AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -imetR_rpxx_opreg_300.orf -g0.290 -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 = 0.29 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 RP716 300 unknown #2 RP743 79 SERINE HYDROXYMETHYLTRANSFERASE (glyA) #3 RP744 102 unknown #4 RP745 52 GLUTAREDOXIN-LIKE PROTEIN GRLA (grxC2) Motif number 1 GAGTACTTTGATTCTCTAATAGAACCC 1 4 1 TCTTTTTTCT 0.993429 -297 ATATCTGATATTCTATTCTTAGCTAAGTTTAAAG 1 56 0 TCTATTTGCT 0.987353 -245 CAATAAAGCTTTCTTTTTTTATCTTAAGAGTATG 1 111 1 TCTTTTTTCT 0.993429 -190 ACTCTTTGACTACTATTGGGTTCTCGAAAGCCTT 1 192 1 TCTATGGTCT 0.960063 -109 TTCCATTGATTCCTATGTGTCTCTTTCTAATCCA 1 276 0 TCTATGTTCT 0.987362 -25 CGGTATCTAGTCGTTTATTTTTCTTTGTACTGTA 2 14 1 TGTTTTTTCT 0.984566 -66 TATAGGCTCTTTGTTTTGTTTGCTATTGCTATTC 3 23 1 TGTTTTTGCT 0.977235 -80 * **** ** *** Masking position 6 Map Score: 7.85276 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 47 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 2 CTTTGGGTTCTATTAGAGAATCAAAGTACT 1 12 0 TATTAGAGAA 0.916441 -289 GAATATCAGATATTAGAGTGCTTTAAATCT 1 77 1 TATTAGAGTG 0.816886 -224 AAGAAAGCTTTATTGAAGCAGATTTAAAGC 1 96 0 TATTGAAGCA 0.953632 -205 TTTTTCTTTGTACTGTAGTAACACATATAC 2 31 1 TACTGTAGTA 0.609372 -49 AAAGAGCCTATACTGTAGCACTTA 3 5 0 TACTGTAGCA 0.921452 -98 TCAACTTTAATATTAAAGTAATAAACATAT 3 68 1 TATTAAAGTA 0.816444 -35 AAAATACACTTTCTATAGCAATAT 4 5 0 TTCTATAGCA 0.62967 -48 ATAGAAAGTGTATTTTAGAAAATAATATTT 4 19 1 TATTTTAGAA 0.779353 -34 ********** Masking position 7 Map Score: 4.43467 Number of sites scoring better than the average of aligned sites = 471 Number in coding regions = 361 Number in noncoding regions = 110 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 3 TGGGTTCTATTAGAGAATCAAAGTACTC 1 9 0 TAGAGAATCA 0.864667 -292 TAGCTAAGAATAGAATATCAGATATTAGAG 1 65 1 TAGAATATCA 0.910537 -236 TTTTTATCTTAAGAGTATGAGAAGAGAACA 1 126 1 AAGAGTATGA 0.973537 -175 CCTTACGAATAAGAGCATCATGTCTTAAAC 1 222 1 AAGAGCATCA 0.975645 -79 ATCATGTCTTAAACGCATCAACAAAGATGG 1 238 1 AAACGCATCA 0.959052 -63 TAAATACTAAAAACATATGAGGATGC 2 64 1 AAACATATGA 0.912392 -16 TTAAAGTAATAAACATATGAAATAAAGTAA 3 80 1 AAACATATGA 0.912392 -23 ********** Masking position 7 Map Score: 3.80346 Number of sites scoring better than the average of aligned sites = 143 Number in coding regions = 107 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 4 GATAAAAAAAGAAAGCTTTATTGAAGCAGA 1 104 0 GAAAGCTTTA 0.789099 -197 GAGAAGAGAACATAGCCTTAATCTGACTAG 1 144 1 CATAGCCTTA 0.948921 -157 CAATAGTAGTCAAAGAGTTTTTTGAGATGC 1 180 0 CAAAGAGTTT 0.912532 -121 TTGGGTTCTCGAAAGCCTTACGAATAAGAG 1 207 1 GAAAGCCTTA 0.970882 -94 AACAAAGATGGAAAGATTTTGGATTAGAAA 1 257 1 GAAAGATTTT 0.93687 -44 ********** Masking position 4 Map Score: 1.61985 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 41 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 5 TAGCTAAGTTTAAAGATAATATTGGATATC 1 41 0 TAAAGATAAT 0.933887 -260 TCTCATACTCTTAAGATAAAAAAAGAAAGC 1 118 0 TTAAGATAAA 0.927448 -183 CATCTGTCTAGTCAGATTAAGGCTATGTTC 1 151 0 GTCAGATTAA 0.88646 -150 AACAAAGATGGAAAGATTTTGGATTAGAAA 1 257 1 GAAAGATTTT 0.712874 -44 ACAGTACAAAGAAAAATAAACGACTAGATA 2 17 0 GAAAAATAAA 0.774719 -63 GTAACACATATACAGATAAATACTAAAAAC 2 48 1 TACAGATAAA 0.927695 -32 ATACTCAACTTTAATATTAAAGTAATAAAC 3 64 1 TTAATATTAA 0.478811 -39 AAACCTGATATAAATATTATTTTCTAAAAT 4 30 0 TAAATATTAT 0.764769 -23 ********** Masking position 6 Map Score: 1.34638 Number of sites scoring better than the average of aligned sites = 702 Number in coding regions = 487 Number in noncoding regions = 215 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 6 ********** No masking Map Score: 1.3033e-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 7 GAACATAGCCTTAATCTGACTAGACAGATGC 1 151 1 TTATCTGACT 0.829038 -150 TTTTTTGAGATGCATCTGTCTAGTCAGATTA 1 162 0 TGATCTGTCT 0.985739 -139 CCAAAATCTTTCCATCTTTGTTGATGCGTTT 1 248 0 TCATCTTTGT 0.955265 -53 GATTCCTATGTGTCTCTTTCTAATCCAAAAT 1 272 0 TGCTCTTTCT 0.979356 -29 TAGTCGTTTATTTTTCTTTGTACTGTAGTAA 2 21 1 TTTTCTTTGT 0.885348 -59 AGTATTTATCTGTATATGTGTTACTACAGTA 2 41 0 TGATATGTGT 0.921734 -39 GCTACAGTATAGGCTCTTTGTTTTGTTTGCT 3 16 1 AGCTCTTTGT 0.928259 -87 ** ******** Masking position 5 Map Score: 0.992899 Number of sites scoring better than the average of aligned sites = 86 Number in coding regions = 65 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 8 ********** No masking Map Score: 1.3033e-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: 1.3033e-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: 1.3033e-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