Multiple sequence alignment - TraesCS5D01G164900

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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 TraesCS5D01G164900 chr5D 100.000 2421 0 0 1 2421 256499959 256497539 0 4471
1 TraesCS5D01G164900 chr6D 94.515 2425 122 10 1 2421 200593775 200596192 0 3731
2 TraesCS5D01G164900 chr7A 94.021 2425 129 13 1 2421 412882626 412880214 0 3661
3 TraesCS5D01G164900 chr2D 93.740 2428 132 17 1 2421 377095374 377097788 0 3624
4 TraesCS5D01G164900 chr2D 93.449 2427 140 15 1 2421 72328162 72325749 0 3583
5 TraesCS5D01G164900 chr2D 92.478 2433 135 27 1 2421 70682664 70680268 0 3435
6 TraesCS5D01G164900 chr2D 95.792 713 28 2 1 711 159831110 159831822 0 1149
7 TraesCS5D01G164900 chr2B 92.875 2428 149 18 1 2421 109029282 109026872 0 3504
8 TraesCS5D01G164900 chr1A 91.010 2436 184 27 1 2421 298162829 298165244 0 3253
9 TraesCS5D01G164900 chr2A 92.392 1906 114 20 259 2157 529894340 529896221 0 2687
10 TraesCS5D01G164900 chr3D 93.070 1746 100 15 681 2421 484787211 484788940 0 2534


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 TraesCS5D01G164900 chr5D 256497539 256499959 2420 True 4471 4471 100.000 1 2421 1 chr5D.!!$R1 2420
1 TraesCS5D01G164900 chr6D 200593775 200596192 2417 False 3731 3731 94.515 1 2421 1 chr6D.!!$F1 2420
2 TraesCS5D01G164900 chr7A 412880214 412882626 2412 True 3661 3661 94.021 1 2421 1 chr7A.!!$R1 2420
3 TraesCS5D01G164900 chr2D 377095374 377097788 2414 False 3624 3624 93.740 1 2421 1 chr2D.!!$F2 2420
4 TraesCS5D01G164900 chr2D 72325749 72328162 2413 True 3583 3583 93.449 1 2421 1 chr2D.!!$R2 2420
5 TraesCS5D01G164900 chr2D 70680268 70682664 2396 True 3435 3435 92.478 1 2421 1 chr2D.!!$R1 2420
6 TraesCS5D01G164900 chr2D 159831110 159831822 712 False 1149 1149 95.792 1 711 1 chr2D.!!$F1 710
7 TraesCS5D01G164900 chr2B 109026872 109029282 2410 True 3504 3504 92.875 1 2421 1 chr2B.!!$R1 2420
8 TraesCS5D01G164900 chr1A 298162829 298165244 2415 False 3253 3253 91.010 1 2421 1 chr1A.!!$F1 2420
9 TraesCS5D01G164900 chr2A 529894340 529896221 1881 False 2687 2687 92.392 259 2157 1 chr2A.!!$F1 1898
10 TraesCS5D01G164900 chr3D 484787211 484788940 1729 False 2534 2534 93.070 681 2421 1 chr3D.!!$F1 1740

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
854 864 1.065647 TAAACATTCCCCGTGGGTGA 58.934 50.0 3.83 0.0 44.74 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1990 2026 2.098215 CGATCACGTGCAAAAACACA 57.902 45.0 11.67 0.0 40.73 3.72 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
76 77 2.558380 GAAGTGCCACCCCTGGATCC 62.558 65.000 4.20 4.20 40.55 3.36
93 94 2.743928 CGTGAGGCAGAACAGGGC 60.744 66.667 0.00 0.00 0.00 5.19
256 257 2.647299 ACACCACATAACCCCTCATTCA 59.353 45.455 0.00 0.00 0.00 2.57
260 261 4.538490 ACCACATAACCCCTCATTCACTTA 59.462 41.667 0.00 0.00 0.00 2.24
289 291 9.253832 TCTGATATTTTTCCTTTGCTATTCCAA 57.746 29.630 0.00 0.00 0.00 3.53
658 664 7.823745 AATATGTGAGTGTTCCTTCTTGTTT 57.176 32.000 0.00 0.00 0.00 2.83
769 775 4.178545 GCAACTTATGTGGCAACTTCAT 57.821 40.909 3.29 0.00 42.54 2.57
771 777 4.622740 GCAACTTATGTGGCAACTTCATTC 59.377 41.667 3.29 0.00 42.54 2.67
828 836 7.946207 TGGCAACTTCTTTTAATTACACATGA 58.054 30.769 0.00 0.00 37.61 3.07
829 837 8.417106 TGGCAACTTCTTTTAATTACACATGAA 58.583 29.630 0.00 0.00 37.61 2.57
830 838 8.699749 GGCAACTTCTTTTAATTACACATGAAC 58.300 33.333 0.00 0.00 0.00 3.18
854 864 1.065647 TAAACATTCCCCGTGGGTGA 58.934 50.000 3.83 0.00 44.74 4.02
896 906 4.377431 GCTTTGTCGTTCATGTACCTCTTG 60.377 45.833 0.00 0.00 0.00 3.02
987 1000 9.890629 AACTCTGCTTTTTCTTTCCTTTATTTT 57.109 25.926 0.00 0.00 0.00 1.82
1037 1050 0.536006 GAGCTTGCACCAGACAACCT 60.536 55.000 0.00 0.00 0.00 3.50
1040 1053 1.813513 CTTGCACCAGACAACCTAGG 58.186 55.000 7.41 7.41 0.00 3.02
1264 1277 1.725164 CTACGAAGCAAGGAAACCGAC 59.275 52.381 0.00 0.00 0.00 4.79
1333 1355 4.515191 TGTCACCTCTGCATTGAAGTTTAC 59.485 41.667 0.00 0.00 0.00 2.01
1412 1437 4.453136 GCTTTCACACGTTGGAATACCTTA 59.547 41.667 0.00 0.00 37.04 2.69
1420 1445 5.613329 ACGTTGGAATACCTTACAAAGTGA 58.387 37.500 1.85 0.00 43.50 3.41
1432 1457 1.679680 ACAAAGTGAGAAGGTCGACGA 59.320 47.619 9.92 0.00 0.00 4.20
1448 1473 1.658114 CGAGTCCCTGTCGTCACAA 59.342 57.895 0.00 0.00 32.62 3.33
1477 1502 2.093783 GGTCGTCAAGCTCCGTAAAATG 59.906 50.000 0.00 0.00 0.00 2.32
1527 1552 3.943034 CAACACGCGGGCAAACGA 61.943 61.111 9.12 0.00 35.47 3.85
1567 1592 2.235898 AGCTGTGAAAAAGGCCAACAAA 59.764 40.909 5.01 0.00 0.00 2.83
1601 1626 2.302952 CGTGATGCTCCATACCGCG 61.303 63.158 0.00 0.00 0.00 6.46
1977 2012 7.201974 GGTTAGCATGGTAGGTAGTTCATAAGA 60.202 40.741 4.57 0.00 0.00 2.10
1990 2026 7.387122 GGTAGTTCATAAGAAAACCGTTCTCTT 59.613 37.037 5.23 5.23 34.35 2.85
2028 2067 6.627671 GTGATCGTTTCAACTAGTTTGTTCAC 59.372 38.462 5.07 10.09 35.70 3.18
2029 2068 5.133707 TCGTTTCAACTAGTTTGTTCACG 57.866 39.130 5.07 10.21 36.49 4.35
2193 2235 5.824429 AGTCATTCATACATGGCATTTTCG 58.176 37.500 0.00 0.00 30.53 3.46
2399 2445 0.521735 GACGCCCTTTTGTGATGGAC 59.478 55.000 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 77 2.743928 GCCCTGTTCTGCCTCACG 60.744 66.667 0.00 0.00 0.00 4.35
93 94 3.345808 CGGGTGGTGCGTGAACTG 61.346 66.667 0.00 0.00 0.00 3.16
256 257 9.692325 AGCAAAGGAAAAATATCAGAGATAAGT 57.308 29.630 0.00 0.00 0.00 2.24
676 682 5.476599 AGCATGGCTACTGACAAAACATAAA 59.523 36.000 0.00 0.00 36.99 1.40
769 775 7.872113 AAACAAAGTTGCCCAATATTTTGAA 57.128 28.000 15.76 0.00 34.60 2.69
828 836 4.888917 CCACGGGGAATGTTTATTTTGTT 58.111 39.130 0.00 0.00 35.59 2.83
829 837 4.529109 CCACGGGGAATGTTTATTTTGT 57.471 40.909 0.00 0.00 35.59 2.83
987 1000 2.554344 GGGGAACATGACCTGCAAGTAA 60.554 50.000 0.00 0.00 0.00 2.24
1287 1300 5.520748 AAGGTTTAGGATTGATGTGGAGT 57.479 39.130 0.00 0.00 0.00 3.85
1333 1355 6.848296 GTGAACTCAAGAGAACAGAAAAATCG 59.152 38.462 3.73 0.00 0.00 3.34
1412 1437 1.679680 TCGTCGACCTTCTCACTTTGT 59.320 47.619 10.58 0.00 0.00 2.83
1420 1445 0.961358 CAGGGACTCGTCGACCTTCT 60.961 60.000 10.58 0.00 34.60 2.85
1432 1457 0.389391 CAGTTGTGACGACAGGGACT 59.611 55.000 5.65 0.00 43.88 3.85
1448 1473 0.250467 AGCTTGACGACCATTGCAGT 60.250 50.000 0.00 0.00 0.00 4.40
1477 1502 4.323417 TCATCAACCAGTTCCATGTGTAC 58.677 43.478 0.00 0.00 0.00 2.90
1527 1552 4.020543 AGCTTCCTCTATGAACTCTCGTT 58.979 43.478 0.00 0.00 35.68 3.85
1567 1592 4.152402 GCATCACGTGATCACTTGTACTTT 59.848 41.667 27.79 0.39 33.02 2.66
1601 1626 3.564225 GCCACATAATGTAAGGTAGGCAC 59.436 47.826 0.00 0.00 39.35 5.01
1977 2012 4.387559 GCAAAAACACAAGAGAACGGTTTT 59.612 37.500 0.00 0.00 41.79 2.43
1990 2026 2.098215 CGATCACGTGCAAAAACACA 57.902 45.000 11.67 0.00 40.73 3.72
2028 2067 8.272866 CACACATATTGTATTGTACACATACCG 58.727 37.037 17.82 9.25 38.63 4.02
2029 2068 8.556194 CCACACATATTGTATTGTACACATACC 58.444 37.037 17.82 7.54 38.63 2.73
2193 2235 4.278170 TGTTGGTGGACATCAGAATTTGAC 59.722 41.667 0.00 0.00 38.99 3.18
2318 2364 5.349543 AGCAAAGCACAAGAAAACAAAGAAG 59.650 36.000 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.