AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i241_synecho_ctra_300.orf -o241_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 RCY52962 217 Synechocystis #2 RCY32002 68 Synechocystis #3 RCY10628 106 Synechocystis #4 RCY33025 54 Synechocystis #5 RCY40193 300 Synechocystis #6 RCY15045 300 Synechocystis #7 RCY08865 31 Synechocystis #8 RCY01023 53 Synechocystis #9 RCY42273 33 Synechocystis #10 RCY18626 124 Synechocystis #11 RCY28673 246 Synechocystis #12 RCT00247 300 Chlamydia_trachomatis Motif number 1 ATTGTGCTGTCAATGTTCCCCAGAGGATCTACC 1 13 0 CATGTCCCAG 0.883275 -205 TAACTTACTCCTACTCCCCCCAGGGTCATGGCC 1 60 1 CACTCCCCAG 0.972254 -158 CACTAAGGACCGTTCCCCCTAAGATGGGGAGGG 1 100 1 CTTCCCCTAG 0.774601 -118 TGACAATTGACAACCCTCCCCATCTTAGGGGGA 1 113 0 CACCCCCCAT 0.980116 -105 CCCCACAAAACCCGTCGCCCCAGTCAAAATAAT 1 189 0 CCGTCCCCAG 0.937762 -29 CAATTTACATCAAGGCATCCTAGCATCTTCATT 2 31 0 CAGGCTCCAG 0.89352 -38 ATTTTACCCACCATCCAGCCGAGGTTAATAGAA 3 29 1 CATCCGCCAG 0.971219 -78 CTGATTTTTTCACCATACCTAAGGGGATGTCGT 6 219 1 CCCATCCTAG 0.539222 -82 ACAATCCTCCTTAGTACTGGCAAC 7 18 0 CATCCCCTAG 0.95614 -14 CCAGTTTTAGCCCCCCGGCCAAGACTTTCTCTA 11 15 1 CCCCCGCCAG 0.987097 -232 GATGGAATCACTCCCCGTCCTAGGCGTATTTTT 11 97 1 CCCCCTCCAG 0.991269 -150 GCCGCTGTTTCCCCGCTCCCAATATAGAATCAT 11 160 1 CCCGCCCCAT 0.960244 -87 TGTCCCTGTCCGATCTGTCCAATGATTCTATAT 11 181 0 CATCTTCCAT 0.625887 -66 ATTCTCCCCCCCCCCCCTCCCATCAAACAGAAG 12 81 0 CCCCCTCCAT 0.961001 -220 AAAATCTTTGCTATACCTCCGAGAATCTTAAGC 12 229 1 CATACTCCAG 0.885473 -72 CACGCCCTCTCCGCCCAAGGAATTTCCAT 12 282 0 CCTCCCCCAG 0.995025 -19 * **** *** ** Masking position 12 Map Score: 22.3475 Number of sites scoring better than the average of aligned sites = 1350 Number in coding regions = 1205 Number in noncoding regions = 145 Number of orfs with sites within 600 bp upstream = 171 Fraction of orfs with sites within 600 bp upstream = 0.0274655 Motif number 2 AACGGTCCTTAGTGACCAACTGGCCATGACCCTGG 1 79 0 AGACACTGCC 0.913155 -139 GATTTTGACAATTGACAACCCTCCCCATCTTAGGG 1 116 0 AGACACCTCC 0.861102 -102 CCAATCCCCAAAATAGCCCCAATGAAGA 2 4 1 ACCCAATACC 0.762485 -65 AGCCCATTTTACCCACCATCCAGCCGAGGTTAATA 3 24 1 ACACACCACC 0.960517 -83 GGGGCTGAGTCCGCCCAAACCTATCAGACCCTTAC 3 76 1 CCCCACCTTC 0.894593 -31 CAAACCTATCAGACCCTTACCAGCCA 3 91 1 ACCCTCCACC 0.922533 -16 AAGACAAGCACTCTCTCTCTGCCCACTAAAAACT 4 10 1 ACTCCCTGCC 0.923023 -45 CATAAATTTAATTCCCTATCTTCCCATTCCGTATT 5 247 1 ACCCACTTCC 0.985647 -54 TTTCCTGAGGATGCCCAAGCTGTTCAAATTACGTT 10 38 1 ACCCACTGTC 0.955964 -87 GGTAAGATGGAATCACTCCCCGTCCTAGGCGTATT 11 92 1 ACACCCCGCC 0.98445 -155 CGAACTGTCCCTGTCCGATCTGTCCAATGATTCTA 11 184 0 CTCCACTGCC 0.898914 -63 CACAGTAAACCCGCCCGAACTGTCCCTGTCCGATC 11 199 0 CCCCACTGCC 0.991996 -48 TTTTATTCTCCCCCCCCCCCCTCCCATCAAACAGA 12 83 0 CCCCCCCTCC 0.981704 -218 CACGCCCTCTCCGCCCAAGGAATTTC 12 285 0 ACCCCCCGCC 0.99548 -16 * *** * *** ** Masking position 6 Map Score: 16.9428 Number of sites scoring better than the average of aligned sites = 1291 Number in coding regions = 1170 Number in noncoding regions = 121 Number of orfs with sites within 600 bp upstream = 122 Fraction of orfs with sites within 600 bp upstream = 0.0195952 Motif number 3 CATGACCCTGGGGGGAGTAGGAGTAAGTTAAAATGAAAA 1 51 0 GGGGGGAGTT 0.99561 -167 CCCCATCTTAGGGGGAACGGTCCTTAGTGACCAACTGGC 1 90 0 GGGGGGAGTG 0.981477 -128 GATAGGTTTGGGCGGACTCAGCCCCAGTTTATCTTGTTT 3 62 0 GGCGGAAGTT 0.988689 -45 CCATACCTAAGGGGATGTCGTCCATGGTTTTAACTTCCA 6 231 1 GGGGAGGGTT 0.933808 -70 GGCTGACTGTGGCGGTTTAATGTTTGTTTTTATGAGGAT 8 17 1 GGCGGAGTTT 0.963715 -37 GTCTTGGCCGGGGGGCTAAAACTGGAGTT 11 1 0 GGGGGAAGTT 0.993017 -246 TTGTTGTCTGGGAGGCAATAGAGAAAGTCTTGGCCGGGG 11 27 0 GGAGGAAGTC 0.900639 -220 CTGCCAATGTGGCGGTTATGCCGCTGTTTCCCCGCTCCC 11 141 1 GGCGGGGTTT 0.976935 -106 GGGAGGGGGGGGGGGGAGAATAAAAATTTCTTCTTCCTA 12 93 1 GGGGGAATTT 0.98379 -208 TAAGATTCTCGGAGGTATAGCAAAGATTTTTTTAAAAAA 12 220 0 GGAGGGATTT 0.963506 -81 ***** * **** Masking position 18 Map Score: 10.1188 Number of sites scoring better than the average of aligned sites = 519 Number in coding regions = 444 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 4 TCAACCCAAGCCCATTTTACCCACCATCCAGC 3 16 1 CCCTTTTACC 0.99324 -91 GCTTACTCTAAGTCTTTTAACCACGATTTACA 5 114 1 AGTTTTTACC 0.872875 -187 ACAGCATTTGCCCGTTTTATCCTGAATCCTTT 6 153 1 CCCTTTTACC 0.99324 -148 TATCCTGAATCCTTTTTTAACCCATAGATGGG 6 170 1 CCTTTTTACC 0.986139 -131 TCTAGCAATCTGTGTTTTACCCATTGTCGACA 10 89 1 TGTTTTTACC 0.795662 -36 AACTCCAGTTTTAGCCCCCCGGCCAA 11 5 1 CCATTTTACC 0.965702 -242 TGGAGATAGACCCTCTTTACACAAACTTTTTT 12 137 1 CCCCTTTAAC 0.899258 -164 CAGATTAACAACCTTTTTATACAGATAAAAGT 12 180 1 ACCTTTTAAC 0.901652 -121 *** ***** ** Masking position 9 Map Score: 5.21963 Number of sites scoring better than the average of aligned sites = 513 Number in coding regions = 446 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 5 ACGAAGACACAAAAAGAAGAGAGGCTATCAGC 5 154 1 AAAAAGAAGA 0.914187 -147 ATTAGGGATTACATAGGTGCGACCGCTGATAG 5 178 0 ACATAGGTGA 0.760844 -123 ACTGATACAAAGAAAGGACTAAAGGAAA 5 283 0 ACAAAGAAGA 0.954401 -18 CTATGGGTTAAAAAAGGATTCAGGATAAAACG 6 165 0 AAAAAGGACA 0.963292 -136 AATGACCCAAACAATGGACTGAAACTAGCAAA 9 11 0 ACAATGGAGA 0.919644 -23 CCCATTGTCGACAAAGGAATCAGGATT 10 108 1 ACAAAGGACA 0.980973 -17 ATCGCCTAGGACAAAGGTAAGATGGAATCACT 11 77 1 ACAAAGGTGA 0.952788 -170 CTTATTAAAAGGGAGGCAACTTTTGATA 12 7 1 AAAAGGGACA 0.87453 -294 GATTTTTTTAAAAAAGAAAGCAAACTTTTATC 12 203 0 AAAAAGAACA 0.895839 -98 ******** ** Masking position 3 Map Score: 5.24452 Number of sites scoring better than the average of aligned sites = 153 Number in coding regions = 122 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 6 CTGCATTGTGCTGTCAATGTTCCCCAGAGG 1 20 0 CTGTCAATGT 0.907 -198 TAGTGACCAACTGGCCATGACCCTGGGGGG 1 75 0 CTGGCCATGA 0.905373 -143 ATTGACAACCCTCCCCATCTTAGGGGGAAC 1 111 0 CTCCCCATCT 0.872958 -107 AAGACAAGCACTCTCTCTCTGCCC 4 5 1 CAAGCACTCT 0.784357 -50 TTTTAGGAGACTAGCCATGTTTAAGGATGA 5 53 1 CTAGCCATGT 0.963741 -248 CCACGATTTACAGGCAATGTACGAAGACAC 5 134 1 CAGGCAATGT 0.950757 -167 TTTTTTAGCTCTAGCAATCTGTGTTTTACC 10 80 1 CTAGCAATCT 0.91858 -45 ATGGTAAAGACTGCCAATGTGGCGGTTATG 11 131 1 CTGCCAATGT 0.937833 -116 CCCGCCCGAACTGTCCCTGTCCGATCTGTC 11 195 0 CTGTCCCTGT 0.917174 -52 CACGCCCTCTCCGCCCAAGG 12 291 0 CACGCCCTCT 0.862289 -10 ********** Masking position 8 Map Score: 5.5899 Number of sites scoring better than the average of aligned sites = 626 Number in coding regions = 574 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 7 CATCTTCATTGGGGCTATTTTGGGGATTGG 2 6 0 GGGTATTTTG 0.908426 -63 TAGAAAATTGGGTTAGTTTTTAGTGGGCAGAGAGA 4 24 0 GTTGTTTTTG 0.972234 -31 GGGTTTCTTCGTGTTTTTTTTCAGGATGGACATTA 5 206 0 GGTTTTTTTG 0.982601 -95 GCGGTTTAATGTTTGTTTTTATGAGGATTCTTATT 8 28 1 GTTTTTTTAG 0.798227 -26 TGTTAGTCCAGCGGAGTTTTTCCTGAGGATGCCCA 10 20 1 GGGGTTTTTG 0.988739 -105 AAATTACGTTGATGAGTTTTTTTAGCTCTAGCAAT 10 63 1 GTGGTTTTTG 0.971688 -62 CCCGTCCTAGGCGTATTTTTTATGGTAAAGACTGC 11 110 1 GGTTTTTTTG 0.982601 -137 CTATACTTAAGTGTTGTTTTTTCGGCAGAGTAAAA 12 44 1 GGTGTTTTTG 0.98896 -257 * ** ****** * Masking position 8 Map Score: 6.32394 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 69 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 8 CTCGGCTGGATGGTGGGTAAAATGGGCTTG 3 22 0 TGGTGGGTAA 0.867547 -85 TGGCTGGTAAGGGTCTGATA 3 97 0 TGGCTGGTAA 0.951967 -10 GACTTACCACTGGCTGTTTTCCTAAATGGA 6 77 0 TGGCTGTTTT 0.91025 -224 CAGTTTGGCTTGGCAGGTAACCCATCTATG 6 192 0 TGGCAGGTAA 0.965985 -109 GATGTACTAATGGAAGTTAAAACCATGGAC 6 250 0 TGGAAGTTAA 0.711254 -51 TGGCTGACTGTGGCGGTTTAATGTTTGTTT 8 16 1 TGGCGGTTTA 0.973669 -38 ACCGCCACATTGGCAGTCTTTACCATAAAA 11 127 0 TGGCAGTCTT 0.772491 -120 ACTGCCAATGTGGCGGTTATGCCGCTGTTT 11 140 1 TGGCGGTTAT 0.973669 -107 GGGACAGTTCGGGCGGGTTTACTGTGCTAT 11 208 1 GGGCGGGTTT 0.900284 -39 ********** Masking position 6 Map Score: 5.6492 Number of sites scoring better than the average of aligned sites = 767 Number in coding regions = 698 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 9 ATCTTAGGGGGAACGGTCCTTAGTGACCAA 1 95 0 GAACGGTCCT 0.983252 -123 ATACAAAGTGGATCGGTCATCGGCGGGACA 6 33 1 GATCGGTCAT 0.941589 -268 AAAATCAAGAGCTCTGTCCTGGGTTCACGG 6 121 0 GCTCTGTCCT 0.972303 -180 GTCCCTGTCCGATCTGTCCAATGATTCTAT 11 183 0 GATCTGTCCA 0.968595 -64 AAACCCGCCCGAACTGTCCCTGTCCGATCT 11 198 0 GAACTGTCCC 0.969606 -49 ********** Masking position 7 Map Score: 1.29295 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 41 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 10 GTAGGAGTAAGTTAAAATGAAAACCTGCAT 1 44 0 GTTAAAATGA 0.887096 -174 GTTGTCAATTGTCAAAATCACATTACTGCT 1 132 1 GTCAAAATCA 0.98421 -86 CGTCGCCCCAGTCAAAATAATTTTCATTAA 1 180 0 GTCAAAATAA 0.922746 -38 CCAGTGGTAAGTCAAAATCACTCGACACCG 6 94 1 GTCAAAATCA 0.98421 -207 TAGGTATGGTGAAAAAATCAGTTTGGCTTG 6 210 0 GAAAAAATCA 0.794681 -91 ACTAATGGAAGTTAAAACCATGGACGACAT 6 245 0 GTTAAAACCA 0.910036 -56 ********** Masking position 5 Map Score: 2.03366 Number of sites scoring better than the average of aligned sites = 151 Number in coding regions = 131 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 11 GACCGTTCCCCCTAAGATGGGGAGGGTTGT 1 107 1 CCTAAGATGG 0.841756 -111 CTTTTTTAACCCATAGATGGGTTACCTGCC 6 181 1 CCATAGATGG 0.913825 -120 GAAGTTAAAACCATGGACGACATCCCCTTA 6 238 0 CCATGGACGA 0.955934 -63 GATCCTTTGACCTTAGCCGGAATATTTGAT 6 277 0 CCTTAGCCGG 0.982976 -24 TGTGTTTTACCCATTGTCGACAAAGGAATC 10 99 1 CCATTGTCGA 0.507098 -26 ATAGAGAAAGTCTTGGCCGGGGGGCTAAAA 11 19 0 TCTTGGCCGG 0.899829 -228 AAAAAATACGCCTAGGACGGGGAGTGATTC 11 101 0 CCTAGGACGG 0.977241 -146 CAAGGAATTTCCATAGACGGTTGATAAATC 12 266 0 CCATAGACGG 0.98441 -35 TATGGAAATTCCTTGGGCGGAGAGGGCGTG 12 281 1 CCTTGGGCGG 0.980303 -20 ********** Masking position 2 Map Score: 8.34455 Number of sites scoring better than the average of aligned sites = 782 Number in coding regions = 713 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 12 AACTTACTCCTACTCCCCCCAGGGTCATGG 1 61 1 TACTCCCCCC 0.972642 -157 ATTAATGTACGTCTCCCACCACCAGCAGTA 1 155 0 GTCTCCCACC 0.957948 -63 GGTTTGGGCGGACTCAGCCCCAGTTTATCT 3 67 0 GACTCAGCCC 0.868764 -40 CAAGCACTCTCTCTCTGCCCACTAAAAACT 4 15 1 CTCTCTGCCC 0.916313 -40 TACCGATACTGTTTACGCCCTATGAACTTT 5 26 1 GTTTACGCCC 0.80793 -275 AACTCCAGTTTTAGCCCCCCGGCCAAGACT 11 11 1 TTAGCCCCCC 0.773223 -236 TTATGCCGCTGTTTCCCCGCTCCCAATATA 11 156 1 GTTTCCCCGC 0.885352 -91 GAAATTTTTATTCTCCCCCCCCCCCCTCCC 12 93 0 TTCTCCCCCC 0.99119 -208 CACGCCCTCTCCGCCCAAGGAATTTC 12 285 0 CTCTCCGCCC 0.989904 -16 ********** Masking position 10 Map Score: 5.56468 Number of sites scoring better than the average of aligned sites = 1176 Number in coding regions = 1028 Number in noncoding regions = 148 Number of orfs with sites within 600 bp upstream = 156 Fraction of orfs with sites within 600 bp upstream = 0.0250562 Motif number 13 ********** No masking Map Score: -1.16996e-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: -1.16996e-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: -1.16996e-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