AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i036_tpal_bbur_300.orf -o036_tpal_bbur_300.ace -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/synecho.fna -g0.40 -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 = 0.4 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RTP00410 181 AE000520 #2 RTP00411 70 AE000520 #3 RTP00413 137 AE000520 #4 RTP00194 66 AE000520 #5 RTP01039 60 AE000520 #6 RTP00195 72 AE000520 #7 RTP00196 111 AE000520 #8 RBB00167 154 3615 #9 RBB00847 84 3615 #10 RBB00136 96 3615 Motif number 1 GTGTTCTTTCCTCAGCCGGTGAAGGCCCAGGATTGGGTGC 1 36 0 CCGCGGGGCG 0.984228 -146 CGGCTGAGGAAAGAACACGCGCTGGTACTGTAACACCTTT 1 58 1 AGACCGGGCG 0.732405 -124 ACAAAGATCCCCGAACCCATGTCCGTTGCGACGCTACCCT 1 149 1 CGACCAGGGG 0.703573 -33 GCACGACGGGGGTCTGTGCAGGATCAACAGA 2 50 0 CCACGGGGCG 0.599374 -21 CATTTGTGCGCAGCACGGGAGTTGGGTGCGCAGCAGGTGC 3 29 0 CGACGGGGGG 0.998589 -109 AGTTAGCGCGCTGTGCCGGTGAAGTGTGGGTAGACGGTGG 3 85 0 CGGCGGGTGG 0.993689 -53 AAAGACACTATCCAGCAGGGGTACGGTCAGGT 4 3 0 TCGCGGGGCG 0.984441 -64 CTGGCAAATACTGAGCAGGGGTCTGGACAAAAGCATTAGC 6 18 0 CGGCGGGGCA 0.984625 -55 CAGTATTTGCCAGAAGACGAGTTTGAGGCGCAGAACGA 6 45 1 CGAGCGGGGG 0.985444 -28 CGGCAGCGTGCGGTACAGGGGGTCGGTGTGCGGTATGGCA 7 49 0 CGACGGGGGG 0.999154 -63 GAATTCAGCGACGCGCGGGTGTCGGCAGCGTGCGGTACAG 7 71 0 AGGCGGGGGG 0.981388 -41 * * ** ** * * * * Masking position 11 Map Score: 26.7907 Number of sites scoring better than the average of aligned sites = 415 Number in coding regions = 120 Number in noncoding regions = 295 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 2 CTCAAACACCGTAAAAAATGAACGCACCCA 1 13 1 GTAAAAAATG 0.908418 -169 CACCGTATTCAAAAAGAAAG 3 128 1 AAAAAGAAAG 0.942611 -10 CAACAATATACAGAAAGCCGGGGTCTC 5 8 1 ATACAGAAAG 0.962131 -53 TATTAATAGCATAAAAAAAGGGAAAACTGA 8 11 0 ATAAAAAAAG 0.988093 -144 TGGCTTTTTTGTAAAAAATGATATAAATAT 8 109 1 GTAAAAAATG 0.908418 -46 CACACTCCTTATAATAAAAGAATATTTATA 8 130 0 ATAATAAAAG 0.921117 -25 AAAATCATGTATGAAAAAAGATTTTTTATT 9 34 1 ATGAAAAAAG 0.945376 -51 TTGATAATGCATAAAAAAAGACATTTTAAA 9 63 0 ATAAAAAAAG 0.988093 -22 CACATTATATATAAAGAAAGTAATAATACC 10 32 1 ATAAAGAAAG 0.983358 -65 TAAATTAATTAAACAAAAAGGTAAAAA 10 80 1 AAACAAAAAG 0.908418 -17 ********** Masking position 7 Map Score: 15.4933 Number of sites scoring better than the average of aligned sites = 92 Number in coding regions = 28 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 3 GCGTGTTCTTTCCTCAGCCGGTGAAGGCCCA 1 47 0 TCCCAGCCGG 0.98072 -135 GGGAGTTGGGTGCGCAGCAGGTGCTGATAGG 3 22 0 TGCCAGCAGG 0.997709 -116 TGCGCATTTGTGCGCAGCACGGGAGTTGGGT 3 42 0 TGCCAGCACG 0.996352 -96 ACACTTCACCGGCACAGCGCGCTAACTCTCC 3 98 1 GGCCAGCGCG 0.972243 -40 TGAAAGACACTATCCAGCAGGGGTACGGTCA 4 14 0 TATCAGCAGG 0.975572 -53 TACCCACTGCTACCCAGCCGTGAAAGACACT 4 34 0 TACCAGCCGT 0.90797 -33 TCGTCCATCTTACCCCGCAGGAAATACAGGA 5 40 1 TACCCGCAGG 0.990033 -21 TTCTGGCAAATACTGAGCAGGGGTCTGGACA 6 29 0 TACGAGCAGG 0.967653 -44 ACGAGTTTGAGGCGCAGAACGA 6 61 1 GGCCAGAACG 0.919894 -12 ACCGACCCCCTGTACCGCACGCTGCCGACAC 7 62 1 TGTCCGCACG 0.958019 -50 *** ******* Masking position 7 Map Score: 15.148 Number of sites scoring better than the average of aligned sites = 337 Number in coding regions = 90 Number in noncoding regions = 247 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 4 AGGCCCAGGATTGGGTGCGTTCATTTTTTA 1 24 0 TTGGGTGCGT 0.968098 -158 GCGTGCTGATGTGGTTGCACGTTACC 2 7 0 GTGGTTGCAC 0.967888 -64 AGCACGGGAGTTGGGTGCGCAGCAGGTGCT 3 28 0 TTGGGTGCGC 0.996333 -110 CCGGTGAAGTGTGGGTAGACGGTGGTATTC 3 80 0 GTGGGTAGAC 0.934394 -58 CTGGGTAGCAGTGGGTACACGACTCTTTT 4 48 1 GTGGGTACAC 0.983952 -19 GAGTGTGCTCTTAGGTGCGCTCTTT 7 6 0 TTAGGTGCGC 0.972413 -106 TCTTTTTAAGGTGAGTGTGCTCTTAGGTGC 7 18 0 GTGAGTGTGC 0.95491 -94 GGTACAGGGGGTCGGTGTGCGGTATGGCAC 7 48 0 GTCGGTGTGC 0.973304 -64 ********** Masking position 6 Map Score: 9.79677 Number of sites scoring better than the average of aligned sites = 206 Number in coding regions = 65 Number in noncoding regions = 141 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 5 CTCTCCACCGTATTCAAAAAGAAAG 3 123 1 TATTCAAAAA 0.80024 -15 ATGCTATTAATATTGTAATATGGATAGGAT 8 29 1 TATTGTAATA 0.870875 -126 TTGTAAAAGATATTGAAAAAAAATATCCTA 8 53 0 TATTGAAAAA 0.903734 -102 TTGAAAGAATTTTTGTAAAAGATATTGAAA 8 65 0 TTTTGTAAAA 0.905808 -90 ATTGAATTGCTTTTGAAAGAATTTTTGTAA 8 77 0 TTTTGAAAGA 0.853284 -78 ATTTTGGCTTTTTTGTAAAAAATGATATAA 8 105 1 TTTTGTAAAA 0.905808 -50 AAAGATTTTTTATTTTAAAATGTCTTTTTT 9 50 1 TATTTTAAAA 0.72937 -35 ********** Masking position 7 Map Score: 4.94244 Number of sites scoring better than the average of aligned sites = 104 Number in coding regions = 28 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 6 GTACGTCTTCCCTAAAAGCGGCGATTATTT 1 108 0 CCTAAAAGCG 0.967866 -74 AACGTGCAACCACATCAGCACGCTCTTCAG 2 14 1 CACATCAGCA 0.944634 -57 AAAAGGACGCCCTATCAGCACCTGCTGCGC 3 12 1 CCTATCAGCA 0.944636 -126 CCGTGCTGCGCACAAATGCGCATAACTGCG 3 51 1 CACAAATGCG 0.928154 -87 CACAAATGCGCATAACTGCGAATACCACCG 3 61 1 CATAACTGCG 0.944632 -77 CAGGGGTCTGGACAAAAGCATTAGCGTACA 6 13 0 GACAAAAGCA 0.827442 -60 AAAGAGCGCACCTAAGAGCACACTCACCTT 7 11 1 CCTAAGAGCA 0.936024 -101 ********** Masking position 4 Map Score: 1.51695 Number of sites scoring better than the average of aligned sites = 431 Number in coding regions = 117 Number in noncoding regions = 314 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 7 ********** No masking Map Score: -2.17893e-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 8 ********** No masking Map Score: -2.17893e-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 9 ********** No masking Map Score: -2.17893e-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