AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -icrp_pyro_opreg_300.orf -g0.419 -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 = 0.419 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 PH0024 36 284aa long hypothetical sugar transport membrane protein #2 PH0025 169 426aa long hypothetical protein #3 PH0124 300 437aa long hypothetical protein #4 PH0194 60 375aa long hypothetical multiple sugar-binding transport ATP-binding protein #5 PH0206 132 544aa long hypothetical protein #6 PH0207 206 428aa long hypothetical protein #7 PH0209 300 131aa long hypothetical protein #8 PH0365 54 327aa long hypothetical galactose-1-phosphate uridyltransferase #9 PH0369 92 350aa long hypothetical galactokinase #10 PH0378 56 318aa long hypothetical UDP-glucose 4-epimerase #11 PH0857 300 394aa long hypothetical threonine synthase #12 PH0864 300 208aa long hypothetical transcription initiation factor IIB #13 PH1332 300 155aa long hypothetical protein #14 PH1337 300 197aa long hypothetical protein #15 PH1338 26 202aa long hypothetical protein #16 PH1340 58 120aa long hypothetical protein #17 PH1361 274 537aa long hypothetical proline permease #18 PH1363 211 493aa long hypothetical protein #19 PH1463 40 438aa long hypothetical L-asparaginase #20 PH1497 109 197aa long hypothetical protein #21 PH1598 94 503aa long hypothetical pyrimidine-nucleoside phosphorylase #22 PH1742 55 306aa long hypothetical UDP-glucose 4-epimerase #23 PH1952 30 263aa long hypothetical protein #24 PH1953 110 705aa long hypothetical phosphoribosylformylglycinamidine synthase II Motif number 1 GGCAAAAACAGAAAAATAAATAAAGATTTAGGGCA 2 121 1 GAAAAATAAG 0.81734 -49 GACGAATTAAGAAAGTACACTAAAATTGAAAAGTC 5 90 0 GAAAGTTAAA 0.701247 -43 ATTATTTCAAGAAAGGAAATATAAAT 6 2 0 GAAAGGAAAA 0.87812 -205 AAGTACATTGGAAAAGTTGATGAAATTGTAATTGA 7 156 1 GAAAAGTAAA 0.945069 -145 GCACTACCAGGAGAAAGGGTTGGAGTTCCTTACGA 7 225 1 GAGAAATGAG 0.818515 -76 TCACATTGTCGAAAATTTTATTAAGTTTTTGACTA 9 24 0 GAAAATTAAG 0.701247 -69 TAGAAGGAAAGAAAAATTCCTGGAAACTCATCGTT 11 69 1 GAAAAATGAA 0.845678 -232 ACTTGTCTTGGAGAAAGGTCATGAAAGACGTCTTT 11 219 1 GAGAAAAGAA 0.73756 -82 AATTGACCAAGAAAAGTTAATGGAGGGTGCAAA 11 278 1 GAAAAGTGAG 0.934036 -23 ATTTTTTAGAGAAAGGTATTTAAAGTTTACCTTCC 12 93 1 GAAAGGTAAG 0.920396 -208 TCTATTTAAAGAAAAACTATTAGAAAGCTCAATAA 13 75 0 GAAAAATGAA 0.845678 -226 TCCACTCGACGAGAAGGAGATTGAACTTCTATTTA 13 102 0 GAGAAGTGAA 0.945477 -199 TCGTCGAGTGGAGAAGTCATTAAAAATTCTCCTCT 13 125 1 GAGAAGTAAA 0.945273 -176 CGATCCCAGGGAAAGGGAAGTCGAAGTTGTCACGT 14 114 1 GAAAGGTGAA 0.934036 -187 AGAGATATGCGAGAGAATTTATGAAAGCAAAGGAA 14 203 1 GAGAGAAGAA 0.697328 -98 ATGAAAAAGAGAGAATTACTTAAAGGTTTACCAGA 14 247 1 GAGAATTAAG 0.702073 -54 AGTTCCGATAGAAAAGAGTGAGAAAATAAAGGTTG 18 47 1 GAAAAGAAAA 0.897841 -165 AAAATGTTAAGAGAGGGGATATAAACC 19 3 0 GAGAGGAAAA 0.878541 -38 TTGGTTAATTGAGAAGATTTAAAAGACTTATGGTG 20 47 1 GAGAAGAAAG 0.878541 -63 TTATGGTGAAGAAAAGTATTTTAAATCGCCTGAAA 20 74 1 GAAAAGTAAA 0.945069 -36 TTGAAGAAGCGAAAGGAGGAATAAAAGG 23 4 0 GAAAGGAAAA 0.87812 -27 ****** * *** Masking position 4 Map Score: 20.4887 Number of sites scoring better than the average of aligned sites = 1080 Number in coding regions = 1001 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 2 TTTCTCTATTTCTTTTTTATCTGGG 1 2 1 TCTCTTCTTT 0.808448 -35 AGATCCCTTATGCCCTAAATCTTTATTTATTTTT 2 132 0 TCCCTTCTTT 0.973218 -38 TATATCAGCTTCCCGTACATCTTTGATAATTCCA 7 109 0 TCCGTTCTTT 0.86717 -192 TATCCCTTAACCCACTAGACCTTACAGTTATATA 10 30 0 CCACTCCTTA 0.588354 -27 CCTGGAAACTCATCGTTCCTCCTTATTCAGGAGA 11 87 1 CTCGTTCCTT 0.557468 -214 AGTCCTAAATCACCCTTCTTCCTACTTCATTCTT 11 179 0 CCCCTTCCTA 0.955947 -122 ATCCGAAGTTCCCTTACTCCTAAACTTAGGGG 12 279 0 TCCCTTCCTA 0.938919 -22 TCCAGGATCCTTCCCTTTACCCTAATCTCTCCAT 13 197 1 TCCCTCCCTA 0.926606 -104 GCATCGAATATCTCCTTAGCCTTTAAAACCTCGG 14 23 0 TTCCTCCTTT 0.832413 -278 ATATCTGCTTTCCCCTAATCCTTTGGGATAGCTC 14 64 0 TCCCTCCTTT 0.967581 -237 TTTTTCATTTCTCCCTCTTCCTTTGCTTTCATAA 14 221 0 CCCCTCCTTT 0.976816 -80 CATATAAATACCCCCTAAATCTTTATATACTATA 17 45 1 CCCCTTCTTT 0.980879 -230 GCAACCTTTATTTTCTCACTCTTTTCTATCGGAA 18 49 0 TTTCTTCTTT 0.412593 -163 TACTTTTCTTCACCATAAGTCTTTTAAATCTTCT 20 58 0 CCCATTCTTT 0.771627 -52 GTCAATCACTCACCCTAAATCCTATCAACTGAAA 24 16 0 CCCCTTCCTA 0.955947 -95 * **** ***** Masking position 6 Map Score: 12.3939 Number of sites scoring better than the average of aligned sites = 551 Number in coding regions = 512 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 3 TGTATCTTCCTAAAATTCAAATCTATTATGT 2 38 1 TAAAATTAAA 0.949186 -132 TACTACAATGTAAACATGAAATGCACAGCAT 3 25 1 TAAACATAAA 0.88878 -276 ATGCATGTCCAAAAAATGAAAAATATCTCAT 3 114 0 AAAAAATAAA 0.775 -187 CTCTTCTTAAAAATAAAATTGCATGAGA 4 43 0 TAAAAATAAA 0.906438 -18 GAAAGTACACTAAAATTGAAAAGTCCAATGT 5 84 0 TAAAATTAAA 0.949186 -49 TTTACAAAAGTAAACATGAAAATCAGGAAAT 6 150 1 TAAACATAAA 0.88878 -57 TATGAACTAGTAAATTTAAAAGTATTAGTAG 7 51 0 TAAATTTAAA 0.907395 -250 CCTTGAAGTTTAAATTTCAAATTTTTTAGAG 12 73 1 TAAATTTAAA 0.907395 -228 ACTTGGAAGGTAAACTTTAAATACCTTTCTC 12 101 0 TAAACTTAAA 0.939053 -200 TCACCTCCAATAAATTTCAAAATGTAAATAT 17 85 0 TAAATTTAAA 0.907395 -190 CCCTCCAAAAATTGAAACAAATTCAAC 18 195 0 AAAAATTAAA 0.86913 -17 AATAAATCTTAAAAATTTAAAATTTTTACAT 24 63 1 AAAAATTAAA 0.86913 -48 ******* *** Masking position 4 Map Score: 12.2492 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 43 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 4 AGCTACATAATTTTCCAGGAGAAGCAGGGGAT 3 66 0 TTTTCCGGGA 0.978944 -235 AGCAATGTTTTTCCAGGAAATGTTTTTAGT 4 9 1 TTTTCCGGAA 0.938277 -52 CCAATGTAAGTTATTCGGGGTATTTAAAAAGT 5 59 0 TTATTCGGTA 0.791787 -74 TCGTTCCTCCTTATTCAGGAGATGTTATGAAG 11 99 1 TTATTCGGGA 0.967016 -202 AAATTGTGGATTTTCCTGGGAAACAAAGGTTA 13 30 0 TTTTCCGGAA 0.938419 -271 GGGAAAGCAGATATTCAGGGGATTCTACCCCG 14 84 1 ATATTCGGGA 0.929948 -217 TTGAGGATATATATCCCGGTGAGGTAG 14 284 1 ATATCCGGGA 0.934991 -17 TCTCTTAACATTTTTCTGGGGGTATTC 19 24 1 TTTTTCGGGG 0.899511 -17 CTTTCCTAAATTTTCAGGCGATTTAAAATAC 20 89 0 ATTTTCGGGA 0.951065 -21 AATTTTTACATTTTTCTGGCAAATAAGGAGGT 24 83 1 TTTTTCGGAA 0.933631 -28 ****** ** ** Masking position 4 Map Score: 9.90361 Number of sites scoring better than the average of aligned sites = 45 Number in coding regions = 35 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 5 TTATGCCCTAAATCTTTATTTATTTTTCTGT 2 128 0 AATCTTTTTT 0.841506 -42 AACAGTTTTTATCCTTTATTTGACAAATGCA 3 140 0 ATCCTTTTTT 0.895299 -161 GAAATGCCGAAACATTTATATTTAATTGACG 6 176 1 AACATTTTAT 0.757895 -31 CAAGTATTAGAACCTTTCCTTCGCCCTCCTT 7 195 0 AACCTTTCTT 0.929711 -106 CAGCGTATCTATCCTTTTTATAGTGAGGGAG 11 21 1 ATCCTTTTAT 0.834484 -280 TTCTAGAGCGAACCTTAGTATACTCCCTCAC 11 43 0 AACCTTATAT 0.720799 -258 CTAGGGTTAGAACATTTTCTTCTCCCCCTAA 12 255 1 AACATTTCTT 0.670807 -46 TAATCCTTCTAACCTTTGTTTCCCAGGAAAA 13 21 1 AACCTTTTTT 0.9718 -280 ATACCCCCTAAATCTTTATATACTATAAGTC 17 52 1 AATCTTTTAT 0.757895 -223 TTGCCCTTGCAACCTTTATTTTCTCACTCTT 18 60 0 AACCTTTTTT 0.971802 -152 GGCCTTCTTTAACCTTTTTTTGCTAACCTAA 18 132 1 AACCTTTTTT 0.971801 -80 ******* *** Masking position 1 Map Score: 8.93947 Number of sites scoring better than the average of aligned sites = 136 Number in coding regions = 118 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 6 TTTCTTTTTTATCTGGGAGGGCGTTAAA 1 19 1 ATCGGGAGGG 0.978573 -18 TGTAATTGACATCAAGGAGGGCGAAGGAAAG 7 182 1 ATCAGGAGGG 0.937374 -119 ACATAGCACTTTAAAGGAGGATAGTAGGTTG 11 132 1 TTAAGGAGGA 0.709026 -169 CCAAGAAAAGTTAATGGAGGGTGCAAA 11 284 1 TTATGGAGGG 0.968648 -17 ATATTATATATACTTGGAAGGTAAACTTTAA 12 112 0 TACTGGAAGG 0.828205 -189 AAAGGGAAGGATCCTGGAGGAACCAACGTCA 13 184 0 ATCTGGAGGA 0.752358 -117 GAGATTAGGGTAAAGGGAAGGATCCTGGAGG 13 195 0 TAAGGGAAGG 0.831423 -106 ATTTTGAAATTTATTGGAGGTGACTTAGATG 17 93 1 TTATGGAGGT 0.689136 -182 GGGACAAAATTACGGGGAAGGAGTACTATGT 17 203 1 TACGGGAAGG 0.901664 -72 TGAAGAGCTTACCAAGGAGGGTAGAGC 17 258 1 ACCAGGAGGG 0.757371 -17 TTTGTTTCAATTTTTGGAGGG 18 201 1 TTTTGGAGGG 0.865124 -11 CAGAAAAATGTTAAGAGAGGGGATATAAACC 19 11 0 TTAGAGAGGG 0.781518 -30 GAACGATGACTAAAGGGAGGGATGG 20 5 0 TAAGGGAGGG 0.964544 -105 TTTAAACGATTTCGGGGAGGGTA 22 3 0 TTCGGGAGGG 0.99093 -53 *** ******* Masking position 8 Map Score: 11.5851 Number of sites scoring better than the average of aligned sites = 450 Number in coding regions = 402 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 7 TGTTATCTGTTTTTAATGTAAATTAGGCATTAGT 2 75 1 TTTAGAAATT 0.686366 -95 TTCCAATGTTTCCTATGGAAAATTTGACAATAAC 3 200 1 TCTTGAAATT 0.970592 -101 GTTTTTAGTCTTCTCATGCAATTTTATTTTTAAG 4 32 1 TCTAGAATTT 0.796255 -29 ATTTTACCTATTCTGAGAGAAATTAATATCTAAC 5 19 1 TCTAAAAATT 0.910749 -114 TTTTCATGTTTACTTTTGTAAAGTTGTAGGTTAC 6 138 0 TCTTGAAAGT 0.861392 -69 TAAGGAGCCTTGCTTATAAAAATTTGCTACTAAT 7 25 1 TCTAAAAATT 0.910748 -276 TTAAATACCTTTCTCTAAAAAATTTGAAATTTAA 12 82 0 TCTTAAAATT 0.923816 -219 GTGAATACTGTCCTTAAGAAAATTAAAGATGGAG 13 225 0 TCTAGAAATT 0.965247 -76 TCTATGCTTTTACTCTCGTAAATTCCGCTAAGCA 14 149 0 TCTTGAAATT 0.970591 -152 CCTCTTCCTTTGCTTTCATAAATTCTCTCGCATA 14 208 0 TCTTAAAATT 0.923814 -93 TCTCACTCTTTTCTATCGGAACTTTTTTAAAGAG 18 36 0 TCTTGAACTT 0.873146 -176 * ** * * ***** Masking position 10 Map Score: 7.83682 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 42 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 8 TAATTCGTCCTCTAAGGGGGGTGAAAG 5 116 1 TCTAAGGGGG 0.800433 -17 ACATCTCCTGAATAAGGAGGAACGATGAGT 11 94 0 AATAAGGAGG 0.919891 -207 AAGTATATATAATATGGGGGATCCAAGATT 12 128 1 AATATGGGGG 0.891369 -173 CAAAGGATTTAATTACGTGGCCGCACTCTG 12 222 0 AATTACGTGG 0.718257 -79 TTACTCCTAAACTTAGGGGGAGAAGAAAAT 12 268 0 ACTTAGGGGG 0.976598 -33 AAATATCATAAATTAGGGGGTGAAAACTAT 17 11 0 AATTAGGGGG 0.988423 -264 GTATATAAAGATTTAGGGGGTATTTATATG 17 45 0 ATTTAGGGGG 0.93865 -230 TTTGGGACAAAATTACGGGGAAGGAGTACT 17 200 1 AATTACGGGG 0.958035 -75 AATTTTTAATAATTAGGGGCCCCAT 22 41 1 AATTAGGGGC 0.917048 -15 TTTTCTGGCAAATAAGGAGGTGTCACG 24 94 1 AATAAGGAGG 0.919891 -17 ********** Masking position 3 Map Score: 10.2087 Number of sites scoring better than the average of aligned sites = 93 Number in coding regions = 78 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 9 AGATATTTTTCATTTTTTGGACATGCATTTGTC 3 117 1 CATTTTGGCA 0.628829 -184 CAGTTTTTATCCTTTATTTGACAAATGCATGTC 3 136 0 CCTTTTTGCA 0.964325 -165 ATTCCATAACCATTTAGTTCACCATTCCCTAAC 7 82 0 CATTTTTCCC 0.952312 -219 AGTATTAGAACCTTTCCTTCGCCCTCCTTGATG 7 191 0 CCTTTTTCCC 0.980489 -110 CCCTCCATTAACTTTTCTTGGTCAATTACCCGT 11 272 0 ACTTTTTGTC 0.64635 -29 AGGGTTAGAACATTTTCTTCTCCCCCTAAGTTT 12 257 1 CATTTTTCCC 0.952312 -44 ATCCTTCTAACCTTTGTTTCCCAGGAAAATCCA 13 23 1 CCTTTTTCCA 0.964325 -278 GCCCTTGCAACCTTTATTTTCTCACTCTTTTCT 18 56 0 CCTTTTTTTC 0.652012 -156 CCTTCTTTAACCTTTTTTTGCTAACCTAATGTT 18 134 1 CCTTTTTGTA 0.885973 -78 GATTTAAAATACTTTTCTTCACCATAAGTCTTT 20 68 0 ACTTTTTCCC 0.864099 -42 CCTTTTATTCCTCCTTTCGCTTC 23 1 1 CCTTTTTCTC 0.935254 -30 GAGTGATTGACATTTCTTTGTCAAAATAAATCT 24 39 1 CATTTTTGCA 0.914831 -72 AAAATTTTTACATTTTTCTGGCAAATAAGGAGG 24 81 1 CATTTCTGCA 0.628829 -30 ***** *** ** Masking position 5 Map Score: 8.35541 Number of sites scoring better than the average of aligned sites = 369 Number in coding regions = 335 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 10 TCAATGCTGTGCATTTCATGTTTACATTGT 3 29 0 GCATTTCATG 0.844222 -272 ATTGATCATTGCATCCCCTGCTTCTCCTGG 3 54 1 GCATCCCCTG 0.950576 -247 AAGACTAAAAACATTTCCTGGAAAAACATT 4 14 0 ACATTTCCTG 0.951594 -47 CTTAAAAATAAAATTGCATGAGAAGACTAA 4 36 0 AAATTGCATG 0.546842 -25 AAATGTTTCGGCATTTCCTGATTTTCATGT 6 163 0 GCATTTCCTG 0.969088 -44 GAAGGAAAGAAAAATTCCTGGAAACTCATC 11 71 1 AAAATTCCTG 0.634311 -230 GTTCTTCATAACATCTCCTGAATAAGGAGG 11 104 0 ACATCTCCTG 0.955153 -197 ACAAATTGTGGATTTTCCTGGGAAACAAAG 13 34 0 GATTTTCCTG 0.734475 -267 GATCGGGGTAGAATCCCCTGAATATCTGCT 14 89 0 GAATCCCCTG 0.923433 -212 AAAGTATTTTAAATCGCCTGAAAATTTAGG 20 86 1 AAATCGCCTG 0.883216 -24 ********** Masking position 9 Map Score: 4.39813 Number of sites scoring better than the average of aligned sites = 144 Number in coding regions = 131 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 11 GCATTGATCATTGCATCCCCTGCTTCTCCT 3 52 1 TTGCATCCCC 0.978611 -249 CTTTCACCCCCCTTAGAGGAC 5 122 0 TTTCACCCCC 0.96 -11 TTGGGCGGGTTATTACCCCCGCATCTTTTC 6 80 1 TATTACCCCC 0.80945 -127 TGGACTAAAATTATATCTCCAACTGCTGTA 7 266 0 TTATATCTCC 0.599506 -35 ATGTTCTTCATAACATCTCCTGAATAAGGA 11 106 0 TAACATCTCC 0.634239 -195 TTTGCACCCTCCATTAACTTT 11 290 0 TTGCACCCTC 0.812408 -11 ACACCTAATCTTGGATCCCCCATATTATAT 12 134 0 TTGGATCCCC 0.912967 -167 GGGATCGGGGTAGAATCCCCTGAATATCTG 14 91 0 TAGAATCCCC 0.762186 -210 ATAGTTTTCACCCCCTAATTTATGA 17 6 1 TTTCACCCCC 0.96 -269 GGTTTATATCCCCTCTCTTAACA 19 4 1 TTATATCCCC 0.896472 -37 ********** Masking position 5 Map Score: 4.57835 Number of sites scoring better than the average of aligned sites = 191 Number in coding regions = 163 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 12 TTTAATTTTCTTTTAATAGCACATTAAGAC 3 258 0 TTTTAATAGC 0.800989 -43 TTAAAAGAAAATTAAATAGCGATTAGTGTT 3 272 1 ATTAAATAGC 0.818485 -29 CGAAACACTTTTTAAATACCCCGAATAACT 5 53 1 TTTAAATACC 0.950889 -80 AGCAAGGCTCCTTAAATAGCCCCTTTGT 7 9 0 CTTAAATAGC 0.869845 -292 GAAGGTAAACTTTAAATACCTTTCTCTAAA 12 97 0 TTTAAATACC 0.950889 -204 ATAGTTTTTCTTTAAATAGAAGTTCAATCT 13 90 1 TTTAAATAGA 0.714207 -211 ATTTTTTTCATATAAATACCCCCTAAATCT 17 37 1 TATAAATACC 0.731501 -238 TCGGAACTTTTTTAAAGAGCTCCTTATGCA 18 25 0 TTTAAAGAGC 0.856432 -187 AGAAAAGTATTTTAAATCGCCTGAAAATTT 20 83 1 TTTAAATCGC 0.869845 -27 CCCGAAATCGTTTAAATGCCTCAAATTTTT 22 18 1 TTTAAATGCC 0.818966 -38 ********** Masking position 5 Map Score: 4.15548 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 33 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 13 GTTTTGTTTTCAAAGGCAAAAACAGAAAAAT 2 107 1 CAAGGCAAAA 0.94815 -63 AATAACGTTCCAATTTCAAAAGCTGTTCATG 3 228 1 CAATTCAAAA 0.950102 -73 AATGATGCCTCAAATGTAAAATATCTAGAAA 6 106 0 CAATGTAAAA 0.785752 -101 TTACCCGTCCCAACTTCAAAACTCCCAAAGA 11 249 0 CAATTCAAAA 0.950102 -52 AATATCGTGATAACTGCAAAGAGATATGCGA 14 184 1 TAATGCAAAG 0.67127 -117 CACCTCCAATAAATTTCAAAATGTAAATATT 17 84 0 AAATTCAAAA 0.680134 -191 ATAAAGGTTGCAAGGGCAAAGAGCCAAGCTG 18 72 1 CAAGGCAAAG 0.89938 -140 AGGCCGGAAGCAATTGCAAAATCAAAGACGT 18 106 0 CAATGCAAAA 0.973965 -106 AAAATTGAAACAAATTCAACATTACCTATGT 18 184 0 CAATTCAACA 0.816474 -28 *** ******* Masking position 8 Map Score: 2.62436 Number of sites scoring better than the average of aligned sites = 71 Number in coding regions = 64 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 14 TAGGAAGATACATTTTTAATTGGTAAATTT 2 20 0 CATTTTTAAT 0.626538 -150 GCTTCCCGTACATCTTTGATAATTCCATAA 7 106 0 CATCTTTGAT 0.94192 -195 TTACGACCACCTTTAATATACTTTGAA 8 8 1 CACCTTTAAT 0.799611 -47 CCTGGAAACTCATCGTTCCTCCTTATTCAG 11 87 1 CATCGTTCCT 0.780365 -214 CTCCCAAAGACGTCTTTCATGACCTTTCTC 11 229 0 CGTCTTTCAT 0.930445 -72 CTAATCTCTCCATCTTTAATTTTCTTAAGG 13 218 1 CATCTTTAAT 0.937591 -83 AAGCTGAAAACGTCTTTGATTTTGCAATTG 18 97 1 CGTCTTTGAT 0.901803 -115 TCCCTTTAGTCATCGTTCATCTGTCGAGCT 20 18 1 CATCGTTCAT 0.930445 -92 ********** Masking position 6 Map Score: 0.645839 Number of sites scoring better than the average of aligned sites = 91 Number in coding regions = 85 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 15 GCGATTAGTGTTATATTTCCA 3 290 1 TTATATTTCC 0.890661 -11 ATTTATATTTCCTTTCTTGAAA 6 3 1 TTATATTTCC 0.890661 -204 CGTACATCTTTGATAATTCCATAACCATTT 7 100 0 TGATAATTCC 0.7612 -201 TGGACTAAAATTATATCTCCAACTGCTGTA 7 266 0 TTATATCTCC 0.799272 -35 GATAGTAGGTTGCTAGTTCCTGATTTCCAA 11 151 1 TGCTAGTTCC 0.95539 -150 TAAATAGAAGTTCAATCTCCTTCTCGTCGA 13 102 1 TTCAATCTCC 0.728934 -199 GCCTCATGTATTCAAGTTCCAGTGACGTTG 13 162 1 TTCAAGTTCC 0.897185 -139 AATATCTCGTTGAAAGTTTCTACTTCG 13 284 1 TGAAAGTTTC 0.461049 -17 TGGGCCACGCTGCTAGTTCCAACGATTCTT 17 142 1 TGCTAGTTCC 0.95539 -133 ********** Masking position 5 Map Score: 0.545313 Number of sites scoring better than the average of aligned sites = 264 Number in coding regions = 240 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542