AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i064_aful_mthe_300.orf -o064_aful_mthe_300.ace -a/home/amcguire/alignace/lib/ORF_aful.txt -z/skink1/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: RAG48457 25 Archaeoglobus_fulgidus Input sequences: #1 RAG18763 209 Archaeoglobus_fulgidus #2 RAG14978 75 Archaeoglobus_fulgidus #3 RAG15094 200 Archaeoglobus_fulgidus #4 RAG00432 102 Archaeoglobus_fulgidus #5 RAG22490 30 Archaeoglobus_fulgidus #6 RAG22489 109 Archaeoglobus_fulgidus #7 RAG29246 201 Archaeoglobus_fulgidus #8 RAG50219 136 Archaeoglobus_fulgidus #9 RAG50216 152 Archaeoglobus_fulgidus #10 RAG50214 54 Archaeoglobus_fulgidus #11 RAG32775 72 Archaeoglobus_fulgidus #12 RAG35275 48 Archaeoglobus_fulgidus #13 RTH01080 300 M.thermo #14 RTH02062 231 M.thermo #15 RTH02127 159 M.thermo #16 RTH01004 66 M.thermo #17 RTH01088 218 M.thermo #18 RTH00663 79 M.thermo #19 RTH00777 35 M.thermo #20 RTH00316 57 M.thermo #21 RTH00321 44 M.thermo #22 RTH01047 56 M.thermo #23 RTH02145 30 M.thermo #24 RTH00013 16 M.thermo #25 RTH00133 56 M.thermo #26 RTH01743 127 M.thermo #27 RTH00602 189 M.thermo #28 RTH00576 116 M.thermo #29 RTH00954 31 M.thermo #30 RTH00250 30 M.thermo #31 RTH00057 21 M.thermo #32 RTH01659 205 M.thermo #33 RTH01211 72 M.thermo #34 RTH00503 300 M.thermo Motif number 1 GCCTTCTTATCCCCGGGATGCAGAACATTGC 1 96 1 CCCGGGATGC 0.98155 -114 TCTTGGGCCACCGCGGGATAGATGAGAAGGA 1 168 1 CCCGGGATAG 0.987959 -42 ATTTTGAGGGCTGCAGGATAGATATAGTTTG 2 52 0 CTCAGGATAG 0.751207 -24 GCCTTAATTACCGCTGGATACAGGCTTGGAA 3 109 1 CCCTGGATAC 0.846671 -92 TAAAAAATTTCTTCGGGATAGGTTTTTAAGG 11 30 0 CTCGGGATAG 0.959782 -43 GTAGTCATATCCATGGGATGAATTCCAACCA 13 132 1 CCTGGGATGA 0.784088 -169 GAGGCTGTGCCCAGGGGATGGCCCATGATTC 14 20 1 CCGGGGATGG 0.968735 -212 TACCTATAATCCAGGGGAGAGTGTGAC 14 215 1 CCGGGGAGAG 0.939399 -17 CTGAAATGCTCCACGGAATGCCCCAACAATG 22 24 0 CCCGGAATGC 0.725151 -33 TTCTGGATGGCTCCGGGAGAAAAAAATCAGT 25 33 0 CTCGGGAGAA 0.831162 -24 CGTTTCTGGATGGCTCCGGGAGA 25 44 0 TTCTGGATGG 0.719583 -13 TGGATATGAATCATGGGATGGATTTGCATCA 28 49 1 TCTGGGATGG 0.800465 -68 TTAACTCAGGTCACTGGAGAG 29 1 0 TCCTGGAGAG 0.815294 -31 CAACCTCCTCCCCCTGGAGGAGGCCAGTGCT 33 20 0 CCCTGGAGGA 0.900871 -53 TTGACCTCCATTTCGGGAGGGCCTCCCAGTT 33 48 1 TTCGGGAGGG 0.925197 -25 TGATAACGCCCCACAGGAGGGCCATGAGAAC 34 12 1 CCCAGGAGGG 0.964114 -289 ACCTGCTGCACACCGGGAGGGAGACC 34 285 1 CACGGGAGGG 0.938408 -16 ** ******** Masking position 8 Map Score: 18.0904 Number of sites scoring better than the average of aligned sites = 603 Number in coding regions = 567 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 2 AATTGAAATCATATAAATAGTTTGCCTGCATA 4 20 0 AATAAAAGTT 0.83062 -83 ATTGATTTATCAATAAAAAGTTTTTCAAAATA 6 23 1 CATAAAAGTT 0.550472 -87 AATTTTACTAAAATAAAAATTGAGGATAGCTT 7 116 1 AATAAAATTG 0.919091 -86 TTAAAGAAAAAGTTAAAAATTTTTC 9 138 1 ATTAAAATTT 0.876528 -15 ACATTTGCCAATATAAAAAATTTCTTCGGGAT 11 42 0 AATAAAAATT 0.552441 -31 TAAACTTATTATTTAAAAATTTTGGTCCATTA 13 43 1 ATTAAAATTT 0.876527 -258 CCACAGATTAATATAAAAATTGCAAATGGTAG 13 104 1 AATAAAATTG 0.919107 -197 ATATGCTTTCACTTAAACATTGGTTGATGGTT 13 158 0 ATTAAAATTG 0.874278 -143 AATTCCAGTAATATAAACATTTATTTATATGC 13 184 0 AATAAAATTT 0.920623 -117 CGCTGATGGTAAATAAATATTGTAAGTACCAT 14 162 0 AATAAAATTG 0.918149 -70 TTACCATCAGCGATAAATATTGTTGCCATAGG 14 182 1 CATAAAATTG 0.739373 -50 AAAGTTAACCATTTAAATATTTTCTCATCAAC 17 128 1 ATTAAAATTT 0.876495 -91 TCTTCTTACAATATAAAGATATATTATTACAT 18 42 1 AATAAAATAT 0.49811 -38 GAATCACCAGAAATAAAGAGTTGACGGAT 23 8 0 AATAAAAGTT 0.830627 -23 TTAAAGAACTATTTAAAACTTTACTGTACATA 26 42 0 ATTAAACTTT 0.639327 -86 ATAAGGGAGTATTTAAATCTTGACATGGTGGT 32 56 0 ATTAAACTTG 0.634556 -150 * ***** **** Masking position 6 Map Score: 13.0685 Number of sites scoring better than the average of aligned sites = 66 Number in coding regions = 27 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 3 GCGAGGTAGTAGGGTGGTTGGATAATCCTCTTC 1 43 0 AGGGTTGGAT 0.82195 -167 TGCTCTGAATAGGGGGTGGGGATATTAATACTT 2 11 1 AGGTGGGGAT 0.916456 -65 CTTTAGTGTTAAAGCGGTGGGTTTTATAAGC 3 9 0 AGGGTGGGTT 0.970934 -192 GCTTGGAAAGACGGAGAGGGGATACCTCATTGA 3 132 1 AGGAGGGGAT 0.916456 -69 TACCGCAGGCAAAAGGTGGGGTT 4 90 1 AAGTGGGGTT 0.90669 -13 GCTGTTCTCAACTAAGGGTGGTTGAATGAGGTA 7 148 1 AAGGGTGGTT 0.94878 -54 GACTGTTCTGACCATCGGTGGTTTG 8 122 1 AACGGTGGTT 0.852917 -15 TGAAAAAGTTAGGGCGAATGGTTAGTTTTATGG 13 271 0 AGGAATGGTT 0.731676 -30 TTCGGATCCCAAGGTCGGGGGTTCAAATCCCCC 17 41 0 AGCGGGGGTT 0.979326 -178 AACTGGAGGGGGTTGC 24 2 1 AGAGGGGGTT 0.922619 -15 TATGTACATCAAAGGGAATGGTTAATAAACA 26 9 0 AGGAATGGTT 0.731676 -119 CGTCACCTCAAATGTCTGTGGTTATGCAACATG 28 90 0 AGCTGTGGTT 0.847117 -27 TCATAAATCTAGGAAGGTGGGTTAATC 30 14 1 AAGGTGGGTT 0.896476 -17 ACACTGAGTTATTGAGGGGGGTTCTCTATCCGG 34 223 0 AGGGGGGGTT 0.993435 -78 * * ******** Masking position 1 Map Score: 13.5343 Number of sites scoring better than the average of aligned sites = 185 Number in coding regions = 172 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 4 GAATTCATCCCATGGATATGACTACCATTTG 13 126 0 CATGGAATGA 0.992645 -175 TATAAAGTTTCATGGAGATAAACT 15 4 0 CATGGAATAA 0.945965 -156 TATCTTACTGCATGGAAATGATGATTTCATC 26 77 1 CATGGAATGA 0.992645 -51 TTAATCAATCCATGGATATGAATCATGGGAT 28 37 1 CATGGAATGA 0.992645 -80 GCTGTGTGGTCATGAATATGAACAGCCAGTT 32 18 0 CATGAAATGA 0.973558 -188 CCATGAGAACCATTGAGATGATTAAACATGA 34 33 1 CATTGAATGA 0.945965 -268 ATAATCTCCACATGAACATGGTAGTGGAGTG 34 143 0 CATGAAATGG 0.918891 -158 ****** **** Masking position 6 Map Score: 8.95991 Number of sites scoring better than the average of aligned sites = 14 Number in coding regions = 14 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 5 ATTATCCAACCACCCTACTACCTCGCAACTG 1 50 1 CCCCTACTAC 0.785361 -160 AAGTATTAATATCCCCACCCCCTATTCAGAG 2 13 0 ACCCCACCCC 0.903857 -63 TCAATGAGGTATCCCCTCTCCGTCTTTCCAA 3 134 0 ACCCCTCTCC 0.934406 -67 TTAACCTTTTCTTCCCACTCCTTAAG 5 15 1 CTCCCACTCC 0.946485 -16 GGTTTTTATCCTCCCACTCCCTTAAAAACC 11 10 1 CTCCCACTCC 0.946485 -63 CCATTAGATGCCCCCTAATCCAAATTAAGGA 13 69 1 CCCCTAATCC 0.922882 -232 GGGGGATTTGAACCCCCGACCTTGGGATCCG 17 41 1 ACCCCCGACC 0.738436 -178 AGACTACGGGCCCCCTACACACATCTCTATT 17 96 1 CCCCTACACA 0.763705 -123 GCAACCCCCTCCAGTT 24 5 0 CACCCCCTCC 0.953462 -12 ACCCCTCCACCACCTCACCCC 25 1 1 ACCCTCCACC 0.919456 -56 GACCACACAGCACCCCAAACCACCATGTCAA 32 38 1 CCCCCAAACC 0.921459 -168 GATTTAAATACTCCCTTATCCTATTATAGAG 32 69 1 CCCCTTATCC 0.790868 -137 AAATGGAGGTCAACCTCCTCCCCCTGGAGGA 33 30 0 CACCTCCTCC 0.906319 -43 CCGGATAGAGAACCCCCCTCAATAACTCAGT 34 223 1 ACCCCCCTCA 0.858458 -78 * ********* Masking position 5 Map Score: 10.6872 Number of sites scoring better than the average of aligned sites = 1196 Number in coding regions = 1149 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 6 CTTTTCGTTCTGCATCATGGCTTTAGTGTT 3 32 0 TGCATCATGG 0.991065 -169 ACATGTAACCGGAATCATGGGCCATCCCCT 14 32 0 GGAATCATGG 0.962678 -200 TCCATGGATATGAATCATGGGATGGATTTG 28 45 1 TGAATCATGG 0.986023 -72 GGGATGGATTTGCATCATGGTTCCAGCCAT 28 63 1 TGCATCATGG 0.991065 -54 TCTGTGGTTATGCAACATGGCTGGAACCAT 28 79 0 TGCAACATGG 0.964746 -38 TATGTAACTCTAAATCATGGTTAACCAGTT 32 118 1 TAAATCATGG 0.91606 -88 ********** Masking position 4 Map Score: 7.25773 Number of sites scoring better than the average of aligned sites = 9 Number in coding regions = 8 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 7 ATGCAGAACGAAAAGGTCAAGGTCTACTTC 3 47 1 AAAAGGTCAA 0.775461 -154 GAGTGGGAAGAAAAGGTTAAAAAA 5 5 0 AAAAGGTTAA 0.943053 -26 ACTAATACCAGCAAGGTTAACGGAATTAAC 7 181 0 GCAAGGTTAA 0.84633 -21 CTATTTAAAGAAAAAGTTAAAAATTTTTC 9 134 1 AAAAAGTTAA 0.591304 -19 AAGTTAGGGCGAATGGTTAGTTTTATGGAG 13 269 0 GAATGGTTAG 0.84633 -32 GAAAATATTTAAATGGTTAACTTTAAATAG 17 122 0 AAATGGTTAA 0.943053 -97 GAAAGGTTAATGCGTTTTGA 19 26 0 GAAAGGTTAA 0.963515 -10 ACATCAAAGGGAATGGTTAATAAACA 26 7 0 GAATGGTTAA 0.963515 -121 ATCCCTCGATGACTGGTTAAATTTATTTTA 27 167 0 GACTGGTTAA 0.919062 -23 ATTCATATTTAACTGGTTAACCATGATTTA 32 128 0 AACTGGTTAA 0.876856 -78 ********** Masking position 7 Map Score: 7.21354 Number of sites scoring better than the average of aligned sites = 49 Number in coding regions = 34 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 8 AAAAGAATTCAAACTTATATACCGCAGGCA 4 71 1 AAACTTATAT 0.78537 -32 TGATAATAAATCACTTATAAATAGCTTTGT 6 85 0 TCACTTATAA 0.86549 -25 AAAACTGATAATAAATCACTT 6 99 0 AAACTGATAA 0.849852 -11 TAAAATTTTTTTACTTATAAATTTTATCCT 7 93 0 TTACTTATAA 0.702291 -109 AGTTTAATACACACTTATAAGGAGACTGAG 13 19 0 ACACTTATAA 0.86549 -282 AGTGTGTATTAAACTTATTATTTAAAAATT 13 34 1 AAACTTATTA 0.649397 -267 CCGGGGTGATAAACTGATAACTGGAAAAAC 14 62 0 AAACTGATAA 0.849852 -170 AACCACCTTATAACTTATAAGTTCTAACTT 27 13 1 TAACTTATAA 0.929396 -177 TTATAAGTTCTAACTTATAATCGGTCAGGG 27 27 1 TAACTTATAA 0.929396 -163 CACTGGAGATTAACTTATATCTCTTTCAGG 27 86 0 TAACTTATAT 0.78537 -104 ********** Masking position 5 Map Score: 6.03729 Number of sites scoring better than the average of aligned sites = 10 Number in coding regions = 3 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 9 CGGCAACGCTTGCGTGAAAATCGATACTTGCT 1 130 1 TGCTGAAAAC 0.810919 -80 TATAAAATTTGCCTTTAAAACCCTCATTAACA 8 54 0 GCCTTAAAAC 0.963185 -83 AAGTAATTCATCCCTTAAAAACTGTTGGAACG 8 86 1 TCCTTAAAAC 0.972814 -51 CCTCCAATTTTCCATTAAAAGCCCACAAAACT 9 93 1 TCCTTAAAAC 0.972795 -60 ATCCTCCCACTCCCTTAAAAACCTATCCCGAA 11 18 1 TCCTTAAAAC 0.972814 -55 AAAATTTTGGTCCATTAGATGCCCCCTAATCC 13 58 1 TCCTTAGATC 0.903168 -243 GCGGTATATGCCCTGAAATGCTCCACGGAAT 22 36 0 GCCTGAAATC 0.884853 -21 TGATTAATATTCATTTAGAAGCTTACATATAT 28 12 0 TCATTAGAAC 0.743061 -105 CCACAGGAGGGCCATGAGAACCATTGAGATGA 34 22 1 GCCTGAGAAC 0.952566 -279 *** ****** * Masking position 7 Map Score: 4.76752 Number of sites scoring better than the average of aligned sites = 115 Number in coding regions = 107 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 10 TAGTTATTGAAACCATCAATCCCTACCTCCGGA 6 53 1 AACATCACCC 0.969302 -57 CATCATACACTATCATCATACACCGAATCGCTT 7 42 0 TACATCACAC 0.971334 -160 TTATTGTGAGTACCATCATACACTATCATCATA 7 55 0 TACATCACAC 0.971334 -147 GATGAATTCCAACCATCAACCAATGTTTAAGTG 13 148 1 AACATCACAA 0.970483 -153 GCAGCTACAGAAACATCACTCAAGATTGTAACC 15 66 1 AACATCACAA 0.970483 -94 GTAGCTACAGAAACATCAGTCAAGATAAATTCC 15 101 1 AACATCACAA 0.970483 -59 AGTATATTATTATCATCATTTAC 16 1 0 TACATCATAC 0.869663 -66 CTACTGATGAAATCATCATTTCCATGCAGTAAG 26 80 0 AACATCATCC 0.861449 -48 ACATGGCTGGAACCATGATGCAAATCCATCCCA 28 62 0 AACATGACAA 0.826868 -55 ** ***** *** Masking position 6 Map Score: 6.5535 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 47 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 11 AATTCAAACTTATATACCGCAGGCAAAAGG 4 76 1 TATATACCGC 0.787748 -27 ACACTATCATCATACACCGAATCGCTTGAT 7 39 0 CATACACCGA 0.966364 -163 TGAGTACCATCATACACTATCATCATACAC 7 52 0 CATACACTAT 0.719782 -150 CATTTCAGGGCATATACCGC 22 47 1 CATATACCGC 0.970791 -10 TTTAGAGTTACATACACCGCCAGTATGGAA 32 102 0 CATACACCGC 0.988376 -104 CATGACCTCACATCCACCACAACGGCAAGG 34 59 1 CATCCACCAC 0.837803 -242 GAGACGTCTCCATATACTGTTTGATTTCCT 34 94 1 CATATACTGT 0.814464 -207 TTAAGATGCACATACACTGAGTTATTGAGG 34 239 0 CATACACTGA 0.918236 -62 ********** Masking position 6 Map Score: 2.45081 Number of sites scoring better than the average of aligned sites = 90 Number in coding regions = 88 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 12 TTTCACGCAAGCGTTGCCGGAAGCAATGTTCTG 1 116 0 GCGTTGCGAG 0.592198 -94 CATCTATCCCGCGGTGGCCCAAGAAATTTCAGC 1 159 0 GCGGTGCCAG 0.949878 -51 GAACGCGACGGCTGTCGCGAGTA 1 197 1 GCTGTCCGGA 0.710888 -13 TCTTTCCAAGCCTGTATCCAGCGGTAATTAAGG 3 110 0 CCTGTACCGG 0.906353 -91 AACCCCACCTTTTGCCTGCGGTATATAAGT 4 83 0 CCTTTTCCGG 0.681177 -20 CTTATAAATAGCTTTGTCCGGAGGTAGGGATTG 6 69 0 GCTTTGCCGG 0.969876 -41 TGGGCGAGAGGCTGTGCCCAGGGGATGGCCCAT 14 13 1 GCTGTGCCGG 0.993189 -219 TAATAAAAAAGCGGACCCGGGGGGATTTGAACC 17 22 1 GCGGACCGGG 0.877759 -197 AAAGCTGTCTGCTGTCCCCTGAGTCTGGTCTTC 17 169 0 GCTGTCCCGG 0.989972 -50 GGAGGATGACCCTGTCCCCGGCGGATACATC 20 9 0 CCTGTCCCGG 0.980585 -49 CTCTCCAGTGACCTGAGTTAACCGAGA 29 5 1 CCAGTGCCGG 0.930419 -27 CCTCCCCCTGGAGGAGGCCAGTGCTATCCTCAT 33 12 0 GAGGAGCCGG 0.686793 -61 ****** ** * * Masking position 8 Map Score: 6.19513 Number of sites scoring better than the average of aligned sites = 195 Number in coding regions = 176 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 13 GGTAGTATGTTTGAGGTGTTTTCGTTAATT 1 12 1 TTGAGGTGTT 0.869371 -198 TTGCGAGGTAGTAGGGTGGTTGGATAATCC 1 48 0 GTAGGGTGGT 0.882041 -162 AAAAACCAGCTTGGGGTGGTCAACGTCAAT 3 160 0 TTGGGGTGGT 0.97766 -41 TGTTCTCAACTAAGGGTGGTTGAATGAGGT 7 150 1 TAAGGGTGGT 0.6492 -52 GGGTGGTTGAATGAGGTAGTTAATTCCGTT 7 163 1 ATGAGGTAGT 0.630082 -39 AAAGGATTAATTAAGGTTGTTCTACTCGAC 12 13 0 TTAAGGTTGT 0.629532 -36 ATCAGTAGGGGTGAGGTGGTGGAGGGGT 25 9 0 GTGAGGTGGT 0.962443 -48 AGTTCCAGCCATGAGGTGAT 26 118 1 ATGAGGTGAT 0.897136 -10 CTTATAAGTTATAAGGTGGTTCC 27 4 0 ATAAGGTGGT 0.904152 -186 CCACAGACATTTGAGGTGACGTAAT 28 102 1 TTGAGGTGAC 0.775461 -15 ACATGGTGGTTTGGGGTGCTGTGTGGTCAT 32 36 0 TTGGGGTGCT 0.878686 -170 GTGTTAAAGATTAAGGTGATATA 32 193 1 TTAAGGTGAT 0.896919 -13 ATGAGAACCATTGAGATGATTAAACATGAC 34 35 1 TTGAGATGAT 0.590536 -266 ********** Masking position 7 Map Score: 6.12289 Number of sites scoring better than the average of aligned sites = 584 Number in coding regions = 538 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 14 AAACTATATCTATCCTGCAGCCCTCAAAAT 2 53 1 TATCCTGCAG 0.960117 -23 TTATAAATTTTATCCTTCAGATTATTGTGA 7 79 0 TATCCTTCAG 0.728871 -123 TAATTCCGTTAACCTTGCTGGTATTAGTT 7 183 1 AACCTTGCTG 0.782053 -19 CTGCAGATGTAACCCTGCAGCTACAGAAAC 15 50 1 AACCCTGCAG 0.988736 -110 TCAAGATTGTAACCCTGTAGCTACAGAAAC 15 85 1 AACCCTGTAG 0.907422 -75 AAGAATGATAGATCCTGCAGATGAACGGAT 27 116 1 GATCCTGCAG 0.952906 -74 TGAACGGATAAACCCTGCAGGAGCTTAATG 27 137 1 AACCCTGCAG 0.988736 -53 ATTTATGTTAAATCCAGCTGTTTTTACGGT 32 165 1 AATCCAGCTG 0.784038 -41 ********** Masking position 2 Map Score: 5.43918 Number of sites scoring better than the average of aligned sites = 186 Number in coding regions = 176 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 15 TATGATTTTCGAACTTCGGAACGTGTGAAC 9 46 0 GAACTTCGGA 0.824674 -107 AATTAAGGAATGACCACAGATTAATATAAA 13 91 1 TGACCACAGA 0.929806 -210 CACAACTTACGGACTTCACATTTATCACGG 15 133 1 GGACTTCACA 0.928882 -27 ATGATCCGGTGAACTTCAGAGTATATTATT 16 23 0 GAACTTCAGA 0.892547 -44 ATATGACGTGGGACTTCGGATCCCAAGGTC 17 58 0 GGACTTCGGA 0.923273 -161 CCATGTTGCATAACCACAGACATTTGAGGT 28 89 1 TAACCACAGA 0.838131 -28 TTCATATTCATGACCACACAGCACCCCAAA 32 27 1 TGACCACACA 0.890611 -179 TGATTAAACATGACCTCACATCCACCACAA 34 51 1 TGACCTCACA 0.928882 -250 ********** Masking position 3 Map Score: 1.08142 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 101 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617