Multiple sequence alignment - TraesCS5D01G511100

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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 TraesCS5D01G511100 chr5D 100.000 1455 0 0 1 1455 535873539 535874993 0.000000e+00 2687
1 TraesCS5D01G511100 chr5D 91.890 1455 112 5 1 1455 271850570 271849122 0.000000e+00 2028
2 TraesCS5D01G511100 chr5D 100.000 635 0 0 1765 2399 535875303 535875937 0.000000e+00 1173
3 TraesCS5D01G511100 chr5D 84.431 334 43 6 2063 2390 535807957 535808287 1.070000e-83 320
4 TraesCS5D01G511100 chr5D 83.969 131 13 5 2271 2394 535842260 535842389 4.190000e-23 119
5 TraesCS5D01G511100 chr2B 88.942 1456 154 6 1 1455 546866733 546868182 0.000000e+00 1790
6 TraesCS5D01G511100 chr6B 87.569 1456 174 6 1 1455 671145310 671146759 0.000000e+00 1679
7 TraesCS5D01G511100 chr2D 87.491 1455 177 4 1 1455 10068165 10069614 0.000000e+00 1674
8 TraesCS5D01G511100 chr2D 83.926 1462 217 17 1 1455 642787465 642786015 0.000000e+00 1382
9 TraesCS5D01G511100 chr5B 86.589 1454 172 8 3 1455 658444860 658446291 0.000000e+00 1583
10 TraesCS5D01G511100 chr5B 84.109 516 34 17 1914 2394 676305434 676305936 2.810000e-124 455
11 TraesCS5D01G511100 chr1B 86.960 1365 168 9 94 1455 637980656 637979299 0.000000e+00 1526
12 TraesCS5D01G511100 chr1D 85.155 1455 204 11 4 1455 452586838 452585393 0.000000e+00 1480
13 TraesCS5D01G511100 chr1D 84.536 1455 211 13 4 1455 452581288 452579845 0.000000e+00 1428
14 TraesCS5D01G511100 chr4A 89.835 423 32 6 1974 2394 636037673 636037260 1.260000e-147 532
15 TraesCS5D01G511100 chr4A 83.626 342 35 5 2063 2390 636108667 636108333 3.880000e-78 302
16 TraesCS5D01G511100 chr4A 86.099 223 20 3 2045 2266 636060197 636059985 1.850000e-56 230
17 TraesCS5D01G511100 chr4A 88.344 163 5 2 2232 2389 636093190 636093037 1.460000e-42 183


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 TraesCS5D01G511100 chr5D 535873539 535875937 2398 False 1930 2687 100.000 1 2399 2 chr5D.!!$F3 2398
1 TraesCS5D01G511100 chr5D 271849122 271850570 1448 True 2028 2028 91.890 1 1455 1 chr5D.!!$R1 1454
2 TraesCS5D01G511100 chr2B 546866733 546868182 1449 False 1790 1790 88.942 1 1455 1 chr2B.!!$F1 1454
3 TraesCS5D01G511100 chr6B 671145310 671146759 1449 False 1679 1679 87.569 1 1455 1 chr6B.!!$F1 1454
4 TraesCS5D01G511100 chr2D 10068165 10069614 1449 False 1674 1674 87.491 1 1455 1 chr2D.!!$F1 1454
5 TraesCS5D01G511100 chr2D 642786015 642787465 1450 True 1382 1382 83.926 1 1455 1 chr2D.!!$R1 1454
6 TraesCS5D01G511100 chr5B 658444860 658446291 1431 False 1583 1583 86.589 3 1455 1 chr5B.!!$F1 1452
7 TraesCS5D01G511100 chr5B 676305434 676305936 502 False 455 455 84.109 1914 2394 1 chr5B.!!$F2 480
8 TraesCS5D01G511100 chr1B 637979299 637980656 1357 True 1526 1526 86.960 94 1455 1 chr1B.!!$R1 1361
9 TraesCS5D01G511100 chr1D 452585393 452586838 1445 True 1480 1480 85.155 4 1455 1 chr1D.!!$R2 1451
10 TraesCS5D01G511100 chr1D 452579845 452581288 1443 True 1428 1428 84.536 4 1455 1 chr1D.!!$R1 1451

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
348 349 0.827368 GAGGTCTCTGGTAGCTTGGG 59.173 60.0 0.0 0.0 0.0 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1910 1915 0.179 CGGGGAGAATGGGACTTCAG 59.821 60.0 0.0 0.0 0.0 3.02 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
46 47 1.297664 GCTGCAGCTCTTGGATGTAG 58.702 55.000 31.33 0.00 44.71 2.74
50 51 2.290514 TGCAGCTCTTGGATGTAGCTTT 60.291 45.455 0.00 0.00 43.97 3.51
74 75 3.069729 CCTCCTTCCCGTTAATCTACCTG 59.930 52.174 0.00 0.00 0.00 4.00
212 213 1.572085 CTTTGCTGACTGCGGTCCTG 61.572 60.000 22.81 15.92 46.63 3.86
256 257 6.586344 TCATGTCTATTTTCTGCCTTCCTAG 58.414 40.000 0.00 0.00 0.00 3.02
284 285 3.702548 TCCTAGTTAAGCTTGACGCCATA 59.297 43.478 14.94 2.41 40.39 2.74
302 303 4.625083 GCCATAAGGAGAGCTTTCTTCTGT 60.625 45.833 4.01 0.00 36.89 3.41
326 327 2.877691 GAGGAAACATGCACGGGC 59.122 61.111 0.34 0.34 41.68 6.13
348 349 0.827368 GAGGTCTCTGGTAGCTTGGG 59.173 60.000 0.00 0.00 0.00 4.12
462 463 2.071778 ACTGCAACACCCAAACATCT 57.928 45.000 0.00 0.00 0.00 2.90
552 554 6.877611 TCCTCTGGAAAATAGTGAACAAAC 57.122 37.500 0.00 0.00 0.00 2.93
590 592 1.800805 AGCACTCCTTTGTGATCACG 58.199 50.000 20.54 7.89 40.12 4.35
711 714 1.472188 AGGTCTTAGTGGCTACCGTC 58.528 55.000 0.00 0.00 37.09 4.79
744 747 6.157211 CAGCTTATTATCGAACCTACGGAAT 58.843 40.000 0.00 0.00 0.00 3.01
768 771 1.260033 CTTACTAATGCTGCTGCTCGC 59.740 52.381 17.00 4.33 40.48 5.03
817 820 3.005684 GCAGGATTTCCAACATGTTGACA 59.994 43.478 34.76 20.29 42.93 3.58
852 855 2.825836 CTCACGCATGGGCTTCCC 60.826 66.667 10.10 0.00 45.71 3.97
923 926 4.201851 CGATCCACACCATGATTTTGTCTC 60.202 45.833 0.00 0.00 0.00 3.36
979 982 1.949847 ATGGCTTCTCCTCCACGACG 61.950 60.000 0.00 0.00 34.81 5.12
1104 1107 4.023980 ACTGCTCCTATGCTACACAAGTA 58.976 43.478 0.00 0.00 0.00 2.24
1145 1148 3.077556 CCCGACCTCCCTCACTGG 61.078 72.222 0.00 0.00 0.00 4.00
1279 1282 2.284405 ACCACCCACCCCGAGTAG 60.284 66.667 0.00 0.00 0.00 2.57
1287 1290 0.314302 CACCCCGAGTAGCGATAAGG 59.686 60.000 0.00 0.00 44.57 2.69
1317 1320 1.190643 CAGACTTCTCCCTCTGGGTC 58.809 60.000 2.25 0.00 44.74 4.46
1348 1351 7.148623 GGTTCAAAAAGACTGAAGATAGTACCG 60.149 40.741 0.00 0.00 33.56 4.02
1394 1398 1.377725 CCGCTGCAATCCCTTCTGT 60.378 57.895 0.00 0.00 0.00 3.41
1397 1401 1.093159 GCTGCAATCCCTTCTGTCTG 58.907 55.000 0.00 0.00 0.00 3.51
1410 1415 5.316987 CCTTCTGTCTGAAAATTGTACCCT 58.683 41.667 0.00 0.00 33.79 4.34
1440 1445 4.870426 TGCTGTAATTCTCGAATCCTTCAC 59.130 41.667 0.00 0.00 0.00 3.18
1441 1446 4.870426 GCTGTAATTCTCGAATCCTTCACA 59.130 41.667 0.00 0.00 0.00 3.58
1791 1796 3.985805 CGATTAGCGTCATTGCGAG 57.014 52.632 4.97 0.00 40.67 5.03
1792 1797 1.200483 CGATTAGCGTCATTGCGAGT 58.800 50.000 4.97 0.00 40.67 4.18
1793 1798 2.381589 CGATTAGCGTCATTGCGAGTA 58.618 47.619 4.97 0.00 40.67 2.59
1794 1799 2.787129 CGATTAGCGTCATTGCGAGTAA 59.213 45.455 4.97 2.92 40.67 2.24
1795 1800 3.242016 CGATTAGCGTCATTGCGAGTAAA 59.758 43.478 4.97 0.00 40.67 2.01
1796 1801 4.259650 CGATTAGCGTCATTGCGAGTAAAA 60.260 41.667 4.97 0.00 40.67 1.52
1797 1802 5.556382 CGATTAGCGTCATTGCGAGTAAAAT 60.556 40.000 4.97 0.00 40.67 1.82
1798 1803 5.539582 TTAGCGTCATTGCGAGTAAAATT 57.460 34.783 4.97 0.00 40.67 1.82
1799 1804 4.419522 AGCGTCATTGCGAGTAAAATTT 57.580 36.364 4.97 0.00 40.67 1.82
1800 1805 4.403453 AGCGTCATTGCGAGTAAAATTTC 58.597 39.130 0.00 0.00 40.67 2.17
1801 1806 4.154195 AGCGTCATTGCGAGTAAAATTTCT 59.846 37.500 0.00 0.00 40.67 2.52
1802 1807 4.492294 GCGTCATTGCGAGTAAAATTTCTC 59.508 41.667 0.00 0.00 0.00 2.87
1803 1808 5.617609 CGTCATTGCGAGTAAAATTTCTCA 58.382 37.500 7.45 0.00 0.00 3.27
1804 1809 6.077197 CGTCATTGCGAGTAAAATTTCTCAA 58.923 36.000 7.45 0.00 0.00 3.02
1805 1810 6.577055 CGTCATTGCGAGTAAAATTTCTCAAA 59.423 34.615 7.45 2.60 0.00 2.69
1806 1811 7.408290 CGTCATTGCGAGTAAAATTTCTCAAAC 60.408 37.037 7.45 0.00 0.00 2.93
1807 1812 7.378461 GTCATTGCGAGTAAAATTTCTCAAACA 59.622 33.333 7.45 0.98 0.00 2.83
1808 1813 8.081633 TCATTGCGAGTAAAATTTCTCAAACAT 58.918 29.630 7.45 0.00 0.00 2.71
1809 1814 8.702438 CATTGCGAGTAAAATTTCTCAAACATT 58.298 29.630 7.45 0.00 0.00 2.71
1810 1815 9.906660 ATTGCGAGTAAAATTTCTCAAACATTA 57.093 25.926 7.45 0.00 0.00 1.90
1811 1816 8.948853 TGCGAGTAAAATTTCTCAAACATTAG 57.051 30.769 7.45 0.00 0.00 1.73
1812 1817 7.537306 TGCGAGTAAAATTTCTCAAACATTAGC 59.463 33.333 7.45 1.85 0.00 3.09
1813 1818 7.252995 GCGAGTAAAATTTCTCAAACATTAGCG 60.253 37.037 7.45 0.00 0.00 4.26
1814 1819 7.744715 CGAGTAAAATTTCTCAAACATTAGCGT 59.255 33.333 7.45 0.00 0.00 5.07
1815 1820 8.728088 AGTAAAATTTCTCAAACATTAGCGTG 57.272 30.769 0.00 0.00 0.00 5.34
1816 1821 8.564574 AGTAAAATTTCTCAAACATTAGCGTGA 58.435 29.630 0.00 0.00 0.00 4.35
1817 1822 9.341899 GTAAAATTTCTCAAACATTAGCGTGAT 57.658 29.630 0.00 0.00 0.00 3.06
1818 1823 8.452989 AAAATTTCTCAAACATTAGCGTGATC 57.547 30.769 0.00 0.00 0.00 2.92
1819 1824 5.545658 TTTCTCAAACATTAGCGTGATCC 57.454 39.130 0.00 0.00 0.00 3.36
1820 1825 4.471904 TCTCAAACATTAGCGTGATCCT 57.528 40.909 0.00 0.00 0.00 3.24
1821 1826 4.832248 TCTCAAACATTAGCGTGATCCTT 58.168 39.130 0.00 0.00 0.00 3.36
1822 1827 4.870426 TCTCAAACATTAGCGTGATCCTTC 59.130 41.667 0.00 0.00 0.00 3.46
1823 1828 4.832248 TCAAACATTAGCGTGATCCTTCT 58.168 39.130 0.00 0.00 0.00 2.85
1824 1829 4.631377 TCAAACATTAGCGTGATCCTTCTG 59.369 41.667 0.00 0.00 0.00 3.02
1825 1830 4.471904 AACATTAGCGTGATCCTTCTGA 57.528 40.909 0.00 0.00 0.00 3.27
1826 1831 4.471904 ACATTAGCGTGATCCTTCTGAA 57.528 40.909 0.00 0.00 0.00 3.02
1827 1832 4.184629 ACATTAGCGTGATCCTTCTGAAC 58.815 43.478 0.00 0.00 0.00 3.18
1828 1833 3.953712 TTAGCGTGATCCTTCTGAACA 57.046 42.857 0.00 0.00 0.00 3.18
1829 1834 4.471904 TTAGCGTGATCCTTCTGAACAT 57.528 40.909 0.00 0.00 0.00 2.71
1830 1835 2.625737 AGCGTGATCCTTCTGAACATG 58.374 47.619 0.00 0.00 36.22 3.21
1831 1836 1.063174 GCGTGATCCTTCTGAACATGC 59.937 52.381 7.04 7.04 46.98 4.06
1832 1837 2.625737 CGTGATCCTTCTGAACATGCT 58.374 47.619 0.00 0.00 0.00 3.79
1833 1838 3.785486 CGTGATCCTTCTGAACATGCTA 58.215 45.455 0.00 0.00 0.00 3.49
1834 1839 4.183865 CGTGATCCTTCTGAACATGCTAA 58.816 43.478 0.00 0.00 0.00 3.09
1835 1840 4.033358 CGTGATCCTTCTGAACATGCTAAC 59.967 45.833 0.00 0.00 0.00 2.34
1836 1841 4.033358 GTGATCCTTCTGAACATGCTAACG 59.967 45.833 0.00 0.00 0.00 3.18
1837 1842 3.678056 TCCTTCTGAACATGCTAACGT 57.322 42.857 0.00 0.00 0.00 3.99
1838 1843 4.002906 TCCTTCTGAACATGCTAACGTT 57.997 40.909 5.88 5.88 0.00 3.99
1839 1844 3.745975 TCCTTCTGAACATGCTAACGTTG 59.254 43.478 11.99 2.07 0.00 4.10
1840 1845 3.745975 CCTTCTGAACATGCTAACGTTGA 59.254 43.478 11.99 0.00 0.00 3.18
1841 1846 4.213270 CCTTCTGAACATGCTAACGTTGAA 59.787 41.667 11.99 0.67 0.00 2.69
1842 1847 5.277779 CCTTCTGAACATGCTAACGTTGAAA 60.278 40.000 11.99 0.00 0.00 2.69
1843 1848 5.940192 TCTGAACATGCTAACGTTGAAAT 57.060 34.783 11.99 0.00 0.00 2.17
1844 1849 7.360861 CCTTCTGAACATGCTAACGTTGAAATA 60.361 37.037 11.99 0.00 0.00 1.40
1845 1850 7.060600 TCTGAACATGCTAACGTTGAAATAG 57.939 36.000 11.99 0.19 0.00 1.73
1846 1851 5.627172 TGAACATGCTAACGTTGAAATAGC 58.373 37.500 11.99 12.05 41.84 2.97
1847 1852 4.258935 ACATGCTAACGTTGAAATAGCG 57.741 40.909 11.99 2.44 43.86 4.26
1848 1853 2.798834 TGCTAACGTTGAAATAGCGC 57.201 45.000 11.99 0.00 43.86 5.92
1849 1854 1.059979 TGCTAACGTTGAAATAGCGCG 59.940 47.619 11.99 0.00 43.86 6.86
1850 1855 1.715030 CTAACGTTGAAATAGCGCGC 58.285 50.000 26.66 26.66 36.36 6.86
1851 1856 1.323534 CTAACGTTGAAATAGCGCGCT 59.676 47.619 38.01 38.01 36.36 5.92
1852 1857 1.352114 AACGTTGAAATAGCGCGCTA 58.648 45.000 39.72 39.72 36.36 4.26
1853 1858 1.567504 ACGTTGAAATAGCGCGCTAT 58.432 45.000 40.32 40.32 40.63 2.97
1892 1897 7.864108 AAAATCAAATCACACTGATATCCGA 57.136 32.000 0.00 0.00 35.76 4.55
1893 1898 8.455903 AAAATCAAATCACACTGATATCCGAT 57.544 30.769 0.00 0.00 35.76 4.18
1894 1899 7.430992 AATCAAATCACACTGATATCCGATG 57.569 36.000 0.00 0.00 35.76 3.84
1895 1900 5.299949 TCAAATCACACTGATATCCGATGG 58.700 41.667 0.00 0.00 35.76 3.51
1896 1901 2.820059 TCACACTGATATCCGATGGC 57.180 50.000 0.00 0.00 0.00 4.40
1897 1902 1.000274 TCACACTGATATCCGATGGCG 60.000 52.381 0.00 0.00 37.24 5.69
1898 1903 1.000274 CACACTGATATCCGATGGCGA 60.000 52.381 0.00 0.00 40.82 5.54
1899 1904 1.895798 ACACTGATATCCGATGGCGAT 59.104 47.619 0.00 0.00 40.82 4.58
1900 1905 2.300152 ACACTGATATCCGATGGCGATT 59.700 45.455 0.00 0.00 40.82 3.34
1901 1906 3.244215 ACACTGATATCCGATGGCGATTT 60.244 43.478 0.00 0.00 40.82 2.17
1902 1907 4.021456 ACACTGATATCCGATGGCGATTTA 60.021 41.667 0.00 0.00 40.82 1.40
1903 1908 4.929211 CACTGATATCCGATGGCGATTTAA 59.071 41.667 0.00 0.00 40.82 1.52
1904 1909 5.582269 CACTGATATCCGATGGCGATTTAAT 59.418 40.000 0.00 0.00 40.82 1.40
1905 1910 6.756542 CACTGATATCCGATGGCGATTTAATA 59.243 38.462 0.00 0.00 40.82 0.98
1906 1911 7.277760 CACTGATATCCGATGGCGATTTAATAA 59.722 37.037 0.00 0.00 40.82 1.40
1907 1912 7.822334 ACTGATATCCGATGGCGATTTAATAAA 59.178 33.333 0.00 0.00 40.82 1.40
1908 1913 8.731275 TGATATCCGATGGCGATTTAATAAAT 57.269 30.769 0.00 0.00 40.82 1.40
1909 1914 9.825109 TGATATCCGATGGCGATTTAATAAATA 57.175 29.630 0.00 0.00 40.82 1.40
1911 1916 9.832445 ATATCCGATGGCGATTTAATAAATACT 57.168 29.630 0.00 0.00 40.82 2.12
1912 1917 7.359262 TCCGATGGCGATTTAATAAATACTG 57.641 36.000 0.00 0.00 40.82 2.74
1928 1933 1.290134 ACTGAAGTCCCATTCTCCCC 58.710 55.000 0.00 0.00 0.00 4.81
1929 1934 0.179000 CTGAAGTCCCATTCTCCCCG 59.821 60.000 0.00 0.00 0.00 5.73
1930 1935 0.252513 TGAAGTCCCATTCTCCCCGA 60.253 55.000 0.00 0.00 0.00 5.14
1931 1936 0.466124 GAAGTCCCATTCTCCCCGAG 59.534 60.000 0.00 0.00 0.00 4.63
1935 1947 0.691078 TCCCATTCTCCCCGAGGAAG 60.691 60.000 0.00 0.00 43.40 3.46
1936 1948 0.983378 CCCATTCTCCCCGAGGAAGT 60.983 60.000 0.00 0.00 43.40 3.01
1998 2010 2.119886 CTTCTCGAGGAATCCGGCT 58.880 57.895 13.56 0.00 33.01 5.52
1999 2011 1.319541 CTTCTCGAGGAATCCGGCTA 58.680 55.000 13.56 0.00 33.01 3.93
2000 2012 1.268352 CTTCTCGAGGAATCCGGCTAG 59.732 57.143 13.56 0.00 33.01 3.42
2001 2013 1.173444 TCTCGAGGAATCCGGCTAGC 61.173 60.000 13.56 6.04 0.00 3.42
2002 2014 2.049985 CGAGGAATCCGGCTAGCG 60.050 66.667 9.00 4.07 0.00 4.26
2041 2053 2.579738 GACGCCTCCAACCTCCTC 59.420 66.667 0.00 0.00 0.00 3.71
2117 2129 2.764128 GGAGGCGGAGATGGACCA 60.764 66.667 0.00 0.00 0.00 4.02
2120 2132 3.458163 GGCGGAGATGGACCACGA 61.458 66.667 0.00 0.00 0.00 4.35
2122 2134 2.711922 GCGGAGATGGACCACGACT 61.712 63.158 0.00 0.00 0.00 4.18
2130 2142 2.254651 GACCACGACTTCTCGCGT 59.745 61.111 5.77 0.00 44.33 6.01
2163 2175 0.580104 CCAGTTTCGAGTTCGCGTTT 59.420 50.000 5.77 0.00 39.60 3.60
2174 2186 4.089493 CGAGTTCGCGTTTAATTCAGAGAA 59.911 41.667 5.77 0.00 0.00 2.87
2249 2276 1.689582 GATCCCTCCCCGACTTGGT 60.690 63.158 0.00 0.00 35.15 3.67
2306 2333 1.215647 CAGGTCCGTACAGTGCCTC 59.784 63.158 0.00 0.00 0.00 4.70
2309 2336 1.533469 GGTCCGTACAGTGCCTCACT 61.533 60.000 0.00 0.00 46.51 3.41
2312 2340 1.251527 CCGTACAGTGCCTCACTCCT 61.252 60.000 0.00 0.00 43.43 3.69
2314 2342 0.533032 GTACAGTGCCTCACTCCTCC 59.467 60.000 0.00 0.00 43.43 4.30
2321 2349 3.775654 CTCACTCCTCCCACGCCC 61.776 72.222 0.00 0.00 0.00 6.13
2330 2358 0.254747 CTCCCACGCCCTTGGAATTA 59.745 55.000 0.00 0.00 39.24 1.40
2333 2361 1.379527 CCACGCCCTTGGAATTAGAC 58.620 55.000 0.00 0.00 39.24 2.59
2338 2366 2.745152 CGCCCTTGGAATTAGACGGATT 60.745 50.000 0.00 0.00 0.00 3.01
2347 2390 6.826668 TGGAATTAGACGGATTCATGTGTAT 58.173 36.000 0.00 0.00 35.66 2.29
2361 2404 5.354767 TCATGTGTATGATTCTCTGCTGTC 58.645 41.667 0.00 0.00 38.37 3.51
2364 2407 5.895928 TGTGTATGATTCTCTGCTGTCTAC 58.104 41.667 0.00 0.00 0.00 2.59
2377 2420 2.031069 GCTGTCTACCGCGATTCAGATA 60.031 50.000 8.23 1.61 0.00 1.98
2394 2437 5.928976 TCAGATATGGATCCGTGTGAAATT 58.071 37.500 17.25 0.00 31.81 1.82
2395 2438 5.991606 TCAGATATGGATCCGTGTGAAATTC 59.008 40.000 17.25 0.00 31.81 2.17
2396 2439 4.991056 AGATATGGATCCGTGTGAAATTCG 59.009 41.667 17.25 0.00 31.81 3.34
2397 2440 2.465860 TGGATCCGTGTGAAATTCGT 57.534 45.000 7.39 0.00 0.00 3.85
2398 2441 2.073056 TGGATCCGTGTGAAATTCGTG 58.927 47.619 7.39 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 2.484742 TAACGGGAAGGAGGAAAAGC 57.515 50.000 0.00 0.00 0.00 3.51
50 51 3.708121 GGTAGATTAACGGGAAGGAGGAA 59.292 47.826 0.00 0.00 0.00 3.36
212 213 3.830755 TGAAATATACGGCTAGGGAGTCC 59.169 47.826 0.00 0.00 0.00 3.85
256 257 5.521544 CGTCAAGCTTAACTAGGATAGACC 58.478 45.833 0.00 0.00 42.77 3.85
284 285 3.392616 TGGAACAGAAGAAAGCTCTCCTT 59.607 43.478 0.00 0.00 34.51 3.36
326 327 1.658686 AAGCTACCAGAGACCTCGCG 61.659 60.000 0.00 0.00 34.09 5.87
334 335 2.076863 CGTTTTCCCAAGCTACCAGAG 58.923 52.381 0.00 0.00 0.00 3.35
348 349 6.309494 AGTTCTTTAGGTTTGCAAACGTTTTC 59.691 34.615 34.41 21.14 39.77 2.29
462 463 4.352893 TGATGATACCACTGAGTCCAAGA 58.647 43.478 0.00 0.00 0.00 3.02
552 554 2.422093 GCTCAATAAGGAGGGGAAGGTG 60.422 54.545 0.00 0.00 35.41 4.00
625 627 1.713078 AGGGGAGTTGAGAAGCCATTT 59.287 47.619 0.00 0.00 0.00 2.32
711 714 5.484173 TCGATAATAAGCTGTTTTGCCAG 57.516 39.130 0.00 0.00 35.49 4.85
744 747 2.166459 AGCAGCAGCATTAGTAAGACGA 59.834 45.455 3.17 0.00 45.49 4.20
768 771 3.119990 ACAACAAAACACAGTCCAACTCG 60.120 43.478 0.00 0.00 0.00 4.18
852 855 4.197750 AGTATGCATTCTTGGCTGAGAAG 58.802 43.478 3.54 0.00 38.90 2.85
923 926 0.179108 GATCGGGACCTTGGAAGACG 60.179 60.000 0.00 0.00 0.00 4.18
979 982 1.674441 GTTGGCCTTCGTATTTAGCCC 59.326 52.381 3.32 0.00 43.18 5.19
1028 1031 2.124570 GACATCGTGGGCAGGCAT 60.125 61.111 0.00 0.00 0.00 4.40
1145 1148 2.668550 GCGGGTGTTGGTGGAGAC 60.669 66.667 0.00 0.00 0.00 3.36
1279 1282 6.159988 AGTCTGCTACAATATTCCTTATCGC 58.840 40.000 0.00 0.00 0.00 4.58
1287 1290 6.041523 AGAGGGAGAAGTCTGCTACAATATTC 59.958 42.308 0.00 0.00 34.50 1.75
1317 1320 4.574828 TCTTCAGTCTTTTTGAACCGGAAG 59.425 41.667 9.46 0.00 31.66 3.46
1394 1398 6.430000 GCAGAAGTAAGGGTACAATTTTCAGA 59.570 38.462 0.00 0.00 32.12 3.27
1397 1401 6.206829 ACAGCAGAAGTAAGGGTACAATTTTC 59.793 38.462 0.00 0.00 32.12 2.29
1410 1415 6.757010 GGATTCGAGAATTACAGCAGAAGTAA 59.243 38.462 0.00 0.00 36.06 2.24
1773 1778 1.200483 ACTCGCAATGACGCTAATCG 58.800 50.000 0.00 0.00 45.38 3.34
1774 1779 4.772046 TTTACTCGCAATGACGCTAATC 57.228 40.909 0.00 0.00 0.00 1.75
1775 1780 5.734855 ATTTTACTCGCAATGACGCTAAT 57.265 34.783 0.00 0.00 0.00 1.73
1776 1781 5.539582 AATTTTACTCGCAATGACGCTAA 57.460 34.783 0.00 0.00 0.00 3.09
1777 1782 5.350365 AGAAATTTTACTCGCAATGACGCTA 59.650 36.000 0.00 0.00 0.00 4.26
1778 1783 4.154195 AGAAATTTTACTCGCAATGACGCT 59.846 37.500 0.00 0.00 0.00 5.07
1779 1784 4.403453 AGAAATTTTACTCGCAATGACGC 58.597 39.130 0.00 0.00 0.00 5.19
1780 1785 5.617609 TGAGAAATTTTACTCGCAATGACG 58.382 37.500 0.00 0.00 36.11 4.35
1781 1786 7.378461 TGTTTGAGAAATTTTACTCGCAATGAC 59.622 33.333 0.00 0.00 36.11 3.06
1782 1787 7.421599 TGTTTGAGAAATTTTACTCGCAATGA 58.578 30.769 0.00 0.00 36.11 2.57
1783 1788 7.621832 TGTTTGAGAAATTTTACTCGCAATG 57.378 32.000 0.00 0.00 36.11 2.82
1784 1789 8.816640 AATGTTTGAGAAATTTTACTCGCAAT 57.183 26.923 0.00 0.00 36.11 3.56
1785 1790 9.393249 CTAATGTTTGAGAAATTTTACTCGCAA 57.607 29.630 0.00 0.00 36.11 4.85
1786 1791 7.537306 GCTAATGTTTGAGAAATTTTACTCGCA 59.463 33.333 0.00 0.00 36.11 5.10
1787 1792 7.252995 CGCTAATGTTTGAGAAATTTTACTCGC 60.253 37.037 0.00 0.00 36.11 5.03
1788 1793 7.744715 ACGCTAATGTTTGAGAAATTTTACTCG 59.255 33.333 0.00 0.00 36.11 4.18
1789 1794 8.840867 CACGCTAATGTTTGAGAAATTTTACTC 58.159 33.333 0.00 0.00 0.00 2.59
1790 1795 8.564574 TCACGCTAATGTTTGAGAAATTTTACT 58.435 29.630 0.00 0.00 0.00 2.24
1791 1796 8.722342 TCACGCTAATGTTTGAGAAATTTTAC 57.278 30.769 0.00 0.00 0.00 2.01
1792 1797 9.554724 GATCACGCTAATGTTTGAGAAATTTTA 57.445 29.630 0.00 0.00 0.00 1.52
1793 1798 7.542130 GGATCACGCTAATGTTTGAGAAATTTT 59.458 33.333 0.00 0.00 0.00 1.82
1794 1799 7.029563 GGATCACGCTAATGTTTGAGAAATTT 58.970 34.615 0.00 0.00 0.00 1.82
1795 1800 6.375455 AGGATCACGCTAATGTTTGAGAAATT 59.625 34.615 0.00 0.00 0.00 1.82
1796 1801 5.882557 AGGATCACGCTAATGTTTGAGAAAT 59.117 36.000 0.00 0.00 0.00 2.17
1797 1802 5.245531 AGGATCACGCTAATGTTTGAGAAA 58.754 37.500 0.00 0.00 0.00 2.52
1798 1803 4.832248 AGGATCACGCTAATGTTTGAGAA 58.168 39.130 0.00 0.00 0.00 2.87
1799 1804 4.471904 AGGATCACGCTAATGTTTGAGA 57.528 40.909 0.00 0.00 0.00 3.27
1800 1805 4.872691 AGAAGGATCACGCTAATGTTTGAG 59.127 41.667 0.00 0.00 0.00 3.02
1801 1806 4.631377 CAGAAGGATCACGCTAATGTTTGA 59.369 41.667 0.00 0.00 0.00 2.69
1802 1807 4.631377 TCAGAAGGATCACGCTAATGTTTG 59.369 41.667 0.00 0.00 0.00 2.93
1803 1808 4.832248 TCAGAAGGATCACGCTAATGTTT 58.168 39.130 0.00 0.00 0.00 2.83
1804 1809 4.471904 TCAGAAGGATCACGCTAATGTT 57.528 40.909 0.00 0.00 0.00 2.71
1805 1810 4.184629 GTTCAGAAGGATCACGCTAATGT 58.815 43.478 0.00 0.00 0.00 2.71
1806 1811 4.183865 TGTTCAGAAGGATCACGCTAATG 58.816 43.478 0.00 0.00 0.00 1.90
1807 1812 4.471904 TGTTCAGAAGGATCACGCTAAT 57.528 40.909 0.00 0.00 0.00 1.73
1808 1813 3.953712 TGTTCAGAAGGATCACGCTAA 57.046 42.857 0.00 0.00 0.00 3.09
1809 1814 3.785486 CATGTTCAGAAGGATCACGCTA 58.215 45.455 0.00 0.00 0.00 4.26
1810 1815 2.625737 CATGTTCAGAAGGATCACGCT 58.374 47.619 0.00 0.00 0.00 5.07
1811 1816 1.063174 GCATGTTCAGAAGGATCACGC 59.937 52.381 0.00 0.00 28.67 5.34
1812 1817 2.625737 AGCATGTTCAGAAGGATCACG 58.374 47.619 0.00 0.00 0.00 4.35
1813 1818 4.033358 CGTTAGCATGTTCAGAAGGATCAC 59.967 45.833 0.00 0.00 0.00 3.06
1814 1819 4.183865 CGTTAGCATGTTCAGAAGGATCA 58.816 43.478 0.00 0.00 0.00 2.92
1815 1820 4.184629 ACGTTAGCATGTTCAGAAGGATC 58.815 43.478 0.00 0.00 0.00 3.36
1816 1821 4.207891 ACGTTAGCATGTTCAGAAGGAT 57.792 40.909 0.00 0.00 0.00 3.24
1817 1822 3.678056 ACGTTAGCATGTTCAGAAGGA 57.322 42.857 0.00 0.00 0.00 3.36
1818 1823 3.745975 TCAACGTTAGCATGTTCAGAAGG 59.254 43.478 0.00 0.00 28.84 3.46
1819 1824 4.990543 TCAACGTTAGCATGTTCAGAAG 57.009 40.909 0.00 0.00 28.84 2.85
1820 1825 5.743026 TTTCAACGTTAGCATGTTCAGAA 57.257 34.783 0.00 0.00 28.84 3.02
1821 1826 5.940192 ATTTCAACGTTAGCATGTTCAGA 57.060 34.783 0.00 0.00 28.84 3.27
1822 1827 5.734498 GCTATTTCAACGTTAGCATGTTCAG 59.266 40.000 13.71 0.00 38.53 3.02
1823 1828 5.627172 GCTATTTCAACGTTAGCATGTTCA 58.373 37.500 13.71 0.00 38.53 3.18
1824 1829 4.723862 CGCTATTTCAACGTTAGCATGTTC 59.276 41.667 17.53 0.00 38.58 3.18
1825 1830 4.647964 CGCTATTTCAACGTTAGCATGTT 58.352 39.130 17.53 0.00 38.58 2.71
1826 1831 3.485216 GCGCTATTTCAACGTTAGCATGT 60.485 43.478 17.53 0.00 38.58 3.21
1827 1832 3.029074 GCGCTATTTCAACGTTAGCATG 58.971 45.455 17.53 5.88 38.58 4.06
1828 1833 2.285602 CGCGCTATTTCAACGTTAGCAT 60.286 45.455 17.53 5.83 38.58 3.79
1829 1834 1.059979 CGCGCTATTTCAACGTTAGCA 59.940 47.619 17.53 0.00 38.58 3.49
1830 1835 1.715030 CGCGCTATTTCAACGTTAGC 58.285 50.000 5.56 5.08 35.97 3.09
1831 1836 1.323534 AGCGCGCTATTTCAACGTTAG 59.676 47.619 35.79 0.00 0.00 2.34
1832 1837 1.352114 AGCGCGCTATTTCAACGTTA 58.648 45.000 35.79 0.00 0.00 3.18
1833 1838 1.352114 TAGCGCGCTATTTCAACGTT 58.648 45.000 35.48 11.63 0.00 3.99
1834 1839 1.567504 ATAGCGCGCTATTTCAACGT 58.432 45.000 40.32 22.25 35.92 3.99
1835 1840 2.645628 AATAGCGCGCTATTTCAACG 57.354 45.000 44.70 1.35 44.18 4.10
1866 1871 9.389755 TCGGATATCAGTGTGATTTGATTTTTA 57.610 29.630 4.83 0.00 38.26 1.52
1867 1872 8.279970 TCGGATATCAGTGTGATTTGATTTTT 57.720 30.769 4.83 0.00 38.26 1.94
1868 1873 7.864108 TCGGATATCAGTGTGATTTGATTTT 57.136 32.000 4.83 0.00 38.26 1.82
1869 1874 7.040892 CCATCGGATATCAGTGTGATTTGATTT 60.041 37.037 4.83 0.00 38.26 2.17
1870 1875 6.429078 CCATCGGATATCAGTGTGATTTGATT 59.571 38.462 4.83 0.00 38.26 2.57
1871 1876 5.936372 CCATCGGATATCAGTGTGATTTGAT 59.064 40.000 4.83 0.00 38.26 2.57
1872 1877 5.299949 CCATCGGATATCAGTGTGATTTGA 58.700 41.667 4.83 0.00 38.26 2.69
1873 1878 4.083643 GCCATCGGATATCAGTGTGATTTG 60.084 45.833 4.83 0.00 38.26 2.32
1874 1879 4.067896 GCCATCGGATATCAGTGTGATTT 58.932 43.478 4.83 0.00 38.26 2.17
1875 1880 3.668447 GCCATCGGATATCAGTGTGATT 58.332 45.455 4.83 0.00 38.26 2.57
1876 1881 2.353109 CGCCATCGGATATCAGTGTGAT 60.353 50.000 4.83 0.00 40.72 3.06
1877 1882 1.000274 CGCCATCGGATATCAGTGTGA 60.000 52.381 4.83 0.00 0.00 3.58
1878 1883 1.000274 TCGCCATCGGATATCAGTGTG 60.000 52.381 4.83 4.83 36.13 3.82
1879 1884 1.328279 TCGCCATCGGATATCAGTGT 58.672 50.000 4.83 0.00 36.13 3.55
1880 1885 2.662006 ATCGCCATCGGATATCAGTG 57.338 50.000 4.83 2.32 36.13 3.66
1881 1886 3.685139 AAATCGCCATCGGATATCAGT 57.315 42.857 4.83 0.00 36.13 3.41
1882 1887 7.770801 TTATTAAATCGCCATCGGATATCAG 57.229 36.000 4.83 0.00 36.13 2.90
1883 1888 8.731275 ATTTATTAAATCGCCATCGGATATCA 57.269 30.769 4.83 0.00 36.13 2.15
1885 1890 9.832445 AGTATTTATTAAATCGCCATCGGATAT 57.168 29.630 4.94 0.00 36.13 1.63
1886 1891 9.093970 CAGTATTTATTAAATCGCCATCGGATA 57.906 33.333 4.94 0.00 36.13 2.59
1887 1892 7.822334 TCAGTATTTATTAAATCGCCATCGGAT 59.178 33.333 4.94 0.00 36.13 4.18
1888 1893 7.156000 TCAGTATTTATTAAATCGCCATCGGA 58.844 34.615 4.94 0.00 36.13 4.55
1889 1894 7.359262 TCAGTATTTATTAAATCGCCATCGG 57.641 36.000 4.94 0.00 36.13 4.18
1890 1895 8.495949 ACTTCAGTATTTATTAAATCGCCATCG 58.504 33.333 4.94 0.00 32.38 3.84
1891 1896 9.813080 GACTTCAGTATTTATTAAATCGCCATC 57.187 33.333 4.94 0.00 32.38 3.51
1892 1897 8.784043 GGACTTCAGTATTTATTAAATCGCCAT 58.216 33.333 4.94 0.00 32.38 4.40
1893 1898 7.227910 GGGACTTCAGTATTTATTAAATCGCCA 59.772 37.037 4.94 0.00 32.38 5.69
1894 1899 7.227910 TGGGACTTCAGTATTTATTAAATCGCC 59.772 37.037 4.94 0.00 32.38 5.54
1895 1900 8.149973 TGGGACTTCAGTATTTATTAAATCGC 57.850 34.615 4.94 1.31 32.38 4.58
1900 1905 9.847224 GGAGAATGGGACTTCAGTATTTATTAA 57.153 33.333 0.00 0.00 0.00 1.40
1901 1906 8.437575 GGGAGAATGGGACTTCAGTATTTATTA 58.562 37.037 0.00 0.00 0.00 0.98
1902 1907 7.290813 GGGAGAATGGGACTTCAGTATTTATT 58.709 38.462 0.00 0.00 0.00 1.40
1903 1908 6.183361 GGGGAGAATGGGACTTCAGTATTTAT 60.183 42.308 0.00 0.00 0.00 1.40
1904 1909 5.132144 GGGGAGAATGGGACTTCAGTATTTA 59.868 44.000 0.00 0.00 0.00 1.40
1905 1910 4.079730 GGGGAGAATGGGACTTCAGTATTT 60.080 45.833 0.00 0.00 0.00 1.40
1906 1911 3.459969 GGGGAGAATGGGACTTCAGTATT 59.540 47.826 0.00 0.00 0.00 1.89
1907 1912 3.049344 GGGGAGAATGGGACTTCAGTAT 58.951 50.000 0.00 0.00 0.00 2.12
1908 1913 2.478292 GGGGAGAATGGGACTTCAGTA 58.522 52.381 0.00 0.00 0.00 2.74
1909 1914 1.290134 GGGGAGAATGGGACTTCAGT 58.710 55.000 0.00 0.00 0.00 3.41
1910 1915 0.179000 CGGGGAGAATGGGACTTCAG 59.821 60.000 0.00 0.00 0.00 3.02
1911 1916 0.252513 TCGGGGAGAATGGGACTTCA 60.253 55.000 0.00 0.00 0.00 3.02
1912 1917 0.466124 CTCGGGGAGAATGGGACTTC 59.534 60.000 0.00 0.00 0.00 3.01
1988 2000 1.289380 CCTACGCTAGCCGGATTCC 59.711 63.158 5.05 0.00 42.52 3.01
2025 2037 0.684805 CTAGAGGAGGTTGGAGGCGT 60.685 60.000 0.00 0.00 0.00 5.68
2106 2118 1.135333 GAGAAGTCGTGGTCCATCTCC 59.865 57.143 7.87 0.00 0.00 3.71
2148 2160 4.445052 TCTGAATTAAACGCGAACTCGAAA 59.555 37.500 15.93 0.00 43.02 3.46
2174 2186 3.692406 GCACCCGGTCGGAGAAGT 61.692 66.667 11.39 0.00 39.69 3.01
2249 2276 4.373116 GCTCCTCGCGGTGGAACA 62.373 66.667 19.12 2.09 39.98 3.18
2306 2333 3.322466 AAGGGCGTGGGAGGAGTG 61.322 66.667 0.00 0.00 0.00 3.51
2309 2336 4.649705 TCCAAGGGCGTGGGAGGA 62.650 66.667 0.00 0.00 39.34 3.71
2312 2340 0.254747 CTAATTCCAAGGGCGTGGGA 59.745 55.000 0.00 0.00 39.34 4.37
2314 2342 1.379527 GTCTAATTCCAAGGGCGTGG 58.620 55.000 0.00 0.00 40.33 4.94
2321 2349 5.586243 ACACATGAATCCGTCTAATTCCAAG 59.414 40.000 0.00 0.00 33.13 3.61
2330 2358 6.041409 AGAGAATCATACACATGAATCCGTCT 59.959 38.462 0.00 0.00 44.27 4.18
2333 2361 5.107182 GCAGAGAATCATACACATGAATCCG 60.107 44.000 0.00 0.00 44.27 4.18
2338 2366 5.128335 AGACAGCAGAGAATCATACACATGA 59.872 40.000 0.00 0.00 45.15 3.07
2347 2390 1.135139 GCGGTAGACAGCAGAGAATCA 59.865 52.381 0.00 0.00 37.82 2.57
2361 2404 3.850122 TCCATATCTGAATCGCGGTAG 57.150 47.619 6.13 0.00 0.00 3.18
2364 2407 2.544685 GGATCCATATCTGAATCGCGG 58.455 52.381 6.95 0.00 32.29 6.46
2377 2420 2.677836 CACGAATTTCACACGGATCCAT 59.322 45.455 13.41 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.