AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i220_Ribosomal_Operon_7_ecoli_hinf_reg_100.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 galP 300 galactose-proton symport of transport system #2 sprT 76 orf, hypothetical protein #3 endA 94 DNA-specific endonuclease I #4 yggJ 52 orf, hypothetical protein #5 yhdT 108 orf, hypothetical protein #6 HI0301 300 hemolysin, putative #7 HI0303 49 conserved hypothetical protein #8 HI0976 119 conserved hypothetical protein #9 HI0978 40 ribosomal protein L11 methyltransferase (prmA) Motif number 1 ATAGATTAAACGCTGTTATCTGCAATTAAGA 1 127 0 CGCGTTATCT 0.841691 -174 TCCCCAAGCTTCCTCCCATCGCGGAGGAAGC 2 13 1 TCCCCCATCG 0.94109 -64 AGCCACCTCTTGCAGTCATCTTTTCTTCGCT 2 41 1 TGCGTCATCT 0.983206 -36 GGCCGGAAAATCCGGCCTTTTGACGCTTTAG 5 16 0 TCCGCCTTTT 0.958653 -93 GGCCGGATTTTCCGGCCTTTTTTATTACTGG 5 30 1 TCCGCCTTTT 0.958653 -79 AAGGTACAATCCCCGCTTTCTTCACCCATCA 5 78 1 CCCGCTTTCT 0.796519 -31 TAAGGATCTTTGCCCTCTTTTTACGAGATCA 6 29 1 TGCCTCTTTT 0.945134 -272 TCTAGAATTTTCCCCTCTCCGTAAAAATTGT 6 145 1 TCCCTCTCCG 0.855761 -156 AAACCCAATGTGCGGTTATTTTTTATTGATT 6 201 1 TGCGTTATTT 0.900519 -100 TTATTGATTTTCCTCTTTTCGCGTTTTGCGA 6 223 1 TCCCTTTTCG 0.843701 -78 AATGAAAAAGTGCGGTCATTTTAACTGGTGT 7 13 0 TGCGTCATTT 0.969223 -37 TTAATCAATATGCTGTCACCTTCTTCTAAAT 8 14 1 TGCGTCACCT 0.948709 -106 AATATCACCTTCCTCTCATTTAGAAGAAGGT 8 31 0 TCCCTCATTT 0.958644 -89 *** ******* Masking position 3 Map Score: 11.9171 Number of sites scoring better than the average of aligned sites = 1295 Number in coding regions = 1157 Number in noncoding regions = 138 Number of orfs with sites within 600 bp upstream = 144 Fraction of orfs with sites within 600 bp upstream = 0.0231288 Motif number 2 ATTACACTGATGTGATTTGCTTCACATCTTT 1 222 1 TGGATTTGCT 0.687092 -79 CCCTCCAATATGGTTATTTTTTATTGTGAAT 1 276 0 TGTTATTTTT 0.946881 -25 GATTTTTGATTGTGAATTGATCTCGTAAAAA 6 46 0 TGGAATTGAT 0.903829 -255 CCGTAAAAATTGTGTATTTTTAACCGCACTT 6 163 1 TGGTATTTTT 0.976619 -138 ACCCAATGTGCGGTTATTTTTTATTGATTTT 6 203 1 CGTTATTTTT 0.788024 -98 TTTCGCGTTTTGCGATTTTTTCTAAAATATG 6 239 1 TGGATTTTTT 0.920706 -62 TTCTAAAATATGATAATTTTTCGCCGTCAAT 6 258 1 TGTAATTTTT 0.946881 -43 AATGTTTATTTATATGAATGAAA 7 37 0 TGTTATTTAT 0.849239 -13 GATGTATCCCTGTGAATTGTTGCAATTCTAT 8 98 0 TGGAATTGTT 0.96747 -22 TTCAAAATTTTGCGTATTTTTACCGCACT 9 9 0 TGGTATTTTT 0.976619 -32 ** ******** Masking position 7 Map Score: 10.0713 Number of sites scoring better than the average of aligned sites = 272 Number in coding regions = 210 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 3 GTAATCGGTTTCAGTTGTGATGATAATCTGC 1 14 0 TAGTTGTGAT 0.972857 -287 CAAATCTTTGTCTGTTGTGGTTGGTGTAATC 1 39 0 TTGTTGTGGT 0.932231 -262 AACATTTATCTTAGTTATGATTTAAGTGCAT 1 181 0 TAGTTATGAT 0.846667 -120 AAGCGATTACACTGATGTGATTTGCTTCACA 1 217 1 ATGATGTGAT 0.83983 -84 TACGACGTAAAAAGATGTGAAGCAAATCACA 1 232 0 AAGATGTGAA 0.815239 -69 ATGGTTATTTTTTATTGTGAATTAAGATAGG 1 267 0 TTATTGTGAA 0.894849 -34 TTTTGAAGTTTGATGTGATAAGGATCTTT 6 9 1 TTGATGTGAT 0.954817 -292 TAATGGATTTTTGATTGTGAATTGATCTCGT 6 51 0 TGATTGTGAA 0.756793 -250 ATGTTGTGGATAACTTGTGAATAATGGATTT 6 72 0 TACTTGTGAA 0.83311 -229 GAAAAGTATCTATGTTGTGGATAACTTGTGA 6 83 0 TTGTTGTGGA 0.920483 -218 CGATTTTTTCTAAAATATGATAATTTTTCGC 6 251 1 TAAATATGAT 0.478787 -50 * ********* Masking position 6 Map Score: 5.88108 Number of sites scoring better than the average of aligned sites = 424 Number in coding regions = 336 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 108 Fraction of orfs with sites within 600 bp upstream = 0.0173466 Motif number 4 AACTCAATTATTTTCATGCACTTAAATCATAA 1 166 1 TTTTTGCACT 0.916375 -135 GCAGTCATCTTTTCTTCGCTCTATCCTCTGCC 2 52 1 TTTCCGCTCT 0.975742 -25 AAATCCGGCCTTTTGACGCTTTAGCAGTC 5 8 0 TTTTCGCTTT 0.981571 -101 ATTGTGTATTTTTAACCGCACTTTAGGTTTAA 6 171 1 TTTACGCACT 0.954217 -130 GATTTTCCTCTTTTCGCGTTTTGCGATTTTTT 6 228 1 TTTTCGTTTT 0.873557 -73 TGATATTTAATTTTCTCACTTTCAGCAATTTC 8 55 1 TTTTCACTTT 0.873557 -65 TTTTGCGTATTTTTACCGCACT 9 1 0 TTTTCGCACT 0.988302 -40 **** ****** Masking position 3 Map Score: 3.41977 Number of sites scoring better than the average of aligned sites = 312 Number in coding regions = 264 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 5 GTGAGTACGACGTAAAAAGATGTGAAGCAA 1 238 0 CGTAAAAAGA 0.984268 -63 ACTGCTAAAGCGTCAAAAGGCCGGATTTTC 5 12 1 CGTCAAAAGG 0.930646 -97 GAATTGATCTCGTAAAAAGAGGGCAAAGAT 6 34 0 CGTAAAAAGA 0.984268 -267 TTCCCCTCTCCGTAAAAATTGTGTATTTTT 6 154 1 CGTAAAAATT 0.965239 -147 TATGTTTTAGCGTAGAAATTGCTGAAAGTG 8 71 0 CGTAGAAATT 0.91034 -49 AGTGCGGTAAAAATACGCAAAATTT 9 6 1 GGTAAAAATA 0.901215 -35 ********** Masking position 6 Map Score: 3.69022 Number of sites scoring better than the average of aligned sites = 129 Number in coding regions = 104 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 6 CAACTGAAACCGATTACACCAACCACAACAG 1 28 1 CGATTACACA 0.943543 -273 TATTTTCATGCACTTAAATCATAACTAAGAT 1 174 1 CACTTAAACA 0.88912 -127 TCAGTGTAATCGCTTACACTAACATTTATCT 1 201 0 CGCTTACATA 0.943588 -100 CACTTACTCCGTGTTAAAACG 3 84 0 CACTTACTCG 0.908567 -11 CCCTACCCCACGCGTACAACCGC 4 40 1 CGCGTACACC 0.935562 -13 GTACAATCCCCGCTTTCTTCACCCATCAGGG 5 81 1 CGCTTTCTCA 0.960625 -28 TTAATTTTCTCACTTTCAGCAATTTCTACGC 8 61 1 CACTTTCACA 0.963661 -59 ******** ** Masking position 5 Map Score: 0.84646 Number of sites scoring better than the average of aligned sites = 947 Number in coding regions = 901 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 7 ********** No masking Map Score: -1.29786e-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 ********** No masking Map Score: -1.29786e-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: -1.29786e-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