Multiple sequence alignment - TraesCS2D01G031900

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2D01G031900 chr2D 100.000 6706 0 0 1 6706 12690497 12697202 0.000000e+00 12384.0
1 TraesCS2D01G031900 chr2B 93.017 2148 117 20 4564 6706 23122818 23124937 0.000000e+00 3105.0
2 TraesCS2D01G031900 chr2B 94.082 1318 41 12 1859 3155 23119642 23120943 0.000000e+00 1967.0
3 TraesCS2D01G031900 chr2B 88.493 1347 75 27 3260 4563 23121422 23122731 0.000000e+00 1555.0
4 TraesCS2D01G031900 chr2B 93.556 450 21 3 1305 1746 23119192 23119641 0.000000e+00 664.0
5 TraesCS2D01G031900 chr2B 85.569 589 53 18 161 729 23117978 23118554 7.490000e-164 588.0
6 TraesCS2D01G031900 chr2B 87.613 444 34 8 793 1233 23118677 23119102 4.670000e-136 496.0
7 TraesCS2D01G031900 chr2B 93.382 136 7 2 1738 1872 659534375 659534509 4.100000e-47 200.0
8 TraesCS2D01G031900 chr2B 96.552 58 2 0 3206 3263 23121119 23121176 5.540000e-16 97.1
9 TraesCS2D01G031900 chr2A 90.311 1992 119 21 4564 6547 14818041 14819966 0.000000e+00 2542.0
10 TraesCS2D01G031900 chr2A 95.344 1396 29 14 3170 4563 14816564 14817925 0.000000e+00 2185.0
11 TraesCS2D01G031900 chr2A 94.414 1289 47 8 1859 3133 14815050 14816327 0.000000e+00 1958.0
12 TraesCS2D01G031900 chr2A 88.185 1278 75 31 1 1227 14813095 14814347 0.000000e+00 1454.0
13 TraesCS2D01G031900 chr2A 97.500 120 3 0 1743 1862 78845690 78845571 8.820000e-49 206.0
14 TraesCS2D01G031900 chr2A 93.548 62 3 1 6134 6194 14820189 14820250 2.580000e-14 91.6
15 TraesCS2D01G031900 chr5B 90.000 310 12 4 906 1213 440779652 440779944 3.790000e-102 383.0
16 TraesCS2D01G031900 chr5B 79.310 232 27 15 1238 1448 440780064 440780295 7.010000e-30 143.0
17 TraesCS2D01G031900 chr7B 88.172 279 18 7 957 1232 612595535 612595801 1.090000e-82 318.0
18 TraesCS2D01G031900 chr7B 96.721 122 4 0 1740 1861 81424985 81425106 3.170000e-48 204.0
19 TraesCS2D01G031900 chr7B 95.918 98 4 0 1099 1196 629481551 629481454 6.960000e-35 159.0
20 TraesCS2D01G031900 chr1B 96.748 123 4 0 1739 1861 8855862 8855984 8.820000e-49 206.0
21 TraesCS2D01G031900 chr1B 92.701 137 8 2 1728 1863 334306811 334306676 5.310000e-46 196.0
22 TraesCS2D01G031900 chr3B 95.968 124 5 0 1742 1865 829966123 829966246 1.140000e-47 202.0
23 TraesCS2D01G031900 chr3B 95.968 124 5 0 1742 1865 830093610 830093733 1.140000e-47 202.0
24 TraesCS2D01G031900 chr3B 95.968 124 5 0 1742 1865 830140895 830141018 1.140000e-47 202.0
25 TraesCS2D01G031900 chr6B 93.939 132 6 2 1745 1875 187836886 187836756 1.480000e-46 198.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G031900 chr2D 12690497 12697202 6705 False 12384.00 12384 100.000000 1 6706 1 chr2D.!!$F1 6705
1 TraesCS2D01G031900 chr2B 23117978 23124937 6959 False 1210.30 3105 91.268857 161 6706 7 chr2B.!!$F2 6545
2 TraesCS2D01G031900 chr2A 14813095 14820250 7155 False 1646.12 2542 92.360400 1 6547 5 chr2A.!!$F1 6546
3 TraesCS2D01G031900 chr5B 440779652 440780295 643 False 263.00 383 84.655000 906 1448 2 chr5B.!!$F1 542

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
338 350 0.312416 CGCCGCTTGCTATAGACTCT 59.688 55.000 3.21 0.00 38.05 3.24 F
1759 2142 0.033796 ATGTACTCCCTCCGTCCGAA 60.034 55.000 0.00 0.00 0.00 4.30 F
1849 2232 0.036306 GAGGGACAAGCTTTTCCGGA 59.964 55.000 22.30 0.00 32.00 5.14 F
1850 2233 0.250770 AGGGACAAGCTTTTCCGGAC 60.251 55.000 22.30 11.02 32.00 4.79 F
1853 2236 0.601841 GACAAGCTTTTCCGGACGGA 60.602 55.000 1.83 9.76 43.52 4.69 F
1854 2237 0.602905 ACAAGCTTTTCCGGACGGAG 60.603 55.000 13.64 3.27 46.06 4.63 F
2729 3126 0.958822 CTTTCCTCCCCCGTTGTTTG 59.041 55.000 0.00 0.00 0.00 2.93 F
2733 3130 1.362355 CTCCCCCGTTGTTTGTTGC 59.638 57.895 0.00 0.00 0.00 4.17 F
2855 3258 1.873591 CGTGGCTAGTTTTTCTGCAGT 59.126 47.619 14.67 0.00 0.00 4.40 F
2856 3259 3.064207 CGTGGCTAGTTTTTCTGCAGTA 58.936 45.455 14.67 0.00 0.00 2.74 F
2857 3260 3.123621 CGTGGCTAGTTTTTCTGCAGTAG 59.876 47.826 14.67 7.97 0.00 2.57 F
3913 4799 3.244044 TGGGCCTTTTTACTTGTCATTGC 60.244 43.478 4.53 0.00 0.00 3.56 F
4822 5831 3.504863 CACCAACTGCAGCAATCATAAC 58.495 45.455 15.27 0.00 0.00 1.89 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1842 2225 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13 R
2717 3114 0.824182 TAGGCAACAAACAACGGGGG 60.824 55.000 0.00 0.00 41.41 5.40 R
2733 3130 2.354821 GTGCCAAACGAGCCTAAATAGG 59.645 50.000 1.92 1.92 46.42 2.57 R
3162 3565 2.834638 AATCACTGGAATTCAGGGGG 57.165 50.000 7.93 0.00 46.67 5.40 R
3163 3566 3.435601 CCCTAATCACTGGAATTCAGGGG 60.436 52.174 13.15 4.52 46.67 4.79 R
3532 4396 5.188948 ACAAGGCCACTGTAATACTACATGA 59.811 40.000 5.01 0.00 37.41 3.07 R
4420 5314 2.169832 AACACCCACTCATTCTCACG 57.830 50.000 0.00 0.00 0.00 4.35 R
4421 5315 7.103641 TCTATTTAACACCCACTCATTCTCAC 58.896 38.462 0.00 0.00 0.00 3.51 R
4901 5910 5.559427 AAGGGCAATTTCACAAAAACAAC 57.441 34.783 0.00 0.00 0.00 3.32 R
4973 5982 5.878406 ACAGATCCTAAACAGTCCCTATG 57.122 43.478 0.00 0.00 0.00 2.23 R
5010 6019 1.352352 CACCACCCTCCATCTTGAGTT 59.648 52.381 0.00 0.00 0.00 3.01 R
5295 6304 0.463295 CTCATGCGGCCAAGTGATCT 60.463 55.000 2.24 0.00 0.00 2.75 R
6107 7123 0.319211 TCGACGGTACAAAGCTGTGG 60.319 55.000 9.18 0.00 36.96 4.17 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 66 6.950842 AGATGATGACAGTCCAACTTATCAA 58.049 36.000 0.00 0.00 29.90 2.57
98 99 5.839621 TGTACTATATTCGACAAAGCCTCC 58.160 41.667 0.00 0.00 0.00 4.30
233 242 2.234414 GACATGTTTGGTTGGCATCCAT 59.766 45.455 17.58 2.07 34.75 3.41
286 297 5.163499 GGAAAAGTGTTTGGTTGTATCCACA 60.163 40.000 0.00 0.00 37.20 4.17
328 340 0.804544 TAGTCACATACGCCGCTTGC 60.805 55.000 0.00 0.00 0.00 4.01
338 350 0.312416 CGCCGCTTGCTATAGACTCT 59.688 55.000 3.21 0.00 38.05 3.24
370 382 3.535280 ACTTTTGCCACGACCAATTTT 57.465 38.095 0.00 0.00 0.00 1.82
434 447 1.288752 GGCAACCAAACATGTCCGG 59.711 57.895 11.09 11.09 0.00 5.14
438 451 1.460273 AACCAAACATGTCCGGCACC 61.460 55.000 12.31 0.00 0.00 5.01
453 466 1.154225 CACCGGCGCTTGTTCAATC 60.154 57.895 7.64 0.00 0.00 2.67
483 496 2.028925 GGGTTGTGCCGGCAAAAG 59.971 61.111 32.40 0.00 38.44 2.27
522 538 5.871396 TTATCTTGCGATTTACTCCCTCT 57.129 39.130 0.00 0.00 0.00 3.69
552 579 5.679734 AATATTATCTTGGAAGTGCGCAG 57.320 39.130 12.22 0.00 0.00 5.18
597 624 9.284968 CTCTACACAAGAAAAAGGGAGAAAATA 57.715 33.333 0.00 0.00 32.46 1.40
642 669 7.573968 GTCCCAGAGACAAAATAATGCTAAT 57.426 36.000 0.00 0.00 45.55 1.73
924 1035 0.535102 CTCCCGAATCAAATCCCCCG 60.535 60.000 0.00 0.00 0.00 5.73
932 1049 1.077716 CAAATCCCCCGTCACCTCC 60.078 63.158 0.00 0.00 0.00 4.30
933 1050 2.666098 AAATCCCCCGTCACCTCCG 61.666 63.158 0.00 0.00 0.00 4.63
941 1058 4.699522 GTCACCTCCGCCACCACC 62.700 72.222 0.00 0.00 0.00 4.61
954 1071 2.286885 CCACCCCACCCCACCTAT 60.287 66.667 0.00 0.00 0.00 2.57
1227 1367 2.115266 CCCAACACCCCACACCTC 59.885 66.667 0.00 0.00 0.00 3.85
1228 1368 2.281484 CCAACACCCCACACCTCG 60.281 66.667 0.00 0.00 0.00 4.63
1239 1510 1.404315 CCACACCTCGCCTCTAGTTTC 60.404 57.143 0.00 0.00 0.00 2.78
1244 1515 1.470632 CCTCGCCTCTAGTTTCTGCTG 60.471 57.143 0.00 0.00 0.00 4.41
1367 1642 2.047061 TCATGGGCTAGGGTGTGATAC 58.953 52.381 0.00 0.00 0.00 2.24
1377 1669 0.464036 GGTGTGATACGAGATGGGCA 59.536 55.000 0.00 0.00 0.00 5.36
1588 1946 0.919710 GGTCTGGAGGCTTGGGTAAT 59.080 55.000 0.00 0.00 0.00 1.89
1662 2023 4.746729 CCAAATAACATGTGTGGGATGTG 58.253 43.478 0.00 0.00 34.22 3.21
1704 2087 9.764363 ATTTCTTACCTTTTGTTCTGGAAAATC 57.236 29.630 0.00 0.00 0.00 2.17
1752 2135 6.919775 ACTCATTGTATATGTACTCCCTCC 57.080 41.667 1.08 0.00 0.00 4.30
1753 2136 5.477291 ACTCATTGTATATGTACTCCCTCCG 59.523 44.000 1.08 0.00 0.00 4.63
1754 2137 5.391256 TCATTGTATATGTACTCCCTCCGT 58.609 41.667 1.08 0.00 0.00 4.69
1755 2138 5.475909 TCATTGTATATGTACTCCCTCCGTC 59.524 44.000 1.08 0.00 0.00 4.79
1756 2139 3.759581 TGTATATGTACTCCCTCCGTCC 58.240 50.000 1.08 0.00 0.00 4.79
1757 2140 1.906990 ATATGTACTCCCTCCGTCCG 58.093 55.000 0.00 0.00 0.00 4.79
1758 2141 0.839277 TATGTACTCCCTCCGTCCGA 59.161 55.000 0.00 0.00 0.00 4.55
1759 2142 0.033796 ATGTACTCCCTCCGTCCGAA 60.034 55.000 0.00 0.00 0.00 4.30
1760 2143 0.251297 TGTACTCCCTCCGTCCGAAA 60.251 55.000 0.00 0.00 0.00 3.46
1761 2144 0.890683 GTACTCCCTCCGTCCGAAAA 59.109 55.000 0.00 0.00 0.00 2.29
1762 2145 1.273327 GTACTCCCTCCGTCCGAAAAA 59.727 52.381 0.00 0.00 0.00 1.94
1780 2163 3.801114 AAAACTTGTCCCAAGCTTGTC 57.199 42.857 24.35 14.49 0.00 3.18
1781 2164 1.692411 AACTTGTCCCAAGCTTGTCC 58.308 50.000 24.35 12.15 0.00 4.02
1782 2165 0.178990 ACTTGTCCCAAGCTTGTCCC 60.179 55.000 24.35 11.81 0.00 4.46
1783 2166 0.111253 CTTGTCCCAAGCTTGTCCCT 59.889 55.000 24.35 0.00 0.00 4.20
1784 2167 0.110486 TTGTCCCAAGCTTGTCCCTC 59.890 55.000 24.35 10.65 0.00 4.30
1785 2168 1.059584 TGTCCCAAGCTTGTCCCTCA 61.060 55.000 24.35 12.85 0.00 3.86
1786 2169 0.110486 GTCCCAAGCTTGTCCCTCAA 59.890 55.000 24.35 0.00 34.61 3.02
1787 2170 0.850100 TCCCAAGCTTGTCCCTCAAA 59.150 50.000 24.35 0.00 35.48 2.69
1788 2171 1.428912 TCCCAAGCTTGTCCCTCAAAT 59.571 47.619 24.35 0.00 35.48 2.32
1789 2172 1.547372 CCCAAGCTTGTCCCTCAAATG 59.453 52.381 24.35 5.47 35.48 2.32
1790 2173 1.547372 CCAAGCTTGTCCCTCAAATGG 59.453 52.381 24.35 1.81 35.48 3.16
1791 2174 2.517959 CAAGCTTGTCCCTCAAATGGA 58.482 47.619 18.65 0.00 35.48 3.41
1792 2175 3.094572 CAAGCTTGTCCCTCAAATGGAT 58.905 45.455 18.65 0.00 35.48 3.41
1793 2176 2.731572 AGCTTGTCCCTCAAATGGATG 58.268 47.619 0.00 0.00 35.48 3.51
1794 2177 2.042162 AGCTTGTCCCTCAAATGGATGT 59.958 45.455 0.00 0.00 35.48 3.06
1795 2178 3.266772 AGCTTGTCCCTCAAATGGATGTA 59.733 43.478 0.00 0.00 35.48 2.29
1796 2179 4.079558 AGCTTGTCCCTCAAATGGATGTAT 60.080 41.667 0.00 0.00 35.48 2.29
1797 2180 4.276926 GCTTGTCCCTCAAATGGATGTATC 59.723 45.833 0.00 0.00 35.48 2.24
1798 2181 5.688807 CTTGTCCCTCAAATGGATGTATCT 58.311 41.667 0.00 0.00 35.48 1.98
1799 2182 6.688922 GCTTGTCCCTCAAATGGATGTATCTA 60.689 42.308 0.00 0.00 35.48 1.98
1800 2183 6.425210 TGTCCCTCAAATGGATGTATCTAG 57.575 41.667 0.00 0.00 33.65 2.43
1801 2184 5.221722 TGTCCCTCAAATGGATGTATCTAGC 60.222 44.000 0.00 0.00 33.65 3.42
1802 2185 4.907269 TCCCTCAAATGGATGTATCTAGCA 59.093 41.667 0.00 0.00 0.00 3.49
1803 2186 4.999950 CCCTCAAATGGATGTATCTAGCAC 59.000 45.833 0.00 0.00 0.00 4.40
1804 2187 5.221803 CCCTCAAATGGATGTATCTAGCACT 60.222 44.000 0.00 0.00 0.00 4.40
1805 2188 6.014242 CCCTCAAATGGATGTATCTAGCACTA 60.014 42.308 0.00 0.00 0.00 2.74
1806 2189 7.445121 CCTCAAATGGATGTATCTAGCACTAA 58.555 38.462 0.00 0.00 0.00 2.24
1807 2190 7.386299 CCTCAAATGGATGTATCTAGCACTAAC 59.614 40.741 0.00 0.00 0.00 2.34
1808 2191 8.023021 TCAAATGGATGTATCTAGCACTAACT 57.977 34.615 0.00 0.00 0.00 2.24
1809 2192 8.486210 TCAAATGGATGTATCTAGCACTAACTT 58.514 33.333 0.00 0.00 0.00 2.66
1810 2193 8.554528 CAAATGGATGTATCTAGCACTAACTTG 58.445 37.037 0.00 0.00 0.00 3.16
1811 2194 6.161855 TGGATGTATCTAGCACTAACTTGG 57.838 41.667 0.00 0.00 0.00 3.61
1812 2195 5.661312 TGGATGTATCTAGCACTAACTTGGT 59.339 40.000 0.00 0.00 0.00 3.67
1813 2196 5.986135 GGATGTATCTAGCACTAACTTGGTG 59.014 44.000 0.97 0.97 37.70 4.17
1814 2197 5.339008 TGTATCTAGCACTAACTTGGTGG 57.661 43.478 7.33 0.00 35.47 4.61
1815 2198 4.775780 TGTATCTAGCACTAACTTGGTGGT 59.224 41.667 13.64 13.64 45.46 4.16
1816 2199 5.953548 TGTATCTAGCACTAACTTGGTGGTA 59.046 40.000 14.32 14.32 43.66 3.25
1821 2204 5.340439 AGCACTAACTTGGTGGTAGATAC 57.660 43.478 8.10 0.00 42.47 2.24
1822 2205 4.775780 AGCACTAACTTGGTGGTAGATACA 59.224 41.667 8.10 0.00 42.47 2.29
1823 2206 5.425539 AGCACTAACTTGGTGGTAGATACAT 59.574 40.000 8.10 0.00 42.47 2.29
1824 2207 5.753921 GCACTAACTTGGTGGTAGATACATC 59.246 44.000 7.33 0.00 38.19 3.06
1825 2208 6.281405 CACTAACTTGGTGGTAGATACATCC 58.719 44.000 0.00 0.00 38.19 3.51
1826 2209 5.962031 ACTAACTTGGTGGTAGATACATCCA 59.038 40.000 0.00 2.64 38.19 3.41
1827 2210 5.975988 AACTTGGTGGTAGATACATCCAT 57.024 39.130 6.33 0.00 33.19 3.41
1828 2211 5.975988 ACTTGGTGGTAGATACATCCATT 57.024 39.130 6.33 0.00 33.19 3.16
1829 2212 6.327386 ACTTGGTGGTAGATACATCCATTT 57.673 37.500 6.33 0.00 33.19 2.32
1830 2213 6.122277 ACTTGGTGGTAGATACATCCATTTG 58.878 40.000 6.33 4.25 33.19 2.32
1831 2214 5.966853 TGGTGGTAGATACATCCATTTGA 57.033 39.130 0.00 0.00 33.68 2.69
1832 2215 5.928976 TGGTGGTAGATACATCCATTTGAG 58.071 41.667 0.00 0.00 33.68 3.02
1833 2216 5.163205 TGGTGGTAGATACATCCATTTGAGG 60.163 44.000 0.00 0.00 33.68 3.86
1834 2217 5.308825 GTGGTAGATACATCCATTTGAGGG 58.691 45.833 0.00 0.00 33.68 4.30
1835 2218 5.071788 GTGGTAGATACATCCATTTGAGGGA 59.928 44.000 0.00 0.00 39.14 4.20
1836 2219 5.071788 TGGTAGATACATCCATTTGAGGGAC 59.928 44.000 0.00 0.00 37.23 4.46
1837 2220 5.071788 GGTAGATACATCCATTTGAGGGACA 59.928 44.000 0.00 0.00 37.23 4.02
1838 2221 5.715439 AGATACATCCATTTGAGGGACAA 57.285 39.130 0.00 0.00 37.23 3.18
1839 2222 5.688807 AGATACATCCATTTGAGGGACAAG 58.311 41.667 0.00 0.00 39.77 3.16
1840 2223 2.450476 ACATCCATTTGAGGGACAAGC 58.550 47.619 0.00 0.00 39.77 4.01
1841 2224 2.042162 ACATCCATTTGAGGGACAAGCT 59.958 45.455 0.00 0.00 39.77 3.74
1842 2225 2.978156 TCCATTTGAGGGACAAGCTT 57.022 45.000 0.00 0.00 39.77 3.74
1843 2226 3.243359 TCCATTTGAGGGACAAGCTTT 57.757 42.857 0.00 0.00 39.77 3.51
1844 2227 3.575805 TCCATTTGAGGGACAAGCTTTT 58.424 40.909 0.00 0.00 39.77 2.27
1845 2228 3.573967 TCCATTTGAGGGACAAGCTTTTC 59.426 43.478 3.91 3.91 39.77 2.29
1846 2229 3.306294 CCATTTGAGGGACAAGCTTTTCC 60.306 47.826 21.34 21.34 39.77 3.13
1847 2230 1.604604 TTGAGGGACAAGCTTTTCCG 58.395 50.000 22.30 2.85 34.20 4.30
1848 2231 0.250727 TGAGGGACAAGCTTTTCCGG 60.251 55.000 22.30 0.00 32.00 5.14
1849 2232 0.036306 GAGGGACAAGCTTTTCCGGA 59.964 55.000 22.30 0.00 32.00 5.14
1850 2233 0.250770 AGGGACAAGCTTTTCCGGAC 60.251 55.000 22.30 11.02 32.00 4.79
1851 2234 1.574702 GGGACAAGCTTTTCCGGACG 61.575 60.000 22.30 0.00 32.00 4.79
1852 2235 1.574702 GGACAAGCTTTTCCGGACGG 61.575 60.000 15.65 3.96 0.00 4.79
1853 2236 0.601841 GACAAGCTTTTCCGGACGGA 60.602 55.000 1.83 9.76 43.52 4.69
1854 2237 0.602905 ACAAGCTTTTCCGGACGGAG 60.603 55.000 13.64 3.27 46.06 4.63
1855 2238 1.003718 AAGCTTTTCCGGACGGAGG 60.004 57.895 13.64 9.30 46.06 4.30
1856 2239 2.436115 GCTTTTCCGGACGGAGGG 60.436 66.667 13.64 8.97 46.06 4.30
1857 2240 2.951101 GCTTTTCCGGACGGAGGGA 61.951 63.158 13.64 1.83 46.06 4.20
1893 2276 8.121305 AGATGATATTAGAGAAGTACCAGCAG 57.879 38.462 0.00 0.00 0.00 4.24
1898 2281 5.995565 TTAGAGAAGTACCAGCAGCTTTA 57.004 39.130 0.00 0.00 0.00 1.85
1900 2283 3.835395 AGAGAAGTACCAGCAGCTTTACT 59.165 43.478 7.44 7.44 0.00 2.24
2324 2713 2.787249 CAATCGTCTGCTTGGCCG 59.213 61.111 0.00 0.00 0.00 6.13
2414 2803 4.141413 TGCAGCTGTGGATTCCATAACTAT 60.141 41.667 16.64 0.00 35.28 2.12
2528 2925 9.736023 CTGAATTGTAATAAGAATGGGCTTTAC 57.264 33.333 0.00 0.00 0.00 2.01
2576 2973 4.286707 TCTAGTTTAGCCCTGATACTGCA 58.713 43.478 0.00 0.00 0.00 4.41
2577 2974 3.268023 AGTTTAGCCCTGATACTGCAC 57.732 47.619 0.00 0.00 0.00 4.57
2578 2975 2.840651 AGTTTAGCCCTGATACTGCACT 59.159 45.455 0.00 0.00 0.00 4.40
2580 2977 4.469945 AGTTTAGCCCTGATACTGCACTTA 59.530 41.667 0.00 0.00 0.00 2.24
2581 2978 5.131142 AGTTTAGCCCTGATACTGCACTTAT 59.869 40.000 0.00 0.00 0.00 1.73
2582 2979 3.760580 AGCCCTGATACTGCACTTATC 57.239 47.619 4.28 4.28 0.00 1.75
2583 2980 3.041211 AGCCCTGATACTGCACTTATCA 58.959 45.455 11.22 11.22 35.21 2.15
2584 2981 3.070734 AGCCCTGATACTGCACTTATCAG 59.929 47.826 22.99 22.99 46.90 2.90
2630 3027 4.853924 ATGTCCGATCTTGTTGCTTTTT 57.146 36.364 0.00 0.00 0.00 1.94
2655 3052 8.560355 TTTGTCATCTAATTTCCTTCATCGAA 57.440 30.769 0.00 0.00 0.00 3.71
2717 3114 8.662781 TGCATATTACACAGATAACTTTCCTC 57.337 34.615 0.00 0.00 0.00 3.71
2729 3126 0.958822 CTTTCCTCCCCCGTTGTTTG 59.041 55.000 0.00 0.00 0.00 2.93
2733 3130 1.362355 CTCCCCCGTTGTTTGTTGC 59.638 57.895 0.00 0.00 0.00 4.17
2754 3151 2.354821 CCTATTTAGGCTCGTTTGGCAC 59.645 50.000 0.00 0.00 36.53 5.01
2759 3156 2.253452 GCTCGTTTGGCACTGCAG 59.747 61.111 13.48 13.48 0.00 4.41
2855 3258 1.873591 CGTGGCTAGTTTTTCTGCAGT 59.126 47.619 14.67 0.00 0.00 4.40
2856 3259 3.064207 CGTGGCTAGTTTTTCTGCAGTA 58.936 45.455 14.67 0.00 0.00 2.74
2857 3260 3.123621 CGTGGCTAGTTTTTCTGCAGTAG 59.876 47.826 14.67 7.97 0.00 2.57
2858 3261 4.315803 GTGGCTAGTTTTTCTGCAGTAGA 58.684 43.478 14.67 0.00 0.00 2.59
2859 3262 4.938226 GTGGCTAGTTTTTCTGCAGTAGAT 59.062 41.667 14.67 0.00 34.80 1.98
2860 3263 6.106673 GTGGCTAGTTTTTCTGCAGTAGATA 58.893 40.000 14.67 0.28 34.80 1.98
3192 3795 8.561536 TGAATTCCAGTGATTAGGGAACTATA 57.438 34.615 2.27 0.00 43.94 1.31
3193 3796 9.170890 TGAATTCCAGTGATTAGGGAACTATAT 57.829 33.333 2.27 0.00 43.94 0.86
3502 4366 9.969001 AACCTAGTTCCATAGTTTATTTGCTTA 57.031 29.630 0.00 0.00 0.00 3.09
3532 4396 9.328845 ACATTATGCATTCTTTCTTGTGTTTTT 57.671 25.926 3.54 0.00 0.00 1.94
3533 4397 9.801714 CATTATGCATTCTTTCTTGTGTTTTTC 57.198 29.630 3.54 0.00 0.00 2.29
3855 4741 7.591821 ACTGGGATAATAAAAGGCTAAATCCA 58.408 34.615 0.00 0.00 34.39 3.41
3913 4799 3.244044 TGGGCCTTTTTACTTGTCATTGC 60.244 43.478 4.53 0.00 0.00 3.56
3924 4810 8.453238 TTTACTTGTCATTGCTTGTTTACCTA 57.547 30.769 0.00 0.00 0.00 3.08
3936 4822 8.800370 TGCTTGTTTACCTAATTATCACATGA 57.200 30.769 0.00 0.00 0.00 3.07
4420 5314 7.396540 ACATGAATAGACCTGGTCAAATTTC 57.603 36.000 27.48 21.23 34.60 2.17
4421 5315 6.094048 ACATGAATAGACCTGGTCAAATTTCG 59.906 38.462 27.48 17.96 34.60 3.46
4452 5346 5.427157 TGAGTGGGTGTTAAATAGATAGCCA 59.573 40.000 0.00 0.00 36.65 4.75
4679 5688 6.096705 TGACCATTGACAAATGAATGTATCCC 59.903 38.462 0.00 0.00 45.17 3.85
4822 5831 3.504863 CACCAACTGCAGCAATCATAAC 58.495 45.455 15.27 0.00 0.00 1.89
5010 6019 6.627087 AGGATCTGTTTGAGTTTATCCTGA 57.373 37.500 0.00 0.00 41.24 3.86
5190 6199 8.730680 TCCTTGAAGTAGAGCAAAATTTATGAC 58.269 33.333 0.00 0.00 0.00 3.06
5221 6230 9.499479 ACATAATGGCAAAAATATCACAAAACA 57.501 25.926 0.00 0.00 0.00 2.83
5238 6247 5.761234 ACAAAACAATGCATTGAGCTTCATT 59.239 32.000 38.99 21.45 45.94 2.57
5254 6263 7.815549 TGAGCTTCATTTCACATAACTACGTAA 59.184 33.333 0.00 0.00 0.00 3.18
5360 6369 4.219725 TGTCTATCTTGGTGTGATCGTTGA 59.780 41.667 0.00 0.00 0.00 3.18
5418 6428 3.724478 AGGTGTCATCTATGGGTCAAGA 58.276 45.455 0.00 0.00 0.00 3.02
5443 6453 9.301897 GATAGATCCAAAAACCTTAGCCATATT 57.698 33.333 0.00 0.00 0.00 1.28
5733 6743 2.766970 TTGCTTGTACTTTTGCGACC 57.233 45.000 0.00 0.00 0.00 4.79
5736 6746 2.032799 TGCTTGTACTTTTGCGACCAAG 59.967 45.455 0.00 0.00 34.03 3.61
5750 6760 2.433436 GACCAAGTTATTGAAGCGGGT 58.567 47.619 0.00 0.00 38.83 5.28
5771 6781 1.194781 TGGAGTCTCCTGGTTCTGCC 61.195 60.000 19.82 0.00 37.46 4.85
5772 6782 1.194781 GGAGTCTCCTGGTTCTGCCA 61.195 60.000 12.02 0.00 46.95 4.92
5834 6844 1.228429 GTGGTTTGGCCCTGCAGTA 60.228 57.895 13.81 0.00 36.04 2.74
5862 6872 5.280945 TGCTGCTGTTAAAATTGTTCTGTC 58.719 37.500 0.00 0.00 0.00 3.51
5864 6874 5.400485 GCTGCTGTTAAAATTGTTCTGTCTG 59.600 40.000 0.00 0.00 0.00 3.51
5866 6876 7.094508 TGCTGTTAAAATTGTTCTGTCTGAA 57.905 32.000 0.00 0.00 0.00 3.02
5898 6910 3.451141 TTGTGGGAGTTTGCATTTGTC 57.549 42.857 0.00 0.00 0.00 3.18
5921 6933 2.928116 ACGCCGAGCACTAGAATAAAAC 59.072 45.455 0.00 0.00 0.00 2.43
6005 7021 7.095229 CGATTTGATTTGTTCTTCAGTACCTCA 60.095 37.037 0.00 0.00 0.00 3.86
6042 7058 9.797642 TGTAATGTAATGCTGGATCTATTTCAT 57.202 29.630 0.00 0.00 0.00 2.57
6109 7125 5.724370 TGTAAAGATCTGTAATCCTGGTCCA 59.276 40.000 0.00 0.00 0.00 4.02
6124 7140 1.145803 GTCCACAGCTTTGTACCGTC 58.854 55.000 0.00 0.00 0.00 4.79
6131 7147 3.129813 ACAGCTTTGTACCGTCGATATCA 59.870 43.478 3.12 0.00 0.00 2.15
6167 7183 8.181904 AGAAAATTATTGAACATGTGACTGGT 57.818 30.769 0.00 0.00 0.00 4.00
6168 7184 8.641541 AGAAAATTATTGAACATGTGACTGGTT 58.358 29.630 0.00 0.00 0.00 3.67
6169 7185 9.260002 GAAAATTATTGAACATGTGACTGGTTT 57.740 29.630 0.00 0.00 0.00 3.27
6170 7186 8.816640 AAATTATTGAACATGTGACTGGTTTC 57.183 30.769 0.00 0.00 0.00 2.78
6171 7187 6.951062 TTATTGAACATGTGACTGGTTTCA 57.049 33.333 0.00 0.00 0.00 2.69
6172 7188 4.898829 TTGAACATGTGACTGGTTTCAG 57.101 40.909 0.00 0.00 46.10 3.02
6173 7189 4.149511 TGAACATGTGACTGGTTTCAGA 57.850 40.909 0.00 0.00 43.49 3.27
6174 7190 3.876914 TGAACATGTGACTGGTTTCAGAC 59.123 43.478 0.00 0.00 43.49 3.51
6175 7191 3.558931 ACATGTGACTGGTTTCAGACA 57.441 42.857 0.00 0.00 43.49 3.41
6176 7192 4.090761 ACATGTGACTGGTTTCAGACAT 57.909 40.909 0.00 0.00 44.57 3.06
6177 7193 4.414999 CATGTGACTGGTTTCAGACATG 57.585 45.455 11.23 11.23 44.57 3.21
6178 7194 3.558931 TGTGACTGGTTTCAGACATGT 57.441 42.857 0.00 0.00 44.57 3.21
6179 7195 3.884895 TGTGACTGGTTTCAGACATGTT 58.115 40.909 0.00 0.00 44.57 2.71
6180 7196 3.876914 TGTGACTGGTTTCAGACATGTTC 59.123 43.478 0.00 0.00 44.57 3.18
6181 7197 4.130118 GTGACTGGTTTCAGACATGTTCT 58.870 43.478 0.00 0.00 44.57 3.01
6182 7198 5.163353 TGTGACTGGTTTCAGACATGTTCTA 60.163 40.000 0.00 0.00 44.57 2.10
6183 7199 5.758296 GTGACTGGTTTCAGACATGTTCTAA 59.242 40.000 0.00 0.00 44.57 2.10
6184 7200 6.260050 GTGACTGGTTTCAGACATGTTCTAAA 59.740 38.462 0.00 0.00 44.57 1.85
6185 7201 6.826231 TGACTGGTTTCAGACATGTTCTAAAA 59.174 34.615 0.00 0.00 43.49 1.52
6186 7202 7.027778 ACTGGTTTCAGACATGTTCTAAAAC 57.972 36.000 0.00 7.53 40.59 2.43
6187 7203 6.601613 ACTGGTTTCAGACATGTTCTAAAACA 59.398 34.615 18.06 16.19 42.44 2.83
6189 7205 8.783093 CTGGTTTCAGACATGTTCTAAAACATA 58.217 33.333 18.06 10.35 46.45 2.29
6252 7296 7.605449 TCAAATCATCACAAGGGAATCTTTTC 58.395 34.615 0.00 0.00 32.41 2.29
6315 7359 8.389779 TCACAAGCAGTCTTATATCACAAAAA 57.610 30.769 0.00 0.00 0.00 1.94
6372 7418 7.401955 TGAAAGGAAATTGCAATTTGGTTTT 57.598 28.000 35.57 28.55 38.64 2.43
6387 7433 9.369904 CAATTTGGTTTTAGAAAGTATGGATGG 57.630 33.333 0.00 0.00 0.00 3.51
6408 7454 8.255905 GGATGGAATTTCTGAACTGAATTTGAT 58.744 33.333 0.00 0.00 0.00 2.57
6463 7509 7.611855 CCACACTTTCAGGAAGGAAGTTTATAT 59.388 37.037 0.00 0.00 39.79 0.86
6492 7538 7.068103 TGCTTTGGAACTACTGAATGAGAAAAA 59.932 33.333 0.00 0.00 0.00 1.94
6493 7539 7.592903 GCTTTGGAACTACTGAATGAGAAAAAG 59.407 37.037 0.00 0.00 0.00 2.27
6494 7540 8.519799 TTTGGAACTACTGAATGAGAAAAAGT 57.480 30.769 0.00 0.00 0.00 2.66
6579 7626 6.097554 TCAGCTTTATTCCAAGTTTCCAACAA 59.902 34.615 0.00 0.00 0.00 2.83
6583 7630 7.254421 GCTTTATTCCAAGTTTCCAACAAACAG 60.254 37.037 0.40 0.00 32.81 3.16
6637 7685 4.027572 TGCACAACAGTTTGAGCTAAAC 57.972 40.909 8.02 9.46 46.25 2.01
6649 7697 4.546829 TGAGCTAAACTTGTACCGGAAT 57.453 40.909 9.46 0.00 0.00 3.01
6650 7698 4.501071 TGAGCTAAACTTGTACCGGAATC 58.499 43.478 9.46 0.00 0.00 2.52
6655 7703 2.845363 ACTTGTACCGGAATCCGTTT 57.155 45.000 21.12 9.54 46.80 3.60
6682 7730 1.860399 GCGGTATAGTGAGCGACAGTG 60.860 57.143 0.00 0.00 42.83 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 6.042093 ACTGTCATCATCTAATAATCCACCGT 59.958 38.462 0.00 0.00 0.00 4.83
87 88 1.373570 CTGAATCGGGAGGCTTTGTC 58.626 55.000 0.00 0.00 0.00 3.18
98 99 8.986477 ATTTCTTTGTTTAAATCCTGAATCGG 57.014 30.769 0.00 0.00 0.00 4.18
155 157 4.331968 CCTGATGCCACCACTTACTAAAA 58.668 43.478 0.00 0.00 0.00 1.52
233 242 4.713553 TGATAGAAAAGTGTGACAAGGCA 58.286 39.130 0.00 0.00 0.00 4.75
286 297 2.795231 AAGTGTGGCATGCTATGACT 57.205 45.000 18.92 14.52 39.69 3.41
328 340 6.868622 AGTTGGTTAGCAACAGAGTCTATAG 58.131 40.000 25.76 0.00 35.18 1.31
338 350 2.497675 TGGCAAAAGTTGGTTAGCAACA 59.502 40.909 25.76 3.95 35.18 3.33
355 367 1.365633 GGCAAAATTGGTCGTGGCA 59.634 52.632 0.00 0.00 36.61 4.92
434 447 3.267597 ATTGAACAAGCGCCGGTGC 62.268 57.895 32.51 32.51 0.00 5.01
453 466 0.882927 ACAACCCAACATGTCCGACG 60.883 55.000 0.00 0.00 0.00 5.12
483 496 6.357240 GCAAGATAATATTTTTCGCCGACTTC 59.643 38.462 0.00 0.00 0.00 3.01
535 551 1.134699 CCTCTGCGCACTTCCAAGATA 60.135 52.381 5.66 0.00 0.00 1.98
536 552 0.392193 CCTCTGCGCACTTCCAAGAT 60.392 55.000 5.66 0.00 0.00 2.40
537 553 1.004560 CCTCTGCGCACTTCCAAGA 60.005 57.895 5.66 0.00 0.00 3.02
538 554 2.037136 CCCTCTGCGCACTTCCAAG 61.037 63.158 5.66 0.00 0.00 3.61
539 555 2.032528 CCCTCTGCGCACTTCCAA 59.967 61.111 5.66 0.00 0.00 3.53
540 556 2.922503 TCCCTCTGCGCACTTCCA 60.923 61.111 5.66 0.00 0.00 3.53
541 557 2.125350 CTCCCTCTGCGCACTTCC 60.125 66.667 5.66 0.00 0.00 3.46
542 558 1.446966 GACTCCCTCTGCGCACTTC 60.447 63.158 5.66 0.00 0.00 3.01
543 559 2.659610 GACTCCCTCTGCGCACTT 59.340 61.111 5.66 0.00 0.00 3.16
544 560 3.386237 GGACTCCCTCTGCGCACT 61.386 66.667 5.66 0.00 0.00 4.40
546 562 1.768684 AAAAGGACTCCCTCTGCGCA 61.769 55.000 10.98 10.98 43.48 6.09
547 563 1.003233 AAAAGGACTCCCTCTGCGC 60.003 57.895 0.00 0.00 43.48 6.09
548 564 0.321671 TCAAAAGGACTCCCTCTGCG 59.678 55.000 0.00 0.00 43.48 5.18
549 565 2.431454 CTTCAAAAGGACTCCCTCTGC 58.569 52.381 0.00 0.00 43.48 4.26
552 579 1.352687 AGGCTTCAAAAGGACTCCCTC 59.647 52.381 0.00 0.00 43.48 4.30
666 694 6.073819 CGGGTCAAGGTTTCAAATTCAAATTC 60.074 38.462 0.00 0.00 0.00 2.17
672 700 3.611766 GCTCGGGTCAAGGTTTCAAATTC 60.612 47.826 0.00 0.00 0.00 2.17
821 928 8.929487 AGGTATATTCTTTCTCCCTACTCTTTG 58.071 37.037 0.00 0.00 0.00 2.77
924 1035 4.699522 GGTGGTGGCGGAGGTGAC 62.700 72.222 0.00 0.00 0.00 3.67
936 1053 3.217030 ATAGGTGGGGTGGGGTGGT 62.217 63.158 0.00 0.00 0.00 4.16
937 1054 2.286885 ATAGGTGGGGTGGGGTGG 60.287 66.667 0.00 0.00 0.00 4.61
938 1055 2.383601 GGATAGGTGGGGTGGGGTG 61.384 68.421 0.00 0.00 0.00 4.61
939 1056 2.043941 GGATAGGTGGGGTGGGGT 59.956 66.667 0.00 0.00 0.00 4.95
940 1057 2.776963 GGGATAGGTGGGGTGGGG 60.777 72.222 0.00 0.00 0.00 4.96
941 1058 2.776963 GGGGATAGGTGGGGTGGG 60.777 72.222 0.00 0.00 0.00 4.61
942 1059 2.043772 TGGGGATAGGTGGGGTGG 59.956 66.667 0.00 0.00 0.00 4.61
943 1060 2.383601 GGTGGGGATAGGTGGGGTG 61.384 68.421 0.00 0.00 0.00 4.61
944 1061 2.043941 GGTGGGGATAGGTGGGGT 59.956 66.667 0.00 0.00 0.00 4.95
1227 1367 1.996191 GAACAGCAGAAACTAGAGGCG 59.004 52.381 0.00 0.00 0.00 5.52
1228 1368 2.351455 GGAACAGCAGAAACTAGAGGC 58.649 52.381 0.00 0.00 0.00 4.70
1231 1371 2.334977 TGGGGAACAGCAGAAACTAGA 58.665 47.619 0.00 0.00 0.00 2.43
1239 1510 0.179034 GCCTAGATGGGGAACAGCAG 60.179 60.000 0.00 0.00 38.15 4.24
1244 1515 4.838986 TCTACATAAGCCTAGATGGGGAAC 59.161 45.833 0.00 0.00 36.00 3.62
1367 1642 2.280389 CCATCGGTGCCCATCTCG 60.280 66.667 0.00 0.00 0.00 4.04
1394 1687 5.385509 TCACAAGCTTAAATTAACAGGGC 57.614 39.130 0.00 0.00 0.00 5.19
1568 1926 1.205460 TTACCCAAGCCTCCAGACCC 61.205 60.000 0.00 0.00 0.00 4.46
1640 2001 4.381825 CCACATCCCACACATGTTATTTGG 60.382 45.833 0.00 0.33 31.83 3.28
1662 2023 4.338379 AGAAATTACTAGCACGGATCCC 57.662 45.455 6.06 0.00 0.00 3.85
1764 2147 5.893518 TTGAGGGACAAGCTTGGGACAAG 62.894 52.174 29.18 3.71 37.48 3.16
1765 2148 4.092026 TTGAGGGACAAGCTTGGGACAA 62.092 50.000 29.18 21.59 37.48 3.18
1766 2149 1.059584 TGAGGGACAAGCTTGGGACA 61.060 55.000 29.18 17.71 0.00 4.02
1767 2150 0.110486 TTGAGGGACAAGCTTGGGAC 59.890 55.000 29.18 18.90 34.20 4.46
1768 2151 0.850100 TTTGAGGGACAAGCTTGGGA 59.150 50.000 29.18 4.51 39.77 4.37
1769 2152 1.547372 CATTTGAGGGACAAGCTTGGG 59.453 52.381 29.18 6.83 39.77 4.12
1770 2153 1.547372 CCATTTGAGGGACAAGCTTGG 59.453 52.381 29.18 12.28 39.77 3.61
1771 2154 2.517959 TCCATTTGAGGGACAAGCTTG 58.482 47.619 24.84 24.84 39.77 4.01
1772 2155 2.978156 TCCATTTGAGGGACAAGCTT 57.022 45.000 0.00 0.00 39.77 3.74
1773 2156 2.042162 ACATCCATTTGAGGGACAAGCT 59.958 45.455 0.00 0.00 39.77 3.74
1774 2157 2.450476 ACATCCATTTGAGGGACAAGC 58.550 47.619 0.00 0.00 39.77 4.01
1775 2158 5.688807 AGATACATCCATTTGAGGGACAAG 58.311 41.667 0.00 0.00 39.77 3.16
1776 2159 5.715439 AGATACATCCATTTGAGGGACAA 57.285 39.130 0.00 0.00 37.23 3.18
1777 2160 5.221722 GCTAGATACATCCATTTGAGGGACA 60.222 44.000 0.00 0.00 37.23 4.02
1778 2161 5.221722 TGCTAGATACATCCATTTGAGGGAC 60.222 44.000 0.00 0.00 37.23 4.46
1779 2162 4.907269 TGCTAGATACATCCATTTGAGGGA 59.093 41.667 0.00 0.00 39.14 4.20
1780 2163 4.999950 GTGCTAGATACATCCATTTGAGGG 59.000 45.833 0.00 0.00 0.00 4.30
1781 2164 5.862845 AGTGCTAGATACATCCATTTGAGG 58.137 41.667 0.00 0.00 0.00 3.86
1782 2165 8.147058 AGTTAGTGCTAGATACATCCATTTGAG 58.853 37.037 0.00 0.00 0.00 3.02
1783 2166 8.023021 AGTTAGTGCTAGATACATCCATTTGA 57.977 34.615 0.00 0.00 0.00 2.69
1784 2167 8.554528 CAAGTTAGTGCTAGATACATCCATTTG 58.445 37.037 0.00 0.00 0.00 2.32
1785 2168 7.716998 CCAAGTTAGTGCTAGATACATCCATTT 59.283 37.037 0.00 0.00 0.00 2.32
1786 2169 7.147479 ACCAAGTTAGTGCTAGATACATCCATT 60.147 37.037 0.00 0.00 0.00 3.16
1787 2170 6.327626 ACCAAGTTAGTGCTAGATACATCCAT 59.672 38.462 0.00 0.00 0.00 3.41
1788 2171 5.661312 ACCAAGTTAGTGCTAGATACATCCA 59.339 40.000 0.00 0.00 0.00 3.41
1789 2172 5.986135 CACCAAGTTAGTGCTAGATACATCC 59.014 44.000 0.00 0.00 0.00 3.51
1790 2173 5.986135 CCACCAAGTTAGTGCTAGATACATC 59.014 44.000 0.00 0.00 33.75 3.06
1791 2174 5.425539 ACCACCAAGTTAGTGCTAGATACAT 59.574 40.000 0.00 0.00 33.75 2.29
1792 2175 4.775780 ACCACCAAGTTAGTGCTAGATACA 59.224 41.667 0.00 0.00 33.75 2.29
1793 2176 5.340439 ACCACCAAGTTAGTGCTAGATAC 57.660 43.478 0.00 0.00 33.75 2.24
1794 2177 6.429151 TCTACCACCAAGTTAGTGCTAGATA 58.571 40.000 3.26 0.00 30.87 1.98
1795 2178 5.269991 TCTACCACCAAGTTAGTGCTAGAT 58.730 41.667 3.26 0.00 30.87 1.98
1796 2179 4.669700 TCTACCACCAAGTTAGTGCTAGA 58.330 43.478 3.26 3.26 32.55 2.43
1797 2180 5.599999 ATCTACCACCAAGTTAGTGCTAG 57.400 43.478 0.00 0.00 33.75 3.42
1798 2181 5.953548 TGTATCTACCACCAAGTTAGTGCTA 59.046 40.000 0.00 0.00 33.75 3.49
1799 2182 4.775780 TGTATCTACCACCAAGTTAGTGCT 59.224 41.667 0.00 0.00 33.75 4.40
1800 2183 5.080969 TGTATCTACCACCAAGTTAGTGC 57.919 43.478 0.00 0.00 33.75 4.40
1801 2184 6.127168 TGGATGTATCTACCACCAAGTTAGTG 60.127 42.308 0.00 0.00 31.23 2.74
1802 2185 5.962031 TGGATGTATCTACCACCAAGTTAGT 59.038 40.000 0.00 0.00 31.23 2.24
1803 2186 6.479972 TGGATGTATCTACCACCAAGTTAG 57.520 41.667 0.00 0.00 31.23 2.34
1804 2187 7.446106 AATGGATGTATCTACCACCAAGTTA 57.554 36.000 0.00 0.00 36.49 2.24
1805 2188 5.975988 ATGGATGTATCTACCACCAAGTT 57.024 39.130 0.00 0.00 36.49 2.66
1806 2189 5.975988 AATGGATGTATCTACCACCAAGT 57.024 39.130 0.00 0.00 36.49 3.16
1807 2190 6.356556 TCAAATGGATGTATCTACCACCAAG 58.643 40.000 0.00 0.00 36.49 3.61
1808 2191 6.320434 TCAAATGGATGTATCTACCACCAA 57.680 37.500 0.00 0.00 36.49 3.67
1809 2192 5.163205 CCTCAAATGGATGTATCTACCACCA 60.163 44.000 0.00 0.00 36.49 4.17
1810 2193 5.308825 CCTCAAATGGATGTATCTACCACC 58.691 45.833 0.00 0.00 36.49 4.61
1811 2194 5.071788 TCCCTCAAATGGATGTATCTACCAC 59.928 44.000 0.00 0.00 36.49 4.16
1812 2195 5.071788 GTCCCTCAAATGGATGTATCTACCA 59.928 44.000 0.00 0.00 38.09 3.25
1813 2196 5.071788 TGTCCCTCAAATGGATGTATCTACC 59.928 44.000 0.00 0.00 33.65 3.18
1814 2197 6.174720 TGTCCCTCAAATGGATGTATCTAC 57.825 41.667 0.00 0.00 33.65 2.59
1815 2198 6.688922 GCTTGTCCCTCAAATGGATGTATCTA 60.689 42.308 0.00 0.00 35.48 1.98
1816 2199 5.688807 CTTGTCCCTCAAATGGATGTATCT 58.311 41.667 0.00 0.00 35.48 1.98
1817 2200 4.276926 GCTTGTCCCTCAAATGGATGTATC 59.723 45.833 0.00 0.00 35.48 2.24
1818 2201 4.079558 AGCTTGTCCCTCAAATGGATGTAT 60.080 41.667 0.00 0.00 35.48 2.29
1819 2202 3.266772 AGCTTGTCCCTCAAATGGATGTA 59.733 43.478 0.00 0.00 35.48 2.29
1820 2203 2.042162 AGCTTGTCCCTCAAATGGATGT 59.958 45.455 0.00 0.00 35.48 3.06
1821 2204 2.731572 AGCTTGTCCCTCAAATGGATG 58.268 47.619 0.00 0.00 35.48 3.51
1822 2205 3.463048 AAGCTTGTCCCTCAAATGGAT 57.537 42.857 0.00 0.00 35.48 3.41
1823 2206 2.978156 AAGCTTGTCCCTCAAATGGA 57.022 45.000 0.00 0.00 35.48 3.41
1824 2207 3.306294 GGAAAAGCTTGTCCCTCAAATGG 60.306 47.826 23.49 0.00 35.48 3.16
1825 2208 3.612479 CGGAAAAGCTTGTCCCTCAAATG 60.612 47.826 26.94 9.69 35.48 2.32
1826 2209 2.558359 CGGAAAAGCTTGTCCCTCAAAT 59.442 45.455 26.94 0.00 35.48 2.32
1827 2210 1.953686 CGGAAAAGCTTGTCCCTCAAA 59.046 47.619 26.94 0.00 35.48 2.69
1828 2211 1.604604 CGGAAAAGCTTGTCCCTCAA 58.395 50.000 26.94 0.00 34.61 3.02
1829 2212 0.250727 CCGGAAAAGCTTGTCCCTCA 60.251 55.000 26.94 0.00 0.00 3.86
1830 2213 0.036306 TCCGGAAAAGCTTGTCCCTC 59.964 55.000 26.94 5.77 0.00 4.30
1831 2214 0.250770 GTCCGGAAAAGCTTGTCCCT 60.251 55.000 26.94 0.00 0.00 4.20
1832 2215 1.574702 CGTCCGGAAAAGCTTGTCCC 61.575 60.000 26.94 13.97 0.00 4.46
1833 2216 1.574702 CCGTCCGGAAAAGCTTGTCC 61.575 60.000 24.00 24.00 37.50 4.02
1834 2217 0.601841 TCCGTCCGGAAAAGCTTGTC 60.602 55.000 5.23 8.23 42.05 3.18
1835 2218 0.602905 CTCCGTCCGGAAAAGCTTGT 60.603 55.000 5.23 0.00 44.66 3.16
1836 2219 1.298859 CCTCCGTCCGGAAAAGCTTG 61.299 60.000 5.23 0.00 44.66 4.01
1837 2220 1.003718 CCTCCGTCCGGAAAAGCTT 60.004 57.895 5.23 0.00 44.66 3.74
1838 2221 2.663196 CCTCCGTCCGGAAAAGCT 59.337 61.111 5.23 0.00 44.66 3.74
1839 2222 2.436115 CCCTCCGTCCGGAAAAGC 60.436 66.667 5.23 0.00 44.66 3.51
1840 2223 1.218316 CTCCCTCCGTCCGGAAAAG 59.782 63.158 5.23 3.59 44.66 2.27
1841 2224 0.251742 TACTCCCTCCGTCCGGAAAA 60.252 55.000 5.23 0.00 44.66 2.29
1842 2225 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13
1843 2226 0.754217 CATACTCCCTCCGTCCGGAA 60.754 60.000 5.23 0.00 44.66 4.30
1844 2227 1.152819 CATACTCCCTCCGTCCGGA 60.153 63.158 0.00 0.00 42.90 5.14
1845 2228 2.857744 GCATACTCCCTCCGTCCGG 61.858 68.421 0.00 0.00 0.00 5.14
1846 2229 1.392710 AAGCATACTCCCTCCGTCCG 61.393 60.000 0.00 0.00 0.00 4.79
1847 2230 0.105039 CAAGCATACTCCCTCCGTCC 59.895 60.000 0.00 0.00 0.00 4.79
1848 2231 0.824759 ACAAGCATACTCCCTCCGTC 59.175 55.000 0.00 0.00 0.00 4.79
1849 2232 2.032620 CTACAAGCATACTCCCTCCGT 58.967 52.381 0.00 0.00 0.00 4.69
1850 2233 2.307768 TCTACAAGCATACTCCCTCCG 58.692 52.381 0.00 0.00 0.00 4.63
1851 2234 3.898123 TCATCTACAAGCATACTCCCTCC 59.102 47.826 0.00 0.00 0.00 4.30
1852 2235 5.736951 ATCATCTACAAGCATACTCCCTC 57.263 43.478 0.00 0.00 0.00 4.30
1853 2236 7.805083 AATATCATCTACAAGCATACTCCCT 57.195 36.000 0.00 0.00 0.00 4.20
1854 2237 8.972127 TCTAATATCATCTACAAGCATACTCCC 58.028 37.037 0.00 0.00 0.00 4.30
1881 2264 3.926616 TCAGTAAAGCTGCTGGTACTTC 58.073 45.455 18.58 1.80 44.66 3.01
1893 2276 7.599245 ACACACTAGTCATTTACTCAGTAAAGC 59.401 37.037 15.20 8.26 40.58 3.51
1898 2281 6.183360 ACACACACACTAGTCATTTACTCAGT 60.183 38.462 0.00 0.00 39.80 3.41
1900 2283 5.983118 CACACACACACTAGTCATTTACTCA 59.017 40.000 0.00 0.00 39.80 3.41
1939 2322 2.282110 CATCCCGCACAACACCCA 60.282 61.111 0.00 0.00 0.00 4.51
2324 2713 4.683334 GTGCTGTTGCCGGCGAAC 62.683 66.667 20.60 23.75 46.53 3.95
2414 2803 1.256812 TCACCTGAGCACGAGATGAA 58.743 50.000 0.00 0.00 0.00 2.57
2469 2866 8.257306 GGACAATATTTACCAACAACCATCATT 58.743 33.333 3.59 0.00 0.00 2.57
2472 2869 7.257722 CAGGACAATATTTACCAACAACCATC 58.742 38.462 9.46 0.00 0.00 3.51
2576 2973 6.515862 GCTCTAATGATGACGACCTGATAAGT 60.516 42.308 0.00 0.00 0.00 2.24
2577 2974 5.861251 GCTCTAATGATGACGACCTGATAAG 59.139 44.000 0.00 0.00 0.00 1.73
2578 2975 5.279006 GGCTCTAATGATGACGACCTGATAA 60.279 44.000 0.00 0.00 0.00 1.75
2580 2977 3.006323 GGCTCTAATGATGACGACCTGAT 59.994 47.826 0.00 0.00 0.00 2.90
2581 2978 2.362397 GGCTCTAATGATGACGACCTGA 59.638 50.000 0.00 0.00 0.00 3.86
2582 2979 2.363680 AGGCTCTAATGATGACGACCTG 59.636 50.000 0.00 0.00 0.00 4.00
2583 2980 2.672098 AGGCTCTAATGATGACGACCT 58.328 47.619 0.00 0.00 0.00 3.85
2584 2981 3.460857 AAGGCTCTAATGATGACGACC 57.539 47.619 0.00 0.00 0.00 4.79
2586 2983 8.367911 ACATATTAAAGGCTCTAATGATGACGA 58.632 33.333 3.32 0.00 0.00 4.20
2587 2984 8.539770 ACATATTAAAGGCTCTAATGATGACG 57.460 34.615 3.32 0.00 0.00 4.35
2630 3027 8.560355 TTCGATGAAGGAAATTAGATGACAAA 57.440 30.769 0.00 0.00 0.00 2.83
2633 3030 9.050601 AGAATTCGATGAAGGAAATTAGATGAC 57.949 33.333 0.00 0.00 0.00 3.06
2642 3039 5.902613 AATGCAGAATTCGATGAAGGAAA 57.097 34.783 0.00 0.00 0.00 3.13
2702 3099 1.838077 CGGGGGAGGAAAGTTATCTGT 59.162 52.381 0.00 0.00 0.00 3.41
2717 3114 0.824182 TAGGCAACAAACAACGGGGG 60.824 55.000 0.00 0.00 41.41 5.40
2733 3130 2.354821 GTGCCAAACGAGCCTAAATAGG 59.645 50.000 1.92 1.92 46.42 2.57
2754 3151 7.329499 AGCTAGATTATCATAATCCACTGCAG 58.671 38.462 13.48 13.48 0.00 4.41
2759 3156 9.507329 TGGAAAAGCTAGATTATCATAATCCAC 57.493 33.333 13.01 4.27 0.00 4.02
3162 3565 2.834638 AATCACTGGAATTCAGGGGG 57.165 50.000 7.93 0.00 46.67 5.40
3163 3566 3.435601 CCCTAATCACTGGAATTCAGGGG 60.436 52.174 13.15 4.52 46.67 4.79
3167 3570 5.779241 AGTTCCCTAATCACTGGAATTCA 57.221 39.130 7.93 0.00 40.11 2.57
3168 3571 9.660180 GATATAGTTCCCTAATCACTGGAATTC 57.340 37.037 0.00 0.00 40.11 2.17
3192 3795 8.689972 CCTTTTGAAAAGGCAAGTATATCAGAT 58.310 33.333 22.36 0.00 0.00 2.90
3193 3796 7.669722 ACCTTTTGAAAAGGCAAGTATATCAGA 59.330 33.333 30.92 0.00 41.10 3.27
3489 4353 8.310382 TGCATAATGTGGTTAAGCAAATAAACT 58.690 29.630 10.68 0.00 42.21 2.66
3498 4362 7.260603 AGAAAGAATGCATAATGTGGTTAAGC 58.739 34.615 0.00 0.00 37.48 3.09
3502 4366 6.869913 CACAAGAAAGAATGCATAATGTGGTT 59.130 34.615 0.00 0.00 33.76 3.67
3532 4396 5.188948 ACAAGGCCACTGTAATACTACATGA 59.811 40.000 5.01 0.00 37.41 3.07
3533 4397 5.428253 ACAAGGCCACTGTAATACTACATG 58.572 41.667 5.01 0.00 37.41 3.21
3855 4741 8.230472 CTGAAAGTGGATAATTAGCATTTCCT 57.770 34.615 16.20 0.00 0.00 3.36
3945 4831 6.941436 TGCTGCCTTTAATCAAATTGGAAATT 59.059 30.769 0.00 0.00 0.00 1.82
4420 5314 2.169832 AACACCCACTCATTCTCACG 57.830 50.000 0.00 0.00 0.00 4.35
4421 5315 7.103641 TCTATTTAACACCCACTCATTCTCAC 58.896 38.462 0.00 0.00 0.00 3.51
4901 5910 5.559427 AAGGGCAATTTCACAAAAACAAC 57.441 34.783 0.00 0.00 0.00 3.32
4973 5982 5.878406 ACAGATCCTAAACAGTCCCTATG 57.122 43.478 0.00 0.00 0.00 2.23
5010 6019 1.352352 CACCACCCTCCATCTTGAGTT 59.648 52.381 0.00 0.00 0.00 3.01
5190 6199 7.980662 TGTGATATTTTTGCCATTATGTTGGAG 59.019 33.333 0.18 0.00 39.25 3.86
5221 6230 5.142061 TGTGAAATGAAGCTCAATGCATT 57.858 34.783 5.99 5.99 45.94 3.56
5254 6263 8.961294 ACAAGATGTAACTCTCTATACGTACT 57.039 34.615 0.00 0.00 0.00 2.73
5255 6264 9.044150 AGACAAGATGTAACTCTCTATACGTAC 57.956 37.037 0.00 0.00 0.00 3.67
5256 6265 9.610705 AAGACAAGATGTAACTCTCTATACGTA 57.389 33.333 0.00 0.00 0.00 3.57
5257 6266 8.399425 CAAGACAAGATGTAACTCTCTATACGT 58.601 37.037 0.00 0.00 0.00 3.57
5258 6267 8.399425 ACAAGACAAGATGTAACTCTCTATACG 58.601 37.037 0.00 0.00 0.00 3.06
5295 6304 0.463295 CTCATGCGGCCAAGTGATCT 60.463 55.000 2.24 0.00 0.00 2.75
5296 6305 2.020131 CTCATGCGGCCAAGTGATC 58.980 57.895 2.24 0.00 0.00 2.92
5297 6306 2.117156 GCTCATGCGGCCAAGTGAT 61.117 57.895 2.24 0.00 0.00 3.06
5298 6307 2.747460 GCTCATGCGGCCAAGTGA 60.747 61.111 2.24 1.82 0.00 3.41
5386 6395 0.914644 ATGACACCTATGCTGCTGGT 59.085 50.000 0.00 3.98 33.87 4.00
5733 6743 2.095263 CCACACCCGCTTCAATAACTTG 60.095 50.000 0.00 0.00 0.00 3.16
5736 6746 1.737793 CTCCACACCCGCTTCAATAAC 59.262 52.381 0.00 0.00 0.00 1.89
5750 6760 1.342074 CAGAACCAGGAGACTCCACA 58.658 55.000 23.60 0.00 39.61 4.17
5771 6781 4.498520 AGCGACCGATCAGCCGTG 62.499 66.667 0.00 0.00 0.00 4.94
5772 6782 4.498520 CAGCGACCGATCAGCCGT 62.499 66.667 0.00 0.00 0.00 5.68
5792 6802 2.747446 ACATAACAACAATCCTGGCGAC 59.253 45.455 0.00 0.00 0.00 5.19
5793 6803 3.066291 ACATAACAACAATCCTGGCGA 57.934 42.857 0.00 0.00 0.00 5.54
5834 6844 7.596248 CAGAACAATTTTAACAGCAGCATAAGT 59.404 33.333 0.00 0.00 0.00 2.24
5862 6872 8.511604 ACTCCCACAAACAATATTAGATTCAG 57.488 34.615 0.00 0.00 0.00 3.02
5864 6874 9.573133 CAAACTCCCACAAACAATATTAGATTC 57.427 33.333 0.00 0.00 0.00 2.52
5866 6876 7.178274 TGCAAACTCCCACAAACAATATTAGAT 59.822 33.333 0.00 0.00 0.00 1.98
5898 6910 3.620929 TTATTCTAGTGCTCGGCGTAG 57.379 47.619 6.85 4.28 0.00 3.51
5921 6933 3.314553 ACACTTCGACATACAGGAAACG 58.685 45.455 0.00 0.00 0.00 3.60
5989 7005 3.388024 AGCTGTTGAGGTACTGAAGAACA 59.612 43.478 0.00 0.00 41.55 3.18
6005 7021 7.040892 CCAGCATTACATTACATCATAGCTGTT 60.041 37.037 0.00 0.00 42.91 3.16
6042 7058 4.020396 ACAATAAAATCCAGCATTGCCACA 60.020 37.500 4.70 0.00 32.76 4.17
6080 7096 7.112779 CCAGGATTACAGATCTTTACAAGGTT 58.887 38.462 0.00 0.00 0.00 3.50
6105 7121 1.145803 GACGGTACAAAGCTGTGGAC 58.854 55.000 11.22 11.22 36.96 4.02
6107 7123 0.319211 TCGACGGTACAAAGCTGTGG 60.319 55.000 9.18 0.00 36.96 4.17
6109 7125 3.129813 TGATATCGACGGTACAAAGCTGT 59.870 43.478 0.00 0.00 39.75 4.40
6153 7169 3.876914 TGTCTGAAACCAGTCACATGTTC 59.123 43.478 0.00 0.00 33.49 3.18
6177 7193 8.394667 GCATGTTAGCCTTTATGTTTTAGAAC 57.605 34.615 0.00 0.00 36.29 3.01
6232 7276 8.163408 TCTAAAGAAAAGATTCCCTTGTGATGA 58.837 33.333 0.00 0.00 36.12 2.92
6240 7284 7.177878 TCAAGCATCTAAAGAAAAGATTCCCT 58.822 34.615 0.00 0.00 36.12 4.20
6283 7327 8.531982 TGATATAAGACTGCTTGTGAGTACTTT 58.468 33.333 0.00 0.00 35.56 2.66
6318 7362 7.437713 TCCTACCTTACAGACATGATGATTT 57.562 36.000 0.00 0.00 0.00 2.17
6319 7363 7.448420 CATCCTACCTTACAGACATGATGATT 58.552 38.462 0.00 0.00 31.12 2.57
6372 7418 9.396022 GTTCAGAAATTCCATCCATACTTTCTA 57.604 33.333 0.00 0.00 33.07 2.10
6438 7484 6.884280 ATAAACTTCCTTCCTGAAAGTGTG 57.116 37.500 0.00 0.00 32.69 3.82
6439 7485 7.829706 GGATATAAACTTCCTTCCTGAAAGTGT 59.170 37.037 0.00 0.00 32.69 3.55
6463 7509 4.041567 TCATTCAGTAGTTCCAAAGCAGGA 59.958 41.667 0.00 0.00 35.41 3.86
6570 7617 2.639065 ACGAGCTCTGTTTGTTGGAAA 58.361 42.857 12.85 0.00 0.00 3.13
6579 7626 2.230266 GGAGAAGAGAACGAGCTCTGTT 59.770 50.000 19.23 19.23 44.18 3.16
6583 7630 1.178276 TGGGAGAAGAGAACGAGCTC 58.822 55.000 2.73 2.73 35.11 4.09
6652 7700 5.499047 GCTCACTATACCGCAATAACAAAC 58.501 41.667 0.00 0.00 0.00 2.93
6655 7703 3.067040 TCGCTCACTATACCGCAATAACA 59.933 43.478 0.00 0.00 0.00 2.41
6685 7733 1.835693 GGGAAGATCTGCCCTCAGG 59.164 63.158 29.88 0.00 41.31 3.86


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.