AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i298_synecho_ctra_300.orf -o298_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 RCY20391 256 Synechocystis #2 RCY49700 117 Synechocystis #3 RCY39680 96 Synechocystis #4 RCY41334 295 Synechocystis #5 RCY24823 47 Synechocystis #6 RCY42786 46 Synechocystis #7 RCY33128 300 Synechocystis #8 RCT00022 75 Chlamydia_trachomatis #9 RCT00023 187 Chlamydia_trachomatis #10 RCT00025 59 Chlamydia_trachomatis #11 RCT00028 25 Chlamydia_trachomatis #12 RCT00029 63 Chlamydia_trachomatis #13 RCT00748 194 Chlamydia_trachomatis Motif number 1 AGCCCATTTAGTCTCCCCTTACCC 1 5 0 GTCTCCCCTT 0.983032 -252 GGCCACCGCTGTCGCCCCTCACCCCATTGC 2 72 1 GTCGCCCCTC 0.945776 -46 GCTGGCCTCATTCCCCCATTTGTCTGGGTT 3 28 0 TTCCCCCATT 0.868213 -69 GGCCAGCATTTTCTCCCCTTCCACTAGAAT 3 51 1 TTCTCCCCTT 0.973115 -46 TAAAAAGAATTTCCCCCATTCTAGTGGAAG 3 68 0 TTCCCCCATT 0.868213 -29 CAAGAATTAAGTCTTCCCTCGGAGCAAGCA 4 111 1 GTCTTCCCTC 0.785308 -185 ATGCCCCCTCCTCCGTCTTCGGTTCCGCCC 4 225 1 CTCCGTCTTC 0.706847 -71 CAAGCAAAACCGCTCCCCGCCAAAACCCAT 4 265 0 CGCTCCCCGC 0.817363 -31 GGAGTTTTTCCGCTGCCTTTAGAGAGTATT 7 66 1 CGCTGCCTTT 0.852231 -235 AGTCGGCTAACTCCCCCATTTTTAGGCAAA 7 103 1 CTCCCCCATT 0.913378 -198 TAGAATTTTAGTCTGCCTTCTACAGTGAGT 7 173 0 GTCTGCCTTC 0.946226 -128 TTCGGGTATGCTCTCCCTTCTGTTATGTGA 8 17 1 CTCTCCCTTC 0.982267 -59 AAGCGGGGTGTTCGCCCCGCTTTTCTCTAG 9 33 0 TTCGCCCCGC 0.70479 -155 GTTTTAATAAGTCTCTCTTTTTGAATCTGA 9 68 1 GTCTCTCTTT 0.929464 -120 GAACGACTTCTTCTGCCTTTACTCTAGTAT 9 168 0 TTCTGCCTTT 0.913789 -20 GGCTTAATGCCGCTCTCTTTTCTTTA 12 7 0 CGCTCTCTTT 0.817508 -57 TCTCATAATTTTCTCTCTTTGTTTAATTGT 13 44 1 TTCTCTCTTT 0.891692 -151 CCGGAACAATGTCTCTCTTTACAACCTGTG 13 159 1 GTCTCTCTTT 0.929464 -36 ********** Masking position 7 Map Score: 20.816 Number of sites scoring better than the average of aligned sites = 1585 Number in coding regions = 1310 Number in noncoding regions = 275 Number of orfs with sites within 600 bp upstream = 273 Fraction of orfs with sites within 600 bp upstream = 0.0438484 Motif number 2 CATTTAGTCTCCCCTTACCC 1 1 0 CCCCTTACCC 0.898912 -256 AGGGTAACGGATCTTTTCCCCGGAGCGCTT 1 71 1 ATCTTTTCCC 0.713494 -186 CTATATTGCTATCTAGCCCCTGTTTTTGCT 1 185 1 ATCTAGCCCC 0.949973 -72 GGTTGTTTAAATCCTTCCCCACCAGAAACT 2 39 1 ATCCTTCCCC 0.984151 -79 GCCCCTCACCCCATTGCCCCCGTAGTTGAC 2 85 1 CCATTGCCCC 0.826823 -33 AAATGCTGGCCTCATTCCCCCATTTGTCTG 3 32 0 CTCATTCCCC 0.981693 -65 AGCATTTTCTCCCCTTCCACTAGAATGGGG 3 55 1 CCCCTTCCAC 0.890082 -42 AACGTATAAACTCCATCCCCCAATGGTTAG 4 81 1 CTCCATCCCC 0.98614 -215 CCCCTGGGTAATCTATCCCCAATTTCCCGA 4 187 1 ATCTATCCCC 0.942504 -109 CCCGATGTCCATCATGCCCCCTCCTCCGTC 4 212 1 ATCATGCCCC 0.965656 -84 CCCGCCAAAACCCATGCCCCTGATGGGGCG 4 250 0 CCCATGCCCC 0.980807 -46 TACAAAAAAACTCCAGCGCCGGGGGAGACT 7 233 0 CTCCAGCGCC 0.897595 -68 ********** Masking position 10 Map Score: 16.3558 Number of sites scoring better than the average of aligned sites = 2280 Number in coding regions = 2009 Number in noncoding regions = 271 Number of orfs with sites within 600 bp upstream = 265 Fraction of orfs with sites within 600 bp upstream = 0.0425634 Motif number 3 ACATCCGTGTAAACTTTTCTTAAAGATTAGC 1 32 0 AACTTTTCTT 0.656195 -225 AGCGGTGGCCACAAGTTTCTGGTGGGGAAGG 2 51 0 AAAGTTTCTG 0.933546 -67 GAATGAGGCCAGCATTTTCTCCCCTTCCACT 3 45 1 ACATTTTCTC 0.948503 -52 AAGTTTAAACAAAATTTACTGAATTTTTGAT 4 25 0 AAATTTACTG 0.738136 -271 GATGGAGTTTATACGTTTCTCCATACCACCA 4 67 0 AACGTTTCTC 0.953337 -229 GCCTTTAGAGAGTATTTTCTCCAAGTCGGCT 7 80 1 ATATTTTCTC 0.891005 -221 AAATAGATAAAAAACTTTCACATTATACCGC 7 270 0 AAACTTTCAC 0.697774 -31 TTTGAACAGAACTTTCTGTTATCTAGAG 9 8 1 AAACTTTCTG 0.914495 -180 TTTTGTTTTAATAAGTCTCTCTTTTTGAATC 9 64 1 AAAGTCTCTC 0.818003 -124 GGGGAACACTAGACTTTACTCTGAAAAGTCA 9 95 0 AACTTTACTC 0.803901 -93 AAAATTATCTAATATTTTCTCCTCACTTTTT 10 27 1 ATATTTTCTC 0.891005 -33 AGCGGCATTAAGCCCTTTCTGCTGTTCTCAA 12 23 1 ACCCTTTCTG 0.798575 -41 CTCCCTAATAACCAGTTTCTCATAATTTTCT 13 27 1 ACAGTTTCTC 0.945131 -168 CCAGTTTCTCATAATTTTCTCTCTTTGTTTA 13 38 1 AAATTTTCTC 0.970542 -157 * ********* Masking position 1 Map Score: 13.1745 Number of sites scoring better than the average of aligned sites = 285 Number in coding regions = 229 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 4 AGCGCTCCGGGGAAAAGATCCGTTACCCTAG 1 69 0 GGAAAAGATC 0.928624 -188 TAGTGGAAGGGGAGAAAATGCTGGCCTCATT 3 46 0 GGAGAAAATC 0.992081 -51 CACTAGAATGGGGGAAATTCTTTTTACGGGG 3 72 1 GGGGAAATTT 0.85215 -25 AGATTACCCAGGGGAAAATGCCGGAGCTACC 4 170 0 GGGGAAAATC 0.986116 -126 TAAAGGCAGCGGAAAAACTCCCTAGAGCAGA 7 56 0 GGAAAAACTC 0.931014 -245 TAGCCGACTTGGAGAAAATACTCTCTAAAGG 7 81 0 GGAGAAAATC 0.992081 -220 ACTCCCAGTTGGAATAAATTTTTAGTCTCCC 7 210 1 GGAATAAATT 0.774487 -91 TAAAAAGTGAGGAGAAAATATTAGATAATTT 10 28 0 GGAGAAAATT 0.980011 -32 ********* * Masking position 6 Map Score: 6.40053 Number of sites scoring better than the average of aligned sites = 473 Number in coding regions = 420 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 5 TAAATGGGCTAATCTTTAAGAAAAGTTTAC 1 25 1 AATCTTTAAG 0.82708 -232 GTTTGGCTCGACTTTTTAGTAAGCACAACC 1 130 0 ACTTTTTAGT 0.76613 -127 TTTTTTCATTAATCTTTGGGCTGGTTATGG 2 11 1 AATCTTTGGG 0.964187 -107 AAATTTACTGAATTTTTGATAGGGCTAATA 4 15 0 AATTTTTGAT 0.805023 -281 CTAACTCCCCCATTTTTAGGCAAAATCATA 7 109 1 CATTTTTAGG 0.909054 -192 AGTTGGAATAAATTTTTAGTCTCCCCCGGC 7 216 1 AATTTTTAGT 0.933427 -85 ATTGGCAATCAATTTTTGGGGAACACTAGA 9 113 0 AATTTTTGGG 0.982168 -75 AATATTAGATAATTTTTGCGATAAAGAACT 10 13 0 AATTTTTGCG 0.913708 -47 AAAAAGAATTTTTAGGTGAAATACA 11 7 1 AATTTTTAGG 0.977159 -19 ********** Masking position 5 Map Score: 6.47233 Number of sites scoring better than the average of aligned sites = 409 Number in coding regions = 342 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 6 TTTAGTAAGCACAACCTTAAAATCCTCAAATA 1 114 0 ACAACCAAAA 0.964632 -143 GAAGGAATTAACAAGCAAAAACAGGGGCTAGA 1 196 0 ACAAGCAAAC 0.987762 -61 AAGGATTTAAACAACCATAACCAGCCCAAAGA 2 23 0 ACAACCAACC 0.985276 -95 ACCAGTTTAAACAAGTTTAAACAAAATTTACT 4 36 0 ACAAGTAAAC 0.925854 -260 AAAAATCAAGACAAGCAAAACCGCTCCCCGCC 4 274 0 ACAAGCAACC 0.985276 -22 TTGACAACCCCAAAATCACTATCTT 8 61 0 ACAACCAAAA 0.964632 -15 ****** **** Masking position 4 Map Score: 3.83895 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 29 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 7 TGGTAGCTCCGGCATTTTCCCCTGGGTAATC 4 169 1 GGCATTTCCC 0.848375 -127 TCAGGGGCATGGGTTTTGGCGGGGAGCGGTT 4 257 1 GGGTTTTGCG 0.919859 -39 AGATTTACGAGGGATTTTGCCATTTTGCTTC 6 26 0 GGGATTTGCC 0.987952 -21 ATCTGCTCTAGGGAGTTTTTCCGCTGCCTTT 7 55 1 GGGAGTTTTC 0.78935 -246 CTAAAAATGGGGGAGTTAGCCGACTTGGAGA 7 97 0 GGGAGTTGCC 0.995627 -204 AAAAAAAGCGGGGTGTTCGCCCCGCTTTTCT 9 37 0 GGGTGTTGCC 0.989482 -151 AAAAGAGAGCGGCATTAAGCCCTTTCTGCTG 12 16 1 GGCATTAGCC 0.802303 -48 CTGGTTATTAGGGAGCTTGCTCATCGCATGT 13 11 0 GGGAGCTGCT 0.899091 -184 ******* *** Masking position 2 Map Score: 4.74134 Number of sites scoring better than the average of aligned sites = 659 Number in coding regions = 605 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 8 GCTATATTGCTATCTAGCCCCTGTTTTTGC 1 184 1 TATCTAGCCC 0.968312 -73 TAAACAACCATAACCAGCCCAAAGATTAAT 2 18 0 TAACCAGCCC 0.933376 -100 TGGTTGTTTAAATCCTTCCCCACCAGAAAC 2 38 1 AATCCTTCCC 0.898296 -80 TTTATACGTTTCTCCATACCACCACCAGTT 4 61 0 TCTCCATACC 0.84362 -235 AAACGTATAAACTCCATCCCCCAATGGTTA 4 80 1 ACTCCATCCC 0.97972 -216 TCCCCTGGGTAATCTATCCCCAATTTCCCG 4 186 1 AATCTATCCC 0.950655 -110 CTACAAAAAAACTCCAGCGCCGGGGGAGAC 7 234 0 ACTCCAGCGC 0.926905 -67 GGAATTGCTTTATCTAGCCTTTAATATGAT 13 76 1 TATCTAGCCT 0.773362 -119 ********** Masking position 4 Map Score: 3.16431 Number of sites scoring better than the average of aligned sites = 1049 Number in coding regions = 934 Number in noncoding regions = 115 Number of orfs with sites within 600 bp upstream = 134 Fraction of orfs with sites within 600 bp upstream = 0.0215226 Motif number 9 ACGGATGTAAATTCCTAGGGTAACGGATCT 1 55 1 ATTCCTAGGG 0.956697 -202 GGAGCGCTTCGTTCCTAGGGAGTATTTGAG 1 92 1 GTTCCTAGGG 0.871762 -165 TTGCTTGTTAATTCCTTCGGGGGTTACTCA 1 210 1 ATTCCTTCGG 0.969862 -47 GTCTGGGTTAATCCGTTCGGCCAACT 3 7 0 ATCCGTTCGG 0.942814 -90 TCATTCCCCCATTTGTCTGGGTTAATCCGT 3 21 0 ATTTGTCTGG 0.760649 -76 ATTGCAATGAATTCGTCTGGGCTGATAACC 13 121 1 ATTCGTCTGG 0.960785 -74 TGATAACCTTATCCCTCCGGAACAATGTCT 13 143 1 ATCCCTCCGG 0.979916 -52 ********** Masking position 6 Map Score: 1.76056 Number of sites scoring better than the average of aligned sites = 297 Number in coding regions = 272 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 10 GGAGACTAAATGGGCTAATCTTTAAGAAAA 1 19 1 TGGGCTAATC 0.983135 -238 CATTAATCTTTGGGCTGGTTATGGTTGTTT 2 17 1 TGGGCTGGTT 0.922618 -101 CCCATTTGTCTGGGTTAATCCGTTCGGCCA 3 14 0 TGGGTTAATC 0.951686 -83 AATTTTTGATAGGGCTAATACTGT 4 5 0 AGGGCTAATA 0.885013 -291 GATGTAACATTGGGTTGAGACAAGGAATTA 5 21 0 TGGGTTGAGA 0.823157 -27 CTGGCAATATTGGGATAGTCTGTATATGAT 7 133 0 TGGGATAGTC 0.882586 -168 TGAATTCGTCTGGGCTGATAACCTTATCCC 13 128 1 TGGGCTGATA 0.978151 -67 ********** Masking position 6 Map Score: 2.5019 Number of sites scoring better than the average of aligned sites = 308 Number in coding regions = 269 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 11 TGAACTTCCACCCAGTATTGCCCAGCTATAT 1 160 1 CCCAGTATGC 0.951081 -97 GGGGCTAGATAGCAATATAGCTGGGCAATAC 1 174 0 AGCAATATGC 0.958836 -83 AATCAAGACAAGCAAAACCGCTCCCCGCCAA 4 272 0 AGCAAAACGC 0.846258 -24 CTTGTCTCAACCCAATGTTACATCAACATCC 5 27 1 CCCAATGTAC 0.841373 -21 TTGGGATTGAAGCAAAATGGCAAAATCCCTC 6 18 1 AGCAAAATGC 0.947053 -29 TACAGACTATCCCAATATTGCCAGAGCTTTG 7 139 1 CCCAATATGC 0.984418 -162 TTGACAACCCCAAAATCACTATCTTAGTA 8 57 0 CCCAAAATAC 0.929768 -19 ******** ** Masking position 4 Map Score: 0.845932 Number of sites scoring better than the average of aligned sites = 397 Number in coding regions = 342 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 12 ********** No masking Map Score: 2.23354e-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: 2.23354e-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: 2.23354e-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