Multiple sequence alignment - TraesCS1B01G405100

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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 TraesCS1B01G405100 chr1B 100.000 2675 0 0 1 2675 633717783 633720457 0 4940
1 TraesCS1B01G405100 chr5A 98.067 1707 25 4 1 1700 559031137 559029432 0 2963
2 TraesCS1B01G405100 chr5A 98.169 983 17 1 1694 2675 559029476 559028494 0 1714
3 TraesCS1B01G405100 chr5B 97.891 1707 28 4 1 1700 57514312 57512607 0 2946
4 TraesCS1B01G405100 chr3A 97.713 1705 33 2 1 1700 105556145 105554442 0 2928
5 TraesCS1B01G405100 chr3A 97.864 983 20 1 1694 2675 593308995 593309977 0 1698
6 TraesCS1B01G405100 chr5D 97.550 1714 25 6 1 1700 299971182 299969472 0 2916
7 TraesCS1B01G405100 chr5D 97.141 1714 31 6 1 1700 503340250 503341959 0 2878
8 TraesCS1B01G405100 chr5D 96.614 1713 39 6 1 1700 6252464 6250758 0 2824
9 TraesCS1B01G405100 chr5D 97.762 983 21 1 1694 2675 503341915 503342897 0 1692
10 TraesCS1B01G405100 chr5D 97.660 983 22 1 1694 2675 6250802 6249820 0 1687
11 TraesCS1B01G405100 chr5D 97.558 983 23 1 1694 2675 503315976 503316958 0 1681
12 TraesCS1B01G405100 chr1D 97.014 1708 34 7 1 1700 254460221 254461919 0 2856
13 TraesCS1B01G405100 chr7A 95.738 1713 52 7 1 1700 537840599 537838895 0 2739
14 TraesCS1B01G405100 chr4D 94.804 1713 67 8 1 1700 19901535 19903238 0 2651
15 TraesCS1B01G405100 chr1A 98.271 983 16 1 1694 2675 554484495 554485477 0 1720
16 TraesCS1B01G405100 chr2B 98.067 983 18 1 1694 2675 683729915 683730897 0 1709
17 TraesCS1B01G405100 chrUn 97.762 983 21 1 1694 2675 345936757 345935775 0 1692
18 TraesCS1B01G405100 chr7B 97.762 983 21 1 1694 2675 662752596 662751614 0 1692


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 TraesCS1B01G405100 chr1B 633717783 633720457 2674 False 4940.0 4940 100.0000 1 2675 1 chr1B.!!$F1 2674
1 TraesCS1B01G405100 chr5A 559028494 559031137 2643 True 2338.5 2963 98.1180 1 2675 2 chr5A.!!$R1 2674
2 TraesCS1B01G405100 chr5B 57512607 57514312 1705 True 2946.0 2946 97.8910 1 1700 1 chr5B.!!$R1 1699
3 TraesCS1B01G405100 chr3A 105554442 105556145 1703 True 2928.0 2928 97.7130 1 1700 1 chr3A.!!$R1 1699
4 TraesCS1B01G405100 chr3A 593308995 593309977 982 False 1698.0 1698 97.8640 1694 2675 1 chr3A.!!$F1 981
5 TraesCS1B01G405100 chr5D 299969472 299971182 1710 True 2916.0 2916 97.5500 1 1700 1 chr5D.!!$R1 1699
6 TraesCS1B01G405100 chr5D 503340250 503342897 2647 False 2285.0 2878 97.4515 1 2675 2 chr5D.!!$F2 2674
7 TraesCS1B01G405100 chr5D 6249820 6252464 2644 True 2255.5 2824 97.1370 1 2675 2 chr5D.!!$R2 2674
8 TraesCS1B01G405100 chr5D 503315976 503316958 982 False 1681.0 1681 97.5580 1694 2675 1 chr5D.!!$F1 981
9 TraesCS1B01G405100 chr1D 254460221 254461919 1698 False 2856.0 2856 97.0140 1 1700 1 chr1D.!!$F1 1699
10 TraesCS1B01G405100 chr7A 537838895 537840599 1704 True 2739.0 2739 95.7380 1 1700 1 chr7A.!!$R1 1699
11 TraesCS1B01G405100 chr4D 19901535 19903238 1703 False 2651.0 2651 94.8040 1 1700 1 chr4D.!!$F1 1699
12 TraesCS1B01G405100 chr1A 554484495 554485477 982 False 1720.0 1720 98.2710 1694 2675 1 chr1A.!!$F1 981
13 TraesCS1B01G405100 chr2B 683729915 683730897 982 False 1709.0 1709 98.0670 1694 2675 1 chr2B.!!$F1 981
14 TraesCS1B01G405100 chrUn 345935775 345936757 982 True 1692.0 1692 97.7620 1694 2675 1 chrUn.!!$R1 981
15 TraesCS1B01G405100 chr7B 662751614 662752596 982 True 1692.0 1692 97.7620 1694 2675 1 chr7B.!!$R1 981

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
877 899 4.913345 CCGTACGATTCGTGCTAATATTGA 59.087 41.667 21.4 0.0 41.39 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1678 1700 0.179045 ATGTAGCAGGTGAATCCGCC 60.179 55.0 0.0 0.0 43.25 6.13 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
877 899 4.913345 CCGTACGATTCGTGCTAATATTGA 59.087 41.667 21.40 0.00 41.39 2.57
910 932 5.513962 GGTCCCTGGAATGGAAGAGATAATC 60.514 48.000 0.00 0.00 30.32 1.75
1126 1148 2.154462 GGGATGGGATTGCTCGTATTG 58.846 52.381 0.00 0.00 0.00 1.90
1148 1170 8.650143 ATTGTAGGTCTTGGTGAAATAATGTT 57.350 30.769 0.00 0.00 0.00 2.71
1421 1443 4.207165 GCTCCAAGTATAATTTCCAGGCA 58.793 43.478 0.00 0.00 0.00 4.75
1433 1455 3.417069 TTCCAGGCATTCCATATACGG 57.583 47.619 0.00 0.00 33.74 4.02
1546 1568 4.497006 GCAAAATAGCAGTAGCCACAGATG 60.497 45.833 0.00 0.00 43.56 2.90
1607 1629 8.630037 TGTTTATGTAGCTATCGATCAAAGAGA 58.370 33.333 0.00 0.00 0.00 3.10
1626 1648 2.428890 AGAATCCTCCGTAGCTCAAGTG 59.571 50.000 0.00 0.00 0.00 3.16
1660 1682 2.046855 AGGAGGGGGCCATGGAAT 59.953 61.111 18.40 0.00 0.00 3.01
1661 1683 0.772124 GAGGAGGGGGCCATGGAATA 60.772 60.000 18.40 0.00 0.00 1.75
1662 1684 0.103173 AGGAGGGGGCCATGGAATAT 60.103 55.000 18.40 0.00 0.00 1.28
1663 1685 0.786435 GGAGGGGGCCATGGAATATT 59.214 55.000 18.40 0.00 0.00 1.28
1664 1686 1.550869 GGAGGGGGCCATGGAATATTG 60.551 57.143 18.40 0.00 0.00 1.90
1665 1687 1.147817 GAGGGGGCCATGGAATATTGT 59.852 52.381 18.40 0.00 0.00 2.71
1666 1688 2.378547 GAGGGGGCCATGGAATATTGTA 59.621 50.000 18.40 0.00 0.00 2.41
1667 1689 2.379907 AGGGGGCCATGGAATATTGTAG 59.620 50.000 18.40 0.00 0.00 2.74
1668 1690 2.110011 GGGGGCCATGGAATATTGTAGT 59.890 50.000 18.40 0.00 0.00 2.73
1669 1691 3.332485 GGGGGCCATGGAATATTGTAGTA 59.668 47.826 18.40 0.00 0.00 1.82
1670 1692 4.567747 GGGGGCCATGGAATATTGTAGTAG 60.568 50.000 18.40 0.00 0.00 2.57
1671 1693 4.010349 GGGCCATGGAATATTGTAGTAGC 58.990 47.826 18.40 0.00 0.00 3.58
1672 1694 4.263506 GGGCCATGGAATATTGTAGTAGCT 60.264 45.833 18.40 0.00 0.00 3.32
1673 1695 4.697352 GGCCATGGAATATTGTAGTAGCTG 59.303 45.833 18.40 0.00 0.00 4.24
1674 1696 5.513094 GGCCATGGAATATTGTAGTAGCTGA 60.513 44.000 18.40 0.00 0.00 4.26
1675 1697 5.997746 GCCATGGAATATTGTAGTAGCTGAA 59.002 40.000 18.40 0.00 0.00 3.02
1676 1698 6.486657 GCCATGGAATATTGTAGTAGCTGAAA 59.513 38.462 18.40 0.00 0.00 2.69
1677 1699 7.175641 GCCATGGAATATTGTAGTAGCTGAAAT 59.824 37.037 18.40 0.00 0.00 2.17
1678 1700 8.509690 CCATGGAATATTGTAGTAGCTGAAATG 58.490 37.037 5.56 0.00 0.00 2.32
1679 1701 8.509690 CATGGAATATTGTAGTAGCTGAAATGG 58.490 37.037 0.00 0.00 0.00 3.16
1680 1702 6.486657 TGGAATATTGTAGTAGCTGAAATGGC 59.513 38.462 0.00 0.00 0.00 4.40
1681 1703 6.347725 GGAATATTGTAGTAGCTGAAATGGCG 60.348 42.308 0.00 0.00 34.52 5.69
1682 1704 2.309528 TGTAGTAGCTGAAATGGCGG 57.690 50.000 0.00 0.00 34.52 6.13
1683 1705 1.828595 TGTAGTAGCTGAAATGGCGGA 59.171 47.619 0.00 0.00 34.52 5.54
1684 1706 2.434336 TGTAGTAGCTGAAATGGCGGAT 59.566 45.455 0.00 0.00 34.52 4.18
1685 1707 2.717639 AGTAGCTGAAATGGCGGATT 57.282 45.000 0.00 0.00 34.52 3.01
1686 1708 2.565841 AGTAGCTGAAATGGCGGATTC 58.434 47.619 0.00 0.00 34.52 2.52
1687 1709 2.092968 AGTAGCTGAAATGGCGGATTCA 60.093 45.455 0.00 0.56 34.57 2.57
1688 1710 1.098050 AGCTGAAATGGCGGATTCAC 58.902 50.000 0.00 0.00 32.46 3.18
1689 1711 0.101219 GCTGAAATGGCGGATTCACC 59.899 55.000 0.00 0.00 32.46 4.02
1690 1712 1.755179 CTGAAATGGCGGATTCACCT 58.245 50.000 0.00 0.00 36.31 4.00
1691 1713 1.402968 CTGAAATGGCGGATTCACCTG 59.597 52.381 0.00 0.00 36.31 4.00
1692 1714 0.101219 GAAATGGCGGATTCACCTGC 59.899 55.000 0.00 0.00 37.42 4.85
1697 1719 0.179045 GGCGGATTCACCTGCTACAT 60.179 55.000 0.00 0.00 37.93 2.29
1933 1955 5.356882 TGTTCATTCACGCCTTTTAGAAG 57.643 39.130 0.00 0.00 0.00 2.85
2011 2033 4.155709 AGTTGAGACTCAATCTGGAGACA 58.844 43.478 20.43 0.00 38.79 3.41
2173 2195 7.938140 ATTAAAGCCATGAAACAAGTAGCTA 57.062 32.000 0.00 0.00 0.00 3.32
2217 2239 3.664107 TCAATTCGCAGAGTTACAAGCT 58.336 40.909 0.00 0.00 32.99 3.74
2307 2329 4.843516 AGGGAATTGCTTAAACAATCCCAA 59.156 37.500 25.08 5.19 43.08 4.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
730 752 9.480538 GTTTTTCAAAATAAAGGGTTTCGTTTC 57.519 29.630 0.00 0.00 33.64 2.78
877 899 0.546747 TTCCAGGGACCCGAGAATGT 60.547 55.000 12.78 0.00 0.00 2.71
910 932 9.788960 GTAGAAGTTCAAGGCCTAATTAATTTG 57.211 33.333 5.16 4.28 0.00 2.32
984 1006 5.472137 GGTTGCCATTAGTGTTTCTTGACTA 59.528 40.000 0.00 0.00 0.00 2.59
1126 1148 7.827729 ACCTAACATTATTTCACCAAGACCTAC 59.172 37.037 0.00 0.00 0.00 3.18
1148 1170 7.994425 TCTGCAAATTTGACTAATTCACCTA 57.006 32.000 22.31 0.00 35.39 3.08
1421 1443 6.126883 TGTTTGAAGAGGTCCGTATATGGAAT 60.127 38.462 15.48 7.42 40.44 3.01
1433 1455 2.278332 AAGCCCTGTTTGAAGAGGTC 57.722 50.000 6.23 0.00 37.75 3.85
1483 1505 0.530744 ATTAACTCTCGCTGACCGCA 59.469 50.000 0.00 0.00 39.08 5.69
1546 1568 4.317488 TGCCCTTTTTGATTGAGAATTGC 58.683 39.130 0.00 0.00 0.00 3.56
1598 1620 3.964031 AGCTACGGAGGATTCTCTTTGAT 59.036 43.478 0.00 0.00 39.86 2.57
1607 1629 1.482593 CCACTTGAGCTACGGAGGATT 59.517 52.381 0.00 0.00 0.00 3.01
1626 1648 4.141688 CCCTCCTCATGGAAAGTAGTTACC 60.142 50.000 0.00 0.00 42.66 2.85
1660 1682 4.100344 TCCGCCATTTCAGCTACTACAATA 59.900 41.667 0.00 0.00 0.00 1.90
1661 1683 3.118408 TCCGCCATTTCAGCTACTACAAT 60.118 43.478 0.00 0.00 0.00 2.71
1662 1684 2.235155 TCCGCCATTTCAGCTACTACAA 59.765 45.455 0.00 0.00 0.00 2.41
1663 1685 1.828595 TCCGCCATTTCAGCTACTACA 59.171 47.619 0.00 0.00 0.00 2.74
1664 1686 2.596904 TCCGCCATTTCAGCTACTAC 57.403 50.000 0.00 0.00 0.00 2.73
1665 1687 3.133901 TGAATCCGCCATTTCAGCTACTA 59.866 43.478 0.00 0.00 0.00 1.82
1666 1688 2.092968 TGAATCCGCCATTTCAGCTACT 60.093 45.455 0.00 0.00 0.00 2.57
1667 1689 2.032178 GTGAATCCGCCATTTCAGCTAC 59.968 50.000 0.00 0.00 32.79 3.58
1668 1690 2.288666 GTGAATCCGCCATTTCAGCTA 58.711 47.619 0.00 0.00 32.79 3.32
1669 1691 1.098050 GTGAATCCGCCATTTCAGCT 58.902 50.000 0.00 0.00 32.79 4.24
1670 1692 0.101219 GGTGAATCCGCCATTTCAGC 59.899 55.000 0.00 0.00 42.48 4.26
1671 1693 1.402968 CAGGTGAATCCGCCATTTCAG 59.597 52.381 0.00 0.00 45.32 3.02
1672 1694 1.462616 CAGGTGAATCCGCCATTTCA 58.537 50.000 0.00 0.00 45.32 2.69
1673 1695 0.101219 GCAGGTGAATCCGCCATTTC 59.899 55.000 0.00 0.00 45.32 2.17
1674 1696 0.323725 AGCAGGTGAATCCGCCATTT 60.324 50.000 0.00 0.00 45.32 2.32
1675 1697 0.546122 TAGCAGGTGAATCCGCCATT 59.454 50.000 0.00 0.00 45.32 3.16
1676 1698 0.179045 GTAGCAGGTGAATCCGCCAT 60.179 55.000 0.00 0.00 45.32 4.40
1677 1699 1.220749 GTAGCAGGTGAATCCGCCA 59.779 57.895 0.00 0.00 45.32 5.69
1678 1700 0.179045 ATGTAGCAGGTGAATCCGCC 60.179 55.000 0.00 0.00 43.25 6.13
1679 1701 1.668419 AATGTAGCAGGTGAATCCGC 58.332 50.000 0.00 0.00 41.99 5.54
1680 1702 4.816385 ACAATAATGTAGCAGGTGAATCCG 59.184 41.667 0.00 0.00 38.24 4.18
1697 1719 4.814234 CCGCCATTTCAGCTACTACAATAA 59.186 41.667 0.00 0.00 0.00 1.40
1912 1934 4.723248 CCTTCTAAAAGGCGTGAATGAAC 58.277 43.478 0.00 0.00 45.50 3.18
2011 2033 8.147244 ACATTAGTAGGAATATAGGCGGAAAT 57.853 34.615 0.00 0.00 0.00 2.17
2173 2195 6.015180 TGAGCTAGTTCCAATTTTGATTTGCT 60.015 34.615 3.94 0.00 0.00 3.91
2217 2239 1.602668 GCAGAGGCGAATTGTGCAAAA 60.603 47.619 0.00 0.00 34.18 2.44
2307 2329 0.622665 CCACTGGGAGAGGATTTGCT 59.377 55.000 0.00 0.00 35.59 3.91
2471 2493 1.796796 GCTTGCTCGGTGAATGTCC 59.203 57.895 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.