AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i217_Ribosomal_Operon_4_bbur_reg_300.orf -o217_borburg_300.ace -a/home/amcguire/genomes/ORF_borburg.txt -z/home/amcguire/genomes/borburg.fna -g0.28 -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 = 0.28 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RBB00315 172 3615 #2 RBB00314 240 3615 #3 RBB00313 90 3615 #4 RBB00312 91 3615 Motif number 1 AATTTATCTGTGTCTAGATTTTAATTAA 1 7 0 TGTCTATTTT 0.820805 -166 GATATTATTTTTTTTTTAATGTAGAATTTATC 1 31 0 TTTTTAATGT 0.929692 -142 TTTTTAAAAGTTTTTGGTATTTCCTATGTAAT 1 64 0 TTTTTTATTT 0.861219 -109 ATCTAAATTGTTTGTGAATTTTTAAAAGTTTT 1 82 0 TTTGTATTTT 0.948234 -91 TTTTTTGTCCTTGTTGGTTTTAGCACTATACT 1 151 0 TTGTTTTTTA 0.7475 -22 TTTAAAATAATTTTTGATTCTTCAATTAAGT 2 10 0 TTTTTTTCTT 0.828296 -231 ATAAATTATTTGGTTCAATTGTTTAAAATAAT 2 31 0 TGGTTATTGT 0.967207 -210 GGTTGTTTTTTTGTTGTATTTTTGATAAATTA 2 55 0 TTGTTATTTT 0.981391 -186 AGTAAATATCTTGTTAAATTGTAGGTTGTTTT 2 78 0 TTGTTATTGT 0.984637 -163 TACTGTTTGATTGTTTAATTGTATTTAATACT 2 120 0 TTGTTATTGT 0.984637 -121 GGATTTTGTATTTTTATTTTTTATAGATATAT 2 171 0 TTTTTTTTTT 0.970648 -70 TTAATAAGATTTTGTGGATTTTGTATTTTTAT 2 186 0 TTTGTATTTT 0.948234 -55 TCAATATTGTTTTTTGCATTGTGGTATAAAAA 3 63 1 TTTTTATTGT 0.986007 -28 ACCATGTTAGTGTTTAATTTGTAGCTTGGCAG 4 41 1 TGTTTTTTGT 0.948706 -51 ***** ***** Masking position 5 Map Score: 19.897 Number of sites scoring better than the average of aligned sites = 1689 Number in coding regions = 1092 Number in noncoding regions = 597 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 2 CATTAAAAAAAAAATAATATCTATTACATA 1 42 1 AAAATAATAT 0.891443 -131 TAAAAATTCACAAACAATTTAGATAGAATC 1 90 1 CAAACAATTT 0.954215 -83 AATTTAACATTATACTATATAATGTTAAAA 1 122 1 TATACTATAT 0.742805 -51 TCAATTGTTTAAAATAATTTTTGATTCTTC 2 19 0 AAAATAATTT 0.887871 -222 ACAATTGAACCAAATAATTTATCAAAAATA 2 41 1 CAAATAATTT 0.805728 -200 AAAAAAACAACCTACAATTTAACAAGATAT 2 75 1 CCTACAATTT 0.888485 -166 AATTGTATTTAATACTATATGATGCAAGTA 2 106 0 AATACTATAT 0.957859 -135 TATAGTATTAAATACAATTAAACAATCAAA 2 117 1 AATACAATTA 0.842555 -124 TACTACTATTACTACTATATATCTATAAAA 2 155 1 ACTACTATAT 0.868381 -86 AAAAAATAAAAATACAAAATCCACAAAATC 2 181 1 AATACAAAAT 0.842556 -60 GATAAAATGTAATAGAATATATAAGGAGGC 2 218 1 AATAGAATAT 0.86394 -23 GTGAGTTATTAATGCTATTTTGAATATTAA 3 12 1 AATGCTATTT 0.768287 -79 CACAATGCAAAAAACAATATTGAATAAACC 3 56 0 AAAACAATAT 0.976349 -35 TCCTCCATTAAAAACAATTTTATGCTGCCA 4 67 0 AAAACAATTT 0.97623 -25 ********** Masking position 7 Map Score: 15.0642 Number of sites scoring better than the average of aligned sites = 670 Number in coding regions = 456 Number in noncoding regions = 214 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 3 TACCAAAAACTTTTAAAAATTCACAAACAA 1 77 1 TTTTAAAAAT 0.915049 -96 TAGAATCCTAATTTAACATTATACTATATA 1 113 1 ATTTAACATT 0.884784 -60 AGCACTATACTTTTAACATTATATAGTATA 1 132 0 TTTTAACATT 0.918966 -41 TTAATTGAAGAATCAAAAATTATTTTAAAC 2 13 1 AATCAAAAAT 0.803268 -228 CAAAAATTATTTTAAACAATTGAACCAAAT 2 26 1 TTTAAACAAT 0.964448 -215 CCAAATAATTTATCAAAAATACAACAAAAA 2 50 1 TATCAAAAAT 0.857684 -191 ACAACCTACAATTTAACAAGATATTTACTT 2 81 1 ATTTAACAAG 0.713849 -160 ATTAAATACAATTAAACAATCAAACAGTAG 2 123 1 ATTAAACAAT 0.948354 -118 ACTATATATCTATAAAAAATAAAAATACAA 2 168 1 TATAAAAAAT 0.879601 -73 GAAAAGCTTATTTTAATATTCAAAATAGCA 3 24 0 TTTTAATATT 0.662187 -67 TTCTAGGTTTATTCAATATTGTTTTTTGCA 3 51 1 ATTCAATATT 0.522837 -40 TGCATTGTGGTATAAAAAATTGAT 3 77 1 TATAAAAAAT 0.879601 -14 TTATTATTGACAATTGCATTTATA 4 5 1 TATTGACAAT 0.713853 -87 CAAGCTACAAATTAAACACTAACATGGTAT 4 39 0 ATTAAACACT 0.775914 -53 GCTCCTCCATTAAAAACAATTTTATGCTGC 4 69 0 TAAAAACAAT 0.627312 -23 ********** Masking position 6 Map Score: 12.56 Number of sites scoring better than the average of aligned sites = 2337 Number in coding regions = 1514 Number in noncoding regions = 823 Number of orfs with sites within 600 bp upstream = 144 Fraction of orfs with sites within 600 bp upstream = 0.0231288 Motif number 4 TGGTATTTCCTATGTAATAGATATTATTTT 1 52 0 TATGTAATAG 0.956382 -121 TGTTTAATTGTATTTAATACTATATGATGC 2 111 0 TATTTAATAC 0.804165 -130 ATTAAGATAAAATGTAATAGAATATATAAG 2 213 1 AATGTAATAG 0.943943 -28 GTGAGTTATTAATGCTATTTTGAATATTAA 3 12 1 AATGCTATTT 0.744976 -79 TTTCTAGGTTTATTCAATATTGTTTTTTGC 3 50 1 TATTCAATAT 0.845748 -41 ATAGCATATAAATGCAATTGTCAATAATAA 4 11 0 AATGCAATTG 0.938002 -81 ATTGCATTTATATGCTATACCATGTTAGTG 4 23 1 TATGCTATAC 0.931153 -69 ********** Masking position 7 Map Score: 1.66185 Number of sites scoring better than the average of aligned sites = 258 Number in coding regions = 174 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 5 ********** No masking Map Score: -1.14154e-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 6 ********** No masking Map Score: -1.14154e-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 7 ********** No masking Map Score: -1.14154e-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