Multiple sequence alignment - TraesCS7D01G212900

Loading Multiple Alignment...

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 TraesCS7D01G212900 chr7D 100.000 3850 0 0 1 3850 171309881 171306032 0.000000e+00 7110
1 TraesCS7D01G212900 chr7D 95.480 177 4 4 1731 1905 363554546 363554720 2.930000e-71 279
2 TraesCS7D01G212900 chr7D 95.455 176 7 1 1727 1901 498339422 498339597 2.930000e-71 279
3 TraesCS7D01G212900 chr7B 95.429 1969 65 12 1891 3850 137789680 137787728 0.000000e+00 3114
4 TraesCS7D01G212900 chr7B 93.193 1763 75 19 3 1732 137791429 137789679 0.000000e+00 2549
5 TraesCS7D01G212900 chr7A 93.539 1981 92 19 1888 3850 174200405 174198443 0.000000e+00 2916
6 TraesCS7D01G212900 chr7A 94.493 1707 70 6 2 1685 174202156 174200451 0.000000e+00 2610
7 TraesCS7D01G212900 chr7A 92.670 191 8 6 1731 1919 67503818 67504004 1.760000e-68 270
8 TraesCS7D01G212900 chr6A 84.663 326 48 2 3428 3752 521458819 521459143 1.330000e-84 324
9 TraesCS7D01G212900 chr6B 83.436 326 52 2 3428 3752 567408028 567408352 6.250000e-78 302
10 TraesCS7D01G212900 chr6D 99.387 163 0 1 1731 1892 266777479 266777641 1.050000e-75 294
11 TraesCS7D01G212900 chr2B 95.135 185 5 4 1728 1908 797534653 797534837 4.870000e-74 289
12 TraesCS7D01G212900 chr2B 82.039 206 27 10 1729 1927 677039130 677039332 2.380000e-37 167
13 TraesCS7D01G212900 chr5D 96.532 173 5 1 1721 1892 472291167 472290995 6.300000e-73 285
14 TraesCS7D01G212900 chr5D 93.989 183 10 1 1719 1900 127451968 127452150 3.790000e-70 276
15 TraesCS7D01G212900 chrUn 95.506 178 5 3 1727 1902 115107898 115108074 8.140000e-72 281
16 TraesCS7D01G212900 chr1D 94.022 184 8 3 1716 1897 436432529 436432711 3.790000e-70 276


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 TraesCS7D01G212900 chr7D 171306032 171309881 3849 True 7110.0 7110 100.000 1 3850 1 chr7D.!!$R1 3849
1 TraesCS7D01G212900 chr7B 137787728 137791429 3701 True 2831.5 3114 94.311 3 3850 2 chr7B.!!$R1 3847
2 TraesCS7D01G212900 chr7A 174198443 174202156 3713 True 2763.0 2916 94.016 2 3850 2 chr7A.!!$R1 3848

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
433 448 1.073897 GTCCCTGTTGCTTCCAGCT 59.926 57.895 0.0 0.0 42.97 4.24 F
1267 1306 0.740149 CACTCTTTTGGCTGCACACA 59.260 50.000 0.5 0.0 0.00 3.72 F
1392 1431 0.461870 CGGCAACCATGATCGGAGAA 60.462 55.000 0.0 0.0 43.58 2.87 F
2012 2053 0.463833 GGCCTTACTGGGATGTTCCG 60.464 60.000 0.0 0.0 37.43 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1327 1366 0.034337 CAGCCCTGCAGCAAACAAAT 59.966 50.000 8.66 0.0 34.23 2.32 R
2226 2277 0.804989 GCTTACAGCGCCTGATTGTT 59.195 50.000 2.29 0.0 35.18 2.83 R
2549 2609 1.009552 TCCAAGGGGCAGATCTCCTTA 59.990 52.381 12.57 0.0 38.70 2.69 R
3796 3856 1.164411 CATAACTGCAAACGCCCTGA 58.836 50.000 0.00 0.0 0.00 3.86 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
99 100 3.132925 GTTACGGTTTACCTGCAGAACA 58.867 45.455 17.39 0.00 0.00 3.18
334 343 2.798262 CTTTTCGCGTGCTGCTGC 60.798 61.111 5.77 8.89 43.27 5.25
427 442 1.880027 GACGAAATGTCCCTGTTGCTT 59.120 47.619 0.00 0.00 42.04 3.91
433 448 1.073897 GTCCCTGTTGCTTCCAGCT 59.926 57.895 0.00 0.00 42.97 4.24
511 526 5.501156 GGAAGGTGATCTAACAATGGAACT 58.499 41.667 0.00 0.00 0.00 3.01
608 626 6.656693 CACCTGTTGATCTGAGTTCCTTTTAT 59.343 38.462 0.00 0.00 0.00 1.40
741 760 1.334384 ACCCAAAGCCACCAAACACC 61.334 55.000 0.00 0.00 0.00 4.16
844 883 1.880027 GCTTACTCCACCAACCACAAG 59.120 52.381 0.00 0.00 0.00 3.16
886 925 5.470368 TCTTGACCAGTTTCTCTTCATACG 58.530 41.667 0.00 0.00 0.00 3.06
917 956 6.481643 AGGCCTGTCTTACTTTGCTATAAAA 58.518 36.000 3.11 0.00 0.00 1.52
926 965 5.736951 ACTTTGCTATAAAACCCATGCAA 57.263 34.783 0.00 0.00 38.41 4.08
930 969 4.489810 TGCTATAAAACCCATGCAAAACG 58.510 39.130 0.00 0.00 0.00 3.60
933 972 2.524569 AAAACCCATGCAAAACGAGG 57.475 45.000 0.00 0.00 0.00 4.63
1238 1277 1.014352 GACTGTTTCGTGCAGGTTGT 58.986 50.000 6.26 0.01 38.22 3.32
1267 1306 0.740149 CACTCTTTTGGCTGCACACA 59.260 50.000 0.50 0.00 0.00 3.72
1276 1315 1.576421 GCTGCACACACTAACCTGC 59.424 57.895 0.00 0.00 0.00 4.85
1294 1333 2.547211 CTGCATGCTTATACTGTGGAGC 59.453 50.000 20.33 0.00 35.74 4.70
1326 1365 5.125356 TGAGTTTGCTCTGAACATCTGAAA 58.875 37.500 0.00 0.00 42.13 2.69
1327 1366 5.589855 TGAGTTTGCTCTGAACATCTGAAAA 59.410 36.000 0.00 0.00 42.13 2.29
1336 1375 7.467557 TCTGAACATCTGAAAATTTGTTTGC 57.532 32.000 0.00 0.00 32.73 3.68
1377 1416 2.661537 CTGCTTGACGACACGGCA 60.662 61.111 12.27 12.27 45.89 5.69
1392 1431 0.461870 CGGCAACCATGATCGGAGAA 60.462 55.000 0.00 0.00 43.58 2.87
1419 1458 2.079925 GCAGACCAGAATGTGAACTCC 58.920 52.381 0.00 0.00 0.00 3.85
1420 1459 2.289945 GCAGACCAGAATGTGAACTCCT 60.290 50.000 0.00 0.00 0.00 3.69
1425 1464 4.392940 ACCAGAATGTGAACTCCTTGAAG 58.607 43.478 0.00 0.00 0.00 3.02
1509 1548 2.417933 CTGTGCTGACTTACTTGCCATC 59.582 50.000 0.00 0.00 0.00 3.51
1543 1583 6.380095 ACGCAGTTGTCTTGGTAAATAAAA 57.620 33.333 0.00 0.00 37.78 1.52
1572 1612 9.606631 AAACCTATGTTCAGAGTATTGATTCTC 57.393 33.333 0.00 0.00 32.15 2.87
1581 1621 4.081972 AGAGTATTGATTCTCGTGCAGTGT 60.082 41.667 0.00 0.00 36.03 3.55
1602 1642 6.263168 AGTGTCTTAGTTACTTTTGCTTGCAT 59.737 34.615 0.00 0.00 0.00 3.96
1612 1652 4.748102 ACTTTTGCTTGCATCACTTTCATG 59.252 37.500 0.00 0.00 0.00 3.07
1626 1666 1.538047 TTCATGTCAGGCTTGCCTTC 58.462 50.000 11.99 8.77 0.00 3.46
1712 1753 5.303259 TGATATAACCTGCTGTGCCATTA 57.697 39.130 0.00 0.00 0.00 1.90
1732 1773 6.647067 CCATTAGGATGCTGTTTAGCTACTAC 59.353 42.308 0.00 0.00 43.78 2.73
1738 1779 4.310357 GCTGTTTAGCTACTACTCCCTC 57.690 50.000 0.00 0.00 46.57 4.30
1739 1780 3.068448 GCTGTTTAGCTACTACTCCCTCC 59.932 52.174 0.00 0.00 46.57 4.30
1740 1781 3.285484 TGTTTAGCTACTACTCCCTCCG 58.715 50.000 0.00 0.00 0.00 4.63
1743 1784 2.055684 AGCTACTACTCCCTCCGTTC 57.944 55.000 0.00 0.00 0.00 3.95
1744 1785 1.031235 GCTACTACTCCCTCCGTTCC 58.969 60.000 0.00 0.00 0.00 3.62
1745 1786 1.409942 GCTACTACTCCCTCCGTTCCT 60.410 57.143 0.00 0.00 0.00 3.36
1747 1788 3.686691 GCTACTACTCCCTCCGTTCCTAA 60.687 52.174 0.00 0.00 0.00 2.69
1748 1789 3.463048 ACTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
1749 1790 3.991683 ACTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
1750 1791 5.134725 ACTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
1751 1792 5.713807 ACTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
1752 1793 6.856757 ACTACTCCCTCCGTTCCTAAATATA 58.143 40.000 0.00 0.00 0.00 0.86
1753 1794 7.300658 ACTACTCCCTCCGTTCCTAAATATAA 58.699 38.462 0.00 0.00 0.00 0.98
1754 1795 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
1755 1796 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
1756 1797 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
1757 1798 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
1758 1799 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
1759 1800 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
1760 1801 7.441458 CCCTCCGTTCCTAAATATAAGTCTTTG 59.559 40.741 0.00 0.00 0.00 2.77
1761 1802 7.985752 CCTCCGTTCCTAAATATAAGTCTTTGT 59.014 37.037 0.00 0.00 0.00 2.83
1772 1813 8.950208 AATATAAGTCTTTGTAGAGCTTCCAC 57.050 34.615 0.00 0.00 0.00 4.02
1773 1814 4.965200 AAGTCTTTGTAGAGCTTCCACT 57.035 40.909 0.00 0.00 0.00 4.00
1774 1815 7.719871 ATAAGTCTTTGTAGAGCTTCCACTA 57.280 36.000 0.00 0.00 0.00 2.74
1775 1816 6.613153 AAGTCTTTGTAGAGCTTCCACTAT 57.387 37.500 0.00 0.00 0.00 2.12
1776 1817 5.971763 AGTCTTTGTAGAGCTTCCACTATG 58.028 41.667 0.00 0.00 0.00 2.23
1777 1818 5.717178 AGTCTTTGTAGAGCTTCCACTATGA 59.283 40.000 0.00 0.00 0.00 2.15
1778 1819 6.211584 AGTCTTTGTAGAGCTTCCACTATGAA 59.788 38.462 0.00 0.00 0.00 2.57
1779 1820 6.311690 GTCTTTGTAGAGCTTCCACTATGAAC 59.688 42.308 0.00 0.00 0.00 3.18
1780 1821 5.738619 TTGTAGAGCTTCCACTATGAACA 57.261 39.130 0.00 0.00 0.00 3.18
1781 1822 5.073311 TGTAGAGCTTCCACTATGAACAC 57.927 43.478 0.00 0.00 0.00 3.32
1782 1823 4.526650 TGTAGAGCTTCCACTATGAACACA 59.473 41.667 0.00 0.00 0.00 3.72
1783 1824 4.833478 AGAGCTTCCACTATGAACACAT 57.167 40.909 0.00 0.00 0.00 3.21
1784 1825 5.939764 AGAGCTTCCACTATGAACACATA 57.060 39.130 0.00 0.00 0.00 2.29
1785 1826 5.665459 AGAGCTTCCACTATGAACACATAC 58.335 41.667 0.00 0.00 0.00 2.39
1786 1827 4.433615 AGCTTCCACTATGAACACATACG 58.566 43.478 0.00 0.00 0.00 3.06
1787 1828 3.555956 GCTTCCACTATGAACACATACGG 59.444 47.826 0.00 0.00 0.00 4.02
1788 1829 4.679639 GCTTCCACTATGAACACATACGGA 60.680 45.833 0.00 0.00 0.00 4.69
1789 1830 5.601662 CTTCCACTATGAACACATACGGAT 58.398 41.667 0.00 0.00 30.16 4.18
1790 1831 4.944048 TCCACTATGAACACATACGGATG 58.056 43.478 5.94 5.94 39.16 3.51
1792 1833 5.595133 TCCACTATGAACACATACGGATGTA 59.405 40.000 14.23 0.00 44.82 2.29
1793 1834 6.266786 TCCACTATGAACACATACGGATGTAT 59.733 38.462 14.23 0.00 44.82 2.29
1794 1835 7.449086 TCCACTATGAACACATACGGATGTATA 59.551 37.037 14.23 6.86 44.82 1.47
1795 1836 8.251026 CCACTATGAACACATACGGATGTATAT 58.749 37.037 14.23 8.03 44.82 0.86
1801 1842 7.973944 TGAACACATACGGATGTATATAGATGC 59.026 37.037 14.23 0.00 44.82 3.91
1802 1843 7.404671 ACACATACGGATGTATATAGATGCA 57.595 36.000 14.23 0.00 44.82 3.96
1803 1844 8.011844 ACACATACGGATGTATATAGATGCAT 57.988 34.615 14.23 0.00 44.82 3.96
1804 1845 8.478066 ACACATACGGATGTATATAGATGCATT 58.522 33.333 14.23 1.23 44.82 3.56
1805 1846 9.317936 CACATACGGATGTATATAGATGCATTT 57.682 33.333 14.23 0.00 44.82 2.32
1806 1847 9.890629 ACATACGGATGTATATAGATGCATTTT 57.109 29.630 12.79 0.00 44.77 1.82
1810 1851 9.944376 ACGGATGTATATAGATGCATTTTAAGT 57.056 29.630 11.19 0.00 38.38 2.24
1832 1873 7.093322 AGTGTAGATTCATTCATTTTGCTCC 57.907 36.000 0.00 0.00 0.00 4.70
1833 1874 5.967674 GTGTAGATTCATTCATTTTGCTCCG 59.032 40.000 0.00 0.00 0.00 4.63
1834 1875 5.647658 TGTAGATTCATTCATTTTGCTCCGT 59.352 36.000 0.00 0.00 0.00 4.69
1835 1876 6.821160 TGTAGATTCATTCATTTTGCTCCGTA 59.179 34.615 0.00 0.00 0.00 4.02
1836 1877 6.949352 AGATTCATTCATTTTGCTCCGTAT 57.051 33.333 0.00 0.00 0.00 3.06
1837 1878 6.732154 AGATTCATTCATTTTGCTCCGTATG 58.268 36.000 0.00 0.00 0.00 2.39
1838 1879 5.895636 TTCATTCATTTTGCTCCGTATGT 57.104 34.783 0.00 0.00 0.00 2.29
1839 1880 6.993786 TTCATTCATTTTGCTCCGTATGTA 57.006 33.333 0.00 0.00 0.00 2.29
1840 1881 6.603237 TCATTCATTTTGCTCCGTATGTAG 57.397 37.500 0.00 0.00 0.00 2.74
1841 1882 6.112734 TCATTCATTTTGCTCCGTATGTAGT 58.887 36.000 0.00 0.00 0.00 2.73
1842 1883 6.257849 TCATTCATTTTGCTCCGTATGTAGTC 59.742 38.462 0.00 0.00 0.00 2.59
1843 1884 4.439057 TCATTTTGCTCCGTATGTAGTCC 58.561 43.478 0.00 0.00 0.00 3.85
1844 1885 3.965379 TTTTGCTCCGTATGTAGTCCA 57.035 42.857 0.00 0.00 0.00 4.02
1845 1886 2.953466 TTGCTCCGTATGTAGTCCAC 57.047 50.000 0.00 0.00 0.00 4.02
1846 1887 1.108776 TGCTCCGTATGTAGTCCACC 58.891 55.000 0.00 0.00 0.00 4.61
1847 1888 1.341679 TGCTCCGTATGTAGTCCACCT 60.342 52.381 0.00 0.00 0.00 4.00
1848 1889 2.092267 TGCTCCGTATGTAGTCCACCTA 60.092 50.000 0.00 0.00 0.00 3.08
1849 1890 2.553172 GCTCCGTATGTAGTCCACCTAG 59.447 54.545 0.00 0.00 0.00 3.02
1850 1891 3.818180 CTCCGTATGTAGTCCACCTAGT 58.182 50.000 0.00 0.00 0.00 2.57
1851 1892 3.548770 TCCGTATGTAGTCCACCTAGTG 58.451 50.000 0.00 0.00 0.00 2.74
1866 1907 6.531503 CACCTAGTGGAATCTCTACAAAGA 57.468 41.667 0.00 0.00 37.04 2.52
1867 1908 6.334202 CACCTAGTGGAATCTCTACAAAGAC 58.666 44.000 0.00 0.00 37.04 3.01
1868 1909 6.153680 CACCTAGTGGAATCTCTACAAAGACT 59.846 42.308 0.00 0.00 37.04 3.24
1869 1910 6.726764 ACCTAGTGGAATCTCTACAAAGACTT 59.273 38.462 0.00 0.00 37.04 3.01
1870 1911 7.894364 ACCTAGTGGAATCTCTACAAAGACTTA 59.106 37.037 0.00 0.00 37.04 2.24
1871 1912 8.919145 CCTAGTGGAATCTCTACAAAGACTTAT 58.081 37.037 0.00 0.00 34.57 1.73
1885 1926 8.943909 ACAAAGACTTATATTTAGGAACGGAG 57.056 34.615 0.00 0.00 0.00 4.63
1886 1927 7.985752 ACAAAGACTTATATTTAGGAACGGAGG 59.014 37.037 0.00 0.00 0.00 4.30
1918 1959 5.283294 TGCAAACAAAGAACATGACAGATG 58.717 37.500 0.00 0.00 0.00 2.90
1933 1974 5.214417 TGACAGATGCATTTCTTGAAAACG 58.786 37.500 0.00 0.00 0.00 3.60
1943 1984 6.343924 GCATTTCTTGAAAACGAAACACTACG 60.344 38.462 0.00 0.00 32.55 3.51
1965 2006 6.740110 ACGAACTCCATATCTATCTGACAAC 58.260 40.000 0.00 0.00 0.00 3.32
1966 2007 6.321435 ACGAACTCCATATCTATCTGACAACA 59.679 38.462 0.00 0.00 0.00 3.33
1967 2008 7.147897 ACGAACTCCATATCTATCTGACAACAA 60.148 37.037 0.00 0.00 0.00 2.83
1976 2017 6.139679 TCTATCTGACAACAAGGGGAAAAT 57.860 37.500 0.00 0.00 0.00 1.82
1977 2018 7.265599 TCTATCTGACAACAAGGGGAAAATA 57.734 36.000 0.00 0.00 0.00 1.40
1979 2020 8.998814 TCTATCTGACAACAAGGGGAAAATATA 58.001 33.333 0.00 0.00 0.00 0.86
2012 2053 0.463833 GGCCTTACTGGGATGTTCCG 60.464 60.000 0.00 0.00 37.43 4.30
2075 2116 3.728373 AAGGACATCCCCACCGCC 61.728 66.667 0.00 0.00 36.42 6.13
2150 2191 0.540365 CTGACATGGTGGCCCTTGTT 60.540 55.000 0.00 1.22 46.17 2.83
2189 2232 8.023128 TCTTTTGACAGCTGCAGTTTATATTTC 58.977 33.333 15.27 0.00 0.00 2.17
2226 2277 7.119699 CAGTTCAGCTCATATTAACAGAACCAA 59.880 37.037 0.00 0.00 35.86 3.67
2304 2363 8.156994 AGTAGGAGATACTCGTTTACATCTTC 57.843 38.462 0.00 0.00 40.99 2.87
2305 2365 6.394025 AGGAGATACTCGTTTACATCTTCC 57.606 41.667 0.00 0.00 0.00 3.46
2403 2463 7.148340 CCCTTGTTATCTTCTTAAGCTGAACAG 60.148 40.741 0.00 0.00 30.94 3.16
2406 2466 6.147821 TGTTATCTTCTTAAGCTGAACAGTGC 59.852 38.462 0.00 0.00 0.00 4.40
2414 2474 4.351874 AAGCTGAACAGTGCCTTACTAA 57.648 40.909 3.77 0.00 37.60 2.24
2420 2480 6.402226 GCTGAACAGTGCCTTACTAAACATAC 60.402 42.308 3.77 0.00 37.60 2.39
2431 2491 6.959311 CCTTACTAAACATACGACATTTGCAC 59.041 38.462 0.00 0.00 0.00 4.57
2459 2519 1.348250 CCACACGATTGGATTCGCG 59.652 57.895 0.00 0.00 42.82 5.87
2549 2609 0.247736 CGACCTACCTCAGCAAGCTT 59.752 55.000 0.00 0.00 0.00 3.74
2959 3019 4.631377 TGGTATAGGTATTATCGTCGTCGG 59.369 45.833 1.55 0.00 37.69 4.79
2966 3026 1.311859 TTATCGTCGTCGGGCTACAT 58.688 50.000 1.55 0.00 37.69 2.29
3030 3090 4.804108 TCATGTATTTTGAGGGTTTTGCG 58.196 39.130 0.00 0.00 0.00 4.85
3042 3102 2.094234 GGGTTTTGCGCAACCTGATATT 60.094 45.455 26.09 0.00 45.12 1.28
3043 3103 3.129638 GGGTTTTGCGCAACCTGATATTA 59.870 43.478 26.09 6.26 45.12 0.98
3044 3104 4.202111 GGGTTTTGCGCAACCTGATATTAT 60.202 41.667 26.09 0.00 45.12 1.28
3119 3179 3.556775 TGAAAATGCAGCAAGAAAAGCAC 59.443 39.130 0.00 0.00 40.14 4.40
3121 3181 2.144482 ATGCAGCAAGAAAAGCACAC 57.856 45.000 0.00 0.00 40.14 3.82
3122 3182 0.816373 TGCAGCAAGAAAAGCACACA 59.184 45.000 0.00 0.00 31.05 3.72
3123 3183 1.203065 GCAGCAAGAAAAGCACACAC 58.797 50.000 0.00 0.00 0.00 3.82
3762 3822 3.603532 TCTTCACCTGATCATCAAGCAC 58.396 45.455 0.00 0.00 0.00 4.40
3796 3856 5.605534 AGCTAACTTAAGCATCATCGATGT 58.394 37.500 24.09 9.70 45.30 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
99 100 4.652822 CCTAAACCAGCCTTTAACAGTCT 58.347 43.478 0.00 0.00 0.00 3.24
334 343 1.757699 TGAGGAAAACAAAAACGGGGG 59.242 47.619 0.00 0.00 0.00 5.40
427 442 2.187100 TGTATCCATCACACAGCTGGA 58.813 47.619 19.93 6.11 45.91 3.86
511 526 6.151985 TGACTTAAGTTGCTGAAAAACCTCAA 59.848 34.615 10.02 0.00 0.00 3.02
608 626 4.443457 GGATGCTTCCACTGCTATGTTAGA 60.443 45.833 13.60 0.00 42.12 2.10
741 760 3.068165 TCTCTCTCTCTCTCTCTGTAGCG 59.932 52.174 0.00 0.00 0.00 4.26
844 883 3.832527 AGAGGGAGATGAGCTAACTCTC 58.167 50.000 9.96 9.96 43.85 3.20
917 956 0.958822 GTTCCTCGTTTTGCATGGGT 59.041 50.000 0.00 0.00 0.00 4.51
926 965 1.757682 TTGTGGCAAGTTCCTCGTTT 58.242 45.000 0.00 0.00 0.00 3.60
930 969 3.518634 TGTTTTTGTGGCAAGTTCCTC 57.481 42.857 0.00 0.00 0.00 3.71
933 972 4.681744 TCAGATGTTTTTGTGGCAAGTTC 58.318 39.130 0.00 0.00 0.00 3.01
1238 1277 1.270625 CCAAAAGAGTGTGCGGGTAGA 60.271 52.381 0.00 0.00 0.00 2.59
1267 1306 5.118990 CACAGTATAAGCATGCAGGTTAGT 58.881 41.667 21.98 7.10 42.86 2.24
1294 1333 6.646653 TGTTCAGAGCAAACTCAATACTACTG 59.353 38.462 0.00 0.00 46.09 2.74
1295 1334 6.759272 TGTTCAGAGCAAACTCAATACTACT 58.241 36.000 0.00 0.00 46.09 2.57
1299 1338 6.369890 TCAGATGTTCAGAGCAAACTCAATAC 59.630 38.462 0.00 0.00 46.09 1.89
1326 1365 0.760572 AGCCCTGCAGCAAACAAATT 59.239 45.000 8.66 0.00 34.23 1.82
1327 1366 0.034337 CAGCCCTGCAGCAAACAAAT 59.966 50.000 8.66 0.00 34.23 2.32
1336 1375 0.818445 GATCCATCACAGCCCTGCAG 60.818 60.000 6.78 6.78 0.00 4.41
1377 1416 3.012518 CTGCTTTTCTCCGATCATGGTT 58.987 45.455 0.00 0.00 0.00 3.67
1392 1431 1.202976 ACATTCTGGTCTGCCTGCTTT 60.203 47.619 0.00 0.00 34.18 3.51
1419 1458 3.160679 ACCACCTCAAATCCCTTCAAG 57.839 47.619 0.00 0.00 0.00 3.02
1420 1459 3.117322 TCAACCACCTCAAATCCCTTCAA 60.117 43.478 0.00 0.00 0.00 2.69
1425 1464 2.286365 TGTCAACCACCTCAAATCCC 57.714 50.000 0.00 0.00 0.00 3.85
1543 1583 7.016153 TCAATACTCTGAACATAGGTTTGGT 57.984 36.000 0.00 0.00 37.36 3.67
1572 1612 5.432157 CAAAAGTAACTAAGACACTGCACG 58.568 41.667 0.00 0.00 0.00 5.34
1581 1621 6.486657 AGTGATGCAAGCAAAAGTAACTAAGA 59.513 34.615 0.00 0.00 28.10 2.10
1602 1642 1.881973 GCAAGCCTGACATGAAAGTGA 59.118 47.619 0.00 0.00 0.00 3.41
1664 1705 7.880195 AGGTAGCAGCAGGTTATAATGAAATAG 59.120 37.037 0.00 0.00 0.00 1.73
1712 1753 4.342665 GGAGTAGTAGCTAAACAGCATCCT 59.657 45.833 0.00 0.00 37.25 3.24
1732 1773 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
1736 1777 8.943909 ACAAAGACTTATATTTAGGAACGGAG 57.056 34.615 0.00 0.00 0.00 4.63
1747 1788 8.763601 AGTGGAAGCTCTACAAAGACTTATATT 58.236 33.333 0.00 0.00 29.47 1.28
1748 1789 8.312669 AGTGGAAGCTCTACAAAGACTTATAT 57.687 34.615 0.00 0.00 29.47 0.86
1749 1790 7.719871 AGTGGAAGCTCTACAAAGACTTATA 57.280 36.000 0.00 0.00 29.47 0.98
1750 1791 6.613153 AGTGGAAGCTCTACAAAGACTTAT 57.387 37.500 0.00 0.00 29.47 1.73
1751 1792 7.396339 TCATAGTGGAAGCTCTACAAAGACTTA 59.604 37.037 0.00 0.00 29.47 2.24
1752 1793 4.965200 AGTGGAAGCTCTACAAAGACTT 57.035 40.909 0.00 0.00 29.47 3.01
1753 1794 5.717178 TCATAGTGGAAGCTCTACAAAGACT 59.283 40.000 0.00 0.00 29.47 3.24
1754 1795 5.967088 TCATAGTGGAAGCTCTACAAAGAC 58.033 41.667 0.00 0.00 29.47 3.01
1755 1796 6.014584 TGTTCATAGTGGAAGCTCTACAAAGA 60.015 38.462 0.00 0.00 29.47 2.52
1756 1797 6.091441 GTGTTCATAGTGGAAGCTCTACAAAG 59.909 42.308 0.00 0.00 29.47 2.77
1757 1798 5.932303 GTGTTCATAGTGGAAGCTCTACAAA 59.068 40.000 0.00 0.00 29.47 2.83
1758 1799 5.011635 TGTGTTCATAGTGGAAGCTCTACAA 59.988 40.000 0.00 0.00 29.47 2.41
1759 1800 4.526650 TGTGTTCATAGTGGAAGCTCTACA 59.473 41.667 0.00 0.00 29.47 2.74
1760 1801 5.073311 TGTGTTCATAGTGGAAGCTCTAC 57.927 43.478 0.00 0.00 0.00 2.59
1761 1802 5.939764 ATGTGTTCATAGTGGAAGCTCTA 57.060 39.130 0.00 0.00 31.89 2.43
1762 1803 4.833478 ATGTGTTCATAGTGGAAGCTCT 57.167 40.909 0.00 0.00 31.89 4.09
1763 1804 4.504461 CGTATGTGTTCATAGTGGAAGCTC 59.496 45.833 0.00 0.00 37.23 4.09
1764 1805 4.433615 CGTATGTGTTCATAGTGGAAGCT 58.566 43.478 0.00 0.00 37.23 3.74
1765 1806 3.555956 CCGTATGTGTTCATAGTGGAAGC 59.444 47.826 0.00 0.00 37.23 3.86
1766 1807 5.006153 TCCGTATGTGTTCATAGTGGAAG 57.994 43.478 6.65 0.00 38.35 3.46
1767 1808 5.105106 ACATCCGTATGTGTTCATAGTGGAA 60.105 40.000 0.00 0.00 44.79 3.53
1768 1809 4.404394 ACATCCGTATGTGTTCATAGTGGA 59.596 41.667 0.00 9.81 44.79 4.02
1769 1810 4.693283 ACATCCGTATGTGTTCATAGTGG 58.307 43.478 0.00 0.00 44.79 4.00
1775 1816 7.973944 GCATCTATATACATCCGTATGTGTTCA 59.026 37.037 3.56 0.00 45.99 3.18
1776 1817 7.973944 TGCATCTATATACATCCGTATGTGTTC 59.026 37.037 3.56 0.00 45.99 3.18
1777 1818 7.836842 TGCATCTATATACATCCGTATGTGTT 58.163 34.615 3.56 0.00 45.99 3.32
1778 1819 7.404671 TGCATCTATATACATCCGTATGTGT 57.595 36.000 3.56 0.00 45.99 3.72
1779 1820 8.877808 AATGCATCTATATACATCCGTATGTG 57.122 34.615 3.56 0.00 45.99 3.21
1784 1825 9.944376 ACTTAAAATGCATCTATATACATCCGT 57.056 29.630 0.00 0.00 0.00 4.69
1806 1847 8.677300 GGAGCAAAATGAATGAATCTACACTTA 58.323 33.333 0.00 0.00 0.00 2.24
1807 1848 7.542025 GGAGCAAAATGAATGAATCTACACTT 58.458 34.615 0.00 0.00 0.00 3.16
1808 1849 6.183360 CGGAGCAAAATGAATGAATCTACACT 60.183 38.462 0.00 0.00 0.00 3.55
1809 1850 5.967674 CGGAGCAAAATGAATGAATCTACAC 59.032 40.000 0.00 0.00 0.00 2.90
1810 1851 5.647658 ACGGAGCAAAATGAATGAATCTACA 59.352 36.000 0.00 0.00 0.00 2.74
1811 1852 6.124088 ACGGAGCAAAATGAATGAATCTAC 57.876 37.500 0.00 0.00 0.00 2.59
1812 1853 7.498900 ACATACGGAGCAAAATGAATGAATCTA 59.501 33.333 0.00 0.00 0.00 1.98
1813 1854 6.319658 ACATACGGAGCAAAATGAATGAATCT 59.680 34.615 0.00 0.00 0.00 2.40
1814 1855 6.498304 ACATACGGAGCAAAATGAATGAATC 58.502 36.000 0.00 0.00 0.00 2.52
1815 1856 6.455360 ACATACGGAGCAAAATGAATGAAT 57.545 33.333 0.00 0.00 0.00 2.57
1816 1857 5.895636 ACATACGGAGCAAAATGAATGAA 57.104 34.783 0.00 0.00 0.00 2.57
1817 1858 6.112734 ACTACATACGGAGCAAAATGAATGA 58.887 36.000 0.00 0.00 0.00 2.57
1818 1859 6.363577 ACTACATACGGAGCAAAATGAATG 57.636 37.500 0.00 0.00 0.00 2.67
1819 1860 5.527582 GGACTACATACGGAGCAAAATGAAT 59.472 40.000 0.00 0.00 0.00 2.57
1820 1861 4.873827 GGACTACATACGGAGCAAAATGAA 59.126 41.667 0.00 0.00 0.00 2.57
1821 1862 4.081365 TGGACTACATACGGAGCAAAATGA 60.081 41.667 0.00 0.00 0.00 2.57
1822 1863 4.034048 GTGGACTACATACGGAGCAAAATG 59.966 45.833 0.00 0.00 0.00 2.32
1823 1864 4.189231 GTGGACTACATACGGAGCAAAAT 58.811 43.478 0.00 0.00 0.00 1.82
1824 1865 3.592059 GTGGACTACATACGGAGCAAAA 58.408 45.455 0.00 0.00 0.00 2.44
1825 1866 2.093869 GGTGGACTACATACGGAGCAAA 60.094 50.000 0.00 0.00 0.00 3.68
1826 1867 1.479323 GGTGGACTACATACGGAGCAA 59.521 52.381 0.00 0.00 0.00 3.91
1827 1868 1.108776 GGTGGACTACATACGGAGCA 58.891 55.000 0.00 0.00 0.00 4.26
1828 1869 1.400737 AGGTGGACTACATACGGAGC 58.599 55.000 0.00 0.00 0.00 4.70
1829 1870 3.564644 CACTAGGTGGACTACATACGGAG 59.435 52.174 0.00 0.00 0.00 4.63
1830 1871 3.548770 CACTAGGTGGACTACATACGGA 58.451 50.000 0.00 0.00 0.00 4.69
1831 1872 3.984508 CACTAGGTGGACTACATACGG 57.015 52.381 0.00 0.00 0.00 4.02
1843 1884 6.153680 AGTCTTTGTAGAGATTCCACTAGGTG 59.846 42.308 0.00 0.00 35.89 4.00
1844 1885 6.257586 AGTCTTTGTAGAGATTCCACTAGGT 58.742 40.000 0.00 0.00 35.89 3.08
1845 1886 6.783708 AGTCTTTGTAGAGATTCCACTAGG 57.216 41.667 0.00 0.00 0.00 3.02
1860 1901 7.985752 CCTCCGTTCCTAAATATAAGTCTTTGT 59.014 37.037 0.00 0.00 0.00 2.83
1861 1902 7.441458 CCCTCCGTTCCTAAATATAAGTCTTTG 59.559 40.741 0.00 0.00 0.00 2.77
1862 1903 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
1863 1904 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
1864 1905 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
1865 1906 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
1866 1907 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
1867 1908 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
1868 1909 7.300658 ACTACTCCCTCCGTTCCTAAATATAA 58.699 38.462 0.00 0.00 0.00 0.98
1869 1910 6.856757 ACTACTCCCTCCGTTCCTAAATATA 58.143 40.000 0.00 0.00 0.00 0.86
1870 1911 5.713807 ACTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
1871 1912 5.134725 ACTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
1872 1913 3.991683 ACTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
1873 1914 3.463048 ACTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
1874 1915 4.467769 CATACTACTCCCTCCGTTCCTAA 58.532 47.826 0.00 0.00 0.00 2.69
1875 1916 3.749954 GCATACTACTCCCTCCGTTCCTA 60.750 52.174 0.00 0.00 0.00 2.94
1876 1917 2.946785 CATACTACTCCCTCCGTTCCT 58.053 52.381 0.00 0.00 0.00 3.36
1877 1918 1.340568 GCATACTACTCCCTCCGTTCC 59.659 57.143 0.00 0.00 0.00 3.62
1878 1919 2.029623 TGCATACTACTCCCTCCGTTC 58.970 52.381 0.00 0.00 0.00 3.95
1879 1920 2.154567 TGCATACTACTCCCTCCGTT 57.845 50.000 0.00 0.00 0.00 4.44
1880 1921 2.154567 TTGCATACTACTCCCTCCGT 57.845 50.000 0.00 0.00 0.00 4.69
1881 1922 2.167693 TGTTTGCATACTACTCCCTCCG 59.832 50.000 8.78 0.00 0.00 4.63
1882 1923 3.906720 TGTTTGCATACTACTCCCTCC 57.093 47.619 8.78 0.00 0.00 4.30
1883 1924 5.488341 TCTTTGTTTGCATACTACTCCCTC 58.512 41.667 8.78 0.00 0.00 4.30
1884 1925 5.499004 TCTTTGTTTGCATACTACTCCCT 57.501 39.130 8.78 0.00 0.00 4.20
1885 1926 5.472137 TGTTCTTTGTTTGCATACTACTCCC 59.528 40.000 8.78 0.00 0.00 4.30
1886 1927 6.554334 TGTTCTTTGTTTGCATACTACTCC 57.446 37.500 8.78 0.00 0.00 3.85
1918 1959 5.949233 AGTGTTTCGTTTTCAAGAAATGC 57.051 34.783 0.00 0.00 38.43 3.56
1933 1974 8.569641 AGATAGATATGGAGTTCGTAGTGTTTC 58.430 37.037 0.00 0.00 0.00 2.78
1943 1984 7.655328 CCTTGTTGTCAGATAGATATGGAGTTC 59.345 40.741 0.00 0.00 0.00 3.01
1965 2006 7.125659 ACCAACCTGAAATATATTTTCCCCTTG 59.874 37.037 11.92 9.66 0.00 3.61
1966 2007 7.125659 CACCAACCTGAAATATATTTTCCCCTT 59.874 37.037 11.92 0.00 0.00 3.95
1967 2008 6.611236 CACCAACCTGAAATATATTTTCCCCT 59.389 38.462 11.92 0.00 0.00 4.79
1976 2017 2.856231 AGGCCCACCAACCTGAAATATA 59.144 45.455 0.00 0.00 39.06 0.86
1977 2018 1.645919 AGGCCCACCAACCTGAAATAT 59.354 47.619 0.00 0.00 39.06 1.28
1979 2020 0.190815 AAGGCCCACCAACCTGAAAT 59.809 50.000 0.00 0.00 39.06 2.17
2012 2053 3.118223 CCTTGGAGTCCAATCTTCCTACC 60.118 52.174 24.78 0.00 43.07 3.18
2150 2191 5.877012 GCTGTCAAAAGAGAAGATCATACCA 59.123 40.000 0.00 0.00 0.00 3.25
2200 2243 6.595326 TGGTTCTGTTAATATGAGCTGAACTG 59.405 38.462 19.42 4.91 38.74 3.16
2208 2251 9.778993 CTGATTGTTTGGTTCTGTTAATATGAG 57.221 33.333 0.00 0.00 0.00 2.90
2226 2277 0.804989 GCTTACAGCGCCTGATTGTT 59.195 50.000 2.29 0.00 35.18 2.83
2299 2358 9.887862 ATCTCCATATTGGTATTTTTGGAAGAT 57.112 29.630 0.00 0.00 39.03 2.40
2304 2363 7.053316 TGCATCTCCATATTGGTATTTTTGG 57.947 36.000 0.00 0.00 39.03 3.28
2305 2365 8.199449 AGTTGCATCTCCATATTGGTATTTTTG 58.801 33.333 0.00 0.00 39.03 2.44
2403 2463 6.657836 AATGTCGTATGTTTAGTAAGGCAC 57.342 37.500 0.00 0.00 0.00 5.01
2406 2466 6.959311 GTGCAAATGTCGTATGTTTAGTAAGG 59.041 38.462 0.00 0.00 0.00 2.69
2414 2474 4.083324 CCTTCAGTGCAAATGTCGTATGTT 60.083 41.667 0.00 0.00 31.21 2.71
2420 2480 2.096496 GGATCCTTCAGTGCAAATGTCG 59.904 50.000 3.84 0.00 31.21 4.35
2431 2491 2.283298 CAATCGTGTGGGATCCTTCAG 58.717 52.381 12.58 0.13 0.00 3.02
2549 2609 1.009552 TCCAAGGGGCAGATCTCCTTA 59.990 52.381 12.57 0.00 38.70 2.69
2959 3019 6.340522 ACAGCCAAAATATTTCAATGTAGCC 58.659 36.000 0.10 0.00 0.00 3.93
2966 3026 7.716799 ACTCCATACAGCCAAAATATTTCAA 57.283 32.000 0.10 0.00 0.00 2.69
3042 3102 8.922931 AATCCATTGCTGATGTGTACATAATA 57.077 30.769 0.00 0.00 36.57 0.98
3043 3103 7.722728 AGAATCCATTGCTGATGTGTACATAAT 59.277 33.333 0.00 0.00 36.57 1.28
3044 3104 7.012610 CAGAATCCATTGCTGATGTGTACATAA 59.987 37.037 0.00 0.00 36.57 1.90
3762 3822 4.033817 GCTTAAGTTAGCTCATGACAGCAG 59.966 45.833 9.38 0.00 42.40 4.24
3796 3856 1.164411 CATAACTGCAAACGCCCTGA 58.836 50.000 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.