AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i030_tpal_bbur_300.orf -o030_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 RBB00500 300 3615 #2 RBB00498 42 3615 #3 RBB00782 53 3615 #4 RBB00783 71 3615 Motif number 1 AAAACAAAAAATCCTTAAACAA 1 1 1 AACAAAAAAT 0.792123 -300 AAACAAATTTTAGAAAAGAAATTCATAATTTA 1 27 1 TAAAAGAAAT 0.939379 -274 AGAAATTCATAATTTAAAAATTAAAATTCTTA 1 43 1 AATAAAAATT 0.78044 -258 TAATGTCAATAATTTAAGAATTTTAATTTTTA 1 57 0 AATAAGAATT 0.758363 -244 CATTAATCTTAATTAAAAATAAGATATTAAAT 1 84 1 AAAAAAATAA 0.969706 -217 ATAAAAGCCTTATTAAAATTATATTTAATATC 1 106 0 TAAAAATTAT 0.663412 -195 AAGGCTTTTATTAGAAAAATTAATTTTTTTTA 1 127 1 TTAAAAATTA 0.648677 -174 TAGTCTCTTTTATTAAAAAAAATTAATTTTTC 1 140 0 TAAAAAAAAA 0.92229 -161 AAAGAGACTAAAATAAAAAAATTCTAACCATC 1 162 1 AAAAAAAAAT 0.969703 -139 TGCAAAAAACAAAATAAAATTTAATTAAAAGA 1 195 1 AATAAAATTT 0.840826 -106 ATAAAATTTAATTAAAAGATTTAATATTATTC 1 208 1 ATAAAGATTT 0.814449 -93 CAGATTAAAAAATCAAAAATTAAAACTTCTTA 1 239 1 AAAAAAATTA 0.946183 -62 AAAACTTCTTAATAAAAAATAAAATAGTTATA 1 260 1 AAAAAAATAA 0.969708 -41 AATAAAATAGTTATAAAGATAAGGAGATATAA 1 277 1 TTAAAGATAA 0.74767 -24 AAGAAAAAATATTTATCTTTAT 2 1 1 AAAAAAATAT 0.979348 -42 CTTTTTCCTTTAATAAAGATAAATATTTTTTC 2 13 0 TAAAAGATAA 0.939378 -30 AAGTTCAAAACAAAGCTTTAAGATTATAA 3 8 1 AAAAAGCTTT 0.825734 -46 TTTAAGATTATAACAAAAATATACTGGTAACA 3 27 1 TAAAAAATAT 0.963024 -27 AATTAAAACAAATGGTCTTTTC 4 1 1 AAAAAACAAA 0.816876 -71 TTTAACTAAAAAGAAAAGAAATTAACCAAA 4 52 1 AAAAAGAAAT 0.965771 -20 ** ******** Masking position 6 Map Score: 27.1834 Number of sites scoring better than the average of aligned sites = 1389 Number in coding regions = 368 Number in noncoding regions = 1021 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 2 AAAAATCCTTAAACAAATTTTAGAAAAGAA 1 17 1 AAACAAATTT 0.767685 -284 TAGAAAAGAAATTCATAATTTAAAAATTAA 1 37 1 ATTCATAATT 0.705429 -264 ATAATTTAAAAATTAAAATTCTTAAATTAT 1 51 1 AATTAAAATT 0.500623 -250 TATTGACATTAATCTTAATTAAAAATAAGA 1 78 1 AATCTTAATT 0.737498 -223 TTATATTTAATATCTTATTTTTAATTAAGA 1 90 0 TATCTTATTT 0.875765 -211 GCCTTATTAAAATTATATTTAATATCTTAT 1 102 0 AATTATATTT 0.548218 -199 TTTATTAGAAAAATTAATTTTTTTTAATAA 1 133 1 AAATTAATTT 0.487935 -168 TGGTTAGAATTTTTTTATTTTAGTCTCTTT 1 162 0 TTTTTTATTT 0.767642 -139 TAAATCTTTTAATTAAATTTTATTTTGTTT 1 201 0 AATTAAATTT 0.562126 -100 ATCTGAATAATATTAAATCTTTTAATTAAA 1 214 0 TATTAAATCT 0.899533 -87 AATTTTTGATTTTTTAATCTGAATAATATT 1 230 0 TTTTTAATCT 0.713575 -71 AAAAATCAAAAATTAAAACTTCTTAATAAA 1 246 1 AATTAAAACT 0.759071 -55 TCTTTATAACTATTTTATTTTTTATTAAGA 1 266 0 TATTTTATTT 0.855329 -35 AATTATATCTCCTTATCTTT 1 291 0 AATTATATCT 0.87115 -10 AAGAAAAAATATTTATCTTTATTAAAGG 2 9 1 ATATTTATCT 0.584918 -34 AATATACTGGTAACAAAATT 3 44 1 TAACAAAATT 0.595062 -10 ********** Masking position 7 Map Score: 16.826 Number of sites scoring better than the average of aligned sites = 1443 Number in coding regions = 411 Number in noncoding regions = 1032 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 3 AAAACAAAAAATCCTTAAACAAATTTT 1 8 1 AAAATCCTTA 0.937924 -293 TTTAAAAATTAAAATTCTTAAATTATTGAC 1 55 1 AAAATTCTTA 0.905091 -246 ATTATTGACATTAATCTTAATTAAAAATAA 1 76 1 TTAATCTTAA 0.357611 -225 AATTAAAAATAAGATATTAAATATAATTTT 1 94 1 AAGATATTAA 0.894026 -207 GATATTAAATATAATTTTAATAAGGCTTTT 1 106 1 ATAATTTTAA 0.836381 -195 TTTTTCTAATAAAAGCCTTATTAAAATTAT 1 116 0 AAAAGCCTTA 0.827081 -185 CTTTTATTAAAAAAAATTAATTTTTCTAAT 1 136 0 AAAAAATTAA 0.857825 -165 TTTTTAATAAAAGAGACTAAAATAAAAAAA 1 153 1 AAGAGACTAA 0.743456 -148 CTAAAATAAAAAAATTCTAACCATCTTGCA 1 169 1 AAAATTCTAA 0.923979 -132 AAAAAACAAAATAAAATTTAATTAAAAGAT 1 198 1 ATAAAATTTA 0.687741 -103 TTTAATCTGAATAATATTAAATCTTTTAAT 1 218 0 ATAATATTAA 0.895807 -83 TCAAAAATTAAAACTTCTTAATAAAAAATA 1 251 1 AAACTTCTTA 0.547795 -50 AATAAAAAATAAAATAGTTATAAAGATAAG 1 270 1 AAAATAGTTA 0.777071 -31 AAGAAAAAATATTTATCTTTATTAA 2 6 1 AAAATATTTA 0.919705 -37 TATTTTTGTTATAATCTTAAAGCTTTGTTT 3 18 0 ATAATCTTAA 0.888464 -36 CTAAAAAGAAAAGAAATTAACCAAA 4 57 1 AAGAAATTAA 0.712117 -15 ********** Masking position 8 Map Score: 18.4539 Number of sites scoring better than the average of aligned sites = 1171 Number in coding regions = 348 Number in noncoding regions = 823 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 4 ********** No masking Map Score: 2.79544e-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 5 ********** No masking Map Score: 2.79544e-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 6 ********** No masking Map Score: 2.79544e-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