AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i293_tpal_bbur_100.orf -o293_tpal_bbur_100.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 RTP00005 105 AE000520 #2 RTP00906 121 AE000520 #3 RTP00907 59 AE000520 #4 RTP00138 102 AE000520 #5 RTP00552 92 AE000520 #6 RTP00770 34 AE000520 #7 RTP00771 204 AE000520 #8 RBB00505 32 3615 #9 RBB00504 148 3615 #10 RBB00429 50 3615 #11 RBB00693 115 3615 #12 RBB00686 63 3615 Motif number 1 GCGTCGTTAGCGTAGATATGGTTGGGTCTTGACTGA 1 46 0 CGGATAGGGG 0.97092 -60 CGTTTTGGAGAGATGGTGTGTGCAGATCGTTAAGGG 2 22 0 AGGGTGGTGA 0.981903 -100 GTGGACCATACGCCTAAGCGTTTTGGAGAGATGGTG 2 40 0 CGTAAGGTGG 0.801981 -82 TTGATTTTCCCGTGGGGGGGGGGTGGACCATACGCC 2 62 0 CGGGGGGGGG 0.998666 -60 ATGCTTTTTCCGCGTGGGAGTAGTGACCATTTTGAC 3 31 0 CGTGGGGTGA 0.942616 -29 ATGCCGCTTTCGATGGAGGGGATAGAGCGCGTGCAC 4 47 0 CGGGAGGGGA 0.992484 -56 TGCCGCTAACAGCAAGTGAGTACGGGCGT 4 84 1 AGAGTGGTGG 0.914956 -19 GAAATGGGCACGGGGGTGCAGGTGGGGAAT 5 5 0 CGGGTGAGGG 0.987458 -88 AGTAGGTGCGTTTTGAAAGAAGCGGA 7 1 1 AGGGTGGTGA 0.981903 -204 GCGTTTTGAAAGAAGCGGAGGGCGGGGAAATCTGTT 7 18 1 AGGCGGGGGG 0.965359 -187 TTTCTGTGTGCGGGGATGTGGGGAGATTTCGTAGGC 7 116 1 CGGATGGGGA 0.990554 -89 ATTTCGTAGGCACGGGTGAGGAAAGGATCGCGGGTA 7 141 1 CAGGTGGGGG 0.987459 -64 AGGAAAGGATCGCGGGTAGGGATAGGACGGAAGAAG 7 159 1 CGGGTAGGGG 0.993432 -46 ** **** ** ** Masking position 15 Map Score: 22.1959 Number of sites scoring better than the average of aligned sites = 1062 Number in coding regions = 298 Number in noncoding regions = 764 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 2 GCGTCGTTAGCGTAGATATGGTTGGGTCTTG 1 51 0 CGTAGAATGG 0.804589 -55 TTGATTTTCCCGTGGGGGGGGGGTGGACCAT 2 67 0 CGTGGGGGGG 0.997823 -55 GCTTTTTCCGCGTGGGAGTAGTGACCATTTT 3 34 0 CGTGGGGTAG 0.982136 -26 ATGCCGCTTTCGATGGAGGGGATAGAGCGCG 4 52 0 CGATGGGGGG 0.936181 -51 GAAATGGGCACGGGGGTGCAGGTGGGGAAT 5 10 0 CGGGGGGCAG 0.991095 -83 CACTGCCGTGCGCAGGAGCGACCAGCTTGCC 5 53 1 CGCAGGGCGA 0.953009 -40 ACCAGCTTGCCGTGGGCGCAAAGTGCATGC 5 73 1 CGTGGGGCAA 0.945928 -20 TTGAAAGAAGCGGAGGGCGGGGAAATCTGTT 7 23 1 CGGAGGCGGG 0.969452 -182 TTTCTGTGTGCGGGGATGTGGGGAGATTTCG 7 116 1 CGGGGAGTGG 0.971028 -89 GGGGAGATTTCGTAGGCACGGGTGAGGAAAG 7 135 1 CGTAGGACGG 0.982205 -70 AGGAAAGGATCGCGGGTAGGGATAGGACGGA 7 159 1 CGCGGGAGGG 0.98864 -46 ****** **** Masking position 1 Map Score: 15.3911 Number of sites scoring better than the average of aligned sites = 1203 Number in coding regions = 382 Number in noncoding regions = 821 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 3 TTTTCCTCTTTTTTACTATTATTAGTAACAT 9 9 1 TTTTATATTA 0.757941 -140 AACATAATGGTGTAATATATTTAACATTATCAT 9 37 1 TTATAATTTA 0.837277 -112 TAACATTATCATTAATAATTTTATATGATAGTA 9 58 1 ATATATTTTA 0.891899 -91 TTTATATGATAGTATTAATTTTTTTGTATTATT 9 77 1 ATATATTTTT 0.907532 -72 TTAATTTTTTTGTATTATTTTTTGGAAAAGTTA 9 91 1 TTATATTTTT 0.961003 -58 TAATACACTTTATTATACTTTTTCATTATAATT 10 17 0 TTTTATTTTT 0.966975 -34 TTTAGTTTTTTTAATTAATTTTAATTAAACTAA 11 15 0 TAATATTTTA 0.836478 -101 TTTTTATGATATTTTTAGTTTTTTTAATTAATT 11 28 0 ATTTATTTTT 0.921039 -88 ATCTAAAATATTTTCTATTTTTTGTAAACACGT 11 60 0 TTTTATTTTT 0.96698 -56 AAATAGAAAATATTTTAGATTTAAGTTATGTAC 11 73 1 TTTTAATTTA 0.85944 -43 TAGATTTAAGTTATGTACTTTTTGCGGGAGGCT 11 88 1 TATTATTTTT 0.879023 -28 * ** ** ***** Masking position 7 Map Score: 7.92005 Number of sites scoring better than the average of aligned sites = 180 Number in coding regions = 50 Number in noncoding regions = 130 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 4 ATACACAATTGATTTTCCCGTGGGGGGGGG 2 76 0 GATTTTCCCG 0.929369 -46 TGACCATTTTGACTGTGCCGCATTCGTGCG 3 14 0 GACTGTGCCG 0.983931 -46 TCAATGCTTTTTCCGCGTGGGAGTA 3 45 0 GCTTTTTCCG 0.949761 -15 ATCGAAAGCGGCATCTGCCGCTAACAGCAA 4 69 1 GCATCTGCCG 0.984969 -34 ATCAGCAACCGACACTGCCGTGCGCAGGAG 5 41 1 GACACTGCCG 0.98945 -52 ACTTATCATTGACACTGCTGGCCGT 6 6 0 GACACTGCTG 0.924044 -29 GGTCACATGTGCTTCTTCCGTCCTATCCCT 7 176 0 GCTTCTTCCG 0.98244 -29 ********** Masking position 6 Map Score: 4.95024 Number of sites scoring better than the average of aligned sites = 512 Number in coding regions = 163 Number in noncoding regions = 349 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 5 TTGATGCTGTATCATAAATACACAATTGATT 2 92 0 ATCATAAAAC 0.979743 -30 ATGATACAGCATCAAAAAATCATC 2 108 1 ATCAAAAATC 0.885214 -14 CTCTAATAAAATCAAAAAGAAAT 8 3 0 ATCAAAAAAA 0.947322 -30 ATTTAACATTATCATTAATAATTTTATATGA 9 55 1 ATCATTAAAA 0.829406 -94 AATTAATACTATCATATAAAATTATTAATGA 9 66 0 ATCATATAAA 0.829407 -83 ATTAAAATTAATTAAAAAAACTAAAAATATC 11 23 1 ATTAAAAAAC 0.828127 -93 AACTAAAAATATCATAAAAACGTGTTTACAA 11 41 1 ATCATAAAAC 0.97974 -75 ******** ** Masking position 4 Map Score: 3.68431 Number of sites scoring better than the average of aligned sites = 116 Number in coding regions = 26 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 6 CCCCTTAACGATCTGCACACACCATCTCTC 2 21 1 ATCTGCACAC 0.873093 -101 GGTGGACCATACGCCTAAGCGTTTTGGAGA 2 47 0 ACGCCTAAGC 0.457351 -75 CGTATGGTCCACCCCCCCCCCACGGGAAAA 2 64 1 ACCCCCCCCC 0.984836 -58 ACCCGCACGAATGCGGCACA 3 1 1 ACCCGCACGA 0.967899 -59 AATGGTCACTACTCCCACGCGGAAAAAGCA 3 36 1 ACTCCCACGC 0.93052 -24 CGGTCAACGTACGCGTACCAAAAAGCACGT 4 19 1 ACGCGTACCA 0.762574 -84 ACCAAAAAGCACGTGCACGCGCTCTATCCC 4 35 1 ACGTGCACGC 0.935931 -68 CACGCGCTCTATCCCCTCCATCGAAAGCGG 4 50 1 ATCCCCTCCA 0.628986 -53 ATTCCCCACCTGCACCCCCGTGCCCAT 5 8 1 ACCTGCACCC 0.982004 -85 CTCCCCACATCCCCGCACACAGAAACCCAC 7 111 0 CCCCGCACAC 0.919059 -94 TGCCTACGAAATCTCCCCACATCCCCGCAC 7 123 0 ATCTCCCCAC 0.725349 -82 CTTCCGTCCTATCCCTACCCGCGATCCTTT 7 162 0 ATCCCTACCC 0.923362 -43 ********** Masking position 1 Map Score: 7.27423 Number of sites scoring better than the average of aligned sites = 2648 Number in coding regions = 729 Number in noncoding regions = 1919 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 7 AACGATCTGCACACACCATCTCTCCAAAAC 2 27 1 ACACACCATC 0.805763 -95 ATGGTCCACCCCCCCCCCACGGGAAAATCA 2 67 1 CCCCCCCCAC 0.969948 -55 CGCGCTCTATCCCCTCCATCGAAAGCGGCA 4 52 1 CCCCTCCATC 0.949364 -51 CGGCATCTGCCGCTAACAGCAAGTGAGTAC 4 77 1 CGCTAACAGC 0.611161 -26 ATTCCCCACCTGCACCCCCGTGC 5 4 1 CCCCACCTGC 0.974716 -89 CGTGCGCAGGAGCGACCAGCTTGCCGTGGG 5 59 1 AGCGACCAGC 0.918843 -34 CAACAGATTTCCCCGCCCTCCGCTTCTTTC 7 25 0 CCCCGCCCTC 0.96173 -180 TTCTACGATCACCGACCAACAGATTTCCCC 7 41 0 ACCGACCAAC 0.869255 -164 AAATCTCCCCACATCCCCGCACACAGAAAC 7 115 0 ACATCCCCGC 0.7893 -90 TCCGTCCTATCCCTACCCGCGATCCTTTCC 7 160 0 CCCTACCCGC 0.987904 -45 TTATAAGCCTCCCGCAAAAAGTACA 11 101 0 AGCCTCCCGC 0.949193 -15 ********** Masking position 7 Map Score: 8.85246 Number of sites scoring better than the average of aligned sites = 2585 Number in coding regions = 682 Number in noncoding regions = 1903 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 8 ********** No masking Map Score: 2.38275e-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 CTCCTTCAATTGCTCAGACTGGACAGAAA 1 87 1 TCTCAAGGAC 0.958285 -19 CAATGACGTACTTATCATTGACACTGCTGGCC 6 13 0 TCTTACTGAC 0.991615 -22 CCCACCGTGCTGCTCGCCTTTGACTCGGATATCA 7 82 0 TCTCGCTGAC 0.985505 -123 CGCGATCCTTTCCTCACCCGTGCCTACGAAATCT 7 139 0 TCTCACTGCC 0.985505 -66 TTCCTTACCGGTCACATGTGCTTCT 7 190 0 TCTTACTCAC 0.964433 -15 ACCTTATTAATACTTACAATTGACAAGCATACAA 12 38 0 TCTTAATGAC 0.975587 -26 * **** * **** Masking position 4 Map Score: 1.03169 Number of sites scoring better than the average of aligned sites = 125 Number in coding regions = 40 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 10 ********** No masking Map Score: 2.38275e-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: 2.38275e-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 12 ********** No masking Map Score: 2.38275e-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