AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i262_tpal_bbur_300.orf -o262_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 RTP00651 75 AE000520 #2 RTP00654 39 AE000520 #3 RBB00553 213 3615 #4 RBB00769 20 3615 #5 RBB00550 22 3615 #6 RBB00549 89 3615 Motif number 1 GCCGGAGAGGAAAAAATAACCCGGTGCT 2 9 0 AAAAAATAAC 0.924151 -31 CTCTAATTCTTAAAATTAAACCTCCCAGGA 3 22 0 TAAAATTAAA 0.969421 -192 AGATGTCGCAAAAAAATAACTCTAATTCTT 3 41 0 AAAAAATAAC 0.924151 -173 TATCATTGACTAAAAATATTCAAATTCCTA 3 80 0 TAAAAATATT 0.947569 -134 ATTCAGAGGTTAAGAATAAAAATTCCGCCT 3 120 1 TAAGAATAAA 0.888627 -94 TAGCGCTAAATAAAAATGTTCTTATGTTGG 3 157 1 TAAAAATGTT 0.740584 -57 ATAATAATCCTTAAAATAAATTAAACTCCC 3 193 0 TTAAAATAAA 0.904613 -21 ATCTATCTCCTAAAATTATT 4 1 0 TAAAATTATT 0.925434 -20 ATATTAAATTAAAGGGGAAGAA 5 4 1 TTAAATTAAA 0.869847 -19 TACATTCACTAAAAAGTAAATTCTAGGAAT 6 12 0 AAAAAGTAAA 0.851049 -78 GAATGTATAATAAAATTAATTATTAATGTT 6 35 1 TAAAATTAAT 0.965164 -55 AATTAATAATTAACATTAATAATTAATTTT 6 46 0 TAACATTAAT 0.82984 -44 CTAAAAAATATATACTCCTAAA 6 78 0 AAAAAATATA 0.908605 -12 ********** Masking position 5 Map Score: 15.8744 Number of sites scoring better than the average of aligned sites = 838 Number in coding regions = 236 Number in noncoding regions = 602 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 2 AAATAACTCTAATTCTTAAAATTAAACCTC 3 28 0 AATTCTTAAA 0.973404 -186 TTTTTGCGACATCTCATAAAATTTAGGAAT 3 57 1 ATCTCATAAA 0.854927 -157 AAAATATTCAAATTCCTAAATTTTATGAGA 3 68 0 AATTCCTAAA 0.989433 -146 GCGGAATTTTTATTCTTAACCTCTGAATTG 3 118 0 TATTCTTAAC 0.817707 -96 AAATAAATTAAACTCCCAAAAAGCCAACAT 3 180 0 AACTCCCAAA 0.965712 -34 AATAATAATCCTTAAAATAAATTAAA 3 198 0 AATCCTTAAA 0.895302 -16 ATCTATCTCCTAAAATTATT 4 7 0 ATCTCCTAAA 0.97442 -14 TATTCCTAGAATTTACTTTT 6 1 1 TATTCCTAGA 0.919844 -89 AAAAAATATATACTCCTAAATCAATTAATA 6 68 0 TACTCCTAAA 0.984432 -22 ********** Masking position 8 Map Score: 12.4 Number of sites scoring better than the average of aligned sites = 344 Number in coding regions = 114 Number in noncoding regions = 230 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 3 ACCGCGCACCGCACAGTTTTACGGGAG 1 8 1 ACCGCACAGT 0.976735 -68 GGGCGTGCGTACCGTACAGG 1 66 1 ACCGTACAGG 0.900492 -10 TTTTTCCTCTCCGGCACAGGATTTGA 2 24 1 CCGGCACAGG 0.954082 -16 TTAAAATTAAACCTCCCAGGAGCTTTGATT 3 13 0 ACCTCCCAGG 0.990736 -201 ********** Masking position 8 Map Score: 3.89696 Number of sites scoring better than the average of aligned sites = 178 Number in coding regions = 58 Number in noncoding regions = 120 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 4 CCGGAGAGGAAAAAATAACCCGGTGCT 2 7 0 AAAATAACCC 0.742248 -33 AAAATCAAAGCTCCTGGGAGGTTT 3 4 1 ATAAAGCTCC 0.966936 -210 AATTCTTAAAATTAAACCTCCCAGGAGCTTT 3 17 0 ATAAACCTCC 0.940796 -197 GACTAAAAATATTCAAATTCCTAAATTTTAT 3 72 0 ATCAAATTCC 0.920673 -142 GAGGTTAAGAATAAAAATTCCGCCTTGAAAA 3 125 1 ATAAAATTCC 0.974173 -89 AGCGCTAAATAAAAATGTTCTTATGTTGGCT 3 158 1 AAAATGTTCT 0.685233 -56 CCTTAAAATAAATTAAACTCCCAAAAAGCCA 3 184 0 AATAAACTCC 0.96912 -30 AATAATAATCCTTAAAATAAA 3 203 0 AAAATAATCC 0.93247 -11 ATTCACTAAAAAGTAAATTCTAGGAATA 6 8 0 AATAAATTCT 0.773776 -82 CTAAAAAATATATACTCCTAAATCAATT 6 72 0 ATTATACTCC 0.955429 -18 ** ******** Masking position 5 Map Score: 7.59482 Number of sites scoring better than the average of aligned sites = 1121 Number in coding regions = 317 Number in noncoding regions = 804 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 5 ACGCACGCCCCCATGACAAATAATTTCTAC 1 46 0 CCATGACAAA 0.973363 -30 TTTTGGCTATCATTGACTAAAAATATTCAA 3 87 0 CATTGACTAA 0.985816 -127 AAAAATTCCGCCTTGAAAAATAGCGCTAAA 3 137 1 CCTTGAAAAA 0.958741 -77 TTTTATTATACATTCACTAAAAAGTAAATT 6 20 0 CATTCACTAA 0.962863 -70 ACTCCTAAATCAATTAATAATTAACATTAA 6 57 0 CAATTAATAA 0.844145 -33 ********** Masking position 6 Map Score: 1.92286 Number of sites scoring better than the average of aligned sites = 373 Number in coding regions = 122 Number in noncoding regions = 251 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 6 CCGTAAAACTGTGCGGTGCGCGGT 1 5 0 GTGCGGTGCG 0.983871 -71 CCGCACAGTTTTACGGGAGAACATGCGGTA 1 19 1 TTACGGGAGA 0.956577 -57 ACGGGAGAACATGCGGTAGAAATTATTTGT 1 31 1 ATGCGGTAGA 0.978718 -45 CCTGTACGGTACGCACGCCCCCA 1 63 0 GTACGGTACG 0.983633 -13 TCAAATCCTGTGCCGGAGAGGAAAAAATA 2 21 0 GTGCCGGAGA 0.982442 -19 ********** Masking position 2 Map Score: 1.30115 Number of sites scoring better than the average of aligned sites = 448 Number in coding regions = 130 Number in noncoding regions = 318 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: 7.76924e-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 8 ********** No masking Map Score: 7.76924e-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 9 ********** No masking Map Score: 7.76924e-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