Multiple sequence alignment - TraesCS2A01G423200

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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 TraesCS2A01G423200 chr2A 100.000 1531 0 0 857 2387 678126321 678127851 0 2828
1 TraesCS2A01G423200 chr2A 97.714 1531 35 0 857 2387 718924150 718922620 0 2634
2 TraesCS2A01G423200 chr2A 100.000 529 0 0 1 529 678125465 678125993 0 977
3 TraesCS2A01G423200 chr2A 97.921 529 11 0 1 529 718924718 718924190 0 917
4 TraesCS2A01G423200 chr2A 94.707 529 28 0 1 529 207349414 207348886 0 822
5 TraesCS2A01G423200 chr3A 97.715 1532 34 1 857 2387 601340149 601338618 0 2634
6 TraesCS2A01G423200 chr3A 97.164 529 15 0 1 529 601340717 601340189 0 894
7 TraesCS2A01G423200 chr7A 96.410 1504 54 0 882 2385 35448447 35446944 0 2479
8 TraesCS2A01G423200 chr5B 95.104 1532 73 2 857 2387 392102420 392103950 0 2412
9 TraesCS2A01G423200 chr5B 95.020 1526 72 4 864 2387 392043689 392045212 0 2394
10 TraesCS2A01G423200 chr5B 94.452 1532 83 2 857 2387 392058909 392060439 0 2357
11 TraesCS2A01G423200 chr5B 92.439 529 40 0 1 529 392101852 392102380 0 756
12 TraesCS2A01G423200 chr5B 91.969 523 42 0 1 523 392058013 392058535 0 734
13 TraesCS2A01G423200 chr5B 91.767 498 41 0 1 498 392042992 392043489 0 693
14 TraesCS2A01G423200 chr1B 95.039 1532 75 1 857 2387 42064852 42063321 0 2407
15 TraesCS2A01G423200 chr1B 92.628 529 39 0 1 529 42065420 42064892 0 761
16 TraesCS2A01G423200 chr3B 94.419 1541 76 2 857 2387 373619434 373617894 0 2361
17 TraesCS2A01G423200 chr3B 93.864 1532 93 1 857 2387 28333451 28331920 0 2307
18 TraesCS2A01G423200 chr3B 92.952 525 37 0 5 529 28334014 28333490 0 765
19 TraesCS2A01G423200 chr6B 95.094 530 23 2 2 529 663186622 663187150 0 832


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 TraesCS2A01G423200 chr2A 678125465 678127851 2386 False 1902.5 2828 100.0000 1 2387 2 chr2A.!!$F1 2386
1 TraesCS2A01G423200 chr2A 718922620 718924718 2098 True 1775.5 2634 97.8175 1 2387 2 chr2A.!!$R2 2386
2 TraesCS2A01G423200 chr2A 207348886 207349414 528 True 822.0 822 94.7070 1 529 1 chr2A.!!$R1 528
3 TraesCS2A01G423200 chr3A 601338618 601340717 2099 True 1764.0 2634 97.4395 1 2387 2 chr3A.!!$R1 2386
4 TraesCS2A01G423200 chr7A 35446944 35448447 1503 True 2479.0 2479 96.4100 882 2385 1 chr7A.!!$R1 1503
5 TraesCS2A01G423200 chr5B 392101852 392103950 2098 False 1584.0 2412 93.7715 1 2387 2 chr5B.!!$F3 2386
6 TraesCS2A01G423200 chr5B 392058013 392060439 2426 False 1545.5 2357 93.2105 1 2387 2 chr5B.!!$F2 2386
7 TraesCS2A01G423200 chr5B 392042992 392045212 2220 False 1543.5 2394 93.3935 1 2387 2 chr5B.!!$F1 2386
8 TraesCS2A01G423200 chr1B 42063321 42065420 2099 True 1584.0 2407 93.8335 1 2387 2 chr1B.!!$R1 2386
9 TraesCS2A01G423200 chr3B 373617894 373619434 1540 True 2361.0 2361 94.4190 857 2387 1 chr3B.!!$R1 1530
10 TraesCS2A01G423200 chr3B 28331920 28334014 2094 True 1536.0 2307 93.4080 5 2387 2 chr3B.!!$R2 2382
11 TraesCS2A01G423200 chr6B 663186622 663187150 528 False 832.0 832 95.0940 2 529 1 chr6B.!!$F1 527

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
402 403 3.426568 GTGCTGCCTCGACTTGCC 61.427 66.667 0.0 0.0 0.0 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2242 2297 0.174389 GTCATCTGCGAGGAGAAGCA 59.826 55.0 0.0 0.0 41.55 3.91 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
402 403 3.426568 GTGCTGCCTCGACTTGCC 61.427 66.667 0.00 0.00 0.00 4.52
1087 1130 1.527034 CAGTGCAAGGCTCAAAGCTA 58.473 50.000 0.00 0.00 41.99 3.32
1162 1205 0.259065 TGCTCGTAGTCTGGGGATCT 59.741 55.000 0.00 0.00 0.00 2.75
1461 1515 3.763360 CCATGTGTGTTGGTCCATGTAAT 59.237 43.478 0.00 0.00 34.30 1.89
1503 1557 2.880890 CAAGCATAACCATAGCTGGGTC 59.119 50.000 11.79 0.98 38.42 4.46
1534 1588 1.601759 TGGCCAAGCTCAGAAGTGC 60.602 57.895 0.61 0.00 34.56 4.40
1600 1654 0.912487 AATGTCCGGGGCCTCAACTA 60.912 55.000 1.96 0.00 0.00 2.24
1664 1718 5.316167 TCTTCTTGCCATATTGTGTGTCTT 58.684 37.500 0.00 0.00 0.00 3.01
2123 2178 1.707427 AGGAGGTTCACTTGGAGCAAT 59.293 47.619 0.00 0.00 0.00 3.56
2146 2201 2.910977 AGAGGGAAAACCCGACTATGTT 59.089 45.455 0.00 0.00 41.63 2.71
2211 2266 1.345415 TCAGCACTCATCTGCTTCACA 59.655 47.619 0.00 0.00 45.64 3.58
2219 2274 1.277273 CATCTGCTTCACACCCTCTCA 59.723 52.381 0.00 0.00 0.00 3.27
2231 2286 3.726859 ACACCCTCTCATCCTCTCTATCT 59.273 47.826 0.00 0.00 0.00 1.98
2242 2297 3.139957 TCCTCTCTATCTGATCACTGCCT 59.860 47.826 0.00 0.00 0.00 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
70 71 2.681778 CCTGGACAGGGAGCGACT 60.682 66.667 10.55 0.00 44.87 4.18
402 403 2.363018 TCGTCCCTCCTGGAGCAG 60.363 66.667 18.51 11.49 46.38 4.24
898 941 1.078356 CAGCTGGCTGCAGATCAGT 60.078 57.895 27.00 16.80 44.66 3.41
1000 1043 1.202582 AGCAAGAGTCTTACGACGCAT 59.797 47.619 4.74 0.00 44.93 4.73
1001 1044 0.596577 AGCAAGAGTCTTACGACGCA 59.403 50.000 4.74 0.00 44.93 5.24
1087 1130 2.433446 CACCCTTGCTCTGCCAGT 59.567 61.111 0.00 0.00 0.00 4.00
1162 1205 4.617530 CGTGATGTCTTCTCCGTCCTTAAA 60.618 45.833 0.00 0.00 0.00 1.52
1461 1515 2.037620 GCCATGCAACCCAACCACAA 62.038 55.000 0.00 0.00 0.00 3.33
1600 1654 2.224572 ACAGTAGCTCGTCTATCCGGAT 60.225 50.000 22.95 22.95 0.00 4.18
1664 1718 4.402155 ACATTGTGAAGCTTTGTTTCCTGA 59.598 37.500 0.00 0.00 0.00 3.86
1938 1992 1.330655 TTGGGCGGTTTTTGGCTGAA 61.331 50.000 0.00 0.00 0.00 3.02
2211 2266 3.986817 TCAGATAGAGAGGATGAGAGGGT 59.013 47.826 0.00 0.00 0.00 4.34
2219 2274 4.088634 GGCAGTGATCAGATAGAGAGGAT 58.911 47.826 0.00 0.00 0.00 3.24
2231 2286 0.251354 GGAGAAGCAGGCAGTGATCA 59.749 55.000 0.00 0.00 0.00 2.92
2242 2297 0.174389 GTCATCTGCGAGGAGAAGCA 59.826 55.000 0.00 0.00 41.55 3.91


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

AutoCloner maintained by Alex Coulton.