AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i300_synecho_ctra_300.orf -o300_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 RCY43669 195 Synechocystis #2 RCY43837 121 Synechocystis #3 RCY26609 38 Synechocystis #4 RCY32578 235 Synechocystis #5 RCT00313 295 Chlamydia_trachomatis #6 RCT00316 275 Chlamydia_trachomatis #7 RCT00598 55 Chlamydia_trachomatis #8 RCT00599 52 Chlamydia_trachomatis #9 RCT00600 178 Chlamydia_trachomatis Motif number 1 AATCTCCTTGCCAAAACTCCTATGATTC 1 8 1 TTGCAAAACT 0.950023 -188 GTTACAGTTCTTGACAAAGCCAGATGGTAAC 1 119 1 TTGCAAAGCC 0.892442 -77 ACTTGCACAATTGGCAGAAGTTTAACTAACG 2 35 1 TTGCAGAAGT 0.960995 -87 ACGGGCGAATTTGTTAAAGGCACTACTGAAC 2 63 1 TTGTAAAGGC 0.807498 -59 AAAGAGCGAACTGTCAAAGGTTCAGTAGTGC 2 82 0 CTGCAAAGGT 0.955162 -40 TCTTTCAATGTTGGCAAAGGTTTT 2 108 1 TTGCAAAGGT 0.985386 -14 TTAGTAATCTTTGTTAAAAATTATGACATCT 4 43 1 TTGTAAAAAT 0.624248 -193 TGTGAGAAGTCTGAAAAAAGTTCCATAATTT 4 191 1 CTGAAAAAGT 0.84996 -45 TAAGCCTTCCTTGCAAGAAATCGAGTATTAC 5 127 1 TTGAAGAAAT 0.610107 -169 TGGGCCCAAGTTGGAAATGGTTTTCTGTGAG 5 226 0 TTGAAATGGT 0.724996 -70 CTTAATGGGATTGCCTGAAGTATCTACTGCG 6 229 0 TTGCTGAAGT 0.723901 -47 CAACCTTTGTTTGACAAAGGTTGTTTC 7 7 0 TTGCAAAGGT 0.985386 -49 CTGAGGCTCTTTGAAAAAACTATTTTTGTTG 9 122 1 TTGAAAAACT 0.87475 -57 *** ******* Masking position 2 Map Score: 11.1787 Number of sites scoring better than the average of aligned sites = 1073 Number in coding regions = 925 Number in noncoding regions = 148 Number of orfs with sites within 600 bp upstream = 177 Fraction of orfs with sites within 600 bp upstream = 0.0284292 Motif number 2 GAGATGCTCTACCCATTGTCCTGGGGAGCA 1 75 1 ACCCATTGTC 0.927325 -121 CCGTTAGTTAAACTTCTGCCAATTGTGCAA 2 37 0 AACTTCTGCC 0.822768 -85 GGCACTACTGAACCTTTGACAGTTCGCTCT 2 81 1 AACCTTTGAC 0.9522 -41 AAAACCTTTGCCAACATTGAAA 2 110 0 AACCTTTGCC 0.992294 -12 CATCTTCGCTACCCTTTTCCCCAGCCTTCT 4 69 1 ACCCTTTTCC 0.959397 -167 TAAATTATGGAACTTTTTTCAGACTTCTCA 4 193 0 AACTTTTTTC 0.828624 -43 ACTCACAGAAAACCATTTCCAACTTGGGCC 5 225 1 AACCATTTCC 0.961364 -71 GAATAAGAGAAAACATTTCCTCATAGATAG 6 126 0 AAACATTTCC 0.684933 -150 GAAACAACCTTTGTCAAACAAAGGT 7 6 1 AACCTTTGTC 0.98497 -50 TTTTCTCATCAACCTTTGTTTGACAAAGGT 7 17 0 AACCTTTGTT 0.851274 -39 ********** Masking position 7 Map Score: 10.9571 Number of sites scoring better than the average of aligned sites = 1176 Number in coding regions = 1058 Number in noncoding regions = 118 Number of orfs with sites within 600 bp upstream = 135 Fraction of orfs with sites within 600 bp upstream = 0.0216833 Motif number 3 CTCGATTACACCAACCTACTGGGCGTTCTA 1 42 1 CCAACCTACT 0.883004 -154 ACCCTTTTCCCCAGCCTTCTCAATGGGGAT 4 79 1 CCAGCCTTCT 0.989075 -157 CCAACTTGGGCCCACCTTCTCCACTCTGAG 5 243 1 CCCACCTTCT 0.9857 -53 ACCGTTATACAGCGCCTTCTGGTTTTACAG 6 56 1 AGCGCCTTCT 0.98544 -220 ACAGTCCTCAAGCGCCTTCTGTAAAACCAG 6 74 0 AGCGCCTTCT 0.98544 -202 ATCTAAGCAACTGCCTTCTTTTTCTCATC 7 37 0 ACTGCCTTCT 0.970283 -19 ********** Masking position 7 Map Score: 6.23644 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 34 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 4 TTCTATCTCGATTACACCAACCTACTGGGC 1 36 1 ATTACACCAA 0.915016 -160 GAACTGTAACATTTCACCAAATTCTGCTCC 1 99 0 ATTTCACCAA 0.915016 -97 AAAACCAACTATTTAAGCAAATTCACAGAA 5 25 1 ATTTAAGCAA 0.961312 -271 AGAGATTTATATCAAAGCAATAGAAAATAA 5 85 1 ATCAAAGCAA 0.975044 -211 ACTCTGAGCCATCAAAGCAATTTGTTTTCG 5 265 1 ATCAAAGCAA 0.975044 -31 ATCTAAGCAACTGCCTTCTT 7 46 0 ATCTAAGCAA 0.975044 -10 ********** Masking position 6 Map Score: 4.94655 Number of sites scoring better than the average of aligned sites = 93 Number in coding regions = 77 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 5 TTGTCTTACTTTTTTCTGTGAATTTGCTTAA 5 37 0 TTTTTCTGTA 0.982227 -259 TGTGAGTTTCTTTGTCTGTAAACATGAGATT 5 201 0 TTTGTCTGTA 0.93622 -95 GTTGGAAATGGTTTTCTGTGAGTTTCTTTGT 5 217 0 GTTTTCTGTA 0.981874 -79 AAAGCAATTTGTTTTCGGTAATTGGAAA 5 278 1 GTTTTCGGTA 0.968429 -18 ATGAGGAAATGTTTTCTCTTATTCAAGAAGG 6 132 1 GTTTTCTCTA 0.958085 -144 TTCTCTCAAATTTTTCGATCAAAAACTAGAT 9 12 1 TTTTTCGATA 0.82881 -167 TAGACTACACTTGTTCTGTGATAAACAGCTC 9 55 0 TTGTTCTGTA 0.93622 -124 AGATATCGGTTTTTTTTCTGAGGCTCTTTGA 9 105 1 TTTTTTTCTA 0.722544 -74 ********* * Masking position 11 Map Score: 4.75142 Number of sites scoring better than the average of aligned sites = 131 Number in coding regions = 94 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 6 GGTTACCATCTGGCTTTGTCAAGAACTGTA 1 121 0 TGGCTTTGTC 0.864566 -75 GGTTCACCGAATGTTTTGTCCAGACTGTGA 4 117 1 ATGTTTTGTC 0.856117 -119 TTGTCTTACTTTTTTCTGTGAATTTGCTTA 5 38 0 TTTTTCTGTG 0.775611 -258 TTTCTGTGAGTTTCTTTGTCTGTAAACATG 5 206 0 TTTCTTTGTC 0.76676 -90 AAGTTGGAAATGGTTTTCTGTGAGTTTCTT 5 220 0 TGGTTTTCTG 0.923114 -76 TCAAAGCAATTTGTTTTCGGTAATTGGAAA 5 276 1 TTGTTTTCGG 0.766943 -20 CTATGAGGAAATGTTTTCTCTTATTCAAGA 6 130 1 ATGTTTTCTC 0.856117 -146 ATGGTTCAAATTGGTTTCTCCTTCTTGAAT 6 152 0 TTGGTTTCTC 0.847054 -124 TAAACCCCGATGGTTCTGTCGCAGTAGATA 6 210 1 TGGTTCTGTC 0.902899 -66 GCAACTGCCTTCTTTTTCTCATCAACCTTT 7 30 0 TCTTTTTCTC 0.666809 -26 TAGACTACACTTGTTCTGTGATAAACAGCT 9 56 0 TTGTTCTGTG 0.914651 -123 AGATATCGGTTTTTTTTCTGAGGCTCTTTG 9 105 1 TTTTTTTCTG 0.860781 -74 ********** Masking position 5 Map Score: 5.81416 Number of sites scoring better than the average of aligned sites = 515 Number in coding regions = 416 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 7 CCAATGATGAATCCCCATTGAGAAGGCTGGG 4 88 0 ATCCCCATGA 0.979155 -148 TAGGTTGGAAAACCCCAGTCACAGTCTGGAC 4 134 0 AACCCCATCA 0.954039 -102 TCTCACACTTTAACCCATTGGGTGAAGGGAA 4 167 0 TAACCCATGG 0.939298 -69 GCTACAATTAAACCCCGATGGTTCTGTCGCA 6 202 1 AACCCCGTGG 0.975681 -74 ACAGATTCCCCAGGGATAAAAGGATG 6 260 0 TTCCCCAGGA 0.881954 -16 AACCCCAGAGGGTGTTTAAAT 8 1 1 AACCCCAAGG 0.96985 -52 ATAAATAAACCCATTGAACTATTAGAT 9 162 0 AAACCCATGA 0.967165 -17 ******* *** Masking position 6 Map Score: 2.88526 Number of sites scoring better than the average of aligned sites = 651 Number in coding regions = 600 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 8 TCACCCCTACCTGTAAAATGGGCTCTAG 3 21 1 CTGAAAATGG 0.960125 -18 TGTGAGAAGTCTGAAAAAAGTTCCATAATTTA 4 191 1 CTGAAAAAGT 0.788366 -45 ATGAGATTTGCTGAATAACCTGTGCATGTATT 5 177 0 CTGATAACCG 0.984172 -119 CCGAGATTTCCTGCATGACCGG 6 1 0 CTGATGACCG 0.956719 -275 CCAGAAGGCGCTGTATAACGGTGTCCAGATGA 6 46 0 CTGATAACGT 0.937222 -230 CAAGCGCCTTCTGTAAAACCAGAAGGCGCTGT 6 64 0 CTGAAAACCG 0.988038 -212 TTAATTGTAGCTGAAAACTCAGCTGTTCGACA 6 181 0 CTGAAACTCG 0.904577 -95 *** ****** * Masking position 5 Map Score: 1.59474 Number of sites scoring better than the average of aligned sites = 234 Number in coding regions = 215 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 9 ********** No masking Map Score: 1.86405e-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 10 ********** No masking Map Score: 1.86405e-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: 1.86405e-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