Multiple sequence alignment - TraesCS1B01G262900

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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 TraesCS1B01G262900 chr1B 100.000 2465 0 0 1 2465 461439044 461441508 0 4553
1 TraesCS1B01G262900 chr1B 99.536 646 2 1 1820 2464 683708887 683708242 0 1175
2 TraesCS1B01G262900 chr4D 98.869 1768 19 1 1 1768 123450063 123448297 0 3153
3 TraesCS1B01G262900 chr3A 98.812 1768 20 1 1 1768 495105837 495104071 0 3147
4 TraesCS1B01G262900 chr3B 98.812 1768 17 3 1 1768 92297809 92296046 0 3145
5 TraesCS1B01G262900 chr3B 98.699 1768 22 1 1 1768 6011843 6010077 0 3136
6 TraesCS1B01G262900 chr2B 98.756 1768 21 1 1 1768 234542237 234540471 0 3142
7 TraesCS1B01G262900 chrUn 98.699 1768 22 1 1 1768 217906591 217908357 0 3136
8 TraesCS1B01G262900 chrUn 99.691 647 1 1 1820 2465 67966045 67965399 0 1182
9 TraesCS1B01G262900 chr7A 98.643 1768 23 1 1 1768 563523175 563521409 0 3131
10 TraesCS1B01G262900 chr7A 98.585 1767 24 1 2 1768 708281822 708280057 0 3123
11 TraesCS1B01G262900 chr7A 99.227 647 4 1 1820 2465 671971205 671970559 0 1166
12 TraesCS1B01G262900 chr7A 99.073 647 5 1 1820 2465 671993773 671994419 0 1160
13 TraesCS1B01G262900 chr6D 98.474 1769 24 3 1 1768 108484131 108485897 0 3114
14 TraesCS1B01G262900 chr6D 98.918 647 5 2 1820 2465 108475888 108475243 0 1155
15 TraesCS1B01G262900 chr7B 99.691 647 1 1 1820 2465 698164745 698165391 0 1182
16 TraesCS1B01G262900 chr7B 98.918 647 5 2 1820 2465 743054894 743055539 0 1155
17 TraesCS1B01G262900 chr1D 99.073 647 5 1 1820 2465 141338654 141339300 0 1160
18 TraesCS1B01G262900 chr2A 98.918 647 6 1 1820 2465 563281250 563281896 0 1155


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 TraesCS1B01G262900 chr1B 461439044 461441508 2464 False 4553 4553 100.000 1 2465 1 chr1B.!!$F1 2464
1 TraesCS1B01G262900 chr1B 683708242 683708887 645 True 1175 1175 99.536 1820 2464 1 chr1B.!!$R1 644
2 TraesCS1B01G262900 chr4D 123448297 123450063 1766 True 3153 3153 98.869 1 1768 1 chr4D.!!$R1 1767
3 TraesCS1B01G262900 chr3A 495104071 495105837 1766 True 3147 3147 98.812 1 1768 1 chr3A.!!$R1 1767
4 TraesCS1B01G262900 chr3B 92296046 92297809 1763 True 3145 3145 98.812 1 1768 1 chr3B.!!$R2 1767
5 TraesCS1B01G262900 chr3B 6010077 6011843 1766 True 3136 3136 98.699 1 1768 1 chr3B.!!$R1 1767
6 TraesCS1B01G262900 chr2B 234540471 234542237 1766 True 3142 3142 98.756 1 1768 1 chr2B.!!$R1 1767
7 TraesCS1B01G262900 chrUn 217906591 217908357 1766 False 3136 3136 98.699 1 1768 1 chrUn.!!$F1 1767
8 TraesCS1B01G262900 chrUn 67965399 67966045 646 True 1182 1182 99.691 1820 2465 1 chrUn.!!$R1 645
9 TraesCS1B01G262900 chr7A 563521409 563523175 1766 True 3131 3131 98.643 1 1768 1 chr7A.!!$R1 1767
10 TraesCS1B01G262900 chr7A 708280057 708281822 1765 True 3123 3123 98.585 2 1768 1 chr7A.!!$R3 1766
11 TraesCS1B01G262900 chr7A 671970559 671971205 646 True 1166 1166 99.227 1820 2465 1 chr7A.!!$R2 645
12 TraesCS1B01G262900 chr7A 671993773 671994419 646 False 1160 1160 99.073 1820 2465 1 chr7A.!!$F1 645
13 TraesCS1B01G262900 chr6D 108484131 108485897 1766 False 3114 3114 98.474 1 1768 1 chr6D.!!$F1 1767
14 TraesCS1B01G262900 chr6D 108475243 108475888 645 True 1155 1155 98.918 1820 2465 1 chr6D.!!$R1 645
15 TraesCS1B01G262900 chr7B 698164745 698165391 646 False 1182 1182 99.691 1820 2465 1 chr7B.!!$F1 645
16 TraesCS1B01G262900 chr7B 743054894 743055539 645 False 1155 1155 98.918 1820 2465 1 chr7B.!!$F2 645
17 TraesCS1B01G262900 chr1D 141338654 141339300 646 False 1160 1160 99.073 1820 2465 1 chr1D.!!$F1 645
18 TraesCS1B01G262900 chr2A 563281250 563281896 646 False 1155 1155 98.918 1820 2465 1 chr2A.!!$F1 645

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
499 500 0.802494 CCGGTCTTCATTTCCAACGG 59.198 55.0 0.0 0.0 0.0 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1786 1788 1.006162 ACGAGAACCCTTCCTAGCTCT 59.994 52.381 0.0 0.0 0.0 4.09 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
141 142 0.966370 GACAGAGGGCTCGTGGTACT 60.966 60.000 0.00 0.00 34.09 2.73
499 500 0.802494 CCGGTCTTCATTTCCAACGG 59.198 55.000 0.00 0.00 0.00 4.44
528 529 5.221342 GGAAACAGGTCGAGATAGATGACAT 60.221 44.000 0.00 0.00 34.32 3.06
776 778 3.011708 AGCCCCACTCATATTCAAAAGGT 59.988 43.478 0.00 0.00 0.00 3.50
967 969 4.093850 AGCTGTCGTAAAGTTTCGTTGTTT 59.906 37.500 0.00 0.00 0.00 2.83
1606 1608 2.439104 GGCTAGGGTGAGCTGAGGG 61.439 68.421 0.00 0.00 42.43 4.30
1639 1641 3.660501 AGTGAGCGAATGTGTGTAAGA 57.339 42.857 0.00 0.00 0.00 2.10
1754 1756 1.809619 CACGTCGGAACCGCATGAT 60.810 57.895 8.48 0.00 39.59 2.45
1768 1770 1.037030 CATGATTTCACCGGGGTGGG 61.037 60.000 17.31 0.00 45.43 4.61
1769 1771 1.211567 ATGATTTCACCGGGGTGGGA 61.212 55.000 17.31 7.19 45.43 4.37
1770 1772 1.077716 GATTTCACCGGGGTGGGAG 60.078 63.158 17.31 0.00 45.43 4.30
1771 1773 1.848886 GATTTCACCGGGGTGGGAGT 61.849 60.000 17.31 4.27 45.43 3.85
1772 1774 1.432023 ATTTCACCGGGGTGGGAGTT 61.432 55.000 17.31 0.00 45.43 3.01
1773 1775 1.647334 TTTCACCGGGGTGGGAGTTT 61.647 55.000 17.31 0.00 45.43 2.66
1774 1776 1.647334 TTCACCGGGGTGGGAGTTTT 61.647 55.000 17.31 0.00 45.43 2.43
1775 1777 1.602605 CACCGGGGTGGGAGTTTTC 60.603 63.158 6.32 0.00 44.64 2.29
1776 1778 1.772979 ACCGGGGTGGGAGTTTTCT 60.773 57.895 6.32 0.00 44.64 2.52
1777 1779 1.002502 CCGGGGTGGGAGTTTTCTC 60.003 63.158 0.00 0.00 45.49 2.87
1790 1792 5.544136 GAGTTTTCTCCTTGATCAAGAGC 57.456 43.478 32.49 16.32 40.79 4.09
1791 1793 5.240013 AGTTTTCTCCTTGATCAAGAGCT 57.760 39.130 32.49 18.10 40.79 4.09
1792 1794 6.365970 AGTTTTCTCCTTGATCAAGAGCTA 57.634 37.500 32.49 15.71 40.79 3.32
1793 1795 6.405538 AGTTTTCTCCTTGATCAAGAGCTAG 58.594 40.000 32.49 22.54 40.79 3.42
1794 1796 5.350504 TTTCTCCTTGATCAAGAGCTAGG 57.649 43.478 32.49 18.22 40.28 3.02
1795 1797 4.256983 TCTCCTTGATCAAGAGCTAGGA 57.743 45.455 32.49 21.15 44.14 2.94
1796 1798 4.614475 TCTCCTTGATCAAGAGCTAGGAA 58.386 43.478 32.49 11.76 45.21 3.36
1797 1799 4.648762 TCTCCTTGATCAAGAGCTAGGAAG 59.351 45.833 32.49 14.89 45.21 3.46
1798 1800 3.708631 TCCTTGATCAAGAGCTAGGAAGG 59.291 47.826 32.49 15.44 43.58 3.46
1799 1801 3.181456 CCTTGATCAAGAGCTAGGAAGGG 60.181 52.174 32.49 11.62 41.17 3.95
1800 1802 3.121929 TGATCAAGAGCTAGGAAGGGT 57.878 47.619 0.00 0.00 0.00 4.34
1801 1803 3.454858 TGATCAAGAGCTAGGAAGGGTT 58.545 45.455 0.00 0.00 0.00 4.11
1802 1804 3.452627 TGATCAAGAGCTAGGAAGGGTTC 59.547 47.826 0.00 0.00 0.00 3.62
1803 1805 3.191888 TCAAGAGCTAGGAAGGGTTCT 57.808 47.619 0.00 0.00 0.00 3.01
1804 1806 3.100671 TCAAGAGCTAGGAAGGGTTCTC 58.899 50.000 0.00 0.00 0.00 2.87
1805 1807 1.770294 AGAGCTAGGAAGGGTTCTCG 58.230 55.000 0.00 0.00 0.00 4.04
1806 1808 1.006162 AGAGCTAGGAAGGGTTCTCGT 59.994 52.381 0.00 0.00 0.00 4.18
1807 1809 2.241685 AGAGCTAGGAAGGGTTCTCGTA 59.758 50.000 0.00 0.00 0.00 3.43
1808 1810 3.117436 AGAGCTAGGAAGGGTTCTCGTAT 60.117 47.826 0.00 0.00 0.00 3.06
1809 1811 3.637694 GAGCTAGGAAGGGTTCTCGTATT 59.362 47.826 0.00 0.00 0.00 1.89
1810 1812 3.385111 AGCTAGGAAGGGTTCTCGTATTG 59.615 47.826 0.00 0.00 0.00 1.90
1811 1813 3.492829 GCTAGGAAGGGTTCTCGTATTGG 60.493 52.174 0.00 0.00 0.00 3.16
1812 1814 2.547990 AGGAAGGGTTCTCGTATTGGT 58.452 47.619 0.00 0.00 0.00 3.67
1813 1815 2.910977 AGGAAGGGTTCTCGTATTGGTT 59.089 45.455 0.00 0.00 0.00 3.67
1814 1816 3.055312 AGGAAGGGTTCTCGTATTGGTTC 60.055 47.826 0.00 0.00 0.00 3.62
1815 1817 2.667473 AGGGTTCTCGTATTGGTTCG 57.333 50.000 0.00 0.00 0.00 3.95
1816 1818 2.173519 AGGGTTCTCGTATTGGTTCGA 58.826 47.619 0.00 0.00 34.88 3.71
1817 1819 2.094338 AGGGTTCTCGTATTGGTTCGAC 60.094 50.000 0.00 0.00 32.65 4.20
1818 1820 2.265683 GGTTCTCGTATTGGTTCGACC 58.734 52.381 0.00 0.00 39.22 4.79
2133 2136 2.039624 ATCCGTGGACAGGCTCCT 59.960 61.111 0.00 0.00 40.26 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
499 500 1.446272 CTCGACCTGTTTCCCGAGC 60.446 63.158 0.00 0.00 41.31 5.03
528 529 6.575649 CGGTAAGGAAGAGGATAAAAAGGTGA 60.576 42.308 0.00 0.00 0.00 4.02
603 605 0.927029 GGGGGCTGGGTTCTATTTCT 59.073 55.000 0.00 0.00 0.00 2.52
776 778 0.036732 ATCGTCTTGAAAGCTGGGCA 59.963 50.000 0.00 0.00 0.00 5.36
967 969 1.203052 GATAGGGTCAACGACGGAACA 59.797 52.381 0.00 0.00 32.65 3.18
1102 1104 7.385752 TGAAGCAAGTGAATGATTTGAAATTCC 59.614 33.333 0.00 0.00 32.81 3.01
1606 1608 1.218316 CTCACTTACGCTGTCCCCC 59.782 63.158 0.00 0.00 0.00 5.40
1768 1770 5.244755 AGCTCTTGATCAAGGAGAAAACTC 58.755 41.667 30.33 14.20 38.88 3.01
1769 1771 5.240013 AGCTCTTGATCAAGGAGAAAACT 57.760 39.130 30.33 16.51 38.88 2.66
1770 1772 5.584251 CCTAGCTCTTGATCAAGGAGAAAAC 59.416 44.000 30.33 15.01 38.88 2.43
1771 1773 5.485353 TCCTAGCTCTTGATCAAGGAGAAAA 59.515 40.000 30.33 12.77 38.88 2.29
1772 1774 5.026121 TCCTAGCTCTTGATCAAGGAGAAA 58.974 41.667 30.33 13.43 38.88 2.52
1773 1775 4.614475 TCCTAGCTCTTGATCAAGGAGAA 58.386 43.478 30.33 13.77 38.88 2.87
1774 1776 4.256983 TCCTAGCTCTTGATCAAGGAGA 57.743 45.455 30.33 14.41 38.88 3.71
1775 1777 4.202243 CCTTCCTAGCTCTTGATCAAGGAG 60.202 50.000 30.33 25.10 38.88 3.69
1776 1778 3.708631 CCTTCCTAGCTCTTGATCAAGGA 59.291 47.826 30.33 19.27 38.88 3.36
1777 1779 3.181456 CCCTTCCTAGCTCTTGATCAAGG 60.181 52.174 30.33 22.38 38.88 3.61
1778 1780 3.454082 ACCCTTCCTAGCTCTTGATCAAG 59.546 47.826 26.56 26.56 39.71 3.02
1779 1781 3.454858 ACCCTTCCTAGCTCTTGATCAA 58.545 45.455 8.12 8.12 0.00 2.57
1780 1782 3.121929 ACCCTTCCTAGCTCTTGATCA 57.878 47.619 0.00 0.00 0.00 2.92
1781 1783 3.709141 AGAACCCTTCCTAGCTCTTGATC 59.291 47.826 0.00 0.00 0.00 2.92
1782 1784 3.709141 GAGAACCCTTCCTAGCTCTTGAT 59.291 47.826 0.00 0.00 0.00 2.57
1783 1785 3.100671 GAGAACCCTTCCTAGCTCTTGA 58.899 50.000 0.00 0.00 0.00 3.02
1784 1786 2.159170 CGAGAACCCTTCCTAGCTCTTG 60.159 54.545 0.00 0.00 0.00 3.02
1785 1787 2.104170 CGAGAACCCTTCCTAGCTCTT 58.896 52.381 0.00 0.00 0.00 2.85
1786 1788 1.006162 ACGAGAACCCTTCCTAGCTCT 59.994 52.381 0.00 0.00 0.00 4.09
1787 1789 1.476477 ACGAGAACCCTTCCTAGCTC 58.524 55.000 0.00 0.00 0.00 4.09
1788 1790 2.822707 TACGAGAACCCTTCCTAGCT 57.177 50.000 0.00 0.00 0.00 3.32
1789 1791 3.492829 CCAATACGAGAACCCTTCCTAGC 60.493 52.174 0.00 0.00 0.00 3.42
1790 1792 3.705072 ACCAATACGAGAACCCTTCCTAG 59.295 47.826 0.00 0.00 0.00 3.02
1791 1793 3.716431 ACCAATACGAGAACCCTTCCTA 58.284 45.455 0.00 0.00 0.00 2.94
1792 1794 2.547990 ACCAATACGAGAACCCTTCCT 58.452 47.619 0.00 0.00 0.00 3.36
1793 1795 3.268330 GAACCAATACGAGAACCCTTCC 58.732 50.000 0.00 0.00 0.00 3.46
1794 1796 2.928116 CGAACCAATACGAGAACCCTTC 59.072 50.000 0.00 0.00 0.00 3.46
1795 1797 2.564062 TCGAACCAATACGAGAACCCTT 59.436 45.455 0.00 0.00 34.49 3.95
1796 1798 2.094338 GTCGAACCAATACGAGAACCCT 60.094 50.000 0.00 0.00 39.16 4.34
1797 1799 2.265683 GTCGAACCAATACGAGAACCC 58.734 52.381 0.00 0.00 39.16 4.11
1798 1800 2.265683 GGTCGAACCAATACGAGAACC 58.734 52.381 0.00 0.00 38.42 3.62
1811 1813 3.319755 TCGTATTGGTTCTTGGTCGAAC 58.680 45.455 0.00 0.00 41.91 3.95
1812 1814 3.256383 TCTCGTATTGGTTCTTGGTCGAA 59.744 43.478 0.00 0.00 0.00 3.71
1813 1815 2.821378 TCTCGTATTGGTTCTTGGTCGA 59.179 45.455 0.00 0.00 0.00 4.20
1814 1816 3.226346 TCTCGTATTGGTTCTTGGTCG 57.774 47.619 0.00 0.00 0.00 4.79
1815 1817 3.683340 GGTTCTCGTATTGGTTCTTGGTC 59.317 47.826 0.00 0.00 0.00 4.02
1816 1818 3.558533 GGGTTCTCGTATTGGTTCTTGGT 60.559 47.826 0.00 0.00 0.00 3.67
1817 1819 3.007635 GGGTTCTCGTATTGGTTCTTGG 58.992 50.000 0.00 0.00 0.00 3.61
1818 1820 3.939066 AGGGTTCTCGTATTGGTTCTTG 58.061 45.455 0.00 0.00 0.00 3.02
2133 2136 4.408921 AGTCCATAATCCGATTTGACCTCA 59.591 41.667 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.