AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i248_tpal_bbur_100.orf -o248_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 RTP00901 300 AE000520 #2 RTP01017 300 AE000520 #3 RBB00684 79 3615 #4 RBB00663 114 3615 #5 RBB00659 46 3615 #6 RBB00657 36 3615 Motif number 1 TGGAGCCAGACTCTTCTGCAATTCTTGCTGAACT 1 13 0 CTCTTGCAAC 0.980716 -288 GCGCGCGAGCATCCCGCGGAAGTCTATCGTAAGA 1 116 0 ATCCCGGAAC 0.852083 -185 CCGCGGGATGCTCGCGCGCATCACCGGTGATAAG 1 131 1 CTCCCGCATC 0.993516 -170 GTTGTGTGTTCACTTACGCATTGCGGTTTTATGG 1 169 0 CACTCGCATC 0.969167 -132 ATTTGCAGGGCTCGTACGCATCGCGTC 2 4 0 CTCTCGCATC 0.993775 -297 CGACGCGTCACTCATACGTAATTCATCATTTGCA 2 31 0 CTCTCGTAAC 0.962771 -270 GCAGTGATTGCCCTTTTGTATAAGGGTGTGAATT 2 100 1 CCCTTGTATG 0.871965 -201 GCGCCGAACCCCCACGTGCATGGAGACCATTGTC 2 143 0 CCCCTGCATA 0.895224 -158 AAACCCATATCCCTCGCGGAAAAGACGAGTACTA 2 194 0 CCCCCGGAAG 0.943688 -107 TAGACCTACCCTCTTTTGGATACCACTTCATCAC 2 230 0 CTCTTGGATC 0.985859 -71 CACGCATTCTCCCTTTTGGATGCCCACTATAGGT 2 273 1 CCCTTGGATC 0.98692 -28 *** * ***** * Masking position 10 Map Score: 13.0133 Number of sites scoring better than the average of aligned sites = 359 Number in coding regions = 108 Number in noncoding regions = 251 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 2 TAAGACTCCCATAAAACCGCAATGCGTAAGTGA 1 161 1 AAAAACCAAT 0.949542 -140 ACACCCTTATACAAAAGGGCAATCACTGCGATA 2 96 0 AAAAAGCAAT 0.971936 -205 AAATATTTTAAAAAAAGGTCAATT 3 2 0 AAAAAGCAAT 0.971935 -78 TTCATATTATAATAAATAAAAATATTTTAAAAA 3 21 0 ATAAAAAAAT 0.908411 -59 CCAATTACTGATAAATCTACAATTTCATATTAT 3 44 0 AAAATTCAAT 0.910194 -36 TTAAAATTAAAAACCAATTACTGATAAA 3 62 0 ATAAAACAAT 0.97218 -18 TAGTATACCAAATAATTATCAATTTAAAAAAAA 4 42 1 ATAATACAAT 0.940533 -73 TTATCAATTTAAAAAAAAAAAATTATTTGATAT 4 57 1 AAAAAAAAAT 0.935574 -58 TAAAAATGAAAGAAAAAATAAATACATTGCTCA 5 21 1 AAAAAAAAAT 0.935569 -26 ATTTAATAATCTGCAATAAAATAGGAG 6 5 1 ATAATTCAAT 0.87379 -32 * **** * **** Masking position 5 Map Score: 10.874 Number of sites scoring better than the average of aligned sites = 275 Number in coding regions = 88 Number in noncoding regions = 187 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 3 AACTCAAGGCATTCACGCGCAGCATCGTAA 1 58 1 ATTCACGCGC 0.990763 -243 CTTCCGCGGGATGCTCGCGCGCATCACCGG 1 128 1 ATGCTCGCGC 0.991432 -173 GTCCAACAAGATACTCACCCTGACTAAGAC 1 275 1 ATACTCACCC 0.964282 -26 TAAGGAGGAAATTCACACCCTTATACAAAA 2 113 0 ATTCACACCC 0.985552 -188 GGTCTAAAATTTGCACACGCATTCTCCCTT 2 258 1 TTGCACACGC 0.979042 -43 ********** Masking position 2 Map Score: 3.87018 Number of sites scoring better than the average of aligned sites = 9 Number in coding regions = 1 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 4 GTTCAGCAAGAATTGCAGAAGAGTCTGGCT 1 14 1 AATTGCAGAA 0.858333 -287 GCAGCATCGTAATTGCCCAATGCTTTATAG 1 76 1 AATTGCCCAA 0.978749 -225 AACGTGGTGGCGTTGTCGAACCTGTTATGT 1 215 0 CGTTGTCGAA 0.956061 -86 GAACGCACCCCATTGTCCAACAAGATACTC 1 261 1 CATTGTCCAA 0.988595 -40 GCATGGAGACCATTGTCTAAGGAGGAAATT 2 130 0 CATTGTCTAA 0.956173 -171 AAAATAAATACATTGCTCAAAC 5 35 1 CATTGCTCAA 0.963124 -12 ********** Masking position 4 Map Score: 3.44165 Number of sites scoring better than the average of aligned sites = 1226 Number in coding regions = 339 Number in noncoding regions = 887 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 5 ACGAGTACTATCTCCGCTTTTCCCAGAGCG 2 174 0 TCTCCGCTTT 0.980167 -127 CGGAGATAGTACTCGTCTTTTCCGCGAGGG 2 188 1 ACTCGTCTTT 0.911926 -113 ATTTTAGACCTACCCTCTTTTGGATACCAC 2 238 0 TACCCTCTTT 0.912357 -63 GCACACGCATTCTCCCTTTTGGATGCCCAC 2 270 1 TCTCCCTTTT 0.945737 -31 AAAAATCCCCTTTATACAACCTT 4 4 1 AATCCCCTTT 0.942758 -111 AAGTTTGTTCTCCTATTTTATTGCAGAT 6 19 0 TCTCCTATTT 0.941675 -18 ********** Masking position 8 Map Score: 1.04483 Number of sites scoring better than the average of aligned sites = 500 Number in coding regions = 132 Number in noncoding regions = 368 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 6 ATACATAACAGGTTCGACAACGCCACCACG 1 213 1 GGTTCGACAA 0.936038 -88 CAATGGGGTGCGTTCGTTGCATATATGCAA 1 246 0 CGTTCGTTGC 0.970658 -55 GTAGCAGATCCGTTCGACGCGTCACTCATA 2 49 0 CGTTCGACGC 0.995546 -252 TGCACGTGGGGGTTCGGCGCTCTGGGAAAA 2 157 1 GGTTCGGCGC 0.994703 -144 ********** Masking position 4 Map Score: 0.76685 Number of sites scoring better than the average of aligned sites = 11 Number in coding regions = 5 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 7 ATATATGCAAAAACGTGGTGGCGTTGTCGA 1 226 0 AAACGTGGTG 0.993353 -75 TCTGCTACTAAAACGTCGTGCCAGGTATCG 2 71 1 AAACGTCGTG 0.987869 -230 GATGCCCACTATAGGTGGTG 2 291 1 ATAGGTGGTG 0.978827 -10 ********** Masking position 3 Map Score: 0.0405893 Number of sites scoring better than the average of aligned sites = 4 Number in coding regions = 1 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 8 AATTACGATGCTGCGCGTGAATGCCTTGAG 1 60 0 CTGCGCGTGA 0.945541 -241 CACCGGTGATGCGCGCGAGCATCCCGCGGA 1 130 0 GCGCGCGAGC 0.720842 -171 AAACCGCAATGCGTAAGTGAACACACAACA 1 174 1 GCGTAAGTGA 0.890817 -127 GACGCGATGCGTACGAGCCCTGCAAATG 2 9 1 GCGTACGAGC 0.962822 -292 AGCGCCGAACCCCCACGTGCATGGAGACCA 2 148 0 CCCCACGTGC 0.952974 -153 CTCGTCTTTTCCGCGAGGGATATGGGTTTG 2 199 1 CCGCGAGGGA 0.956263 -102 ********** Masking position 7 Map Score: 0.222711 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 14 Number in noncoding regions = 37 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: -6.939e-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 10 ********** No masking Map Score: -6.939e-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 11 ********** No masking Map Score: -6.939e-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