AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i054_mjan_pyro_300.orf -o054_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 Input sequences: #1 RMJ14902 160 M_jannaschii_chromosome #2 RMJ08360 300 M_jannaschii_chromosome #3 RMJ07567 167 M_jannaschii_chromosome #4 RMJ10911 194 M_jannaschii_chromosome #5 RMJ08527 300 M_jannaschii_chromosome #6 RMJ05443 300 M_jannaschii_chromosome #7 RMJ09985 300 M_jannaschii_chromosome #8 RPH00392 47 Pyrococcus_OT3 #9 RPH00390 129 Pyrococcus_OT3 #10 RPH01578 34 Pyrococcus_OT3 #11 RPH01579 16 Pyrococcus_OT3 #12 RPH01583 215 Pyrococcus_OT3 #13 RPH01584 238 Pyrococcus_OT3 #14 RPH01754 99 Pyrococcus_OT3 #15 RPH01755 65 Pyrococcus_OT3 Motif number 1 ACTAAGGTAATTAATAAAAATTAAGATTTTAG 1 60 0 TTATAAAATT 0.922242 -101 ACGGCTTCTATTATTTAAAGTTATTGTTTGAT 1 93 1 TTATTAAATT 0.815421 -68 GATAAAGGAATTATTTAAAATTTATCAAACAA 1 116 0 TTATTAAATT 0.815421 -45 TAAAAAGAATATATAAAAAATGAAACACGT 2 9 0 ATAAAAAATG 0.852744 -292 GGATACCATATTATATATTATTTTCGGTTTTT 2 74 1 TTAATATTTT 0.596109 -227 TAAGGATTAGATATAAATACTTCAACATCAAA 2 131 0 ATAAAATATT 0.952046 -170 TTCTATTACAATATAAAAATTTAAAAATTTAT 2 264 1 ATAAAAAATT 0.968135 -37 ATCAATCTAAATAGAAATTTTTGGGGATAAA 3 10 0 ATAAAATTTT 0.837484 -158 CTCACCTATTATATATAAACTGCTAATAATAA 3 51 0 ATAATAAATG 0.683243 -117 AAGCAATAAAATACAAAAAGTTTAAGGATTTA 3 104 1 ATAAAAAATT 0.968138 -64 TTTTTATATCTTACATAAAATTATAAATCCTT 3 127 0 TTAATAAATT 0.896936 -41 TATGTAAGATATAAAAATATTTTGTGAGGGAT 3 142 1 ATAAAATATT 0.952044 -26 TAATATTGCTATAATTAATCTTTTTGGTGATA 4 14 0 ATATTAATTT 0.598602 -181 AGCAATATTAATAAAAATACTTTCACATAAAA 4 36 1 ATAAAATATT 0.952046 -159 ACAACACAAAATATAAATACTTATAATGCATT 4 123 1 ATAAAATATT 0.952046 -72 TAGGGGCACCATACAAAAAATTAAAGAATAGT 5 41 0 ATAAAAAATT 0.968138 -260 AATTGTTTTATTATTAAAAATTCTAATAAGTT 5 168 0 TTATAAAATT 0.922242 -133 TATAAAATAGTTAAAAATAATTTACTTTTTTA 5 207 0 TTAAAATATT 0.938521 -94 TTAATCGTGTTTAAATAATATTGATTATGTTA 5 262 0 TTAATAATTT 0.693148 -39 AAGTTAATAAATAAAAAGAATTACAAAAACAT 6 93 1 ATAAAAGATT 0.862491 -208 CAATTAACTATTAATAATATTTGATGTTTTTG 6 116 0 TTATAATATT 0.885706 -185 AACTACAACAATATAAATAATGGCTCATGATA 6 242 1 ATAAAATATG 0.790955 -59 TCCTGTTTTTTTACAAAAAGTTTATTAAAAAC 7 80 1 TTAAAAAATT 0.958956 -221 CAAAGGTTTTATAAAAAATCTTAAATTATACA 7 177 1 ATAAAAATTT 0.887477 -124 CAGACTTAACTTAATTATAATTCTCAATGTAT 7 204 0 TTATTATATT 0.742697 -97 CTAATTAATATTAATAATATTTCCAGACTTAA 7 227 0 TTATAATATT 0.885706 -74 ACTTTTTAACTTATTAAAACTTCATACCTGAG 9 31 1 TTATAAAATT 0.922242 -99 TTTCTATATAATACTAAGATTTTCGAAAAAAA 12 74 0 ATATAAGATT 0.760994 -142 TTAGTATTATATAGAAAAATTTTCTAAAATTT 12 89 1 ATAAAAAATT 0.968138 -127 GAACCTAGGTATATAAAATTTTCGAGAAATAT 12 154 0 ATAAAAATTT 0.887473 -62 *** ***** ** Masking position 7 Map Score: 41.6147 Number of sites scoring better than the average of aligned sites = 994 Number in coding regions = 591 Number in noncoding regions = 403 Number of orfs with sites within 600 bp upstream = 368 Fraction of orfs with sites within 600 bp upstream = 0.059107 Motif number 2 TCGTTTTATCTAAAATCTTAATTTTTATTAAT 1 51 1 TAAAACTAAT 0.782759 -110 TATGAGTGGATAAAGGAATTATTTAAAATTTA 1 124 0 TAAAGATTAT 0.874391 -37 ATCTAATCCTTAAAATAATTTACAATGGAACT 2 151 1 TAAAAATTTA 0.776225 -150 TTTAAATGCCTAAAGGCATTATTATTCCATAG 2 201 0 TAAAGCTTAT 0.773124 -100 TATATTTTATTAAAGGCATTTAAATGCCTAAA 2 219 0 TAAAGCTTTA 0.477917 -82 ATATAAAAATTTAAAAATTTATGCTGATGGTG 2 274 1 TTAAAATTAT 0.88503 -27 TACAAAAAGTTTAAGGATTTATAATTTTATGT 3 115 1 TTAAGATTAT 0.78748 -53 ATGTAAGATATAAAAATATTTTGTGAGGGATT 3 143 1 TAAAATTTTT 0.756781 -25 TACTTTCACATAAAAATGTTTTGTTGGTGACT 4 53 1 TAAAATTTTT 0.756781 -142 TTACTTCCCTTAAAAGTTTTATTTTTAATTTT 4 153 1 TAAAATTTAT 0.859411 -42 TTTTTAATTTTAAAATCATTTTGGTGATTAA 4 174 1 TAAAACTTTT 0.782504 -21 CTATTTAACTTTAAATCATAATATATATAGAG 5 112 0 TTAAACTAAT 0.69029 -189 TGATTTAAAGTTAAATAGTAAATTATATATGT 5 126 1 TTAAAATAAA 0.737199 -175 TTATATATGTTAAAATTTTTAACTTATTAGAA 5 148 1 TAAAATTTAA 0.496212 -153 TTTTTAATAATAAAACAATTATAACTTTAAAA 5 180 1 TAAAAATTAT 0.941485 -121 ATTATAACTTTAAAAAAGTAAATTATTTTTAA 5 197 1 TAAAAATAAA 0.819886 -104 TATAAAATTATAAAATAGTTAAAAATAATTTA 5 215 0 TAAAAATTAA 0.877061 -86 TTAATCGTGTTTAAATAATATTGATTATGTTA 5 262 0 TTAAAATATT 0.676216 -39 TTCTTAAACAGTTAATTTATTATAA 6 4 1 TTAAAATTAA 0.858684 -297 AAACAGTTCTTAAAAAACTTATAGCACTGAAA 6 50 1 TAAAAATTAT 0.936421 -251 CATGATAATATAAAATAGTTTTTAATAGTATA 6 267 1 TAAAAATTTT 0.880051 -34 TATTTTCAGTTTAAAAAATAAAAGAA 7 5 0 TTAAAATAAA 0.737566 -296 AAAAAGTTTATTAAAAACTAATAAAATCTAAA 7 94 1 TTAAAATAAT 0.81992 -207 AATGTATAATTTAAGATTTTTTATAAAACCTT 7 179 0 TTAAGTTTTT 0.436968 -122 CCTCCAAAAATTAAAAATTAAAAAGGG 10 6 0 TTAAAATAAA 0.718829 -29 AAAAATTTTCTAAAATTTTTAAGATCTTAAAA 12 103 1 TAAAATTTAA 0.496212 -113 TTTTAAGATCTTAAAATTTTATTCGATAATCC 12 119 1 TTAAATTTAT 0.786734 -97 ATAGCAGATTTAAAAAACTAAATCAAACTTTC 13 15 0 TAAAAATAAA 0.815611 -224 GTTAATCCTCTAAAGCAATTTTTAAATAGCCA 14 38 0 TAAAGATTTT 0.761663 -62 ***** * **** Masking position 4 Map Score: 28.649 Number of sites scoring better than the average of aligned sites = 2272 Number in coding regions = 1589 Number in noncoding regions = 683 Number of orfs with sites within 600 bp upstream = 472 Fraction of orfs with sites within 600 bp upstream = 0.0758111 Motif number 3 TATTTAAAGTTATTGTTTGATAAATTTTAAATAATTC 1 104 1 TATTTGATTT 0.540907 -57 ATTTTTTATATATTCTTTTTATATATTCCCACAATAC 2 20 1 TATTTTAATT 0.800703 -281 CCATATTATATATTATTTTCGGTTTTTAGTAAGGTTA 2 79 1 TATTTTTTTT 0.678198 -222 AGTTTGTATATTTTATTAAAGGCATTTAAATGCCTAA 2 220 0 TTTTTACTTT 0.70959 -81 TAAATTTTTATATTGTAATAGAACTTTCGCAGTTTGT 2 250 0 TATTTTATTT 0.92822 -51 CTTTTTGTATTTTATTGCTTATAGTTTTGGAGTATAT 3 87 0 TTTATTATTT 0.848434 -81 CAAAACATTTTTATGTGAAAGTATTTTTATTAATATT 4 39 0 TTATTAATTT 0.433883 -156 TTTTGTGTTGTTTTTTGTTGAGTATTTTAATCATTTT 4 97 0 TTTTTTTTTT 0.763344 -98 ATGGTGCCCCTATTATTTTCCACATTTTTCACAAATG 5 61 1 TATTTTCTTT 0.843542 -240 TATATAGAGGTTTTGTATTATTACATTTGTGAAAAAT 5 84 0 TTTTTTAATT 0.86012 -217 CCTCTATATATATTATGATTTAAAGTTAAATAGTAAA 5 111 1 TATTTTAGTT 0.694662 -190 GTTATAATTGTTTTATTATTAAAAATTCTAATAAGTT 5 168 0 TTTTTTAATT 0.86012 -133 TTAAAAATAATTTACTTTTTTAAAGTTATAATTGTTT 5 192 0 TTTATTAGTT 0.496176 -109 AAAAAGTAAATTATTTTTAACTATTTTATAATTTTAT 5 209 1 TTATTAATTT 0.433883 -92 TTATATTTCATTTTTTGATATAAAATTATAAAATAGT 5 228 0 TTTTTTAATT 0.860119 -73 TTAAGAACTGTTTTATTATTGTATTTTTTATAATAAA 6 26 0 TTTTTTATTT 0.951904 -275 TTGTAATTCTTTTTATTTATTAACTTTGTGTTATATT 6 82 0 TTTTTAATTT 0.854237 -219 GAGCCATTATTTATATTGTTGTAGTTTCTTACGTAAT 6 231 0 TTATTTATTT 0.721319 -70 AACTATTTTATATTATCATGAGCCATTATTTATATTG 6 250 0 TATTTTCATT 0.626179 -51 AGATGCTCTTTATAATATTTTCAGTTTAAAAAATAAA 7 15 0 TATATTATTT 0.785291 -286 AAAATCCTGTTTTTTTACAAAAAGTTTATTAAAAACT 7 76 1 TTTTTAATTT 0.854237 -225 TAATTTAAGATTTTTTATAAAACCTTTGAACGAACCT 7 168 0 TTTTTACTTT 0.70959 -133 CAATTTTCTTTTTATTATTAGGATTTTCTTTGGGAAT 7 266 0 TTTATTATTT 0.848434 -35 TACCTGAGCTTTTTCTAATCCAAGTTTACTTATGTCG 9 55 1 TTTTTTATTT 0.951904 -75 CCCTTTTTAATTTTTAATTTTTGGAGGGAGGT 10 6 1 TTTATTTTTT 0.477067 -29 TCTCTTGCTCTATTGTACTCCTATTTTATAATGTTCA 12 34 1 TATTTTATTT 0.92822 -182 AATTTTTCTATATAATACTAAGATTTTCGAAAAAAAT 12 73 0 TATATTATTT 0.785291 -143 CCGAAAACTCTATTTTTCTTGGCTATTTAAAAATTGC 14 19 1 TATTTTCATT 0.626179 -81 **** * * * *** Masking position 6 Map Score: 28.6952 Number of sites scoring better than the average of aligned sites = 1835 Number in coding regions = 1301 Number in noncoding regions = 534 Number of orfs with sites within 600 bp upstream = 379 Fraction of orfs with sites within 600 bp upstream = 0.0608738 Motif number 4 AGATTTTTGGTAGTTGGTGAGATAAGATGC 1 22 0 TAGTTGGTGA 0.961785 -139 TAAATAGAAATTTTTGGGGATAAA 3 5 0 TTTTTGGGGA 0.8576 -163 AGTTTATATATAATAGGTGAGTTATATATA 3 62 1 TAATAGGTGA 0.655816 -106 GATATAAAAATATTTTGTGAGGGATTGTC 3 149 1 TATTTTGTGA 0.763462 -19 ATAATTAATCTTTTTGGTGATAAGT 4 6 0 TTTTTGGTGA 0.969679 -189 AACAAAACATTTTTATGTGAAAGTATTTTT 4 48 0 TTTTATGTGA 0.498884 -147 TAAAAATGTTTTGTTGGTGACTTAAACCAT 4 63 1 TTGTTGGTGA 0.971948 -132 TTTGTGTTGTTTTTTGTTGAGTATTTTAAT 4 103 0 TTTTTGTTGA 0.696476 -92 TTTTAAAATCATTTTGGTGATTAA 4 181 1 ATTTTGGTGA 0.919159 -14 AATTAAAGAATAGTTGGCGATGACGCTCCC 5 25 0 TAGTTGGCGA 0.825773 -276 AATAAAAAGAAAATTGGTGAAAGG 7 287 1 AAATTGGTGA 0.751463 -14 GGATAAATAGATGTTGGTGAAGTCC 8 6 0 ATGTTGGTGA 0.924915 -42 ********** Masking position 10 Map Score: 10.4119 Number of sites scoring better than the average of aligned sites = 309 Number in coding regions = 207 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 5 CAATAACTTTAAATAATAGAAGCCGTAACTA 1 88 0 AAATAATAAA 0.779957 -73 ATTGTTTGATAAATTTTAAATAATTCCTTTA 1 115 1 AAATTTTAAT 0.738428 -46 TAAAAACCGAAAATAATATATAATATGGTAT 2 76 0 AAATAATAAT 0.795295 -225 TGCCTTTAATAAAATATACAAACTGCGAAAG 2 233 1 AAAATATAAA 0.854382 -68 AAGTTCTATTACAATATAAAAATTTAAAAAT 2 261 1 ACAATATAAA 0.625162 -40 ATCTTACATAAAATTATAAATCCTTAAACTT 3 121 0 AAATTATAAT 0.939818 -47 AAAACAACACAAAATATAAATACTTATAATG 4 120 1 AAAATATAAT 0.865526 -75 AATGATTTTAAAATTAAAAATAAAACTTTTA 4 163 0 AAATTAAAAT 0.865522 -32 ACCATACAAAAAATTAAAGAATAGTTGGCGA 5 35 0 AAATTAAAAA 0.854382 -266 GTTAAATAGTAAATTATATATGTTAAAATTT 5 135 1 AAATTATAAT 0.939752 -166 TTTTGATATAAAATTATAAAATAGTTAAAAA 5 222 0 AAATTATAAA 0.934365 -79 AATTTATTATAAAAAATACAATAATAAAACA 6 24 1 AAAAAATAAA 0.593643 -277 TTATTGAATGAAATTAAATAAATAAGGGCAA 6 164 0 AAATTAAAAA 0.854379 -137 AGAAACTACAACAATATAAATAATGGCTCAT 6 239 1 ACAATATAAT 0.646591 -62 TCAGTTTAAAAAATAAAAGAA 7 1 0 AAATAAAAAA 0.593643 -300 AAAAAATCTTAAATTATACATTGAGAATTAT 7 189 1 AAATTATAAT 0.939818 -112 CAAAATAAAGATAAAGGTTCAA 8 36 0 AAAATAAAAT 0.726234 -12 CTCCCTCCAAAAATTAAAAATTAAAAAGGG 10 10 0 AAATTAAAAT 0.865522 -25 AAAATTGTGAACATTATAAAATAGGAGTACA 12 47 0 ACATTATAAA 0.801848 -169 AAGATCTTAAAAATTTTAGAAAATTTTTCTA 12 100 0 AAATTTTAAA 0.720162 -116 TATTTCTCGAAAATTTTATATACCTAGGTTC 12 155 1 AAATTTTAAT 0.738141 -61 ******** ** Masking position 8 Map Score: 28.1754 Number of sites scoring better than the average of aligned sites = 858 Number in coding regions = 601 Number in noncoding regions = 257 Number of orfs with sites within 600 bp upstream = 254 Fraction of orfs with sites within 600 bp upstream = 0.0407967 Motif number 6 AAAACCTTTTAAGTTTATGAGTGGATAAAGGAA 1 138 0 TTATTTAGTG 0.955252 -23 AAATTTCTATTTAGATTGATTATTGACAGTTATTA 3 22 1 TTATGTATTG 0.941893 -146 ATTGCTATAATTAATCTTTTTGGTGATAAGT 4 7 0 TTATTTGGTG 0.832992 -188 CAACTATTCTTTAATTTTTTGTATGGTGCCCCTAT 5 39 1 TTATTTTATG 0.724801 -262 ATTTACTTTTTTAAAGTTATAATTGTTTTATTATT 5 185 0 TTATTTATTG 0.962799 -116 TAACTTTGTGTTATATTTTTCAGTGCTATAAGTTT 6 64 0 TTATTTAGTG 0.955252 -237 AAATTACACGTTTATGTGGTTATTGAATGAAATTA 6 179 0 TTTTGTATTG 0.673163 -122 CTTAACTTAATTATAATTCTCAATGTATAATTTAA 7 197 0 TTATTTAATG 0.904531 -104 CTTTTTATTATTAGGATTTTCTTTGGGAATAAATA 7 261 0 TTATTTTTTG 0.877964 -40 GTCAATGGACTTACCCTTCTCATTGATACCTTGGA 13 129 0 TTATTTATTG 0.962799 -110 TTGAACTTTCTTAGATTGGTAATTGCCTCTGGTTT 13 165 1 TTATGTATTG 0.941893 -74 *** ** * **** Masking position 7 Map Score: 8.95621 Number of sites scoring better than the average of aligned sites = 140 Number in coding regions = 113 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 7 AACTAAGGTAATTAATAAAAATTAAGATTT 1 63 0 ATTAATAAAA 0.894807 -98 TACGGCTTCTATTATTTAAAGTTATTGTTT 1 92 1 ATTATTTAAA 0.807219 -69 GGATAAAGGAATTATTTAAAATTTATCAAA 1 119 0 ATTATTTAAA 0.807219 -42 TTTAAATGCCTTTAATAAAATATACAAACT 2 227 1 TTTAATAAAA 0.502806 -74 GTTCTATTACAATATAAAAATTTAAAAATT 2 263 1 AATATAAAAA 0.304723 -38 TTATAGCAATATTAATAAAAATACTTTCAC 4 32 1 ATTAATAAAA 0.894807 -163 CATATCAAAAATGATTAAAATACTCAACAA 4 90 1 ATGATTAAAA 0.835159 -105 TATATATATTATGATTTAAAGTTAAATAGT 5 115 1 ATGATTTAAA 0.543916 -186 TAATTGTTTTATTATTAAAAATTCTAATAA 5 171 0 ATTATTAAAA 0.94687 -130 CATAATCAATATTATTTAAACACGATTAAA 5 265 1 ATTATTTAAA 0.807219 -36 TTATTTAAACACGATTAAAATGCATTGGTG 5 276 1 ACGATTAAAA 0.693468 -25 CAGTTAATTTATTATAAAAAATACAATAAT 6 19 1 ATTATAAAAA 0.669653 -282 TAAAAAATACAATAATAAAACAGTTCTTAA 6 33 1 AATAATAAAA 0.647868 -268 CACAAAGTTAATAAATAAAAAGAATTACAA 6 89 1 ATAAATAAAA 0.378442 -212 TTAACAATTAACTATTAATAATATTTGATG 6 122 0 ACTATTAATA 0.475119 -179 CACCTTTTATACTATTAAAAACTATTTTAT 6 276 0 ACTATTAAAA 0.888376 -25 TTACAAAAAGTTTATTAAAAACTAATAAAA 7 90 1 TTTATTAAAA 0.680475 -211 TTTATTAAAAACTAATAAAATCTAAACGCC 7 100 1 ACTAATAAAA 0.791665 -201 GTCTGGAAATATTATTAATATTAATTAGGA 7 231 1 ATTATTAATA 0.66966 -70 AGAAAATCCTAATAATAAAAAGAAAATTGG 7 274 1 AATAATAAAA 0.647868 -27 AACTTTTTAACTTATTAAAACTTCATACCT 9 30 1 CTTATTAAAA 0.641845 -100 CGCAGAAACGATTATTAAAACTCAAGCCTA 9 90 1 ATTATTAAAA 0.94687 -40 ********** Masking position 4 Map Score: 24.6096 Number of sites scoring better than the average of aligned sites = 688 Number in coding regions = 500 Number in noncoding regions = 188 Number of orfs with sites within 600 bp upstream = 181 Fraction of orfs with sites within 600 bp upstream = 0.0290716 Motif number 8 TAACGTTGAGTATTGTGGGAATATATAAAAAGAATA 2 30 0 TTTGGAATAT 0.941141 -271 GTTATTAATTTGATGTTGAAGTATTTATATCTAATC 2 123 1 TTTGAAATTT 0.81643 -178 ACAATGGAACTTTCGTAGGAATAAATGTTCTATGGA 2 172 1 TCTGGAAAAT 0.685233 -129 GGAATAAATGTTCTATGGAATAATAATGCCTTTAGG 2 189 1 TTTGAAATAA 0.698549 -112 TTATTGCTTATAGTTTTGGAGTATATATAACTCACC 3 77 0 TTTGGAATAT 0.941141 -91 ACGTTTATGTGGTTATTGAATGAAATTAAATAAATA 6 171 0 GTTGAAAAAT 0.904662 -130 TATTAGGATTTTCTTTGGGAATAAATATCCTAATTA 7 252 0 TTTGGAAAAT 0.932443 -49 ATAATACTAAGATTTTCGAAAAAAATTGTGAACATT 12 63 0 GTTGAAAAAT 0.904662 -153 AATCTTAGTATTATATAGAAAAATTTTCTAAAATTT 12 85 1 TTTGAAATTT 0.816429 -131 AAATATCTTGGATTATCGAATAAAATTTTAAGATCT 12 124 0 GTTGAAAAAT 0.904662 -92 GGGTGATGAATATTAAGGAAGGAAATA 12 199 1 TTAGAAAAAT 0.666699 -17 TTTTTAAATCTGCTATGGAAGTATATAGCATGAACT 13 31 1 TTTGAAATAT 0.956093 -208 TCATACCCCCTCCTTTTGAATTCTATCTCAAGAAAC 15 40 0 TTTGAACTAT 0.774496 -26 * * * *** **** Masking position 10 Map Score: 5.90961 Number of sites scoring better than the average of aligned sites = 173 Number in coding regions = 151 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 9 AAAACCTTTTAAGTTTATGAGTGGATAAAGG 1 140 0 AAGTTTATAG 0.740186 -21 TTTACAATGGAACTTTCGTAGGAATAAATGT 2 169 1 AACTTTCGAG 0.981982 -132 ATTGTAATAGAACTTTCGCAGTTTGTATATT 2 245 0 AACTTTCGAG 0.981982 -56 TTATTGCTTATAGTTTTGGAGTATATATAAC 3 82 0 TAGTTTTGAG 0.792668 -86 ATAAGTTAAAAAGTTTCGGAGGGGATTGAGT 9 14 0 AAGTTTCGAG 0.981982 -116 TTTAATTTTTAATTTTTGGAGGGAGGTGA 10 16 1 AATTTTTGAG 0.822539 -19 ATTGACGTTGAACTTTCTTAGATTGGTAATT 13 158 1 AACTTTCTAG 0.936977 -81 ******** ** Masking position 2 Map Score: 1.63805 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 41 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 10 ********** No masking Map Score: -5.88086e-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 11 ********** No masking Map Score: -5.88086e-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 12 ********** No masking Map Score: -5.88086e-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