Multiple sequence alignment - TraesCS2B01G146500

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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 TraesCS2B01G146500 chr2B 100.000 2573 0 0 1 2573 112836389 112838961 0.000000e+00 4752
1 TraesCS2B01G146500 chr2B 97.963 2062 41 1 1 2062 391081498 391079438 0.000000e+00 3574
2 TraesCS2B01G146500 chr2B 96.224 1960 53 5 616 2573 357737653 357735713 0.000000e+00 3190
3 TraesCS2B01G146500 chr2B 95.970 1588 59 4 3 1588 757862643 757861059 0.000000e+00 2573
4 TraesCS2B01G146500 chr2B 94.048 1596 89 3 979 2573 343651499 343653089 0.000000e+00 2416
5 TraesCS2B01G146500 chr2B 95.194 1290 61 1 303 1591 757797390 757796101 0.000000e+00 2037
6 TraesCS2B01G146500 chr2B 98.052 308 5 1 1 307 757813020 757812713 3.770000e-148 534
7 TraesCS2B01G146500 chr5A 98.330 2575 41 1 1 2573 19253496 19250922 0.000000e+00 4516
8 TraesCS2B01G146500 chr7B 98.214 2575 44 1 1 2573 716883428 716880854 0.000000e+00 4499
9 TraesCS2B01G146500 chr7B 98.213 2574 45 1 1 2573 716843187 716840614 0.000000e+00 4497
10 TraesCS2B01G146500 chr7B 98.212 2573 46 0 1 2573 742984797 742987369 0.000000e+00 4497
11 TraesCS2B01G146500 chr7A 97.981 2575 45 5 1 2573 120845799 120843230 0.000000e+00 4460
12 TraesCS2B01G146500 chr7A 97.903 2575 50 3 1 2573 60274667 60277239 0.000000e+00 4453


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 TraesCS2B01G146500 chr2B 112836389 112838961 2572 False 4752 4752 100.000 1 2573 1 chr2B.!!$F1 2572
1 TraesCS2B01G146500 chr2B 391079438 391081498 2060 True 3574 3574 97.963 1 2062 1 chr2B.!!$R2 2061
2 TraesCS2B01G146500 chr2B 357735713 357737653 1940 True 3190 3190 96.224 616 2573 1 chr2B.!!$R1 1957
3 TraesCS2B01G146500 chr2B 757861059 757862643 1584 True 2573 2573 95.970 3 1588 1 chr2B.!!$R5 1585
4 TraesCS2B01G146500 chr2B 343651499 343653089 1590 False 2416 2416 94.048 979 2573 1 chr2B.!!$F2 1594
5 TraesCS2B01G146500 chr2B 757796101 757797390 1289 True 2037 2037 95.194 303 1591 1 chr2B.!!$R3 1288
6 TraesCS2B01G146500 chr5A 19250922 19253496 2574 True 4516 4516 98.330 1 2573 1 chr5A.!!$R1 2572
7 TraesCS2B01G146500 chr7B 716880854 716883428 2574 True 4499 4499 98.214 1 2573 1 chr7B.!!$R2 2572
8 TraesCS2B01G146500 chr7B 716840614 716843187 2573 True 4497 4497 98.213 1 2573 1 chr7B.!!$R1 2572
9 TraesCS2B01G146500 chr7B 742984797 742987369 2572 False 4497 4497 98.212 1 2573 1 chr7B.!!$F1 2572
10 TraesCS2B01G146500 chr7A 120843230 120845799 2569 True 4460 4460 97.981 1 2573 1 chr7A.!!$R1 2572
11 TraesCS2B01G146500 chr7A 60274667 60277239 2572 False 4453 4453 97.903 1 2573 1 chr7A.!!$F1 2572

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
762 766 3.242641 GGTTTAGCGGATTCGGAATTGTC 60.243 47.826 4.47 0.0 36.79 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2112 2120 0.259647 CTTCCCCCTCATTGCCATCA 59.74 55.0 0.0 0.0 0.0 3.07 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
74 75 4.367039 ACCTGGTGCTTTGTATTGTAGT 57.633 40.909 0.00 0.0 0.00 2.73
91 92 5.284861 TGTAGTAACCTTGCTTGTTCTCA 57.715 39.130 0.00 0.0 0.00 3.27
265 266 6.062095 GGCAACCCTTTAGATATTGCTTAGA 58.938 40.000 7.15 0.0 44.03 2.10
274 275 9.418045 CTTTAGATATTGCTTAGAGTTAGGCTC 57.582 37.037 0.00 0.0 44.45 4.70
762 766 3.242641 GGTTTAGCGGATTCGGAATTGTC 60.243 47.826 4.47 0.0 36.79 3.18
1218 1225 6.211664 TCTCGAAAACGAAGATTTGAAGTC 57.788 37.500 0.00 0.0 31.10 3.01
1447 1455 7.321153 TCCATTACGAAAAGACTTTCCTCTAG 58.679 38.462 0.00 0.0 38.17 2.43
1487 1495 4.100035 ACGCTATGATGATCCAGAGAAACA 59.900 41.667 2.77 0.0 0.00 2.83
1566 1574 1.066143 CCTTGGGAACAGTGTAGCGAT 60.066 52.381 0.00 0.0 44.54 4.58
1598 1606 5.310068 TCCGAATCTACATAGGTCTAGTCCT 59.690 44.000 13.30 13.3 41.20 3.85
1830 1838 6.703607 CGGTTTCATTGATAGCAGAAGAGTAT 59.296 38.462 7.02 0.0 0.00 2.12
1891 1899 2.561569 CCCTACGGAAACTATTGCCTG 58.438 52.381 0.00 0.0 0.00 4.85
1894 1902 2.851263 ACGGAAACTATTGCCTGTGA 57.149 45.000 0.00 0.0 0.00 3.58
1937 1945 6.729100 TCAGTAGAAGGGAAGAAAAGATGGTA 59.271 38.462 0.00 0.0 0.00 3.25
1950 1958 7.756614 AGAAAAGATGGTAACTCCTTTTAGGT 58.243 34.615 9.57 0.0 43.57 3.08
2112 2120 3.483869 GAGCTGGGGAAGGCCGAT 61.484 66.667 0.00 0.0 33.83 4.18
2335 2343 3.547787 AAGGGGAGAGTGGCCGAGT 62.548 63.158 0.00 0.0 0.00 4.18
2377 2385 9.574516 ACTGTAAATCTGTTGAAGGTTTTCTAT 57.425 29.630 0.00 0.0 39.93 1.98
2386 2394 7.284074 TGTTGAAGGTTTTCTATGTAGGTTCA 58.716 34.615 0.00 0.0 34.31 3.18
2502 2513 3.625313 TGTCGTGAAGTGCAATTTTCTCA 59.375 39.130 0.00 0.0 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
74 75 5.865085 ACTGTATGAGAACAAGCAAGGTTA 58.135 37.500 0.00 0.00 0.00 2.85
691 695 9.142014 ACAGAGCATTAGTACTTATTCTGATCT 57.858 33.333 21.77 11.37 35.84 2.75
762 766 0.038744 AGAACCCAGGATGCTTGGTG 59.961 55.000 10.94 1.33 33.73 4.17
1218 1225 5.913514 CCGAGTACTCAGTAAATTATGGACG 59.086 44.000 22.37 3.34 0.00 4.79
1447 1455 2.102588 AGCGTACTTCCACATATCCACC 59.897 50.000 0.00 0.00 0.00 4.61
1566 1574 7.674348 AGACCTATGTAGATTCGGAATTATCCA 59.326 37.037 4.47 0.99 46.97 3.41
1598 1606 4.405358 GCATTTCCTATTGATTTGTCCCCA 59.595 41.667 0.00 0.00 0.00 4.96
1937 1945 3.262405 TCGCCATGTACCTAAAAGGAGTT 59.738 43.478 0.00 0.00 37.67 3.01
1950 1958 2.223641 CGTAAGTAAGGCTCGCCATGTA 60.224 50.000 11.02 0.00 38.92 2.29
2042 2050 3.095347 GCGGAGGAAAGGAGGCGAT 62.095 63.158 0.00 0.00 0.00 4.58
2112 2120 0.259647 CTTCCCCCTCATTGCCATCA 59.740 55.000 0.00 0.00 0.00 3.07
2335 2343 1.134521 ACAGTCTGTCGCTTTTGACCA 60.135 47.619 0.00 0.00 38.11 4.02
2377 2385 2.912956 AGAGGCAGGATTTGAACCTACA 59.087 45.455 0.00 0.00 35.84 2.74
2386 2394 1.005215 CAAGTGGGAGAGGCAGGATTT 59.995 52.381 0.00 0.00 0.00 2.17
2482 2493 6.545508 CATATGAGAAAATTGCACTTCACGA 58.454 36.000 0.00 0.00 0.00 4.35
2502 2513 4.804139 CGACAACCTCTCTAAAACGCATAT 59.196 41.667 0.00 0.00 0.00 1.78


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

AutoCloner maintained by Alex Coulton.