AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i222_synecho_ctra_100.orf -o222_synecho_ctra_100.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 RCT00453 87 Chlamydia_trachomatis #8 RCT00553 300 Chlamydia_trachomatis #9 RCT00797 300 Chlamydia_trachomatis #10 RCT00798 18 Chlamydia_trachomatis Motif number 1 TGATTGCCTTCATTCTATGGCCCCACACCAT 1 34 1 CATCTATGGC 0.85183 -233 TCTATGGCCCCACACCATTGCGTTAAATATC 1 47 1 CACCCATTGC 0.724948 -220 GTTAAATATCTTTACGATCGCCATTGGCTAG 1 68 1 TTTCGATCGC 0.94154 -199 TGTATTTTAGCTTCCCATGGCTAGCCAATGG 1 88 0 CTTCCATGGC 0.987547 -179 TAGAGTGGCCTTCCCCATCCCATCAACCCTC 2 83 0 TTCCCATCCC 0.931764 -201 CTGAAGGCATTACCCCAGGCCACTCCGGGTC 2 190 0 TACCCAGGCC 0.743728 -94 GCTTGCTTAGTTTGCGATGGCGTCAGCGGCA 2 233 0 TTTCGATGGC 0.962143 -51 CCCATCCCAACTTTCCATGGCACCCAGCGGA 3 42 0 CTTCCATGGC 0.987547 -99 TAGCGGGATTTTCCCCATCCCAACTTTCCAT 3 55 0 TTCCCATCCC 0.931764 -86 ATTTTTCCGCTTTCCTATGGCTTATCAGGTA 5 247 1 TTTCTATGGC 0.941736 -54 GATGTTGGCCTTGACCATGGCCGAGGAAAGA 6 77 1 TTGCCATGGC 0.969601 -126 GTTGATCAACCTGACCAGCGCTAATCAGTAT 6 121 1 CTGCCAGCGC 0.918728 -82 AAACAAGGCCTTTGCTAGGGCGGAATTACGA 6 167 1 TTTCTAGGGC 0.881491 -36 TTCAAAAAAACTCTCGATCGCCCCTGGTAAA 9 18 0 CTCCGATCGC 0.957761 -283 *** ******* Masking position 7 Map Score: 15.9728 Number of sites scoring better than the average of aligned sites = 1874 Number in coding regions = 1698 Number in noncoding regions = 176 Number of orfs with sites within 600 bp upstream = 179 Fraction of orfs with sites within 600 bp upstream = 0.0287504 Motif number 2 TATCCGGCCTGTATTTTAGCTTCCCATGGC 1 98 0 GTATTTTAGC 0.848167 -169 CCGGATAACCCCATTTACCCTTTCCCAAAG 1 121 1 CCATTTACCC 0.786226 -146 CGATTCTCTCGGATTTTCGGCCTGCAATTT 1 177 0 GGATTTTCGG 0.803938 -90 GCTGACTTTGCCATTTTACCGATTCTCTCG 1 196 0 CCATTTTACC 0.965333 -71 GGCAAAGTCAGCATTTTCGCTTGTAAACCC 1 214 1 GCATTTTCGC 0.958112 -53 GAAGGCCACTCTATTTTAGGCTAGTTAGTG 2 101 1 CTATTTTAGG 0.524251 -183 GTAGTTAGCGCTATTTTTGCTCACTTTTCC 3 15 1 CTATTTTTGC 0.857316 -126 AACCCTAGCGGGATTTTCCCCATCCCAACT 3 61 0 GGATTTTCCC 0.971395 -80 CAACAAGCAAGGATTTTTCCGCTTTCCTAT 5 235 1 GGATTTTTCC 0.955131 -66 CAACTTTTTACCATTTTACCCGGCTCAATT 5 279 1 CCATTTTACC 0.965333 -22 TAACAAAGGATTTGCGCTCTCTGCTGG 6 8 1 GGATTTGCGC 0.794899 -195 CGCCCGTTACCGATTCTACCCCAGCAGAGA 6 28 0 CGATTCTACC 0.814418 -175 CGGTAACGGGCGATTTTTCCTAGGTTTAGC 6 46 1 CGATTTTTCC 0.96456 -157 TACGAGAGACCCATTTTTCC 6 193 1 CCATTTTTCC 0.959069 -10 GGAGTGTTTGCCATTGTAGCGTTTCACGGA 8 220 0 CCATTGTAGC 0.747212 -81 CCAAGAAGAGGGATTTCTCCTTCTGGCCTA 9 216 0 GGATTTCTCC 0.756463 -85 ********** Masking position 5 Map Score: 14.9378 Number of sites scoring better than the average of aligned sites = 1081 Number in coding regions = 919 Number in noncoding regions = 162 Number of orfs with sites within 600 bp upstream = 188 Fraction of orfs with sites within 600 bp upstream = 0.030196 Motif number 3 ACATTACCTACAAACTTCAACAAAAAACACCT 1 245 1 CAACCAAAAA 0.861866 -22 TGGGGTAATGCCTTCAGCGATACAATAGATGCCGCTG 2 204 1 CCTCCAACAA 0.955887 -80 AGTATTTGATCCATCCCCATAAACAAGGCCTTTGCTA 6 147 1 CCTCCTAAAG 0.987162 -56 ACTCCTACATCCCTCTCCCTCAAAATACTTGCTACTA 7 15 1 CCTCCTAAAA 0.986106 -73 CCACTTCGTAAAATCTACCAAAAAAAAGCTGCATTTA 7 58 1 AATCCAAAAA 0.794831 -30 GATCTCTATACAATCTCCTAAAAGAAGCTCCTCCGAA 8 140 1 CATCCAAAAG 0.979609 -161 CAATGGCAAACACTCCGCGTAAAAAGAGACGATTCTT 8 234 1 CATCCTAAAA 0.968038 -67 TCCCTCTCCATAAATAAAAAATTTACTG 8 283 0 CCTCCTAAAA 0.986106 -18 AAACTTCACTCCTTCTTCCATAAGAAGAAATGTGTAG 9 83 0 CCTCCAAAAG 0.991195 -218 CACAAGCCACCCTTCTCCAAGAAGAGGGATTTCTCCT 9 225 0 CCTCCAAAAG 0.991193 -76 ** ** * * ** * * Masking position 12 Map Score: 12.7147 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 67 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 4 AACCCCATTTACCCTTTCCCAAAGCCAGAG 1 127 1 ACCCTTTCCC 0.984638 -140 TGCAATTTACTCGCTCTCCCCTAGGGTACT 1 155 0 TCGCTCTCCC 0.962292 -112 AGAGTGGCCTTCCCCATCCCATCAACCCTC 2 83 0 TCCCCATCCC 0.949065 -201 CTATTTTTGCTCACTTTTCCGCTGGGTGCC 3 25 1 TCACTTTTCC 0.896029 -116 AGCGGGATTTTCCCCATCCCAACTTTCCAT 3 55 0 TCCCCATCCC 0.949065 -86 TAACTCCAAAACACTTTCCCAGGTAAAGCT 3 92 1 ACACTTTCCC 0.908045 -49 AACTCCTACATCCCTCTCCCTCAAAATACT 7 14 1 TCCCTCTCCC 0.994952 -74 CCTTTATAAAACCCTTTTGCTTAGTTCCGT 8 195 1 ACCCTTTTGC 0.755228 -106 TCCCTCTCCATAAATAAAAA 8 291 0 TCCCTCTCCA 0.939499 -10 AAAACTTCACTCCTTCTTCCATAAGAAGAA 9 91 0 TCCTTCTTCC 0.86488 -210 GAAGGAGAAATCCCTCTTCTTGGAGAAGGG 9 223 1 TCCCTCTTCT 0.875451 -78 ACCACAAGCCACCCTTCTCCAAGAAGAGGG 9 234 0 ACCCTTCTCC 0.832796 -67 ********** Masking position 2 Map Score: 13.6508 Number of sites scoring better than the average of aligned sites = 1257 Number in coding regions = 1104 Number in noncoding regions = 153 Number of orfs with sites within 600 bp upstream = 174 Fraction of orfs with sites within 600 bp upstream = 0.0279473 Motif number 5 AATTTACTCGCTCTCCCCTAGGGTACTCTGGCTT 1 148 0 CTTCCCGGGT 0.974401 -119 AAATTCGTTAAATTTTCCGAGGGTTGATGGGATG 2 65 1 AATTCCGGGT 0.947848 -219 TTTTTGCTCACTTTTCCGCTGGGTGCCATGGAAA 3 28 1 CTTTCGGGGT 0.972098 -113 GTGCCATGGAAAGTTGGGATGGGGAAAATCCCGC 3 50 1 AATTGGGGGG 0.73096 -91 TAACATGCACCAGTTCACGGGGGTTTAGCTCAGT 5 156 0 CATTACGGGT 0.978568 -145 ACAATTGAGCCGGGTAAAATGGTAA 5 286 0 CATTAGGGGT 0.958948 -15 AGGATTTGCGCTCTCTGCTGGGGTAGAATCGGTA 6 17 1 CTTCGCGGGT 0.952145 -186 GTAACGGGCGATTTTTCCTAGGTTTAGCCGATGT 6 48 1 ATTTCCGGTT 0.663459 -155 AACAAAACTTTTTTCAACCTGGGTTTTTTTCAAG 8 103 0 TTTCACGGGT 0.796917 -198 AGAATCGTCTCTTTTTACGCGGAGTGTTTGCCAT 8 236 0 CTTTACGGAG 0.734665 -65 GGACCTGTTTACCAGGGGCGATCGAGAG 9 5 1 CTTTACGGGG 0.97233 -296 AGCGATTACTAATTTTAGCAGGGTAGAT 9 283 1 AATTAGGGGT 0.895641 -18 ** ** ** **** Masking position 4 Map Score: 6.08874 Number of sites scoring better than the average of aligned sites = 1051 Number in coding regions = 915 Number in noncoding regions = 136 Number of orfs with sites within 600 bp upstream = 161 Fraction of orfs with sites within 600 bp upstream = 0.0258593 Motif number 6 TAAAATGGCAAAGTCAGCATTTTCGCTTGT 1 208 1 AAGTCAGCAT 0.710461 -59 TTCGCTTGTAAACCCAACATTACCTACAAA 1 229 1 AACCCAACAT 0.911617 -38 AAGCTCAATGAACCAAAGTTTCCCACTAAC 2 124 0 AACCAAAGTT 0.902237 -160 ATCGCAAACTAAGCAAGCATTAATACAAAT 2 246 1 AAGCAAGCAT 0.937426 -38 AACTTTAAAAAACTAAAGATAATTTCAGCT 3 118 0 AACTAAAGAT 0.768281 -23 AGTTCACAACAAGCAAGGATTTTTCCGCTT 5 229 1 AAGCAAGGAT 0.936963 -72 TAACAAAGGATTTGCGCTCTC 6 2 1 AACAAAGGAT 0.885979 -201 TCTATAGAACAACCAAGCTTGTTGCTAGCT 8 36 1 AACCAAGCTT 0.946436 -265 TCTTGAAAAAAACCCAGGTTGAAAAAAGTT 8 102 1 AACCCAGGTT 0.916638 -199 AGAGATCCATAACAAAACTTTTTTCAACCT 8 117 0 AACAAAACTT 0.693707 -184 ********** Masking position 6 Map Score: 5.22733 Number of sites scoring better than the average of aligned sites = 484 Number in coding regions = 413 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 7 CATCTATTGTATCGCTGAAGGCATTACCCC 2 205 0 ATCGCTGAAG 0.971296 -79 TACAATAGATGCCGCTGACGCCATCGCAAA 2 224 1 GCCGCTGACG 0.987243 -60 GCGGACTCGAACCGCTGACATCCTGCTTGC 5 108 1 ACCGCTGACA 0.987054 -193 TTTACTGCAAACCGCTGCAAAGAATCGTCT 8 260 0 ACCGCTGCAA 0.938438 -41 AAAATTAGTAATCGCTGACGGAGAGCCTAA 9 269 0 ATCGCTGACG 0.987054 -32 ********** Masking position 6 Map Score: 3.16594 Number of sites scoring better than the average of aligned sites = 87 Number in coding regions = 79 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 8 AGGGTAAATGGGGTTATCCGGCCTGTATTTT 1 111 0 GGGTATCCGG 0.945878 -156 CTCTCCCCTAGGGTACTCTGGCTTTGGGAAA 1 141 0 GGGACTCTGG 0.96903 -126 CATTACCCCAGGCCACTCCGGGTCATGTTTA 2 183 0 GGCACTCCGG 0.991497 -101 TGGCGTCAGCGGCATCTATTGTATCGCTGAA 2 216 0 GGCTCTATTG 0.858435 -68 GGCTACTCCTAGTATATCTAG 5 1 1 GGCACTCCTA 0.879847 -300 GCTTTCCTATGGCTTATCAGGTAACAACTTT 5 255 1 GGCTATCAGG 0.912469 -46 TCTATTGTAGGGCATCTCTTGAAAAAAACCC 8 86 1 GGCTCTCTTG 0.979058 -215 *** ******* Masking position 7 Map Score: 1.46286 Number of sites scoring better than the average of aligned sites = 330 Number in coding regions = 304 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 9 TACTCGCTCTCCCCTAGGGTACTCTGGCTT 1 148 0 CCCCTAGGGT 0.698606 -119 TCGTTAAATTTTCCGAGGGTTGATGGGATG 2 69 1 TTCCGAGGGT 0.91671 -215 GCTCACTTTTCCGCTGGGTGCCATGGAAAG 3 33 1 CCGCTGGGTG 0.815579 -108 GGGGAAAATCCCGCTAGGGTTCTAACTCCA 3 70 1 CCGCTAGGGT 0.969566 -71 ATGCACCAGTTCACGGGGGTTTAGCTCAGT 5 156 0 TCACGGGGGT 0.811918 -145 TTTGCGCTCTCTGCTGGGGTAGAATCGGTA 6 21 1 CTGCTGGGGT 0.975457 -182 CGGGCGATTTTTCCTAGGTTTAGCCGATGT 6 52 1 TTCCTAGGTT 0.816593 -151 AACAAGGCCTTTGCTAGGGCGGAATTACGA 6 168 1 TTGCTAGGGC 0.88724 -35 ********** Masking position 4 Map Score: 2.21779 Number of sites scoring better than the average of aligned sites = 1091 Number in coding regions = 1019 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 10 CTGCCTTGCCAAATTTGTCTAA 1 3 1 GCCTTGCCAA 0.948942 -264 AGCTTCCCATGGCTAGCCAATGGCGATCGT 1 81 0 GGCTAGCCAA 0.943515 -186 TGTGATGTAAGACTAACCTATTAACCTATG 2 28 1 GACTAACCTA 0.873564 -256 GTTTCCCACTAACTAGCCTAAAATAGAGTG 2 107 0 AACTAGCCTA 0.873564 -177 CGCCATCGCAAACTAAGCAAGCATTAATAC 2 242 1 AACTAAGCAA 0.802113 -42 CAATCTTCAGACCTAGCCAAAAAACAACAG 5 36 1 ACCTAGCCAA 0.967675 -265 GCCGATGTTGGCCTTGACCATGGCCGAGGA 6 74 1 GCCTTGACCA 0.609384 -129 CGTTTCACGGAACTAAGCAAAAGGGTTTTA 8 201 0 AACTAAGCAA 0.802113 -100 TCTCCTTCTGGCCTAAACAATCTTTCGCAT 9 201 0 GCCTAAACAA 0.890904 -100 ********** Masking position 4 Map Score: 0.983983 Number of sites scoring better than the average of aligned sites = 616 Number in coding regions = 512 Number in noncoding regions = 104 Number of orfs with sites within 600 bp upstream = 112 Fraction of orfs with sites within 600 bp upstream = 0.0179891 Motif number 11 ********** No masking Map Score: -5.73108e-13 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 AATATCTGAAAACCGGCTCGAAAAAGTATG 5 71 1 AACCGGCTCG 0.859678 -230 TATGGAGATTAGCGGACTCGAACCGCTGAC 5 97 1 AGCGGACTCG 0.905737 -204 CTGCTTGCAAAGCAGGCGCTCTACCAACTG 5 130 1 AGCAGGCGCT 0.964431 -171 TAGAATCGGTAACGGGCGATTTTTCCTAGG 6 40 1 AACGGGCGAT 0.843303 -163 CAGGTTGATCAACAGGGGATAATTGGTCTT 6 104 0 AACAGGGGAT 0.81595 -99 GGACCTGTTTACCAGGGGCGATCGAGAGTT 9 11 1 ACCAGGGGCG 0.93972 -290 GGTACCATGTAGCAGTCTAGAGCGGAGGCG 9 154 1 AGCAGTCTAG 0.738898 -147 AGCAGTCTAGAGCGGAGGCGTCTAGATTAC 9 164 1 AGCGGAGGCG 0.938234 -137 TACTAATTTTAGCAGGGTAGAT 9 289 1 AGCAGGGTAG 0.946276 -12 ********** Masking position 1 Map Score: 0.925323 Number of sites scoring better than the average of aligned sites = 790 Number in coding regions = 732 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 13 GGGGAGAGCGAGTAAATTGCAGGCCGAAAATCCG 1 164 1 AGAATGCAGC 0.936047 -103 AGATGAATTAAGGCAATTACATGCATTTCTC 4 8 0 AGAATACAGC 0.97941 -47 AGACCTAGCCAAAAAACAACAGCCAGGAATATCT 5 44 1 AAAACACACC 0.837458 -257 TTGTTACCAAAGGGCGTAACATGCACCAGTTCAC 5 172 0 AGCGTACAGC 0.955632 -129 TAGCCATAGAAGTTCACAACAAGCAAGGATTTTT 5 219 1 AGCACACAGC 0.985099 -82 TTTAGTGCACAGCTAGCAACAAGCTTGGTTGTTC 8 42 0 AGAGCACAGC 0.985099 -259 GAGAGCCTAAAAAAAACCACAAGCCACCCTTCTC 9 245 0 AAAACACAGC 0.964029 -56 ** *** *** ** Masking position 11 Map Score: 1.20881 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 27 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 14 ********** No masking Map Score: -5.73108e-13 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: -5.73108e-13 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