AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i03010_aful_reg_100.orf -o03010_aful_100.ace -a/home/amcguire/genomes/ORF_aful.txt -z/home/amcguire/genomes/aful.fna -g0.49 -x5 -e 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 = 0.49 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: AF0933 22 branched-chain amino acid aminotransferase (ilvE) AF0938 21 SSU ribosomal protein S10P (rps10P) Input sequences: #1 AF0057 38 LSU ribosomal protein L37AE (rpl37AE) #2 AF0059 97 A. fulgidus predicted coding region AF0059 #3 AF0508 291 ethylene-inducible protein #4 AF0511 32 SSU ribosomal protein S6E (rps6E) #5 AF0535 122 cell division protein (ftsZ-1) #6 AF0764 138 LSU ribosomal protein L7AE (rpl7AE) #7 AF0875 300 snRNP, putative #8 AF0911 24 SSU ribosomal protein S17E (rps17E) #9 AF0912 51 A. fulgidus predicted coding region AF0912 #10 AF0913 144 A. fulgidus predicted coding region AF0913 #11 AF0932 41 conserved hypothetical protein #12 AF0937 57 translation elongation factor EF-1, subunit alpha (tuf) #13 AF1117 62 DNA-directed RNA polymerase, subunit E' (rpoE1) #14 AF1118 111 A. fulgidus predicted coding region AF1118 #15 AF1127 213 LSU ribosomal protein L18E (rpl18E) #16 AF1132 108 enolase (eno) #17 AF1332 70 A. fulgidus predicted coding region AF1332 #18 AF1430 73 LSU ribosomal protein L40E (rpl40E) #19 AF1490 166 LSU ribosomal protein L1P (rpl1P) #20 AF1529 197 LSU ribosomal protein L21E (rpl21E) #21 AF1886 32 DNA-directed RNA polymerase, subunit B'' (rpoB2) #22 AF1926 57 conserved hypothetical protein #23 AF1927 142 conserved hypothetical protein #24 AF2070 63 conserved hypothetical protein #25 AF2071 60 N-acetyl-gamma-glutamyl-phosphate reductase (argC) #26 AF2152 89 SSU ribosomal protein S8E (rps8E) #27 AF2285 104 SSU ribosomal protein S13P (rps13P) #28 AF2320 52 SSU ribosomal protein S3AE (rps3AE) Motif number 1 TCTTATTGCATTTAAACGTTTTCCA 1 5 0 TTTAAAGTTT 0.951204 -34 GCTTGCAAACTAAAAAATTTTGTGAAAATGA 3 195 1 TAAAAATTTT 0.885447 -97 TATTATAAACTATAAATCATTTTCACAAAAT 3 211 0 TATAAACATT 0.537883 -81 CCCGTGCAGTTTTAAAAGTTTTGGTAACACT 6 69 0 TTTAAAGTTT 0.951204 -70 CATGATTCCCTATAAAAGTTTCTTCGGATGG 7 46 1 TATAAAGTTT 0.926913 -255 GCTTCAGGGTTAAAAATGTTTTCGACTTGTG 7 181 1 TAAAAAGTTT 0.932447 -120 GAGGAGTTATTTAAAAATATCGCTGAACCCG 7 243 0 TTAAAATATC 0.429812 -58 CAAATTAATCTTAAAATTTTCTTTCAAAAAA 9 18 0 TTAAAATTTC 0.771545 -34 TAACCGAAAATTTAAAATTTTGCATATACCC 10 40 0 TTTAAATTTT 0.916078 -105 TACGAGGGGTTAAAAACCTTTGACGTCATCA 10 113 0 TAAAAACTTT 0.850208 -32 ATCAGCTGATTTAAAACGTTTTTCCGTT 11 8 0 TTAAAAGTTT 0.95499 -34 ACTTCAATAATTTAAATTTTTTGCTCAGATA 14 24 1 TTTAAATTTT 0.916078 -88 CGCGGAAGGCTAAAAACGATTTCGATATGAG 15 11 0 TAAAAAGATT 0.754962 -203 CATTACGTAATTTAAATCTTTGCCGCATGTT 15 60 0 TTTAAACTTT 0.88908 -154 GTTCATAATCTTTAAATCTTCGGTAGCCAAG 17 18 0 TTTAAACTTC 0.694979 -53 TTTAGCGTTATTTAAACTTTATTGGAGAAAG 18 40 0 TTTAAATTTA 0.579329 -34 ATAAGAGGAATTAAAACGTTTCCCCTTCTGT 19 22 1 TTAAAAGTTT 0.95499 -145 TGTGGGGTGATAAAAAGTATTAGCCCAAATC 22 25 0 TAAAAATATT 0.633064 -33 GTAGTGTTTATTAAAAGTTTTTTTTATATAT 23 97 1 TTAAAATTTT 0.922366 -46 TGGGGCTGTGTAAAAAATTTT 24 1 0 TAAAAATTTT 0.885447 -63 CTTTAATTGTTATAAACGTTTGCTGCTAAAC 26 24 1 TATAAAGTTT 0.926913 -66 CACTTCCGCCTTAAAAAGTTTAGCAGCAAAC 26 41 0 TTAAAAGTTT 0.95499 -49 TGTAAGGATATTTAAAGGTTATGTGCCCCCC 27 56 0 TTTAAAGTTA 0.710926 -49 ****** **** Masking position 10 Map Score: 29.2152 Number of sites scoring better than the average of aligned sites = 343 Number in coding regions = 117 Number in noncoding regions = 226 Number of orfs with sites within 600 bp upstream = 256 Fraction of orfs with sites within 600 bp upstream = 0.0411179 Motif number 2 ATGCTGAGTATGAGCTGAGCATTAAAGAGTA 2 8 1 GAGAGGAGCA 0.969981 -90 TGTTCAGCCTGAAACCGATGAGGATGTAAAGGCT 3 14 0 GACCGGAGGA 0.828017 -278 AGAATCCTTTGCAAGGGATGAGCATCAACTCTTT 3 113 1 GAGGGGAGCA 0.814274 -179 ATCTTGTGTCGAGACAGCTGAGGAGCCAAAGTTT 3 241 1 GGCAGGAGGA 0.988279 -51 GCAGAAGTTGCTTGAGTCGAGGATTTATAAAA 4 10 0 GTGAGGAGGA 0.935334 -23 GGGGAATTAGGGAAGAGCCGATGAATGATGATTT 6 97 1 GAGAGGATGA 0.874218 -42 ATGATTTGATGAAGGAGGTGATGAC 6 124 1 GAGAGGATGA 0.874235 -15 GATAAGGAAGCTGGCAGAGGAGGAAGTCAAATCC 15 132 1 CGCAGGAGGA 0.981629 -82 AGAGTCGTTTTCGACAGCAGGGGAAACGAGACGG 16 44 1 TGCAGGGGGA 0.932631 -65 TTAAAAAGCACAGACAGAAGGGGAAACGTTTTAA 19 32 0 CGCAGGGGGA 0.972551 -135 ACGGACTCCTTAGGGAGTAGTGGAGAGGTATTTT 19 107 0 TGGAGGTGGA 0.901847 -60 CGTCAAAGAACTGTGAGTTCGGCAGGAGTTCAAA 20 41 0 CGGAGCGGCA 0.716523 -157 CTTCCGGTGTCAGTGAGAAGGGGATCGACA 20 178 1 CGGAGGGGGA 0.985829 -20 GGGCAGGCATCGGTGAGAGGAGCATG 24 48 1 CGGAGGAGCA 0.979863 -16 TTCTGAGATGGCGAAAGTTGAGGATGCT 25 5 0 GGAAGGAGGA 0.928798 -56 TTATTCTCTATCAGGAGTGGTGCAGT 26 74 1 TAGAGGTGCA 0.64201 -16 * * *** ***** Masking position 14 Map Score: 14.7123 Number of sites scoring better than the average of aligned sites = 1386 Number in coding regions = 1326 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 3 TGTTCAGCCTGAAACCGATGAGGATGTAAAGG 3 16 0 GAAACGTGAG 0.94875 -276 AGAATCCTTTGCAAGGGATGAGCATCAACTCT 3 113 1 GCAAGGTGAG 0.992293 -179 ATCTTGTGTCGAGACAGCTGAGGAGCCAAAGT 3 241 1 GAGAAGTGAG 0.978032 -51 TTATCCCTTCGCAATGGCTGAATATAAACTTT 3 268 0 GCAAGGTGAA 0.918359 -24 TCCCGACCCAGCAAAGGCTGCGGTGATGATTT 13 40 1 GCAAGGTGCG 0.964095 -23 GAGCGAGTCAGCAAAAAATGAGGCGCCA 15 196 1 GCAAAATGAG 0.85131 -18 CAGGGGAAACGAGACGGTTGAGTGTGAAGTCG 16 61 1 GAGAGGTGAG 0.988697 -48 TCTGCAAAAAGAGAAAGGTGAGATGAC 21 16 1 GAGAAGTGAG 0.978032 -17 TTCTGAGATGGCGAAAGTTGAGGATGCT 25 7 0 GCGAAGTGAG 0.986111 -54 GAGGAAAAGGTTAAGAGGCAAAATA 25 46 0 GAAAGGTAAG 0.875835 -15 **** ** **** Masking position 4 Map Score: 11.8061 Number of sites scoring better than the average of aligned sites = 516 Number in coding regions = 489 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 4 ACGTGGTCTTATTGCATTTAAACGTTTTCCA 1 7 0 ATATTTAAAT 0.880665 -32 GTCTCGACACAAGATATTATAAACTATAAATCATT 3 221 0 AGATTATAAT 0.624555 -71 CTTCGCAATGGCTGAATATAAACTTTGGCTCCTCA 3 259 0 GTATATAAAT 0.752434 -33 ATAGGATGTTAATCCATTTAAATCTTGTGATTACC 6 21 1 ATATTTAAAT 0.880665 -118 GTTGCAGGAGGAGTTATTTAAAAATATCGCTGAAC 7 246 0 GGATTTAAAT 0.974825 -55 ATCCATTAGGAGGATATATAAACCTT 12 2 0 AGATATAAAT 0.922368 -56 CTGGGTCGGGAAGCAATATAAATTTAACTAAGAAT 13 16 0 AGATATAAAT 0.922393 -47 CCGTTACATTACGTAATTTAAATCTTTGCCGCATG 15 62 0 AGATTTAAAT 0.970955 -152 GCAGCGTTTAGCGTTATTTAAACTTTATTGGAGAA 18 42 0 GGATTTAAAT 0.974818 -32 CAGTTTATAAGAGGAATTAAAACGTTTCCCCTTCT 19 16 1 GGATTAAAAT 0.896658 -151 GAGTAGTGGAGAGGTATTTTAAGTTATCGGTTCTC 19 92 0 GGATTTTAAT 0.896658 -75 CAAGCCTGTAAGGATATTTAAAGGTTATGTGCCCC 27 58 0 AGATTTAAAT 0.970955 -47 * * ******* * Masking position 6 Map Score: 9.39494 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 8 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 5 CCTTTCACCAACATCGAAAAAAATTATAAGAA 5 6 1 CACACTCAAA 0.955674 -117 ATAAGAATTTCTCTTCCATCAGAAGCACAGGAAGAGG 5 36 1 CTTCCTCAAA 0.78504 -87 GTCATCACCTCCTTCATCAAATCATCATT 6 120 0 CACCCCCCAA 0.978524 -19 TATTTTTAAATAACTCCTCCTGCAACGAACCTTAGAT 7 255 1 TACCCCCCAG 0.652943 -46 ATTCTTTCCCTCCAGAATTATCTAAGGTTC 7 281 0 CTTCCCCAAA 0.90586 -20 ATTTTGCATATACCCACTTCTTAAAAAGGAGGTTAAG 10 18 0 TACACTCAAA 0.768307 -127 TTGCTCATATCAACTACACCTCAGCGTAGTTTTGACC 15 95 0 CACACCCAGT 0.756393 -119 CGCCTTCGCAACAACCTCCCCAGCAACGACTTCAC 16 84 0 CACACTCCAA 0.893964 -25 CGCACCACCTACACCTCAGGAAGTTTAAGGTT 17 49 0 CACACCCAGA 0.969276 -22 AAATACCTCTCCACTACTCCCTAAGGAGTCCGTAGGA 19 108 1 CCCACCCAAA 0.906993 -59 ATCCCCTTCTCACTGACACCGGAAGTATATTTAAGGC 20 166 0 CATACCCAAA 0.924787 -32 TATTATTTTTCTCCTCGCCCAAAAAGAGAACGGTTAA 23 53 0 CTCCGCCAAA 0.776718 -90 ATTTTTTACACAGCCCCACCAAAAGGAAATGGTAGGG 24 14 1 CACCCCCAAA 0.991491 -50 CATCCTCAACTTTCGCCATCTCAGAAAACTCTTTATT 25 13 1 TTCCCTCAGA 0.590077 -48 GAGAATAAAACACTTCCGCCTTAAAAAGTTTAGCAGC 26 45 0 CATCCCCAAA 0.961862 -45 AACATCACCGTCTAAGAGGAAGCAAGCCT 27 86 0 CACCCTCAGG 0.868302 -19 ** * ** ** ** * Masking position 10 Map Score: 9.99877 Number of sites scoring better than the average of aligned sites = 1434 Number in coding regions = 1361 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 6 TGTAAAACACCCAATCTGCGTTGTTCAGCCTG 3 37 0 CCATCTGCTT 0.911813 -255 AGTTTGCAAGCCTATCCTCATTATGGATTCGT 3 174 0 CCATCCTCTT 0.953542 -118 CTTCCCGCTTAACCTCCTTTTTAAGAAGT 10 8 1 CTAACCTCTT 0.927482 -137 GTCATCAAAGCTAAACCGCATTGCCTATGCAA 10 88 0 CTAACCGCTT 0.970344 -57 GAAGTCAAATCCAAACCTCGTTACTCTCATCG 15 154 1 CCAACCTCTT 0.984837 -60 CCTCCCCAATCGCCTTGGGGTTTATT 20 5 1 CCAATCGCTT 0.970344 -193 GAAAATTACCCCTAACCGCGTCTATACTAAAG 20 78 1 CCAACCGCTC 0.974889 -120 AAGTATTAGCCCAAATCGCTATGCTGGTGCC 22 10 0 CCAATCGCAT 0.837609 -48 ACAATTAAAGCCTAACTACTTTC 26 2 0 CCAACTACTT 0.835033 -88 ** ****** ** Masking position 4 Map Score: 6.01538 Number of sites scoring better than the average of aligned sites = 93 Number in coding regions = 84 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 7 TACATCCTCATCGGTTTCAGGCTGAACAACG 3 20 1 TCGGTTTAGG 0.868191 -272 TTTTTCGATGTTGGTGAAAGG 5 1 0 TTGGTGAAGG 0.986123 -122 CATGCTAGAATTGGTGGTATGTACAGAGCAA 7 19 0 TTGGTGGATG 0.836626 -282 AAAAGTTTCTTCGGATGGAGGCAATTAAAAA 7 59 1 TCGGATGAGG 0.879149 -242 TTATCTAAGGTTCGTTGCAGGAGGAGTTATT 7 263 0 TTCGTTGAGG 0.826371 -38 AAAGCTTATATTGGTTAAAGAACATCATATA 14 89 1 TTGGTTAAGA 0.813727 -23 TTAAACTTTATTGGAGAAAGGTTTATGAGCA 18 29 0 TTGGAGAAGG 0.951815 -45 GATTAAAGGGTTGGTTACAGTTGAGTTTGGT 20 123 0 TTGGTTAAGT 0.813727 -75 TCAAAAACTTTTGGTGATAGG 23 1 0 TTGGTGAAGG 0.986123 -142 AGGGCAGGCATCGGTGAGAGGAGCATG 24 47 1 TCGGTGAAGG 0.980618 -17 ******* *** Masking position 9 Map Score: 7.44933 Number of sites scoring better than the average of aligned sites = 158 Number in coding regions = 140 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 8 TCAGCCATTGCGAAGGGATAACG 3 279 1 CGAAGGATAA 0.757969 -13 TAAAACTGCACGGGGAATTAGGGAAGAGCCG 6 86 1 CGGGGATTAG 0.873168 -53 AACGCCCTTCCGAGGCGTTAGCCCGGGTTCG 7 112 0 CGAGGGTTAG 0.970845 -189 GTTCGTTGCAGGAGGAGTTATTTAAAAATAT 7 254 0 GGAGGGTTAT 0.691465 -47 ATTGATTATACGAGGGGTTAAAAACCTTTGA 10 121 0 CGAGGGTTAA 0.979066 -24 ACTCGGCGAGTTAATCAGCTGATT 11 28 0 CGGCGGTTAA 0.943765 -14 AAACCAGAAAGGAGGAGATAGGT 12 45 1 GGAGGGATAG 0.858796 -13 GCTGGGACTACGGGGTGGTAAG 19 155 1 CGGGGGGTAA 0.950768 -12 CTTAATTGTGTGGGGTGATAAAAAGTATTAG 22 33 0 TGGGGGATAA 0.807791 -25 TCTTTTTGGGCGAGGAGAAAAATAATAGTCT 23 63 1 CGAGGGAAAA 0.80233 -80 AGAGCGGCGAATTAAATGCTAAAAT 27 5 1 CGGCGATTAA 0.7211 -100 ***** ***** Masking position 10 Map Score: 4.44265 Number of sites scoring better than the average of aligned sites = 252 Number in coding regions = 231 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 9 TTTACAATCGCTCCATAATTCTGGGTATTTTGA 3 63 1 CCCATAACTG 0.890527 -229 TTGTTCGCTCCGCCCTCTTCCTGTGCTTCTGAT 5 53 0 CCCCTCTCTG 0.985201 -70 ACCTATCTCCTCCTTTCTGGTTTTTCGTT 12 39 0 CCCTCCTCTG 0.991904 -19 TAAAACGTTTCCCCTTCTGTCTGTGCTTTTTAA 19 33 1 CCCTTCTCTG 0.993279 -134 TGTCGATCCCCTTCTCACTGACACCGGAAG 20 178 0 CCCTTCTCTG 0.993279 -20 TATTAATTGTCCCCTCAAAACTGCAAAAGC 28 33 1 CCCTCAACTG 0.956874 -20 * ****** *** Masking position 12 Map Score: 2.84822 Number of sites scoring better than the average of aligned sites = 144 Number in coding regions = 135 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 10 ATCATTTACAATACTCTTTAATGCTCAGCTC 2 22 0 ATATCTTTAA 0.967542 -76 CGTCCATATTCTTTAAACAATTACCA 2 82 0 ATATCTTTAA 0.967538 -16 ACAAGATATTATAAACTATAAATCATTTTCA 3 217 0 ATAACTATAA 0.632012 -75 TCAATGCAAGATAGTATATAAATTCTTTGTT 5 81 0 ATATATATAA 0.588895 -42 TTTAACCAATATAAGCTTTAAGTTGAGTTGA 14 77 0 ATAGCTTTAA 0.944055 -35 GCTATATGATGTTCTTTAACCAATATAAG 14 93 0 ATGTCTTTAA 0.861432 -19 AAGGTTGTTCATAATCTTTAAATCTTCGGTA 17 24 0 ATATCTTTAA 0.967525 -47 GTCTTAACAAATACTATTTAACCGTTCTCTT 23 36 1 ATATATTTAA 0.837482 -107 GAAAGTAGTTAGGCTTTAATTGTTATAAA 26 9 1 TTAGCTTTAA 0.703705 -81 AGGGGGGCACATAACCTTTAAATATCCTTAC 27 55 1 ATACCTTTAA 0.901678 -50 *** ******* Masking position 7 Map Score: 6.16735 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 27 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 11 TTCACAAAATTTTTTAGTTTGCAAGCCTATCC 3 189 0 TTTTTATTGC 0.883447 -103 TTACCAAAACTTTTAAAACTGCACGGGGAATT 6 73 1 TTTTAACTGC 0.964161 -66 TCGAAAACATTTTTAACCCTGAAGCTCCAGCA 7 174 0 TTTTAACTGA 0.742779 -127 ATATGCAAAATTTTAAATTTTCGGTTACATCA 10 44 1 TTTTAATTTC 0.901678 -101 CGTCAAAGGTTTTTAACCCCTCGTATAATCAA 10 119 1 TTTTAACCTC 0.865482 -26 CGGAAAAACGTTTTAAATCAGCTGATTAACTC 11 13 1 TTTTAACAGC 0.925675 -29 ATCGAAATCGTTTTTAGCCTTCCGCGGAAGGA 15 16 1 TTTTTACTTC 0.896201 -198 GCATGTTAATTTTTAATGTTCCTTCCGCGGAA 15 35 0 TTTTAATTCC 0.708945 -179 AGGGGAAACGTTTTAATTCCTCTTATAAACTG 19 16 0 TTTTAACCTC 0.865482 -151 TGTCTGTGCTTTTTAATTTTGAAATTTTATCT 19 50 1 TTTTAATTGA 0.61236 -117 TGGAGAGGTATTTTAAGTTATCGGTTCTCTGA 19 89 0 TTTTAATATC 0.80936 -78 AAATAGTATTTGTTAAGACTTCCTCAAAAACT 23 23 0 TGTTAACTTC 0.709759 -120 TTAAAAGTTTTTTTTATATATCCAGCGCGCTT 23 107 1 TTTTTATATC 0.686183 -36 AAAATTTTTTACACAGCCCCACCAAAA 24 6 1 TTTTTACAGC 0.865128 -58 CTCAGAAAACTCTTTATTTTGCCTCTTAACCT 25 32 1 TCTTTATTGC 0.525096 -29 ****** **** Masking position 6 Map Score: 6.90428 Number of sites scoring better than the average of aligned sites = 229 Number in coding regions = 156 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 12 CTTGTGTCGAGACAGCTGAGGAGCCAAAGTT 3 243 1 GACAGTGAGG 0.732468 -49 TAAGGTTCGTTGCAGGAGGAGTTATTTAAAA 7 258 0 TGCAGAGGAG 0.802475 -43 CGAAAAACCAGAAAGGAGGAGATAGGT 12 41 1 GAAAGAGGAG 0.85057 -17 AGTCGTTTTCGACAGCAGGGGAAACGAGACG 16 46 1 GACAGAGGGG 0.992587 -63 AAAAAGCACAGACAGAAGGGGAAACGTTTTA 19 33 0 GACAGAGGGG 0.992587 -134 GGACTCCTTAGGGAGTAGTGGAGAGGTATTT 19 108 0 GGGAGAGTGG 0.899828 -59 TCCCTAAGGAGTCCGTAGGAGGCTACGGCCG 19 125 1 GTCCGAGGAG 0.88731 -42 TCCGGTGTCAGTGAGAAGGGGATCGACA 20 180 1 GTGAGAGGGG 0.973248 -18 TTTATTCTCTATCAGGAGTGGTGCAGT 26 73 1 ATCAGAGTGG 0.724248 -17 ***** ***** Masking position 5 Map Score: 1.80697 Number of sites scoring better than the average of aligned sites = 440 Number in coding regions = 414 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 13 TCAATTAAAAGAGTTGATGCTCATCCCTTG 3 124 0 GAGTTGATGC 0.906048 -168 GTAACACTGATATGTGATGATGGTAATCAC 6 47 0 TATGTGATGA 0.836923 -92 GATGAATGATGATTTGATGAAGGAGGTGAT 6 116 1 GATTTGATGA 0.958144 -23 TTTGATGAAGGAGGTGATGAC 6 128 1 GAGGTGATGA 0.97267 -11 ATGCGGTTTAGCTTTGATGACGTCAAAGGT 10 99 1 GCTTTGATGA 0.95733 -46 AGCAAAGGCTGCGGTGATGATTTT 13 49 1 GCGGTGATGA 0.972132 -14 GCTTTAAGTTGAGTTGATGATTATTAGAGT 14 64 0 GAGTTGATGA 0.973197 -48 AACTCACAGTTCTTTGACGATGGAAAATTA 20 56 1 TCTTTGACGA 0.576656 -142 ********** Masking position 7 Map Score: 6.21282 Number of sites scoring better than the average of aligned sites = 148 Number in coding regions = 127 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 14 TTGCAAAGGATTCTTTATGCTCAGGATTTGCTC 3 94 0 TTCTTATGCA 0.904457 -198 AACAATCTTTGCTCTGTACATACCACCAAT 7 8 1 TTTGTCTGCA 0.960346 -293 GAGTGAGCATTTTTATCTGAGCAAAAAATTTAA 14 35 0 TTTTTCTGCA 0.977152 -77 CTGAGGTGTAGTTGATATGAGCAAGATAAGGAA 15 108 1 GTTGTATGCA 0.715454 -106 TATATCGTGATTTTTTCTGCTCATAAACCTTTC 18 12 1 TTTTTCTGCA 0.977152 -62 ACGTTTCCCCTTCTGTCTGTGCTTTTTAATTTT 19 37 1 TTCTTCTGCT 0.812735 -130 AATTTTGAAATTTTATCTGCCCATTTCAGAGAA 19 64 1 TTTTTCTGCA 0.977152 -103 TAAAAGTTTTTTTTATATATCCAGCGCGCTTTT 23 108 1 TTTTTATACA 0.651181 -35 **** **** ** Masking position 6 Map Score: 1.7687 Number of sites scoring better than the average of aligned sites = 86 Number in coding regions = 74 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 15 ********** No masking Map Score: 6.06393e-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