AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i334_synecho_ctra_300.orf -o334_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 RCY03368 177 Synechocystis #2 RCY22330 51 Synechocystis #3 RCY11539 185 Synechocystis #4 RCY38294 42 Synechocystis #5 RCY35677 300 Synechocystis #6 RCY06664 88 Synechocystis #7 RCT00022 75 Chlamydia_trachomatis #8 RCT00023 187 Chlamydia_trachomatis Motif number 1 GGCGCAGGACCGGGGGAGGAATAAC 1 1 1 GCCAGAGGGG 0.998891 -177 GATTGGCTCTGACTCAGGTTTGGGGACCATGGCAT 3 99 0 GCCAGTGGGG 0.999146 -87 TGGCTACGGACCACGAGGTCGGGGGTTCGAGTCCC 5 31 1 CAGAGTGGGG 0.969361 -270 AAAAAAACTGGGCCCAGCTAGGGAGCCCAGCCCGA 5 103 0 GCCAGTGGAG 0.993453 -198 TAGCTTTCCGGCCTGAGCACAGGGGACTATGAATT 5 160 1 GCGAGAGGGG 0.997879 -141 GTTTTGCTAGGCCACAGATATGGGGCAGGAGTTTC 5 272 1 GCCAGTGGGG 0.999145 -29 AATGCAAGGGGAAAAAGCAGGGGGGTCTTGGGGGA 6 24 1 GAAAGAGGGG 0.979198 -65 * * *** * **** Masking position 6 Map Score: 13.4816 Number of sites scoring better than the average of aligned sites = 108 Number in coding regions = 98 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 2 CCACCATCAACCGTAAACCCCCGTAAACAC 1 157 1 CCGTAAACCC 0.955823 -21 CCGTAAACCCCCGTAAACACA 1 167 1 CCGTAAACAC 0.907352 -11 CCAAAATCACTCAGTTATTC 3 1 1 CCAAAATCAC 0.950377 -185 TAGATATATGCCATGGTCCCCAAACCTGAG 3 92 1 CCATGGTCCC 0.912594 -94 ACCTCGTGGTCCGTAGCCACGCGCTCTAAT 5 20 0 CCGTAGCCAC 0.937866 -281 TTGGAGGGACTCGAACCCCCGACCTCGTGG 5 41 0 TCGAACCCCC 0.95681 -260 CCTGGGAAATTCATAGTCCCCTGTGCTCAG 5 172 0 TCATAGTCCC 0.917138 -129 CACGAGTGCGTCAAACTCACCTTGATGCTT 5 243 0 TCAAACTCAC 0.900587 -58 TCTAACTCCCCCAAGACCCCCCTGCTTTTT 6 35 0 CCAAGACCCC 0.923638 -54 AGTCTTCTATTCTAACTCCCCCAAGACCCC 6 45 0 TCTAACTCCC 0.806013 -44 TTGACAACCCCAAAATCACTATCTTAGTA 7 57 0 CCAAAATCAC 0.950377 -19 GAAAAGCGGGGCGAACACCCCGCTTTTTTT 8 38 1 GCGAACACCC 0.863836 -150 ********** Masking position 8 Map Score: 9.68749 Number of sites scoring better than the average of aligned sites = 1966 Number in coding regions = 1721 Number in noncoding regions = 245 Number of orfs with sites within 600 bp upstream = 237 Fraction of orfs with sites within 600 bp upstream = 0.0380662 Motif number 3 TTTGTCTTTGACCTGTTTTTGGTAAGCTGAA 3 163 1 ACCTTTTTTG 0.934323 -23 TCCCTCCAAGCCCGTTTTTTGCATCACGCCG 5 62 1 CCCGTTTTTG 0.993343 -239 CCTAGCTGGGCCCAGTTTTTTTATAGCTATG 5 116 1 CCCATTTTTT 0.962493 -185 GTTTGACGCACTCGTGTTTTGCTAGGCCACA 5 257 1 CTCGGTTTTG 0.928514 -44 CCCAAGACCCCCCTGCTTTTTCCCCTTGCAT 6 25 0 CCCTCTTTTT 0.90712 -64 GGGTGTTCGCCCCGCTTTTCTCTAGATAACA 8 27 0 CCCGTTTTCT 0.94665 -161 GGGCGAACACCCCGCTTTTTTTGTTTTAATA 8 46 1 CCCGTTTTTT 0.987004 -142 TTTAATAAGTCTCTCTTTTTGAATCTGACTT 8 70 1 CTCTTTTTTG 0.959477 -118 TACATTGGCAATCAATTTTTGGGGAACACTA 8 115 0 ATCATTTTTG 0.764917 -73 **** ****** Masking position 7 Map Score: 8.81697 Number of sites scoring better than the average of aligned sites = 584 Number in coding regions = 486 Number in noncoding regions = 98 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 4 AAAAGAATTAATTAATCCCCATCCGCAGTAA 1 96 1 ATTATCCCCA 0.976676 -82 AAAATCACTCAGTTATTCCCACTATCATTTT 3 13 1 AGTATTCCCA 0.967191 -173 CCCAAACCTGAGTCAGAGCCAATCTTAAGAA 3 110 1 AGTAGAGCCA 0.962189 -76 CATCAAGGTGAGTTTGACGCACTCGTGTTTT 5 246 1 AGTTGACGCA 0.810303 -55 TTCCCCTTGCATTGATCGCCAAATGG 6 6 0 ATTATCGCCA 0.9626 -83 AAGACTGAGCATTTTGACCCAAGGCAGACC 6 69 1 ATTTGACCCA 0.942101 -20 AGTAAAGTCTAGTGTTCCCCAAAAATTGATT 8 106 1 AGTTTCCCCA 0.976417 -82 TTCCCCAAAAATTGATTGCCAATGTACACTC 8 120 1 ATTATTGCCA 0.919506 -68 *** ******* Masking position 1 Map Score: 4.84789 Number of sites scoring better than the average of aligned sites = 580 Number in coding regions = 507 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 5 AGTGTCCCCTGGAACGCCAAGCAAACGGTT 1 33 0 GGAACGCCAA 0.904003 -145 AAAGCGCCAAAGTTTGCCCATGCCATGTAT 1 126 1 AGTTTGCCCA 0.833411 -52 GCCCATGCCATGTATGCCACCATCAACCGT 1 141 1 TGTATGCCAC 0.898185 -37 ATATATGCCATGGTCCCCAAACCTGAGTCA 3 95 1 TGGTCCCCAA 0.945482 -91 CCCCTTGCATTGATCGCCAAATGG 6 5 0 TGATCGCCAA 0.988164 -84 AAAAGCGGGGTGTTCGCCCCGCTTTTCTCT 8 35 0 TGTTCGCCCC 0.971933 -153 TAAAGTCTAGTGTTCCCCAAAAATTGATTG 8 108 1 TGTTCCCCAA 0.974694 -80 CCCCAAAAATTGATTGCCAATGTACACTCT 8 122 1 TGATTGCCAA 0.97031 -66 ********** Masking position 7 Map Score: 6.17049 Number of sites scoring better than the average of aligned sites = 1623 Number in coding regions = 1431 Number in noncoding regions = 192 Number of orfs with sites within 600 bp upstream = 202 Fraction of orfs with sites within 600 bp upstream = 0.0324446 Motif number 6 TTTTGAATTTTATGAGTCGGACTTAACC 2 34 1 TATGTCGGAC 0.957554 -18 AAGGGTTTATTTTGCTTCTTTCCACTGGATAC 3 53 1 TTTGTCTTTC 0.875321 -133 ATAGTAGATATATGCCATGGTCCCCAAACCTG 3 88 1 TATGATGGTC 0.74701 -98 ATTTCTTAAGATTGGCTCTGACTCAGGTTTGG 3 111 0 ATTGTCTGAC 0.918478 -75 CCGCTCAACATTTGTCTTTGACCTGTTTTTGG 3 153 1 TTTGTTTGAC 0.975392 -33 TAGCCGAATCTTTGGTTTGGTCCTGGGAAATT 5 191 0 TTTGTTGGTC 0.974906 -110 AGATAGTGATTTTGGGGTTGTCAA 7 62 1 TTTGGTTGTC 0.92422 -14 AGTCTCTCTTTTTGAATCTGACTTTTCAGAGT 8 77 1 TTTGTCTGAC 0.984343 -111 **** ****** Masking position 3 Map Score: 3.41047 Number of sites scoring better than the average of aligned sites = 271 Number in coding regions = 223 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 7 CGGTTATTCCTCCCCCGGTCCTGCGCC 1 8 0 TCCCCCGGTC 0.959031 -170 CAGTGGAGTGTCCCCTGGAACGCCAAGCAA 1 39 0 TCCCCTGGAA 0.9919 -139 CAGGGGACACTCCACTGTATTCTACTTCCA 1 52 1 TCCACTGTAT 0.895158 -126 TTAATCCCCATCCGCAGTAAAAGCGCCAAA 1 107 1 TCCGCAGTAA 0.863064 -71 TCAACCGTAAACCCCCGTAAACACA 1 163 1 ACCCCCGTAA 0.865266 -15 ACATATTCCGCTGGTAATAATAATTT 2 7 1 TCCGCTGGTA 0.962867 -45 TTTGCTTCTTTCCACTGGATACTGGATAGT 3 63 1 TCCACTGGAT 0.943725 -123 AAATTCATAGTCCCCTGTGCTCAGGCCGGA 5 166 0 TCCCCTGTGC 0.946492 -135 CCCTGCTTTTTCCCCTTGCATTGATCGCCA 6 16 0 TCCCCTTGCA 0.834926 -73 ********** Masking position 5 Map Score: 4.60618 Number of sites scoring better than the average of aligned sites = 1747 Number in coding regions = 1585 Number in noncoding regions = 162 Number of orfs with sites within 600 bp upstream = 185 Fraction of orfs with sites within 600 bp upstream = 0.0297141 Motif number 8 ACCGGGGGAGGAATAACCGTTTGCTTGGCG 1 19 1 GAATAACCGT 0.80059 -159 ATGATAGTGGGAATAACTGAGTGATTTTGG 3 11 0 GAATAACTGA 0.756135 -175 ACTGGATACTGGATAGTAGATATATGCCAT 3 76 1 GGATAGTAGA 0.840569 -110 CAATCTTAAGAAATAGCCGTTGTTCCGCTC 3 129 1 AAATAGCCGT 0.825944 -57 TAGCCTCTGTAGATAGCCGAATCTTTGGTT 5 206 0 AGATAGCCGA 0.960971 -95 GGGGGAGTTAGAATAGAAGACTGAGCATTT 6 53 1 GAATAGAAGA 0.69901 -36 AGAAGGGAGAGCATACCCGAACATTTT 7 8 0 GCATACCCGA 0.929322 -68 TGAAAATCTCACATAACAGAAGGGAGAGCA 7 25 0 ACATAACAGA 0.882199 -51 GCTTTTCTCTAGATAACAGAAAGTTCTGTT 8 15 0 AGATAACAGA 0.93476 -173 TCTCTCTAACAAAGACCAGAGTGTACATTG 8 139 0 AAAGACCAGA 0.716788 -49 TTTGTTAGAGAGATACTAGAGTAAAGGCAG 8 156 1 AGATACTAGA 0.749442 -32 ********** Masking position 5 Map Score: 3.30257 Number of sites scoring better than the average of aligned sites = 344 Number in coding regions = 298 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 9 ATTATTATTACCAGCGGAATATGT 2 5 0 CCAGCGGAAT 0.924243 -47 CTAGCCGGATTATCCTCGCC 4 1 1 CTAGCCGGAT 0.977251 -42 CGAGTCCCTCCAAGCCCGTTTTTTGCATCA 5 58 1 CAAGCCCGTT 0.950045 -243 GCTAGGGAGCCCAGCCCGATGATAATAATC 5 92 0 CCAGCCCGAT 0.995993 -209 GGTGGAAACTCCTGCCCCATATCTGTGGCC 5 281 0 CCTGCCCCAT 0.965737 -20 ********** Masking position 10 Map Score: 0.542738 Number of sites scoring better than the average of aligned sites = 230 Number in coding regions = 207 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 10 ********** No masking Map Score: 2.24775e-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: 2.24775e-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: 2.24775e-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