Multiple sequence alignment - TraesCS4D01G160700

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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 TraesCS4D01G160700 chr4D 100.000 6402 0 0 1 6402 238642105 238635704 0.000000e+00 11823
1 TraesCS4D01G160700 chr4B 97.010 3545 76 13 2868 6402 360232459 360228935 0.000000e+00 5932
2 TraesCS4D01G160700 chr4B 97.140 1783 45 4 1 1778 360235570 360233789 0.000000e+00 3005
3 TraesCS4D01G160700 chr4B 93.130 655 25 8 1940 2582 360233790 360233144 0.000000e+00 942
4 TraesCS4D01G160700 chr4B 90.281 391 29 5 2670 3054 426143926 426144313 2.660000e-138 503
5 TraesCS4D01G160700 chr4A 96.831 2840 81 6 3050 5884 298243581 298240746 0.000000e+00 4737
6 TraesCS4D01G160700 chr4A 96.586 1787 50 9 1 1778 298245648 298243864 0.000000e+00 2952
7 TraesCS4D01G160700 chr4A 94.291 508 28 1 5896 6402 298240763 298240256 0.000000e+00 776
8 TraesCS4D01G160700 chr4A 86.564 454 47 12 2594 3039 74584431 74583984 7.460000e-134 488
9 TraesCS4D01G160700 chr2A 88.274 452 34 11 2609 3054 34791173 34791611 2.050000e-144 523
10 TraesCS4D01G160700 chr2A 87.826 345 39 2 2234 2575 182826486 182826830 1.000000e-107 401
11 TraesCS4D01G160700 chr1D 90.561 392 26 9 2670 3056 138778803 138779188 5.730000e-140 508
12 TraesCS4D01G160700 chr5A 87.225 454 46 8 2608 3054 619025143 619025591 2.060000e-139 507
13 TraesCS4D01G160700 chr5A 90.281 391 29 5 2670 3054 704516156 704515769 2.660000e-138 503
14 TraesCS4D01G160700 chr5A 89.526 401 32 6 2670 3063 216940344 216939947 3.450000e-137 499
15 TraesCS4D01G160700 chr5A 86.966 445 40 10 2615 3054 516069979 516069548 9.650000e-133 484
16 TraesCS4D01G160700 chr5A 87.536 345 40 3 2234 2575 567688559 567688215 4.650000e-106 396
17 TraesCS4D01G160700 chr3A 87.444 446 42 12 2608 3045 50272960 50273399 9.580000e-138 501
18 TraesCS4D01G160700 chr7B 92.151 344 23 4 1758 2100 382277454 382277114 3.470000e-132 483
19 TraesCS4D01G160700 chr7B 88.218 348 36 5 2234 2580 167717114 167716771 1.660000e-110 411
20 TraesCS4D01G160700 chr7D 89.914 347 30 5 2231 2574 617491350 617491694 5.890000e-120 442
21 TraesCS4D01G160700 chr3D 90.854 328 27 3 1758 2084 554149785 554150110 2.740000e-118 436
22 TraesCS4D01G160700 chr5D 90.000 330 30 3 1755 2083 27095683 27095356 2.130000e-114 424
23 TraesCS4D01G160700 chr5D 85.610 410 41 14 2234 2633 415720781 415720380 1.280000e-111 414
24 TraesCS4D01G160700 chr5D 88.116 345 38 2 2234 2575 40260821 40260477 2.150000e-109 407
25 TraesCS4D01G160700 chr5D 87.571 354 38 5 2226 2575 91975685 91975334 7.730000e-109 405
26 TraesCS4D01G160700 chr5D 86.872 358 41 5 2234 2588 80365538 80365892 4.650000e-106 396
27 TraesCS4D01G160700 chr5B 89.394 330 30 4 1757 2084 291840777 291840451 1.660000e-110 411
28 TraesCS4D01G160700 chr5B 88.450 329 34 3 1755 2083 27316239 27316563 1.670000e-105 394
29 TraesCS4D01G160700 chr6B 89.362 329 29 5 1758 2083 67539148 67538823 5.970000e-110 409
30 TraesCS4D01G160700 chr2D 89.124 331 30 4 1757 2083 445190010 445189682 2.150000e-109 407
31 TraesCS4D01G160700 chr6D 88.724 337 26 9 1755 2084 41542675 41542344 1.000000e-107 401
32 TraesCS4D01G160700 chr1B 88.685 327 34 3 1758 2083 589887597 589887273 4.650000e-106 396


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 TraesCS4D01G160700 chr4D 238635704 238642105 6401 True 11823.000000 11823 100.000000 1 6402 1 chr4D.!!$R1 6401
1 TraesCS4D01G160700 chr4B 360228935 360235570 6635 True 3293.000000 5932 95.760000 1 6402 3 chr4B.!!$R1 6401
2 TraesCS4D01G160700 chr4A 298240256 298245648 5392 True 2821.666667 4737 95.902667 1 6402 3 chr4A.!!$R2 6401


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
781 787 1.024579 GTGGTCCTAACATGGGCACG 61.025 60.000 0.0 0.0 32.35 5.34 F
1772 1783 1.134189 CCAAATACTCCCTCCGTTCCC 60.134 57.143 0.0 0.0 0.00 3.97 F
2718 2741 1.038280 CGTACTCCCACCCCTCATAC 58.962 60.000 0.0 0.0 0.00 2.39 F
4118 4591 0.394899 ATCACCCTTTGCCTGCTAGC 60.395 55.000 8.1 8.1 0.00 3.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2661 2684 2.493278 CAACCATTTTCCTAGGGTGCAG 59.507 50.000 9.46 0.00 32.66 4.41 R
3217 3689 2.299013 CTGGAAAAGGTTGGGTTAAGCC 59.701 50.000 17.01 17.01 37.49 4.35 R
4339 4812 1.533273 ACCATAGCCGCCTCCGTAT 60.533 57.895 0.00 0.00 0.00 3.06 R
6043 6526 2.784347 TGGTACATCGATTGGCAAACA 58.216 42.857 3.01 0.00 0.00 2.83 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
178 180 5.644636 CGTATGGGCTCTGTTTAGGTTTTTA 59.355 40.000 0.00 0.00 0.00 1.52
237 239 4.767578 AGAGGCTCATGTATGTGTTGAT 57.232 40.909 18.26 0.00 0.00 2.57
258 260 2.536725 GACCGAAAGTCCGAAACCC 58.463 57.895 0.00 0.00 39.84 4.11
685 691 2.868839 GCAGTTGATTTTGCCATGTGCT 60.869 45.455 7.54 0.00 42.00 4.40
689 695 2.768698 TGATTTTGCCATGTGCTTTGG 58.231 42.857 7.54 0.00 42.00 3.28
781 787 1.024579 GTGGTCCTAACATGGGCACG 61.025 60.000 0.00 0.00 32.35 5.34
797 803 1.323534 GCACGCAACATAAGTAGGTCG 59.676 52.381 0.00 0.00 0.00 4.79
822 828 5.039333 GGTGAGTGATGCATGCTTTTATTC 58.961 41.667 20.33 12.00 0.00 1.75
832 838 5.762711 TGCATGCTTTTATTCGGAAGCTATA 59.237 36.000 20.33 0.00 46.39 1.31
1053 1064 4.566360 GCTGACTATTCTGTCTCTGCTTTC 59.434 45.833 0.00 0.00 37.79 2.62
1126 1137 5.263599 TGATTATGCTGAAAATGGAGGTGT 58.736 37.500 0.00 0.00 0.00 4.16
1580 1591 4.510340 ACTGGTTCACAAATACGTGTTCTC 59.490 41.667 0.00 0.00 38.12 2.87
1772 1783 1.134189 CCAAATACTCCCTCCGTTCCC 60.134 57.143 0.00 0.00 0.00 3.97
1776 1787 1.961133 TACTCCCTCCGTTCCCAAAT 58.039 50.000 0.00 0.00 0.00 2.32
1777 1788 1.961133 ACTCCCTCCGTTCCCAAATA 58.039 50.000 0.00 0.00 0.00 1.40
1778 1789 1.558294 ACTCCCTCCGTTCCCAAATAC 59.442 52.381 0.00 0.00 0.00 1.89
1779 1790 1.838077 CTCCCTCCGTTCCCAAATACT 59.162 52.381 0.00 0.00 0.00 2.12
1780 1791 1.835531 TCCCTCCGTTCCCAAATACTC 59.164 52.381 0.00 0.00 0.00 2.59
1781 1792 1.134189 CCCTCCGTTCCCAAATACTCC 60.134 57.143 0.00 0.00 0.00 3.85
1782 1793 1.134189 CCTCCGTTCCCAAATACTCCC 60.134 57.143 0.00 0.00 0.00 4.30
1783 1794 1.838077 CTCCGTTCCCAAATACTCCCT 59.162 52.381 0.00 0.00 0.00 4.20
1784 1795 1.835531 TCCGTTCCCAAATACTCCCTC 59.164 52.381 0.00 0.00 0.00 4.30
1785 1796 1.134189 CCGTTCCCAAATACTCCCTCC 60.134 57.143 0.00 0.00 0.00 4.30
1786 1797 1.472728 CGTTCCCAAATACTCCCTCCG 60.473 57.143 0.00 0.00 0.00 4.63
1787 1798 1.558294 GTTCCCAAATACTCCCTCCGT 59.442 52.381 0.00 0.00 0.00 4.69
1788 1799 1.961133 TCCCAAATACTCCCTCCGTT 58.039 50.000 0.00 0.00 0.00 4.44
1789 1800 1.835531 TCCCAAATACTCCCTCCGTTC 59.164 52.381 0.00 0.00 0.00 3.95
1790 1801 1.134189 CCCAAATACTCCCTCCGTTCC 60.134 57.143 0.00 0.00 0.00 3.62
1791 1802 1.838077 CCAAATACTCCCTCCGTTCCT 59.162 52.381 0.00 0.00 0.00 3.36
1792 1803 3.036091 CCAAATACTCCCTCCGTTCCTA 58.964 50.000 0.00 0.00 0.00 2.94
1793 1804 3.453353 CCAAATACTCCCTCCGTTCCTAA 59.547 47.826 0.00 0.00 0.00 2.69
1794 1805 4.080751 CCAAATACTCCCTCCGTTCCTAAA 60.081 45.833 0.00 0.00 0.00 1.85
1795 1806 5.397559 CCAAATACTCCCTCCGTTCCTAAAT 60.398 44.000 0.00 0.00 0.00 1.40
1796 1807 6.183361 CCAAATACTCCCTCCGTTCCTAAATA 60.183 42.308 0.00 0.00 0.00 1.40
1797 1808 7.450903 CAAATACTCCCTCCGTTCCTAAATAT 58.549 38.462 0.00 0.00 0.00 1.28
1798 1809 7.628501 AATACTCCCTCCGTTCCTAAATATT 57.371 36.000 0.00 0.00 0.00 1.28
1799 1810 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
1800 1811 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
1801 1812 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
1802 1813 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
1803 1814 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
1804 1815 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
1805 1816 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
1806 1817 7.201705 CCCTCCGTTCCTAAATATTTGTCTTTC 60.202 40.741 11.05 0.00 0.00 2.62
1807 1818 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
1808 1819 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
1809 1820 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
1810 1821 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
1823 1834 8.964476 TTGTCTTTCTAGAGATTTCAACAAGT 57.036 30.769 0.00 0.00 0.00 3.16
1824 1835 8.370493 TGTCTTTCTAGAGATTTCAACAAGTG 57.630 34.615 0.00 0.00 0.00 3.16
1825 1836 8.204160 TGTCTTTCTAGAGATTTCAACAAGTGA 58.796 33.333 0.00 0.00 0.00 3.41
1826 1837 8.491950 GTCTTTCTAGAGATTTCAACAAGTGAC 58.508 37.037 0.00 0.00 35.39 3.67
1827 1838 8.424918 TCTTTCTAGAGATTTCAACAAGTGACT 58.575 33.333 0.00 0.00 35.39 3.41
1828 1839 9.698309 CTTTCTAGAGATTTCAACAAGTGACTA 57.302 33.333 0.00 0.00 35.39 2.59
1829 1840 9.477484 TTTCTAGAGATTTCAACAAGTGACTAC 57.523 33.333 0.00 0.00 35.39 2.73
1830 1841 8.178313 TCTAGAGATTTCAACAAGTGACTACA 57.822 34.615 0.00 0.00 35.39 2.74
1831 1842 8.807118 TCTAGAGATTTCAACAAGTGACTACAT 58.193 33.333 0.00 0.00 35.39 2.29
1833 1844 8.764524 AGAGATTTCAACAAGTGACTACATAC 57.235 34.615 0.00 0.00 35.39 2.39
1834 1845 7.542477 AGAGATTTCAACAAGTGACTACATACG 59.458 37.037 0.00 0.00 35.39 3.06
1835 1846 6.590292 AGATTTCAACAAGTGACTACATACGG 59.410 38.462 0.00 0.00 35.39 4.02
1836 1847 5.456548 TTCAACAAGTGACTACATACGGA 57.543 39.130 0.00 0.00 35.39 4.69
1837 1848 5.055642 TCAACAAGTGACTACATACGGAG 57.944 43.478 0.00 0.00 0.00 4.63
1838 1849 3.505464 ACAAGTGACTACATACGGAGC 57.495 47.619 0.00 0.00 0.00 4.70
1839 1850 2.823747 ACAAGTGACTACATACGGAGCA 59.176 45.455 0.00 0.00 0.00 4.26
1840 1851 3.257375 ACAAGTGACTACATACGGAGCAA 59.743 43.478 0.00 0.00 0.00 3.91
1841 1852 4.242475 CAAGTGACTACATACGGAGCAAA 58.758 43.478 0.00 0.00 0.00 3.68
1842 1853 4.530710 AGTGACTACATACGGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
1843 1854 5.086104 AGTGACTACATACGGAGCAAAAT 57.914 39.130 0.00 0.00 0.00 1.82
1844 1855 4.870426 AGTGACTACATACGGAGCAAAATG 59.130 41.667 0.00 0.00 0.00 2.32
1845 1856 4.868171 GTGACTACATACGGAGCAAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
1846 1857 5.005779 GTGACTACATACGGAGCAAAATGAG 59.994 44.000 0.00 0.00 0.00 2.90
1847 1858 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
1848 1859 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
1849 1860 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
1850 1861 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
1851 1862 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
1852 1863 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
1853 1864 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
1854 1865 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
1855 1866 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
1856 1867 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
1857 1868 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
1871 1882 9.469097 AGTGAATCTACACTCTAAAGTATGTCT 57.531 33.333 0.00 0.00 46.36 3.41
1893 1904 9.990868 TGTCTATATACATCCATATGTGGTAGT 57.009 33.333 8.51 10.44 45.99 2.73
1895 1906 9.642343 TCTATATACATCCATATGTGGTAGTCC 57.358 37.037 8.51 0.00 45.99 3.85
1896 1907 9.421399 CTATATACATCCATATGTGGTAGTCCA 57.579 37.037 8.51 1.36 45.99 4.02
1897 1908 8.860517 ATATACATCCATATGTGGTAGTCCAT 57.139 34.615 8.51 3.29 45.99 3.41
1898 1909 5.912149 ACATCCATATGTGGTAGTCCATT 57.088 39.130 8.51 0.00 44.79 3.16
1899 1910 6.266131 ACATCCATATGTGGTAGTCCATTT 57.734 37.500 8.51 0.00 44.79 2.32
1900 1911 6.064060 ACATCCATATGTGGTAGTCCATTTG 58.936 40.000 8.51 0.00 44.79 2.32
1901 1912 5.966853 TCCATATGTGGTAGTCCATTTGA 57.033 39.130 8.51 0.00 46.20 2.69
1902 1913 6.320434 TCCATATGTGGTAGTCCATTTGAA 57.680 37.500 8.51 0.00 46.20 2.69
1903 1914 6.726379 TCCATATGTGGTAGTCCATTTGAAA 58.274 36.000 8.51 0.00 46.20 2.69
1904 1915 7.353525 TCCATATGTGGTAGTCCATTTGAAAT 58.646 34.615 8.51 0.00 46.20 2.17
1905 1916 7.502226 TCCATATGTGGTAGTCCATTTGAAATC 59.498 37.037 8.51 0.00 46.20 2.17
1906 1917 7.503566 CCATATGTGGTAGTCCATTTGAAATCT 59.496 37.037 0.00 0.00 46.20 2.40
1907 1918 8.562892 CATATGTGGTAGTCCATTTGAAATCTC 58.437 37.037 0.00 0.00 46.20 2.75
1908 1919 6.126863 TGTGGTAGTCCATTTGAAATCTCT 57.873 37.500 0.00 0.00 46.20 3.10
1909 1920 7.252612 TGTGGTAGTCCATTTGAAATCTCTA 57.747 36.000 0.00 0.00 46.20 2.43
1910 1921 7.685481 TGTGGTAGTCCATTTGAAATCTCTAA 58.315 34.615 0.00 0.00 46.20 2.10
1911 1922 8.160765 TGTGGTAGTCCATTTGAAATCTCTAAA 58.839 33.333 0.00 0.00 46.20 1.85
1912 1923 9.010029 GTGGTAGTCCATTTGAAATCTCTAAAA 57.990 33.333 0.00 0.00 46.20 1.52
1913 1924 9.581289 TGGTAGTCCATTTGAAATCTCTAAAAA 57.419 29.630 0.00 0.00 39.03 1.94
1917 1928 9.354673 AGTCCATTTGAAATCTCTAAAAAGACA 57.645 29.630 0.00 0.00 0.00 3.41
1918 1929 9.965824 GTCCATTTGAAATCTCTAAAAAGACAA 57.034 29.630 0.00 0.00 0.00 3.18
1935 1946 7.625828 AAAGACAAATATTTAGGAACGGAGG 57.374 36.000 0.00 0.00 0.00 4.30
1936 1947 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
1937 1948 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
1938 1949 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
1991 2002 9.605275 TGTACTACATACGGATGTATATAGACC 57.395 37.037 20.64 7.69 45.42 3.85
2024 2037 6.471146 AGTGTAGATTCACTCATTTTGCTCT 58.529 36.000 0.00 0.00 44.07 4.09
2269 2291 7.671398 CCCCCTCTATTTTAATATCAATGCACT 59.329 37.037 0.00 0.00 0.00 4.40
2581 2604 4.100189 CCCTCGGTGATGAATAGACTTTCT 59.900 45.833 0.00 0.00 0.00 2.52
2582 2605 5.285651 CCTCGGTGATGAATAGACTTTCTC 58.714 45.833 0.00 0.00 0.00 2.87
2583 2606 5.068460 CCTCGGTGATGAATAGACTTTCTCT 59.932 44.000 0.00 0.00 0.00 3.10
2584 2607 6.137794 TCGGTGATGAATAGACTTTCTCTC 57.862 41.667 0.00 0.00 0.00 3.20
2585 2608 5.888724 TCGGTGATGAATAGACTTTCTCTCT 59.111 40.000 0.00 0.00 0.00 3.10
2586 2609 6.038825 TCGGTGATGAATAGACTTTCTCTCTC 59.961 42.308 0.00 0.00 0.00 3.20
2587 2610 6.039270 CGGTGATGAATAGACTTTCTCTCTCT 59.961 42.308 0.00 0.00 0.00 3.10
2588 2611 7.425606 GGTGATGAATAGACTTTCTCTCTCTC 58.574 42.308 0.00 0.00 0.00 3.20
2589 2612 7.285401 GGTGATGAATAGACTTTCTCTCTCTCT 59.715 40.741 0.00 0.00 0.00 3.10
2590 2613 8.345565 GTGATGAATAGACTTTCTCTCTCTCTC 58.654 40.741 0.00 0.00 0.00 3.20
2591 2614 8.274322 TGATGAATAGACTTTCTCTCTCTCTCT 58.726 37.037 0.00 0.00 0.00 3.10
2592 2615 8.682936 ATGAATAGACTTTCTCTCTCTCTCTC 57.317 38.462 0.00 0.00 0.00 3.20
2593 2616 7.861629 TGAATAGACTTTCTCTCTCTCTCTCT 58.138 38.462 0.00 0.00 0.00 3.10
2594 2617 7.987458 TGAATAGACTTTCTCTCTCTCTCTCTC 59.013 40.741 0.00 0.00 0.00 3.20
2595 2618 7.682787 ATAGACTTTCTCTCTCTCTCTCTCT 57.317 40.000 0.00 0.00 0.00 3.10
2596 2619 5.983540 AGACTTTCTCTCTCTCTCTCTCTC 58.016 45.833 0.00 0.00 0.00 3.20
2597 2620 5.723887 AGACTTTCTCTCTCTCTCTCTCTCT 59.276 44.000 0.00 0.00 0.00 3.10
2598 2621 5.983540 ACTTTCTCTCTCTCTCTCTCTCTC 58.016 45.833 0.00 0.00 0.00 3.20
2599 2622 5.723887 ACTTTCTCTCTCTCTCTCTCTCTCT 59.276 44.000 0.00 0.00 0.00 3.10
2600 2623 5.860941 TTCTCTCTCTCTCTCTCTCTCTC 57.139 47.826 0.00 0.00 0.00 3.20
2601 2624 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
2602 2625 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2603 2626 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2604 2627 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2605 2628 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2606 2629 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2607 2630 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2608 2631 6.101881 TCTCTCTCTCTCTCTCTCTCTCTCTA 59.898 46.154 0.00 0.00 0.00 2.43
2609 2632 6.857848 TCTCTCTCTCTCTCTCTCTCTCTAT 58.142 44.000 0.00 0.00 0.00 1.98
2610 2633 7.990055 TCTCTCTCTCTCTCTCTCTCTCTATA 58.010 42.308 0.00 0.00 0.00 1.31
2611 2634 8.619281 TCTCTCTCTCTCTCTCTCTCTCTATAT 58.381 40.741 0.00 0.00 0.00 0.86
2612 2635 9.913310 CTCTCTCTCTCTCTCTCTCTCTATATA 57.087 40.741 0.00 0.00 0.00 0.86
2718 2741 1.038280 CGTACTCCCACCCCTCATAC 58.962 60.000 0.00 0.00 0.00 2.39
2841 2991 8.500773 TGTCTCATATTTTTGAAGGTTTACGTC 58.499 33.333 0.00 0.00 0.00 4.34
2871 3341 8.257306 ACTGATTTGTTTGTATGTGAAAAAGGT 58.743 29.630 0.00 0.00 0.00 3.50
3298 3770 6.099845 AGTTGTAGGGATTACTCCTATGGTTG 59.900 42.308 0.00 0.00 41.74 3.77
3512 3984 2.166459 TGGATAGTTCGAGTGCTGAAGG 59.834 50.000 0.00 0.00 0.00 3.46
3595 4068 8.868916 GCATGATACGTTTCCATGTTTATTTTT 58.131 29.630 18.88 0.00 39.69 1.94
3608 4081 7.416326 CCATGTTTATTTTTAGTAGCAGGTCCC 60.416 40.741 0.00 0.00 0.00 4.46
3952 4425 4.023193 ACGACTCCTTGTTGCCATAAAAAG 60.023 41.667 0.00 0.00 33.33 2.27
4118 4591 0.394899 ATCACCCTTTGCCTGCTAGC 60.395 55.000 8.10 8.10 0.00 3.42
4124 4597 0.671781 CTTTGCCTGCTAGCGTGTCT 60.672 55.000 10.77 0.00 34.65 3.41
4339 4812 5.014858 ACGAACTGAAACCATCTCTAGGTA 58.985 41.667 0.00 0.00 38.76 3.08
4455 4928 4.591498 TGTTGACCATAGTTCTGTGTAGGT 59.409 41.667 0.00 0.00 0.00 3.08
4463 4936 9.662947 ACCATAGTTCTGTGTAGGTAAATAAAC 57.337 33.333 0.00 0.00 0.00 2.01
4575 5049 3.186613 GCTAGTACAATAATCGCTTGCCC 59.813 47.826 0.00 0.00 0.00 5.36
4585 5059 2.960170 GCTTGCCCTTCTGCTGTG 59.040 61.111 0.00 0.00 0.00 3.66
4587 5061 1.228367 CTTGCCCTTCTGCTGTGGT 60.228 57.895 0.00 0.00 0.00 4.16
4693 5168 3.398318 TGCTGTCTATTACTCCCTCCA 57.602 47.619 0.00 0.00 0.00 3.86
4745 5220 7.552687 ACCAATGTACTGATATGTTGGTTGTAG 59.447 37.037 1.98 0.00 44.95 2.74
4787 5263 2.614057 GGAGGGAGTATCATTTTGTGCG 59.386 50.000 0.00 0.00 36.25 5.34
4984 5460 2.305927 CCAACAGGTATGGTTCCTCTGT 59.694 50.000 0.00 0.00 39.97 3.41
5328 5804 0.963355 TGCCCTGCCGTAAATGTTCC 60.963 55.000 0.00 0.00 0.00 3.62
5747 6226 1.342819 TCACAATTCCAAAAAGGGCCG 59.657 47.619 0.00 0.00 38.24 6.13
5897 6377 0.985490 AGCCCTCTCATCCCAACCTC 60.985 60.000 0.00 0.00 0.00 3.85
5941 6424 2.282040 ACCCTGAGCAGCAGCAAC 60.282 61.111 3.17 0.00 45.49 4.17
6043 6526 3.947834 CCAGGACGCTAAATCTTGGATTT 59.052 43.478 9.86 9.86 44.17 2.17
6044 6527 4.201950 CCAGGACGCTAAATCTTGGATTTG 60.202 45.833 13.65 6.82 44.17 2.32
6368 6852 0.821711 TTGCCTGTCCCGAACCAAAG 60.822 55.000 0.00 0.00 0.00 2.77
6391 6875 8.980481 AAGTGGTTGATAATTTACCTATGGAG 57.020 34.615 0.00 0.00 33.05 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
237 239 1.269936 GGTTTCGGACTTTCGGTCTCA 60.270 52.381 0.00 0.00 43.97 3.27
685 691 3.806380 TGTAGGTCAACGCTTAACCAAA 58.194 40.909 0.00 0.00 35.43 3.28
689 695 4.435651 GCAGATTGTAGGTCAACGCTTAAC 60.436 45.833 0.00 0.00 38.97 2.01
700 706 3.835395 GAGGGCTATAGCAGATTGTAGGT 59.165 47.826 25.53 0.00 44.36 3.08
704 710 4.989875 ATTGAGGGCTATAGCAGATTGT 57.010 40.909 25.53 5.18 44.36 2.71
781 787 3.119245 TCACCTCGACCTACTTATGTTGC 60.119 47.826 0.00 0.00 0.00 4.17
797 803 1.747709 AAGCATGCATCACTCACCTC 58.252 50.000 21.98 0.00 0.00 3.85
1024 1035 4.039151 AGACAGAATAGTCAGCGACATG 57.961 45.455 10.52 0.00 40.98 3.21
1053 1064 1.227764 CAGGCCCGACCATGATCTG 60.228 63.158 0.00 0.00 43.14 2.90
1126 1137 5.249163 TCATCACCAGGATTTCTTCTCTTGA 59.751 40.000 0.00 0.00 32.57 3.02
1580 1591 3.411446 TGCAGGAAGGTGTTCATTACTG 58.589 45.455 1.22 1.22 45.66 2.74
1772 1783 4.748277 TTAGGAACGGAGGGAGTATTTG 57.252 45.455 0.00 0.00 0.00 2.32
1776 1787 6.384886 ACAAATATTTAGGAACGGAGGGAGTA 59.615 38.462 0.00 0.00 0.00 2.59
1777 1788 5.191124 ACAAATATTTAGGAACGGAGGGAGT 59.809 40.000 0.00 0.00 0.00 3.85
1778 1789 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
1779 1790 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
1780 1791 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
1781 1792 7.553044 AGAAAGACAAATATTTAGGAACGGAGG 59.447 37.037 0.00 0.00 0.00 4.30
1782 1793 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
1783 1794 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
1784 1795 9.595823 TCTAGAAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
1797 1808 9.396022 ACTTGTTGAAATCTCTAGAAAGACAAA 57.604 29.630 0.00 0.00 0.00 2.83
1798 1809 8.830580 CACTTGTTGAAATCTCTAGAAAGACAA 58.169 33.333 0.00 0.00 0.00 3.18
1799 1810 8.204160 TCACTTGTTGAAATCTCTAGAAAGACA 58.796 33.333 0.00 0.00 0.00 3.41
1800 1811 8.491950 GTCACTTGTTGAAATCTCTAGAAAGAC 58.508 37.037 0.00 0.00 35.39 3.01
1801 1812 8.424918 AGTCACTTGTTGAAATCTCTAGAAAGA 58.575 33.333 0.00 0.00 35.39 2.52
1802 1813 8.600449 AGTCACTTGTTGAAATCTCTAGAAAG 57.400 34.615 0.00 0.00 35.39 2.62
1803 1814 9.477484 GTAGTCACTTGTTGAAATCTCTAGAAA 57.523 33.333 0.00 0.00 35.39 2.52
1804 1815 8.638873 TGTAGTCACTTGTTGAAATCTCTAGAA 58.361 33.333 0.00 0.00 35.39 2.10
1805 1816 8.178313 TGTAGTCACTTGTTGAAATCTCTAGA 57.822 34.615 0.00 0.00 35.39 2.43
1806 1817 8.994429 ATGTAGTCACTTGTTGAAATCTCTAG 57.006 34.615 0.00 0.00 35.39 2.43
1807 1818 9.856488 GTATGTAGTCACTTGTTGAAATCTCTA 57.144 33.333 0.00 0.00 35.39 2.43
1808 1819 7.542477 CGTATGTAGTCACTTGTTGAAATCTCT 59.458 37.037 0.00 0.00 35.39 3.10
1809 1820 7.201444 CCGTATGTAGTCACTTGTTGAAATCTC 60.201 40.741 0.00 0.00 35.39 2.75
1810 1821 6.590292 CCGTATGTAGTCACTTGTTGAAATCT 59.410 38.462 0.00 0.00 35.39 2.40
1811 1822 6.588756 TCCGTATGTAGTCACTTGTTGAAATC 59.411 38.462 0.00 0.00 35.39 2.17
1812 1823 6.460781 TCCGTATGTAGTCACTTGTTGAAAT 58.539 36.000 0.00 0.00 35.39 2.17
1813 1824 5.845103 TCCGTATGTAGTCACTTGTTGAAA 58.155 37.500 0.00 0.00 35.39 2.69
1814 1825 5.456548 TCCGTATGTAGTCACTTGTTGAA 57.543 39.130 0.00 0.00 35.39 2.69
1815 1826 4.617530 GCTCCGTATGTAGTCACTTGTTGA 60.618 45.833 0.00 0.00 0.00 3.18
1816 1827 3.612860 GCTCCGTATGTAGTCACTTGTTG 59.387 47.826 0.00 0.00 0.00 3.33
1817 1828 3.257375 TGCTCCGTATGTAGTCACTTGTT 59.743 43.478 0.00 0.00 0.00 2.83
1818 1829 2.823747 TGCTCCGTATGTAGTCACTTGT 59.176 45.455 0.00 0.00 0.00 3.16
1819 1830 3.503827 TGCTCCGTATGTAGTCACTTG 57.496 47.619 0.00 0.00 0.00 3.16
1820 1831 4.530710 TTTGCTCCGTATGTAGTCACTT 57.469 40.909 0.00 0.00 0.00 3.16
1821 1832 4.530710 TTTTGCTCCGTATGTAGTCACT 57.469 40.909 0.00 0.00 0.00 3.41
1822 1833 4.868171 TCATTTTGCTCCGTATGTAGTCAC 59.132 41.667 0.00 0.00 0.00 3.67
1823 1834 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
1824 1835 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
1825 1836 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
1826 1837 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
1827 1838 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
1828 1839 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
1829 1840 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
1830 1841 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
1831 1842 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
1832 1843 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
1833 1844 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
1834 1845 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
1835 1846 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
1891 1902 9.354673 TGTCTTTTTAGAGATTTCAAATGGACT 57.645 29.630 0.00 0.00 0.00 3.85
1892 1903 9.965824 TTGTCTTTTTAGAGATTTCAAATGGAC 57.034 29.630 0.00 0.00 0.00 4.02
1909 1920 8.520351 CCTCCGTTCCTAAATATTTGTCTTTTT 58.480 33.333 11.05 0.00 0.00 1.94
1910 1921 7.122204 CCCTCCGTTCCTAAATATTTGTCTTTT 59.878 37.037 11.05 0.00 0.00 2.27
1911 1922 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
1912 1923 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
1913 1924 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
1914 1925 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
1915 1926 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
1916 1927 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
1917 1928 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
1918 1929 8.731591 TTATACTCCCTCCGTTCCTAAATATT 57.268 34.615 0.00 0.00 0.00 1.28
1919 1930 7.954620 ACTTATACTCCCTCCGTTCCTAAATAT 59.045 37.037 0.00 0.00 0.00 1.28
1920 1931 7.300658 ACTTATACTCCCTCCGTTCCTAAATA 58.699 38.462 0.00 0.00 0.00 1.40
1921 1932 6.141790 ACTTATACTCCCTCCGTTCCTAAAT 58.858 40.000 0.00 0.00 0.00 1.40
1922 1933 5.522641 ACTTATACTCCCTCCGTTCCTAAA 58.477 41.667 0.00 0.00 0.00 1.85
1923 1934 5.103771 AGACTTATACTCCCTCCGTTCCTAA 60.104 44.000 0.00 0.00 0.00 2.69
1924 1935 4.414846 AGACTTATACTCCCTCCGTTCCTA 59.585 45.833 0.00 0.00 0.00 2.94
1925 1936 3.204831 AGACTTATACTCCCTCCGTTCCT 59.795 47.826 0.00 0.00 0.00 3.36
1926 1937 3.564264 AGACTTATACTCCCTCCGTTCC 58.436 50.000 0.00 0.00 0.00 3.62
1927 1938 5.595257 AAAGACTTATACTCCCTCCGTTC 57.405 43.478 0.00 0.00 0.00 3.95
1928 1939 6.370186 AAAAAGACTTATACTCCCTCCGTT 57.630 37.500 0.00 0.00 0.00 4.44
1929 1940 6.894103 TCTAAAAAGACTTATACTCCCTCCGT 59.106 38.462 0.00 0.00 0.00 4.69
1930 1941 7.284944 TCTCTAAAAAGACTTATACTCCCTCCG 59.715 40.741 0.00 0.00 0.00 4.63
1931 1942 8.536340 TCTCTAAAAAGACTTATACTCCCTCC 57.464 38.462 0.00 0.00 0.00 4.30
2055 2068 8.019652 ACTCCCTCCATTCCTAAATATAAGTCT 58.980 37.037 0.00 0.00 0.00 3.24
2072 2085 5.461516 TGTTGTAGTAGATACTCCCTCCA 57.538 43.478 0.00 0.00 37.73 3.86
2105 2118 6.656314 TGAAATACCTACTGCACATAAACG 57.344 37.500 0.00 0.00 0.00 3.60
2510 2533 8.543774 CCTGAGTTAATCTTACGATCATTTCAC 58.456 37.037 0.00 0.00 0.00 3.18
2519 2542 6.829229 TCTTCACCTGAGTTAATCTTACGA 57.171 37.500 0.00 0.00 0.00 3.43
2562 2585 6.039270 AGAGAGAGAAAGTCTATTCATCACCG 59.961 42.308 0.00 0.00 34.71 4.94
2581 2604 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2582 2605 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2583 2606 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2584 2607 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2585 2608 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
2586 2609 8.821686 ATATAGAGAGAGAGAGAGAGAGAGAG 57.178 42.308 0.00 0.00 0.00 3.20
2655 2678 5.835280 CCATTTTCCTAGGGTGCAGAATATT 59.165 40.000 9.46 0.00 0.00 1.28
2661 2684 2.493278 CAACCATTTTCCTAGGGTGCAG 59.507 50.000 9.46 0.00 32.66 4.41
2666 2689 4.918588 AGTACACAACCATTTTCCTAGGG 58.081 43.478 9.46 0.00 0.00 3.53
2718 2741 9.784531 AGGTATAAAAGATTCATCTATGTGGTG 57.215 33.333 0.00 0.00 35.76 4.17
2806 2956 9.850628 CTTCAAAAATATGAGACACACATGATT 57.149 29.630 0.00 0.00 0.00 2.57
2828 2978 8.308931 ACAAATCAGTATAGACGTAAACCTTCA 58.691 33.333 0.00 0.00 0.00 3.02
2846 2996 8.647143 ACCTTTTTCACATACAAACAAATCAG 57.353 30.769 0.00 0.00 0.00 2.90
2978 3448 7.025365 TCAATATACCTCGTATACGCATTGAC 58.975 38.462 20.42 0.00 34.41 3.18
3217 3689 2.299013 CTGGAAAAGGTTGGGTTAAGCC 59.701 50.000 17.01 17.01 37.49 4.35
3595 4068 5.145564 AGAATTAATCGGGACCTGCTACTA 58.854 41.667 0.00 0.00 0.00 1.82
3608 4081 6.491394 TGGCACGGAAAATTAGAATTAATCG 58.509 36.000 0.00 0.00 0.00 3.34
4118 4591 1.800805 ACTTTGGCTCATCAGACACG 58.199 50.000 0.00 0.00 37.40 4.49
4124 4597 5.129320 TCTGCTTAGATACTTTGGCTCATCA 59.871 40.000 0.00 0.00 0.00 3.07
4339 4812 1.533273 ACCATAGCCGCCTCCGTAT 60.533 57.895 0.00 0.00 0.00 3.06
4478 4951 5.182001 AGGCAGAACTAGCAATTTACACTTG 59.818 40.000 0.00 0.00 0.00 3.16
4585 5059 6.017852 GCTTAATTGTGATTAGGTGCTAGACC 60.018 42.308 0.00 0.00 46.58 3.85
4587 5061 5.753438 CGCTTAATTGTGATTAGGTGCTAGA 59.247 40.000 0.00 0.00 31.43 2.43
4745 5220 7.599245 CCCTCCGTCTCATAATAAAGATGTTAC 59.401 40.741 0.00 0.00 0.00 2.50
4765 5241 2.614057 GCACAAAATGATACTCCCTCCG 59.386 50.000 0.00 0.00 0.00 4.63
4859 5335 6.039616 TGCAAACAGTACCAAGTGAAAAATC 58.960 36.000 0.00 0.00 0.00 2.17
4984 5460 8.962679 TGTAGTCACTATATACATGTCAACACA 58.037 33.333 0.00 0.00 36.78 3.72
5328 5804 4.809426 GTGACCTTCCAATACATAGGTTCG 59.191 45.833 0.00 0.00 40.97 3.95
5912 6395 3.465403 CAGGGTCTCTGGGCCTCG 61.465 72.222 4.53 0.00 39.76 4.63
6043 6526 2.784347 TGGTACATCGATTGGCAAACA 58.216 42.857 3.01 0.00 0.00 2.83
6044 6527 3.057876 TGTTGGTACATCGATTGGCAAAC 60.058 43.478 3.01 0.00 39.30 2.93
6217 6701 1.069935 GGATAGCTTGGGACGCCTC 59.930 63.158 0.00 0.00 0.00 4.70
6368 6852 6.770785 TGCTCCATAGGTAAATTATCAACCAC 59.229 38.462 0.00 0.00 35.64 4.16



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

AutoCloner maintained by Alex Coulton.