AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i190_ribonucleoside_diphos___bsub_reg_300.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 miaA 98 tRNA isopentenylpyrophosphate transferase #2 ymaH 39 similar to host factor-1 protein #3 ymzC 195 ymzC #4 ymzA 81 ymzA #5 ymaA 242 similar to ribonucleoprotein #6 yosL 87 yosL #7 yosK 44 yosK #8 yosI 31 yosI #9 yosH 60 yosH #10 yosG 42 yosG #11 yosD 38 yosD #12 yosC 44 yosC #13 yosB 130 yosB Motif number 1 TCCATTTTGCCCTTTTTTTGCATCGGTAAA 1 18 0 CCTTTTTTTG 0.847047 -81 TATGTATCACTCTCTTTTATAAATCTCCCC 1 79 0 TCTCTTTTAT 0.922044 -20 GTTTCGTCCTCCTTGATTCTCTATATC 2 23 0 CCTCCTTGAT 0.811418 -17 CAAGGCACGGTCTTTTTTTATGAGAACAAC 3 121 1 TCTTTTTTTA 0.728562 -75 GTTTTCACCCTCTGTTTGATCTGTGTCT 4 64 0 CCTCTGTTTG 0.820344 -18 CTCGTTCTGCTCTCTTTTTTGGGCCCTAAT 5 79 1 TCTCTTTTTT 0.945802 -164 ACCTATTCGTCCTCCTTAGGAATTG 6 6 0 CCTCCTTAGG 0.891106 -82 TTTACATCTCCTTATTTTTTGTATTT 6 72 0 TCTCCTTATT 0.950048 -16 AATCCACTAATCTCTTTAAAA 9 2 0 TCTCTTTAAA 0.889091 -59 AGCACAATGCTCCTTTTAATATTTATTT 9 43 0 GCTCCTTTTA 0.854061 -18 ATCTAACTCTCCTTTTGAAAATTTCGG 10 26 0 TCTCCTTTTG 0.981608 -17 TCCTTATAAGTCTCTTTAAAAATTGAATT 11 10 0 TCTCTTTAAA 0.889091 -29 TTATTCACCTCCTTATAAGTCTCTTTA 11 22 0 CCTCCTTATA 0.953772 -17 ATTGCCACCTCCTTTAGTAAGGATAGT 13 8 1 CCTCCTTTAG 0.97515 -123 CTTCATTTTTTCTTTTTTAGACTGAAATCT 13 70 0 TCTTTTTTAG 0.775786 -61 TCATCAACTCTCCTTATTCAACTCTTAA 13 113 0 TCTCCTTATT 0.950048 -18 ********** Masking position 7 Map Score: 18.1912 Number of sites scoring better than the average of aligned sites = 2024 Number in coding regions = 1301 Number in noncoding regions = 723 Number of orfs with sites within 600 bp upstream = 745 Fraction of orfs with sites within 600 bp upstream = 0.119659 Motif number 2 GCGGCCATTTTTAACATGAATCCACTTTTG 3 61 1 TTAACATGAA 0.738973 -135 TATATTATGTATAAAATGAATTTGGGAGTG 3 169 1 ATAAAATGAA 0.90667 -27 ATCCGCTTTGTAAATTCGAATGCTTGTGAA 4 13 0 TAAATTCGAA 0.709172 -69 GATGTATATCATAACATGAAAAAAAACTGC 5 11 0 ATAACATGAA 0.806858 -232 ATACATCGGCTAAAAACGACACCCCGAGTA 5 34 1 TAAAAACGAC 0.792101 -209 TGATTTGATCAAAATATGAATTTTTCATAA 5 126 1 AAAATATGAA 0.942166 -117 GAATTTTTCATAAAAACGAATCTATATATT 5 143 1 TAAAAACGAA 0.934177 -100 GACCTATCAAAAAATATGAATCTCTCATCA 5 213 0 AAAATATGAA 0.942166 -30 AGCTTTATTCAAAATACAAAAAATAAGGAG 6 61 1 AAAATACAAA 0.75954 -27 AGAATAAAAATAAATTAAGAGGAT 8 5 1 TAAAAATAAA 0.803113 -27 TTCTAAATCTAAAAAATAAATATTAAAAGG 9 30 1 AAAAAATAAA 0.857522 -31 AAATTTCGGCTTAAAATAAAACTT 10 5 0 TTAAAATAAA 0.608298 -38 AAGTCTCTTTAAAAATTGAATT 11 3 0 AAAAATTGAA 0.872697 -36 GCAAAGGTTAAAAATTCGACATAGATTTCA 13 48 1 AAAATTCGAC 0.491315 -83 TCTAAAAAAGAAAAAATGAAGACTTTGTCT 13 79 1 AAAAAATGAA 0.962257 -52 ********** Masking position 4 Map Score: 15.62 Number of sites scoring better than the average of aligned sites = 2344 Number in coding regions = 1848 Number in noncoding regions = 496 Number of orfs with sites within 600 bp upstream = 496 Fraction of orfs with sites within 600 bp upstream = 0.0796659 Motif number 3 TATGTATCACTCTCTTTTATAAATCT 1 83 0 TCACTCTCTT 0.916924 -16 GTTTCGTCCTCCTTGATTCTCTA 2 27 0 TCGTCCTCCT 0.995931 -13 GTTTTCACCCTCTGTTTGATCTGT 4 68 0 TCACCCTCTG 0.899444 -14 GAATCATCTCTCGTCCTACTCGGGGTGTCG 5 50 0 TCGTCCTACT 0.964704 -193 GAGATGATTCTCGTTCTGCTCTCTTTTTTG 5 70 1 TCGTTCTGCT 0.929954 -173 CAGTACCTATTCGTCCTCCTTAGGAATTG 6 10 0 TCGTCCTCCT 0.995931 -78 CTATTCGTCCTCCAATTGTTTCTG 7 31 0 TCGTCCTCCA 0.977709 -14 CTTCATCATCCTCTTAATTTATTTT 8 17 0 TCATCCTCTT 0.976093 -15 ATCTAACTCTCCTTTTGAAAATT 10 30 0 TAACTCTCCT 0.767522 -13 ********** Masking position 7 Map Score: 12.6012 Number of sites scoring better than the average of aligned sites = 421 Number in coding regions = 322 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 4 CACTCTCTTTTATAAATCTCCCCCATTATA 1 72 0 TATAAATCTC 0.945631 -27 TATGTATCACTCTCTTTTAT 1 89 0 TATGTATCAC 0.625044 -10 TCCTTGATTCTCTATATCATACAGTTTCGA 2 11 0 TCTATATCAT 0.643 -29 TTGATCTGTGTCTGTATTTAGTTTAGCGGC 4 47 0 TCTGTATTTA 0.615971 -35 TTGATCAAAATATGAATTTTTCATAAAAAC 5 130 1 TATGAATTTT 0.637435 -113 TAAAAACGAATCTATATATTGTGTTTTTGC 5 153 1 TCTATATATT 0.463562 -90 TATCAAAAAATATGAATCTCTCATCACTAA 5 209 0 TATGAATCTC 0.927393 -34 ATTGTTTCTGTATAAATTTCATTGTGTCTT 7 11 0 TATAAATTTC 0.848721 -34 ATTAGTGGATTCTAAATCTAAAAAATAAAT 9 21 1 TCTAAATCTA 0.913778 -40 ATCTAACTCTCCTTTTGAAAA 10 32 0 TCTAACTCTC 0.847364 -11 TTCACCTCCTTATAAGTCTCTTTAAAAATT 11 16 0 TATAAGTCTC 0.749129 -23 TATTTCCCCATCTATATCTTTCCTTT 12 7 0 TCTATATCTT 0.898147 -38 GAAGACTTTGTCTAAATTTAAGAGTTGAAT 13 96 1 TCTAAATTTA 0.773674 -35 ********** Masking position 7 Map Score: 6.24593 Number of sites scoring better than the average of aligned sites = 684 Number in coding regions = 585 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 5 ********** No masking Map Score: 2.97961e-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 GACAGCCTTTCCTCATGTCTTGACATGGCA 3 20 0 CCTCATGTCT 0.943408 -176 GCAGAACGAGAATCATCTCTCGTCCTACTC 5 59 0 AATCATCTCT 0.967626 -184 AATATGAATCTCTCATCACTAACACTATAT 5 201 0 TCTCATCACT 0.868026 -42 TTTAGAATCCACTAATCTCTTTAAAA 9 7 0 ACTAATCTCT 0.91245 -54 AACTCTCCTTATTCAACTCTTAAATTTAGA 13 106 0 ATTCAACTCT 0.900873 -25 TCATCAACTCTCCTTATTCAA 13 120 0 CATCAACTCT 0.945354 -11 ********** Masking position 5 Map Score: 0.0384849 Number of sites scoring better than the average of aligned sites = 221 Number in coding regions = 179 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 7 ********** No masking Map Score: 2.97961e-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 8 TCCTCATGTCTTGACATGGCATTTTTTGAT 3 9 0 TTGCATGCAT 0.900305 -187 AGTTTAGCGGCTGGCATCCGCTTTGTAAATTC 4 26 0 CTGCATCGCT 0.835611 -56 GTTTTCACCCTCTGTTTGATCTG 4 69 0 TTTCACCTCT 0.929875 -13 GCAGTTTTTTTTCATGTTATGATATACATC 5 9 1 TTTCATGTAT 0.640213 -234 CATGTTATGATATACATCGGCTAAAAACGACA 5 23 1 TATCATCGCT 0.840325 -220 GTTTTATCACGACCTATCAAAAAAT 5 228 0 TTACACGCCT 0.880535 -15 TTTACATCTCCTTATTTTTTGT 6 76 0 TTTCATCCCT 0.981655 -12 TTATTCACCTCCTTATAAGTCTC 11 26 0 TATCACCCCT 0.941574 -13 ATTGCCACCTCCTTTAGTAAGGA 13 2 1 TTGCACCCCT 0.986779 -129 TTTTTAACCTTTGCCATACCATATACTATCCT 13 30 0 TTGCATACAT 0.715886 -101 *** **** *** Masking position 6 Map Score: 3.28652 Number of sites scoring better than the average of aligned sites = 871 Number in coding regions = 712 Number in noncoding regions = 159 Number of orfs with sites within 600 bp upstream = 159 Fraction of orfs with sites within 600 bp upstream = 0.0255381 Motif number 9 ********** No masking Map Score: 2.97961e-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 10 ********** No masking Map Score: 2.97961e-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 11 ********** No masking Map Score: 2.97961e-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