Multiple sequence alignment - TraesCS6B01G152400

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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 TraesCS6B01G152400 chr6B 100.000 2754 0 0 1 2754 156374511 156377264 0.000000e+00 5086
1 TraesCS6B01G152400 chr6B 85.694 1419 189 7 3 1420 158075315 158076720 0.000000e+00 1483
2 TraesCS6B01G152400 chr6B 83.082 1655 237 25 2 1642 159397420 159395795 0.000000e+00 1465
3 TraesCS6B01G152400 chr6B 83.615 1422 225 6 1 1420 159379434 159378019 0.000000e+00 1328
4 TraesCS6B01G152400 chr6B 76.347 1429 315 18 6 1420 156531704 156533123 0.000000e+00 745
5 TraesCS6B01G152400 chr6B 85.475 179 24 2 2399 2577 20322926 20322750 4.680000e-43 185
6 TraesCS6B01G152400 chr6B 90.076 131 7 2 1770 1894 209249732 209249862 6.100000e-37 165
7 TraesCS6B01G152400 chr6D 94.719 1742 82 5 1 1734 81672369 81674108 0.000000e+00 2699
8 TraesCS6B01G152400 chr6D 85.894 1432 195 5 3 1434 83045428 83046852 0.000000e+00 1519
9 TraesCS6B01G152400 chr6D 83.011 1654 239 24 1 1642 83526736 83525113 0.000000e+00 1459
10 TraesCS6B01G152400 chr6D 90.865 208 18 1 2136 2342 81674427 81674634 7.510000e-71 278
11 TraesCS6B01G152400 chr6D 91.525 118 10 0 2576 2693 81674777 81674894 2.190000e-36 163
12 TraesCS6B01G152400 chr6D 77.903 267 27 11 1890 2129 81674112 81674373 1.330000e-28 137
13 TraesCS6B01G152400 chr6A 92.645 1781 116 5 1 1776 98063448 98065218 0.000000e+00 2549
14 TraesCS6B01G152400 chr6A 83.031 1656 238 24 1 1642 100756879 100755253 0.000000e+00 1461
15 TraesCS6B01G152400 chr6A 82.164 1654 252 25 1 1640 100798987 100797363 0.000000e+00 1380
16 TraesCS6B01G152400 chr6A 83.251 1421 232 4 1 1420 100739702 100738287 0.000000e+00 1301
17 TraesCS6B01G152400 chr6A 92.035 226 16 1 2136 2359 98065520 98065745 1.590000e-82 316
18 TraesCS6B01G152400 chr6A 83.613 238 20 7 1889 2112 98065219 98065451 3.600000e-49 206
19 TraesCS6B01G152400 chr6A 85.946 185 24 2 2395 2578 85268244 85268061 2.160000e-46 196
20 TraesCS6B01G152400 chr3A 91.398 186 15 1 2397 2581 593351791 593351606 1.270000e-63 254
21 TraesCS6B01G152400 chr4D 92.398 171 13 0 2407 2577 44750817 44750647 7.620000e-61 244
22 TraesCS6B01G152400 chr4D 90.698 129 6 2 1771 1893 465674322 465674450 1.700000e-37 167
23 TraesCS6B01G152400 chr4D 88.194 144 9 4 1763 1900 114329087 114329228 6.100000e-37 165
24 TraesCS6B01G152400 chr5A 87.166 187 18 5 2395 2577 608627188 608627372 1.000000e-49 207
25 TraesCS6B01G152400 chr5A 81.951 205 29 7 2391 2591 594146452 594146652 1.700000e-37 167
26 TraesCS6B01G152400 chr7A 89.172 157 13 3 2422 2577 229030207 229030360 2.800000e-45 193
27 TraesCS6B01G152400 chr3B 84.737 190 21 6 2395 2577 738760586 738760398 1.680000e-42 183
28 TraesCS6B01G152400 chr3B 90.769 130 6 2 1773 1896 463130191 463130320 4.720000e-38 169
29 TraesCS6B01G152400 chr1A 84.574 188 21 7 2395 2578 258741761 258741944 2.180000e-41 180
30 TraesCS6B01G152400 chr3D 90.769 130 6 2 1770 1893 573868971 573869100 4.720000e-38 169
31 TraesCS6B01G152400 chr2B 90.769 130 6 2 1770 1893 526754063 526754192 4.720000e-38 169
32 TraesCS6B01G152400 chr5B 89.630 135 8 2 1770 1898 130514125 130514259 1.700000e-37 167
33 TraesCS6B01G152400 chr1D 90.698 129 6 2 1771 1893 357055577 357055705 1.700000e-37 167
34 TraesCS6B01G152400 chr7B 89.474 133 8 4 1768 1894 715227251 715227119 2.190000e-36 163


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 TraesCS6B01G152400 chr6B 156374511 156377264 2753 False 5086.000000 5086 100.000 1 2754 1 chr6B.!!$F1 2753
1 TraesCS6B01G152400 chr6B 158075315 158076720 1405 False 1483.000000 1483 85.694 3 1420 1 chr6B.!!$F3 1417
2 TraesCS6B01G152400 chr6B 159395795 159397420 1625 True 1465.000000 1465 83.082 2 1642 1 chr6B.!!$R3 1640
3 TraesCS6B01G152400 chr6B 159378019 159379434 1415 True 1328.000000 1328 83.615 1 1420 1 chr6B.!!$R2 1419
4 TraesCS6B01G152400 chr6B 156531704 156533123 1419 False 745.000000 745 76.347 6 1420 1 chr6B.!!$F2 1414
5 TraesCS6B01G152400 chr6D 83045428 83046852 1424 False 1519.000000 1519 85.894 3 1434 1 chr6D.!!$F1 1431
6 TraesCS6B01G152400 chr6D 83525113 83526736 1623 True 1459.000000 1459 83.011 1 1642 1 chr6D.!!$R1 1641
7 TraesCS6B01G152400 chr6D 81672369 81674894 2525 False 819.250000 2699 88.753 1 2693 4 chr6D.!!$F2 2692
8 TraesCS6B01G152400 chr6A 100755253 100756879 1626 True 1461.000000 1461 83.031 1 1642 1 chr6A.!!$R3 1641
9 TraesCS6B01G152400 chr6A 100797363 100798987 1624 True 1380.000000 1380 82.164 1 1640 1 chr6A.!!$R4 1639
10 TraesCS6B01G152400 chr6A 100738287 100739702 1415 True 1301.000000 1301 83.251 1 1420 1 chr6A.!!$R2 1419
11 TraesCS6B01G152400 chr6A 98063448 98065745 2297 False 1023.666667 2549 89.431 1 2359 3 chr6A.!!$F1 2358

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
680 689 0.815734 AGCTTGCTGATGCCATTGAC 59.184 50.0 0.0 0.0 38.71 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2211 2312 0.026933 TATACAAAACCATGCGCGCG 59.973 50.0 28.44 28.44 0.0 6.86 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
87 88 4.196193 TCGGTAGCTTTGATAACCAATGG 58.804 43.478 0.00 0.00 34.23 3.16
227 228 1.984570 TGAGGCTCCTGGAACTCCG 60.985 63.158 19.53 1.38 39.43 4.63
680 689 0.815734 AGCTTGCTGATGCCATTGAC 59.184 50.000 0.00 0.00 38.71 3.18
760 769 3.702048 CGTCCGGAAGAGCCCCAA 61.702 66.667 12.53 0.00 0.00 4.12
761 770 2.046217 GTCCGGAAGAGCCCCAAC 60.046 66.667 5.23 0.00 0.00 3.77
798 807 2.031012 CCGAGCAGGTTCAGCACA 59.969 61.111 0.00 0.00 34.51 4.57
1054 1063 4.385405 GTGGCAGCTCGCTCAGGT 62.385 66.667 7.85 0.00 41.91 4.00
1101 1110 0.877071 CAAGGACAACGATGCTGCTT 59.123 50.000 0.00 0.00 0.00 3.91
1277 1286 1.080354 AGGTGATCCCTTCCCACGA 59.920 57.895 0.00 0.00 42.73 4.35
1288 1297 4.767255 CCCACGAGCAGCAGTCCC 62.767 72.222 0.00 0.00 0.00 4.46
1415 1427 2.047844 GGAGACGAGCAGCAGCAA 60.048 61.111 3.17 0.00 45.49 3.91
1482 1506 0.102481 GCATCTGCATGGCTTTCTGG 59.898 55.000 0.00 0.00 41.59 3.86
1551 1579 2.027625 GAGGAACGGGACACAAGCG 61.028 63.158 0.00 0.00 0.00 4.68
1555 1583 3.767630 AACGGGACACAAGCGGCTT 62.768 57.895 9.94 9.94 0.00 4.35
1596 1624 0.376852 CTCTCTTCTCAGGTCGCTCG 59.623 60.000 0.00 0.00 0.00 5.03
1686 1714 2.293170 TCACACCTTGACATTTTCGCA 58.707 42.857 0.00 0.00 0.00 5.10
1688 1716 2.290367 CACACCTTGACATTTTCGCAGA 59.710 45.455 0.00 0.00 0.00 4.26
1695 1723 2.045926 ATTTTCGCAGAGGCCGCT 60.046 55.556 1.77 1.77 38.43 5.52
1733 1761 4.515191 GGTAAGTTGACTTTGTGCTCATGA 59.485 41.667 1.20 0.00 37.40 3.07
1739 1767 3.570975 TGACTTTGTGCTCATGAATTGCT 59.429 39.130 6.93 0.00 0.00 3.91
1745 1773 2.984471 GTGCTCATGAATTGCTGTGTTG 59.016 45.455 6.93 0.00 0.00 3.33
1776 1804 4.453819 GCAGGCATCCATGATTAAGTACTC 59.546 45.833 0.00 0.00 0.00 2.59
1777 1805 4.999950 CAGGCATCCATGATTAAGTACTCC 59.000 45.833 0.00 0.00 0.00 3.85
1778 1806 4.042187 AGGCATCCATGATTAAGTACTCCC 59.958 45.833 0.00 0.00 0.00 4.30
1780 1808 5.241662 GCATCCATGATTAAGTACTCCCTC 58.758 45.833 0.00 0.00 0.00 4.30
1782 1810 3.895656 TCCATGATTAAGTACTCCCTCCG 59.104 47.826 0.00 0.00 0.00 4.63
1784 1812 4.262079 CCATGATTAAGTACTCCCTCCGTC 60.262 50.000 0.00 0.00 0.00 4.79
1785 1813 3.294214 TGATTAAGTACTCCCTCCGTCC 58.706 50.000 0.00 0.00 0.00 4.79
1786 1814 2.149973 TTAAGTACTCCCTCCGTCCC 57.850 55.000 0.00 0.00 0.00 4.46
1787 1815 1.002069 TAAGTACTCCCTCCGTCCCA 58.998 55.000 0.00 0.00 0.00 4.37
1788 1816 0.115745 AAGTACTCCCTCCGTCCCAA 59.884 55.000 0.00 0.00 0.00 4.12
1789 1817 0.115745 AGTACTCCCTCCGTCCCAAA 59.884 55.000 0.00 0.00 0.00 3.28
1790 1818 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
1791 1819 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
1792 1820 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
1793 1821 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
1794 1822 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
1795 1823 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
1796 1824 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
1797 1825 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
1798 1826 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
1799 1827 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
1800 1828 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
1801 1829 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
1802 1830 5.378332 TCCGTCCCAAAATTCTTGTCTTAA 58.622 37.500 0.00 0.00 0.00 1.85
1803 1831 5.828859 TCCGTCCCAAAATTCTTGTCTTAAA 59.171 36.000 0.00 0.00 0.00 1.52
1804 1832 6.492087 TCCGTCCCAAAATTCTTGTCTTAAAT 59.508 34.615 0.00 0.00 0.00 1.40
1805 1833 7.014808 TCCGTCCCAAAATTCTTGTCTTAAATT 59.985 33.333 0.00 0.00 0.00 1.82
1806 1834 7.655732 CCGTCCCAAAATTCTTGTCTTAAATTT 59.344 33.333 0.00 0.00 34.86 1.82
1807 1835 9.685828 CGTCCCAAAATTCTTGTCTTAAATTTA 57.314 29.630 0.00 0.00 32.84 1.40
1842 1870 9.952030 TGGATGTATCTAACACTAAAACATGAA 57.048 29.630 0.00 0.00 42.09 2.57
1880 1908 9.014297 AGACAAATTTAAGACAAGTATTCTGGG 57.986 33.333 0.00 0.00 0.00 4.45
1881 1909 8.934023 ACAAATTTAAGACAAGTATTCTGGGA 57.066 30.769 0.00 0.00 0.00 4.37
1882 1910 8.793592 ACAAATTTAAGACAAGTATTCTGGGAC 58.206 33.333 0.00 0.00 0.00 4.46
1883 1911 7.611213 AATTTAAGACAAGTATTCTGGGACG 57.389 36.000 0.00 0.00 0.00 4.79
1884 1912 3.611766 AAGACAAGTATTCTGGGACGG 57.388 47.619 0.00 0.00 0.00 4.79
1885 1913 2.816411 AGACAAGTATTCTGGGACGGA 58.184 47.619 0.00 0.00 45.11 4.69
1892 1920 3.845559 TCTGGGACGGAGGGAGTA 58.154 61.111 0.00 0.00 39.80 2.59
1893 1921 1.305623 TCTGGGACGGAGGGAGTAC 59.694 63.158 0.00 0.00 39.80 2.73
1894 1922 1.212934 TCTGGGACGGAGGGAGTACT 61.213 60.000 0.00 0.00 39.80 2.73
1899 1927 3.205056 TGGGACGGAGGGAGTACTTAATA 59.795 47.826 0.00 0.00 0.00 0.98
1901 1929 4.038522 GGGACGGAGGGAGTACTTAATAAC 59.961 50.000 0.00 0.00 0.00 1.89
1907 1935 6.346896 GGAGGGAGTACTTAATAACCTGTTG 58.653 44.000 0.00 0.00 0.00 3.33
1913 1941 6.180472 AGTACTTAATAACCTGTTGCTGCAT 58.820 36.000 1.84 0.00 0.00 3.96
1916 1944 1.843368 ATAACCTGTTGCTGCATGCT 58.157 45.000 20.33 0.00 43.37 3.79
1950 1983 6.857437 TTGATCTCACATCACTTCTCCTAA 57.143 37.500 0.00 0.00 0.00 2.69
1956 1996 2.237392 ACATCACTTCTCCTAACCTGGC 59.763 50.000 0.00 0.00 0.00 4.85
1962 2002 1.927487 TCTCCTAACCTGGCGTGTTA 58.073 50.000 0.00 0.00 0.00 2.41
1969 2009 4.331717 CCTAACCTGGCGTGTTAATACTTG 59.668 45.833 0.65 0.00 0.00 3.16
1993 2033 5.423015 GCAGTCATTCTTGATCAAGTCCTA 58.577 41.667 29.80 16.67 39.38 2.94
1995 2035 6.541641 GCAGTCATTCTTGATCAAGTCCTAAT 59.458 38.462 29.80 20.49 39.38 1.73
1996 2036 7.466996 GCAGTCATTCTTGATCAAGTCCTAATG 60.467 40.741 29.80 27.94 39.38 1.90
1998 2038 6.825721 GTCATTCTTGATCAAGTCCTAATGGT 59.174 38.462 29.12 9.24 39.38 3.55
1999 2039 7.011857 GTCATTCTTGATCAAGTCCTAATGGTC 59.988 40.741 29.12 22.70 39.38 4.02
2002 2042 5.485353 TCTTGATCAAGTCCTAATGGTCTGT 59.515 40.000 29.80 0.00 39.38 3.41
2004 2044 6.867519 TGATCAAGTCCTAATGGTCTGTTA 57.132 37.500 0.00 0.00 32.23 2.41
2014 2054 7.169308 GTCCTAATGGTCTGTTATGTTATGTCG 59.831 40.741 0.00 0.00 34.23 4.35
2015 2055 7.068962 TCCTAATGGTCTGTTATGTTATGTCGA 59.931 37.037 0.00 0.00 34.23 4.20
2063 2114 9.892130 CTAACTGGATTACCTTATCTTGTTCTT 57.108 33.333 0.00 0.00 37.04 2.52
2068 2119 7.824289 TGGATTACCTTATCTTGTTCTTCTGTG 59.176 37.037 0.00 0.00 37.04 3.66
2071 2122 6.867662 ACCTTATCTTGTTCTTCTGTGTTG 57.132 37.500 0.00 0.00 0.00 3.33
2113 2167 7.180229 TGAAGAGTAAATTCACCTCCTGATACA 59.820 37.037 0.00 0.00 31.86 2.29
2119 2173 3.421394 TCACCTCCTGATACATCCCTT 57.579 47.619 0.00 0.00 0.00 3.95
2129 2183 2.157640 TACATCCCTTTTGCCCATGG 57.842 50.000 4.14 4.14 0.00 3.66
2131 2185 3.612856 TCCCTTTTGCCCATGGGA 58.387 55.556 36.00 16.78 45.58 4.37
2132 2186 1.387737 TCCCTTTTGCCCATGGGAG 59.612 57.895 36.00 21.82 43.20 4.30
2133 2187 1.079073 CCCTTTTGCCCATGGGAGT 59.921 57.895 36.00 0.00 42.11 3.85
2134 2188 0.334676 CCCTTTTGCCCATGGGAGTA 59.665 55.000 36.00 16.73 42.11 2.59
2150 2251 1.409064 GAGTATGTGATCGGTGAGGCA 59.591 52.381 0.00 0.00 0.00 4.75
2174 2275 2.752154 AGCATCCAGAGGGAAATGCATC 60.752 50.000 0.00 0.00 46.93 3.91
2229 2330 1.226267 CGCGCGCATGGTTTTGTAT 60.226 52.632 32.61 0.00 0.00 2.29
2283 2385 1.305219 TGATTTTGGAGAAGGCGCGG 61.305 55.000 8.83 0.00 0.00 6.46
2314 2416 3.685592 CGACACGCTGAGCAGATC 58.314 61.111 4.88 0.00 0.00 2.75
2325 2427 2.523245 TGAGCAGATCAGCGGAGATAT 58.477 47.619 4.27 0.00 40.15 1.63
2343 2445 6.349115 GGAGATATGCTGCTTTTGGATACATG 60.349 42.308 0.00 0.00 38.12 3.21
2379 2585 6.542852 TGCATTTATCTGCGTTTTTAGACTC 58.457 36.000 0.00 0.00 45.30 3.36
2380 2586 6.371548 TGCATTTATCTGCGTTTTTAGACTCT 59.628 34.615 0.00 0.00 45.30 3.24
2381 2587 7.547722 TGCATTTATCTGCGTTTTTAGACTCTA 59.452 33.333 0.00 0.00 45.30 2.43
2382 2588 8.388103 GCATTTATCTGCGTTTTTAGACTCTAA 58.612 33.333 0.00 0.00 31.49 2.10
2385 2591 8.997621 TTATCTGCGTTTTTAGACTCTAATGT 57.002 30.769 0.00 0.00 0.00 2.71
2386 2592 7.907214 ATCTGCGTTTTTAGACTCTAATGTT 57.093 32.000 0.00 0.00 0.00 2.71
2387 2593 7.117241 TCTGCGTTTTTAGACTCTAATGTTG 57.883 36.000 0.00 0.00 0.00 3.33
2388 2594 6.147164 TCTGCGTTTTTAGACTCTAATGTTGG 59.853 38.462 0.00 0.00 0.00 3.77
2389 2595 5.761234 TGCGTTTTTAGACTCTAATGTTGGT 59.239 36.000 0.00 0.00 0.00 3.67
2390 2596 6.930164 TGCGTTTTTAGACTCTAATGTTGGTA 59.070 34.615 0.00 0.00 0.00 3.25
2391 2597 7.117236 TGCGTTTTTAGACTCTAATGTTGGTAG 59.883 37.037 0.00 0.00 0.00 3.18
2392 2598 7.117379 GCGTTTTTAGACTCTAATGTTGGTAGT 59.883 37.037 0.00 0.00 0.00 2.73
2393 2599 8.985805 CGTTTTTAGACTCTAATGTTGGTAGTT 58.014 33.333 0.00 0.00 0.00 2.24
2395 2601 8.842358 TTTTAGACTCTAATGTTGGTAGTTGG 57.158 34.615 0.00 0.00 0.00 3.77
2396 2602 7.549147 TTAGACTCTAATGTTGGTAGTTGGT 57.451 36.000 0.00 0.00 0.00 3.67
2397 2603 6.038997 AGACTCTAATGTTGGTAGTTGGTC 57.961 41.667 0.00 0.00 0.00 4.02
2398 2604 5.780793 AGACTCTAATGTTGGTAGTTGGTCT 59.219 40.000 0.00 0.00 0.00 3.85
2399 2605 5.794894 ACTCTAATGTTGGTAGTTGGTCTG 58.205 41.667 0.00 0.00 0.00 3.51
2400 2606 5.307196 ACTCTAATGTTGGTAGTTGGTCTGT 59.693 40.000 0.00 0.00 0.00 3.41
2401 2607 5.790593 TCTAATGTTGGTAGTTGGTCTGTC 58.209 41.667 0.00 0.00 0.00 3.51
2402 2608 4.706842 AATGTTGGTAGTTGGTCTGTCT 57.293 40.909 0.00 0.00 0.00 3.41
2403 2609 5.818678 AATGTTGGTAGTTGGTCTGTCTA 57.181 39.130 0.00 0.00 0.00 2.59
2404 2610 4.866508 TGTTGGTAGTTGGTCTGTCTAG 57.133 45.455 0.00 0.00 0.00 2.43
2405 2611 3.576982 TGTTGGTAGTTGGTCTGTCTAGG 59.423 47.826 0.00 0.00 0.00 3.02
2406 2612 2.816411 TGGTAGTTGGTCTGTCTAGGG 58.184 52.381 0.00 0.00 0.00 3.53
2407 2613 1.481363 GGTAGTTGGTCTGTCTAGGGC 59.519 57.143 0.00 0.00 0.00 5.19
2408 2614 2.176889 GTAGTTGGTCTGTCTAGGGCA 58.823 52.381 0.00 0.00 0.00 5.36
2409 2615 1.958288 AGTTGGTCTGTCTAGGGCAT 58.042 50.000 0.00 0.00 0.00 4.40
2410 2616 3.116096 AGTTGGTCTGTCTAGGGCATA 57.884 47.619 0.00 0.00 0.00 3.14
2411 2617 3.658725 AGTTGGTCTGTCTAGGGCATAT 58.341 45.455 0.00 0.00 0.00 1.78
2412 2618 3.643792 AGTTGGTCTGTCTAGGGCATATC 59.356 47.826 0.00 0.00 0.00 1.63
2413 2619 3.619900 TGGTCTGTCTAGGGCATATCT 57.380 47.619 0.00 0.00 0.00 1.98
2414 2620 4.741928 TGGTCTGTCTAGGGCATATCTA 57.258 45.455 0.00 0.00 0.00 1.98
2415 2621 4.667573 TGGTCTGTCTAGGGCATATCTAG 58.332 47.826 0.00 0.00 36.46 2.43
2416 2622 4.354087 TGGTCTGTCTAGGGCATATCTAGA 59.646 45.833 0.00 0.00 40.38 2.43
2417 2623 5.015710 TGGTCTGTCTAGGGCATATCTAGAT 59.984 44.000 10.73 10.73 43.25 1.98
2418 2624 6.217693 TGGTCTGTCTAGGGCATATCTAGATA 59.782 42.308 14.76 14.76 43.25 1.98
2419 2625 7.091765 TGGTCTGTCTAGGGCATATCTAGATAT 60.092 40.741 17.93 17.93 43.25 1.63
2435 2641 8.970859 ATCTAGATATGCCCTAATTATTGCAC 57.029 34.615 2.53 1.08 36.41 4.57
2436 2642 7.917003 TCTAGATATGCCCTAATTATTGCACA 58.083 34.615 10.27 1.42 36.41 4.57
2437 2643 8.551440 TCTAGATATGCCCTAATTATTGCACAT 58.449 33.333 10.27 5.73 36.41 3.21
2438 2644 7.636150 AGATATGCCCTAATTATTGCACATC 57.364 36.000 14.92 14.92 37.79 3.06
2439 2645 7.408543 AGATATGCCCTAATTATTGCACATCT 58.591 34.615 17.72 17.72 41.68 2.90
2440 2646 8.551440 AGATATGCCCTAATTATTGCACATCTA 58.449 33.333 20.20 8.25 43.88 1.98
2441 2647 8.743085 ATATGCCCTAATTATTGCACATCTAG 57.257 34.615 10.27 0.00 36.41 2.43
2442 2648 5.316167 TGCCCTAATTATTGCACATCTAGG 58.684 41.667 5.26 0.00 0.00 3.02
2443 2649 5.163099 TGCCCTAATTATTGCACATCTAGGT 60.163 40.000 5.26 0.00 0.00 3.08
2444 2650 5.182001 GCCCTAATTATTGCACATCTAGGTG 59.818 44.000 0.04 0.04 41.72 4.00
2455 2661 5.227238 CACATCTAGGTGCTCAATCAAAC 57.773 43.478 1.90 0.00 31.10 2.93
2456 2662 4.940046 CACATCTAGGTGCTCAATCAAACT 59.060 41.667 1.90 0.00 31.10 2.66
2457 2663 6.108687 CACATCTAGGTGCTCAATCAAACTA 58.891 40.000 1.90 0.00 31.10 2.24
2458 2664 6.257411 CACATCTAGGTGCTCAATCAAACTAG 59.743 42.308 1.90 0.00 32.02 2.57
2459 2665 6.155221 ACATCTAGGTGCTCAATCAAACTAGA 59.845 38.462 1.90 0.00 38.26 2.43
2460 2666 6.605471 TCTAGGTGCTCAATCAAACTAGAA 57.395 37.500 0.00 0.00 34.62 2.10
2461 2667 7.004555 TCTAGGTGCTCAATCAAACTAGAAA 57.995 36.000 0.00 0.00 34.62 2.52
2462 2668 7.099764 TCTAGGTGCTCAATCAAACTAGAAAG 58.900 38.462 0.00 0.00 34.62 2.62
2463 2669 5.869579 AGGTGCTCAATCAAACTAGAAAGA 58.130 37.500 0.00 0.00 0.00 2.52
2464 2670 6.299141 AGGTGCTCAATCAAACTAGAAAGAA 58.701 36.000 0.00 0.00 0.00 2.52
2465 2671 6.772716 AGGTGCTCAATCAAACTAGAAAGAAA 59.227 34.615 0.00 0.00 0.00 2.52
2466 2672 7.285401 AGGTGCTCAATCAAACTAGAAAGAAAA 59.715 33.333 0.00 0.00 0.00 2.29
2467 2673 7.920682 GGTGCTCAATCAAACTAGAAAGAAAAA 59.079 33.333 0.00 0.00 0.00 1.94
2495 2701 6.740411 AAAAGACAAAAGAAAATGCTTGCA 57.260 29.167 0.00 0.00 0.00 4.08
2496 2702 6.930667 AAAGACAAAAGAAAATGCTTGCAT 57.069 29.167 1.81 1.81 0.00 3.96
2497 2703 5.917541 AGACAAAAGAAAATGCTTGCATG 57.082 34.783 8.98 0.00 0.00 4.06
2498 2704 5.603596 AGACAAAAGAAAATGCTTGCATGA 58.396 33.333 8.98 0.00 0.00 3.07
2499 2705 6.050432 AGACAAAAGAAAATGCTTGCATGAA 58.950 32.000 8.98 0.00 0.00 2.57
2500 2706 6.708949 AGACAAAAGAAAATGCTTGCATGAAT 59.291 30.769 8.98 0.00 0.00 2.57
2501 2707 7.227910 AGACAAAAGAAAATGCTTGCATGAATT 59.772 29.630 8.98 1.47 0.00 2.17
2502 2708 7.708998 ACAAAAGAAAATGCTTGCATGAATTT 58.291 26.923 11.82 11.82 0.00 1.82
2503 2709 8.192110 ACAAAAGAAAATGCTTGCATGAATTTT 58.808 25.926 24.29 24.29 37.75 1.82
2504 2710 9.666626 CAAAAGAAAATGCTTGCATGAATTTTA 57.333 25.926 24.15 0.00 35.84 1.52
2505 2711 9.887406 AAAAGAAAATGCTTGCATGAATTTTAG 57.113 25.926 24.15 2.69 35.84 1.85
2506 2712 8.611654 AAGAAAATGCTTGCATGAATTTTAGT 57.388 26.923 24.15 15.26 35.84 2.24
2507 2713 8.025243 AGAAAATGCTTGCATGAATTTTAGTG 57.975 30.769 24.15 0.00 35.84 2.74
2508 2714 7.658575 AGAAAATGCTTGCATGAATTTTAGTGT 59.341 29.630 24.15 8.52 35.84 3.55
2509 2715 8.830201 AAAATGCTTGCATGAATTTTAGTGTA 57.170 26.923 23.29 0.00 34.42 2.90
2510 2716 8.830201 AAATGCTTGCATGAATTTTAGTGTAA 57.170 26.923 11.82 0.00 0.00 2.41
2511 2717 8.830201 AATGCTTGCATGAATTTTAGTGTAAA 57.170 26.923 8.98 0.00 0.00 2.01
2512 2718 8.830201 ATGCTTGCATGAATTTTAGTGTAAAA 57.170 26.923 7.35 0.00 41.38 1.52
2513 2719 8.071122 TGCTTGCATGAATTTTAGTGTAAAAC 57.929 30.769 3.33 0.00 40.12 2.43
2514 2720 7.170658 TGCTTGCATGAATTTTAGTGTAAAACC 59.829 33.333 3.33 0.00 40.12 3.27
2515 2721 7.170658 GCTTGCATGAATTTTAGTGTAAAACCA 59.829 33.333 3.33 0.00 40.12 3.67
2516 2722 8.948631 TTGCATGAATTTTAGTGTAAAACCAA 57.051 26.923 0.00 0.00 40.12 3.67
2517 2723 9.553064 TTGCATGAATTTTAGTGTAAAACCAAT 57.447 25.926 0.00 0.00 40.12 3.16
2518 2724 8.986847 TGCATGAATTTTAGTGTAAAACCAATG 58.013 29.630 0.00 1.55 40.12 2.82
2519 2725 9.202273 GCATGAATTTTAGTGTAAAACCAATGA 57.798 29.630 0.00 0.00 40.12 2.57
2560 2766 8.992835 TGCAATACTTATAGCACATCTAGATG 57.007 34.615 27.63 27.63 44.15 2.90
2580 2786 7.042797 AGATGTGCTTTAACAAAACTGATGT 57.957 32.000 0.00 0.00 32.81 3.06
2588 2794 8.487176 GCTTTAACAAAACTGATGTTGGTAATG 58.513 33.333 2.37 0.00 40.95 1.90
2590 2796 6.478512 AACAAAACTGATGTTGGTAATGGT 57.521 33.333 0.00 0.00 39.43 3.55
2596 2802 4.522789 ACTGATGTTGGTAATGGTTGGAAC 59.477 41.667 0.00 0.00 0.00 3.62
2635 2841 4.340617 TCAAGTTGGACAGTTGGTTCTTT 58.659 39.130 2.34 0.00 36.56 2.52
2636 2842 4.157656 TCAAGTTGGACAGTTGGTTCTTTG 59.842 41.667 2.34 0.00 36.56 2.77
2649 2855 3.119173 TGGTTCTTTGTTTTGTGGCTCTG 60.119 43.478 0.00 0.00 0.00 3.35
2667 2873 2.580470 GCATCATCAGTCGCGGTCG 61.580 63.158 6.13 0.00 0.00 4.79
2677 2883 0.378257 GTCGCGGTCGGTATAGTGAA 59.622 55.000 6.13 0.00 36.13 3.18
2683 2889 3.442977 GCGGTCGGTATAGTGAATATCCT 59.557 47.826 0.00 0.00 0.00 3.24
2693 2899 2.620115 AGTGAATATCCTGCGCAAATGG 59.380 45.455 13.05 10.09 0.00 3.16
2694 2900 1.955778 TGAATATCCTGCGCAAATGGG 59.044 47.619 13.05 9.65 0.00 4.00
2701 2907 4.807039 GCGCAAATGGGCCAGCAG 62.807 66.667 13.78 4.83 46.68 4.24
2702 2908 4.807039 CGCAAATGGGCCAGCAGC 62.807 66.667 13.78 14.32 42.60 5.25
2703 2909 3.697747 GCAAATGGGCCAGCAGCA 61.698 61.111 13.78 0.00 46.50 4.41
2710 2916 3.130160 GGCCAGCAGCACACTAGC 61.130 66.667 0.00 0.00 46.50 3.42
2711 2917 2.359107 GCCAGCAGCACACTAGCA 60.359 61.111 0.00 0.00 42.97 3.49
2712 2918 2.396955 GCCAGCAGCACACTAGCAG 61.397 63.158 0.00 0.00 42.97 4.24
2713 2919 2.396955 CCAGCAGCACACTAGCAGC 61.397 63.158 0.00 0.00 45.99 5.25
2714 2920 2.046507 AGCAGCACACTAGCAGCC 60.047 61.111 0.00 0.00 46.72 4.85
2715 2921 3.130160 GCAGCACACTAGCAGCCC 61.130 66.667 0.00 0.00 40.64 5.19
2716 2922 2.348620 CAGCACACTAGCAGCCCA 59.651 61.111 0.00 0.00 36.85 5.36
2717 2923 1.302752 CAGCACACTAGCAGCCCAA 60.303 57.895 0.00 0.00 36.85 4.12
2718 2924 0.890542 CAGCACACTAGCAGCCCAAA 60.891 55.000 0.00 0.00 36.85 3.28
2719 2925 0.178992 AGCACACTAGCAGCCCAAAA 60.179 50.000 0.00 0.00 36.85 2.44
2720 2926 0.890683 GCACACTAGCAGCCCAAAAT 59.109 50.000 0.00 0.00 0.00 1.82
2721 2927 1.273327 GCACACTAGCAGCCCAAAATT 59.727 47.619 0.00 0.00 0.00 1.82
2722 2928 2.491693 GCACACTAGCAGCCCAAAATTA 59.508 45.455 0.00 0.00 0.00 1.40
2723 2929 3.131046 GCACACTAGCAGCCCAAAATTAT 59.869 43.478 0.00 0.00 0.00 1.28
2724 2930 4.338118 GCACACTAGCAGCCCAAAATTATA 59.662 41.667 0.00 0.00 0.00 0.98
2725 2931 5.506317 GCACACTAGCAGCCCAAAATTATAG 60.506 44.000 0.00 0.00 0.00 1.31
2726 2932 5.822519 CACACTAGCAGCCCAAAATTATAGA 59.177 40.000 0.00 0.00 0.00 1.98
2727 2933 6.318648 CACACTAGCAGCCCAAAATTATAGAA 59.681 38.462 0.00 0.00 0.00 2.10
2728 2934 6.889722 ACACTAGCAGCCCAAAATTATAGAAA 59.110 34.615 0.00 0.00 0.00 2.52
2729 2935 7.396055 ACACTAGCAGCCCAAAATTATAGAAAA 59.604 33.333 0.00 0.00 0.00 2.29
2730 2936 8.416329 CACTAGCAGCCCAAAATTATAGAAAAT 58.584 33.333 0.00 0.00 0.00 1.82
2731 2937 8.416329 ACTAGCAGCCCAAAATTATAGAAAATG 58.584 33.333 0.00 0.00 0.00 2.32
2732 2938 6.051074 AGCAGCCCAAAATTATAGAAAATGC 58.949 36.000 0.00 0.00 0.00 3.56
2733 2939 5.816777 GCAGCCCAAAATTATAGAAAATGCA 59.183 36.000 0.00 0.00 0.00 3.96
2734 2940 6.018507 GCAGCCCAAAATTATAGAAAATGCAG 60.019 38.462 0.00 0.00 0.00 4.41
2735 2941 7.043565 CAGCCCAAAATTATAGAAAATGCAGT 58.956 34.615 0.00 0.00 0.00 4.40
2736 2942 7.223387 CAGCCCAAAATTATAGAAAATGCAGTC 59.777 37.037 0.00 0.00 0.00 3.51
2737 2943 6.198966 GCCCAAAATTATAGAAAATGCAGTCG 59.801 38.462 0.00 0.00 0.00 4.18
2738 2944 6.198966 CCCAAAATTATAGAAAATGCAGTCGC 59.801 38.462 0.00 0.00 39.24 5.19
2749 2955 1.948104 TGCAGTCGCAGTTGTTTACT 58.052 45.000 0.00 0.00 45.36 2.24
2750 2956 2.285083 TGCAGTCGCAGTTGTTTACTT 58.715 42.857 0.00 0.00 45.36 2.24
2751 2957 2.680841 TGCAGTCGCAGTTGTTTACTTT 59.319 40.909 0.00 0.00 45.36 2.66
2752 2958 3.035942 GCAGTCGCAGTTGTTTACTTTG 58.964 45.455 0.00 0.00 38.36 2.77
2753 2959 3.035942 CAGTCGCAGTTGTTTACTTTGC 58.964 45.455 0.00 0.00 33.85 3.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
227 228 3.188048 CACAAGCACACTTCAGATCCTTC 59.812 47.826 0.00 0.00 32.29 3.46
243 244 6.151144 ACAACTCCCTTACAAATATCACAAGC 59.849 38.462 0.00 0.00 0.00 4.01
680 689 3.350833 AGCAATGGTTTAGAAGGAGCTG 58.649 45.455 0.00 0.00 0.00 4.24
760 769 0.602905 GCTGGCTACAACAACCTCGT 60.603 55.000 0.00 0.00 0.00 4.18
761 770 1.626654 CGCTGGCTACAACAACCTCG 61.627 60.000 0.00 0.00 0.00 4.63
789 798 3.748048 TCAGTAATTGCTCTGTGCTGAAC 59.252 43.478 3.20 0.00 43.37 3.18
798 807 1.211457 CCAGGGCTCAGTAATTGCTCT 59.789 52.381 0.00 0.00 38.15 4.09
1054 1063 1.694150 CTTCAACCACCTGACTGGAGA 59.306 52.381 5.22 0.00 39.71 3.71
1101 1110 1.069090 GCTGGAGTTGGTGTCGTCA 59.931 57.895 0.00 0.00 0.00 4.35
1277 1286 0.762461 GAGGGATAGGGACTGCTGCT 60.762 60.000 0.00 0.00 41.52 4.24
1288 1297 1.290324 CGACATGGCGGAGGGATAG 59.710 63.158 14.85 0.00 0.00 2.08
1385 1394 1.985116 GTCTCCTTGGCCTCTCCGT 60.985 63.158 3.32 0.00 37.80 4.69
1482 1506 1.471851 GGTTCCCTTCGCTAGCTTCTC 60.472 57.143 13.93 0.00 0.00 2.87
1551 1579 1.244816 ACAAAAAGGAGCCGTAAGCC 58.755 50.000 0.00 0.00 45.47 4.35
1555 1583 3.504520 GGATCAAACAAAAAGGAGCCGTA 59.495 43.478 0.00 0.00 0.00 4.02
1596 1624 2.793278 TTTCTTTTTCCTTCGCCTGC 57.207 45.000 0.00 0.00 0.00 4.85
1686 1714 2.821366 CAATCGCAAGCGGCCTCT 60.821 61.111 14.98 0.00 40.31 3.69
1695 1723 0.320858 TTACCGACAGGCAATCGCAA 60.321 50.000 5.02 0.00 42.76 4.85
1733 1761 5.124457 CCTGCTAACTATCAACACAGCAATT 59.876 40.000 0.00 0.00 38.45 2.32
1739 1767 3.694043 TGCCTGCTAACTATCAACACA 57.306 42.857 0.00 0.00 0.00 3.72
1745 1773 4.277515 TCATGGATGCCTGCTAACTATC 57.722 45.455 0.00 0.00 0.00 2.08
1776 1804 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
1777 1805 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
1778 1806 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
1780 1808 5.699097 TTAAGACAAGAATTTTGGGACGG 57.301 39.130 0.00 0.00 0.00 4.79
1816 1844 9.952030 TTCATGTTTTAGTGTTAGATACATCCA 57.048 29.630 0.00 0.00 39.39 3.41
1854 1882 9.014297 CCCAGAATACTTGTCTTAAATTTGTCT 57.986 33.333 0.00 0.00 0.00 3.41
1855 1883 9.010029 TCCCAGAATACTTGTCTTAAATTTGTC 57.990 33.333 0.00 0.00 0.00 3.18
1856 1884 8.793592 GTCCCAGAATACTTGTCTTAAATTTGT 58.206 33.333 0.00 0.00 0.00 2.83
1857 1885 7.962918 CGTCCCAGAATACTTGTCTTAAATTTG 59.037 37.037 0.00 0.00 0.00 2.32
1858 1886 7.120726 CCGTCCCAGAATACTTGTCTTAAATTT 59.879 37.037 0.00 0.00 0.00 1.82
1859 1887 6.598064 CCGTCCCAGAATACTTGTCTTAAATT 59.402 38.462 0.00 0.00 0.00 1.82
1860 1888 6.070424 TCCGTCCCAGAATACTTGTCTTAAAT 60.070 38.462 0.00 0.00 0.00 1.40
1861 1889 5.246656 TCCGTCCCAGAATACTTGTCTTAAA 59.753 40.000 0.00 0.00 0.00 1.52
1862 1890 4.773674 TCCGTCCCAGAATACTTGTCTTAA 59.226 41.667 0.00 0.00 0.00 1.85
1863 1891 4.346730 TCCGTCCCAGAATACTTGTCTTA 58.653 43.478 0.00 0.00 0.00 2.10
1864 1892 3.170717 TCCGTCCCAGAATACTTGTCTT 58.829 45.455 0.00 0.00 0.00 3.01
1865 1893 2.761208 CTCCGTCCCAGAATACTTGTCT 59.239 50.000 0.00 0.00 0.00 3.41
1866 1894 2.159085 CCTCCGTCCCAGAATACTTGTC 60.159 54.545 0.00 0.00 0.00 3.18
1867 1895 1.831736 CCTCCGTCCCAGAATACTTGT 59.168 52.381 0.00 0.00 0.00 3.16
1868 1896 1.139058 CCCTCCGTCCCAGAATACTTG 59.861 57.143 0.00 0.00 0.00 3.16
1869 1897 1.007963 TCCCTCCGTCCCAGAATACTT 59.992 52.381 0.00 0.00 0.00 2.24
1870 1898 0.635009 TCCCTCCGTCCCAGAATACT 59.365 55.000 0.00 0.00 0.00 2.12
1871 1899 1.041437 CTCCCTCCGTCCCAGAATAC 58.959 60.000 0.00 0.00 0.00 1.89
1872 1900 0.635009 ACTCCCTCCGTCCCAGAATA 59.365 55.000 0.00 0.00 0.00 1.75
1873 1901 0.635009 TACTCCCTCCGTCCCAGAAT 59.365 55.000 0.00 0.00 0.00 2.40
1874 1902 0.324091 GTACTCCCTCCGTCCCAGAA 60.324 60.000 0.00 0.00 0.00 3.02
1875 1903 1.212934 AGTACTCCCTCCGTCCCAGA 61.213 60.000 0.00 0.00 0.00 3.86
1876 1904 0.324460 AAGTACTCCCTCCGTCCCAG 60.324 60.000 0.00 0.00 0.00 4.45
1877 1905 1.002069 TAAGTACTCCCTCCGTCCCA 58.998 55.000 0.00 0.00 0.00 4.37
1878 1906 2.149973 TTAAGTACTCCCTCCGTCCC 57.850 55.000 0.00 0.00 0.00 4.46
1879 1907 4.038522 GGTTATTAAGTACTCCCTCCGTCC 59.961 50.000 0.00 0.00 0.00 4.79
1880 1908 4.892345 AGGTTATTAAGTACTCCCTCCGTC 59.108 45.833 0.00 0.00 0.00 4.79
1881 1909 4.648307 CAGGTTATTAAGTACTCCCTCCGT 59.352 45.833 0.00 0.00 0.00 4.69
1882 1910 4.648307 ACAGGTTATTAAGTACTCCCTCCG 59.352 45.833 0.00 0.00 0.00 4.63
1883 1911 6.346896 CAACAGGTTATTAAGTACTCCCTCC 58.653 44.000 0.00 0.00 0.00 4.30
1884 1912 5.816258 GCAACAGGTTATTAAGTACTCCCTC 59.184 44.000 0.00 0.00 0.00 4.30
1885 1913 5.487845 AGCAACAGGTTATTAAGTACTCCCT 59.512 40.000 0.00 0.00 0.00 4.20
1886 1914 5.585047 CAGCAACAGGTTATTAAGTACTCCC 59.415 44.000 0.00 0.00 0.00 4.30
1887 1915 5.064834 GCAGCAACAGGTTATTAAGTACTCC 59.935 44.000 0.00 0.00 0.00 3.85
1888 1916 5.642063 TGCAGCAACAGGTTATTAAGTACTC 59.358 40.000 0.00 0.00 0.00 2.59
1889 1917 5.556915 TGCAGCAACAGGTTATTAAGTACT 58.443 37.500 0.00 0.00 0.00 2.73
1890 1918 5.873179 TGCAGCAACAGGTTATTAAGTAC 57.127 39.130 0.00 0.00 0.00 2.73
1891 1919 5.163663 GCATGCAGCAACAGGTTATTAAGTA 60.164 40.000 14.21 0.00 44.79 2.24
1892 1920 4.380867 GCATGCAGCAACAGGTTATTAAGT 60.381 41.667 14.21 0.00 44.79 2.24
1893 1921 4.107622 GCATGCAGCAACAGGTTATTAAG 58.892 43.478 14.21 0.00 44.79 1.85
1894 1922 4.108699 GCATGCAGCAACAGGTTATTAA 57.891 40.909 14.21 0.00 44.79 1.40
1907 1935 6.949578 TCAATTAAACTAAAAGCATGCAGC 57.050 33.333 21.98 0.00 46.19 5.25
1950 1983 2.706890 CCAAGTATTAACACGCCAGGT 58.293 47.619 0.00 0.00 0.00 4.00
1956 1996 5.351465 AGAATGACTGCCAAGTATTAACACG 59.649 40.000 0.00 0.00 36.52 4.49
1962 2002 6.182627 TGATCAAGAATGACTGCCAAGTATT 58.817 36.000 0.00 0.00 38.69 1.89
1969 2009 3.376546 GGACTTGATCAAGAATGACTGCC 59.623 47.826 36.15 19.99 40.79 4.85
1993 2033 5.523916 GCTCGACATAACATAACAGACCATT 59.476 40.000 0.00 0.00 0.00 3.16
1995 2035 4.430007 GCTCGACATAACATAACAGACCA 58.570 43.478 0.00 0.00 0.00 4.02
1996 2036 3.486108 CGCTCGACATAACATAACAGACC 59.514 47.826 0.00 0.00 0.00 3.85
1998 2038 4.365899 ACGCTCGACATAACATAACAGA 57.634 40.909 0.00 0.00 0.00 3.41
1999 2039 5.450376 AAACGCTCGACATAACATAACAG 57.550 39.130 0.00 0.00 0.00 3.16
2002 2042 9.904647 GTAAATTAAACGCTCGACATAACATAA 57.095 29.630 0.00 0.00 0.00 1.90
2004 2044 8.193250 AGTAAATTAAACGCTCGACATAACAT 57.807 30.769 0.00 0.00 0.00 2.71
2014 2054 6.776094 AGCAGATCAAGTAAATTAAACGCTC 58.224 36.000 0.00 0.00 0.00 5.03
2015 2055 6.743575 AGCAGATCAAGTAAATTAAACGCT 57.256 33.333 0.00 0.00 0.00 5.07
2063 2114 3.342377 TCTGTCACCAAACAACACAGA 57.658 42.857 0.00 0.00 40.89 3.41
2068 2119 4.695217 TCAGTTTCTGTCACCAAACAAC 57.305 40.909 3.03 0.00 35.33 3.32
2071 2122 4.636206 ACTCTTCAGTTTCTGTCACCAAAC 59.364 41.667 0.00 0.00 32.61 2.93
2113 2167 2.104303 TCCCATGGGCAAAAGGGAT 58.896 52.632 27.41 0.00 45.15 3.85
2119 2173 1.638070 TCACATACTCCCATGGGCAAA 59.362 47.619 27.41 13.43 34.68 3.68
2129 2183 1.269831 GCCTCACCGATCACATACTCC 60.270 57.143 0.00 0.00 0.00 3.85
2131 2185 1.410517 CTGCCTCACCGATCACATACT 59.589 52.381 0.00 0.00 0.00 2.12
2132 2186 1.858091 CTGCCTCACCGATCACATAC 58.142 55.000 0.00 0.00 0.00 2.39
2133 2187 0.104855 GCTGCCTCACCGATCACATA 59.895 55.000 0.00 0.00 0.00 2.29
2134 2188 1.153289 GCTGCCTCACCGATCACAT 60.153 57.895 0.00 0.00 0.00 3.21
2150 2251 0.924823 ATTTCCCTCTGGATGCTGCT 59.075 50.000 0.00 0.00 41.40 4.24
2211 2312 0.026933 TATACAAAACCATGCGCGCG 59.973 50.000 28.44 28.44 0.00 6.86
2227 2328 3.648067 CCCTCCACTTGGATGCTCTTATA 59.352 47.826 0.00 0.00 44.46 0.98
2229 2330 1.839994 CCCTCCACTTGGATGCTCTTA 59.160 52.381 0.00 0.00 44.46 2.10
2283 2385 3.134127 GTCGCATTGCCCTCCACC 61.134 66.667 2.41 0.00 0.00 4.61
2325 2427 2.169330 TGCATGTATCCAAAAGCAGCA 58.831 42.857 0.00 0.00 0.00 4.41
2328 2430 7.784037 AGAAAATATGCATGTATCCAAAAGCA 58.216 30.769 10.16 0.00 33.46 3.91
2343 2445 7.752239 ACGCAGATAAATGCATAGAAAATATGC 59.248 33.333 11.91 11.91 46.87 3.14
2362 2568 7.148407 CCAACATTAGAGTCTAAAAACGCAGAT 60.148 37.037 16.37 0.00 0.00 2.90
2379 2585 5.794894 AGACAGACCAACTACCAACATTAG 58.205 41.667 0.00 0.00 0.00 1.73
2380 2586 5.818678 AGACAGACCAACTACCAACATTA 57.181 39.130 0.00 0.00 0.00 1.90
2381 2587 4.706842 AGACAGACCAACTACCAACATT 57.293 40.909 0.00 0.00 0.00 2.71
2382 2588 4.223032 CCTAGACAGACCAACTACCAACAT 59.777 45.833 0.00 0.00 0.00 2.71
2383 2589 3.576982 CCTAGACAGACCAACTACCAACA 59.423 47.826 0.00 0.00 0.00 3.33
2384 2590 3.056035 CCCTAGACAGACCAACTACCAAC 60.056 52.174 0.00 0.00 0.00 3.77
2385 2591 3.170717 CCCTAGACAGACCAACTACCAA 58.829 50.000 0.00 0.00 0.00 3.67
2386 2592 2.816411 CCCTAGACAGACCAACTACCA 58.184 52.381 0.00 0.00 0.00 3.25
2387 2593 1.481363 GCCCTAGACAGACCAACTACC 59.519 57.143 0.00 0.00 0.00 3.18
2388 2594 2.176889 TGCCCTAGACAGACCAACTAC 58.823 52.381 0.00 0.00 0.00 2.73
2389 2595 2.615986 TGCCCTAGACAGACCAACTA 57.384 50.000 0.00 0.00 0.00 2.24
2390 2596 1.958288 ATGCCCTAGACAGACCAACT 58.042 50.000 0.00 0.00 0.00 3.16
2391 2597 3.643792 AGATATGCCCTAGACAGACCAAC 59.356 47.826 0.00 0.00 0.00 3.77
2392 2598 3.928754 AGATATGCCCTAGACAGACCAA 58.071 45.455 0.00 0.00 0.00 3.67
2393 2599 3.619900 AGATATGCCCTAGACAGACCA 57.380 47.619 0.00 0.00 0.00 4.02
2394 2600 4.924625 TCTAGATATGCCCTAGACAGACC 58.075 47.826 0.00 0.00 38.08 3.85
2395 2601 8.165239 CATATCTAGATATGCCCTAGACAGAC 57.835 42.308 30.49 0.00 43.57 3.51
2410 2616 8.551440 TGTGCAATAATTAGGGCATATCTAGAT 58.449 33.333 10.73 10.73 38.68 1.98
2411 2617 7.917003 TGTGCAATAATTAGGGCATATCTAGA 58.083 34.615 14.61 0.00 38.68 2.43
2412 2618 8.743085 ATGTGCAATAATTAGGGCATATCTAG 57.257 34.615 14.61 0.00 38.68 2.43
2413 2619 8.737168 GATGTGCAATAATTAGGGCATATCTA 57.263 34.615 26.28 11.70 45.54 1.98
2414 2620 7.636150 GATGTGCAATAATTAGGGCATATCT 57.364 36.000 26.28 11.04 45.54 1.98
2416 2622 7.776969 CCTAGATGTGCAATAATTAGGGCATAT 59.223 37.037 17.48 17.48 40.15 1.78
2417 2623 7.112122 CCTAGATGTGCAATAATTAGGGCATA 58.888 38.462 14.61 12.88 38.68 3.14
2418 2624 5.948162 CCTAGATGTGCAATAATTAGGGCAT 59.052 40.000 14.61 2.99 38.68 4.40
2419 2625 5.163099 ACCTAGATGTGCAATAATTAGGGCA 60.163 40.000 9.15 9.15 32.41 5.36
2420 2626 5.182001 CACCTAGATGTGCAATAATTAGGGC 59.818 44.000 13.76 4.62 32.41 5.19
2421 2627 6.808008 CACCTAGATGTGCAATAATTAGGG 57.192 41.667 13.76 3.11 32.41 3.53
2433 2639 4.940046 AGTTTGATTGAGCACCTAGATGTG 59.060 41.667 0.00 0.00 39.29 3.21
2434 2640 5.171339 AGTTTGATTGAGCACCTAGATGT 57.829 39.130 0.00 0.00 0.00 3.06
2435 2641 6.577103 TCTAGTTTGATTGAGCACCTAGATG 58.423 40.000 0.00 0.00 30.06 2.90
2436 2642 6.798427 TCTAGTTTGATTGAGCACCTAGAT 57.202 37.500 0.00 0.00 30.06 1.98
2437 2643 6.605471 TTCTAGTTTGATTGAGCACCTAGA 57.395 37.500 0.00 0.00 31.73 2.43
2438 2644 7.099764 TCTTTCTAGTTTGATTGAGCACCTAG 58.900 38.462 0.00 0.00 0.00 3.02
2439 2645 7.004555 TCTTTCTAGTTTGATTGAGCACCTA 57.995 36.000 0.00 0.00 0.00 3.08
2440 2646 5.869579 TCTTTCTAGTTTGATTGAGCACCT 58.130 37.500 0.00 0.00 0.00 4.00
2441 2647 6.560253 TTCTTTCTAGTTTGATTGAGCACC 57.440 37.500 0.00 0.00 0.00 5.01
2442 2648 8.856490 TTTTTCTTTCTAGTTTGATTGAGCAC 57.144 30.769 0.00 0.00 0.00 4.40
2471 2677 7.143514 TGCAAGCATTTTCTTTTGTCTTTTT 57.856 28.000 0.00 0.00 0.00 1.94
2472 2678 6.740411 TGCAAGCATTTTCTTTTGTCTTTT 57.260 29.167 0.00 0.00 0.00 2.27
2473 2679 6.539464 TCATGCAAGCATTTTCTTTTGTCTTT 59.461 30.769 4.52 0.00 33.90 2.52
2474 2680 6.050432 TCATGCAAGCATTTTCTTTTGTCTT 58.950 32.000 4.52 0.00 33.90 3.01
2475 2681 5.603596 TCATGCAAGCATTTTCTTTTGTCT 58.396 33.333 4.52 0.00 33.90 3.41
2476 2682 5.910637 TCATGCAAGCATTTTCTTTTGTC 57.089 34.783 4.52 0.00 33.90 3.18
2477 2683 6.870971 ATTCATGCAAGCATTTTCTTTTGT 57.129 29.167 4.52 0.00 33.90 2.83
2478 2684 8.568732 AAAATTCATGCAAGCATTTTCTTTTG 57.431 26.923 4.52 0.00 33.90 2.44
2479 2685 9.887406 CTAAAATTCATGCAAGCATTTTCTTTT 57.113 25.926 14.02 10.81 33.90 2.27
2480 2686 9.059260 ACTAAAATTCATGCAAGCATTTTCTTT 57.941 25.926 14.02 6.10 33.90 2.52
2481 2687 8.500773 CACTAAAATTCATGCAAGCATTTTCTT 58.499 29.630 14.02 2.51 33.90 2.52
2482 2688 7.658575 ACACTAAAATTCATGCAAGCATTTTCT 59.341 29.630 14.02 1.23 33.90 2.52
2483 2689 7.799784 ACACTAAAATTCATGCAAGCATTTTC 58.200 30.769 14.02 0.00 33.90 2.29
2484 2690 7.733402 ACACTAAAATTCATGCAAGCATTTT 57.267 28.000 14.79 14.79 33.90 1.82
2485 2691 8.830201 TTACACTAAAATTCATGCAAGCATTT 57.170 26.923 4.52 0.00 33.90 2.32
2486 2692 8.830201 TTTACACTAAAATTCATGCAAGCATT 57.170 26.923 4.52 0.00 33.90 3.56
2487 2693 8.711457 GTTTTACACTAAAATTCATGCAAGCAT 58.289 29.630 0.86 0.86 39.56 3.79
2488 2694 7.170658 GGTTTTACACTAAAATTCATGCAAGCA 59.829 33.333 0.00 0.00 39.56 3.91
2489 2695 7.170658 TGGTTTTACACTAAAATTCATGCAAGC 59.829 33.333 0.00 0.00 39.56 4.01
2490 2696 8.586570 TGGTTTTACACTAAAATTCATGCAAG 57.413 30.769 0.00 0.00 39.56 4.01
2491 2697 8.948631 TTGGTTTTACACTAAAATTCATGCAA 57.051 26.923 0.00 0.00 39.56 4.08
2492 2698 8.986847 CATTGGTTTTACACTAAAATTCATGCA 58.013 29.630 0.00 0.00 39.56 3.96
2493 2699 9.202273 TCATTGGTTTTACACTAAAATTCATGC 57.798 29.630 0.00 0.00 39.56 4.06
2534 2740 9.428097 CATCTAGATGTGCTATAAGTATTGCAA 57.572 33.333 22.42 0.00 43.76 4.08
2535 2741 8.992835 CATCTAGATGTGCTATAAGTATTGCA 57.007 34.615 22.42 3.73 40.96 4.08
2551 2757 8.506437 TCAGTTTTGTTAAAGCACATCTAGATG 58.494 33.333 27.63 27.63 44.15 2.90
2552 2758 8.621532 TCAGTTTTGTTAAAGCACATCTAGAT 57.378 30.769 0.00 0.00 0.00 1.98
2553 2759 8.506437 CATCAGTTTTGTTAAAGCACATCTAGA 58.494 33.333 0.00 0.00 0.00 2.43
2554 2760 8.292448 ACATCAGTTTTGTTAAAGCACATCTAG 58.708 33.333 0.00 0.00 0.00 2.43
2555 2761 8.165239 ACATCAGTTTTGTTAAAGCACATCTA 57.835 30.769 0.00 0.00 0.00 1.98
2556 2762 7.042797 ACATCAGTTTTGTTAAAGCACATCT 57.957 32.000 0.00 0.00 0.00 2.90
2557 2763 7.306749 CCAACATCAGTTTTGTTAAAGCACATC 60.307 37.037 0.00 0.00 35.61 3.06
2558 2764 6.479660 CCAACATCAGTTTTGTTAAAGCACAT 59.520 34.615 0.00 0.00 35.61 3.21
2559 2765 5.809562 CCAACATCAGTTTTGTTAAAGCACA 59.190 36.000 0.00 0.00 35.61 4.57
2560 2766 5.810074 ACCAACATCAGTTTTGTTAAAGCAC 59.190 36.000 0.00 0.00 35.61 4.40
2561 2767 5.971763 ACCAACATCAGTTTTGTTAAAGCA 58.028 33.333 0.00 0.00 35.61 3.91
2562 2768 7.995463 TTACCAACATCAGTTTTGTTAAAGC 57.005 32.000 0.00 0.00 35.61 3.51
2563 2769 8.977505 CCATTACCAACATCAGTTTTGTTAAAG 58.022 33.333 0.00 0.00 35.61 1.85
2564 2770 8.478877 ACCATTACCAACATCAGTTTTGTTAAA 58.521 29.630 0.00 0.00 35.61 1.52
2565 2771 8.012957 ACCATTACCAACATCAGTTTTGTTAA 57.987 30.769 0.00 0.00 35.61 2.01
2566 2772 7.589958 ACCATTACCAACATCAGTTTTGTTA 57.410 32.000 0.00 0.00 35.61 2.41
2567 2773 6.478512 ACCATTACCAACATCAGTTTTGTT 57.521 33.333 0.00 0.00 37.79 2.83
2568 2774 6.279882 CAACCATTACCAACATCAGTTTTGT 58.720 36.000 0.00 0.00 35.28 2.83
2569 2775 5.695816 CCAACCATTACCAACATCAGTTTTG 59.304 40.000 0.00 0.00 35.28 2.44
2570 2776 5.600484 TCCAACCATTACCAACATCAGTTTT 59.400 36.000 0.00 0.00 35.28 2.43
2571 2777 5.144100 TCCAACCATTACCAACATCAGTTT 58.856 37.500 0.00 0.00 35.28 2.66
2572 2778 4.735369 TCCAACCATTACCAACATCAGTT 58.265 39.130 0.00 0.00 38.88 3.16
2573 2779 4.380843 TCCAACCATTACCAACATCAGT 57.619 40.909 0.00 0.00 0.00 3.41
2574 2780 4.522405 TGTTCCAACCATTACCAACATCAG 59.478 41.667 0.00 0.00 0.00 2.90
2580 2786 2.243810 GCCTGTTCCAACCATTACCAA 58.756 47.619 0.00 0.00 0.00 3.67
2588 2794 0.030235 GAAACACGCCTGTTCCAACC 59.970 55.000 1.42 0.00 39.88 3.77
2590 2796 1.021202 CAGAAACACGCCTGTTCCAA 58.979 50.000 1.42 0.00 39.88 3.53
2596 2802 1.021202 TGAAACCAGAAACACGCCTG 58.979 50.000 0.00 0.00 0.00 4.85
2635 2841 1.689984 TGATGCAGAGCCACAAAACA 58.310 45.000 0.00 0.00 0.00 2.83
2636 2842 2.229543 TGATGATGCAGAGCCACAAAAC 59.770 45.455 0.00 0.00 0.00 2.43
2649 2855 2.580470 CGACCGCGACTGATGATGC 61.580 63.158 8.23 0.00 40.82 3.91
2667 2873 4.188247 TGCGCAGGATATTCACTATACC 57.812 45.455 5.66 0.00 0.00 2.73
2677 2883 1.181098 GGCCCATTTGCGCAGGATAT 61.181 55.000 16.91 4.29 0.00 1.63
2693 2899 3.130160 GCTAGTGTGCTGCTGGCC 61.130 66.667 0.00 0.00 40.92 5.36
2694 2900 2.359107 TGCTAGTGTGCTGCTGGC 60.359 61.111 0.00 0.00 40.25 4.85
2695 2901 3.886340 CTGCTAGTGTGCTGCTGG 58.114 61.111 0.00 0.00 0.00 4.85
2699 2905 0.890542 TTTGGGCTGCTAGTGTGCTG 60.891 55.000 0.00 0.00 35.44 4.41
2700 2906 0.178992 TTTTGGGCTGCTAGTGTGCT 60.179 50.000 0.00 0.00 0.00 4.40
2701 2907 0.890683 ATTTTGGGCTGCTAGTGTGC 59.109 50.000 0.00 0.00 0.00 4.57
2702 2908 4.989279 ATAATTTTGGGCTGCTAGTGTG 57.011 40.909 0.00 0.00 0.00 3.82
2703 2909 6.001449 TCTATAATTTTGGGCTGCTAGTGT 57.999 37.500 0.00 0.00 0.00 3.55
2704 2910 6.942532 TTCTATAATTTTGGGCTGCTAGTG 57.057 37.500 0.00 0.00 0.00 2.74
2705 2911 7.954666 TTTTCTATAATTTTGGGCTGCTAGT 57.045 32.000 0.00 0.00 0.00 2.57
2706 2912 7.383300 GCATTTTCTATAATTTTGGGCTGCTAG 59.617 37.037 0.00 0.00 0.00 3.42
2707 2913 7.147759 TGCATTTTCTATAATTTTGGGCTGCTA 60.148 33.333 0.00 0.00 0.00 3.49
2708 2914 6.051074 GCATTTTCTATAATTTTGGGCTGCT 58.949 36.000 0.00 0.00 0.00 4.24
2709 2915 5.816777 TGCATTTTCTATAATTTTGGGCTGC 59.183 36.000 0.00 0.00 0.00 5.25
2710 2916 7.043565 ACTGCATTTTCTATAATTTTGGGCTG 58.956 34.615 0.00 0.00 0.00 4.85
2711 2917 7.186570 ACTGCATTTTCTATAATTTTGGGCT 57.813 32.000 0.00 0.00 0.00 5.19
2712 2918 6.198966 CGACTGCATTTTCTATAATTTTGGGC 59.801 38.462 0.00 0.00 0.00 5.36
2713 2919 6.198966 GCGACTGCATTTTCTATAATTTTGGG 59.801 38.462 0.00 0.00 42.15 4.12
2714 2920 7.153478 GCGACTGCATTTTCTATAATTTTGG 57.847 36.000 0.00 0.00 42.15 3.28
2731 2937 3.035942 CAAAGTAAACAACTGCGACTGC 58.964 45.455 0.00 0.00 38.88 4.40
2732 2938 3.035942 GCAAAGTAAACAACTGCGACTG 58.964 45.455 0.00 0.00 38.88 3.51
2733 2939 3.334272 GCAAAGTAAACAACTGCGACT 57.666 42.857 0.00 0.00 38.88 4.18


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

AutoCloner maintained by Alex Coulton.