Multiple sequence alignment - TraesCS5B01G027000

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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 TraesCS5B01G027000 chr5B 100.000 2549 0 0 1 2549 26059946 26057398 0 4708
1 TraesCS5B01G027000 chr2D 96.125 1987 68 6 569 2549 64508698 64510681 0 3234
2 TraesCS5B01G027000 chr2D 94.025 569 28 2 1 568 52713958 52713395 0 857
3 TraesCS5B01G027000 chr2D 93.170 571 31 6 1 568 507252799 507253364 0 832
4 TraesCS5B01G027000 chr2D 92.970 569 34 3 1 568 600834297 600833734 0 824
5 TraesCS5B01G027000 chr2B 95.368 1986 74 11 568 2548 546410285 546412257 0 3142
6 TraesCS5B01G027000 chrUn 95.178 1991 83 6 569 2549 60558711 60560698 0 3133
7 TraesCS5B01G027000 chr3B 94.869 1988 86 9 569 2549 53523443 53525421 0 3092
8 TraesCS5B01G027000 chr3B 94.724 1990 95 8 567 2549 687040064 687042050 0 3085
9 TraesCS5B01G027000 chr3B 94.257 1985 103 6 568 2549 804661031 804663007 0 3024
10 TraesCS5B01G027000 chr1B 94.584 1994 96 6 564 2549 542264934 542266923 0 3073
11 TraesCS5B01G027000 chr4B 94.144 1998 107 7 558 2549 645967807 645965814 0 3033
12 TraesCS5B01G027000 chr4B 94.147 1982 108 4 567 2547 585994907 585996881 0 3011
13 TraesCS5B01G027000 chr4B 92.982 570 33 3 1 569 297817655 297817092 0 824
14 TraesCS5B01G027000 chr6D 93.750 560 30 1 1 560 185385139 185385693 0 835
15 TraesCS5B01G027000 chr3D 93.761 561 28 3 1 560 486531357 486531911 0 835
16 TraesCS5B01G027000 chr7D 93.594 562 29 5 1 560 222918304 222918860 0 832
17 TraesCS5B01G027000 chr4D 93.728 558 29 4 1 557 443496676 443497228 0 832
18 TraesCS5B01G027000 chr1D 93.158 570 32 3 1 568 255259313 255259877 0 830


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 TraesCS5B01G027000 chr5B 26057398 26059946 2548 True 4708 4708 100.000 1 2549 1 chr5B.!!$R1 2548
1 TraesCS5B01G027000 chr2D 64508698 64510681 1983 False 3234 3234 96.125 569 2549 1 chr2D.!!$F1 1980
2 TraesCS5B01G027000 chr2D 52713395 52713958 563 True 857 857 94.025 1 568 1 chr2D.!!$R1 567
3 TraesCS5B01G027000 chr2D 507252799 507253364 565 False 832 832 93.170 1 568 1 chr2D.!!$F2 567
4 TraesCS5B01G027000 chr2D 600833734 600834297 563 True 824 824 92.970 1 568 1 chr2D.!!$R2 567
5 TraesCS5B01G027000 chr2B 546410285 546412257 1972 False 3142 3142 95.368 568 2548 1 chr2B.!!$F1 1980
6 TraesCS5B01G027000 chrUn 60558711 60560698 1987 False 3133 3133 95.178 569 2549 1 chrUn.!!$F1 1980
7 TraesCS5B01G027000 chr3B 53523443 53525421 1978 False 3092 3092 94.869 569 2549 1 chr3B.!!$F1 1980
8 TraesCS5B01G027000 chr3B 687040064 687042050 1986 False 3085 3085 94.724 567 2549 1 chr3B.!!$F2 1982
9 TraesCS5B01G027000 chr3B 804661031 804663007 1976 False 3024 3024 94.257 568 2549 1 chr3B.!!$F3 1981
10 TraesCS5B01G027000 chr1B 542264934 542266923 1989 False 3073 3073 94.584 564 2549 1 chr1B.!!$F1 1985
11 TraesCS5B01G027000 chr4B 645965814 645967807 1993 True 3033 3033 94.144 558 2549 1 chr4B.!!$R2 1991
12 TraesCS5B01G027000 chr4B 585994907 585996881 1974 False 3011 3011 94.147 567 2547 1 chr4B.!!$F1 1980
13 TraesCS5B01G027000 chr4B 297817092 297817655 563 True 824 824 92.982 1 569 1 chr4B.!!$R1 568
14 TraesCS5B01G027000 chr6D 185385139 185385693 554 False 835 835 93.750 1 560 1 chr6D.!!$F1 559
15 TraesCS5B01G027000 chr3D 486531357 486531911 554 False 835 835 93.761 1 560 1 chr3D.!!$F1 559
16 TraesCS5B01G027000 chr7D 222918304 222918860 556 False 832 832 93.594 1 560 1 chr7D.!!$F1 559
17 TraesCS5B01G027000 chr4D 443496676 443497228 552 False 832 832 93.728 1 557 1 chr4D.!!$F1 556
18 TraesCS5B01G027000 chr1D 255259313 255259877 564 False 830 830 93.158 1 568 1 chr1D.!!$F1 567

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
813 818 1.407258 GAGAGCCGTTGAGCATAGAGT 59.593 52.381 0.0 0.0 34.23 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2050 2069 1.881973 TGTCAAACTCTTGCCATCTGC 59.118 47.619 0.0 0.0 41.77 4.26 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
135 136 6.489603 TGGAGAACCCAAGCTTATGAAAATA 58.510 36.000 0.00 0.00 43.29 1.40
241 244 9.607988 TCTTTGTACAACTCTTGTTTCAGATTA 57.392 29.630 8.07 0.00 42.22 1.75
474 477 3.743521 TCCAGAACACTCCAGAATTGTG 58.256 45.455 0.00 0.00 37.67 3.33
475 478 2.816087 CCAGAACACTCCAGAATTGTGG 59.184 50.000 15.46 15.46 39.19 4.17
476 479 3.496692 CCAGAACACTCCAGAATTGTGGA 60.497 47.826 22.08 22.08 44.82 4.02
477 480 4.136796 CAGAACACTCCAGAATTGTGGAA 58.863 43.478 23.38 9.19 46.29 3.53
478 481 4.580167 CAGAACACTCCAGAATTGTGGAAA 59.420 41.667 23.38 4.43 46.29 3.13
516 519 4.411327 CGTGATACGGTAAGTAAACGGAA 58.589 43.478 0.00 0.00 41.62 4.30
616 621 3.141398 GTGTCCATCTGCTCAGTTTTGA 58.859 45.455 0.00 0.00 0.00 2.69
760 765 3.096092 AGAGGCGGCCAATTTTATTCAA 58.904 40.909 23.09 0.00 0.00 2.69
813 818 1.407258 GAGAGCCGTTGAGCATAGAGT 59.593 52.381 0.00 0.00 34.23 3.24
819 824 2.596452 CGTTGAGCATAGAGTCGTTGT 58.404 47.619 0.00 0.00 0.00 3.32
1175 1185 3.716872 GAGAATGGGGTAAGAATCAGGGA 59.283 47.826 0.00 0.00 0.00 4.20
1214 1224 3.055891 TGGTCGAGATCTTTGAGCAATCA 60.056 43.478 21.42 5.48 43.09 2.57
1437 1449 5.352846 GCTTAGGATGTTGAAGAAGAAGGTC 59.647 44.000 0.00 0.00 0.00 3.85
1520 1532 1.750193 ATGGTAATCGCACTGGTTGG 58.250 50.000 0.00 0.00 0.00 3.77
1665 1680 9.965902 AGAAGAAGTGACCAACATTTAGATATT 57.034 29.630 0.00 0.00 0.00 1.28
1719 1737 9.820725 TTCAGAAACTTTTGATCAATGAAATGT 57.179 25.926 9.40 0.00 0.00 2.71
1904 1922 6.099341 CACCTAGTGCCAAAATAAATGAACC 58.901 40.000 0.00 0.00 0.00 3.62
2050 2069 2.106332 CGCTGGTAACCGCTAGGG 59.894 66.667 0.00 0.00 43.47 3.53
2256 2282 4.139038 GGTTAGAGTGGCACTTGGTTTAA 58.861 43.478 22.98 12.25 0.00 1.52
2406 2440 4.021456 TCGAGCTTCATGACTTGGTTTAGA 60.021 41.667 0.00 0.00 0.00 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
639 644 0.679960 GCACGGACTAGGGGCAAAAT 60.680 55.000 0.00 0.0 0.00 1.82
813 818 3.620427 AATATAGCACACCCACAACGA 57.380 42.857 0.00 0.0 0.00 3.85
1198 1208 6.416415 AGATCAACTGATTGCTCAAAGATCT 58.584 36.000 0.00 0.0 37.89 2.75
1214 1224 4.319766 GCATGAACACGAAACAGATCAACT 60.320 41.667 0.00 0.0 0.00 3.16
1226 1236 0.105778 TGTCACCTGCATGAACACGA 59.894 50.000 0.00 0.0 0.00 4.35
1356 1368 0.826715 CCATCTCTTCTTCCGGAGCA 59.173 55.000 3.34 0.0 0.00 4.26
1520 1532 6.873076 TGCCTTTCCATACATTTTCAACATTC 59.127 34.615 0.00 0.0 0.00 2.67
1637 1650 8.697507 ATCTAAATGTTGGTCACTTCTTCTTT 57.302 30.769 0.00 0.0 0.00 2.52
1638 1651 9.965902 ATATCTAAATGTTGGTCACTTCTTCTT 57.034 29.630 0.00 0.0 0.00 2.52
1673 1689 7.465116 TCTGAATTCCTCATTTCTTCTCCTTT 58.535 34.615 2.27 0.0 32.14 3.11
1719 1737 7.078249 TGGCTCTGGAATAATTCATTAGCTA 57.922 36.000 0.00 0.0 32.75 3.32
1946 1964 3.454082 TGCACTTTCCACCCTTCATTTTT 59.546 39.130 0.00 0.0 0.00 1.94
2050 2069 1.881973 TGTCAAACTCTTGCCATCTGC 59.118 47.619 0.00 0.0 41.77 4.26
2256 2282 3.508845 AACCAAGTGCCACTCTAACAT 57.491 42.857 0.00 0.0 0.00 2.71


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

AutoCloner maintained by Alex Coulton.