Multiple sequence alignment - TraesCS2A01G402100

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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 TraesCS2A01G402100 chr2A 100.000 2722 0 0 1 2722 655909851 655907130 0.000000e+00 5027
1 TraesCS2A01G402100 chr2A 96.026 1409 45 6 796 2203 774011847 774010449 0.000000e+00 2281
2 TraesCS2A01G402100 chr7A 97.707 2748 32 7 1 2722 644066760 644064018 0.000000e+00 4697
3 TraesCS2A01G402100 chr7A 97.505 2204 26 9 1 2203 49623174 49620999 0.000000e+00 3738
4 TraesCS2A01G402100 chr7A 95.861 2078 48 15 1 2075 633712557 633710515 0.000000e+00 3326
5 TraesCS2A01G402100 chr7A 97.871 1409 28 2 796 2203 1550089 1548682 0.000000e+00 2435
6 TraesCS2A01G402100 chr7A 97.857 1400 27 3 806 2203 579482645 579481247 0.000000e+00 2416
7 TraesCS2A01G402100 chr7A 98.664 524 7 0 2199 2722 633708827 633708304 0.000000e+00 929
8 TraesCS2A01G402100 chr7A 98.282 524 9 0 2199 2722 49620848 49620325 0.000000e+00 918
9 TraesCS2A01G402100 chr7A 99.237 131 1 0 2073 2203 639859365 639859235 1.260000e-58 237
10 TraesCS2A01G402100 chr1A 97.761 2724 57 4 1 2722 443853356 443856077 0.000000e+00 4689
11 TraesCS2A01G402100 chr1A 98.074 2129 34 6 598 2722 497975696 497977821 0.000000e+00 3698
12 TraesCS2A01G402100 chr5A 96.806 2724 54 15 1 2722 168400263 168397571 0.000000e+00 4518
13 TraesCS2A01G402100 chr5A 94.714 1627 60 7 1 1605 133817750 133819372 0.000000e+00 2505
14 TraesCS2A01G402100 chr5A 98.013 1409 27 1 796 2203 572301287 572302695 0.000000e+00 2446
15 TraesCS2A01G402100 chr3A 94.147 1623 71 15 1 1605 513294964 513296580 0.000000e+00 2449
16 TraesCS2A01G402100 chr4A 93.904 1624 73 16 1 1605 490340961 490342577 0.000000e+00 2427
17 TraesCS2A01G402100 chr4A 93.519 1620 82 18 1 1605 429488137 429489748 0.000000e+00 2388
18 TraesCS2A01G402100 chr6B 98.282 524 9 0 2199 2722 180277292 180276769 0.000000e+00 918
19 TraesCS2A01G402100 chr3B 98.282 524 9 0 2199 2722 62765236 62764713 0.000000e+00 918
20 TraesCS2A01G402100 chr3B 98.282 524 9 0 2199 2722 62766562 62766039 0.000000e+00 918


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 TraesCS2A01G402100 chr2A 655907130 655909851 2721 True 5027.0 5027 100.0000 1 2722 1 chr2A.!!$R1 2721
1 TraesCS2A01G402100 chr2A 774010449 774011847 1398 True 2281.0 2281 96.0260 796 2203 1 chr2A.!!$R2 1407
2 TraesCS2A01G402100 chr7A 644064018 644066760 2742 True 4697.0 4697 97.7070 1 2722 1 chr7A.!!$R4 2721
3 TraesCS2A01G402100 chr7A 1548682 1550089 1407 True 2435.0 2435 97.8710 796 2203 1 chr7A.!!$R1 1407
4 TraesCS2A01G402100 chr7A 579481247 579482645 1398 True 2416.0 2416 97.8570 806 2203 1 chr7A.!!$R2 1397
5 TraesCS2A01G402100 chr7A 49620325 49623174 2849 True 2328.0 3738 97.8935 1 2722 2 chr7A.!!$R5 2721
6 TraesCS2A01G402100 chr7A 633708304 633712557 4253 True 2127.5 3326 97.2625 1 2722 2 chr7A.!!$R6 2721
7 TraesCS2A01G402100 chr1A 443853356 443856077 2721 False 4689.0 4689 97.7610 1 2722 1 chr1A.!!$F1 2721
8 TraesCS2A01G402100 chr1A 497975696 497977821 2125 False 3698.0 3698 98.0740 598 2722 1 chr1A.!!$F2 2124
9 TraesCS2A01G402100 chr5A 168397571 168400263 2692 True 4518.0 4518 96.8060 1 2722 1 chr5A.!!$R1 2721
10 TraesCS2A01G402100 chr5A 133817750 133819372 1622 False 2505.0 2505 94.7140 1 1605 1 chr5A.!!$F1 1604
11 TraesCS2A01G402100 chr5A 572301287 572302695 1408 False 2446.0 2446 98.0130 796 2203 1 chr5A.!!$F2 1407
12 TraesCS2A01G402100 chr3A 513294964 513296580 1616 False 2449.0 2449 94.1470 1 1605 1 chr3A.!!$F1 1604
13 TraesCS2A01G402100 chr4A 490340961 490342577 1616 False 2427.0 2427 93.9040 1 1605 1 chr4A.!!$F2 1604
14 TraesCS2A01G402100 chr4A 429488137 429489748 1611 False 2388.0 2388 93.5190 1 1605 1 chr4A.!!$F1 1604
15 TraesCS2A01G402100 chr6B 180276769 180277292 523 True 918.0 918 98.2820 2199 2722 1 chr6B.!!$R1 523
16 TraesCS2A01G402100 chr3B 62764713 62766562 1849 True 918.0 918 98.2820 2199 2722 2 chr3B.!!$R1 523

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
664 667 3.73883 AATGTTCACAAGTGCATTGCT 57.261 38.095 10.49 0.0 43.15 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2408 5712 1.001378 GAGCCGTGCAAATCTGTTGTT 60.001 47.619 0.0 0.0 0.0 2.83 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
467 470 6.936968 ATCTAGGGTTCAGTTCTTAAGTGT 57.063 37.500 1.63 0.00 33.51 3.55
518 521 9.574577 TGGGAAGATATGGTCCATTTATAGTAT 57.425 33.333 10.33 0.00 0.00 2.12
664 667 3.738830 AATGTTCACAAGTGCATTGCT 57.261 38.095 10.49 0.00 43.15 3.91
767 771 7.690256 ACTTGGTTCTGTTCCTATTTATGTCT 58.310 34.615 0.00 0.00 0.00 3.41
772 776 8.475639 GGTTCTGTTCCTATTTATGTCTAGTCA 58.524 37.037 0.00 0.00 0.00 3.41
1306 1311 1.633945 TCCTTTTGGCTTCCTCTACCC 59.366 52.381 0.00 0.00 40.12 3.69
1543 1695 4.175489 CGACGACCTCGCGATGGT 62.175 66.667 24.15 24.15 44.43 3.55
1544 1696 2.579787 GACGACCTCGCGATGGTG 60.580 66.667 27.44 21.47 44.43 4.17
1545 1697 4.129737 ACGACCTCGCGATGGTGG 62.130 66.667 27.44 26.68 44.43 4.61
1546 1698 4.129737 CGACCTCGCGATGGTGGT 62.130 66.667 27.44 22.72 38.03 4.16
1547 1699 2.509336 GACCTCGCGATGGTGGTG 60.509 66.667 27.44 8.42 38.03 4.17
1548 1700 4.082523 ACCTCGCGATGGTGGTGG 62.083 66.667 23.55 16.07 36.30 4.61
1553 1705 4.856801 GCGATGGTGGTGGCGGAT 62.857 66.667 0.00 0.00 0.00 4.18
1554 1706 2.896854 CGATGGTGGTGGCGGATG 60.897 66.667 0.00 0.00 0.00 3.51
1555 1707 2.589540 GATGGTGGTGGCGGATGA 59.410 61.111 0.00 0.00 0.00 2.92
1556 1708 1.819632 GATGGTGGTGGCGGATGAC 60.820 63.158 0.00 0.00 0.00 3.06
1567 1719 2.722487 GGATGACGACCTCGCGAT 59.278 61.111 10.36 0.00 44.43 4.58
2408 5712 3.284617 CAGGCATTCCATCACAGAATCA 58.715 45.455 0.00 0.00 31.56 2.57
2624 5930 2.729882 CTCAAAAACGACCTACCACGAG 59.270 50.000 0.00 0.00 0.00 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
467 470 5.594725 TGTGCTACATTTTGTTAGAACCCAA 59.405 36.000 0.00 0.00 0.00 4.12
518 521 9.332713 TGGACCATATCTACAATGAACCATATA 57.667 33.333 0.00 0.00 30.45 0.86
767 771 4.960938 AGAAGCACTTGTGAACATGACTA 58.039 39.130 0.00 0.00 0.00 2.59
772 776 3.817647 GAGGAAGAAGCACTTGTGAACAT 59.182 43.478 4.79 0.00 39.13 2.71
1306 1311 0.179217 CATGGTGTTGTCATCGTGCG 60.179 55.000 0.00 0.00 35.35 5.34
1541 1693 4.077184 TCGTCATCCGCCACCACC 62.077 66.667 0.00 0.00 36.19 4.61
1542 1694 2.813908 GTCGTCATCCGCCACCAC 60.814 66.667 0.00 0.00 36.19 4.16
1543 1695 4.077184 GGTCGTCATCCGCCACCA 62.077 66.667 0.00 0.00 34.46 4.17
1544 1696 3.718210 GAGGTCGTCATCCGCCACC 62.718 68.421 0.00 0.00 35.87 4.61
1545 1697 2.202756 GAGGTCGTCATCCGCCAC 60.203 66.667 0.00 0.00 35.87 5.01
1546 1698 3.822192 CGAGGTCGTCATCCGCCA 61.822 66.667 0.00 0.00 35.87 5.69
1549 1701 3.182472 ATCGCGAGGTCGTCATCCG 62.182 63.158 16.66 0.00 42.22 4.18
1550 1702 1.658717 CATCGCGAGGTCGTCATCC 60.659 63.158 16.66 0.00 42.22 3.51
1551 1703 1.658717 CCATCGCGAGGTCGTCATC 60.659 63.158 20.35 0.00 42.22 2.92
1552 1704 2.413351 CCATCGCGAGGTCGTCAT 59.587 61.111 20.35 0.00 42.22 3.06
1553 1705 3.060000 ACCATCGCGAGGTCGTCA 61.060 61.111 20.35 0.00 42.22 4.35
1554 1706 2.579787 CACCATCGCGAGGTCGTC 60.580 66.667 22.16 0.00 42.22 4.20
1555 1707 4.129737 CCACCATCGCGAGGTCGT 62.130 66.667 22.16 11.33 42.22 4.34
1556 1708 4.129737 ACCACCATCGCGAGGTCG 62.130 66.667 22.16 19.16 37.23 4.79
1557 1709 2.509336 CACCACCATCGCGAGGTC 60.509 66.667 22.16 0.00 37.23 3.85
1558 1710 4.082523 CCACCACCATCGCGAGGT 62.083 66.667 20.35 20.23 40.85 3.85
1565 1717 4.077184 TCGTCCGCCACCACCATC 62.077 66.667 0.00 0.00 0.00 3.51
1566 1718 4.388499 GTCGTCCGCCACCACCAT 62.388 66.667 0.00 0.00 0.00 3.55
2408 5712 1.001378 GAGCCGTGCAAATCTGTTGTT 60.001 47.619 0.00 0.00 0.00 2.83
2624 5930 3.432782 CTTGAAAGCCATGAATCTTCGC 58.567 45.455 0.00 0.00 0.00 4.70


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

AutoCloner maintained by Alex Coulton.