AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i222_synecho_ctra_300.orf -o222_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 RCY30362 266 Synechocystis #2 RCY37275 283 Synechocystis #3 RCY38704 140 Synechocystis #4 RCY05947 54 Synechocystis #5 RCY42648 300 Synechocystis #6 RCY26670 202 Synechocystis #7 RCY31923 135 Synechocystis #8 RCY04429 240 Synechocystis #9 RCY45916 300 Synechocystis #10 RCT00453 87 Chlamydia_trachomatis #11 RCT00553 300 Chlamydia_trachomatis #12 RCT00797 300 Chlamydia_trachomatis #13 RCT00798 18 Chlamydia_trachomatis Motif number 1 CATTGCGTTAAATATCTTTACGATCGCCATTGGCTAGCCATGGG 1 62 1 ATTCTCCGGC 0.990301 -205 GGTTATCCGGCCTGTATTTTAGCTTCCCATGGCTAGCCAATGGC 1 87 0 CTTATCCGCT 0.954101 -180 GGCCGGATAACCCCATTTACCCTTTCCCAAAGCCAGAGTACCCT 1 119 1 CATCTCCGCC 0.980078 -148 TTCGGCCTGCAATTTACTCGCTCTCCCCTAGGGTACTCTGGCTT 1 148 0 ATTCTCCGGT 0.989487 -119 ATGCTGTATTAAATTCGTTAAATTTTCCGAGGGTTGATGGGATG 2 55 1 ATTATCCGGT 0.956877 -229 ACAACAAGCAAGGATTTTTCCGCTTTCCTATGGCTTATCAGGTA 5 234 1 ATTCTCCGGC 0.990301 -67 ATCAGGTAACAACTTTTTACCATTTTACCCGGCTCAATTGT 5 270 1 ATTCTACGCT 0.85848 -31 CTAGGTTTAGCCGATGTTGGCCTTGACCATGGCCGAGGAAAGAC 6 65 1 CTTCTCCGCC 0.98964 -138 CAATTATCCCCTGTTGATCAACCTGACCAGCGCTAATCAGTATT 6 109 1 CTTATCCGCT 0.954101 -94 GTCTAATAATACCAAATTGCCTTGGCCCAGAGCTTTTGAGTTAG 7 58 0 AATCGCCGCT 0.889525 -78 TGACCTAGTAAGAAAATTTTAACTACCCAAGGCTGA 8 215 1 AATATCCGCT 0.928721 -26 TTAATAACAACTTCTATTGACCATTGCCCCTGGTCTACAGTGAA 9 126 1 CTTCTCCGGT 0.987229 -175 AATGGTTTGGATTGTATTTTCAGAGTCCTACGCCACTAAAAATT 9 186 1 ATTCACCGCC 0.919657 -115 ATGTTTATGAACCCATTGCTCCCTCCCCTGTGGCCA 9 275 1 AAGCTCCGGC 0.877067 -26 TTTTATTTCAAAAAAACTCTCGATCGCCCCTGGTAAACAGGTCC 12 11 0 AATCTCCGGT 0.979788 -290 * * * * * ** *** Masking position 18 Map Score: 18.9557 Number of sites scoring better than the average of aligned sites = 737 Number in coding regions = 683 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 2 ACATTACCTACAAACTTCAACAAAAAACACCT 1 245 1 CAACTCAAAA 0.892759 -22 AGTATTTGATCCATCCCCATAAACAAGGCCTTTGC 6 147 1 CCTCCCTAAA 0.976283 -56 ACTCCTACATCCCTCTCCCTCAAAATACTTGCTAC 10 15 1 CCTCTCTAAA 0.988265 -73 CCACTTCGTAAAATCTACCAAAAAAAAGCTGCATT 10 58 1 AATCTCAAAA 0.838111 -30 GATCTCTATACAATCTCCTAAAAGAAGCTCCTCCG 11 140 1 CATCTCAAAA 0.981414 -161 CAATGGCAAACACTCCGCGTAAAAAGAGACGATTC 11 234 1 CATCCCTAAA 0.954446 -67 TCCCTCTCCATAAATAAAAAATTTAC 11 285 0 CCTCTCTAAA 0.988265 -16 AAACTTCACTCCTTCTTCCATAAGAAGAAATGTGT 12 85 0 CCTCTCAAAA 0.99042 -216 CACAAGCCACCCTTCTCCAAGAAGAGGGATTTCTC 12 227 0 CCTCTCAAAA 0.988818 -74 ** *** * * ** * Masking position 12 Map Score: 9.7259 Number of sites scoring better than the average of aligned sites = 87 Number in coding regions = 70 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 3 AACCCCATTTACCCTTTCCCAAAGCCAGAG 1 127 1 ACCCTTTCCC 0.880259 -140 TGCAATTTACTCGCTCTCCCCTAGGGTACT 1 155 0 TCGCTCTCCC 0.987846 -112 AGAGTGGCCTTCCCCATCCCATCAACCCTC 2 83 0 TCCCCATCCC 0.980954 -201 AGCGGGATTTTCCCCATCCCAACTTTCCAT 3 55 0 TCCCCATCCC 0.980954 -86 TGCAAAGCAGGCGCTCTACCAACTGAGCTA 5 135 1 GCGCTCTACC 0.859303 -166 TGAACCCATTGCTCCCTCCCCTGTGGCCA 9 282 1 GCTCCCTCCC 0.951583 -19 AACTCCTACATCCCTCTCCCTCAAAATACT 10 14 1 TCCCTCTCCC 0.994835 -74 TCCCTCTCCATAAATAAAAA 11 291 0 TCCCTCTCCA 0.955574 -10 ********** Masking position 7 Map Score: 8.62447 Number of sites scoring better than the average of aligned sites = 486 Number in coding regions = 435 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 4 GCCGGATAACCCCATTTACCCTTTCCCAAAG 1 120 1 CCCATTACCC 0.817557 -147 TGCTGACTTTGCCATTTTACCGATTCTCTCG 1 196 0 GCCATTTACC 0.936897 -71 TATCGCTGAAGGCATTACCCCAGGCCACTCC 2 195 0 GGCATTCCCC 0.940005 -89 GAACCCTAGCGGGATTTTCCCCATCCCAACT 3 61 0 GGGATTTCCC 0.940555 -80 ACAACAAGCAAGGATTTTTCCGCTTTCCTAT 5 234 1 AGGATTTTCC 0.818504 -67 ACAACTTTTTACCATTTTACCCGGCTCAATT 5 278 1 ACCATTTACC 0.829527 -23 TCGCCCGTTACCGATTCTACCCCAGCAGAGA 6 28 0 CCGATTTACC 0.914656 -175 TCGGTAACGGGCGATTTTTCCTAGGTTTAGC 6 45 1 GCGATTTTCC 0.960564 -158 CGAGGAAAGACCAATTATCCCCTGTTGATCA 6 98 1 CCAATTTCCC 0.780481 -105 TTACGAGAGACCCATTTTTCC 6 192 1 CCCATTTTCC 0.959566 -11 AAGCTTTTCGGGGATTCTTACTTTGGGTAGA 8 74 1 GGGATTTTAC 0.455818 -167 ACTTCTATTGACCATTGCCCCTGGTCTACAG 9 135 1 ACCATTCCCC 0.901391 -166 TGTTTATGAACCCATTGCTCCCTCCCCTGTG 9 276 1 CCCATTCTCC 0.945729 -25 TCCAAGAAGAGGGATTTCTCCTTCTGGCCTA 12 216 0 GGGATTCTCC 0.909928 -85 ****** **** Masking position 4 Map Score: 13.8876 Number of sites scoring better than the average of aligned sites = 1108 Number in coding regions = 952 Number in noncoding regions = 156 Number of orfs with sites within 600 bp upstream = 186 Fraction of orfs with sites within 600 bp upstream = 0.0298747 Motif number 5 GGGTAAATGGGGTTATCCGGCCTGTATTTT 1 111 0 GGTTATCCGG 0.956089 -156 CACACCATCTGGTGAACCGGA 2 2 0 GGTGAACCGG 0.932399 -282 ATACAGCATAGGTTAATAGGTTAGTCTTAC 2 34 0 GGTTAATAGG 0.664134 -250 CTTTCCTATGGCTTATCAGGTAACAACTTT 5 256 1 GCTTATCAGG 0.97881 -45 ACTGATTAGCGCTGGTCAGGTTGATCAACA 6 120 0 GCTGGTCAGG 0.929481 -83 CCTGACCAGCGCTAATCAGTATTTGATCCA 6 130 1 GCTAATCAGT 0.712572 -73 ATGCCTAATTGCTGATCTGGTAGTTGTACC 7 109 0 GCTGATCTGG 0.921878 -27 TCCCCGAAAAGCTTATCAGGGAAGCCTCGA 8 58 0 GCTTATCAGG 0.97881 -183 GATCGCCCCTGGTAAACAGGTCC 12 4 0 GGTAAACAGG 0.915328 -297 ********** Masking position 3 Map Score: 6.04064 Number of sites scoring better than the average of aligned sites = 262 Number in coding regions = 232 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 6 GAGTAAATTGCAGGCCGAAAATCCGAGAGAA 1 173 1 CGGCCGAAAA 0.969805 -94 GTTGGGTTTACAAGCGAAAATGCTGACTTTG 1 216 0 CAGCGAAAAT 0.762596 -51 TTCCCACTAACTAGCCTAAAATAGAGTGGCC 2 104 0 CAGCCTAAAA 0.969525 -180 TCCATGGCACCCAGCGGAAAAGTGAGCAAAA 3 29 0 CAGCGGAAAA 0.981498 -112 ATCTTCAGACCTAGCCAAAAAACAACAGCCA 5 38 1 CAGCCAAAAA 0.956902 -263 AAGCCATAGGAAAGCGGAAAAATCCTTGCTT 5 239 0 AAGCGGAAAA 0.912631 -62 AGCGATAATTCAAGGGGAAAATTATGACTCT 8 167 0 CAGGGGAAAA 0.885159 -74 ATTTCTCCTTCTGGCCTAAACAATCTTTCGC 12 203 0 CGGCCTAAAC 0.805084 -98 TCGCTGACGGAGAGCCTAAAAAAAACCACAA 12 257 0 AAGCCTAAAA 0.862347 -44 * ********* Masking position 8 Map Score: 4.38776 Number of sites scoring better than the average of aligned sites = 336 Number in coding regions = 302 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 7 TCATTCTATGGCCCCACACCATTGCGTTAAATATC 1 43 1 GCCCACCAGC 0.975957 -224 AAGCCAGAGTACCCTAGGGGAGAGCGAGTAAATTG 1 148 1 ACCCAGGAGC 0.888552 -119 AAAATAGAGTGGCCTTCCCCATCCCATCAACCCTC 2 83 0 GGCCTCCACC 0.830885 -201 TGAAGGCATTACCCCAGGCCACTCCGGGTCATGTT 2 185 0 ACCCAGCACC 0.976552 -99 TACCGATTCTACCCCAGCAGAGAGCGCAAATCCTT 6 16 0 ACCCAGAAGC 0.962991 -187 CCTTGACCATGGCCGAGGAAAGACCAATTATCCCC 6 85 1 GGCCAGAACC 0.981183 -118 TCGTAATTCCGCCCTAGCAAAGGCCTTGTTTATGG 6 163 0 GCCCAGAACC 0.899018 -40 CCGCTCAATCGCCCCACTAAAATCCCTACTCAAAC 9 28 1 GCCCACAACC 0.989639 -273 TTCAAGAGATGCCCTACAATAGATCCTTATTTTTT 11 74 0 GCCCACAATC 0.925002 -227 GCTGACGGAGAGCCTAAAAAAAACCACAAGCCACC 12 251 0 AGCCAAAACC 0.776065 -50 **** ** * * ** Masking position 11 Map Score: 6.57946 Number of sites scoring better than the average of aligned sites = 541 Number in coding regions = 506 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 8 CATGGGAAGCTAAAATACAGGCCGGATAACCCC 1 100 1 TAAATCAGCC 0.978968 -167 GGAGAGCGAGTAAATTGCAGGCCGAAAATCCGA 1 166 1 TAAATCAGCC 0.978967 -101 CCTTCAGCGATACAATAGATGCCGCTGACGCCA 2 214 1 TACATGAGCC 0.986521 -70 ACTCTGAAAATACAATCCAAACCATTCACTGAG 9 179 0 TACATCAACC 0.925757 -122 CATAAACATTTACATTGGATGTCATCTCTAAGC 9 251 0 TACATGAGTC 0.904677 -50 AAATACTTGCTACTATACACGCCACTTCGTAAA 10 37 1 TACTTCAGCC 0.976647 -51 ATTCGCGACGTAATCTAGACGCCTCCGCTCTAG 12 170 0 TAATTGAGCC 0.939084 -131 **** * ** *** Masking position 9 Map Score: 3.06391 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 40 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 9 TTATCTTTAGTTTTTTAAAGTTACT 3 126 1 TTTTTTAAAG 0.924669 -15 AGTTAGATTATTTTTTCAAGATTATTAGAA 7 34 0 TTTTTTCAAG 0.973384 -102 CAACCTGGGTTTTTTTCAAGAGATGCCCTA 11 93 0 TTTTTTCAAG 0.973384 -208 ATAACAAAACTTTTTTCAACCTGGGTTTTT 11 109 0 TTTTTTCAAC 0.893527 -192 AGCAAAAGGGTTTTATAAAGGATAAAATGA 11 186 0 TTTTATAAAG 0.85884 -115 AGATGAGGATTATTATCAAGTATTGCGCCT 12 121 0 TATTATCAAG 0.828767 -180 ********** Masking position 6 Map Score: 2.2881 Number of sites scoring better than the average of aligned sites = 54 Number in coding regions = 37 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 10 GCTAGCCATGGGAAGCTAAAATACAGGCCG 1 94 1 GGAAGCTAAA 0.975662 -173 TTATAGCTCTGGAAGCTCAATGAACCAAAG 2 136 0 GGAAGCTCAA 0.936141 -148 TCAGCAATTAGGCATTTAAACC 7 124 1 GGCATTTAAA 0.902917 -12 TATAGTCTTAGGAATCTAAACTTAGTCTAG 8 138 0 GGAATCTAAA 0.931258 -103 TCAGCCTTGGGTAGTTAAAATTTTCTTAC 8 222 0 GGTAGTTAAA 0.909835 -19 ATTGAGGTGTGGCAGTTAAATCTCCCCCTT 9 63 0 GGCAGTTAAA 0.964942 -238 ********** Masking position 4 Map Score: 2.2695 Number of sites scoring better than the average of aligned sites = 123 Number in coding regions = 107 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 11 CATCTATTGTATCGCTGAAGGCATTACCCC 2 205 0 ATCGCTGAAG 0.947769 -79 TACAATAGATGCCGCTGACGCCATCGCAAA 2 224 1 GCCGCTGACG 0.968628 -60 GCGGACTCGAACCGCTGACATCCTGCTTGC 5 108 1 ACCGCTGACA 0.981719 -193 CCCTTGAATTATCGCTCCCATCACCTCGCA 8 182 1 ATCGCTCCCA 0.86652 -59 TTTACTGCAAACCGCTGCAAAGAATCGTCT 11 260 0 ACCGCTGCAA 0.937669 -41 AAAATTAGTAATCGCTGACGGAGAGCCTAA 12 269 0 ATCGCTGACG 0.981719 -32 ********** Masking position 6 Map Score: 2.18905 Number of sites scoring better than the average of aligned sites = 168 Number in coding regions = 154 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 12 ATTTACTCGCTCTCCCCTAGGGTACTCTGG 1 151 0 TCTCCCCTAG 0.955059 -116 GTCTGAAGATTGCGCCCTAGATATACTAGG 5 18 0 TGCGCCCTAG 0.979543 -283 GGCGCAATCTTCAGACCTAGCCAAAAAACA 5 32 1 TCAGACCTAG 0.946696 -269 CTCTCGTAATTCCGCCCTAGCAAAGGCCTT 6 171 0 TCCGCCCTAG 0.995234 -32 CACCTCGCAAACTGACCTAGTAAGAAAATT 8 203 1 ACTGACCTAG 0.885405 -38 TCTAGACGCCTCCGCTCTAGACTGCTACAT 12 160 0 TCCGCTCTAG 0.969976 -141 ********** Masking position 8 Map Score: 2.97591 Number of sites scoring better than the average of aligned sites = 202 Number in coding regions = 170 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 13 CCCGTTACCGATTCTACCCCAGCAGAGAGC 6 26 0 ATTCTACCCC 0.732918 -177 CATCCCGCTCAATCGCCCCACTAAAATCCC 9 24 1 AATCGCCCCA 0.918105 -277 GTGGCAGTTAAATCTCCCCCTTGTTTGAGT 9 55 0 AATCTCCCCC 0.985283 -246 GATAAGGCAAAAGCTCCCCAATTTTTAGTG 9 219 0 AAGCTCCCCA 0.965989 -82 AAAAACTCCTACATCCCTCTCC 10 3 1 AAACTCCTAC 0.716201 -85 CACTTCGTAAAATCTACCAAAAAAAAGCTG 10 59 1 AATCTACCAA 0.790517 -29 ATCTCTATACAATCTCCTAAAAGAAGCTCC 11 141 1 AATCTCCTAA 0.865757 -160 CTCCTAAAAGAAGCTCCTCCGAACTCAGAT 11 154 1 AAGCTCCTCC 0.946265 -147 ********** Masking position 1 Map Score: 1.39932 Number of sites scoring better than the average of aligned sites = 750 Number in coding regions = 606 Number in noncoding regions = 144 Number of orfs with sites within 600 bp upstream = 139 Fraction of orfs with sites within 600 bp upstream = 0.0223257 Motif number 14 CTGCCTTGCCAAATTTGTCT 1 1 1 CTGCCTTGCC 0.907402 -266 GTCTAATTGATTGCCTTCATTCTATGGCCC 1 27 1 TTGCCTTCAT 0.874812 -240 TAAAATAGAGTGGCCTTCCCCATCCCATCA 2 89 0 TGGCCTTCCC 0.96128 -195 ATGCATGTAATTGCCTTAATTCATCTGAAA 4 16 1 TTGCCTTAAT 0.866191 -39 TAGCCGATGTTGGCCTTGACCATGGCCGAG 6 72 1 TGGCCTTGAC 0.977589 -131 TAATACCAAATTGCCTTGGCCCAGAGCTTT 7 66 0 TTGCCTTGGC 0.952489 -70 TGGGGAGCTTTTGCCTTATCCTGCTTAGAG 9 229 1 TTGCCTTATC 0.895857 -72 TTTCTCCTTCTGGCCTAAACAATCTTTCGC 12 203 0 TGGCCTAAAC 0.832533 -98 ********** Masking position 6 Map Score: 1.47398 Number of sites scoring better than the average of aligned sites = 373 Number in coding regions = 326 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 15 ********** No masking Map Score: -3.65686e-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