AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i321_synecho_ctra_300.orf -o321_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 RCY27247 105 Synechocystis #2 RCY39891 95 Synechocystis #3 RCY49697 163 Synechocystis #4 RCY03645 137 Synechocystis #5 RCY22631 194 Synechocystis #6 RCY51824 142 Synechocystis #7 RCY41663 68 Synechocystis #8 RCY29812 279 Synechocystis #9 RCY31507 78 Synechocystis #10 RCY30551 132 Synechocystis #11 RCY27696 181 Synechocystis #12 RCY02760 42 Synechocystis #13 RCY52673 35 Synechocystis #14 RCT00181 62 Chlamydia_trachomatis #15 RCT00182 300 Chlamydia_trachomatis #16 RCT00566 84 Chlamydia_trachomatis #17 RCT00567 152 Chlamydia_trachomatis Motif number 1 CAACCATTTGGCCTTCCCAAGGGAAAGGACGG 1 14 0 GCCTCCCAAG 0.990559 -92 CATTGTCGTGGCGTCCCCAAACTGTTAGAATA 2 16 1 GCGCCCCAAC 0.912463 -80 AGGCTTTGGGCCGATCGCCACGGCCACTGATG 3 38 0 CCGTCGCCAG 0.981005 -126 GGGAGATCTTGCGATCCCTAGCCAAAGCAAGT 3 139 0 GCGTCCCTAC 0.936422 -25 GGCGATCGCCGACGTTAGTGTTC 4 125 0 GCGTCGCCGC 0.882814 -13 GTGCAAAGTACCCTTGCCAACGCCCTCTACCT 5 45 1 CCCTGCCAAG 0.982257 -150 CCGGCCAATGGCGATCGCCAAGCGTCGTATAT 5 98 1 GCGTCGCCAG 0.985077 -97 GAGCCGCTGGGCCTTGCCACTGTCAGGATTGG 5 142 1 GCCTGCCACG 0.949975 -53 GGTAATCCAGGCCCTCCCAATCCTGACAGTGG 5 158 0 GCCTCCCAAC 0.98798 -37 CCTGGATTACCCCGTCCCCAACCTCC 5 179 1 CCCTCCCCAC 0.991565 -16 GGCCCTGCCCAACTTTGTTACCC 7 56 0 GCCTGCCCAC 0.990216 -13 CAGTCGCTAACCCTTGGCCACGGTCCCATTAT 8 103 1 CCCTGGCCAG 0.972055 -177 TCAATTACAACCGCTGCCCCCGTTTCCTTCCA 8 141 0 CCGTGCCCCG 0.964498 -139 GATTTTTGGTGCGTTCCCAAGCCTCTTCTGGT 11 43 1 GCGTCCCAAC 0.987952 -139 ATGGAACCAGCCCATACCCAAGCTTAACGGAA 11 116 0 CCCTACCCAG 0.929214 -66 TCAGCAGTTCCCGGTGCCAAAGTTAAAGAGAT 15 258 1 CCGTGCCAAG 0.982256 -43 *** ****** * Masking position 8 Map Score: 29.7159 Number of sites scoring better than the average of aligned sites = 1619 Number in coding regions = 1479 Number in noncoding regions = 140 Number of orfs with sites within 600 bp upstream = 152 Fraction of orfs with sites within 600 bp upstream = 0.0244137 Motif number 2 GGTATTCTAGCTGGGGAAAACCTCTGGTTT 1 77 1 CTGGGGAAAA 0.984488 -29 AACCAAAAATCTAGACAAAAATTTACCAAG 3 84 0 CTAGACAAAA 0.914098 -80 GCATAGTTGCCCAGGGAAAAATC 6 4 0 CCAGGGAAAA 0.990006 -139 AGTTAAAACAGCAGGGAAAATTAAGTATTA 7 16 1 GCAGGGAAAA 0.935038 -53 TCAGTTGGCCCTAGGCAAAATCATTCACAT 9 24 1 CTAGGCAAAA 0.970121 -55 TGGATTTCCTCCAGAGAAAAAAGTCAACAA 10 111 0 CCAGAGAAAA 0.97012 -22 AACTGGGAAAAACAATCATGGC 13 3 1 CTGGGAAAAA 0.945396 -33 ACAAATGGTCCCGGAGAAAATGTTTTGCAT 15 31 0 CCGGAGAAAA 0.964003 -270 GTATGAAATTCTAGGAAAGAAGTATAATGG 15 113 1 CTAGGAAAGA 0.83063 -188 ********** Masking position 7 Map Score: 9.01088 Number of sites scoring better than the average of aligned sites = 992 Number in coding regions = 821 Number in noncoding regions = 171 Number of orfs with sites within 600 bp upstream = 201 Fraction of orfs with sites within 600 bp upstream = 0.032284 Motif number 3 GACCAAAAATATTGCAACCATTTGGCCTTCC 1 29 0 ATTGCACCAT 0.893663 -77 ACTGATCACCAATGGCACCATGGCCCAAGCC 8 34 0 AATGGACCAT 0.977367 -246 CAAGCTGAATAATGGGACCGTGGCCAAGGGT 8 112 0 AATGGACCGT 0.972696 -168 ATATTACAAAAATGCAGGCATAGTGGCTTAA 8 211 1 AATGCGGCAT 0.924973 -69 AGAAGTGGGAAATGCCGCCATCAAAACGGCT 10 71 0 AATGCGCCAT 0.987853 -62 TGGACAGAAAAAAGCAGCCGTCCTGCAATCA 11 83 0 AAAGCGCCGT 0.916795 -99 TCAATAAGACAATGGAACCAGCCCATACCCA 11 128 0 AATGGACCAG 0.954777 -54 AATAAATAATGCCGCCATGATTGTTTTT 13 18 0 AATGCGCCAT 0.987853 -18 AAATGAGACAAATGGTCCCGGAGAAAATGTT 15 37 0 AATGGCCCGG 0.886941 -264 ***** ***** Masking position 1 Map Score: 7.60739 Number of sites scoring better than the average of aligned sites = 229 Number in coding regions = 207 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 4 TTTCCCTTGGGAAGGCCAAATGGTTGCAATATTTT 1 20 1 GAGGAAGGTT 0.952119 -86 AGGGACTAATGCAGGTAGAGGGCGTTGGCAAGGGT 5 54 0 GAGGAGGCGT 0.944944 -141 CTGACAGTGGCAAGGCCCAGCGGCTCAATATATGC 5 133 0 CAGGAGGGCT 0.988767 -62 GCTTAGAAAGGGAGGAGAAGGGGCTCCGTATTCTA 6 76 0 GAGGAGGGCT 0.99418 -67 GGACCGTGGCCAAGGGTTAGCGACTGGAGTTGGCA 8 94 0 CAGGAGGACT 0.977075 -186 TTACAAAAATGCAGGCATAGTGGCTTAATGGCTTG 8 214 1 GAGGAGGGCT 0.99418 -66 TCAGTTGGCCCTAGGCAAAATCATTCACATCGATT 9 24 1 CAGGAACATT 0.601798 -55 TCCTGTTCCCGCAGGAGCAAAGACTAACCGTTGGG 10 20 1 GAGGAAGACT 0.976795 -113 CAAAGATCATGAAGGAAGAAGCCCTTTTAGCGGAA 16 32 0 GAGGAACCCT 0.932618 -53 * *** ** **** Masking position 9 Map Score: 6.92177 Number of sites scoring better than the average of aligned sites = 230 Number in coding regions = 202 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 5 GATCAATACAGTTGACCAAAAATATTGCAACC 1 41 0 GTACCAAAAA 0.961867 -65 AGTAACCAAAAACCAGAGGTTT 1 94 0 ATACCAAAAA 0.978044 -12 GCACTGTCAAGCGAACCAAAAATCTAGACAAA 3 95 0 GGACCAAAAA 0.954363 -69 TCACTCTGCAAATAGCCAAAAACTGATCACCA 8 54 0 ATGCCAAAAA 0.961867 -226 AGGCTTGGGAACGCACCAAAAATCCTAATCGT 11 35 0 AGACCAAAAA 0.973635 -147 GGAGCAAAAAAAAGACCAAAAAACCGTCTTAA 11 159 0 AAACCAAAAA 0.959798 -23 CATTTGTCTCATTTGCGAAAAATTCTTGCGGG 15 54 1 ATGCGAAAAA 0.806736 -247 GCAATTCATTACATACCAAAAAGGATCTTGGT 17 69 0 AAACCAAAAA 0.959798 -84 * * ******** Masking position 8 Map Score: 6.69504 Number of sites scoring better than the average of aligned sites = 206 Number in coding regions = 170 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 6 GGGTTCATAAAGATCAGAATTGTTATTCTAACAGTTTG 2 33 0 AACAAGTTTC 0.979422 -63 TTCAGTAAATCCAACTCAATGGTTTTGCCAGATTGTTT 4 44 0 CACAAGTTGC 0.987201 -94 AAATCAAACTCTAACTGAAGTGTAGCTTAGAATACGGA 6 49 1 CACAAGTATT 0.743776 -94 GGCTATTTGCAGAGTGAAAGTGTTTTGCCAACTCCAGT 8 69 1 AATAAGTTGC 0.793764 -211 TTGCCTAGGGCCAACTGAAATGTTGGTCGAC 9 4 0 CACAAGTTTC 0.98942 -75 TCTTAAACTACTAACCCAACGGTTAGTCTTTGCTCCTG 10 31 0 CACAAGTTTC 0.98942 -102 GGAAATGCCGCCATCAAAACGGCTTATCTTAAACTACT 10 57 0 CACAAGCTTC 0.956234 -76 AACGCACCAAAAATCCTAATCGTTTTGCAGAAACAAAG 11 20 0 AACAAGTTGC 0.975161 -162 AAATCATCAAACAACAGAAGAGTTGTTTTTGTTTTTGC 17 99 0 AACAAGTTTT 0.903591 -54 * * * ** *** ** Masking position 9 Map Score: 6.08626 Number of sites scoring better than the average of aligned sites = 89 Number in coding regions = 71 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 7 GCACCGTCCTTTCCCTTGGGAAGGCCA 1 5 1 CGCTTCCCTT 0.970266 -101 ACATGGGGGACAAGTTTCCCCTT 5 1 0 CAGTCCCCTT 0.865399 -194 TGAGGATGCAAAGCCGTCTCCTTTAGCTTAGAA 6 103 0 AACTCTCCTT 0.891045 -40 TTTGCATCCTCACCACTCCCCTTGACCCC 6 124 1 CACTCCCCTT 0.980258 -19 ACAACCGCTGCCCCCGTTTCCTTCCAAGCTGAA 8 134 0 CCCTTTCCTT 0.928655 -146 GTAATTGAAGCGACAATTTCCTGGGTAATTTGG 8 165 1 CGCTTTCCTG 0.979089 -115 TTTAATCACGCGCCACTATCCTGTCAAGCCATT 8 240 0 CGCTATCCTG 0.906728 -40 AAATCATTCACATCGATTTCCTGTTCATTCCTT 9 41 1 CACTTTCCTG 0.98496 -38 ATTTCCTGTTCATTCCTTTCCTTCCCTCAATTT 9 56 1 CATTTTCCTT 0.810663 -23 CAAGCTTTCTCCTGTTCCCGCAGG 10 2 1 AACTCTCCTG 0.916483 -131 CGAATTCATTCAGCAGTTCCCGGTGCCAAAGTT 15 249 1 CACTTCCCGG 0.919477 -52 ** * ******* Masking position 7 Map Score: 6.57528 Number of sites scoring better than the average of aligned sites = 692 Number in coding regions = 627 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 8 CCGTCCTTTCCCTTGGGAAGGCCAAATGGT 1 14 1 CCTTGGGAAG 0.865548 -92 ATAATCGGATCCAAGGGCATCAGTGGCCGT 3 21 1 CCAAGGGCAT 0.787662 -143 TGGAGTGAGGCTTTGGGCCGATCGCCACGG 3 47 0 CTTTGGGCCG 0.944218 -117 CTGCATTAGTCCCTGGGCAGTTTCCGGCCA 5 75 1 CCCTGGGCAG 0.991516 -120 TTGGCGATCGCCATTGGCCGGAAACTGCCC 5 89 0 CCATTGGCCG 0.941168 -106 TATATTGAGCCGCTGGGCCTTGCCACTGTC 5 136 1 CGCTGGGCCT 0.930777 -59 GATTTTTCCCTGGGCAACTATGCGGTC 6 8 1 CCCTGGGCAA 0.98661 -135 GGTGGTCTAGGCTTGGGCCATGGTGCCATT 8 25 1 GCTTGGGCCA 0.933756 -255 CAGTCGCTAACCCTTGGCCACGGTCCCATT 8 103 1 CCCTTGGCCA 0.967583 -177 AATGATTTTGCCTAGGGCCAACTGAAATGT 9 19 0 CCTAGGGCCA 0.96801 -60 ********** Masking position 6 Map Score: 9.26541 Number of sites scoring better than the average of aligned sites = 1734 Number in coding regions = 1597 Number in noncoding regions = 137 Number of orfs with sites within 600 bp upstream = 156 Fraction of orfs with sites within 600 bp upstream = 0.0250562 Motif number 9 CTAACTGAAGTGTAGCTTAGAATACGGAGCCC 6 59 1 TGAGCTTGAA 0.938011 -84 AGCCGTCTCCTTTAGCTTAGAAAGGGAGGAGA 6 93 0 TTAGCTTGAA 0.98007 -50 GGTCCCATTATTCAGCTTGGAAGGAAACGGGG 8 124 1 TTAGCTTGAA 0.980038 -156 TTTCGTTTAGAATTGAACCGCCAACGG 12 6 1 TTAGAATGAA 0.908254 -37 TTCTTCTTTATTTAGCATGGTAGTTCTGTCTC 14 11 0 TTAGCATGTA 0.930041 -52 GATTCTCCCATTAAGCATGCAAAACATTTTCT 15 15 1 TTAGCATCAA 0.924871 -286 GCTATAGGGCTTAAGGATGGAATTTTATCGAT 15 153 1 TTAGGATGAA 0.936234 -148 ** ***** *** Masking position 4 Map Score: 2.35018 Number of sites scoring better than the average of aligned sites = 29 Number in coding regions = 24 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 10 ACCAAAAATATTGCAACCATTTGGCCTTCC 1 29 0 TTGCAACCAT 0.909965 -77 CTGATCACCAATGGCACCATGGCCCAAGCC 8 34 0 ATGGCACCAT 0.556041 -246 TATTACAAAAATGCAGGCATAGTGGCTTAA 8 212 1 ATGCAGGCAT 0.599313 -68 GAAGTGGGAAATGCCGCCATCAAAACGGCT 10 71 0 ATGCCGCCAT 0.516489 -62 CAATAAGACAATGGAACCAGCCCATACCCA 11 128 0 ATGGAACCAG 0.879816 -54 AATAAATAATGCCGCCATGATTGTTTTT 13 18 0 ATGCCGCCAT 0.516489 -18 ********** Masking position 2 Map Score: 2.2505 Number of sites scoring better than the average of aligned sites = 308 Number in coding regions = 289 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 11 TCAAACAATCTGGCAAAACCATTGAGTTGG 4 42 1 TGGCAAAACC 0.987891 -96 ATCCTGACAGTGGCAAGGCCCAGCGGCTCA 5 141 0 TGGCAAGGCC 0.879749 -54 AGTGGTGAGGATGCAAAGCCGTCTCCTTTA 6 111 0 ATGCAAAGCC 0.908766 -32 CGACTGGAGTTGGCAAAACACTTTCACTCT 8 79 0 TGGCAAAACA 0.933791 -201 AGTTGGCCCTAGGCAAAATCATTCACATCG 9 26 1 AGGCAAAATC 0.827343 -53 CCTAATCGTTTTGCAGAAACAAAGGGATGC 11 14 0 TTGCAGAAAC 0.77762 -168 AACTGGGAAAAACAATCATGGCG 13 4 1 TGGGAAAAAC 0.775905 -32 CCCATTAAGCATGCAAAACATTTTCTCCGG 15 21 1 ATGCAAAACA 0.800187 -280 ATGTAATGAATTGCAAAAACAAAAACAACT 17 87 1 TTGCAAAAAC 0.943717 -66 GTTTGATGATTTGCTAAACCGGAGAGAGTG 17 125 1 TTGCTAAACC 0.87803 -28 ********** Masking position 3 Map Score: 3.96853 Number of sites scoring better than the average of aligned sites = 1188 Number in coding regions = 1056 Number in noncoding regions = 132 Number of orfs with sites within 600 bp upstream = 150 Fraction of orfs with sites within 600 bp upstream = 0.0240925 Motif number 12 ATTCTAACAGTTTGGGGACGCCACGACAAT 2 17 0 TTTGGGGACG 0.853731 -79 CCAGGGACTAATGCAGGTAGAGGGCGTTGG 5 61 0 ATGCAGGTAG 0.715678 -134 AAATTGAGGGAAGGAAAGGAATG 9 66 0 TTGAGGGAAG 0.975205 -13 GCTGTCTTGATTGCAGGACGGCTGCTTTTT 11 76 1 TTGCAGGACG 0.950162 -106 CTTCAAGATTTTTAGGGACGATGATTTCTT 14 38 0 TTTAGGGACG 0.928349 -25 ATCAAAGATCATGAAGGAAGAAGCCCTTTT 16 39 0 ATGAAGGAAG 0.935999 -46 AAGATTGATTATGAGGGAAGT 16 74 1 ATGAGGGAAG 0.967954 -11 ********** Masking position 2 Map Score: 2.04802 Number of sites scoring better than the average of aligned sites = 320 Number in coding regions = 288 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 13 ********** No masking Map Score: -2.74737e-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: -2.74737e-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: -2.74737e-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