Multiple sequence alignment - TraesCS3A01G068400

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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 TraesCS3A01G068400 chr3A 100.000 2421 0 0 1 2421 40979127 40976707 0.000000e+00 4471.0
1 TraesCS3A01G068400 chr3A 98.212 1622 26 3 1 1620 500029420 500031040 0.000000e+00 2832.0
2 TraesCS3A01G068400 chr3A 97.519 806 19 1 1616 2421 500038670 500039474 0.000000e+00 1376.0
3 TraesCS3A01G068400 chr5D 98.061 2424 43 3 1 2421 545193077 545195499 0.000000e+00 4213.0
4 TraesCS3A01G068400 chr4D 97.937 2424 45 5 1 2421 400125093 400127514 0.000000e+00 4194.0
5 TraesCS3A01G068400 chr4D 100.000 41 0 0 1406 1446 400126539 400126579 2.580000e-10 76.8
6 TraesCS3A01G068400 chr6D 97.730 2423 51 4 1 2421 348875 346455 0.000000e+00 4167.0
7 TraesCS3A01G068400 chr6D 100.000 41 0 0 1406 1446 347430 347390 2.580000e-10 76.8
8 TraesCS3A01G068400 chr1A 97.567 2425 42 5 1 2421 45391982 45394393 0.000000e+00 4135.0
9 TraesCS3A01G068400 chrUn 97.684 2375 50 3 1 2371 43102356 43099983 0.000000e+00 4076.0
10 TraesCS3A01G068400 chr4A 96.145 1686 64 1 737 2421 507108534 507106849 0.000000e+00 2752.0


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 TraesCS3A01G068400 chr3A 40976707 40979127 2420 True 4471.0 4471 100.0000 1 2421 1 chr3A.!!$R1 2420
1 TraesCS3A01G068400 chr3A 500029420 500031040 1620 False 2832.0 2832 98.2120 1 1620 1 chr3A.!!$F1 1619
2 TraesCS3A01G068400 chr3A 500038670 500039474 804 False 1376.0 1376 97.5190 1616 2421 1 chr3A.!!$F2 805
3 TraesCS3A01G068400 chr5D 545193077 545195499 2422 False 4213.0 4213 98.0610 1 2421 1 chr5D.!!$F1 2420
4 TraesCS3A01G068400 chr4D 400125093 400127514 2421 False 2135.4 4194 98.9685 1 2421 2 chr4D.!!$F1 2420
5 TraesCS3A01G068400 chr6D 346455 348875 2420 True 2121.9 4167 98.8650 1 2421 2 chr6D.!!$R1 2420
6 TraesCS3A01G068400 chr1A 45391982 45394393 2411 False 4135.0 4135 97.5670 1 2421 1 chr1A.!!$F1 2420
7 TraesCS3A01G068400 chrUn 43099983 43102356 2373 True 4076.0 4076 97.6840 1 2371 1 chrUn.!!$R1 2370
8 TraesCS3A01G068400 chr4A 507106849 507108534 1685 True 2752.0 2752 96.1450 737 2421 1 chr4A.!!$R1 1684

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
413 414 2.39659 ACAAATACCCAGCCACTACG 57.603 50.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2318 2323 1.204704 CCTGATGTGCGTCTTCCTGTA 59.795 52.381 0.0 0.0 0.0 2.74 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
197 198 4.830600 TGCATGCAGGAATTGATACATCAT 59.169 37.500 18.46 0.0 36.56 2.45
391 392 6.073327 TCTCATAGGAGCGTACTAACAATG 57.927 41.667 0.00 0.0 41.13 2.82
413 414 2.396590 ACAAATACCCAGCCACTACG 57.603 50.000 0.00 0.0 0.00 3.51
525 529 4.699735 ACCATCATTGCGTACAAGAATCAA 59.300 37.500 0.00 0.0 39.69 2.57
533 537 3.372206 GCGTACAAGAATCAACAGAGCAT 59.628 43.478 0.00 0.0 0.00 3.79
952 956 4.681074 TTTTCCAAAACATTGGGAGGTC 57.319 40.909 7.69 0.0 42.32 3.85
971 975 4.351407 AGGTCCTATCGGAGAGAACTATCA 59.649 45.833 0.23 0.0 43.63 2.15
987 991 9.499479 GAGAACTATCATATGTTTGTGGATGAT 57.501 33.333 1.90 0.0 40.99 2.45
1128 1132 4.847198 TCAGCATTTTTCATAGCCTCTCA 58.153 39.130 0.00 0.0 0.00 3.27
1272 1276 2.468831 GCGGTCAACTTTGCATTCAAA 58.531 42.857 0.00 0.0 39.67 2.69
1504 1508 5.126067 GCCTCTCATTATATTGTGTGTGGT 58.874 41.667 9.76 0.0 0.00 4.16
1652 1657 4.276431 TGTACGGTCAAATTTCAAGGTTCC 59.724 41.667 0.00 0.0 0.00 3.62
1695 1700 2.475155 TGTAGAGGGACGAGGAGACTA 58.525 52.381 0.00 0.0 44.43 2.59
1773 1778 9.381033 GATCATGGTCTAATGAAGAATCATAGG 57.619 37.037 0.00 0.0 45.60 2.57
2318 2323 4.225942 TGTTGAGCAGATATTGGGAACTCT 59.774 41.667 0.00 0.0 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
197 198 4.665009 AGTTGGAGCCCCATTCAGATAATA 59.335 41.667 0.00 0.00 43.12 0.98
341 342 6.405397 GGTTTTGGTCACAAGAGCTAGAAAAA 60.405 38.462 0.00 0.00 42.66 1.94
391 392 4.056050 CGTAGTGGCTGGGTATTTGTATC 58.944 47.826 0.00 0.00 0.00 2.24
413 414 3.869065 TGTACCCATGCTAGCTACAAAC 58.131 45.455 17.23 7.86 0.00 2.93
525 529 4.005650 CTGATGTTGGTTGTATGCTCTGT 58.994 43.478 0.00 0.00 0.00 3.41
533 537 5.235850 ACATGTACCTGATGTTGGTTGTA 57.764 39.130 5.05 0.00 38.88 2.41
971 975 4.646040 CCACCACATCATCCACAAACATAT 59.354 41.667 0.00 0.00 0.00 1.78
987 991 4.537751 TCCTTTTCATGTAAACCACCACA 58.462 39.130 0.00 0.00 0.00 4.17
1272 1276 7.050377 AGCATCAGTACTGTATGCTTTGTATT 58.950 34.615 33.63 21.61 44.25 1.89
1504 1508 4.365723 CGTATTTTTCGGCTAAGCTCCTA 58.634 43.478 0.00 0.00 0.00 2.94
1555 1560 6.074994 CGAGTACGATTTTGAACCAGCTATAC 60.075 42.308 0.00 0.00 42.66 1.47
1695 1700 6.272558 AGTTGTAGAATAGTTGGTTCCTTCCT 59.727 38.462 0.00 0.00 0.00 3.36
1770 1775 7.759489 AAATGTTTCTCACATAAACAGCCTA 57.241 32.000 7.38 0.00 46.23 3.93
1773 1778 7.928908 TGAAAATGTTTCTCACATAAACAGC 57.071 32.000 7.38 0.00 46.23 4.40
2000 2005 3.470709 CCACGAGGCTTCAATGATGTAT 58.529 45.455 0.00 0.00 0.00 2.29
2318 2323 1.204704 CCTGATGTGCGTCTTCCTGTA 59.795 52.381 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.