AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i223_Pseudouridylate_Synthase_ecoli_hinf_reg_300.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -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 = 0.46 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 yciV 137 putative enzymes #2 yciQ 27 orf, hypothetical protein #3 yciL 210 orf, hypothetical protein #4 yjbC 211 orf, hypothetical protein #5 HI1194 300 glycine cleavage system transcriptional activator (gcvA) #6 HI1196 35 succinyl-CoA synthetase, beta subunit (sucC) #7 HI1198 120 conserved hypothetical protein #8 HI1199 47 conserved hypothetical protein Motif number 1 CGAACTAGTTAACTAGTACGCAAGTTCACG 1 28 0 AACTAGTACG 0.919286 -110 CGTACTAGTTAACTAGTTCGATGATTAATT 1 38 1 AACTAGTTCG 0.919286 -100 AAGGCGACACCAAAAGGAAGCTCT 3 197 1 CAAAAGGAAG 0.721172 -14 TGGAAATAACAAATAGTTCGCTCATGACTA 4 141 1 AAATAGTTCG 0.939433 -71 TTTATCAACCCAAAGGTACGGTATATTCCG 4 174 1 CAAAGGTACG 0.860673 -38 CAAATTGTTACTCAAGTTCGGTTTCCCGAA 5 96 1 CTCAAGTTCG 0.858277 -205 TTGTGTTTGCATATAGTTCGGGAAACCGAA 5 112 0 ATATAGTTCG 0.877759 -189 GAAACTCATTAACTAGTAAGGAATTACCAA 5 158 1 AACTAGTAAG 0.766018 -143 TATTGTAAGGAAAAGGGTAGGAAAGGACAA 5 204 1 AAAAGGGTAG 0.5497 -97 TTTCATAACCAAAAAGGACGTCGCGA 6 20 1 AAAAAGGACG 0.924551 -16 CTTTAGAAAACTAAAGTGCGG 7 2 0 CTAAAGTGCG 0.889917 -119 GCTCGCCATTATAAAGTGAGCACAAAATTG 7 66 1 ATAAAGTGAG 0.759958 -55 TCTTCCTTAAAAAATGTGCGCTGATTATAG 7 96 0 AAAATGTGCG 0.751436 -25 ********** Masking position 6 Map Score: 8.36551 Number of sites scoring better than the average of aligned sites = 1071 Number in coding regions = 903 Number in noncoding regions = 168 Number of orfs with sites within 600 bp upstream = 165 Fraction of orfs with sites within 600 bp upstream = 0.0265018 Motif number 2 GTGTAGTATGTTGCGCCTCAAAGCCAGGCC 3 53 1 TTGCGCCTCA 0.915145 -158 CAGAACTTACATCTGACTCACTGATAGTAA 3 131 0 ATCTGACTCA 0.947497 -80 CAGATGTAAGTTCTGACTCACTGTTGCACA 3 146 1 TTCTGACTCA 0.990167 -65 CTCCCGTGATTTCTTACTAACCGGAGAAGT 4 12 0 TTCTTACTAA 0.907581 -200 GAGTAACAATTTGTTACTCATTTACTTCCT 5 79 0 TTGTTACTCA 0.975014 -222 GAGTAACAAATTGTTACTCAAGTTCGGTTT 5 90 1 TTGTTACTCA 0.975014 -211 GTTAATGAGTTTCAGACTTAAGTATGATGT 5 141 0 TTCAGACTTA 0.850818 -160 GTGTTTCTTCCTTAAAAAATGTGC 7 107 0 TTCTTCCTTA 0.907471 -14 ********** Masking position 10 Map Score: 6.69541 Number of sites scoring better than the average of aligned sites = 146 Number in coding regions = 122 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 3 CAAGTTCACGTAAAAAGGGTATCGACA 1 6 0 TAAAAAGGAT 0.868979 -132 ATGTCGGCGCAAAAAACATTATCCAGAACGGG 1 108 1 AAAAAACAAT 0.8961 -30 TGGGTTGATAAAAAATAGTCATGAGCGAACTA 4 154 0 AAAAATAGAT 0.817348 -58 ATTCTCCTGTAAAAAACGGAATATACCGTACC 4 188 0 AAAAAACGAT 0.985183 -24 TAAAATCGGGATGAAAAAAACG 5 1 1 TAAAATCGAT 0.926382 -300 ATCGGGATGAAAAAAACGCCACTCAATGAGAG 5 15 1 AAAAAACGAC 0.978139 -286 ACCTCAAATAAAAAAACGTCACTTGTCCTTTC 5 224 0 AAAAAACGAC 0.978139 -77 ******** ** Masking position 5 Map Score: 2.99231 Number of sites scoring better than the average of aligned sites = 293 Number in coding regions = 230 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 4 CGATGATTAATTGTCAACAGCTCATTTCAGA 1 56 1 TTGTCACAGC 0.927468 -82 TTCAGAATATTTGCCAGAACCGTTATGATGT 1 81 1 TTGCCAAACC 0.955137 -57 CTCAAATCACTTTCCAGAAGCAATGTGCGAC 4 89 0 TTTCCAAAGC 0.976499 -123 CATGACTATTTTTTATCAACCCAAAGGTACG 4 163 1 TTTTATAACC 0.726256 -49 GTGAACTGTTTTCATAACCAAAAAGGACG 6 9 1 TTTTCAAACC 0.979166 -27 CGCACTTTAGTTTTCTAAAGCGTAGATTGGC 7 12 1 TTTTCTAAGC 0.964109 -109 GGAAAGGTCGCTTTCACAAGCGTCTATAAG 8 10 0 CTTTCAAAGC 0.950004 -38 ****** **** Masking position 9 Map Score: 2.77879 Number of sites scoring better than the average of aligned sites = 277 Number in coding regions = 236 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 5 CTTCCATCCGTGGAACGCAATTTG 2 5 0 TGGAACGCAA 0.918858 -23 TCAGACGCCTGGGAAGGCGACACCAAAAGG 3 184 1 GGGAAGGCGA 0.992547 -27 ACATTGCTTCTGGAAAGTGATTTGAGCAGG 4 94 1 TGGAAAGTGA 0.950759 -118 CATATAGTTCGGGAAACCGAACTTGAGTAA 5 103 0 GGGAAACCGA 0.984728 -198 ATAGACGCTTGTGAAAGCGACCTTTCCATT 8 14 1 GTGAAAGCGA 0.977529 -34 ********** Masking position 5 Map Score: 1.30635 Number of sites scoring better than the average of aligned sites = 317 Number in coding regions = 292 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 6 CTTTCCTACCCTTTTCCTTACAATACAACC 5 199 0 CTTTTCCTTA 0.939219 -102 AAAAACGTCACTTGTCCTTTCCTACCCTTT 5 215 0 CTTGTCCTTT 0.983712 -86 TGAAATAAATCTTGTCCATTATAGACGAAA 5 272 1 CTTGTCCATT 0.983706 -29 GTGAAAGCGACCTTTCCATTATTCAAGGAA 8 24 1 CCTTTCCATT 0.958163 -24 ********** Masking position 5 Map Score: 0.837214 Number of sites scoring better than the average of aligned sites = 45 Number in coding regions = 37 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 7 TCTGGCAAATATTCTGAAATGAGCTGTTGA 1 69 0 ATTCTGAAAT 0.76739 -69 ACTATCAGTGAGTCAGATGTAAGTTCTGAC 3 133 1 AGTCAGATGT 0.924913 -78 TGCAACAGTGAGTCAGAACTTACATCTGAC 3 144 0 AGTCAGAACT 0.927187 -67 CCTTCCCAGGCGTCTGATATGCTTTTGTGC 3 171 0 CGTCTGATAT 0.804887 -40 TTCTCCGGTTAGTAAGAAATCACGGGAGGC 4 14 1 AGTAAGAAAT 0.954762 -198 GAAGTAAATGAGTAACAAATTGTTACTCAA 5 81 1 AGTAACAAAT 0.754101 -220 TTCAGACTTAAGTATGATGTTGTGTTTGCA 5 131 0 AGTATGATGT 0.835765 -170 ATCATACTTAAGTCTGAAACTCATTAACTA 5 143 1 AGTCTGAAAC 0.887185 -158 CTCATTAACTAGTAAGGAATTACCAATCAT 5 162 1 AGTAAGGAAT 0.831353 -139 ********** Masking position 3 Map Score: 1.84231 Number of sites scoring better than the average of aligned sites = 484 Number in coding regions = 402 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 8 ********** No masking Map Score: -1.83077e-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 9 ********** No masking Map Score: -1.83077e-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: -1.83077e-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