AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_synecho.txt -z/skink1/amcguire/genomes/synecho.fna -inarL_synecho_opreg_300.orf -g0.48 -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 = 0.48 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 ccsA 186 c-type cytochrome synthesis protein #2 1652073 254 hypothetical protein #3 narB 300 nitrate reductase #4 1652597 300 hypothetical protein #5 frdA 175 succinate dehydrogenase flavoprotein subunit #6 sdhB 293 succinate dehydrogenase iron- sulphur protein subunit #7 1652855 163 ABC transporter #8 1653267 249 hypothetical protein #9 1653591 298 hypothetical protein #10 1001440 300 beta transducin-like protein #11 1001143 47 hypothetical protein #12 1001144 160 hypothetical protein #13 1001145 74 hypothetical protein #14 1001146 273 hypothetical protein #15 cysG 195 uroporphyrin-III C-methyltransferase #16 mfd 147 transcription-repair coupling factor #17 1001662 300 hypothetical protein #18 sdhB 166 succinate dehydrogenase iron-sulfur protein #19 1673322 163 hypothetical protein #20 1001796 300 hypothetical protein Motif number 1 CTCAACGATTTTTGCCCTGGGGTCGGTCCCCC 1 17 1 TTCCCTGGGG 0.990605 -170 ATTTACTCATTTTCCCCAGTTGGTGGAATGGA 2 95 0 TTCCCAGTTG 0.828455 -160 TTGATGTTTTTTAACCCTGGCCATGGATGGAG 2 159 0 TTCCCTGGCC 0.988813 -96 GTTTCCCCACTTTACCTTGGGGGCTAAATTTC 2 209 0 TTCCTTGGGG 0.948391 -46 CAGTTTTTCCTTATTCCAGGTGCCATCAATAA 3 112 0 TTTCCAGGTG 0.767761 -189 GAAAAACTGATTTTTCCTGGCGAACAGTTATT 3 135 1 TTTCCTGGCG 0.943095 -166 TAATAGTTAATTTGTCCTGAGGGCTAGCCCAA 3 170 0 TTTCCTGAGG 0.631379 -131 ACCATTGACTTTCACCTTGCCCATCTGGCTAA 4 179 0 TTCCTTGCCC 0.840346 -122 ATGACTACTTTTCACCCAGTCCTAGAGCATA 6 10 0 TTCCCAGTCC 0.890108 -284 AATCATTCGCTGCCCCCTGGGCATTAACCCAT 6 55 1 TGCCCTGGGC 0.930121 -239 CCCATATTGCTTTTCCCAGGGTATTTCCT 6 275 1 TTCCCAGGGT 0.682265 -19 AGGCCGGACCATTTTCCTGCCCTAATCCAGAG 7 62 1 ATTCCTGCCC 0.48272 -102 AAATTTGAAGTTATTCTTGTGGCTATCATGGG 8 34 0 TTTCTTGTGG 0.449169 -216 TTTACTTCAGATTTCCCTGCCCTAGGCGATTG 8 160 0 ATCCCTGCCC 0.842627 -90 CCAAGTTTTCTTTCCCCTGGGGAGAGTGTTGG 8 215 1 TTCCCTGGGG 0.990605 -35 ACGGTAAGCCTTATCCCAGGGCCGCTGGAACT 9 55 1 TTCCCAGGGC 0.972433 -244 TCGAATAGGCTTTTCCCTGCCCATAATTGTAC 10 266 1 TTCCCTGCCC 0.967949 -35 CAGTTCTGGGTGCCCCCAGTCCACTGCC 11 7 0 TGCCCAGTCC 0.523817 -41 GTGGGGCCCATTGGCCCTGGTGAACAGTGACA 12 17 1 TTCCCTGGTG 0.981378 -144 AATACAATGATTAGCCCTGATGACCTTAAAAT 14 36 0 TTCCCTGATG 0.830855 -238 TAAAAATTAGTTTGCCTTGGACTTAACTTATC 14 242 0 TTCCTTGGAC 0.573726 -32 AGGAAAACTTTTGCCCTTGTTCAGTTATCAAA 16 96 0 TTCCTTGTTC 0.684915 -52 AGGGCAAAAGTTTTCCTAGGGGTCGACCTTAC 16 111 1 TTCCTAGGGG 0.868665 -37 CATGTATCAGATCTCCCTGCTGGAATCCTGTT 17 36 1 ATCCCTGCTG 0.761475 -265 GCAATAATTTTTATTCCTGGTCCCGGCAAAAT 18 85 0 TTTCCTGGTC 0.895154 -82 ATAAAAATTATTGCCCCCGGCCCTTCCGTAAT 18 103 1 TTCCCCGGCC 0.894178 -64 TCGAGCCTTTTTTGCCCTGTTGATTTCCTCAT 18 142 1 TTCCCTGTTG 0.930641 -25 TTGCCTAGCAATAACCCTGGGGCAATTCTGAT 20 207 1 ATCCCTGGGG 0.949222 -94 ** ******** Masking position 6 Map Score: 34.8546 Number of sites scoring better than the average of aligned sites = 3647 Number in coding regions = 3329 Number in noncoding regions = 318 Number of orfs with sites within 600 bp upstream = 348 Fraction of orfs with sites within 600 bp upstream = 0.0558946 Motif number 2 AATGGAAATCGCCCTTCTCCCCTAGATGGAGAGAAAGGGA 2 61 0 GCCTCCCAGA 0.910033 -194 CCCAAATTTACTCATTTTCCCCAGTTGGTGGAATGGAAAT 2 92 0 CTCTCCCGTG 0.787259 -163 GGCTAAATTTCCCGGTAAACCCAGGCAGTTTGATGTTTTT 2 180 0 CCCTCCCGTT 0.978931 -75 GTTAAAGTTAACCTTCATGGCCAAGGCTGGTTGGAAGTAA 4 28 0 ACCCGCCAGG 0.419474 -273 ATCCCTAGGGGCCTGCCTTCCCTAATGCTGAATCATTTTT 5 116 0 GCCCCCCATG 0.975277 -60 CTAGAATTGTGCCTATTTTCCCAAGTCTTTGACACCATTG 6 174 0 GCCTCCCATT 0.966458 -120 TGTACCTAAACCCACCAAGGCCGGACCATTTTCCTGCCCT 7 45 1 CCCCGCCGTT 0.809321 -119 AAAGTCCATTGCCCATCGACCCACATTTGGCTCGGTAACC 7 101 1 GCCTCCCCGG 0.94076 -63 ACTCGGCGATCGCCCTAGCCCCAGCATCGTACTGAAATTG 9 191 1 CGCTCCCGGT 0.728194 -108 GTGATTTAGTCCCCCCTATCCCCGTCCCTGGCAGTGTCAA 10 109 1 CCCCCCCGTG 0.984524 -192 GTTCACCAGGGCCAATGGGCCCCACCCAGGG 12 2 0 GCCTCCCAGG 0.978642 -159 ACCCAAACTAGCCCATATCCCCAATCGTTACAATCCTCTA 14 99 1 GCCTCCCATA 0.919851 -175 TTATTCCGCCCCCTAAATTCCCCAATAATGGGGGACTTTC 15 69 1 CCCACCCATG 0.864249 -127 TTTTAAAAGCCCCTCTGGCCCCTCAAATTAGGAGGAATAC 15 114 0 CCCTCCCCTA 0.831899 -82 GGCCAATCATCCCTAGTAAGGTCGACCCCTA 16 127 0 GCCTCCCAGG 0.978642 -21 TTGGTCAACCACCAACTCTCCCGACCCTTTGCCAAGACTG 17 119 0 ACCCCCCATT 0.790772 -182 ATTAGTCTTACCCCCCAGACCCCAAGCAGTTACCTTACCA 17 186 1 CCCCCCCAGT 0.95996 -115 ACGATCCTTGGCCAATAGCCCCAGTGGTTGACTTGGTGAT 17 247 1 GCCTCCCGTG 0.985376 -54 AAATTTTATCCCCATTAGTCCCAGCAAATTAGCC 18 5 0 CCCTCCCGTT 0.978931 -162 GAAGGTCGAGCCTTTTTTGCCCTGTTGATTTCCTCATACC 18 137 1 CCTTCCCGTT 0.660329 -30 *** * *** * ** Masking position 11 Map Score: 25.1857 Number of sites scoring better than the average of aligned sites = 1915 Number in coding regions = 1641 Number in noncoding regions = 274 Number of orfs with sites within 600 bp upstream = 194 Fraction of orfs with sites within 600 bp upstream = 0.0311597 Motif number 3 ATGCCAGACTGGCGATCGCCGTTGCCGGAA 1 105 1 GGCGATCGCC 0.499944 -82 TTGGTGGAATGGAAATCGCCCTTCTCCCCT 2 78 0 GGAAATCGCC 0.90274 -177 AAAAAAATTGATCAATCACCAAAAATGATT 5 96 1 ATCAATCACC 0.86204 -80 GGATTTTAGGGGCGATCGCCTTGGGAATTT 6 119 1 GGCGATCGCC 0.499944 -175 TCTCAACTAAATCAATCGCCTAGGGCAGGG 8 148 1 ATCAATCGCC 0.944039 -102 TGCTCAACTCGGCGATCGCCCTAGCCCCAG 9 185 1 GGCGATCGCC 0.499944 -114 ATAGGGGGGACTAAATCACCACTAATAACC 10 98 0 CTAAATCACC 0.684453 -203 CCAAAAATGGCTCAATCGCCATG 17 4 0 CTCAATCGCC 0.974124 -297 AAATTCTTTGGTCAACCACCAACTCTCCCG 17 136 0 GTCAACCACC 0.837254 -165 TCTGATCAATCTCAATCACCGAAAACTTGA 19 144 1 CTCAATCACC 0.933677 -20 ATGAGATTATGGCGATCGCCGGAGTAATTC 20 26 1 GGCGATCGCC 0.499944 -275 ********** Masking position 5 Map Score: 16.7476 Number of sites scoring better than the average of aligned sites = 6615 Number in coding regions = 6006 Number in noncoding regions = 609 Number of orfs with sites within 600 bp upstream = 395 Fraction of orfs with sites within 600 bp upstream = 0.0634436 Motif number 4 CCAAGCAAATGCCAGACTGGCGATCGCCGTT 1 97 1 GCCAGATGGC 0.718165 -90 TGCTACTATCGCAATAGTGGCAATAAATTAC 3 72 1 GCAATATGGC 0.915025 -229 AAGATACTTAGCCAGATGGGCAAGGTGAAAG 4 172 1 GCCAGAGGGC 0.960013 -129 CAAAGACTTGGGAAAATAGGCACAATTCTAG 6 183 1 GGAAAAAGGC 0.815 -111 CCTGGGAAAAGCAATATGGGCGGAGGCTACC 6 264 0 GCAATAGGGC 0.935326 -30 GATTAGGGCAGGAAAATGGTCCGGCCTTGGT 7 58 0 GGAAAAGGTC 0.671408 -106 GACAACGCTAGCAAAACTGTCACCGTTCAAT 9 149 1 GCAAAATGTC 0.90159 -150 AATTTGAGGGGCCAGAGGGGCTTTTAAAACA 15 125 1 GCCAGAGGGC 0.969424 -71 GATACATGGACCAAAAATGGCTCAATCGCCA 17 13 0 CCAAAATGGC 0.910417 -288 AATCCTGTTGGCAAAAAAGTCCCATCAAGGA 17 59 1 GCAAAAAGTC 0.862329 -242 CGACCCTTTGCCAAGACTGGCTAAGCATACC 17 107 0 CCAAGATGGC 0.911883 -194 AGTTACCTTACCAAAGAGGGCAGGGAGTTAT 17 213 1 CCAAAGGGGC 0.649239 -88 AATCAACAGGGCAAAAAAGGCTCGACCTTCC 18 136 0 GCAAAAAGGC 0.963646 -31 GTAGCAAGGAGCAAAAGAGTCAACCATTCCT 19 86 1 GCAAAAAGTC 0.862329 -78 TAAGCTATTTGCCAGAATGGTAGGGGATAAC 20 98 1 GCCAGATGGT 0.573898 -203 ****** **** Masking position 4 Map Score: 14.5684 Number of sites scoring better than the average of aligned sites = 759 Number in coding regions = 700 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 5 TCCTATAGCAGGAGAGATTGGAC 2 2 0 GGAGATTGGA 0.823666 -253 TCCCCTAGATGGAGAGAAAGGGAGTTAAGAAT 2 52 0 GGAGAAAGGG 0.966874 -203 GGTATTTCGCGGGTAGCCAGGGATAGATGTCC 4 90 1 GGAGCCAGGG 0.952 -211 ATTAACCCATGGAAAGTATGGAAAATACGGCT 6 77 1 GGAGTATGGA 0.911629 -217 TTATTCTTGTGGCTATCATGGGAGTAATTGCT 8 24 0 GGATCATGGG 0.897232 -226 GAAATGGCCGGGCTAGCAAAGGGCAGTTTGGT 9 98 0 GGAGCAAAGG 0.842713 -201 AGCGTTGTCTGGAGAGAATGGAGACAATGAAA 9 126 0 GGAGAATGGA 0.887922 -173 TAGAATGGAGGGTCAGTTCGGGGAATTAGCTC 12 132 0 GGAGTTCGGG 0.873339 -29 TGGGGATATGGGCTAGTTTGGGTGAGTACATG 14 90 0 GGAGTTTGGG 0.949641 -184 CCCATTATTGGGGAATTTAGGGGGCGGAATAA 15 69 0 GGATTTAGGG 0.756896 -127 AATATAAGCAGGGTAGCAAGGAGCAAAAGAGT 19 74 1 GGAGCAAGGA 0.960135 -90 GATCAGAATTGGTAAGCAAGGGAAGATTAGTC 19 119 0 GGAGCAAGGG 0.986785 -45 ** ******** Masking position 5 Map Score: 10.8361 Number of sites scoring better than the average of aligned sites = 589 Number in coding regions = 517 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 6 TTTGATTACTCCATCCATGGCCAGGGTTAAA 2 151 1 CATCCATGGC 0.940121 -104 TTACTTCCAACCAGCCTTGGCCATGAAGGTT 4 28 1 CAGCCTTGGC 0.876126 -273 CATCGGACATCTATCCCTGGCTACCCGCGAA 4 95 0 CATCCCTGGC 0.949899 -206 AGCAAAGGCAAAGTCCATTGCCCATCGACCC 7 92 1 AGTCCATTGC 0.757619 -72 TCAGATTTCCCTGCCCTAGGCGATTGATTTA 8 155 0 CGCCCTAGGC 0.971985 -95 ACTCACCAAACTGCCCTTTGCTAGCCCGGCC 9 94 1 CGCCCTTTGC 0.968599 -205 CCCCCTATCCCCGTCCCTGGCAGTGTCAACG 10 120 1 CGTCCCTGGC 0.981664 -181 ATAGCGAGGAAAGCCCTAGGCGTTAGCTTCA 10 172 0 AGCCCTAGGC 0.873534 -129 TGGGTGCCCCCAGTCCACTGCC 11 2 0 CGTCCACTGC 0.907693 -46 ACTCGAATCCCTGACCTCTGCGGTGCGATCG 12 85 1 CGACCTCTGC 0.749299 -76 ATGATAAGTTAAGTCCAAGGCAAACTAATTT 14 240 1 AGTCCAAGGC 0.778549 -34 CCAACTCTCCCGACCCTTTGCCAAGACTGGC 17 117 0 CACCCTTTGC 0.916135 -184 AGTTATGCTACGATCCTTGGCCAATAGCCCC 17 238 1 CATCCTTGGC 0.963806 -63 ATAAAAATTATTGCCCCCGGCCCTTCCGTAA 18 103 1 TGCCCCCGGC 0.753729 -64 * ********* Masking position 6 Map Score: 10.8267 Number of sites scoring better than the average of aligned sites = 1197 Number in coding regions = 1108 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 7 CAAACAGAGTTCTCAGCTATCAACCCAAATTTACTCATTT 2 115 0 TAGACACAAT 0.951575 -140 TTTGGTCAATTAGTGGTCAACTAATCAAATTCGCTTCAAT 3 254 1 TGGACACAAT 0.993441 -47 TGAAAAGTAGTCATGGTTACCCATCCAAATCATTCGCTGC 6 28 1 TGGACACAAT 0.993428 -266 GCTCTCCAATTCTAGGTTACCGAGCCAAATGTGGGTCGAT 7 115 0 TGGACACAAT 0.993442 -49 TGTAGTTGCGTGGAGGTGAGCAATACACTTAAGCTATTTT 8 78 0 TGGACACATT 0.969185 -172 AATTTCAGGGTGGAGGGAAGCTAAACAAATTCTGCAATTA 16 19 0 TGGACACAAT 0.993442 -129 GCCAGAATGGTAGGGGATAACAAATTAGATGGCACAATTA 20 108 1 TGGACATAAT 0.951575 -193 * ** * * * ** ** Masking position 9 Map Score: 4.92077 Number of sites scoring better than the average of aligned sites = 13 Number in coding regions = 9 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 8 TAGTGATAGCCCAAGCAAATGCCAGACTGGCG 1 87 1 CAACAAATGC 0.938458 -100 TAGTGGTCAACTAATCAAATTCGCTTCAATTA 3 264 1 CAACAAATTC 0.960548 -37 CCACCAAGGCCGGACCATTTTCCTGCCCTAAT 7 56 1 CGACATTTTC 0.709955 -108 TGCCCTAATCCAGAGCAAAGGCAAAGTCCATT 7 79 1 CGACAAAGGC 0.810165 -85 CAATGATTGGCAGATCAATTTCAGTACGATGC 9 214 0 CGACAATTTC 0.950652 -85 AAAGTTTTTACCAAACAAATTCGGGCGGCTTT 10 28 0 CAACAAATTC 0.960548 -273 TGAACAGTGACAAAACAATTGCACGATAGAGT 12 37 1 CAACAATTGC 0.899909 -124 GCTCTACCAACTGAGCTAATTCCCCGAACTGA 12 120 1 CGACTAATTC 0.805882 -41 TGGAGGGAAGCTAAACAAATTCTGCAATTAGA 16 17 0 CAACAAATTC 0.960548 -131 GCGGTGACCCACAATCAAATTCTTTGGTCAAC 17 150 0 AAACAAATTC 0.657345 -151 CTTACCAATTCTGATCAATCTCAATCACCGAA 19 135 1 CGACAATCTC 0.800699 -29 * ** ******* Masking position 4 Map Score: 6.58823 Number of sites scoring better than the average of aligned sites = 223 Number in coding regions = 188 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 9 CCTGGGGTCGGTCCCCCACTAGGATCAAAA 1 32 1 GTCCCCCACT 0.979523 -155 CATTGTTTTAGTCCACCATTGTAATTACCA 9 268 1 GTCCACCATT 0.96651 -31 TGGTGATTTAGTCCCCCCTATCCCCGTCCC 10 107 1 GTCCCCCCTA 0.88509 -194 CTGAGTGAAAGTCCCCCATTATTGGGGAAT 15 85 0 GTCCCCCATT 0.973791 -111 CCCTAGTAAGGTCGACCCCTAGGAAAACTT 16 118 0 GTCGACCCCT 0.828303 -30 AAATTCTTTGGTCAACCACCAACTCTCCCG 17 136 0 GTCAACCACC 0.817148 -165 TCATCACCAAGTCAACCACTGGGGCTATTG 17 259 0 GTCAACCACT 0.935582 -42 GTAGGAGGATGTCCCCCTTAAATTTTATCC 18 34 0 GTCCCCCTTA 0.738486 -133 GAGCAAAAGAGTCAACCATTCCTTCGACTA 19 94 1 GTCAACCATT 0.918574 -70 ********** Masking position 2 Map Score: 5.43266 Number of sites scoring better than the average of aligned sites = 279 Number in coding regions = 234 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 10 CTTGGGGGCTAAATTTCCCGGTAAACCCAG 2 196 0 AAATTTCCCG 0.956231 -59 AATCCAATCTAAATTAGCCGTATTTTCCAT 6 94 0 AAATTAGCCG 0.873876 -200 TTAAATACCAAATTTTCCCGATCTCAACTA 8 127 1 AATTTTCCCG 0.873478 -123 GTTTGGTAAAAACTTTGCCGCCTGGTTTGA 10 44 1 AACTTTGCCG 0.928971 -257 AGTTTTACAAAAATTTCCTGGCACAGTTGA 13 21 1 AAATTTCCTG 0.903132 -54 TTGCTGCGATTAATTTGCTGAAAGTTTCTT 13 50 0 TAATTTGCTG 0.853832 -25 AAAATGTTAAAAATTTGACGTGAATGACGT 15 19 1 AAATTTGACG 0.811395 -177 CTCCACCCTGAAATTTGCTAGGAGTTGGGA 16 44 1 AAATTTGCTA 0.647382 -104 GGCTAATTTGCTGGGACTAATGG 18 4 1 TAATTTGCTG 0.853832 -163 TGATCTATGGAATTTTGCCGGGACCAGGAA 18 74 1 AATTTTGCCG 0.939616 -93 ********** Masking position 5 Map Score: 4.69339 Number of sites scoring better than the average of aligned sites = 603 Number in coding regions = 533 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 11 CTGGCGATCGCCGTTGCCGGAAACTCAACA 1 113 1 CCGTTGCCGG 0.921622 -74 TCATTTTCCCCAGTTGGTGGAATGGAAATC 2 91 0 CAGTTGGTGG 0.972659 -164 GTCATGGATCGAGTTGCTAGGAGGTGAGAG 3 27 0 GAGTTGCTAG 0.820128 -274 GATTAAGACCCCGTTGCTGGCTTTTTTTGT 6 224 0 CCGTTGCTGG 0.982586 -70 AAATGGTCCGGCCTTGGTGGGTTTAGGTAC 7 46 0 GCCTTGGTGG 0.843113 -118 ATAAGGCTTACCGTCGGTGACATTTTTTTC 9 39 0 CCGTCGGTGA 0.750335 -260 ACCAAACTGCCCTTTGCTAGCCCGGCCATT 9 98 1 CCTTTGCTAG 0.70245 -201 TTTCCCTCCGTTGGTAATTACAATGGT 9 282 0 CCGTTGGTAA 0.860139 -17 GGAATTAGCTCAGTTGGTAGAGCGCTGCGA 12 113 0 CAGTTGGTAG 0.938203 -48 AGGGTCGGGAGAGTTGGTGGTTGACCAAAG 17 131 1 GAGTTGGTGG 0.940419 -170 ********** Masking position 4 Map Score: 4.57922 Number of sites scoring better than the average of aligned sites = 941 Number in coding regions = 879 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 12 ATTTAGATTGGATTTTAGGGGCGATCGCCTT 6 110 1 GATTTAGGGG 0.899891 -184 TCGCCTTGGGAATTTTAGTGGCAGGCTTAGT 6 134 1 AATTTAGTGG 0.928421 -160 AAATAGGCACAATTCTAGGGGGTTCTCGACA 6 196 1 AATTTAGGGG 0.98126 -98 CGTTAGCTTCAATTCTAGTGACAATATGTCA 10 152 0 AATTTAGTGA 0.741153 -149 CATGGGCAGGAATTAAAGTGATAAGAAATAC 14 63 0 AATTAAGTGA 0.628004 -211 ATTATTGGGGAATTTAGGGGGCGGAATAAAA 15 67 0 AATTAGGGGG 0.84127 -129 TATTCCTCCTAATTTGAGGGGCCAGAGGGGC 15 115 1 AATTGAGGGG 0.932922 -81 CCTTTGTAGAAATTATAGAGATAGAAAAATA 15 175 0 AATTTAGAGA 0.531221 -21 ATGGGGATAAAATTTAAGGGGGACATCCTCC 18 30 1 AATTAAGGGG 0.968626 -137 ATCAATGGGGAATTGTAGGAGGATGTCCCCC 18 47 0 AATTTAGGAG 0.78979 -120 ATAAATAGTTAATTTAATGGGATAGTTG 19 8 0 AATTAATGGG 0.688979 -156 TATTTGCCAGAATGGTAGGGGATAACAAATT 20 103 1 AATGTAGGGG 0.899891 -198 **** ****** Masking position 2 Map Score: 6.4701 Number of sites scoring better than the average of aligned sites = 442 Number in coding regions = 337 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 13 TAATTATTGATGGCACCTGGAATAAGGAAAAA 3 109 1 TGCACCTGGA 0.709906 -192 CCCAAGTCTTTGACACCATTGAGCAACATCAC 6 163 0 TGCACCATTA 0.893372 -131 CGCAACTACATGTAACCGGTTAAATACCAAAT 8 108 1 TGAACCGGTA 0.941559 -142 CCAGGGCCGCTGGAACTGGTTAAAACTCACCA 9 70 1 TGAACTGGTA 0.760339 -229 CTAGCAAAACTGTCACCGTTCAATCATTTTGC 9 156 1 TGCACCGTTA 0.97978 -143 AGTGACAATATGTCAGCGTTGACACTGCCAGG 10 135 0 TGCAGCGTTA 0.862559 -166 GCAATTGTTTTGTCACTGTTCACCAGGGCCAA 12 27 0 TGCACTGTTA 0.905156 -134 AAAAATTTCCTGGCACAGTTGAAGAAACTTTC 13 29 1 TGCACAGTTA 0.905159 -46 TGTCAACGGTTAAAAATTAGTT 14 262 0 TGCAACGGTA 0.850355 -12 ACAAATTAGATGGCACAATTAATAAACTAATT 20 127 1 TGCACAATTA 0.622622 -174 TTTTGGCAATTGAAACCGGGCAAAAGCGAAGA 20 161 1 TGAACCGGGA 0.86041 -140 ** ******* * Masking position 5 Map Score: 3.4385 Number of sites scoring better than the average of aligned sites = 588 Number in coding regions = 546 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 14 TCTGCCCTCAACGATTTTTGCCCTGGGG 1 8 1 TCAAGATTTT 0.822928 -179 CCAATCAGAATCAAAGGTTTTGATCCTAGTG 1 48 0 TCAAGGTTTT 0.843353 -139 AGAAAGGGAGTTAAGAATTTTTGATACAATC 2 39 0 TTAAAATTTT 0.624793 -216 CCAGGTGCCATCAATAATTATCTGCTGTAAT 3 98 0 TCAAAATTAT 0.555936 -203 GGCAATAATTTTGAGAAATGAA 7 2 1 GCAAAATTTT 0.898905 -162 CTGTCACCGTTCAATCATTTTGCTCAACTCG 9 165 1 TCAACATTTT 0.716337 -134 ACTCTATCGTGCAATTGTTTTGTCACTGTTC 12 38 0 GCAATGTTTT 0.618855 -123 AGAACGTGTTTAAAAAGTTTTATTCCGCCCC 15 50 1 TAAAAGTTTT 0.522422 -146 AGAAAAATATTCAACAGTTTTTAGAGCCTGT 15 153 0 TCAAAGTTTT 0.926036 -43 CTGAACAAGGGCAAAAGTTTTCCTAGGGGTC 16 104 1 GCAAAGTTTT 0.911508 -44 AGGGCCGGGGGCAATAATTTTTATTCCTGGT 18 96 0 GCAAAATTTT 0.898905 -71 GGCAAATAGCTTAACAATTTTTTTCAAATAC 20 80 0 TTAAAATTTT 0.624782 -221 **** ****** Masking position 4 Map Score: 2.59814 Number of sites scoring better than the average of aligned sites = 330 Number in coding regions = 265 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 15 CAAGGCGATCGCCCCTAAAATCCAATCTAA 6 112 0 GCCCCTAAAA 0.920788 -182 TTGTCGAGAACCCCCTAGAATTGTGCCTAT 6 198 0 CCCCCTAGAA 0.948816 -96 GTGATTTAGTCCCCCCTATCCCCGTCCCTG 10 109 1 CCCCCCTATC 0.685519 -192 TGGACTGGGGGCACCCAGAACTGAAAATTT 11 16 1 GCACCCAGAA 0.852722 -32 GTTTTATTCCGCCCCCTAAATTCCCCAATA 15 66 1 GCCCCCTAAA 0.958051 -130 AGCCCCTCTGGCCCCTCAAATTAGGAGGAA 15 117 0 GCCCCTCAAA 0.839655 -79 TAGCTTCCCTCCACCCTGAAATTTGCTAGG 16 36 1 CCACCCTGAA 0.877626 -112 ATTAGTCTTACCCCCCAGACCCCAAGCAGT 17 186 1 CCCCCCAGAC 0.946816 -115 AGGAGGATGTCCCCCTTAAATTTTATCCCC 18 32 0 CCCCCTTAAA 0.935059 -135 ********** Masking position 5 Map Score: 2.21688 Number of sites scoring better than the average of aligned sites = 734 Number in coding regions = 566 Number in noncoding regions = 168 Number of orfs with sites within 600 bp upstream = 124 Fraction of orfs with sites within 600 bp upstream = 0.0199165