Multiple sequence alignment - TraesCS7A01G522700

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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 TraesCS7A01G522700 chr7A 100.000 2270 0 0 1 2270 705675560 705677829 0.000000e+00 4193
1 TraesCS7A01G522700 chr7A 93.548 341 17 1 1712 2052 705632988 705632653 9.360000e-139 503
2 TraesCS7A01G522700 chr7A 90.691 333 27 2 1717 2045 393038957 393039289 7.440000e-120 440
3 TraesCS7A01G522700 chr2D 95.374 1362 56 1 1 1362 647561049 647562403 0.000000e+00 2159
4 TraesCS7A01G522700 chr2A 95.074 1360 66 1 3 1362 772828873 772827515 0.000000e+00 2139
5 TraesCS7A01G522700 chr1B 94.282 1364 77 1 1 1364 470422234 470423596 0.000000e+00 2085
6 TraesCS7A01G522700 chr7B 94.273 1362 77 1 1 1362 556334253 556335613 0.000000e+00 2082
7 TraesCS7A01G522700 chr7B 89.189 111 12 0 2125 2235 705109683 705109793 3.040000e-29 139
8 TraesCS7A01G522700 chr2B 94.183 1358 79 0 1 1358 115849608 115850965 0.000000e+00 2071
9 TraesCS7A01G522700 chr3B 94.053 1362 81 0 1 1362 136796488 136797849 0.000000e+00 2067
10 TraesCS7A01G522700 chr3B 93.260 1365 87 3 1 1360 226965369 226964005 0.000000e+00 2006
11 TraesCS7A01G522700 chr4B 93.660 1325 84 0 38 1362 535245157 535243833 0.000000e+00 1982
12 TraesCS7A01G522700 chr4B 92.642 1359 95 3 1 1358 122553988 122552634 0.000000e+00 1951
13 TraesCS7A01G522700 chr4A 93.675 332 20 1 1714 2045 474967068 474966738 1.570000e-136 496
14 TraesCS7A01G522700 chr4A 92.560 336 20 1 1718 2048 88712608 88712273 5.670000e-131 477
15 TraesCS7A01G522700 chr5A 93.902 328 19 1 1718 2044 510287412 510287085 5.630000e-136 494
16 TraesCS7A01G522700 chr5A 91.793 329 23 1 1718 2046 447364770 447364446 2.660000e-124 455
17 TraesCS7A01G522700 chr3A 92.537 335 20 1 1718 2047 143479705 143480039 2.040000e-130 475
18 TraesCS7A01G522700 chr6A 92.926 311 21 1 1736 2045 397484272 397484582 3.440000e-123 451
19 TraesCS7A01G522700 chr6A 91.239 331 26 2 1718 2045 581811294 581810964 4.450000e-122 448
20 TraesCS7A01G522700 chr7D 84.715 386 33 10 1357 1717 613798316 613798700 1.660000e-96 363
21 TraesCS7A01G522700 chr7D 90.000 110 10 1 2125 2234 613798815 613798923 8.450000e-30 141


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 TraesCS7A01G522700 chr7A 705675560 705677829 2269 False 4193 4193 100.0000 1 2270 1 chr7A.!!$F2 2269
1 TraesCS7A01G522700 chr2D 647561049 647562403 1354 False 2159 2159 95.3740 1 1362 1 chr2D.!!$F1 1361
2 TraesCS7A01G522700 chr2A 772827515 772828873 1358 True 2139 2139 95.0740 3 1362 1 chr2A.!!$R1 1359
3 TraesCS7A01G522700 chr1B 470422234 470423596 1362 False 2085 2085 94.2820 1 1364 1 chr1B.!!$F1 1363
4 TraesCS7A01G522700 chr7B 556334253 556335613 1360 False 2082 2082 94.2730 1 1362 1 chr7B.!!$F1 1361
5 TraesCS7A01G522700 chr2B 115849608 115850965 1357 False 2071 2071 94.1830 1 1358 1 chr2B.!!$F1 1357
6 TraesCS7A01G522700 chr3B 136796488 136797849 1361 False 2067 2067 94.0530 1 1362 1 chr3B.!!$F1 1361
7 TraesCS7A01G522700 chr3B 226964005 226965369 1364 True 2006 2006 93.2600 1 1360 1 chr3B.!!$R1 1359
8 TraesCS7A01G522700 chr4B 535243833 535245157 1324 True 1982 1982 93.6600 38 1362 1 chr4B.!!$R2 1324
9 TraesCS7A01G522700 chr4B 122552634 122553988 1354 True 1951 1951 92.6420 1 1358 1 chr4B.!!$R1 1357
10 TraesCS7A01G522700 chr7D 613798316 613798923 607 False 252 363 87.3575 1357 2234 2 chr7D.!!$F1 877

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
443 445 0.034337 GCCACTACGGTCCTTGTTGA 59.966 55.0 0.0 0.0 36.97 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1655 1688 0.029035 AGTTATGCGCTACCTCGTCG 59.971 55.0 9.73 0.0 0.0 5.12 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
30 31 2.893637 CGAATCCACTTCCAGTACCTG 58.106 52.381 0.00 0.00 0.00 4.00
87 88 1.364626 GAAGACATGTGGCCTCTGCG 61.365 60.000 1.15 0.00 38.85 5.18
110 111 2.567985 CCGTGTGGTTCTTGTTAAGGT 58.432 47.619 0.00 0.00 0.00 3.50
215 216 1.342275 TGCATATCTTTGGGCAGGCTT 60.342 47.619 0.00 0.00 0.00 4.35
266 268 1.178276 AACTGGGAGCTCGTCTGTAG 58.822 55.000 7.83 2.18 0.00 2.74
352 354 2.951642 CGATGGCTATGGTTTGAATGGT 59.048 45.455 0.00 0.00 0.00 3.55
443 445 0.034337 GCCACTACGGTCCTTGTTGA 59.966 55.000 0.00 0.00 36.97 3.18
476 478 1.656095 GACGCAATTCTGGAACTCGAG 59.344 52.381 11.84 11.84 0.00 4.04
486 488 0.390472 GGAACTCGAGGTGGCTCAAG 60.390 60.000 18.41 0.00 0.00 3.02
517 519 2.432456 GTGACATCGCGCCAGACA 60.432 61.111 0.00 0.00 0.00 3.41
519 521 1.079197 TGACATCGCGCCAGACATT 60.079 52.632 0.00 0.00 0.00 2.71
551 553 0.110644 CGCAAGAAGAACTCAACGGC 60.111 55.000 0.00 0.00 43.02 5.68
574 576 1.774110 ACAAGCCATGACCAACAACA 58.226 45.000 0.00 0.00 0.00 3.33
608 610 1.488390 ATTGATGGCACCAATGGTCC 58.512 50.000 6.21 7.94 31.02 4.46
672 675 0.693622 TATCAACGGTGGCCCTTGAA 59.306 50.000 0.00 0.00 34.07 2.69
674 677 2.115266 AACGGTGGCCCTTGAAGG 59.885 61.111 3.69 3.69 34.30 3.46
684 687 1.407989 GCCCTTGAAGGAGATGTGGAG 60.408 57.143 13.97 0.00 37.67 3.86
725 728 7.272144 AGTTCACTAAGGATGGGATTTACTT 57.728 36.000 0.00 0.00 0.00 2.24
792 795 4.342092 TCTGATCTTGTCAAGTCTGTGTGA 59.658 41.667 12.30 1.58 36.14 3.58
801 804 2.088104 AGTCTGTGTGAAGGGTCTGA 57.912 50.000 0.00 0.00 0.00 3.27
857 863 7.414540 GCTCGTTCTTCAAAACAGAATATGGAT 60.415 37.037 0.00 0.00 32.86 3.41
867 873 6.918067 AACAGAATATGGATATCAGACCGA 57.082 37.500 4.83 0.00 0.00 4.69
869 875 8.595362 AACAGAATATGGATATCAGACCGATA 57.405 34.615 4.83 0.00 40.90 2.92
876 882 3.003897 GGATATCAGACCGATAGATCCGC 59.996 52.174 4.83 0.00 39.98 5.54
884 890 1.583495 CGATAGATCCGCCGTGGCTA 61.583 60.000 9.55 0.00 37.33 3.93
931 937 1.055849 TAAGCAAGCACAGGAGTCCA 58.944 50.000 12.86 0.00 0.00 4.02
962 968 1.340405 ACTCTTCCAATGCCGCTTCAT 60.340 47.619 0.00 0.00 0.00 2.57
967 973 2.653726 TCCAATGCCGCTTCATATTGT 58.346 42.857 0.00 0.00 0.00 2.71
990 996 4.773674 TGCATTTGGAATGACATTCTTCCT 59.226 37.500 23.87 7.76 41.29 3.36
998 1004 3.507162 TGACATTCTTCCTTGGCTTGA 57.493 42.857 0.00 0.00 0.00 3.02
1077 1083 3.399330 GGACAACAACCTTCAGATTCGA 58.601 45.455 0.00 0.00 0.00 3.71
1190 1196 1.339631 GGTTCCATCGGTGGTCATCAA 60.340 52.381 15.92 0.00 46.16 2.57
1274 1281 4.393680 TGTAATGCCGCGAGAGTAATTTTT 59.606 37.500 8.23 0.00 0.00 1.94
1283 1290 6.090358 CCGCGAGAGTAATTTTTCTTTGTCTA 59.910 38.462 8.23 0.00 0.00 2.59
1390 1398 2.036387 GGTAATATTTGGCCACCCCAC 58.964 52.381 3.88 0.00 45.34 4.61
1414 1422 5.596845 GAAACCCAAAATAAGCACAACTCA 58.403 37.500 0.00 0.00 0.00 3.41
1422 1430 0.109342 AAGCACAACTCAGACCCCTG 59.891 55.000 0.00 0.00 41.74 4.45
1434 1442 4.431131 CCCCTGAGGCATGCGGTT 62.431 66.667 12.44 0.00 0.00 4.44
1476 1484 4.101898 TCCTTGAGTTTTGCTACACCTACA 59.898 41.667 0.00 0.00 0.00 2.74
1541 1549 0.462759 GAGCTTTAGTGGAGGCGCAT 60.463 55.000 10.83 0.00 0.00 4.73
1564 1597 1.624813 CCGGTTAAGGTGTAAGGGACA 59.375 52.381 0.00 0.00 34.94 4.02
1577 1610 2.154567 AGGGACATTCGTAGGCTACA 57.845 50.000 23.46 6.32 0.00 2.74
1593 1626 8.072567 CGTAGGCTACATAAGAAGTTTACGTAT 58.927 37.037 23.46 0.00 0.00 3.06
1621 1654 2.474410 TTTTCGCCCTCTTCTCTTCC 57.526 50.000 0.00 0.00 0.00 3.46
1622 1655 1.348064 TTTCGCCCTCTTCTCTTCCA 58.652 50.000 0.00 0.00 0.00 3.53
1624 1657 1.573108 TCGCCCTCTTCTCTTCCATT 58.427 50.000 0.00 0.00 0.00 3.16
1632 1665 4.383989 CCTCTTCTCTTCCATTCCTCCTTG 60.384 50.000 0.00 0.00 0.00 3.61
1646 1679 2.237392 CCTCCTTGGAGAAAATCGACCT 59.763 50.000 17.55 0.00 38.35 3.85
1651 1684 1.831736 TGGAGAAAATCGACCTCCTCC 59.168 52.381 19.28 17.26 45.08 4.30
1653 1686 1.749634 GAGAAAATCGACCTCCTCCGA 59.250 52.381 0.00 0.00 39.25 4.55
1655 1688 2.362717 AGAAAATCGACCTCCTCCGATC 59.637 50.000 0.00 0.00 43.72 3.69
1659 1692 2.883468 CGACCTCCTCCGATCGACG 61.883 68.421 18.66 6.66 36.70 5.12
1663 1696 1.524165 CTCCTCCGATCGACGAGGT 60.524 63.158 28.55 0.00 45.77 3.85
1667 1700 2.160487 CTCCGATCGACGAGGTAGCG 62.160 65.000 18.66 2.12 45.77 4.26
1671 1704 0.516001 GATCGACGAGGTAGCGCATA 59.484 55.000 11.47 0.00 33.86 3.14
1675 1708 1.478137 GACGAGGTAGCGCATAACTG 58.522 55.000 11.47 5.24 28.84 3.16
1690 1723 0.976641 AACTGGAATCTCGCAGGTGA 59.023 50.000 0.00 0.00 0.00 4.02
1710 1743 3.787001 GCGCAAGGGCCTCCTACT 61.787 66.667 6.46 0.00 44.07 2.57
1711 1744 2.501610 CGCAAGGGCCTCCTACTC 59.498 66.667 6.46 0.00 44.07 2.59
1712 1745 2.911928 GCAAGGGCCTCCTACTCC 59.088 66.667 6.46 0.00 44.07 3.85
1713 1746 1.690985 GCAAGGGCCTCCTACTCCT 60.691 63.158 6.46 0.00 44.07 3.69
1714 1747 0.398664 GCAAGGGCCTCCTACTCCTA 60.399 60.000 6.46 0.00 44.07 2.94
1715 1748 1.710816 CAAGGGCCTCCTACTCCTAG 58.289 60.000 6.46 0.00 44.07 3.02
1716 1749 1.062810 CAAGGGCCTCCTACTCCTAGT 60.063 57.143 6.46 0.00 44.07 2.57
1717 1750 1.320962 AGGGCCTCCTACTCCTAGTT 58.679 55.000 0.00 0.00 42.75 2.24
1718 1751 2.511420 AGGGCCTCCTACTCCTAGTTA 58.489 52.381 0.00 0.00 42.75 2.24
1719 1752 2.447811 AGGGCCTCCTACTCCTAGTTAG 59.552 54.545 0.00 0.00 42.75 2.34
1720 1753 2.446285 GGGCCTCCTACTCCTAGTTAGA 59.554 54.545 0.84 0.00 0.00 2.10
1721 1754 3.489355 GGCCTCCTACTCCTAGTTAGAC 58.511 54.545 0.00 0.00 0.00 2.59
1722 1755 3.489355 GCCTCCTACTCCTAGTTAGACC 58.511 54.545 0.00 0.00 0.00 3.85
1723 1756 3.138839 GCCTCCTACTCCTAGTTAGACCT 59.861 52.174 0.00 0.00 0.00 3.85
1724 1757 4.721132 CCTCCTACTCCTAGTTAGACCTG 58.279 52.174 0.00 0.00 0.00 4.00
1725 1758 4.446600 CCTCCTACTCCTAGTTAGACCTGG 60.447 54.167 0.00 0.00 0.00 4.45
1726 1759 3.117587 TCCTACTCCTAGTTAGACCTGGC 60.118 52.174 0.00 0.00 0.00 4.85
1727 1760 2.162264 ACTCCTAGTTAGACCTGGCC 57.838 55.000 0.00 0.00 0.00 5.36
1728 1761 1.361543 ACTCCTAGTTAGACCTGGCCA 59.638 52.381 4.71 4.71 0.00 5.36
1729 1762 2.022918 ACTCCTAGTTAGACCTGGCCAT 60.023 50.000 5.51 0.00 0.00 4.40
1730 1763 2.366916 CTCCTAGTTAGACCTGGCCATG 59.633 54.545 5.51 6.06 0.00 3.66
1731 1764 1.417890 CCTAGTTAGACCTGGCCATGG 59.582 57.143 5.51 13.05 0.00 3.66
1732 1765 1.417890 CTAGTTAGACCTGGCCATGGG 59.582 57.143 20.97 16.10 0.00 4.00
1765 1798 3.744719 GGCCCGAAAAAGCCCGAC 61.745 66.667 0.00 0.00 43.76 4.79
1766 1799 3.744719 GCCCGAAAAAGCCCGACC 61.745 66.667 0.00 0.00 0.00 4.79
1767 1800 3.060000 CCCGAAAAAGCCCGACCC 61.060 66.667 0.00 0.00 0.00 4.46
1768 1801 3.428282 CCGAAAAAGCCCGACCCG 61.428 66.667 0.00 0.00 0.00 5.28
1787 1820 4.222847 CCCGGCCCGAAGCTACTC 62.223 72.222 3.71 0.00 43.05 2.59
1788 1821 4.222847 CCGGCCCGAAGCTACTCC 62.223 72.222 3.71 0.00 43.05 3.85
1789 1822 4.222847 CGGCCCGAAGCTACTCCC 62.223 72.222 0.00 0.00 43.05 4.30
1790 1823 4.222847 GGCCCGAAGCTACTCCCG 62.223 72.222 0.00 0.00 43.05 5.14
1791 1824 4.222847 GCCCGAAGCTACTCCCGG 62.223 72.222 0.00 0.00 41.47 5.73
1793 1826 4.222847 CCGAAGCTACTCCCGGGC 62.223 72.222 18.49 2.86 38.42 6.13
1794 1827 4.222847 CGAAGCTACTCCCGGGCC 62.223 72.222 18.49 0.00 0.00 5.80
1795 1828 4.222847 GAAGCTACTCCCGGGCCG 62.223 72.222 21.46 21.46 0.00 6.13
1815 1848 3.780624 GCTCGGGCCTAGATTTTGA 57.219 52.632 9.63 0.00 0.00 2.69
1816 1849 1.587547 GCTCGGGCCTAGATTTTGAG 58.412 55.000 9.63 2.79 0.00 3.02
1817 1850 1.587547 CTCGGGCCTAGATTTTGAGC 58.412 55.000 0.84 0.00 0.00 4.26
1818 1851 0.180406 TCGGGCCTAGATTTTGAGCC 59.820 55.000 0.84 0.00 43.09 4.70
1819 1852 0.181350 CGGGCCTAGATTTTGAGCCT 59.819 55.000 0.84 0.00 43.36 4.58
1820 1853 1.685148 GGGCCTAGATTTTGAGCCTG 58.315 55.000 0.84 0.00 43.36 4.85
1821 1854 1.685148 GGCCTAGATTTTGAGCCTGG 58.315 55.000 0.00 0.00 40.57 4.45
1822 1855 1.064389 GGCCTAGATTTTGAGCCTGGT 60.064 52.381 0.00 0.00 40.57 4.00
1823 1856 2.621668 GGCCTAGATTTTGAGCCTGGTT 60.622 50.000 0.00 0.00 40.57 3.67
1824 1857 2.424956 GCCTAGATTTTGAGCCTGGTTG 59.575 50.000 0.00 0.00 0.00 3.77
1825 1858 2.424956 CCTAGATTTTGAGCCTGGTTGC 59.575 50.000 0.00 0.00 0.00 4.17
1826 1859 1.260544 AGATTTTGAGCCTGGTTGCC 58.739 50.000 0.00 0.00 0.00 4.52
1827 1860 1.203100 AGATTTTGAGCCTGGTTGCCT 60.203 47.619 0.00 0.00 0.00 4.75
1828 1861 0.971386 ATTTTGAGCCTGGTTGCCTG 59.029 50.000 0.00 0.00 0.00 4.85
1829 1862 1.114722 TTTTGAGCCTGGTTGCCTGG 61.115 55.000 6.71 6.71 44.16 4.45
1854 1887 4.115199 GAGCCTGGGCCCGACATT 62.115 66.667 19.37 0.45 43.17 2.71
1855 1888 3.645268 GAGCCTGGGCCCGACATTT 62.645 63.158 19.37 0.00 43.17 2.32
1856 1889 2.679996 GCCTGGGCCCGACATTTT 60.680 61.111 19.37 0.00 34.56 1.82
1857 1890 2.282783 GCCTGGGCCCGACATTTTT 61.283 57.895 19.37 0.00 34.56 1.94
1858 1891 0.968393 GCCTGGGCCCGACATTTTTA 60.968 55.000 19.37 0.00 34.56 1.52
1859 1892 0.815095 CCTGGGCCCGACATTTTTAC 59.185 55.000 19.37 0.00 0.00 2.01
1860 1893 1.540267 CTGGGCCCGACATTTTTACA 58.460 50.000 19.37 0.00 0.00 2.41
1861 1894 1.472480 CTGGGCCCGACATTTTTACAG 59.528 52.381 19.37 0.00 0.00 2.74
1862 1895 1.202952 TGGGCCCGACATTTTTACAGT 60.203 47.619 19.37 0.00 0.00 3.55
1863 1896 1.890489 GGGCCCGACATTTTTACAGTT 59.110 47.619 5.69 0.00 0.00 3.16
1864 1897 2.297880 GGGCCCGACATTTTTACAGTTT 59.702 45.455 5.69 0.00 0.00 2.66
1865 1898 3.243941 GGGCCCGACATTTTTACAGTTTT 60.244 43.478 5.69 0.00 0.00 2.43
1866 1899 3.985279 GGCCCGACATTTTTACAGTTTTC 59.015 43.478 0.00 0.00 0.00 2.29
1867 1900 4.261867 GGCCCGACATTTTTACAGTTTTCT 60.262 41.667 0.00 0.00 0.00 2.52
1868 1901 5.048573 GGCCCGACATTTTTACAGTTTTCTA 60.049 40.000 0.00 0.00 0.00 2.10
1869 1902 6.440436 GCCCGACATTTTTACAGTTTTCTAA 58.560 36.000 0.00 0.00 0.00 2.10
1870 1903 6.919115 GCCCGACATTTTTACAGTTTTCTAAA 59.081 34.615 0.00 0.00 0.00 1.85
1871 1904 7.114388 GCCCGACATTTTTACAGTTTTCTAAAG 59.886 37.037 0.00 0.00 0.00 1.85
1872 1905 7.593644 CCCGACATTTTTACAGTTTTCTAAAGG 59.406 37.037 0.00 0.00 0.00 3.11
1873 1906 7.593644 CCGACATTTTTACAGTTTTCTAAAGGG 59.406 37.037 0.00 0.00 0.00 3.95
1874 1907 7.593644 CGACATTTTTACAGTTTTCTAAAGGGG 59.406 37.037 0.00 0.00 0.00 4.79
1875 1908 7.214381 ACATTTTTACAGTTTTCTAAAGGGGC 58.786 34.615 0.00 0.00 0.00 5.80
1876 1909 5.794726 TTTTACAGTTTTCTAAAGGGGCC 57.205 39.130 0.00 0.00 0.00 5.80
1877 1910 2.304221 ACAGTTTTCTAAAGGGGCCC 57.696 50.000 17.12 17.12 0.00 5.80
1878 1911 1.173913 CAGTTTTCTAAAGGGGCCCG 58.826 55.000 18.95 2.19 0.00 6.13
1879 1912 0.039180 AGTTTTCTAAAGGGGCCCGG 59.961 55.000 18.95 9.21 0.00 5.73
1880 1913 1.304630 TTTTCTAAAGGGGCCCGGC 60.305 57.895 18.95 1.91 0.00 6.13
1919 1952 3.860717 GCTTTTGCATGTTCGGGC 58.139 55.556 0.00 0.00 46.58 6.13
1920 1953 1.737735 GCTTTTGCATGTTCGGGCC 60.738 57.895 0.00 0.00 46.58 5.80
1921 1954 1.444212 CTTTTGCATGTTCGGGCCG 60.444 57.895 22.51 22.51 0.00 6.13
1922 1955 1.861542 CTTTTGCATGTTCGGGCCGA 61.862 55.000 27.46 27.46 0.00 5.54
1923 1956 1.861542 TTTTGCATGTTCGGGCCGAG 61.862 55.000 29.30 18.36 37.14 4.63
1926 1959 2.436646 CATGTTCGGGCCGAGCTT 60.437 61.111 36.45 29.59 37.92 3.74
1927 1960 2.436646 ATGTTCGGGCCGAGCTTG 60.437 61.111 36.45 5.91 37.92 4.01
1928 1961 3.976701 ATGTTCGGGCCGAGCTTGG 62.977 63.158 36.45 16.53 37.92 3.61
1936 1969 2.600173 CCGAGCTTGGGCCCAAAA 60.600 61.111 36.16 17.69 39.73 2.44
1937 1970 2.206536 CCGAGCTTGGGCCCAAAAA 61.207 57.895 36.16 16.88 39.73 1.94
1938 1971 1.006220 CGAGCTTGGGCCCAAAAAC 60.006 57.895 36.16 27.04 39.73 2.43
1939 1972 1.463553 CGAGCTTGGGCCCAAAAACT 61.464 55.000 36.16 30.79 39.73 2.66
1940 1973 1.627864 GAGCTTGGGCCCAAAAACTA 58.372 50.000 36.16 15.25 39.73 2.24
1941 1974 1.546029 GAGCTTGGGCCCAAAAACTAG 59.454 52.381 36.16 24.77 39.73 2.57
1942 1975 0.608130 GCTTGGGCCCAAAAACTAGG 59.392 55.000 36.16 23.64 35.33 3.02
1943 1976 0.608130 CTTGGGCCCAAAAACTAGGC 59.392 55.000 36.16 0.00 46.37 3.93
1946 1979 3.284336 GCCCAAAAACTAGGCCCG 58.716 61.111 0.00 0.00 41.00 6.13
1947 1980 1.303806 GCCCAAAAACTAGGCCCGA 60.304 57.895 0.00 0.00 41.00 5.14
1948 1981 0.683179 GCCCAAAAACTAGGCCCGAT 60.683 55.000 0.00 0.00 41.00 4.18
1949 1982 1.102978 CCCAAAAACTAGGCCCGATG 58.897 55.000 0.00 0.00 0.00 3.84
1950 1983 1.102978 CCAAAAACTAGGCCCGATGG 58.897 55.000 0.00 0.00 0.00 3.51
1982 2015 2.600470 GCTCGGGCCCAGGTTTTT 60.600 61.111 24.92 0.00 0.00 1.94
1997 2030 1.971418 TTTTTGGCTCGGGATTGGC 59.029 52.632 0.00 0.00 0.00 4.52
1998 2031 0.541764 TTTTTGGCTCGGGATTGGCT 60.542 50.000 0.00 0.00 0.00 4.75
1999 2032 0.329931 TTTTGGCTCGGGATTGGCTA 59.670 50.000 0.00 0.00 0.00 3.93
2000 2033 0.107214 TTTGGCTCGGGATTGGCTAG 60.107 55.000 0.00 0.00 0.00 3.42
2001 2034 1.983119 TTGGCTCGGGATTGGCTAGG 61.983 60.000 0.00 0.00 0.00 3.02
2002 2035 2.281139 GCTCGGGATTGGCTAGGC 60.281 66.667 9.85 9.85 0.00 3.93
2040 2073 3.451894 GCCCGATGTTTGGCCAGG 61.452 66.667 5.11 2.45 41.97 4.45
2041 2074 2.035626 CCCGATGTTTGGCCAGGT 59.964 61.111 5.11 0.00 0.00 4.00
2042 2075 1.301623 CCCGATGTTTGGCCAGGTA 59.698 57.895 5.11 0.00 0.00 3.08
2043 2076 0.106719 CCCGATGTTTGGCCAGGTAT 60.107 55.000 5.11 0.87 0.00 2.73
2055 2088 3.206866 TGGCCAGGTATACTCCTAGTCTT 59.793 47.826 0.00 0.00 35.87 3.01
2062 2095 5.310068 AGGTATACTCCTAGTCTTCGGATGA 59.690 44.000 2.25 0.00 35.87 2.92
2077 2110 2.223900 CGGATGATAGCACAAGAGAGCA 60.224 50.000 0.00 0.00 33.43 4.26
2082 2115 3.067883 TGATAGCACAAGAGAGCAGCTAG 59.932 47.826 0.00 0.00 40.66 3.42
2103 2149 3.583086 GCGCCCCTTATCCGCAAC 61.583 66.667 0.00 0.00 46.32 4.17
2106 2152 1.077716 GCCCCTTATCCGCAACAGT 60.078 57.895 0.00 0.00 0.00 3.55
2192 2268 7.877003 TCTTACTTTTTATTTGAACGATGGCA 58.123 30.769 0.00 0.00 0.00 4.92
2193 2269 8.020819 TCTTACTTTTTATTTGAACGATGGCAG 58.979 33.333 0.00 0.00 0.00 4.85
2195 2271 2.823196 TTATTTGAACGATGGCAGCG 57.177 45.000 24.95 24.95 0.00 5.18
2198 2274 2.017138 TTTGAACGATGGCAGCGATA 57.983 45.000 33.22 14.08 0.00 2.92
2201 2277 2.560504 TGAACGATGGCAGCGATAATT 58.439 42.857 33.22 15.63 0.00 1.40
2206 2282 7.262048 TGAACGATGGCAGCGATAATTATATA 58.738 34.615 33.22 2.80 0.00 0.86
2208 2284 7.643528 ACGATGGCAGCGATAATTATATATG 57.356 36.000 33.22 0.00 0.00 1.78
2234 2310 5.601729 TGGAGATGCTCTGAGATTTGAGTAT 59.398 40.000 9.28 0.00 38.11 2.12
2235 2311 6.099413 TGGAGATGCTCTGAGATTTGAGTATT 59.901 38.462 9.28 0.00 36.15 1.89
2236 2312 6.991531 GGAGATGCTCTGAGATTTGAGTATTT 59.008 38.462 9.28 0.00 36.15 1.40
2237 2313 7.498570 GGAGATGCTCTGAGATTTGAGTATTTT 59.501 37.037 9.28 0.00 36.15 1.82
2238 2314 8.804912 AGATGCTCTGAGATTTGAGTATTTTT 57.195 30.769 9.28 0.00 36.15 1.94
2239 2315 8.675504 AGATGCTCTGAGATTTGAGTATTTTTG 58.324 33.333 9.28 0.00 36.15 2.44
2240 2316 7.984422 TGCTCTGAGATTTGAGTATTTTTGA 57.016 32.000 9.28 0.00 33.22 2.69
2241 2317 8.394971 TGCTCTGAGATTTGAGTATTTTTGAA 57.605 30.769 9.28 0.00 33.22 2.69
2242 2318 9.017509 TGCTCTGAGATTTGAGTATTTTTGAAT 57.982 29.630 9.28 0.00 33.22 2.57
2257 2333 9.226345 GTATTTTTGAATAGGAGAAATTCAGCG 57.774 33.333 0.00 0.00 42.58 5.18
2258 2334 7.447374 TTTTTGAATAGGAGAAATTCAGCGA 57.553 32.000 0.00 0.00 42.58 4.93
2259 2335 7.447374 TTTTGAATAGGAGAAATTCAGCGAA 57.553 32.000 0.00 0.00 42.58 4.70
2260 2336 6.422776 TTGAATAGGAGAAATTCAGCGAAC 57.577 37.500 0.00 0.00 42.58 3.95
2261 2337 4.876107 TGAATAGGAGAAATTCAGCGAACC 59.124 41.667 0.00 0.00 38.19 3.62
2262 2338 2.859165 AGGAGAAATTCAGCGAACCA 57.141 45.000 0.00 0.00 0.00 3.67
2263 2339 3.140325 AGGAGAAATTCAGCGAACCAA 57.860 42.857 0.00 0.00 0.00 3.67
2264 2340 3.690460 AGGAGAAATTCAGCGAACCAAT 58.310 40.909 0.00 0.00 0.00 3.16
2265 2341 3.691609 AGGAGAAATTCAGCGAACCAATC 59.308 43.478 0.00 0.00 0.00 2.67
2266 2342 3.691609 GGAGAAATTCAGCGAACCAATCT 59.308 43.478 0.00 0.00 0.00 2.40
2267 2343 4.201861 GGAGAAATTCAGCGAACCAATCTC 60.202 45.833 0.00 0.00 0.00 2.75
2268 2344 4.583871 AGAAATTCAGCGAACCAATCTCT 58.416 39.130 0.00 0.00 0.00 3.10
2269 2345 5.734720 AGAAATTCAGCGAACCAATCTCTA 58.265 37.500 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 3.447742 CTTGCCCGCAATTTTATCTTCC 58.552 45.455 1.98 0.00 35.20 3.46
87 88 0.535553 TAACAAGAACCACACGGCCC 60.536 55.000 0.00 0.00 34.57 5.80
110 111 0.613260 AGCAATGGCAGTTAGGACGA 59.387 50.000 0.00 0.00 44.61 4.20
231 232 3.306710 CCCAGTTAACCTTGCATTTTCCC 60.307 47.826 0.88 0.00 0.00 3.97
352 354 1.612462 CCATGGCTTGCTCTTGTCAGA 60.612 52.381 0.00 0.00 0.00 3.27
443 445 3.026311 GCGTCGTTCGTCCGTTGT 61.026 61.111 0.00 0.00 42.13 3.32
476 478 3.376918 GCAAGCCCTTGAGCCACC 61.377 66.667 11.96 0.00 42.93 4.61
513 515 6.262273 TCTTGCGAGAAAGGTTAAAAATGTCT 59.738 34.615 0.00 0.00 0.00 3.41
517 519 7.272037 TCTTCTTGCGAGAAAGGTTAAAAAT 57.728 32.000 17.16 0.00 41.19 1.82
519 521 6.317893 AGTTCTTCTTGCGAGAAAGGTTAAAA 59.682 34.615 17.16 1.79 41.19 1.52
551 553 0.318120 GTTGGTCATGGCTTGTTGGG 59.682 55.000 0.00 0.00 0.00 4.12
574 576 6.432162 GTGCCATCAATATTAGTGATCCACAT 59.568 38.462 19.30 0.00 36.13 3.21
608 610 3.450152 CGATATGCGCGACGGACG 61.450 66.667 12.10 5.59 45.66 4.79
725 728 2.016318 CCTTGTATGCCGATGAAGCAA 58.984 47.619 0.00 0.00 44.83 3.91
792 795 2.285743 GGGGGAGCTCAGACCCTT 60.286 66.667 25.09 0.00 44.97 3.95
857 863 2.366533 GGCGGATCTATCGGTCTGATA 58.633 52.381 1.38 1.38 38.57 2.15
876 882 2.436646 CAGTTGGGCTAGCCACGG 60.437 66.667 34.09 21.07 37.98 4.94
931 937 2.310779 TGGAAGAGTAGGTGAGCAGT 57.689 50.000 0.00 0.00 0.00 4.40
962 968 7.172868 AGAATGTCATTCCAAATGCACAATA 57.827 32.000 19.80 0.00 40.13 1.90
967 973 4.773674 AGGAAGAATGTCATTCCAAATGCA 59.226 37.500 19.80 0.00 46.21 3.96
990 996 1.117994 TGTGGTGCATTTCAAGCCAA 58.882 45.000 0.00 0.00 0.00 4.52
998 1004 5.683876 AGTAGTAGAGATGTGGTGCATTT 57.316 39.130 0.00 0.00 38.06 2.32
1077 1083 2.665603 GCTTTGGGAGAGCCGAGT 59.334 61.111 0.00 0.00 34.06 4.18
1190 1196 2.490903 GCCTCATGCTTGATCTTGTTGT 59.509 45.455 2.33 0.00 36.87 3.32
1274 1281 2.822306 CGCAAGCGGTAGACAAAGA 58.178 52.632 6.55 0.00 35.56 2.52
1390 1398 4.616953 AGTTGTGCTTATTTTGGGTTTCG 58.383 39.130 0.00 0.00 0.00 3.46
1414 1422 3.790437 CGCATGCCTCAGGGGTCT 61.790 66.667 13.15 0.00 37.43 3.85
1446 1454 1.318576 CAAAACTCAAGGAGCGGGTT 58.681 50.000 0.00 0.00 32.04 4.11
1451 1459 2.226674 GGTGTAGCAAAACTCAAGGAGC 59.773 50.000 0.00 0.00 32.04 4.70
1476 1484 6.011981 TCACATAACTCCCCTTGTAATCCTTT 60.012 38.462 0.00 0.00 0.00 3.11
1486 1494 5.831103 ACAAATCATCACATAACTCCCCTT 58.169 37.500 0.00 0.00 0.00 3.95
1492 1500 5.245531 ACACCGACAAATCATCACATAACT 58.754 37.500 0.00 0.00 0.00 2.24
1541 1549 1.832998 CCCTTACACCTTAACCGGCTA 59.167 52.381 0.00 0.00 0.00 3.93
1564 1597 7.646922 CGTAAACTTCTTATGTAGCCTACGAAT 59.353 37.037 0.00 0.00 32.01 3.34
1593 1626 1.555075 AGAGGGCGAAAATGCTAGACA 59.445 47.619 0.00 0.00 34.52 3.41
1624 1657 2.236395 GGTCGATTTTCTCCAAGGAGGA 59.764 50.000 15.74 4.46 46.75 3.71
1632 1665 1.202428 CGGAGGAGGTCGATTTTCTCC 60.202 57.143 13.80 13.80 45.46 3.71
1640 1673 1.523258 GTCGATCGGAGGAGGTCGA 60.523 63.158 16.41 0.00 40.38 4.20
1641 1674 2.883468 CGTCGATCGGAGGAGGTCG 61.883 68.421 16.41 4.26 35.71 4.79
1646 1679 0.249784 CTACCTCGTCGATCGGAGGA 60.250 60.000 33.62 21.41 38.88 3.71
1651 1684 2.425448 GCGCTACCTCGTCGATCG 60.425 66.667 9.36 9.36 41.41 3.69
1653 1686 0.949397 TTATGCGCTACCTCGTCGAT 59.051 50.000 9.73 0.00 0.00 3.59
1655 1688 0.029035 AGTTATGCGCTACCTCGTCG 59.971 55.000 9.73 0.00 0.00 5.12
1659 1692 2.596904 TTCCAGTTATGCGCTACCTC 57.403 50.000 9.73 0.00 0.00 3.85
1663 1696 2.862530 GCGAGATTCCAGTTATGCGCTA 60.863 50.000 9.73 0.00 40.03 4.26
1667 1700 1.869767 CCTGCGAGATTCCAGTTATGC 59.130 52.381 0.00 0.00 0.00 3.14
1671 1704 0.976641 TCACCTGCGAGATTCCAGTT 59.023 50.000 0.00 0.00 0.00 3.16
1675 1708 1.162800 GCCATCACCTGCGAGATTCC 61.163 60.000 0.00 0.00 0.00 3.01
1708 1741 1.361543 TGGCCAGGTCTAACTAGGAGT 59.638 52.381 0.00 0.00 0.00 3.85
1709 1742 2.160721 TGGCCAGGTCTAACTAGGAG 57.839 55.000 0.00 0.00 0.00 3.69
1710 1743 2.398588 CATGGCCAGGTCTAACTAGGA 58.601 52.381 13.05 0.00 0.00 2.94
1711 1744 1.417890 CCATGGCCAGGTCTAACTAGG 59.582 57.143 17.55 0.00 0.00 3.02
1712 1745 1.417890 CCCATGGCCAGGTCTAACTAG 59.582 57.143 17.55 0.00 0.00 2.57
1713 1746 1.507140 CCCATGGCCAGGTCTAACTA 58.493 55.000 17.55 0.00 0.00 2.24
1714 1747 1.926426 GCCCATGGCCAGGTCTAACT 61.926 60.000 17.55 0.00 44.06 2.24
1715 1748 1.453928 GCCCATGGCCAGGTCTAAC 60.454 63.158 17.55 0.00 44.06 2.34
1716 1749 3.006677 GCCCATGGCCAGGTCTAA 58.993 61.111 17.55 0.00 44.06 2.10
1748 1781 3.744719 GTCGGGCTTTTTCGGGCC 61.745 66.667 0.00 0.00 46.89 5.80
1749 1782 3.744719 GGTCGGGCTTTTTCGGGC 61.745 66.667 0.00 0.00 0.00 6.13
1750 1783 3.060000 GGGTCGGGCTTTTTCGGG 61.060 66.667 0.00 0.00 0.00 5.14
1751 1784 3.428282 CGGGTCGGGCTTTTTCGG 61.428 66.667 0.00 0.00 0.00 4.30
1752 1785 3.428282 CCGGGTCGGGCTTTTTCG 61.428 66.667 0.00 0.00 44.15 3.46
1770 1803 4.222847 GAGTAGCTTCGGGCCGGG 62.223 72.222 27.98 19.79 43.05 5.73
1771 1804 4.222847 GGAGTAGCTTCGGGCCGG 62.223 72.222 27.98 12.42 43.05 6.13
1772 1805 4.222847 GGGAGTAGCTTCGGGCCG 62.223 72.222 22.51 22.51 43.05 6.13
1773 1806 4.222847 CGGGAGTAGCTTCGGGCC 62.223 72.222 0.00 0.00 43.05 5.80
1774 1807 4.222847 CCGGGAGTAGCTTCGGGC 62.223 72.222 0.00 0.00 38.93 6.13
1776 1809 4.222847 GCCCGGGAGTAGCTTCGG 62.223 72.222 29.31 0.00 41.90 4.30
1777 1810 4.222847 GGCCCGGGAGTAGCTTCG 62.223 72.222 29.31 0.00 0.00 3.79
1778 1811 4.222847 CGGCCCGGGAGTAGCTTC 62.223 72.222 29.31 2.59 0.00 3.86
1797 1830 1.587547 CTCAAAATCTAGGCCCGAGC 58.412 55.000 0.00 0.00 38.76 5.03
1798 1831 1.587547 GCTCAAAATCTAGGCCCGAG 58.412 55.000 0.00 0.00 0.00 4.63
1799 1832 0.180406 GGCTCAAAATCTAGGCCCGA 59.820 55.000 0.00 0.00 37.12 5.14
1800 1833 0.181350 AGGCTCAAAATCTAGGCCCG 59.819 55.000 0.00 0.00 43.36 6.13
1801 1834 1.685148 CAGGCTCAAAATCTAGGCCC 58.315 55.000 0.00 0.00 43.36 5.80
1802 1835 1.064389 ACCAGGCTCAAAATCTAGGCC 60.064 52.381 0.00 0.00 42.74 5.19
1803 1836 2.424956 CAACCAGGCTCAAAATCTAGGC 59.575 50.000 0.00 0.00 38.50 3.93
1804 1837 2.424956 GCAACCAGGCTCAAAATCTAGG 59.575 50.000 0.00 0.00 0.00 3.02
1805 1838 2.424956 GGCAACCAGGCTCAAAATCTAG 59.575 50.000 0.00 0.00 40.24 2.43
1806 1839 2.446435 GGCAACCAGGCTCAAAATCTA 58.554 47.619 0.00 0.00 40.24 1.98
1807 1840 1.260544 GGCAACCAGGCTCAAAATCT 58.739 50.000 0.00 0.00 40.24 2.40
1808 1841 3.820595 GGCAACCAGGCTCAAAATC 57.179 52.632 0.00 0.00 40.24 2.17
1837 1870 3.645268 AAATGTCGGGCCCAGGCTC 62.645 63.158 24.92 2.88 41.60 4.70
1838 1871 2.730129 AAAAATGTCGGGCCCAGGCT 62.730 55.000 24.92 0.00 41.60 4.58
1839 1872 0.968393 TAAAAATGTCGGGCCCAGGC 60.968 55.000 24.92 16.99 41.06 4.85
1840 1873 0.815095 GTAAAAATGTCGGGCCCAGG 59.185 55.000 24.92 6.44 0.00 4.45
1841 1874 1.472480 CTGTAAAAATGTCGGGCCCAG 59.528 52.381 24.92 15.19 0.00 4.45
1842 1875 1.202952 ACTGTAAAAATGTCGGGCCCA 60.203 47.619 24.92 6.15 0.00 5.36
1843 1876 1.541379 ACTGTAAAAATGTCGGGCCC 58.459 50.000 13.57 13.57 0.00 5.80
1844 1877 3.653539 AAACTGTAAAAATGTCGGGCC 57.346 42.857 0.00 0.00 0.00 5.80
1845 1878 4.866921 AGAAAACTGTAAAAATGTCGGGC 58.133 39.130 0.00 0.00 0.00 6.13
1846 1879 7.593644 CCTTTAGAAAACTGTAAAAATGTCGGG 59.406 37.037 0.00 0.00 0.00 5.14
1847 1880 7.593644 CCCTTTAGAAAACTGTAAAAATGTCGG 59.406 37.037 0.00 0.00 0.00 4.79
1848 1881 7.593644 CCCCTTTAGAAAACTGTAAAAATGTCG 59.406 37.037 0.00 0.00 0.00 4.35
1849 1882 7.384115 GCCCCTTTAGAAAACTGTAAAAATGTC 59.616 37.037 0.00 0.00 0.00 3.06
1850 1883 7.214381 GCCCCTTTAGAAAACTGTAAAAATGT 58.786 34.615 0.00 0.00 0.00 2.71
1851 1884 6.649141 GGCCCCTTTAGAAAACTGTAAAAATG 59.351 38.462 0.00 0.00 0.00 2.32
1852 1885 6.239772 GGGCCCCTTTAGAAAACTGTAAAAAT 60.240 38.462 12.23 0.00 0.00 1.82
1853 1886 5.070714 GGGCCCCTTTAGAAAACTGTAAAAA 59.929 40.000 12.23 0.00 0.00 1.94
1854 1887 4.589798 GGGCCCCTTTAGAAAACTGTAAAA 59.410 41.667 12.23 0.00 0.00 1.52
1855 1888 4.154176 GGGCCCCTTTAGAAAACTGTAAA 58.846 43.478 12.23 0.00 0.00 2.01
1856 1889 3.770046 GGGCCCCTTTAGAAAACTGTAA 58.230 45.455 12.23 0.00 0.00 2.41
1857 1890 2.290450 CGGGCCCCTTTAGAAAACTGTA 60.290 50.000 18.66 0.00 0.00 2.74
1858 1891 1.546998 CGGGCCCCTTTAGAAAACTGT 60.547 52.381 18.66 0.00 0.00 3.55
1859 1892 1.173913 CGGGCCCCTTTAGAAAACTG 58.826 55.000 18.66 0.00 0.00 3.16
1860 1893 0.039180 CCGGGCCCCTTTAGAAAACT 59.961 55.000 18.66 0.00 0.00 2.66
1861 1894 1.601419 GCCGGGCCCCTTTAGAAAAC 61.601 60.000 18.66 0.00 0.00 2.43
1862 1895 1.304630 GCCGGGCCCCTTTAGAAAA 60.305 57.895 18.66 0.00 0.00 2.29
1863 1896 2.357446 GCCGGGCCCCTTTAGAAA 59.643 61.111 18.66 0.00 0.00 2.52
1864 1897 3.735097 GGCCGGGCCCCTTTAGAA 61.735 66.667 28.23 0.00 44.06 2.10
1895 1928 4.799824 CATGCAAAAGCCCGCCGG 62.800 66.667 0.00 0.00 0.00 6.13
1896 1929 3.572196 AACATGCAAAAGCCCGCCG 62.572 57.895 0.00 0.00 0.00 6.46
1897 1930 1.737735 GAACATGCAAAAGCCCGCC 60.738 57.895 0.00 0.00 0.00 6.13
1898 1931 2.088178 CGAACATGCAAAAGCCCGC 61.088 57.895 0.00 0.00 0.00 6.13
1899 1932 1.444212 CCGAACATGCAAAAGCCCG 60.444 57.895 0.00 0.00 0.00 6.13
1900 1933 1.079888 CCCGAACATGCAAAAGCCC 60.080 57.895 0.00 0.00 0.00 5.19
1901 1934 1.737735 GCCCGAACATGCAAAAGCC 60.738 57.895 0.00 0.00 0.00 4.35
1902 1935 1.737735 GGCCCGAACATGCAAAAGC 60.738 57.895 0.00 0.00 0.00 3.51
1903 1936 1.444212 CGGCCCGAACATGCAAAAG 60.444 57.895 0.00 0.00 0.00 2.27
1904 1937 1.861542 CTCGGCCCGAACATGCAAAA 61.862 55.000 7.50 0.00 34.74 2.44
1905 1938 2.281831 TCGGCCCGAACATGCAAA 60.282 55.556 1.70 0.00 31.06 3.68
1906 1939 2.745884 CTCGGCCCGAACATGCAA 60.746 61.111 7.50 0.00 34.74 4.08
1909 1942 2.436646 AAGCTCGGCCCGAACATG 60.437 61.111 7.50 0.00 34.74 3.21
1910 1943 2.436646 CAAGCTCGGCCCGAACAT 60.437 61.111 7.50 0.00 34.74 2.71
1911 1944 4.697756 CCAAGCTCGGCCCGAACA 62.698 66.667 7.50 0.00 34.74 3.18
1919 1952 2.206536 TTTTTGGGCCCAAGCTCGG 61.207 57.895 35.02 0.00 45.33 4.63
1920 1953 1.006220 GTTTTTGGGCCCAAGCTCG 60.006 57.895 35.02 0.00 45.33 5.03
1921 1954 1.546029 CTAGTTTTTGGGCCCAAGCTC 59.454 52.381 35.02 26.42 41.29 4.09
1922 1955 1.632589 CTAGTTTTTGGGCCCAAGCT 58.367 50.000 35.02 31.40 39.73 3.74
1923 1956 0.608130 CCTAGTTTTTGGGCCCAAGC 59.392 55.000 35.02 27.17 37.24 4.01
1924 1957 0.608130 GCCTAGTTTTTGGGCCCAAG 59.392 55.000 35.02 23.09 39.96 3.61
1925 1958 2.753319 GCCTAGTTTTTGGGCCCAA 58.247 52.632 34.07 34.07 39.96 4.12
1926 1959 4.531351 GCCTAGTTTTTGGGCCCA 57.469 55.556 24.45 24.45 39.96 5.36
1929 1962 0.683179 ATCGGGCCTAGTTTTTGGGC 60.683 55.000 0.84 0.00 46.59 5.36
1930 1963 1.102978 CATCGGGCCTAGTTTTTGGG 58.897 55.000 0.84 0.00 0.00 4.12
1931 1964 1.102978 CCATCGGGCCTAGTTTTTGG 58.897 55.000 0.84 0.00 0.00 3.28
1965 1998 2.600470 AAAAACCTGGGCCCGAGC 60.600 61.111 19.37 0.00 38.76 5.03
1979 2012 0.541764 AGCCAATCCCGAGCCAAAAA 60.542 50.000 0.00 0.00 0.00 1.94
1980 2013 0.329931 TAGCCAATCCCGAGCCAAAA 59.670 50.000 0.00 0.00 0.00 2.44
1981 2014 0.107214 CTAGCCAATCCCGAGCCAAA 60.107 55.000 0.00 0.00 0.00 3.28
1982 2015 1.526887 CTAGCCAATCCCGAGCCAA 59.473 57.895 0.00 0.00 0.00 4.52
1983 2016 2.443394 CCTAGCCAATCCCGAGCCA 61.443 63.158 0.00 0.00 0.00 4.75
1984 2017 2.427753 CCTAGCCAATCCCGAGCC 59.572 66.667 0.00 0.00 0.00 4.70
1985 2018 2.281139 GCCTAGCCAATCCCGAGC 60.281 66.667 0.00 0.00 0.00 5.03
2024 2057 0.106719 ATACCTGGCCAAACATCGGG 60.107 55.000 7.01 4.92 0.00 5.14
2025 2058 2.158813 AGTATACCTGGCCAAACATCGG 60.159 50.000 7.01 5.79 0.00 4.18
2026 2059 3.131396 GAGTATACCTGGCCAAACATCG 58.869 50.000 7.01 0.00 0.00 3.84
2027 2060 3.136626 AGGAGTATACCTGGCCAAACATC 59.863 47.826 7.01 0.00 39.01 3.06
2028 2061 3.123273 AGGAGTATACCTGGCCAAACAT 58.877 45.455 7.01 2.09 39.01 2.71
2029 2062 2.557869 AGGAGTATACCTGGCCAAACA 58.442 47.619 7.01 0.00 39.01 2.83
2030 2063 3.710165 ACTAGGAGTATACCTGGCCAAAC 59.290 47.826 7.01 0.00 41.30 2.93
2031 2064 3.965347 GACTAGGAGTATACCTGGCCAAA 59.035 47.826 7.01 0.00 41.30 3.28
2032 2065 3.206866 AGACTAGGAGTATACCTGGCCAA 59.793 47.826 7.01 0.00 41.30 4.52
2033 2066 2.789992 AGACTAGGAGTATACCTGGCCA 59.210 50.000 4.71 4.71 41.30 5.36
2034 2067 3.529216 AGACTAGGAGTATACCTGGCC 57.471 52.381 0.00 0.00 41.30 5.36
2035 2068 3.502979 CGAAGACTAGGAGTATACCTGGC 59.497 52.174 0.00 0.00 41.30 4.85
2036 2069 4.073549 CCGAAGACTAGGAGTATACCTGG 58.926 52.174 0.00 0.00 42.88 4.45
2037 2070 4.970711 TCCGAAGACTAGGAGTATACCTG 58.029 47.826 0.00 0.00 40.81 4.00
2038 2071 5.310068 TCATCCGAAGACTAGGAGTATACCT 59.690 44.000 0.00 0.00 40.26 3.08
2039 2072 5.558818 TCATCCGAAGACTAGGAGTATACC 58.441 45.833 0.00 0.00 40.26 2.73
2040 2073 7.011669 GCTATCATCCGAAGACTAGGAGTATAC 59.988 44.444 0.00 0.00 40.26 1.47
2041 2074 7.049133 GCTATCATCCGAAGACTAGGAGTATA 58.951 42.308 5.90 5.36 40.26 1.47
2042 2075 5.883673 GCTATCATCCGAAGACTAGGAGTAT 59.116 44.000 5.90 4.66 40.26 2.12
2043 2076 5.221864 TGCTATCATCCGAAGACTAGGAGTA 60.222 44.000 5.90 0.00 40.26 2.59
2055 2088 2.035193 GCTCTCTTGTGCTATCATCCGA 59.965 50.000 0.00 0.00 0.00 4.55
2062 2095 2.364970 CCTAGCTGCTCTCTTGTGCTAT 59.635 50.000 4.91 0.00 35.96 2.97
2091 2137 1.065418 AGGGAACTGTTGCGGATAAGG 60.065 52.381 5.95 0.00 41.13 2.69
2093 2139 2.817258 CAAAGGGAACTGTTGCGGATAA 59.183 45.455 5.95 0.00 42.68 1.75
2162 2238 7.597643 CGTTCAAATAAAAAGTAAGAACGCA 57.402 32.000 11.07 0.00 46.30 5.24
2183 2259 7.710907 ACATATATAATTATCGCTGCCATCGTT 59.289 33.333 0.00 0.00 0.00 3.85
2187 2263 7.992608 TCCAACATATATAATTATCGCTGCCAT 59.007 33.333 0.00 0.00 0.00 4.40
2192 2268 9.265901 GCATCTCCAACATATATAATTATCGCT 57.734 33.333 0.00 0.00 0.00 4.93
2193 2269 9.265901 AGCATCTCCAACATATATAATTATCGC 57.734 33.333 0.00 0.00 0.00 4.58
2234 2310 7.447374 TCGCTGAATTTCTCCTATTCAAAAA 57.553 32.000 0.00 0.00 40.42 1.94
2235 2311 7.305474 GTTCGCTGAATTTCTCCTATTCAAAA 58.695 34.615 0.00 0.00 40.42 2.44
2236 2312 6.128007 GGTTCGCTGAATTTCTCCTATTCAAA 60.128 38.462 0.00 0.00 40.42 2.69
2237 2313 5.354234 GGTTCGCTGAATTTCTCCTATTCAA 59.646 40.000 0.00 0.00 40.42 2.69
2238 2314 4.876107 GGTTCGCTGAATTTCTCCTATTCA 59.124 41.667 0.00 0.00 39.12 2.57
2239 2315 4.876107 TGGTTCGCTGAATTTCTCCTATTC 59.124 41.667 0.00 0.00 33.58 1.75
2240 2316 4.843728 TGGTTCGCTGAATTTCTCCTATT 58.156 39.130 0.00 0.00 0.00 1.73
2241 2317 4.487714 TGGTTCGCTGAATTTCTCCTAT 57.512 40.909 0.00 0.00 0.00 2.57
2242 2318 3.973206 TGGTTCGCTGAATTTCTCCTA 57.027 42.857 0.00 0.00 0.00 2.94
2243 2319 2.859165 TGGTTCGCTGAATTTCTCCT 57.141 45.000 0.00 0.00 0.00 3.69
2244 2320 3.691609 AGATTGGTTCGCTGAATTTCTCC 59.308 43.478 0.00 0.00 0.00 3.71
2245 2321 4.633565 AGAGATTGGTTCGCTGAATTTCTC 59.366 41.667 0.00 0.00 32.71 2.87
2246 2322 4.583871 AGAGATTGGTTCGCTGAATTTCT 58.416 39.130 0.00 0.00 32.71 2.52
2247 2323 4.954092 AGAGATTGGTTCGCTGAATTTC 57.046 40.909 0.00 0.00 32.71 2.17


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

AutoCloner maintained by Alex Coulton.