Multiple sequence alignment - TraesCS3D01G266600

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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 TraesCS3D01G266600 chr3D 100.000 2726 0 0 1 2726 370105433 370108158 0.000000e+00 5035
1 TraesCS3D01G266600 chr3D 96.250 80 3 0 1792 1871 610203813 610203734 6.120000e-27 132
2 TraesCS3D01G266600 chr3D 93.976 83 5 0 1792 1874 4630172 4630254 2.850000e-25 126
3 TraesCS3D01G266600 chr3B 93.597 937 35 12 747 1667 481615990 481616917 0.000000e+00 1375
4 TraesCS3D01G266600 chr3B 91.289 861 45 14 1872 2726 481617196 481618032 0.000000e+00 1147
5 TraesCS3D01G266600 chr3B 81.463 410 55 9 2003 2403 468713575 468713972 1.580000e-82 316
6 TraesCS3D01G266600 chr3B 91.549 142 11 1 1872 2013 468711741 468711881 7.700000e-46 195
7 TraesCS3D01G266600 chr3B 92.135 89 6 1 1784 1872 25369870 25369783 1.020000e-24 124
8 TraesCS3D01G266600 chr3A 91.597 952 58 11 752 1689 491178616 491179559 0.000000e+00 1295
9 TraesCS3D01G266600 chr3A 91.512 860 66 5 1872 2726 491179749 491180606 0.000000e+00 1177
10 TraesCS3D01G266600 chrUn 93.001 743 51 1 1 742 42062863 42062121 0.000000e+00 1083
11 TraesCS3D01G266600 chr1D 92.533 750 42 6 1 747 287642842 287643580 0.000000e+00 1062
12 TraesCS3D01G266600 chr6A 93.072 433 28 2 318 748 410840854 410840422 1.380000e-177 632
13 TraesCS3D01G266600 chr6A 86.290 124 17 0 614 737 397224278 397224401 4.730000e-28 135
14 TraesCS3D01G266600 chr1B 91.117 349 30 1 398 745 389383093 389383441 3.180000e-129 472
15 TraesCS3D01G266600 chr1B 93.269 312 20 1 1 311 389376022 389376333 2.470000e-125 459
16 TraesCS3D01G266600 chr1B 92.308 312 23 1 1 311 389342725 389343036 2.490000e-120 442
17 TraesCS3D01G266600 chr1B 92.308 312 23 1 1 311 389359472 389359783 2.490000e-120 442
18 TraesCS3D01G266600 chr1B 93.976 83 5 0 1792 1874 58566040 58565958 2.850000e-25 126
19 TraesCS3D01G266600 chr2B 90.741 216 20 0 448 663 724396249 724396464 3.430000e-74 289
20 TraesCS3D01G266600 chr2B 91.542 201 17 0 375 575 763057013 763056813 7.430000e-71 278
21 TraesCS3D01G266600 chr2D 71.197 618 163 11 3 615 34065952 34066559 1.020000e-29 141
22 TraesCS3D01G266600 chr2D 79.641 167 34 0 3 169 34093030 34093196 1.330000e-23 121
23 TraesCS3D01G266600 chr6D 96.250 80 3 0 1792 1871 255009638 255009559 6.120000e-27 132
24 TraesCS3D01G266600 chr6D 93.976 83 5 0 1792 1874 18165066 18164984 2.850000e-25 126
25 TraesCS3D01G266600 chr5B 95.062 81 4 0 1792 1872 689864493 689864573 7.920000e-26 128
26 TraesCS3D01G266600 chr5A 95.062 81 4 0 1792 1872 662007283 662007203 7.920000e-26 128
27 TraesCS3D01G266600 chr2A 93.976 83 5 0 1792 1874 611003886 611003804 2.850000e-25 126


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 TraesCS3D01G266600 chr3D 370105433 370108158 2725 False 5035.0 5035 100.0000 1 2726 1 chr3D.!!$F2 2725
1 TraesCS3D01G266600 chr3B 481615990 481618032 2042 False 1261.0 1375 92.4430 747 2726 2 chr3B.!!$F2 1979
2 TraesCS3D01G266600 chr3B 468711741 468713972 2231 False 255.5 316 86.5060 1872 2403 2 chr3B.!!$F1 531
3 TraesCS3D01G266600 chr3A 491178616 491180606 1990 False 1236.0 1295 91.5545 752 2726 2 chr3A.!!$F1 1974
4 TraesCS3D01G266600 chrUn 42062121 42062863 742 True 1083.0 1083 93.0010 1 742 1 chrUn.!!$R1 741
5 TraesCS3D01G266600 chr1D 287642842 287643580 738 False 1062.0 1062 92.5330 1 747 1 chr1D.!!$F1 746

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
642 646 0.179161 TTGGTCGTTTGCAACAACGG 60.179 50.0 20.25 5.58 42.17 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1844 2056 0.030369 GTGCATGCTCTAGCCAATGC 59.97 55.0 20.33 16.33 45.25 3.56 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
31 32 8.000127 TCATTGATGATTATGTGGAGGATTTGA 59.000 33.333 0.00 0.00 0.00 2.69
53 54 1.139989 CGCGCGGAATGAGATTACAT 58.860 50.000 24.84 0.00 0.00 2.29
61 62 6.035005 CGCGGAATGAGATTACATACCATAAG 59.965 42.308 0.00 0.00 0.00 1.73
140 141 4.579753 TCATCGCAATCAAGCAATATCCAA 59.420 37.500 0.00 0.00 0.00 3.53
195 196 4.405358 TGATCTTTCTGGGCACAAACTTTT 59.595 37.500 0.00 0.00 0.00 2.27
254 256 2.507102 CTGCTAGTGGACACGCGG 60.507 66.667 12.47 1.27 36.20 6.46
315 318 2.836154 GGGGCCGGCATGATTCTA 59.164 61.111 30.85 0.00 0.00 2.10
333 336 2.523740 TACGTGATCAGGAGGGGGCA 62.524 60.000 21.63 0.00 0.00 5.36
396 399 0.538057 CCCTTGAAGCTGAGTTGGCA 60.538 55.000 0.00 0.00 0.00 4.92
446 449 1.134401 TCATTGGACGGAGCTTCCATC 60.134 52.381 6.45 0.00 42.88 3.51
492 495 0.321475 TGTTGCAGATGATCCGTGCA 60.321 50.000 5.38 5.38 45.30 4.57
524 527 7.533289 TCGATAAATCCAGGTATACACATCA 57.467 36.000 5.01 0.00 0.00 3.07
547 550 8.718158 TCATATTAGTGAGATCAGAAGGATGT 57.282 34.615 0.00 0.00 36.00 3.06
561 564 4.039245 AGAAGGATGTTGACTCACGAAAGA 59.961 41.667 0.00 0.00 0.00 2.52
579 582 8.922676 CACGAAAGAAACATAAGTCTAGCTAAA 58.077 33.333 0.00 0.00 0.00 1.85
619 622 2.521465 CCAGCCACACCCTTGCAA 60.521 61.111 0.00 0.00 0.00 4.08
621 624 1.529010 CAGCCACACCCTTGCAAGA 60.529 57.895 28.05 0.00 0.00 3.02
624 628 0.681175 GCCACACCCTTGCAAGAATT 59.319 50.000 28.05 8.27 0.00 2.17
642 646 0.179161 TTGGTCGTTTGCAACAACGG 60.179 50.000 20.25 5.58 42.17 4.44
728 732 6.024552 TCACCCAGTTTGATTAATGAAAGC 57.975 37.500 0.00 0.00 0.00 3.51
731 735 6.012745 ACCCAGTTTGATTAATGAAAGCTCT 58.987 36.000 0.00 0.00 0.00 4.09
772 776 5.353394 ACGAATGTATTGGGTGTCACTAT 57.647 39.130 2.35 0.00 0.00 2.12
796 800 3.490348 ACACCCAAAGTCTCATGGAAAG 58.510 45.455 6.26 0.00 39.12 2.62
813 817 4.285003 TGGAAAGGAAACAAGAGGATCGTA 59.715 41.667 0.00 0.00 42.67 3.43
839 843 4.521062 CGCCCAGAGGAAGCTCCG 62.521 72.222 0.00 0.00 42.75 4.63
1058 1074 1.597027 ACTCGAGCAAACCAACCGG 60.597 57.895 13.61 0.00 38.77 5.28
1059 1075 2.966309 CTCGAGCAAACCAACCGGC 61.966 63.158 0.00 0.00 34.57 6.13
1060 1076 4.383602 CGAGCAAACCAACCGGCG 62.384 66.667 0.00 0.00 34.57 6.46
1086 1102 3.607987 GCGCGCTGCTACGTACTG 61.608 66.667 26.67 0.00 41.73 2.74
1561 1584 1.781786 ATGCATGTCGACCTAGTCCT 58.218 50.000 14.12 0.00 0.00 3.85
1562 1585 1.103803 TGCATGTCGACCTAGTCCTC 58.896 55.000 14.12 0.00 0.00 3.71
1647 1680 4.357947 TGGTCACTCGCCACTCGC 62.358 66.667 0.00 0.00 38.27 5.03
1668 1701 4.076394 GCCCATGTACTTTGTTCAGGTAA 58.924 43.478 0.00 0.00 0.00 2.85
1689 1722 0.875059 GTAGTTGCAAGAGGTGGCAC 59.125 55.000 9.70 9.70 40.23 5.01
1693 1726 3.058160 GCAAGAGGTGGCACGCAT 61.058 61.111 12.17 0.00 43.02 4.73
1703 1736 2.485122 GCACGCATGGCAAGTACC 59.515 61.111 0.00 0.00 0.00 3.34
1705 1738 1.861542 GCACGCATGGCAAGTACCAA 61.862 55.000 0.00 0.00 44.65 3.67
1706 1739 0.595588 CACGCATGGCAAGTACCAAA 59.404 50.000 0.00 0.00 44.65 3.28
1707 1740 1.202114 CACGCATGGCAAGTACCAAAT 59.798 47.619 0.00 0.00 44.65 2.32
1712 1745 4.515191 CGCATGGCAAGTACCAAATACTAT 59.485 41.667 0.00 0.00 43.79 2.12
1713 1746 5.560760 CGCATGGCAAGTACCAAATACTATG 60.561 44.000 0.00 0.00 43.79 2.23
1714 1747 5.530915 GCATGGCAAGTACCAAATACTATGA 59.469 40.000 0.00 0.00 43.79 2.15
1715 1748 6.293626 GCATGGCAAGTACCAAATACTATGAG 60.294 42.308 0.00 0.00 43.79 2.90
1716 1749 6.308015 TGGCAAGTACCAAATACTATGAGT 57.692 37.500 0.00 0.00 43.79 3.41
1717 1750 6.112734 TGGCAAGTACCAAATACTATGAGTG 58.887 40.000 0.00 0.00 43.79 3.51
1718 1751 6.070481 TGGCAAGTACCAAATACTATGAGTGA 60.070 38.462 0.00 0.00 43.79 3.41
1719 1752 6.992715 GGCAAGTACCAAATACTATGAGTGAT 59.007 38.462 0.00 0.00 43.79 3.06
1721 1754 7.710907 GCAAGTACCAAATACTATGAGTGATGA 59.289 37.037 0.00 0.00 43.79 2.92
1724 1757 9.770097 AGTACCAAATACTATGAGTGATGATTG 57.230 33.333 0.00 0.00 42.69 2.67
1773 1985 0.314302 CTCCATAAGCTACGACCCCG 59.686 60.000 0.00 0.00 42.50 5.73
1791 2003 1.535204 CGGCCCCTTTCATGCAAGTT 61.535 55.000 4.38 0.00 0.00 2.66
1792 2004 0.037046 GGCCCCTTTCATGCAAGTTG 60.037 55.000 4.38 0.00 0.00 3.16
1793 2005 0.681175 GCCCCTTTCATGCAAGTTGT 59.319 50.000 4.48 0.00 0.00 3.32
1794 2006 1.337167 GCCCCTTTCATGCAAGTTGTC 60.337 52.381 4.48 0.00 0.00 3.18
1795 2007 1.068333 CCCCTTTCATGCAAGTTGTCG 60.068 52.381 4.48 0.00 0.00 4.35
1796 2008 1.879380 CCCTTTCATGCAAGTTGTCGA 59.121 47.619 4.48 0.00 0.00 4.20
1797 2009 2.350772 CCCTTTCATGCAAGTTGTCGAC 60.351 50.000 9.11 9.11 0.00 4.20
1798 2010 2.563976 CTTTCATGCAAGTTGTCGACG 58.436 47.619 11.62 0.00 0.00 5.12
1799 2011 1.577468 TTCATGCAAGTTGTCGACGT 58.423 45.000 11.62 0.00 0.00 4.34
1800 2012 2.425578 TCATGCAAGTTGTCGACGTA 57.574 45.000 11.62 0.00 0.00 3.57
1801 2013 2.954316 TCATGCAAGTTGTCGACGTAT 58.046 42.857 11.62 0.00 0.00 3.06
1802 2014 4.099380 TCATGCAAGTTGTCGACGTATA 57.901 40.909 11.62 0.00 0.00 1.47
1803 2015 4.487019 TCATGCAAGTTGTCGACGTATAA 58.513 39.130 11.62 0.00 0.00 0.98
1804 2016 5.106442 TCATGCAAGTTGTCGACGTATAAT 58.894 37.500 11.62 0.00 0.00 1.28
1805 2017 4.833469 TGCAAGTTGTCGACGTATAATG 57.167 40.909 11.62 6.32 0.00 1.90
1806 2018 4.239304 TGCAAGTTGTCGACGTATAATGT 58.761 39.130 11.62 0.00 0.00 2.71
1807 2019 4.090786 TGCAAGTTGTCGACGTATAATGTG 59.909 41.667 11.62 3.50 0.00 3.21
1808 2020 4.565229 CAAGTTGTCGACGTATAATGTGC 58.435 43.478 11.62 0.00 0.00 4.57
1809 2021 4.106029 AGTTGTCGACGTATAATGTGCT 57.894 40.909 11.62 0.00 0.00 4.40
1810 2022 3.857665 AGTTGTCGACGTATAATGTGCTG 59.142 43.478 11.62 0.00 0.00 4.41
1811 2023 2.190161 TGTCGACGTATAATGTGCTGC 58.810 47.619 11.62 0.00 0.00 5.25
1812 2024 1.521423 GTCGACGTATAATGTGCTGCC 59.479 52.381 0.00 0.00 0.00 4.85
1813 2025 1.407618 TCGACGTATAATGTGCTGCCT 59.592 47.619 0.00 0.00 0.00 4.75
1814 2026 2.619646 TCGACGTATAATGTGCTGCCTA 59.380 45.455 0.00 0.00 0.00 3.93
1815 2027 2.980476 CGACGTATAATGTGCTGCCTAG 59.020 50.000 0.00 0.00 0.00 3.02
1816 2028 3.550233 CGACGTATAATGTGCTGCCTAGT 60.550 47.826 0.00 0.00 0.00 2.57
1817 2029 3.978687 ACGTATAATGTGCTGCCTAGTC 58.021 45.455 0.00 0.00 0.00 2.59
1818 2030 3.637229 ACGTATAATGTGCTGCCTAGTCT 59.363 43.478 0.00 0.00 0.00 3.24
1819 2031 4.099573 ACGTATAATGTGCTGCCTAGTCTT 59.900 41.667 0.00 0.00 0.00 3.01
1820 2032 5.050490 CGTATAATGTGCTGCCTAGTCTTT 58.950 41.667 0.00 0.00 0.00 2.52
1821 2033 5.523916 CGTATAATGTGCTGCCTAGTCTTTT 59.476 40.000 0.00 0.00 0.00 2.27
1822 2034 6.037172 CGTATAATGTGCTGCCTAGTCTTTTT 59.963 38.462 0.00 0.00 0.00 1.94
1823 2035 4.773323 AATGTGCTGCCTAGTCTTTTTC 57.227 40.909 0.00 0.00 0.00 2.29
1824 2036 3.207265 TGTGCTGCCTAGTCTTTTTCA 57.793 42.857 0.00 0.00 0.00 2.69
1825 2037 3.754965 TGTGCTGCCTAGTCTTTTTCAT 58.245 40.909 0.00 0.00 0.00 2.57
1826 2038 3.753272 TGTGCTGCCTAGTCTTTTTCATC 59.247 43.478 0.00 0.00 0.00 2.92
1827 2039 3.753272 GTGCTGCCTAGTCTTTTTCATCA 59.247 43.478 0.00 0.00 0.00 3.07
1828 2040 4.216257 GTGCTGCCTAGTCTTTTTCATCAA 59.784 41.667 0.00 0.00 0.00 2.57
1829 2041 4.826733 TGCTGCCTAGTCTTTTTCATCAAA 59.173 37.500 0.00 0.00 0.00 2.69
1830 2042 5.477984 TGCTGCCTAGTCTTTTTCATCAAAT 59.522 36.000 0.00 0.00 0.00 2.32
1831 2043 5.803967 GCTGCCTAGTCTTTTTCATCAAATG 59.196 40.000 0.00 0.00 0.00 2.32
1832 2044 6.271488 TGCCTAGTCTTTTTCATCAAATGG 57.729 37.500 0.00 0.00 0.00 3.16
1833 2045 5.185635 TGCCTAGTCTTTTTCATCAAATGGG 59.814 40.000 0.00 0.00 0.00 4.00
1834 2046 5.185828 GCCTAGTCTTTTTCATCAAATGGGT 59.814 40.000 0.00 0.00 0.00 4.51
1835 2047 6.625960 GCCTAGTCTTTTTCATCAAATGGGTC 60.626 42.308 0.00 0.00 0.00 4.46
1836 2048 6.660949 CCTAGTCTTTTTCATCAAATGGGTCT 59.339 38.462 0.00 0.00 0.00 3.85
1837 2049 6.983906 AGTCTTTTTCATCAAATGGGTCTT 57.016 33.333 0.00 0.00 0.00 3.01
1838 2050 7.365497 AGTCTTTTTCATCAAATGGGTCTTT 57.635 32.000 0.00 0.00 0.00 2.52
1839 2051 7.795047 AGTCTTTTTCATCAAATGGGTCTTTT 58.205 30.769 0.00 0.00 0.00 2.27
1840 2052 7.712205 AGTCTTTTTCATCAAATGGGTCTTTTG 59.288 33.333 0.00 0.00 35.79 2.44
1841 2053 6.991531 TCTTTTTCATCAAATGGGTCTTTTGG 59.008 34.615 6.48 0.00 35.31 3.28
1842 2054 5.885449 TTTCATCAAATGGGTCTTTTGGT 57.115 34.783 6.48 0.00 35.31 3.67
1843 2055 5.885449 TTCATCAAATGGGTCTTTTGGTT 57.115 34.783 6.48 0.00 35.31 3.67
1844 2056 5.212532 TCATCAAATGGGTCTTTTGGTTG 57.787 39.130 6.48 5.66 35.31 3.77
1845 2057 3.467374 TCAAATGGGTCTTTTGGTTGC 57.533 42.857 6.48 0.00 35.31 4.17
1846 2058 2.768527 TCAAATGGGTCTTTTGGTTGCA 59.231 40.909 6.48 0.00 35.31 4.08
1847 2059 3.390639 TCAAATGGGTCTTTTGGTTGCAT 59.609 39.130 0.00 0.00 35.31 3.96
1848 2060 4.136051 CAAATGGGTCTTTTGGTTGCATT 58.864 39.130 0.00 0.00 31.82 3.56
1849 2061 2.906691 TGGGTCTTTTGGTTGCATTG 57.093 45.000 0.00 0.00 0.00 2.82
1850 2062 1.415659 TGGGTCTTTTGGTTGCATTGG 59.584 47.619 0.00 0.00 0.00 3.16
1851 2063 1.511850 GGTCTTTTGGTTGCATTGGC 58.488 50.000 0.00 0.00 41.68 4.52
1852 2064 1.070601 GGTCTTTTGGTTGCATTGGCT 59.929 47.619 0.00 0.00 41.91 4.75
1853 2065 2.298729 GGTCTTTTGGTTGCATTGGCTA 59.701 45.455 0.00 0.00 41.91 3.93
1854 2066 3.578688 GTCTTTTGGTTGCATTGGCTAG 58.421 45.455 0.00 0.00 41.91 3.42
1855 2067 3.255642 GTCTTTTGGTTGCATTGGCTAGA 59.744 43.478 0.00 0.00 41.91 2.43
1856 2068 3.507233 TCTTTTGGTTGCATTGGCTAGAG 59.493 43.478 0.00 0.00 41.91 2.43
1857 2069 1.176527 TTGGTTGCATTGGCTAGAGC 58.823 50.000 0.00 0.00 41.91 4.09
1858 2070 0.038021 TGGTTGCATTGGCTAGAGCA 59.962 50.000 3.54 0.00 44.36 4.26
1859 2071 1.341285 TGGTTGCATTGGCTAGAGCAT 60.341 47.619 3.54 0.00 44.36 3.79
1860 2072 1.066605 GGTTGCATTGGCTAGAGCATG 59.933 52.381 3.54 0.90 44.36 4.06
1861 2073 0.742505 TTGCATTGGCTAGAGCATGC 59.257 50.000 10.51 10.51 45.25 4.06
1862 2074 2.411535 GCATTGGCTAGAGCATGCA 58.588 52.632 21.98 0.00 44.74 3.96
1863 2075 0.030369 GCATTGGCTAGAGCATGCAC 59.970 55.000 21.98 14.59 44.74 4.57
1864 2076 1.676746 CATTGGCTAGAGCATGCACT 58.323 50.000 21.45 21.45 44.36 4.40
1865 2077 2.022195 CATTGGCTAGAGCATGCACTT 58.978 47.619 22.83 8.33 44.36 3.16
1866 2078 1.742761 TTGGCTAGAGCATGCACTTC 58.257 50.000 22.83 14.30 44.36 3.01
1867 2079 0.907486 TGGCTAGAGCATGCACTTCT 59.093 50.000 22.83 17.00 44.36 2.85
1868 2080 2.110578 TGGCTAGAGCATGCACTTCTA 58.889 47.619 22.83 17.21 44.36 2.10
1869 2081 2.159043 TGGCTAGAGCATGCACTTCTAC 60.159 50.000 22.83 12.67 44.36 2.59
1870 2082 2.159043 GGCTAGAGCATGCACTTCTACA 60.159 50.000 22.83 3.70 44.36 2.74
1897 2109 8.842280 CAAGTAAACAAAAGGGTACAAGTATGA 58.158 33.333 0.00 0.00 0.00 2.15
1974 2186 2.409870 CCCCAAAGCTCGCACCATC 61.410 63.158 0.00 0.00 0.00 3.51
1999 2211 1.098050 AAGAACGCCCATGCATTCTC 58.902 50.000 0.00 0.00 46.32 2.87
2100 4025 1.574428 CGGAAGGAAAGCAACACGG 59.426 57.895 0.00 0.00 0.00 4.94
2301 4228 0.451783 CCCGCATTTTTCTCCCTTCG 59.548 55.000 0.00 0.00 0.00 3.79
2348 4275 3.250040 GCAAGCGACTTTTACCTCTGAAA 59.750 43.478 0.00 0.00 0.00 2.69
2362 4289 1.606668 TCTGAAATTTCCACCACACGC 59.393 47.619 15.48 0.00 0.00 5.34
2437 4364 3.476740 GGATTCCGTGAATGCCAGA 57.523 52.632 4.18 0.00 34.96 3.86
2440 4367 0.620556 ATTCCGTGAATGCCAGAGGT 59.379 50.000 0.00 0.00 30.42 3.85
2469 4397 4.578871 GCCTTTGGCCACTTGATAAAATT 58.421 39.130 3.88 0.00 44.06 1.82
2471 4399 5.569428 GCCTTTGGCCACTTGATAAAATTCT 60.569 40.000 3.88 0.00 44.06 2.40
2481 4409 5.181245 ACTTGATAAAATTCTGTCACCACCG 59.819 40.000 0.00 0.00 0.00 4.94
2598 4528 1.883084 GCAACGTGAGGCCTATCCG 60.883 63.158 4.42 11.24 40.77 4.18
2614 4544 0.179181 TCCGAGACCGTTTCGAATCG 60.179 55.000 19.20 19.20 40.36 3.34
2627 4561 5.164031 CGTTTCGAATCGAACATGGTAAAGA 60.164 40.000 18.30 0.00 45.64 2.52
2659 4593 2.359850 GCAACCGAGACATGGGCA 60.360 61.111 0.00 0.00 0.00 5.36
2660 4594 2.690778 GCAACCGAGACATGGGCAC 61.691 63.158 0.00 0.00 0.00 5.01
2680 4614 4.681978 GACCGCTGCCCACGTCTT 62.682 66.667 0.00 0.00 0.00 3.01
2699 4633 3.576118 TCTTGATGAGTAGCCATAGGAGC 59.424 47.826 0.00 0.00 0.00 4.70
2714 4648 5.065731 CCATAGGAGCAGTTCACTTGATTTC 59.934 44.000 0.00 0.00 0.00 2.17
2719 4653 4.883083 AGCAGTTCACTTGATTTCGTCTA 58.117 39.130 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 2.287970 TGTAATCTCATTCCGCGCGTAT 60.288 45.455 29.95 18.53 0.00 3.06
53 54 1.760613 CGGAACTGGAGGCTTATGGTA 59.239 52.381 0.00 0.00 0.00 3.25
61 62 1.373570 CTTCAATCGGAACTGGAGGC 58.626 55.000 0.00 0.00 0.00 4.70
116 117 4.579753 TGGATATTGCTTGATTGCGATGAA 59.420 37.500 0.00 0.00 37.59 2.57
140 141 4.164843 TGCCTTTCACCAAGTCTACTTT 57.835 40.909 0.00 0.00 33.11 2.66
195 196 8.347771 GCTTTGCTATGATTTCATGTGATTCTA 58.652 33.333 3.30 0.00 37.15 2.10
254 256 1.034292 GGCCCCTCAACATTCAGCTC 61.034 60.000 0.00 0.00 0.00 4.09
315 318 3.083997 GCCCCCTCCTGATCACGT 61.084 66.667 0.00 0.00 0.00 4.49
333 336 1.251251 GGGTTGCAGCAAAGATGACT 58.749 50.000 10.11 0.00 0.00 3.41
396 399 1.885163 GCAAGCCTTCCTGCATTGCT 61.885 55.000 10.49 1.48 39.78 3.91
446 449 1.354040 GCAGTCTGTCTCCACAATCG 58.646 55.000 0.93 0.00 29.82 3.34
492 495 3.117888 ACCTGGATTTATCGATGCCACTT 60.118 43.478 8.54 0.00 0.00 3.16
524 527 9.152327 TCAACATCCTTCTGATCTCACTAATAT 57.848 33.333 0.00 0.00 0.00 1.28
547 550 6.984474 AGACTTATGTTTCTTTCGTGAGTCAA 59.016 34.615 0.00 0.00 38.80 3.18
579 582 3.487376 CCGCATTTGCATGTCGACTAATT 60.487 43.478 17.92 0.00 42.21 1.40
642 646 1.438651 TACGAAGCCAACATGCAGTC 58.561 50.000 0.00 0.00 0.00 3.51
747 751 2.569853 TGACACCCAATACATTCGTCCT 59.430 45.455 0.00 0.00 0.00 3.85
748 752 2.676342 GTGACACCCAATACATTCGTCC 59.324 50.000 0.00 0.00 0.00 4.79
749 753 3.596214 AGTGACACCCAATACATTCGTC 58.404 45.455 0.84 0.00 0.00 4.20
750 754 3.695830 AGTGACACCCAATACATTCGT 57.304 42.857 0.84 0.00 0.00 3.85
796 800 5.012328 ACTGATACGATCCTCTTGTTTCC 57.988 43.478 0.00 0.00 0.00 3.13
813 817 0.904865 TCCTCTGGGCGTGAACTGAT 60.905 55.000 0.00 0.00 0.00 2.90
879 883 3.477346 GTAGACCGGGGAAGGGCC 61.477 72.222 6.32 0.00 41.33 5.80
1082 1098 3.181507 GCTCCGTGAACGTATGTACAGTA 60.182 47.826 0.33 0.00 37.74 2.74
1083 1099 2.415090 GCTCCGTGAACGTATGTACAGT 60.415 50.000 0.33 0.00 37.74 3.55
1084 1100 2.159421 AGCTCCGTGAACGTATGTACAG 60.159 50.000 0.33 0.00 37.74 2.74
1085 1101 1.814394 AGCTCCGTGAACGTATGTACA 59.186 47.619 0.00 0.00 37.74 2.90
1086 1102 2.556534 AGCTCCGTGAACGTATGTAC 57.443 50.000 1.75 0.00 37.74 2.90
1417 1436 2.026879 GTGAGCTCGGCGATCCTC 59.973 66.667 22.90 22.90 0.00 3.71
1647 1680 4.153475 CGTTACCTGAACAAAGTACATGGG 59.847 45.833 0.00 0.00 37.99 4.00
1668 1701 0.602905 GCCACCTCTTGCAACTACGT 60.603 55.000 0.00 0.00 0.00 3.57
1689 1722 2.682856 AGTATTTGGTACTTGCCATGCG 59.317 45.455 0.00 0.00 40.80 4.73
1693 1726 6.070481 TCACTCATAGTATTTGGTACTTGCCA 60.070 38.462 0.00 0.00 40.80 4.92
1755 1967 1.111116 CCGGGGTCGTAGCTTATGGA 61.111 60.000 0.00 0.00 33.95 3.41
1773 1985 0.037046 CAACTTGCATGAAAGGGGCC 60.037 55.000 18.01 0.00 0.00 5.80
1791 2003 2.190161 GCAGCACATTATACGTCGACA 58.810 47.619 17.16 0.00 0.00 4.35
1792 2004 1.521423 GGCAGCACATTATACGTCGAC 59.479 52.381 5.18 5.18 0.00 4.20
1793 2005 1.407618 AGGCAGCACATTATACGTCGA 59.592 47.619 0.00 0.00 0.00 4.20
1794 2006 1.852942 AGGCAGCACATTATACGTCG 58.147 50.000 0.00 0.00 0.00 5.12
1795 2007 3.978687 ACTAGGCAGCACATTATACGTC 58.021 45.455 0.00 0.00 0.00 4.34
1796 2008 3.637229 AGACTAGGCAGCACATTATACGT 59.363 43.478 0.00 0.00 0.00 3.57
1797 2009 4.244425 AGACTAGGCAGCACATTATACG 57.756 45.455 0.00 0.00 0.00 3.06
1798 2010 6.927294 AAAAGACTAGGCAGCACATTATAC 57.073 37.500 0.00 0.00 0.00 1.47
1799 2011 7.109501 TGAAAAAGACTAGGCAGCACATTATA 58.890 34.615 0.00 0.00 0.00 0.98
1800 2012 5.945784 TGAAAAAGACTAGGCAGCACATTAT 59.054 36.000 0.00 0.00 0.00 1.28
1801 2013 5.312895 TGAAAAAGACTAGGCAGCACATTA 58.687 37.500 0.00 0.00 0.00 1.90
1802 2014 4.144297 TGAAAAAGACTAGGCAGCACATT 58.856 39.130 0.00 0.00 0.00 2.71
1803 2015 3.754965 TGAAAAAGACTAGGCAGCACAT 58.245 40.909 0.00 0.00 0.00 3.21
1804 2016 3.207265 TGAAAAAGACTAGGCAGCACA 57.793 42.857 0.00 0.00 0.00 4.57
1805 2017 3.753272 TGATGAAAAAGACTAGGCAGCAC 59.247 43.478 0.00 0.00 0.00 4.40
1806 2018 4.019792 TGATGAAAAAGACTAGGCAGCA 57.980 40.909 0.00 0.00 0.00 4.41
1807 2019 5.376854 TTTGATGAAAAAGACTAGGCAGC 57.623 39.130 0.00 0.00 0.00 5.25
1808 2020 6.327934 CCATTTGATGAAAAAGACTAGGCAG 58.672 40.000 0.00 0.00 0.00 4.85
1809 2021 5.185635 CCCATTTGATGAAAAAGACTAGGCA 59.814 40.000 0.00 0.00 0.00 4.75
1810 2022 5.185828 ACCCATTTGATGAAAAAGACTAGGC 59.814 40.000 0.00 0.00 0.00 3.93
1811 2023 6.660949 AGACCCATTTGATGAAAAAGACTAGG 59.339 38.462 0.00 0.00 0.00 3.02
1812 2024 7.693969 AGACCCATTTGATGAAAAAGACTAG 57.306 36.000 0.00 0.00 0.00 2.57
1813 2025 8.477419 AAAGACCCATTTGATGAAAAAGACTA 57.523 30.769 0.00 0.00 0.00 2.59
1814 2026 6.983906 AAGACCCATTTGATGAAAAAGACT 57.016 33.333 0.00 0.00 0.00 3.24
1815 2027 7.041848 CCAAAAGACCCATTTGATGAAAAAGAC 60.042 37.037 0.83 0.00 39.56 3.01
1816 2028 6.991531 CCAAAAGACCCATTTGATGAAAAAGA 59.008 34.615 0.83 0.00 39.56 2.52
1817 2029 6.767423 ACCAAAAGACCCATTTGATGAAAAAG 59.233 34.615 0.83 0.00 39.56 2.27
1818 2030 6.657875 ACCAAAAGACCCATTTGATGAAAAA 58.342 32.000 0.83 0.00 39.56 1.94
1819 2031 6.245890 ACCAAAAGACCCATTTGATGAAAA 57.754 33.333 0.83 0.00 39.56 2.29
1820 2032 5.885449 ACCAAAAGACCCATTTGATGAAA 57.115 34.783 0.83 0.00 39.56 2.69
1821 2033 5.609423 CAACCAAAAGACCCATTTGATGAA 58.391 37.500 0.83 0.00 39.56 2.57
1822 2034 4.502950 GCAACCAAAAGACCCATTTGATGA 60.503 41.667 0.83 0.00 39.56 2.92
1823 2035 3.747529 GCAACCAAAAGACCCATTTGATG 59.252 43.478 0.83 1.80 39.56 3.07
1824 2036 3.390639 TGCAACCAAAAGACCCATTTGAT 59.609 39.130 0.83 0.00 39.56 2.57
1825 2037 2.768527 TGCAACCAAAAGACCCATTTGA 59.231 40.909 0.83 0.00 39.56 2.69
1826 2038 3.191078 TGCAACCAAAAGACCCATTTG 57.809 42.857 0.00 0.00 37.48 2.32
1827 2039 4.136051 CAATGCAACCAAAAGACCCATTT 58.864 39.130 0.00 0.00 0.00 2.32
1828 2040 3.496515 CCAATGCAACCAAAAGACCCATT 60.497 43.478 0.00 0.00 0.00 3.16
1829 2041 2.038820 CCAATGCAACCAAAAGACCCAT 59.961 45.455 0.00 0.00 0.00 4.00
1830 2042 1.415659 CCAATGCAACCAAAAGACCCA 59.584 47.619 0.00 0.00 0.00 4.51
1831 2043 1.877680 GCCAATGCAACCAAAAGACCC 60.878 52.381 0.00 0.00 37.47 4.46
1832 2044 1.070601 AGCCAATGCAACCAAAAGACC 59.929 47.619 0.00 0.00 41.13 3.85
1833 2045 2.531522 AGCCAATGCAACCAAAAGAC 57.468 45.000 0.00 0.00 41.13 3.01
1834 2046 3.495331 TCTAGCCAATGCAACCAAAAGA 58.505 40.909 0.00 0.00 41.13 2.52
1835 2047 3.841643 CTCTAGCCAATGCAACCAAAAG 58.158 45.455 0.00 0.00 41.13 2.27
1836 2048 2.029110 GCTCTAGCCAATGCAACCAAAA 60.029 45.455 0.00 0.00 41.13 2.44
1837 2049 1.545582 GCTCTAGCCAATGCAACCAAA 59.454 47.619 0.00 0.00 41.13 3.28
1838 2050 1.176527 GCTCTAGCCAATGCAACCAA 58.823 50.000 0.00 0.00 41.13 3.67
1839 2051 0.038021 TGCTCTAGCCAATGCAACCA 59.962 50.000 0.00 0.00 41.13 3.67
1840 2052 1.066605 CATGCTCTAGCCAATGCAACC 59.933 52.381 0.00 0.00 41.13 3.77
1841 2053 1.535437 GCATGCTCTAGCCAATGCAAC 60.535 52.381 11.37 2.38 44.74 4.17
1842 2054 0.742505 GCATGCTCTAGCCAATGCAA 59.257 50.000 11.37 0.00 44.74 4.08
1843 2055 2.411535 GCATGCTCTAGCCAATGCA 58.588 52.632 11.37 0.00 44.74 3.96
1844 2056 0.030369 GTGCATGCTCTAGCCAATGC 59.970 55.000 20.33 16.33 45.25 3.56
1845 2057 1.676746 AGTGCATGCTCTAGCCAATG 58.323 50.000 20.22 0.00 41.18 2.82
1846 2058 2.092538 AGAAGTGCATGCTCTAGCCAAT 60.093 45.455 21.70 5.92 41.18 3.16
1847 2059 1.280133 AGAAGTGCATGCTCTAGCCAA 59.720 47.619 21.70 0.00 41.18 4.52
1848 2060 0.907486 AGAAGTGCATGCTCTAGCCA 59.093 50.000 21.70 0.00 41.18 4.75
1849 2061 2.159043 TGTAGAAGTGCATGCTCTAGCC 60.159 50.000 21.70 13.81 41.18 3.93
1850 2062 2.863137 GTGTAGAAGTGCATGCTCTAGC 59.137 50.000 21.70 16.29 42.50 3.42
1851 2063 4.115401 TGTGTAGAAGTGCATGCTCTAG 57.885 45.455 21.70 0.00 0.00 2.43
1852 2064 4.021104 ACTTGTGTAGAAGTGCATGCTCTA 60.021 41.667 21.70 15.62 34.79 2.43
1853 2065 3.244353 ACTTGTGTAGAAGTGCATGCTCT 60.244 43.478 20.33 18.23 34.79 4.09
1854 2066 3.070018 ACTTGTGTAGAAGTGCATGCTC 58.930 45.455 20.33 15.94 34.79 4.26
1855 2067 3.131709 ACTTGTGTAGAAGTGCATGCT 57.868 42.857 20.33 0.00 34.79 3.79
1856 2068 5.147162 GTTTACTTGTGTAGAAGTGCATGC 58.853 41.667 11.82 11.82 36.80 4.06
1857 2069 6.299023 TGTTTACTTGTGTAGAAGTGCATG 57.701 37.500 4.83 0.00 36.80 4.06
1858 2070 6.935741 TTGTTTACTTGTGTAGAAGTGCAT 57.064 33.333 4.83 0.00 36.80 3.96
1859 2071 6.745159 TTTGTTTACTTGTGTAGAAGTGCA 57.255 33.333 4.83 0.00 36.80 4.57
1860 2072 6.691388 CCTTTTGTTTACTTGTGTAGAAGTGC 59.309 38.462 4.83 0.00 36.80 4.40
1861 2073 7.148137 ACCCTTTTGTTTACTTGTGTAGAAGTG 60.148 37.037 4.83 0.00 36.80 3.16
1862 2074 6.888088 ACCCTTTTGTTTACTTGTGTAGAAGT 59.112 34.615 0.03 0.03 39.54 3.01
1863 2075 7.329588 ACCCTTTTGTTTACTTGTGTAGAAG 57.670 36.000 0.00 0.00 0.00 2.85
1864 2076 7.828223 TGTACCCTTTTGTTTACTTGTGTAGAA 59.172 33.333 0.00 0.00 0.00 2.10
1865 2077 7.337167 TGTACCCTTTTGTTTACTTGTGTAGA 58.663 34.615 0.00 0.00 0.00 2.59
1866 2078 7.556733 TGTACCCTTTTGTTTACTTGTGTAG 57.443 36.000 0.00 0.00 0.00 2.74
1867 2079 7.611079 ACTTGTACCCTTTTGTTTACTTGTGTA 59.389 33.333 0.00 0.00 0.00 2.90
1868 2080 6.434965 ACTTGTACCCTTTTGTTTACTTGTGT 59.565 34.615 0.00 0.00 0.00 3.72
1869 2081 6.859017 ACTTGTACCCTTTTGTTTACTTGTG 58.141 36.000 0.00 0.00 0.00 3.33
1870 2082 8.626526 CATACTTGTACCCTTTTGTTTACTTGT 58.373 33.333 0.00 0.00 0.00 3.16
1897 2109 5.344665 CGTGTTTGTGTTTTGATTTGTCTGT 59.655 36.000 0.00 0.00 0.00 3.41
2020 3936 1.271379 GCTTGCCCTCTTCCTGTTACA 60.271 52.381 0.00 0.00 0.00 2.41
2077 4002 1.671054 TTGCTTTCCTTCCGCTCGG 60.671 57.895 1.14 1.14 0.00 4.63
2170 4095 1.450312 CCATGCCTCTGGACCGAAC 60.450 63.158 0.00 0.00 38.69 3.95
2301 4228 1.743394 CCGATTGGTGGAGGTTAAAGC 59.257 52.381 0.00 0.00 0.00 3.51
2348 4275 0.179004 TTCAGGCGTGTGGTGGAAAT 60.179 50.000 6.26 0.00 0.00 2.17
2362 4289 3.380479 TTCTACGTGACCAAGTTCAGG 57.620 47.619 0.00 0.00 37.40 3.86
2437 4364 2.854076 CCAAAGGCCCCTCAACCT 59.146 61.111 0.00 0.00 38.14 3.50
2469 4397 2.200370 AGGTCCGGTGGTGACAGA 59.800 61.111 0.00 0.00 44.46 3.41
2471 4399 2.123208 TCAGGTCCGGTGGTGACA 60.123 61.111 0.00 0.00 34.36 3.58
2481 4409 4.502962 CAAGAATCTCTTCACTCAGGTCC 58.497 47.826 0.00 0.00 33.78 4.46
2614 4544 6.560253 TTGCTTTCTCTCTTTACCATGTTC 57.440 37.500 0.00 0.00 0.00 3.18
2627 4561 1.269257 GGTTGCGCTTTTGCTTTCTCT 60.269 47.619 9.73 0.00 44.80 3.10
2666 4600 2.434884 ATCAAGACGTGGGCAGCG 60.435 61.111 0.00 0.00 0.00 5.18
2677 4611 3.576118 GCTCCTATGGCTACTCATCAAGA 59.424 47.826 0.00 0.00 0.00 3.02
2680 4614 2.896044 CTGCTCCTATGGCTACTCATCA 59.104 50.000 0.00 0.00 0.00 3.07
2699 4633 5.470368 TCCTAGACGAAATCAAGTGAACTG 58.530 41.667 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.