AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i232_synecho_ctra_300.orf -o232_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 RCY19112 300 Synechocystis #2 RCY33905 157 Synechocystis #3 RCY28443 110 Synechocystis #4 RCY06942 53 Synechocystis #5 RCY41351 138 Synechocystis #6 RCY10129 213 Synechocystis #7 RCT00336 274 Chlamydia_trachomatis #8 RCT00337 60 Chlamydia_trachomatis #9 RCT00338 300 Chlamydia_trachomatis #10 RCT00507 100 Chlamydia_trachomatis #11 RCT00508 63 Chlamydia_trachomatis #12 RCT00509 258 Chlamydia_trachomatis #13 RCT00511 62 Chlamydia_trachomatis #14 RCT00512 300 Chlamydia_trachomatis Motif number 1 GGTTTTACTTCAACTTTCCCTAGAGTTAGCA 1 166 0 CACTTTCCCT 0.875387 -135 TAGGCTCAATCAACCTCCCCAATCCTAACAA 3 37 0 CACCTCCCCA 0.993124 -74 TATTTTTAGGCATCTTCCCCAGGATTGAGTC 3 66 1 CACTTCCCCA 0.969592 -45 TCCGGTTTTTTCTCCTTCCCATCACC 3 95 1 TCCCTTCCCA 0.960082 -16 AACTCCGTGCCACCCTTCCCCGCCTTTT 8 8 0 CACCTTCCCC 0.96348 -53 CGGCTGGGTCCCTCCTCCCCTATAGCTTTTA 9 127 1 CCCCTCCCCT 0.993707 -174 TTGGATCTTACCGCCTCCCTAGAGATGTGGC 9 213 0 CCCCTCCCTA 0.969808 -88 TTGGGTTGTTCCTCCTCCCCTTTTTCTTTGG 9 240 0 CCCCTCCCCT 0.993707 -61 CAGGCCCACCTCTACTCCCCAGTCATCTCTG 12 62 0 TCACTCCCCA 0.84253 -197 TCTTCTTTATTATCCTTCCTCACATCACCCT 12 138 0 TACCTTCCTC 0.541765 -121 ATTCAGGATGCCCCTACCCCTAGAGCATGGG 14 119 1 CCCTACCCCT 0.801495 -182 AAAACAGGCCTAACCTCCCCATGCTCTAGGG 14 136 0 TACCTCCCCA 0.978987 -165 ** ******** Masking position 8 Map Score: 18.5101 Number of sites scoring better than the average of aligned sites = 1140 Number in coding regions = 1031 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 115 Fraction of orfs with sites within 600 bp upstream = 0.0184709 Motif number 2 TCTAGGAATTTTTCAAAAATTGTCGATCCCGCCGAGGA 1 267 0 TTAAATCGAC 0.947636 -34 TTCGCTATGGTTTAAAAGGTTTGCTTACCGTTGCCCGT 5 39 0 TTAAATCTTC 0.960749 -100 AAACCTATGATCTAAAAAATTCCCTAGCGTCTTCTGAC 7 198 0 TTAAATCTAC 0.987254 -77 CAGCTTATATTCTAAAAAAGAACCTACCCTCGTCCTAG 9 159 0 TTAAAACTAC 0.960749 -142 AACCCAAAATTCTTAAGGTTTTTCTACCTAAAAACTAC 9 264 1 TTAAGTCTAC 0.974267 -37 ACTACCTAGTTCTAAAACACTTGCTATC 10 1 0 TTAAATCTAC 0.987254 -100 AAGCAAGCGATATCAAAAAATTACTACCTAGTTCTAAA 10 23 0 TTAAATCTAC 0.987254 -78 CGATCACATCTATAAAATATTCCCTAACGACTTAAATA 12 202 1 TTAAATCTAC 0.987254 -57 CCAGCCTCCTTCTAAAGGGAAGCCTTTCCGCCCATATC 14 218 0 TTAAGACTTC 0.790831 -83 * * *** * *** * Masking position 6 Map Score: 9.92413 Number of sites scoring better than the average of aligned sites = 22 Number in coding regions = 20 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 3 CGATGGGGAATTTTGCTGTCCGTTGGCGATCGCCA 1 42 0 TTTTCTGTTG 0.910596 -259 TAACCATAAGTTTTTCTTAATTTCTCTATGAAAAA 1 107 0 TTTTCTTTCT 0.925266 -194 GAGTTAGCAAATTTGCTTAACCTTTTCATAGTCTA 1 140 0 ATTTCTTTTT 0.834069 -161 ACAATGGCGGTTTTACTTCAACTTTCCCTAGAGTT 1 170 0 TTTTCTTTTT 0.972769 -131 GGTTTAAAAGGTTTGCTTACCGTTGCCCGTTTGAC 5 34 0 GTTTCTTTTG 0.918561 -105 TGAATGAAACTTTTTCTTCACTTTGACGATACTAG 7 124 1 TTTTCTTTTG 0.967092 -151 CAAAAATGTATTTTTCTGGAATTTTTTCACTTAAA 9 44 0 TTTTCTGTTT 0.925266 -257 ATACATTTTTGTTTCCTTTGGCTTGAGGATATAAC 9 68 1 GTTTCTTTTG 0.918561 -233 CCTCCTCCCCTTTTTCTTTGGATCTTACCGCCTCC 9 226 0 TTTTCTTTCT 0.925266 -75 ACCCCGTATATTATCCTTTTTTTTTTTTAGCAAGC 10 57 0 TTATCTTTTT 0.888938 -44 GCAGAAACTTTTTTCCTTTTATCTTCTTTATTATC 12 155 0 TTTTCTTCTT 0.859799 -104 ACTTATCCTTACTTTTTTCAGTTGCTT 14 284 0 TTATCTTTTT 0.888938 -17 **** *** *** Masking position 7 Map Score: 9.64888 Number of sites scoring better than the average of aligned sites = 125 Number in coding regions = 92 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 4 GAAAAAGTGGGGCAAAACCTTCAA 1 3 1 AAAAGGGGCA 0.571478 -298 TATGAAAAACTGGAGCGGGGCCAAGTGATCGT 1 84 0 TGGAGGGGCC 0.911441 -217 GGAAGATGCCTAAAAATAGGCTCAATCAACCT 3 52 0 TAAATAGGCT 0.688595 -59 CATCTTCCCCAGGATTGAGTCCGGTTTTTTCT 3 76 1 AGGAGAGTCC 0.737807 -35 TGATTTTGTTAAGATGTAGTCCAAGACCCCAT 5 91 1 AAGATAGTCC 0.899264 -48 GACCCCATTGTTGAGATAGGCCCGTAGAACGT 5 115 1 TTGATAGGCC 0.91689 -24 TCAAAAAGGGTAGATTTAGTCCGATGAACTAC 6 23 1 TAGATAGTCC 0.899264 -191 TAAAGGTGTAATGAACTGGGCAGACTTTCTAG 6 185 1 ATGATGGGCA 0.644384 -29 CAAAGTCTCAAAAAGATAGGCCGTTCCGATAA 7 234 0 AAAATAGGCC 0.899264 -41 GCAAGTGTTTTAGAACTAGGTAGTAATTTTTT 10 15 1 TAGATAGGTA 0.586196 -86 GACTGGGGAGTAGAGGTGGGCCTGTAACTCTG 12 69 1 TAGATGGGCC 0.970282 -190 GAGACTAGTCAAGATAGAGGCTATTAGACTCA 12 100 1 AAGAGAGGCT 0.917312 -159 ACCAAGAGTTAGGTCCCGACCAACC 13 48 0 AAGATAGGTC 0.851166 -15 GGCTTCCCTTTAGAAGGAGGCTGGTGATTAAA 14 232 1 TAGAGAGGCT 0.917312 -69 **** ****** Masking position 4 Map Score: 5.86688 Number of sites scoring better than the average of aligned sites = 711 Number in coding regions = 624 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 5 ATTCTGCGAAAAATCCTCGGCGGGATCGAC 1 254 1 AAATCCTCGG 0.961076 -47 ATTTTTGAAAAATTCCTAGATTATCT 1 285 1 AATTCCTAGA 0.842157 -16 ATAAGGGACTAATCCCTTGGCGATCGGGCT 2 77 0 AATCCCTTGG 0.87182 -81 TGTCGAGCCGAAATCATAGGCAATGCAGTT 4 33 0 AAATCATAGG 0.949436 -21 AAAATTCATAGGATGTGTAACT 5 3 1 AATTCATAGG 0.967869 -136 GTACAGTCGTAGTTCATCGGACTAAATCTA 6 33 0 AGTTCATCGG 0.933955 -181 GGAATTTTTTAGATCATAGGTTTATCGGAA 7 213 1 AGATCATAGG 0.914036 -62 AAAATCAAGAAATTCCTTGGAGGA 12 5 0 AATTCCTTGG 0.962417 -254 ********** Masking position 1 Map Score: 3.97888 Number of sites scoring better than the average of aligned sites = 347 Number in coding regions = 307 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 6 GAGAAATTAAGAAAAACTTATGGTTAGACT 1 116 1 GAAAAACTTA 0.94823 -185 GTTAGACTATGAAAAGGTTAAGCAAATTTG 1 138 1 GAAAAGGTTA 0.744125 -163 AACGGGGAACGAAAAAGCTAAGCTCAAGGG 1 206 1 GAAAAAGCTA 0.903694 -95 TCAAAGTGAAGAAAAAGTTTCATTCATACA 7 120 0 GAAAAAGTTT 0.896827 -155 ATATTTAAGTGAAAAAATTCCAGAAAAATA 9 41 1 GAAAAAATTC 0.856464 -260 TTTTTAGGTAGAAAAACCTTAAGAATTTTG 9 268 0 GAAAAACCTT 0.884832 -33 AAGATAAAAGGAAAAAAGTTTCTGCCAGCT 12 165 1 GAAAAAAGTT 0.8442 -94 GAATTCAAATGAAAAACTTCTATGTCGAGC 14 26 0 GAAAAACTTC 0.924939 -275 AAGTCTTATTGAAAAACGTAATGAGCTTGT 14 57 1 GAAAAACGTA 0.947238 -244 TTAAGCAACTGAAAAAAGTAAGGATAAGT 14 282 1 GAAAAAAGTA 0.896828 -19 ********** Masking position 5 Map Score: 6.51312 Number of sites scoring better than the average of aligned sites = 386 Number in coding regions = 325 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 7 GTAAAACCGCCATTGTCAACGGGGAACGAAA 1 189 1 CATTGTAACG 0.868097 -112 CAATTCTTTACATTGTTAAGGGTAATTAAGA 6 144 1 CATTGTAAGG 0.972402 -70 CTAGAGCAGACATTGTGATGGAAAAGAAGAT 7 55 0 CATTGTATGG 0.961071 -220 CTTTTTGAGACTTTGTATAGGGATCTGTGGG 7 251 1 CTTTGTTAGG 0.95247 -24 ATATAAGCTGCTTTGTTTGGGTGTTTGCCAC 9 187 1 CTTTGTTGGG 0.955819 -114 TACGGGGTCTCTTTGTCAGGGTTTTGC 10 84 1 CTTTGTAGGG 0.978991 -17 CCCCAGTCATCTCTGTAATGGATAGTAGTCT 12 46 0 CTCTGTATGG 0.908191 -213 ****** **** Masking position 6 Map Score: 3.84635 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 62 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 8 ATTGACCGGTGTTAAGTTCGCC 2 3 0 GTTAAGTTCG 0.879444 -155 GAATGCTTGCGTTAGGATTGTCTGTGGTTA 2 47 1 GTTAGGATTG 0.928303 -111 ATTGTCTGTGGTTAAGCCCGATCGCCAAGG 2 63 1 GTTAAGCCCG 0.971385 -95 TTCCAGGCTTGTTAGGATTGGGGAGGTTGA 3 29 1 GTTAGGATTG 0.928303 -82 CCATTGTTGAGATAGGCCCGTAGAACGTCC 5 119 1 GATAGGCCCG 0.962735 -20 ACCAAGAGTTAGGTCCCGACCAACCCT 13 46 0 GTTAGGTCCC 0.913925 -17 GCATGGGGAGGTTAGGCCTGTTTTGCTTTT 14 143 1 GTTAGGCCTG 0.983674 -158 ********** Masking position 4 Map Score: 3.02713 Number of sites scoring better than the average of aligned sites = 127 Number in coding regions = 112 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 9 GTCCTTCACCGATGGGGAATTTTGCTGTCCGTTGG 1 51 0 GATGGGATGC 0.953123 -250 TCAATCTCTCTAGGTGGGAGAATGCTTGCGTTAGG 2 28 1 TAGGGGAAGC 0.931718 -130 AAATTCATAGGATGTGTAACTAGTCAAACGGGCAA 5 12 1 GATGGTAATC 0.803019 -127 ATATCGAAAAGAGGGGTAACTAAGAGCAAAACAC 9 10 0 GAGGGTAAGA 0.898296 -291 AGCTATAGGGGAGGAGGGACCCAGCCGTCAGAACA 9 119 0 GAGGGGACGC 0.989236 -182 CCTCCCTAGAGATGTGGCAAACACCCAAACAAAGC 9 196 0 GATGGGACCC 0.976486 -105 CATCTCTAGGGAGGCGGTAAGATCCAAAGAAAAAG 9 217 1 GAGGGGAACC 0.987728 -84 AGAAAAAGGGGAGGAGGAACAACCCAAAATTCTTA 9 244 1 GAGGGGAACC 0.987627 -57 TTACATTCAAGATGAGAGAAAAAGAATCCCCTTAG 11 18 0 GATGGAAAGA 0.687113 -46 TTATAGATGTGATCGGTTATACAGCTGGCAGAAAC 12 182 0 GATCGTACGC 0.774091 -77 **** ** * * ** Masking position 9 Map Score: 3.08945 Number of sites scoring better than the average of aligned sites = 320 Number in coding regions = 291 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 10 TCGGTGCTGGCGATCGCCAACGGACAGCAA 1 35 1 CGATCGCCAA 0.986704 -266 ATCCTCGGCGGGATCGACAATTTTTGAAAA 1 266 1 GGATCGACAA 0.985886 -35 TGGTTAAGCCCGATCGCCAAGGGATTAGTC 2 71 1 CGATCGCCAA 0.986704 -87 CTATGATTTCGGCTCGACAA 4 44 1 GGCTCGACAA 0.969207 -10 TCACTGACTAGTATCGTCAAAGTGAAGAAA 7 136 0 GTATCGTCAA 0.883639 -139 ********** Masking position 4 Map Score: 2.40035 Number of sites scoring better than the average of aligned sites = 1120 Number in coding regions = 996 Number in noncoding regions = 124 Number of orfs with sites within 600 bp upstream = 128 Fraction of orfs with sites within 600 bp upstream = 0.0205589 Motif number 11 GAAAGAGAAGTCTTCCTTTCGCTGAATAGC 7 20 0 TCTTCCTTTC 0.975166 -255 TTTCCAAATATCTTCTTTTCCATCACAATG 7 46 1 TCTTCTTTTC 0.973244 -229 AGAACAGTTAACTTCTTTTCTGAGATCA 8 43 1 ACTTCTTTTC 0.962101 -18 ACCTACTCTCACTTCCTTGCAAAAGTATTT 14 178 0 ACTTCCTTGC 0.925066 -123 GCAAACTGATTCTTCTTTTAATCACCAGCC 14 250 0 TCTTCTTTTA 0.874535 -51 ********** Masking position 4 Map Score: 1.44202 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 15 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 12 TAGAGAAATTAAGAAAAACTTATGGTTAGA 1 114 1 AAGAAAAACT 0.823488 -187 TGAAAAGGTTAAGCAAATTTGCTAACTCTA 1 147 1 AAGCAAATTT 0.730839 -154 ACTACATCTTAACAAAATCACGGCCTGGAC 5 81 0 AACAAAATCA 0.77188 -58 GCCGATAGTTAAGCAAATTACAACCAAGTA 6 60 0 AAGCAAATTA 0.881192 -154 GGGTAACTAAGAGCAAAACAC 9 2 0 GAGCAAAACA 0.842987 -299 CTCGATATAGAAGAAAATCAAGAAATTCCT 12 18 0 AAGAAAATCA 0.953367 -241 TATGTCGAGCAAGAAAATCATTTCT 14 6 0 AAGAAAATCA 0.953367 -295 TTTTTACAAAAAGCAAAACAGGCCTAACCT 14 151 0 AAGCAAAACA 0.952861 -150 ********** Masking position 5 Map Score: 3.12663 Number of sites scoring better than the average of aligned sites = 278 Number in coding regions = 231 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 13 GCAAATTTGCTAACTCTAGGGAAAGTTGAA 1 159 1 TAACTCTAGG 0.935339 -142 CGAAAAAGCTAAGCTCAAGGGCGGCACTTT 1 215 1 AAGCTCAAGG 0.931167 -86 AGATAATCTAGGAATTTTTCAA 1 289 0 ATAATCTAGG 0.735995 -12 ATCACAATGTCTGCTCTAGGTGTCTTGGAT 7 67 1 CTGCTCTAGG 0.964435 -208 TCCTAGGTAAAAGCTATAGGGGAGGAGGGA 9 135 0 AAGCTATAGG 0.807572 -166 GTGTTTGCCACATCTCTAGGGAGGCGGTAA 9 207 1 CATCTCTAGG 0.908308 -94 CTAAAAACTACAAATCAAGG 9 291 1 CAAATCAAGG 0.669755 -10 GGTCGGGACCTAACTCTTGGT 13 52 1 TAACTCTTGG 0.695151 -11 TAACCTCCCCATGCTCTAGGGGTAGGGGCA 14 127 0 ATGCTCTAGG 0.957367 -174 ********** Masking position 5 Map Score: 3.0252 Number of sites scoring better than the average of aligned sites = 283 Number in coding regions = 246 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 14 GCAAAACCTTCAATCGGTGCTGGCGATCGC 1 22 1 CAATCGGTGC 0.844113 -279 TCCCCGTTGACAATGGCGGTTTTACTTCAA 1 184 0 CAATGGCGGT 0.951239 -117 AAGCTAAGCTCAAGGGCGGCACTTTACTGT 1 220 1 CAAGGGCGGC 0.990216 -81 GCACATATTGCAATGGAGGCAATGAATAGC 2 137 1 CAATGGAGGC 0.98524 -21 CCTATCTCAACAATGGGGTCTTGGACTACA 5 105 0 CAATGGGGTC 0.930521 -34 TTTTCCATCACAATGTCTGCTCTAGGTGTC 7 61 1 CAATGTCTGC 0.841817 -214 TGCCACATCTCTAGGGAGGCGGTAAGATCC 9 212 1 CTAGGGAGGC 0.90315 -89 ********** Masking position 3 Map Score: 1.82004 Number of sites scoring better than the average of aligned sites = 965 Number in coding regions = 888 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 15 TGCTGGCGATCGCCAACGGACAGCAAAATT 1 39 1 CGCCAACGGA 0.974263 -262 ACTGGAGCGGGGCCAAGTGATCGTCCTTCA 1 78 0 GGCCAAGTGA 0.978751 -223 TAAGCCCGATCGCCAAGGGATTAGTCCCTT 2 75 1 CGCCAAGGGA 0.98638 -83 GACTAGTATCGTCAAAGTGAAGAAAAAGTT 7 131 0 GTCAAAGTGA 0.840231 -144 TCCTCCAAGGAATTTCTTGATT 12 3 1 CTCCAAGGAA 0.791037 -256 GTTGCTTAATGGCAAACTGATTCTTCTTTT 14 261 0 GGCAAACTGA 0.890528 -40 ********** Masking position 5 Map Score: 0.593503 Number of sites scoring better than the average of aligned sites = 660 Number in coding regions = 588 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737