Multiple sequence alignment - TraesCS6B01G324100

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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 TraesCS6B01G324100 chr6B 100.000 2324 0 0 1 2324 573347662 573349985 0.000000e+00 4292
1 TraesCS6B01G324100 chr6B 97.313 1675 39 4 1 1674 18600450 18598781 0.000000e+00 2839
2 TraesCS6B01G324100 chr6B 90.714 560 18 12 1799 2324 556015790 556015231 0.000000e+00 715
3 TraesCS6B01G324100 chr6B 89.565 115 9 3 1775 1887 705877846 705877959 2.410000e-30 143
4 TraesCS6B01G324100 chr7B 95.781 1683 64 5 1 1679 484928865 484927186 0.000000e+00 2708
5 TraesCS6B01G324100 chr7B 98.058 103 2 0 1672 1774 558990899 558991001 1.830000e-41 180
6 TraesCS6B01G324100 chr7B 98.058 103 2 0 1672 1774 665141022 665141124 1.830000e-41 180
7 TraesCS6B01G324100 chr7B 93.269 104 5 2 1672 1774 735818290 735818392 4.000000e-33 152
8 TraesCS6B01G324100 chr5B 90.936 1677 141 9 1 1674 364099712 364098044 0.000000e+00 2244
9 TraesCS6B01G324100 chr5B 92.035 113 8 1 1775 1887 28231179 28231068 8.600000e-35 158
10 TraesCS6B01G324100 chr4A 88.982 1679 173 10 1 1675 700975953 700977623 0.000000e+00 2065
11 TraesCS6B01G324100 chr4A 88.631 1680 174 13 1 1675 632630870 632632537 0.000000e+00 2028
12 TraesCS6B01G324100 chr3B 88.975 1678 171 12 3 1675 629908993 629910661 0.000000e+00 2061
13 TraesCS6B01G324100 chr3B 91.706 422 13 2 1925 2324 511024895 511024474 1.210000e-157 566
14 TraesCS6B01G324100 chr3A 87.679 1680 191 11 1 1675 702515843 702514175 0.000000e+00 1941
15 TraesCS6B01G324100 chr2A 86.833 1686 206 13 1 1680 179276103 179277778 0.000000e+00 1869
16 TraesCS6B01G324100 chr2A 85.850 1682 220 16 1 1674 673275407 673273736 0.000000e+00 1772
17 TraesCS6B01G324100 chrUn 88.475 564 26 7 1799 2324 30417873 30417311 0.000000e+00 645
18 TraesCS6B01G324100 chr5A 87.453 534 27 7 1831 2324 666938388 666937855 1.550000e-161 579
19 TraesCS6B01G324100 chr1B 96.117 103 4 0 1672 1774 554738518 554738620 3.970000e-38 169
20 TraesCS6B01G324100 chr7D 87.591 137 11 5 1775 1905 119017233 119017369 1.110000e-33 154
21 TraesCS6B01G324100 chr7D 87.050 139 10 7 1773 1905 81375555 81375419 1.440000e-32 150
22 TraesCS6B01G324100 chr2B 88.189 127 11 3 1763 1887 11188461 11188337 5.170000e-32 148
23 TraesCS6B01G324100 chr5D 89.167 120 9 4 1770 1887 530634293 530634410 1.860000e-31 147
24 TraesCS6B01G324100 chr2D 87.097 124 16 0 1772 1895 610853163 610853040 8.660000e-30 141
25 TraesCS6B01G324100 chr1D 87.705 122 14 1 1774 1895 411519997 411520117 8.660000e-30 141
26 TraesCS6B01G324100 chr7A 86.992 123 14 2 1774 1895 96059194 96059315 1.120000e-28 137


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 TraesCS6B01G324100 chr6B 573347662 573349985 2323 False 4292 4292 100.000 1 2324 1 chr6B.!!$F1 2323
1 TraesCS6B01G324100 chr6B 18598781 18600450 1669 True 2839 2839 97.313 1 1674 1 chr6B.!!$R1 1673
2 TraesCS6B01G324100 chr6B 556015231 556015790 559 True 715 715 90.714 1799 2324 1 chr6B.!!$R2 525
3 TraesCS6B01G324100 chr7B 484927186 484928865 1679 True 2708 2708 95.781 1 1679 1 chr7B.!!$R1 1678
4 TraesCS6B01G324100 chr5B 364098044 364099712 1668 True 2244 2244 90.936 1 1674 1 chr5B.!!$R2 1673
5 TraesCS6B01G324100 chr4A 700975953 700977623 1670 False 2065 2065 88.982 1 1675 1 chr4A.!!$F2 1674
6 TraesCS6B01G324100 chr4A 632630870 632632537 1667 False 2028 2028 88.631 1 1675 1 chr4A.!!$F1 1674
7 TraesCS6B01G324100 chr3B 629908993 629910661 1668 False 2061 2061 88.975 3 1675 1 chr3B.!!$F1 1672
8 TraesCS6B01G324100 chr3A 702514175 702515843 1668 True 1941 1941 87.679 1 1675 1 chr3A.!!$R1 1674
9 TraesCS6B01G324100 chr2A 179276103 179277778 1675 False 1869 1869 86.833 1 1680 1 chr2A.!!$F1 1679
10 TraesCS6B01G324100 chr2A 673273736 673275407 1671 True 1772 1772 85.850 1 1674 1 chr2A.!!$R1 1673
11 TraesCS6B01G324100 chrUn 30417311 30417873 562 True 645 645 88.475 1799 2324 1 chrUn.!!$R1 525
12 TraesCS6B01G324100 chr5A 666937855 666938388 533 True 579 579 87.453 1831 2324 1 chr5A.!!$R1 493

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
954 957 2.026449 AGAAACCTCCCAGCATCTCTTG 60.026 50.0 0.0 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1878 1890 0.536006 AGAGCCTTGCCTGTGTGTTC 60.536 55.0 0.0 0.0 0.0 3.18 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
231 233 5.141182 GGTTAGATGGTCTAGGATCTGTCA 58.859 45.833 9.05 0.0 29.56 3.58
271 273 4.082125 GTTTGGGTGTGAAAGATCTCCAT 58.918 43.478 0.00 0.0 0.00 3.41
407 409 3.197927 AGGGGAGAATCACTGACTCTT 57.802 47.619 0.00 0.0 39.68 2.85
408 410 3.525862 AGGGGAGAATCACTGACTCTTT 58.474 45.455 0.00 0.0 39.68 2.52
663 665 9.696917 ACTTAATGAACAATGGAAAAAGATGAC 57.303 29.630 0.00 0.0 0.00 3.06
833 835 5.338626 GCCAGAATCCCTTTGAAAATCCAAT 60.339 40.000 0.00 0.0 0.00 3.16
954 957 2.026449 AGAAACCTCCCAGCATCTCTTG 60.026 50.000 0.00 0.0 0.00 3.02
1259 1262 1.270518 TGAGAAGCTGAGAGTTGGTGC 60.271 52.381 0.00 0.0 0.00 5.01
1280 1283 0.108424 GCTCTGCTGAAGGACATCGT 60.108 55.000 0.00 0.0 0.00 3.73
1490 1501 5.305644 ACTGTGAGTTAGATGTTGGAGTCTT 59.694 40.000 0.00 0.0 0.00 3.01
1588 1599 0.467290 TGCTTGAACCCGCTTTCCTT 60.467 50.000 0.00 0.0 0.00 3.36
1593 1604 2.661718 TGAACCCGCTTTCCTTTTTCT 58.338 42.857 0.00 0.0 0.00 2.52
1631 1642 4.585879 ACTTGGCTGTATTTCCGTTATGT 58.414 39.130 0.00 0.0 0.00 2.29
1632 1643 5.007682 ACTTGGCTGTATTTCCGTTATGTT 58.992 37.500 0.00 0.0 0.00 2.71
1633 1644 4.955925 TGGCTGTATTTCCGTTATGTTG 57.044 40.909 0.00 0.0 0.00 3.33
1690 1701 1.961793 AAAAGCAAGTACAGCGACCA 58.038 45.000 0.00 0.0 37.01 4.02
1691 1702 1.226746 AAAGCAAGTACAGCGACCAC 58.773 50.000 0.00 0.0 37.01 4.16
1692 1703 0.944311 AAGCAAGTACAGCGACCACG 60.944 55.000 0.00 0.0 42.93 4.94
1693 1704 2.380410 GCAAGTACAGCGACCACGG 61.380 63.158 0.00 0.0 40.15 4.94
1694 1705 2.048503 AAGTACAGCGACCACGGC 60.049 61.111 0.00 0.0 40.15 5.68
1695 1706 3.584868 AAGTACAGCGACCACGGCC 62.585 63.158 0.00 0.0 40.15 6.13
1725 1736 4.156622 CGTGGAGCTGCGCATGTG 62.157 66.667 19.26 0.0 0.00 3.21
1726 1737 3.807538 GTGGAGCTGCGCATGTGG 61.808 66.667 12.24 0.0 0.00 4.17
1728 1739 4.783621 GGAGCTGCGCATGTGGGA 62.784 66.667 12.24 0.0 0.00 4.37
1729 1740 3.503363 GAGCTGCGCATGTGGGAC 61.503 66.667 12.24 0.0 0.00 4.46
1755 1766 4.421479 CGAGCTCGACGGCACCTT 62.421 66.667 32.06 0.0 43.02 3.50
1756 1767 2.882876 GAGCTCGACGGCACCTTA 59.117 61.111 0.00 0.0 34.17 2.69
1757 1768 1.226717 GAGCTCGACGGCACCTTAG 60.227 63.158 0.00 0.0 34.17 2.18
1758 1769 1.654954 GAGCTCGACGGCACCTTAGA 61.655 60.000 0.00 0.0 34.17 2.10
1759 1770 1.038130 AGCTCGACGGCACCTTAGAT 61.038 55.000 10.28 0.0 34.17 1.98
1760 1771 0.666913 GCTCGACGGCACCTTAGATA 59.333 55.000 0.00 0.0 0.00 1.98
1761 1772 1.269998 GCTCGACGGCACCTTAGATAT 59.730 52.381 0.00 0.0 0.00 1.63
1762 1773 2.288273 GCTCGACGGCACCTTAGATATT 60.288 50.000 0.00 0.0 0.00 1.28
1763 1774 3.799232 GCTCGACGGCACCTTAGATATTT 60.799 47.826 0.00 0.0 0.00 1.40
1764 1775 4.369182 CTCGACGGCACCTTAGATATTTT 58.631 43.478 0.00 0.0 0.00 1.82
1765 1776 4.761975 TCGACGGCACCTTAGATATTTTT 58.238 39.130 0.00 0.0 0.00 1.94
1766 1777 4.807304 TCGACGGCACCTTAGATATTTTTC 59.193 41.667 0.00 0.0 0.00 2.29
1767 1778 4.569162 CGACGGCACCTTAGATATTTTTCA 59.431 41.667 0.00 0.0 0.00 2.69
1768 1779 5.236478 CGACGGCACCTTAGATATTTTTCAT 59.764 40.000 0.00 0.0 0.00 2.57
1769 1780 6.377327 ACGGCACCTTAGATATTTTTCATG 57.623 37.500 0.00 0.0 0.00 3.07
1770 1781 5.885912 ACGGCACCTTAGATATTTTTCATGT 59.114 36.000 0.00 0.0 0.00 3.21
1771 1782 6.183360 ACGGCACCTTAGATATTTTTCATGTG 60.183 38.462 0.00 0.0 0.00 3.21
1772 1783 6.507023 GGCACCTTAGATATTTTTCATGTGG 58.493 40.000 0.00 0.0 0.00 4.17
1773 1784 5.979517 GCACCTTAGATATTTTTCATGTGGC 59.020 40.000 0.00 0.0 0.00 5.01
1774 1785 6.507023 CACCTTAGATATTTTTCATGTGGCC 58.493 40.000 0.00 0.0 0.00 5.36
1775 1786 6.096705 CACCTTAGATATTTTTCATGTGGCCA 59.903 38.462 0.00 0.0 0.00 5.36
1776 1787 6.322201 ACCTTAGATATTTTTCATGTGGCCAG 59.678 38.462 5.11 0.0 0.00 4.85
1777 1788 6.239120 CCTTAGATATTTTTCATGTGGCCAGG 60.239 42.308 5.11 0.0 0.00 4.45
1778 1789 3.962718 AGATATTTTTCATGTGGCCAGGG 59.037 43.478 5.11 0.0 0.00 4.45
1779 1790 1.278537 ATTTTTCATGTGGCCAGGGG 58.721 50.000 5.11 0.0 0.00 4.79
1915 1938 0.537188 CTCCATCTTGCCGGTGTAGT 59.463 55.000 1.90 0.0 0.00 2.73
2260 2334 7.721286 TTTCAAGTTTTCTTCAAACAGCAAA 57.279 28.000 0.61 0.0 46.55 3.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
407 409 6.719370 ACTTTCATAATAGCCTTCCAACACAA 59.281 34.615 0.00 0.00 0.00 3.33
408 410 6.150976 CACTTTCATAATAGCCTTCCAACACA 59.849 38.462 0.00 0.00 0.00 3.72
663 665 1.817357 GGTTTCCCTAACCGTGGAAG 58.183 55.000 0.00 0.00 46.48 3.46
923 926 1.886422 GGAGGTTTCTCTCTCCCCAT 58.114 55.000 0.00 0.00 42.72 4.00
981 984 3.009473 ACATGCAACCAACTACTCTCCAT 59.991 43.478 0.00 0.00 0.00 3.41
1277 1280 2.914059 TCCTCATCATACGAGACACGA 58.086 47.619 0.00 0.00 45.77 4.35
1280 1283 3.254411 GCAGATCCTCATCATACGAGACA 59.746 47.826 0.00 0.00 31.84 3.41
1490 1501 3.025978 ACCCGACGACACTAAATATCCA 58.974 45.455 0.00 0.00 0.00 3.41
1588 1599 4.220821 AGTTCAGCAGATAGGACGAGAAAA 59.779 41.667 0.00 0.00 0.00 2.29
1593 1604 2.166459 CCAAGTTCAGCAGATAGGACGA 59.834 50.000 0.00 0.00 0.00 4.20
1631 1642 5.068215 TCCCCTTTCCATTACTTGAACAA 57.932 39.130 0.00 0.00 0.00 2.83
1632 1643 4.733077 TCCCCTTTCCATTACTTGAACA 57.267 40.909 0.00 0.00 0.00 3.18
1633 1644 5.163652 CGAATCCCCTTTCCATTACTTGAAC 60.164 44.000 0.00 0.00 0.00 3.18
1675 1686 2.380410 CCGTGGTCGCTGTACTTGC 61.380 63.158 0.00 0.00 35.54 4.01
1676 1687 2.380410 GCCGTGGTCGCTGTACTTG 61.380 63.158 0.00 0.00 35.54 3.16
1738 1749 2.921538 CTAAGGTGCCGTCGAGCTCG 62.922 65.000 30.03 30.03 41.45 5.03
1739 1750 1.226717 CTAAGGTGCCGTCGAGCTC 60.227 63.158 2.73 2.73 0.00 4.09
1740 1751 1.038130 ATCTAAGGTGCCGTCGAGCT 61.038 55.000 0.00 0.00 0.00 4.09
1741 1752 0.666913 TATCTAAGGTGCCGTCGAGC 59.333 55.000 0.00 0.00 0.00 5.03
1742 1753 3.644884 AATATCTAAGGTGCCGTCGAG 57.355 47.619 0.00 0.00 0.00 4.04
1743 1754 4.395959 AAAATATCTAAGGTGCCGTCGA 57.604 40.909 0.00 0.00 0.00 4.20
1744 1755 4.569162 TGAAAAATATCTAAGGTGCCGTCG 59.431 41.667 0.00 0.00 0.00 5.12
1745 1756 6.038271 ACATGAAAAATATCTAAGGTGCCGTC 59.962 38.462 0.00 0.00 0.00 4.79
1746 1757 5.885912 ACATGAAAAATATCTAAGGTGCCGT 59.114 36.000 0.00 0.00 0.00 5.68
1747 1758 6.201517 CACATGAAAAATATCTAAGGTGCCG 58.798 40.000 0.00 0.00 0.00 5.69
1748 1759 6.507023 CCACATGAAAAATATCTAAGGTGCC 58.493 40.000 0.00 0.00 0.00 5.01
1749 1760 5.979517 GCCACATGAAAAATATCTAAGGTGC 59.020 40.000 0.00 0.00 0.00 5.01
1750 1761 6.096705 TGGCCACATGAAAAATATCTAAGGTG 59.903 38.462 0.00 0.00 0.00 4.00
1751 1762 6.194235 TGGCCACATGAAAAATATCTAAGGT 58.806 36.000 0.00 0.00 0.00 3.50
1752 1763 6.239120 CCTGGCCACATGAAAAATATCTAAGG 60.239 42.308 0.00 0.00 0.00 2.69
1753 1764 6.239120 CCCTGGCCACATGAAAAATATCTAAG 60.239 42.308 0.00 0.00 0.00 2.18
1754 1765 5.598005 CCCTGGCCACATGAAAAATATCTAA 59.402 40.000 0.00 0.00 0.00 2.10
1755 1766 5.139727 CCCTGGCCACATGAAAAATATCTA 58.860 41.667 0.00 0.00 0.00 1.98
1756 1767 3.962718 CCCTGGCCACATGAAAAATATCT 59.037 43.478 0.00 0.00 0.00 1.98
1757 1768 3.070015 CCCCTGGCCACATGAAAAATATC 59.930 47.826 0.00 0.00 0.00 1.63
1758 1769 3.040477 CCCCTGGCCACATGAAAAATAT 58.960 45.455 0.00 0.00 0.00 1.28
1759 1770 2.465813 CCCCTGGCCACATGAAAAATA 58.534 47.619 0.00 0.00 0.00 1.40
1760 1771 1.278537 CCCCTGGCCACATGAAAAAT 58.721 50.000 0.00 0.00 0.00 1.82
1761 1772 1.479368 GCCCCTGGCCACATGAAAAA 61.479 55.000 0.00 0.00 44.06 1.94
1762 1773 1.912763 GCCCCTGGCCACATGAAAA 60.913 57.895 0.00 0.00 44.06 2.29
1763 1774 2.283821 GCCCCTGGCCACATGAAA 60.284 61.111 0.00 0.00 44.06 2.69
1878 1890 0.536006 AGAGCCTTGCCTGTGTGTTC 60.536 55.000 0.00 0.00 0.00 3.18
1915 1938 3.138798 GTCGTCTGGCTCGGGCTA 61.139 66.667 7.48 0.00 38.73 3.93
2000 2031 3.775654 GGGACTGCAGGGGAGTCG 61.776 72.222 19.93 0.00 40.77 4.18
2260 2334 7.177921 CAGTATTGGGATTTATTGGAGATGCAT 59.822 37.037 0.00 0.00 0.00 3.96


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

AutoCloner maintained by Alex Coulton.