Multiple sequence alignment - TraesCS1A01G082800

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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 TraesCS1A01G082800 chr1A 100.000 2594 0 0 1 2594 65823484 65826077 0.000000e+00 4791.0
1 TraesCS1A01G082800 chr3A 96.615 2600 80 6 1 2594 99311908 99309311 0.000000e+00 4307.0
2 TraesCS1A01G082800 chr5A 96.999 1666 46 4 1 1663 663771049 663772713 0.000000e+00 2796.0
3 TraesCS1A01G082800 chr5A 97.634 930 20 2 1656 2583 663772791 663773720 0.000000e+00 1594.0
4 TraesCS1A01G082800 chr4A 96.759 1666 47 5 1 1663 319843578 319841917 0.000000e+00 2771.0
5 TraesCS1A01G082800 chr4A 98.298 940 15 1 1656 2594 319841838 319840899 0.000000e+00 1646.0
6 TraesCS1A01G082800 chr4A 77.749 391 77 9 2155 2538 668308516 668308903 5.580000e-57 231.0
7 TraesCS1A01G082800 chr5B 84.699 1660 225 18 15 1657 344551010 344552657 0.000000e+00 1631.0
8 TraesCS1A01G082800 chr5B 86.740 905 115 4 1692 2594 344552780 344553681 0.000000e+00 1002.0
9 TraesCS1A01G082800 chr2A 96.468 538 18 1 1656 2193 710381885 710381349 0.000000e+00 887.0
10 TraesCS1A01G082800 chr2A 96.552 377 12 1 2219 2594 710381213 710380837 7.880000e-175 623.0
11 TraesCS1A01G082800 chr2B 74.483 1548 332 46 99 1613 748207421 748208938 1.710000e-171 612.0
12 TraesCS1A01G082800 chr2B 80.556 108 16 5 1478 1582 748358558 748358663 7.700000e-11 78.7
13 TraesCS1A01G082800 chr2D 74.139 1597 352 44 41 1609 357877579 357876016 2.860000e-169 604.0
14 TraesCS1A01G082800 chr6A 76.496 234 45 6 38 266 74652283 74652055 4.530000e-23 119.0


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 TraesCS1A01G082800 chr1A 65823484 65826077 2593 False 4791.0 4791 100.0000 1 2594 1 chr1A.!!$F1 2593
1 TraesCS1A01G082800 chr3A 99309311 99311908 2597 True 4307.0 4307 96.6150 1 2594 1 chr3A.!!$R1 2593
2 TraesCS1A01G082800 chr5A 663771049 663773720 2671 False 2195.0 2796 97.3165 1 2583 2 chr5A.!!$F1 2582
3 TraesCS1A01G082800 chr4A 319840899 319843578 2679 True 2208.5 2771 97.5285 1 2594 2 chr4A.!!$R1 2593
4 TraesCS1A01G082800 chr5B 344551010 344553681 2671 False 1316.5 1631 85.7195 15 2594 2 chr5B.!!$F1 2579
5 TraesCS1A01G082800 chr2A 710380837 710381885 1048 True 755.0 887 96.5100 1656 2594 2 chr2A.!!$R1 938
6 TraesCS1A01G082800 chr2B 748207421 748208938 1517 False 612.0 612 74.4830 99 1613 1 chr2B.!!$F1 1514
7 TraesCS1A01G082800 chr2D 357876016 357877579 1563 True 604.0 604 74.1390 41 1609 1 chr2D.!!$R1 1568

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
618 641 0.107017 CTCCACCGGGCATCAATCTT 60.107 55.0 6.32 0.0 0.0 2.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2217 2449 0.178894 ATTTTGCAAGGAAGCCCCCT 60.179 50.0 0.0 0.0 38.42 4.79 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
69 70 4.776322 CTCACCGCCCGCCAATGA 62.776 66.667 0.00 0.0 0.00 2.57
70 71 4.337177 TCACCGCCCGCCAATGAA 62.337 61.111 0.00 0.0 0.00 2.57
96 97 1.264749 AAGCCACGTGGGAGCTGATA 61.265 55.000 34.58 0.0 40.01 2.15
482 502 4.289672 ACCAACTCTACATCCTCCACAATT 59.710 41.667 0.00 0.0 0.00 2.32
618 641 0.107017 CTCCACCGGGCATCAATCTT 60.107 55.000 6.32 0.0 0.00 2.40
629 652 3.525537 GCATCAATCTTCTTCACCTCGA 58.474 45.455 0.00 0.0 0.00 4.04
826 851 1.596752 GTGTGGCACCGATGTGTGA 60.597 57.895 16.26 0.0 44.65 3.58
841 866 0.550914 TGTGAGTTCCAGGGCAAAGT 59.449 50.000 0.00 0.0 0.00 2.66
860 885 6.972901 GCAAAGTGCAAGGGTTTTACTATATC 59.027 38.462 0.00 0.0 44.26 1.63
871 896 6.147328 GGGTTTTACTATATCCATGACGCTTC 59.853 42.308 0.00 0.0 0.00 3.86
948 973 6.605594 AGAGGGAGAAACATCTACTAGACAAG 59.394 42.308 0.00 0.0 0.00 3.16
1004 1029 2.683859 GCGCTGTTCAGCTCATGCA 61.684 57.895 20.12 0.0 42.74 3.96
1235 1262 1.549243 TATGTTGCCTCGCTGGTGGA 61.549 55.000 0.00 0.0 38.35 4.02
1285 1312 4.129737 ACCGTCCGGCATCTGTCG 62.130 66.667 5.47 0.0 43.72 4.35
1441 1468 5.091261 TGTTCAAGCTTCCTCTAATCCTC 57.909 43.478 0.00 0.0 0.00 3.71
1543 1570 1.063717 GGAAATCTCCCTGCATTCCCA 60.064 52.381 2.15 0.0 35.42 4.37
1628 1661 4.517832 ACACGACCTTGTTTTTAGATTCCC 59.482 41.667 0.00 0.0 0.00 3.97
1684 1805 2.840753 GGTTGGGGAGGCCAAGACA 61.841 63.158 5.01 0.0 0.00 3.41
1836 1957 0.536460 GTTGACGAAAAGGCCAGGGA 60.536 55.000 5.01 0.0 0.00 4.20
1845 1967 2.601367 GGCCAGGGAAGCTGCAAA 60.601 61.111 0.00 0.0 0.00 3.68
1901 2023 5.463724 CCCAACTCTTTTGATACGCTATCTC 59.536 44.000 6.58 0.0 36.17 2.75
1918 2040 7.151308 CGCTATCTCATCCTGAACTTATTCTT 58.849 38.462 0.00 0.0 35.69 2.52
2036 2158 3.933861 AGGACAAACAGACTCAACCTT 57.066 42.857 0.00 0.0 0.00 3.50
2037 2159 3.809905 AGGACAAACAGACTCAACCTTC 58.190 45.455 0.00 0.0 0.00 3.46
2114 2236 9.664332 CTCTTAATATGAACTGGGAGGATAATG 57.336 37.037 0.00 0.0 0.00 1.90
2217 2449 5.437060 ACCTTGCACTAGAAGTCAAAAAGA 58.563 37.500 0.00 0.0 0.00 2.52
2371 2604 4.216472 TGACTACCTGCTTCGCTGATATAG 59.784 45.833 0.00 0.0 0.00 1.31
2553 2787 7.032598 AGAAACCTTGGAGATTATTTCCTGA 57.967 36.000 3.42 0.0 35.67 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 1.973281 CCACGTGGCTTGCATCCTT 60.973 57.895 24.02 0.0 0.00 3.36
70 71 2.360350 CCACGTGGCTTGCATCCT 60.360 61.111 24.02 0.0 0.00 3.24
96 97 2.778278 ATGGGGATGGATGGCCGT 60.778 61.111 0.00 0.0 36.79 5.68
148 149 0.685131 TAGGTCAAGGATCGGGCGAA 60.685 55.000 0.00 0.0 0.00 4.70
331 338 3.015145 CCCCTCCATGGTTCCCGT 61.015 66.667 12.58 0.0 0.00 5.28
618 641 0.904649 ATGTGGCATCGAGGTGAAGA 59.095 50.000 0.00 0.0 0.00 2.87
629 652 4.518278 TTGTATTCCCTGTATGTGGCAT 57.482 40.909 0.00 0.0 0.00 4.40
826 851 0.396974 TTGCACTTTGCCCTGGAACT 60.397 50.000 0.00 0.0 44.23 3.01
841 866 6.770785 GTCATGGATATAGTAAAACCCTTGCA 59.229 38.462 0.00 0.0 0.00 4.08
860 885 1.817099 GGCAGAGGAAGCGTCATGG 60.817 63.158 1.14 0.0 0.00 3.66
871 896 1.815003 CTTTAAGCTGGTTGGCAGAGG 59.185 52.381 1.72 0.0 34.17 3.69
948 973 7.617041 AGTAAGCAGATAAATCAAGTTCCAC 57.383 36.000 0.00 0.0 0.00 4.02
1004 1029 2.993863 ACAAAGGTCCCTGGTCCTATTT 59.006 45.455 2.29 0.0 33.51 1.40
1235 1262 4.946157 CAGCATCTACTTCCAAAGGAACAT 59.054 41.667 0.00 0.0 36.71 2.71
1285 1312 0.107361 CTACAACCAATCCGGACCCC 60.107 60.000 6.12 0.0 38.63 4.95
1543 1570 3.988186 GAATAGGGTCCTATTTTCCCCCT 59.012 47.826 19.72 0.0 45.88 4.79
1628 1661 5.032327 TCATCCATTGTCTCCTGATTGAG 57.968 43.478 0.00 0.0 0.00 3.02
1684 1805 7.615365 TCCACTCTGTATTCATTATTTTTGGCT 59.385 33.333 0.00 0.0 0.00 4.75
1845 1967 5.105675 GGAGTACCTTCGATGTCTCTCTTTT 60.106 44.000 14.26 0.0 0.00 2.27
1901 2023 7.224362 CACAGCTCTAAGAATAAGTTCAGGATG 59.776 40.741 0.00 0.0 36.79 3.51
1918 2040 1.992557 ACCCCCATTTTCACAGCTCTA 59.007 47.619 0.00 0.0 0.00 2.43
2036 2158 1.071314 AAATGTCCCCCACCCACAGA 61.071 55.000 0.00 0.0 0.00 3.41
2037 2159 0.899717 CAAATGTCCCCCACCCACAG 60.900 60.000 0.00 0.0 0.00 3.66
2114 2236 8.225603 ACAAAGTTATCATTATCCACATCACC 57.774 34.615 0.00 0.0 0.00 4.02
2217 2449 0.178894 ATTTTGCAAGGAAGCCCCCT 60.179 50.000 0.00 0.0 38.42 4.79
2243 2476 3.396685 AGGAAGCAGAGTAGATCCACT 57.603 47.619 0.00 0.0 32.47 4.00
2371 2604 5.590663 GGAAGTCCAGGGAATGATCTTTTAC 59.409 44.000 0.00 0.0 35.64 2.01
2553 2787 2.489073 GCATAAGGAATTCACCCCCGAT 60.489 50.000 7.93 0.0 0.00 4.18


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

AutoCloner maintained by Alex Coulton.