AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i001_mjan_pyro_300.orf -o001_mjan_pyro_300.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.37 -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 = 0.37 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: RMJ00185 17 M_jannaschii_chromosome RMJ14288 143 M_jannaschii_chromosome RPH00825 83 Pyrococcus_OT3 RPH01802 66 Pyrococcus_OT3 Input sequences: #1 RMJ07480 92 M_jannaschii_chromosome #2 RMJ11899 120 M_jannaschii_chromosome #3 RMJ08546 99 M_jannaschii_chromosome #4 RMJ01196 300 M_jannaschii_chromosome #5 RMJ00228 94 M_jannaschii_chromosome #6 RMJ14207 63 M_jannaschii_chromosome #7 RMJ08852 76 M_jannaschii_chromosome #8 RMJ02550 225 M_jannaschii_chromosome #9 RMJ01710 300 M_jannaschii_chromosome #10 RMJ05430 300 M_jannaschii_chromosome #11 RMJ07035 147 M_jannaschii_chromosome #12 RMJ04950 24 M_jannaschii_chromosome #13 RMJ11077 65 M_jannaschii_chromosome #14 RPH00824 83 Pyrococcus_OT3 #15 RPH00763 300 Pyrococcus_OT3 #16 RPH00755 157 Pyrococcus_OT3 #17 RPH01799 110 Pyrococcus_OT3 #18 RPH01808 198 Pyrococcus_OT3 #19 RPH01071 300 Pyrococcus_OT3 Motif number 1 TATTTATAACTTATCTTAAAATTTGGTCTTA 1 45 1 TTATTTAAAA 0.519497 -48 TCTCACCATGAAATTTAAGAATTAGTAAGAC 1 70 0 AAATTAAGAA 0.69881 -23 TGCAAATTGGATGTTTAAAAAATTTTTATTC 2 55 1 ATGTTAAAAA 0.507739 -66 AAGAATTAGTAAAATTAAAAAGATAATTTAT 3 13 0 AAAATAAAAA 0.934597 -87 AAGAAAGAAGAAAATTAAGAAGAATTAGTAA 3 32 0 AAAATAAGAA 0.598101 -68 CTTTTAGCAAATAAATAAAAAGAAAGAAGAA 3 51 0 ATAATAAAAA 0.829683 -49 AAAAGTCTAAAAAACTAAAAAAGGGTTTTTA 3 77 1 AAAATAAAAA 0.934597 -23 GAGAATTTAAAATAATAAAAAGTGGCCGGCG 4 99 0 AATATAAAAA 0.818625 -202 TTAATTGTTCTAAAATAAAAAGAAGCCCGGC 4 234 0 TAAATAAAAA 0.890823 -67 ATTAATCGATAAATTTAAATATTTTTAAAAT 4 260 1 AAATTAAATA 0.748228 -41 TTACTTAAGATATTTTAAAAATATTTAAATT 4 271 0 TATTTAAAAA 0.79947 -30 GTAATAATAAAAAAGTAAAAAAGTGGTTTAA 6 16 0 AAAATAAAAA 0.934597 -48 AATATTGCTCATATATAAAAAATGAAATTGC 8 82 0 ATATTAAAAA 0.88365 -144 CTATCTCGAAAAATTTAAATATTGCTCATAT 8 99 0 AAATTAAATA 0.748228 -127 AGTAATTATATAATATCAAAAGCGGGATAGT 8 204 1 TAATTCAAAA 0.80974 -22 CAGTGAAATAAAAAATAAAAATATATCAAAG 9 70 0 AAAATAAAAA 0.934597 -231 TAAAAAGAACTATAGTCAAAACAGTGAAATA 9 91 0 TATATCAAAA 0.463009 -210 TATTACAAAATATTTTAAAAAGAACTATAGT 9 106 0 TATTTAAAAA 0.79947 -195 AGTTCTTTTCAAATGTTAATAAAGTTTATTA 9 187 0 AAATTTAATA 0.425587 -114 ACTTACAATGTAATATAAAAAATTTATAGTT 9 214 0 TAATTAAAAA 0.927116 -87 TGTAAGTATAAAGATTAAAAATTAAATGAGA 9 238 1 AAGATAAAAA 0.659945 -63 TTTAAATTTTAATTATTAAAACTCTCATTTA 9 260 0 AATTTTAAAA 0.636929 -41 CTAAAAATAAACTAAAAATAAGCCTCTT 11 130 0 TAAATAAAAA 0.890823 -18 TTGAAATAAAAATAATAAAAATAAAGATAAT 13 23 0 AATATAAAAA 0.818625 -43 TTTATTATTTTTATTTCAAAAATTTTTGGAG 13 35 1 TTATTCAAAA 0.591922 -31 TTCACCATGTTTATGTAAAAATCATAATACT 14 15 1 TTATTAAAAA 0.812586 -69 TATGTCTAAAAAATCTTAAAAGTATTATGAT 14 35 0 AAATTTAAAA 0.847427 -49 AAATATGGGAATATATAAATATTACTACTTA 15 31 1 ATATTAAATA 0.503255 -270 TTTAATAATTATAAATAAAAAATCCTACGAA 15 89 0 ATAATAAAAA 0.829683 -212 TTTTATTTATAATTATTAAAATCCGAGGCGA 15 100 1 AATTTTAAAA 0.636929 -201 CTACACTACATAATATAAAAATGATTGTTTG 15 174 0 TAATTAAAAA 0.927116 -127 AACTGATTTATATTTTCAAAATGTATCTTTA 16 27 0 TATTTCAAAA 0.572537 -131 ATCACCATATTTAAGTCAAAATTATAAGGTA 16 132 0 TTAATCAAAA 0.482032 -26 TTGTCAAAATAAATCTTAAAAATTTAAAATT 17 56 1 AAATTTAAAA 0.847427 -55 TTTGCCAGAAAAATGTAAAAATTTTAAATTT 17 75 0 AAATTAAAAA 0.957042 -36 AGGGTTTCTAAAATTTAAAAATCAAGGAGAA 18 30 0 AAATTAAAAA 0.957042 -169 **** ****** Masking position 6 Map Score: 39.4571 Number of sites scoring better than the average of aligned sites = 2317 Number in coding regions = 1542 Number in noncoding regions = 775 Number of orfs with sites within 600 bp upstream = 511 Fraction of orfs with sites within 600 bp upstream = 0.0820752 Motif number 2 ATTTATCGCCGTATTGTTTAAGAGTTT 1 2 1 TTTACTTTGT 0.925609 -91 TTCTTCTTAATTTTCTTCTTTCTTTTTATTTATTTG 3 39 1 TTTTCTTTTT 0.905029 -61 ATTAAAAACCCTTTTTTAGTTTTTTAG 3 83 0 TTAACTTTTT 0.846972 -17 CATTATCTCTTATATAACAATTTTTTAATGAGAGAA 5 14 0 TATACTTTTT 0.947661 -81 AAGATTTAAACCACTTTTTTACTTTTTTAT 6 5 1 TTTACTTTTT 0.953671 -59 ATTTTTATTTTTTATTTCACTGTTTTGACTATAGTT 9 79 1 TTTACTTTTT 0.953671 -222 TTGAAATTAGTATAATGCTTTATTGAGGGTAGCTCT 10 140 1 TATACTTTGA 0.655121 -161 AATAAACATTTTATTATCTTTATTTTTATTATTTTT 13 11 1 TTATCTTTTT 0.719289 -55 GTAATATTTATATATTCCCATATTTTATTTTAAGTG 15 20 0 TATACTTTTT 0.947665 -281 GTTTGTGTTCTTTTGTTCACTCTTTTACTTTGGCTT 15 143 0 TTTTCTTTTT 0.905029 -158 ATTTTGAAAATATAAATCAGTTTTGTGTAGGTGGAC 16 36 1 TATACTTTGT 0.916284 -122 CTTTATTTAGTAATTAACTTTTTTGTTAACACGTTT 16 76 1 TAATCTTTGT 0.57671 -82 TTTATATCACCATATTTAAGTCAAAATT 16 140 0 TATACTTTTA 0.758605 -18 TCTTAAGTTTTTTCTACCTTTCTTTTTTGGTTCTAC 19 31 1 TTTCCTTTTT 0.887645 -270 AAACCAACAGTATCACTCCATATTTTTCCCAAAAGT 19 70 0 TATCCTTTTT 0.874209 -231 **** * * **** Masking position 11 Map Score: 12.8826 Number of sites scoring better than the average of aligned sites = 480 Number in coding regions = 414 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 3 CATTATTTGTTTCAATAACTATACGATTTT 2 91 0 TTCAATAACT 0.932135 -30 GCATAAAGGTTTAATAACACATCCTTCAT 7 10 1 TTTAATAACA 0.889196 -67 ACAAATAATATTAATTAACTAATAAGGTGT 7 53 1 TTAATTAACT 0.75254 -24 TATCATTATTTTTAATAACTTCCGTATCAA 8 146 1 TTTAATAACT 0.967582 -80 TAAAATATTTTGTAATAACTAAGGCACTGA 9 120 1 TGTAATAACT 0.801958 -181 GTTAATAAAGTTTATTAATTAAGTTTGAAC 9 174 0 TTTATTAATT 0.813763 -127 ATTAATAAACTTTATTAACATTTGAAAAGA 9 185 1 TTTATTAACA 0.875925 -116 AAATGAGAGTTTTAATAATTAAAATTTAAA 9 261 1 TTTAATAATT 0.832419 -40 TCCTTCGAATTTCATTAACTCTCCTTGCTA 10 64 1 TTCATTAACT 0.923561 -237 AATAAACATTTTATTATCTTTATTTTTAT 13 10 1 TTTATTATCT 0.706187 -56 AAGAAAAAGATTTATTAACTCAATTTATAA 15 59 0 TTTATTAACT 0.96331 -242 CGCCTCGGATTTTAATAATTATAAATAAAA 15 100 0 TTTAATAATT 0.832419 -201 AACTTGTTCCTTCAAAAACTGGAATGTTCA 18 167 1 TTCAAAAACT 0.557009 -32 TTAAGAACCTTTTAATAACTTTCTAA 19 7 0 TTTAATAACT 0.967582 -294 ATAGCTCAAATTTATTAACAATTACGCTTA 19 122 0 TTTATTAACA 0.875925 -179 ********** Masking position 4 Map Score: 16.9752 Number of sites scoring better than the average of aligned sites = 420 Number in coding regions = 358 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 4 ATTTATCGCCGTATTGTTTAAGAGTTTGA 1 4 1 TTCCCGTTTT 0.939301 -89 ACTCTCACCATGAAATTTAAGAATTAGT 1 75 0 TTCCCATTTT 0.850154 -18 AATATCTCCTCATTATTTGTTTCAATAA 2 103 0 TTCCCTCTTT 0.989843 -18 TCTTCTTAATTTTCTTCTTTCTTTTTATTTATTTGC 3 40 1 TTCTCTTTTT 0.764447 -60 TCTATCGCCTCGAAGATATTTTATAATG 5 77 0 TTCCCTCATA 0.880794 -18 AATCTCACCTTTTGCTTTTGGATTAATG 6 46 0 TTCCCTTTTT 0.981588 -18 CTTTTAATGGTATCACCTCAAAATGTTATGGCAATT 8 52 1 TTCCCTCTGT 0.929691 -174 ACTTTCACCTTAGCTATAACTTTAAATT 9 283 0 TTCCCTTATA 0.805809 -18 CTAATGTTTGTCTCGCCGCCTCCCTATCTTCGAGCG 10 94 0 TTCCCGCCTA 0.773024 -207 GATTTCACCTCTCATCTTTTGCCAGATA 14 66 0 TTCCCTCCTT 0.968543 -18 TTTTCGTTTGAATCGCCTCGGATTTTAATAATTATA 15 107 0 ATCCCTCTTT 0.899198 -194 CGTGACACCTCCTTATTTGCCAGAAAAA 17 93 0 TACCCTCTTT 0.89921 -18 TTTCTCCTCCCCTTTAGTTTTCTCCT 18 1 1 TTCCCTCTTA 0.97378 -198 CCCCTTTAGTTTTCTCCTTGATTTTTAAATTTTAGA 18 19 1 TTCCCTTTTT 0.981588 -180 TCGTTAGTTCTTTCGGCTTATCGTTTAGATGACTTT 18 79 1 TTCGCTTTTT 0.827882 -120 * ** **** *** Masking position 7 Map Score: 14.7764 Number of sites scoring better than the average of aligned sites = 283 Number in coding regions = 231 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 5 AGTTATAAATAAATCTTCAAACTCTTAAACAATACGG 1 19 0 AAATTATCTA 0.759617 -74 AACTTATCTTAAAATTTGGTCTTACTAATTCTTAAAT 1 52 1 AAATTCTATA 0.553439 -41 TGGATGTTTAAAAAATTTTTATTCCTACAAAAATCGT 2 62 1 AAATTATCTA 0.758659 -59 ATTATCTTTTTAATTTTACTAATTCTTCTTAATTTTC 3 17 1 TAATTATTTT 0.780149 -83 TAATTCTTCTTAATTTTCTTCTTTCTTTTTATTTATT 3 36 1 TAATTCTTTT 0.598803 -64 GATATTTTAAAAATATTTAAATTTATCGATTAATTGT 4 257 0 AAATTATTTC 0.666089 -44 TAGTGTTATAAAATATTCTCCATTATAAAATATCTTC 5 57 1 AAATTCTTTA 0.851312 -38 TCCGTATCAAAAAGCTTTAAAGTATTAGTAATAATAA 8 166 1 AAATTATATA 0.745336 -60 GTATTAGTAATAATAATAGTAATTATATAATATCAAA 8 187 1 TAAATATTTA 0.329938 -39 ATGTAATATAAAAAATTTATAGTTCTTTTCAAATGTT 9 201 0 AAATTATTTT 0.865004 -100 TTGTAAGTATAAAGATTAAAAATTAAATGAGAGTTTT 9 237 1 AAATTATTAA 0.481183 -64 TTTTAATAATTAAAATTTAAAGTTATAGCTAAGGTGA 9 270 1 TAATTATTTA 0.880889 -31 TTTATTTCAAAAATTTTTGGAGGTATATATTT 13 44 1 AAATTAGTTA 0.727436 -22 TATGTCTAAAAAATCTTAAAAGTATTATGATTTTTAC 14 29 0 AAATTATATA 0.745478 -55 GGGAATATATAAATATTACTACTTATAAATTGAGTTA 15 37 1 AAATTATTTA 0.931687 -264 TAAGTACACATAAATTTATCAATTCTAGGTGAGATA 15 275 1 TAATTATTTA 0.880801 -26 AATAAATCTTAAAAATTTAAAATTTTTACATTTTTCT 17 63 1 AAATTATTTT 0.491072 -48 TTGAAAAAGATAATGTTCAAACTTGTTCCTTCAAAAA 18 148 1 TAATTATTTT 0.780735 -51 AAAGTTATTAAAAGGTTCTTAAGTTTTTTCTACCTTT 19 15 1 AAATTAGTTT 0.545197 -286 AGTTTGTGTATAAAGTTATGCCTTGTAAGCACTACCT 19 225 1 TAATTCTTTA 0.758937 -76 *** ** * ** ** Masking position 7 Map Score: 13.2097 Number of sites scoring better than the average of aligned sites = 565 Number in coding regions = 397 Number in noncoding regions = 168 Number of orfs with sites within 600 bp upstream = 172 Fraction of orfs with sites within 600 bp upstream = 0.0276261 Motif number 6 CTAAAAGTCTAAAAAACTAAAAAAGGGTTTTT 3 75 1 AAAACTAAAA 0.83076 -25 AATATTTTTAAAATATCTTAAGTAAGTGAGGT 4 277 1 AAAACTTAAG 0.965981 -24 AATATTTTAAAAAGAACTATAGTCAAAACAGT 9 97 0 AAAACTATAG 0.799821 -204 TATATGTCTAAAAAATCTTAAAAGTATTATGA 14 36 0 AAAACTTAAA 0.83076 -48 ATTATAAATAAAAAATCCTACGAAAAGAAAAA 15 81 0 AAAACCTACG 0.839998 -220 ATTCAAACGAAAAAAGCCAAAGTAAAAGAGTG 15 130 1 AAAACCAAAG 0.924298 -171 AAAATCAAGGAGAAAACTAAAGGGGAGGAGAA 18 12 0 AGAACTAAAG 0.924298 -187 CTAACGAGAAAGAGAGCTTAAGAGAAGGGTTT 18 54 0 AGAACTTAAG 0.924298 -145 CGATAAGCCGAAAGAACTAACGAGAAAGAGAG 18 70 0 AAAACTAACG 0.924298 -129 AGAAAGGTAGAAAAAACTTAAGAACCTTTTAA 19 22 0 AAAACTTAAG 0.965981 -279 *** * ****** Masking position 5 Map Score: 5.82712 Number of sites scoring better than the average of aligned sites = 174 Number in coding regions = 168 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 7 AAGCCCCCCAGCGATGCCCCGAGTACTGCCATC 4 46 1 GCATGCCCGG 0.989746 -255 CCTTGGCATTACTATGCCCTGGTGGTGTAGCCC 4 138 1 ACATGCCCGT 0.935776 -163 GGTAGCTCTGACTCTGCCCGATGACACCAACCT 10 167 1 ACCTGCCCAG 0.974138 -134 CGATGACACCAACCTGCCCTGTGACCTATCGGC 10 185 1 AACTGCCCGG 0.956625 -116 GGTTTAAGAGGCACTGCCAAGCGTTAGCGAGGC 11 11 1 GCCTGCCAGG 0.974489 -137 TATCCGGGATGCACTGCCTCGCTAACGCTTGGC 11 26 0 GCCTGCCTGT 0.96341 -122 ACACCATAGGGCTCTGCCCTATTGGAATATCCG 11 53 0 GCCTGCCCAT 0.974163 -95 ATTTGAAACAGAGATGCCTAAGGTAGTGCTTAC 19 249 0 GAATGCCTAG 0.701853 -52 ** ****** * * Masking position 5 Map Score: 3.06665 Number of sites scoring better than the average of aligned sites = 28 Number in coding regions = 12 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 8 GGGGCATCGCTGGGGGGCTTAACTTCCGAG 4 36 0 TGGGGGGCTT 0.97083 -265 TACTGCCATCTGGCGGGAAAGGGGCGACGC 4 69 1 TGGCGGGAAA 0.841469 -232 CCGTATGATAGGCCGGGCTACACCACCAGG 4 155 0 GGCCGGGCTA 0.981409 -146 ATGGCGCCCTGGCCGGGATTTGAACCCGAG 4 202 0 GGCCGGGATT 0.946915 -99 GGGCGCCATTTGCCGGGCTTCTTTTTATTT 4 223 1 TGCCGGGCTT 0.984538 -78 GCCCTATTATTGGGGGGCTATTCTCATAGG 8 15 0 TGGGGGGCTA 0.970827 -211 ********** Masking position 5 Map Score: 2.3039 Number of sites scoring better than the average of aligned sites = 12 Number in coding regions = 4 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 9 AGTCTTATACTATTATCTTT 2 1 0 TATTATCTTT 0.941248 -120 AATATCTCCTCATTATTTGTTTCAATAACT 2 101 0 CATTATTTGT 0.906086 -20 AAATAAATTATCTTTTTAATTTTAC 3 6 1 AATTATCTTT 0.829622 -94 CTATCTATGTCATTATCTCTTATATAACAA 5 30 0 CATTATCTCT 0.893166 -65 AGTTAATTAATATTATTTGTGGATATACAA 7 43 0 TATTATTTGT 0.830814 -34 ACAATATTATCATTATTTTTAATAACTTCC 8 139 1 CATTATTTTT 0.951779 -87 GCGAGACAAACATTAGTTTTATATACTTGA 10 114 1 CATTAGTTTT 0.804547 -187 ATAAACATTTTATTATCTTTATTTTTATTA 13 12 1 TATTATCTTT 0.941248 -54 TCTTTATTTTTATTATTTTTATTTCAAAAA 13 27 1 TATTATTTTT 0.909472 -39 CAAGTTTGAACATTATCTTTTTCAAGCTTG 18 143 0 CATTATCTTT 0.969208 -56 ********** Masking position 5 Map Score: 7.64306 Number of sites scoring better than the average of aligned sites = 153 Number in coding regions = 130 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 10 TCACGGGAGTGACAGTCCCGTATGATAGGCCGG 4 169 0 GAGTCCGTAT 0.905095 -132 ATTATTTTTAATAACTTCCGTATCAAAAAGCTT 8 150 1 AACTCCGTAT 0.958293 -76 GAAGGAGTTCATCAGTGCCTTAGTTATTACAAA 9 128 0 AAGTCCTTAG 0.936006 -173 GCTAAAGCTTGGAGCTTCCTTAGCAACAACTA 10 10 0 GGCTCCTTAG 0.853129 -291 AAAATTCCTAAATACTCCCGTAGTGGAGA 10 282 1 AACTCCGTAG 0.968598 -19 TGTGTAGGTGGACACTACTTTATTTAGTAATTA 16 59 1 GACTCTTTAT 0.644259 -99 AACAAAAACCATTAATACCTTATAATTTTGACT 16 117 1 AAATCCTTAT 0.732903 -41 CGTGACACCTCCTTATTTGCCAGAAA 17 95 0 GACCCCTTAT 0.812329 -16 TCAAGCTTGTAAAACTACCTTATATATCTTACT 18 119 0 AACTCCTTAT 0.96089 -80 TATTTTTCCCAAAAGTAACGTAGAACCAAAAAA 19 53 0 AAGTACGTAG 0.518819 -248 ATGCCTTGTAAGCACTACCTTAGGCATCTCTGT 19 242 1 AACTCCTTAG 0.970573 -59 * *** ****** Masking position 12 Map Score: 2.34737 Number of sites scoring better than the average of aligned sites = 106 Number in coding regions = 97 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 11 GAATAAAAATTTTTTAAACATCCAATTTGCATTA 2 52 0 TTTTTAATCA 0.639453 -69 CTATACGATTTTTGTAGGAATAAAAATTTTTTAA 2 69 0 TTTGTGATAA 0.913065 -52 TTTTTTAGACTTTTAGCAAATAAATAAAAAGAAA 3 57 0 TTTTAAATAA 0.71537 -43 ATTAATATTATTTGTGGATATACAAAAAATGAAG 7 34 0 TTTGTAATAA 0.95434 -43 AATATTTAAATTTTTCGAGATAGATTTAACCAAC 8 107 1 TTTTTAATAA 0.918295 -119 TTTATATTACATTGTAAGTATAAAGATTAAAAAT 9 226 1 ATTGTGATAA 0.683086 -75 ACCTCCAAAAATTTTTGAAATAAAAATAATAAAA 13 34 0 ATTTTAATAA 0.696636 -32 TTCAAAAATTTTTGGAGGTATATATTT 13 49 1 TTTGGGATAA 0.665266 -17 AGTATTATGATTTTTACATAAACATGGTGAAATT 14 12 0 TTTTTAAAAA 0.537389 -72 CTTTTAAGATTTTTTAGACATATATCTGGCAAAA 14 44 1 TTTTTAATAA 0.918295 -40 AAAGATACATTTTGAAAATATAAATCAGTTTTGT 16 28 1 TTTGAAATAA 0.824058 -130 ATTAATGGTTTTTGTTTACATAAACGTGTTAACA 16 99 0 TTTGTAATAA 0.94144 -59 TTGACATTTCTTTGTCAAAATAAATCTTAAAAAT 17 45 1 TTTGTAATAA 0.95395 -66 ***** * *** * Masking position 10 Map Score: 7.58278 Number of sites scoring better than the average of aligned sites = 230 Number in coding regions = 175 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 12 AAATCTTCAAACTCTTAAACAATACGGCGA 1 16 0 ACTCTTAAAC 0.718326 -77 GATCTTCTCTCCACCTAAAGGGTGGAGGTT 10 248 0 CCACCTAAAG 0.917937 -53 CTTGGCAGTGCCTCTTAAACC 11 2 0 CCTCTTAAAC 0.942807 -146 AAAGTAGTGTCCACCTACACAAAACTGATT 16 50 0 CCACCTACAC 0.975872 -108 CTCACACCCTCCTGAACATTCCAGTTT 18 182 0 CCTCCTGAAC 0.946916 -17 GTCCTACCACCTACACACTTTAGATC 19 285 0 CCACCTACAC 0.975872 -16 ********** Masking position 6 Map Score: 0.776915 Number of sites scoring better than the average of aligned sites = 29 Number in coding regions = 24 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 13 AAGACTTTCTGTAGTTTAAATATTCCATAATGC 2 25 1 GTGTTAAATT 0.962463 -96 ATTTAAATTTATCGATTAATTGTTCTAAAATAA 4 247 0 ATGTTAATTT 0.815363 -54 AAGTAAAAAAGTGGTTTAAATCTT 6 2 0 GTGTTAAATT 0.962528 -62 AAATTTAAATATTGCTCATATATAAAAAATGAA 8 87 0 ATGTCATATT 0.74821 -139 TGATAATATTGTTGGTTAAATCTATCTCGAAAA 8 118 0 GTGTTAAATT 0.962529 -108 TAGACAGGCTATAGCTCAAATTTATTAACAATT 19 129 0 ATGTCAAATT 0.934695 -172 ATACCCATTTATAGCTTAAATTTGCGGAATAGT 19 173 1 ATGTTAAATT 0.955096 -128 ** * ****** * Masking position 8 Map Score: 0.562749 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 33 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 14 ********** No masking Map Score: 5.53756e-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 15 ********** No masking Map Score: 5.53756e-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