking position 3 Map Score: 4.53976 Number of sites scoring better than the average of aligned sites = 1580 Number in coding regions = 1522 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 7 ACGATGATGTTGATGGTTAATAACAGATTA 1 21 0 TGATGGTTAA 0.978102 -280 CCACAATCAGTGTTGGTAAAGAAAAACCGC 1 71 0 TGTTGGTAAA 0.855199 -230 GGTGACTATTTGTTGGTTCACTTAGGAATT 4 54 1 TGTTGGTTCA 0.880467 -247 GACAGAACTTTGGTGGTTAACCACACACTG 4 87 1 TGGTGGTTAA 0.952655 -214 TAAGGTGTTATGATGGCTAATCGTGAAAGC 6 122 0 TGATGGCTAA 0.932175 -179 ACCTTATTGTTGATGGTCAAAATATTTTTT 6 146 1 TGATGGTCAA 0.942304 -155 TGAATAATCTTGATTGTTAACGATCTCCTT 10 167 1 TGATTGTTAA 0.852805 -134 ********** Masking position 10 Map Score: 3.63423 Number of sites scoring better than the average of aligned sites = 153 Number in coding regions = 136 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 8 TTTCAGGAAAAATTTCTTTCTCAGTTC 3 7 0 AATTCTTTCT 0.893917 -100 CCTGTTTAATAAAATCTTTCTAATTGTCTTA 4 227 1 AAATCTTTCT 0.958362 -74 CTAGATATTTACAAGCCTTCTCATAGGCTCT 10 46 1 ACAGCCTTCT 0.904569 -255 TCACAGAGCTACTAGCTTTCTTAACTTATTG 10 139 0 ACAGCTTTCT 0.972816 -162 TATGTGCCTAAAAAGATTTCTCTCTCATAAA 11 34 0 AAAGATTTCT 0.715855 -83 TTTTACTTGTACTATCTTTCGTGATCTTTCG 13 49 0 ACATCTTTCG 0.906519 -64 GATACGAGAGACCTTCTTTCTTTTTACTTGT 13 70 0 ACTTCTTTCT 0.930391 -43 TTTTCATTGAAAAATCTTTCTATTTCTTTTC 16 217 1 AAATCTTTCT 0.958362 -84 ** ******** Masking position 1 Map Score: 3.41041 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 36 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 9 CAGAAAATTCCCTCGGAGCAAAATGGGGCA 4 127 0 CCTCGGAGCA 0.931232 -174 TTAGCTTTTTGCTTGGTGACCCTTTCCTCG 5 130 1 GCTTGGTGAC 0.941541 -77 GTGACCCTTTCCTCGGTGACCTAAACTGCT 5 145 1 CCTCGGTGAC 0.990486 -62 CCTAGGATTGGCTCGGTGCCGTGGTTTAAT 6 239 1 GCTCGGTGCC 0.988547 -62 CCGGACAAGGCCTCTGTGAAAATCTTAAAA 9 53 0 CCTCTGTGAA 0.957214 -81 AAAGCTAGTAGCTCTGTGAATAATCTTGAT 10 151 1 GCTCTGTGAA 0.957214 -150 ********** Masking position 3 Map Score: 2.95426 Number of sites scoring better than the average of aligned sites = 66 Number in coding regions = 59 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 10 TTTTAGCTTTTCCTCACACCTAATAATGACT 1 250 0 TCTCACACCT 0.942841 -51 ACAGCTTTGATCGTAACCCATTTAACGGTTA 5 31 1 TCTAACCCAT 0.93734 -176 CGATTAGCCATCATAACACCTTATTGTTGAT 6 129 1 TCTAACACCT 0.971219 -172 TTTTCTAATTTCCTCACACCTGTCCTAAGTA 8 57 0 TCTCACACCT 0.942841 -118 GTAAATAACATCATAAATCATACACTTCTAG 10 19 1 TCTAAATCAT 0.833936 -282 CTACTAGCTTTCTTAACTTATTGGATAATGT 10 131 0 TCTAACTTAT 0.714296 -170 GATTTCTCTCTCATAAAACATGGCTTTGCCA 11 20 0 TCTAAAACAT 0.889577 -97 AGAAGGTCTCTCGTATCACATTTCCTCAAAA 13 84 1 TCTATCACAT 0.865761 -29 TTGTTTCTTCTCTTAACTCATGAACAGCAAA 16 266 0 TCTAACTCAT 0.962268 -35 ** ******** Masking position 4 Map Score: 5.64674 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 36 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 11 TTAAAATAACTCACAATTCCCGAAAGTTTT 3 54 0 TCACAATTCC 0.976284 -53 AAAGTTCTGTCCAAAATTCCTAAGTGAACC 4 68 0 CCAAAATTCC 0.916863 -233 AAGGCTTTTCCCGCAACACCAACCCCAGAA 4 152 0 CCGCAACACC 0.884505 -149 AGAAATTCCACAATTCCTTTACCTAAA 7 8 1 CCACAATTCC 0.988375 -79 AAGAGAGAGCCCACAATACCAAAAAAACGA 11 66 0 CCACAATACC 0.973676 -51 TCGTGATCTTTCGCGATTCCATTTTTGTAG 13 32 0 TCGCGATTCC 0.894998 -81 GTCTCTCGTATCACATTTCCTCAAAAGGAG 13 89 1 TCACATTTCC 0.895249 -24 ********** Masking position 2 Map Score: 4.01409 Number of sites scoring better than the average of aligned sites = 326 Number in coding regions = 302 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 12 ATCTTAAGACAATTAGAAAGATTTTATTAAACA 4 229 0 AATAAAGATT 0.961423 -72 AGATGGAGGGGAAAAACAAGATTATCCATTCCC 7 53 1 GAAAAAGATT 0.897933 -34 AATCTTAAAAAAGTATTAAGATTTTAAAAGCTA 9 30 0 AATAAAGATT 0.961423 -104 GGAGATCGTTAACAATCAAGATTATTCACAGAG 10 162 0 AAAAAAGATT 0.939524 -139 ACGAATATGTGCCTAAAAAGATTTCTCTCTCAT 11 37 0 GCTAAAGATT 0.789409 -80 AAGATAGTACAAGTAAAAAGAAAGAAGGTCTCT 13 62 1 AATAAAGAAA 0.620505 -51 TGATTCTTAAAAAAAATAAGAAT 15 1 0 AAAAAAGAAT 0.850467 -68 AAGAGAAAAGAAATAGAAAGATTTTTCAATGAA 16 219 0 AATAAAGATT 0.961424 -82 ** ** ****** Masking position 8 Map Score: 0.461945 Number of sites scoring better than the average of aligned sites = 62 Number in coding regions = 45 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 13 ********** No masking Map Score: 1.18193e-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: 1.18193e-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: 1.18193e-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