AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i166_synecho_ctra_300.orf -o166_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 RCY06888 56 Synechocystis #2 RCY13481 102 Synechocystis #3 RCY15639 83 Synechocystis #4 RCY10985 60 Synechocystis #5 RCY44593 75 Synechocystis #6 RCY02841 300 Synechocystis #7 RCY20200 49 Synechocystis #8 RCY52559 102 Synechocystis #9 RCY34751 215 Synechocystis #10 RCT00172 300 Chlamydia_trachomatis #11 RCT00816 52 Chlamydia_trachomatis Motif number 1 TTGTAATGATGGAAAAAATCTGAC 1 5 0 GGAAAAAATC 0.984261 -52 AATTGTCACAAAGAAAAATCAAAATCCCTC 2 47 0 AAGAAAAATC 0.859647 -56 ATTTTTAAAAAGTCAAAATCAACACAGTAA 3 13 1 AGTCAAAATC 0.861429 -71 ACAACTAGCGGAGAAAAATCG 3 73 1 GAGAAAAATC 0.919269 -11 GGGAAAAAAAGCTAATTGATGT 6 3 1 GAAAAAAAGC 0.874515 -298 TGTAGCTAGTGGCAAAAATCTTTACAAAGC 6 184 0 GGCAAAAATC 0.972537 -117 CTACACGGCGGGACAAAAGCCCGGGAGACT 6 209 1 GGACAAAAGC 0.940958 -92 ATATTTACAAGGAAAAAATCCAGTCTAGGA 8 67 1 GGAAAAAATC 0.984261 -36 GTTGATCGGTAGCCAAAATCACCTTTGTCC 9 132 1 AGCCAAAATC 0.905801 -84 TTGTCCCCTGGGTAAAAAGCTATAAAAAAT 9 156 1 GGTAAAAAGC 0.920365 -60 GTAAAAAGCTATAAAAAATCTTTGCGAAGC 9 167 1 ATAAAAAATC 0.746116 -49 TCTTTCGCACAGAAAAAATCCATTTTTGAT 10 11 1 AGAAAAAATC 0.97113 -290 GACTTCATGAAGGAAGAATCATAGGGGAAG 11 18 0 AGGAAGAATC 0.813993 -35 ********** Masking position 5 Map Score: 18.5904 Number of sites scoring better than the average of aligned sites = 928 Number in coding regions = 773 Number in noncoding regions = 155 Number of orfs with sites within 600 bp upstream = 165 Fraction of orfs with sites within 600 bp upstream = 0.0265018 Motif number 2 TCATTAAAGTCTCCCGGGCTTTTGTCCCGC 6 216 0 CTCCCGGGCT 0.962191 -85 TCATTAATAACTCCTGGGCAGATTTTGTTG 6 263 1 CTCCTGGGCA 0.993561 -38 AGTGATTTGCCCCCTGGGGAAAAGTACCCC 7 16 1 CCCCTGGGGA 0.990852 -34 GGAAAAGTACCCCCTTGACTTTTGTAA 7 33 1 CCCCTTGACT 0.931753 -17 GGCTGGAAAACTCTTGGGCACGAAAAAACA 9 94 0 CTCTTGGGCA 0.972471 -122 TCACCTTTGTCCCCTGGGTAAAAAGCTATA 9 150 1 CCCCTGGGTA 0.988 -66 CTTAAAATCGCTCTTGGATTAAGATGGCGC 10 55 1 CTCTTGGATT 0.744146 -246 TAAGCTAAGTCCCCTTGAGAGCGGCTGTTA 10 106 0 CCCCTTGAGA 0.919659 -195 ********** Masking position 7 Map Score: 8.85346 Number of sites scoring better than the average of aligned sites = 1493 Number in coding regions = 1361 Number in noncoding regions = 132 Number of orfs with sites within 600 bp upstream = 143 Fraction of orfs with sites within 600 bp upstream = 0.0229682 Motif number 3 GCCCTAACCCACCGAGACTAA 4 1 1 GCCCTACCCA 0.956696 -60 TCTCCCAAAGGCGATCGCCGATTATTTCAGA 5 48 0 GCGATGCCGA 0.968583 -28 CTTTAGTTTGGCGATCGCCGATAAAAAGTAG 6 44 1 GCGATGCCGA 0.968583 -257 TCTCGGACCAGCCATTCCCCACATCACCAGG 6 141 0 GCCATCCCCA 0.893489 -160 TAATTTTCATGCGATTACTGCATTGGTGCTG 8 13 0 GCGATACTGC 0.909369 -90 GCAGAGCCAAGCTCTCACTCCTCTGTAATCT 9 38 0 GCTCTACTCC 0.883795 -178 TGAGAGCTTGGCTCTGCCTGCTCCCATTGTA 9 52 1 GCTCTCCTGC 0.878247 -164 CTTGAGAGCGGCTGTTACCGAAGATTCTCAG 10 92 0 GCTGTACCGA 0.95599 -209 AACCAACTGAGCTATAACCGCAGGGATGGAG 10 190 0 GCTATACCGC 0.963869 -111 TCAGTGTCGCGCTCTAACCAACTGAGCTATA 10 205 0 GCTCTACCAA 0.935781 -96 TTCTGGACTTGCGGTTACCAAGACTTGAACT 10 252 0 GCGGTACCAA 0.89722 -49 ***** ***** Masking position 5 Map Score: 10.0895 Number of sites scoring better than the average of aligned sites = 1580 Number in coding regions = 1476 Number in noncoding regions = 104 Number of orfs with sites within 600 bp upstream = 118 Fraction of orfs with sites within 600 bp upstream = 0.0189528 Motif number 4 ATTAAATTAATTGTAAATAATAAAAACC 1 39 1 TTGTAATAAA 0.963172 -18 AGTGAGCAAATTGTCACAAAGAAAAATCAAAA 2 53 0 TTGTCAAAAA 0.904023 -50 TCTCCGCTAGTTGTTAATAACATATAAAACTA 3 55 0 TTGTTATAAA 0.911937 -29 AGTTTCTTGGCAGTAACAGTGGACAAGT 4 43 0 TTGGCATAAA 0.966424 -18 AGCCATCAATTTGGCAATAATTAGTCAAGTTA 5 17 0 TTGGCATAAT 0.888903 -59 TGCTTAGGTGTTGTCATTAATAACTCCTGGGC 6 250 1 TTGTCATAAA 0.985265 -51 TTTGTATAGTTTGTAACTAATAATTAATTTTC 8 36 0 TTGTAATAAA 0.963172 -67 CCTGCTCCCATTGTACATAAATACTCTGTTTT 9 68 1 TTGTACTAAT 0.757712 -148 TAATCTTTTCTTGTGCTTAAAATCGCTCTTGG 10 40 1 TTGTGCTAAA 0.867945 -261 TTACCGAAGATTCTCAGTAACAAAGCGCCATC 10 77 0 TTCTCATAAA 0.89656 -224 ****** *** * Masking position 9 Map Score: 8.47226 Number of sites scoring better than the average of aligned sites = 207 Number in coding regions = 163 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 5 CAGATTTTTTCCATCATTACAAAACTATTAAATTA 1 13 1 CATCATTCAC 0.926657 -44 CACCGAGACTAAATTTTTTATTAACTTGTCCACTG 4 20 1 AATTTTTAAC 0.835586 -41 AGGCGATCGCCGATTATTTCAGAGCCATCAATTTG 5 36 0 CATTATTCAC 0.946653 -40 GTGTTCTGTGCTACTTTTTATCGGCGATCGCCAAA 6 50 0 CACTTTTAGC 0.846493 -251 CTAGTGGCAAAAATCTTTACAAAGCCTAGCCTGTT 6 174 0 AATCTTTCAC 0.927665 -127 CATAAATACTCTGTTTTTTCGTGCCCAAGAGTTTT 9 83 1 CGTTTTTCGC 0.90457 -133 GGCTACCGATCAACTTTTGCAAGGCTGGAAAACTC 9 111 0 CACTTTTCGC 0.951323 -105 AAGCTATAAAAAATCTTTGCGAAGCACACCTAAAC 9 172 1 AATCTTTCAC 0.927665 -44 CCTAAACTGCCCATTTTTGCGGAACT 9 200 1 CATTTTTCAC 0.984577 -16 CAGAAAAAATCCATTTTTGATAATCTTTTCTTGTG 10 20 1 CATTTTTAAC 0.947402 -281 * ****** * * * Masking position 8 Map Score: 6.04453 Number of sites scoring better than the average of aligned sites = 561 Number in coding regions = 470 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 6 GCCCTAACCCACCGAGACTAAATTTTTTA 4 8 1 CCACCGAGCT 0.892413 -53 TAGAAACAATATCCCCTACCCTAGCTAGGGAT 6 98 0 ACCCCTACCT 0.915616 -203 TATTAATGACAACACCTAAGCACTGGTCATTA 6 240 0 ACACCTAACA 0.916262 -61 TGTCATTAATAACTCCTGGGCAGATTTTGTTG 6 261 1 ACTCCTGGCA 0.909743 -40 GGGGAAAAGTACCCCCTTGACTTTTGTAA 7 31 1 ACCCCTTGCT 0.894502 -19 CTGACGATCACATTCCTAGACTGGATTTTTTC 8 78 0 CTTCCTAGCT 0.738013 -25 CTTTGCGAAGCACACCTAAACTGCCCATTTTT 9 186 1 CCACCTAACT 0.96506 -30 CAGATGCTCTACCAACTAAGCTAAGTCCCCTT 10 120 0 ACAACTAACT 0.871695 -181 AGGAGATTCGAACTCCTGACCTTCTGAATGCA 10 155 0 ACTCCTGACT 0.962219 -146 AGGAGTTCGAATCTCCTAGTCTCCATCCCTGC 10 170 1 ACTCCTAGCT 0.982782 -131 TCGCGCTCTAACCAACTGAGCTATAACCGCAG 10 198 0 ACAACTGACT 0.828671 -103 * ******* ** Masking position 6 Map Score: 6.74298 Number of sites scoring better than the average of aligned sites = 470 Number in coding regions = 394 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 7 CACAAAGAAAAATCAAAATCCCTCCGATTACT 2 39 0 AACAAATCCC 0.978365 -64 TCTGTTAGCCAATCAATTTCCCTAATACT 2 84 1 AACAATTCCC 0.988287 -19 GGAACCCTAGAAACAATATCCCCTACCCTAGC 6 105 0 AACAATTCCC 0.988287 -196 TCTCTCGGACCAGCCATTCCCCACATCACCAG 6 142 0 CACCATCCCC 0.937509 -159 TAGCCAAAATCACCTTTGTCCCCTGGGTAAAA 9 141 1 CACTTTTCCC 0.923331 -75 TCTACCAACTAAGCTAAGTCCCCTTGAGAGCG 10 113 0 AACTAATCCC 0.969286 -188 ** **** **** Masking position 2 Map Score: 2.37933 Number of sites scoring better than the average of aligned sites = 176 Number in coding regions = 145 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 8 TTTTATTAACTTGTCCACTGTTACTGCCAA 4 35 1 TTGTCCACTG 0.989337 -26 TCCCAGTGATTTGCCCCCTGGGGAAAAGTA 7 12 1 TTGCCCCCTG 0.995327 -38 AAAATCACCTTTGTCCCCTGGGTAAAAAGC 9 146 1 TTGTCCCCTG 0.996068 -70 ********** Masking position 2 Map Score: 1.93634 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 33 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 9 TTACAATTAATTTAATAGTTTTGTAATGATG 1 24 0 TTTAATATTT 0.939362 -33 GGTTTTTATTATTTACAATTAATT 1 43 0 TTTTATTTTT 0.761408 -14 ATTTTGACTTTTTAAAAATTT 3 1 0 TTTAAAATTT 0.875227 -83 TAAAACTAAATTGAAAAGTTTTACTGTGTTG 3 32 0 TTGAAAATTT 0.751004 -52 TTCAATTTAGTTTTATATGTTATTAACAACT 3 48 1 TTTTATAGTT 0.841245 -36 TGATGTCAGGTTTTAAACTTTAGTTTGGCGA 6 27 1 TTTTAAATTT 0.911265 -274 TTGTAAATATTTGTATAGTTTGTAACTAATA 8 46 0 TTGTATATTT 0.906994 -57 CTCTGTAATCTTTAATATTGTTGCTTTTCAA 9 18 0 TTTAATATGT 0.763631 -198 CGCAAAGATTTTTTATAGCTTTTTACCCAGG 9 162 0 TTTTATACTT 0.841245 -54 TGAAGTCGTTTTTTCTATTTTT 11 41 1 TTTTCTATTT 0.825475 -12 ******* *** Masking position 2 Map Score: 3.44275 Number of sites scoring better than the average of aligned sites = 235 Number in coding regions = 168 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 10 AAATCAAAATCCCTCCGATTACTGGTTGGA 2 32 0 CCCTCCGATT 0.984272 -71 TTCCCAGTGATTTGCCCCCTGG 7 3 1 CCCAGTGATT 0.967178 -47 TAGTCTCCATCCCTGCGGTTATAGCTCAGT 10 186 1 CCCTGCGGTT 0.985411 -115 TGCTCTCTTCCCCTATGATTCTTCCTTCAT 11 12 1 CCCTATGATT 0.964661 -41 ********** Masking position 9 Map Score: 0.0899904 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 34 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 11 ********** No masking Map Score: 3.39172e-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: 3.39172e-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 13 ********** No masking Map Score: 3.39172e-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