AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i216_Ribosomal_Operon_3_bsub_reg_100.orf -aORF_bsub.txt -zbsub.fna -g0.435 -x5 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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 ylxM 176 similar to hypothetical proteins #2 rpsP 105 ribosomal protein S16 (BS17) #3 ylqD 121 ylqD #4 rplS 130 ribosomal protein L19 #5 ylqF 142 similar to hypothetical proteins #6 rnh 70 ribonuclease H Motif number 1 CCCTATTTTAAGGAGGATTTTT 1 2 0 AGGAGGTTTT 0.590896 -175 ATTGTATATGAACCCTATTTTAAGGAGGATT 1 14 0 AACCCTTTTT 0.921696 -163 GGATGATATTTAGCGTATTTTGGAAAAGTTA 1 58 1 TAGCGTTTTT 0.900496 -119 GAAAAGTTAATCGCCGCTTTGACAAGATAAA 1 80 1 TCGCCGTTTG 0.888451 -97 TAACTTAGTTTACACGGTTTTAATGACACTG 1 118 0 TACACGTTTT 0.964244 -59 TTGAGCTCTCCCCTTTGTTAAGTCAAATC 1 158 0 TCCCCTTGTT 0.91666 -19 TTTTTTCTTAACAACGGTTTTATCATGTATA 2 16 0 ACAACGTTTT 0.740199 -90 AAAGTGTTTGTAAAGTGTTTTTTCTTAACAA 2 33 0 TAAAGTTTTT 0.614192 -73 GGCCGGCACCTCCCCTTTTTTTACACGCAAA 3 20 1 TCCCCTTTTT 0.985863 -102 TCTATCAGTTTACCCTTTTTTTGCGTGTAAA 3 39 0 TACCCTTTTT 0.97345 -83 CTTTTACTCGTCCAGGCTTTTCTATTTTGCC 3 76 0 TCCAGGTTTT 0.970278 -46 CGCACCAAGCTCCCCGCTTTTAAAACTTTTA 3 101 0 TCCCCGTTTT 0.992346 -21 TGTTCCGCTGTGCCGGTTTTTGTGGCCAAGA 4 93 1 TGCCGGTTTT 0.966741 -38 ****** **** Masking position 8 Map Score: 14.677 Number of sites scoring better than the average of aligned sites = 1941 Number in coding regions = 1654 Number in noncoding regions = 287 Number of orfs with sites within 600 bp upstream = 274 Fraction of orfs with sites within 600 bp upstream = 0.044009 Motif number 2 AAAACACTTTACAAACACTTTTATCATTGTT 2 43 1 ACAACACTTT 0.817758 -63 TTTACTAGCACCTCCGAAAATATT 2 92 0 ACAGCACCTC 0.990299 -14 AAGGGAGAGGGCCGGCACCTCCCCTTTTTTT 3 11 1 GCGGCACCTC 0.985915 -111 TTTTACTCGTCCAGGCTTTTCTATTTTGCCT 3 75 0 CCGGCTTTTC 0.864862 -47 TGTGGCTTAAGCGGGCTTATCCGCTGCAAGC 4 52 1 GCGGCTTATC 0.836657 -79 GGCCACAAAAACCGGCACAGCGGAACATCGT 4 89 0 ACGGCACAGC 0.971783 -42 GTTACAGGTAACAAGCTCTTTTCGTTCGTTA 5 14 0 ACAGCTCTTT 0.944965 -129 GTTACCTGTAACAAGCTCTTTTTTTATACAG 5 33 1 ACAGCTCTTT 0.944965 -110 AAAATGCCGGACAGGCATCGTAAAATACATA 5 70 1 ACGGCATCGT 0.932011 -73 GTGACACGAACACCGCCTTTATCTTC 5 127 0 ACAACACCGC 0.906728 -16 AAAAATAAAGACCCGCATTTCTGCGCGCCT 6 10 0 ACCGCATTTC 0.914179 -61 ** ******** Masking position 6 Map Score: 7.97555 Number of sites scoring better than the average of aligned sites = 1831 Number in coding regions = 1696 Number in noncoding regions = 135 Number of orfs with sites within 600 bp upstream = 118 Fraction of orfs with sites within 600 bp upstream = 0.0189528 Motif number 3 CTGTCAAGTTTTTATCTTGTCAAAGCGGCGA 1 90 0 TTTTCTTGTC 0.985702 -87 CGTAAAGGGATTTGACTTAACAAAGGGGAGA 1 150 1 TTTACTTAAC 0.929992 -27 TGTAAAGTGTTTTTTCTTAACAACGGTTTTA 2 25 0 TTTTCTTAAC 0.968351 -81 CTTTTAAAACTTTTACTCGTCCAGGCTTTTC 3 85 0 TTTACTCGTC 0.902231 -37 GAACACCGCCTTTATCTTCAGTATGCATGAT 5 115 0 TTTTCTTCAG 0.900978 -28 GGGTCTTTATTTTTTCTTGGCTGAACCGATA 6 27 1 TTTTCTTGGC 0.975868 -44 TTTCTCTTCTCCCTTACTGTA 6 60 0 TTTTCTTCTC 0.979309 -11 *** ******* Masking position 7 Map Score: 5.33866 Number of sites scoring better than the average of aligned sites = 267 Number in coding regions = 208 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 4 ATAGGGTTCATATACAATATCGGAATAAAT 1 27 1 TATACAATAT 0.94096 -150 AATCGCCGCTTTGACAAGATAAAAACTTGA 1 88 1 TTGACAAGAT 0.833794 -89 TCGGTTATACATGATAAAACCGTTG 2 6 1 TATACATGAT 0.950608 -100 GATAGAAGCTTAGGCAAAATAGAAAAGCCT 3 64 1 TAGGCAAAAT 0.928321 -58 TTTCATAGCCTATGCAATAAAAT 4 4 0 TATGCAATAA 0.799827 -127 GCTCTTTTTTTATACAGAATTTGAAAATGC 5 47 1 TATACAGAAT 0.877746 -96 TTATCTTCAGTATGCATGATTCATTGTTGT 5 105 0 TATGCATGAT 0.958749 -38 ********** Masking position 6 Map Score: 1.41646 Number of sites scoring better than the average of aligned sites = 309 Number in coding regions = 243 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 5 TTTTTTGCGTGTAAAAAAAGGGGAGGTGCC 3 24 0 GTAAAAAAAG 0.919587 -98 CAAATTCTGTATAAAAAAAGAGCTTGTTAC 5 40 0 ATAAAAAAAG 0.962101 -103 GCATCGTAAAATACATAAAGGACAACAATG 5 84 1 ATACATAAAG 0.975164 -59 TCAGCCAAGAAAAAATAAAGACCCGCATTT 6 21 0 AAAAATAAAG 0.917054 -50 GGCTGAACCGATACATACAGTAAGGGAGAA 6 45 1 ATACATACAG 0.946491 -26 ********** Masking position 5 Map Score: 1.76422 Number of sites scoring better than the average of aligned sites = 312 Number in coding regions = 170 Number in noncoding regions = 142 Number of orfs with sites within 600 bp upstream = 149 Fraction of orfs with sites within 600 bp upstream = 0.0239319 Motif number 6 TTTAGCGTATTTTGGAAAAGTTAATCGCCGCT 1 66 1 TTTGAAAGTT 0.849776 -111 TTAATCGCCGCTTTGACAAGATAAAAACTTGA 1 86 1 CTTTAAAGAT 0.915923 -91 TCCGAAAATATTTCAACAAGATAGTATATTAA 2 72 0 TTTCAAAGAT 0.908255 -34 TTTGCCTAAGCTTCTATCAGTTTACCCTTTTT 3 50 0 CTTCACAGTT 0.967601 -72 CGTTTTCAAGCTTGCAGCGGATAAGCCCGCTT 4 60 0 CTTGACGGAT 0.965213 -71 CCGCTGCAAGCTTGAAAACGATGTTCCGCTGT 4 72 1 CTTGAACGAT 0.945925 -59 CTCCTTCCAACAGATGCTCTTGGCC 4 116 0 CTTCACAGAT 0.985643 -15 AAAAAAAGAGCTTGTTACAGGTAACAAGCTCT 5 26 0 CTTGTCAGGT 0.855255 -117 **** * ***** Masking position 3 Map Score: 3.13175 Number of sites scoring better than the average of aligned sites = 529 Number in coding regions = 468 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 7 TTGAGCTCTCCCCTTTGTTAAGT 1 164 0 AGCTCTCCCC 0.990437 -13 GAGGTGCCGGCCCTCTCCCTT 3 2 0 CCCTCTCCCT 0.987948 -120 GAGGGCCGGCACCTCCCCTTTTTTTACACG 3 17 1 ACCTCCCCTT 0.97434 -105 CGCACCAAGCTCCCCGCTTTTAAAACT 3 105 0 AGCTCCCCGC 0.976585 -17 TTTCTCTTCTCCCTTACTGTATGT 6 57 0 TCTTCTCCCT 0.913783 -14 ********** Masking position 4 Map Score: 0.684733 Number of sites scoring better than the average of aligned sites = 213 Number in coding regions = 135 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 8 ********** No masking Map Score: -4.38104e-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: -4.38104e-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: -4.38104e-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