Multiple sequence alignment - TraesCS2B01G089200

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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 TraesCS2B01G089200 chr2B 100.000 2993 0 0 1 2993 50388681 50385689 0.000000e+00 5528
1 TraesCS2B01G089200 chr2B 90.674 2434 155 28 1 2402 797508080 797505687 0.000000e+00 3171
2 TraesCS2B01G089200 chr6B 95.658 3017 101 12 1 2993 616551288 616554298 0.000000e+00 4819
3 TraesCS2B01G089200 chr6B 95.625 3017 101 14 1 2993 258480959 258483968 0.000000e+00 4811
4 TraesCS2B01G089200 chr6B 95.435 3023 102 11 1 2993 526753578 526750562 0.000000e+00 4785
5 TraesCS2B01G089200 chr4B 95.593 3018 101 6 1 2993 327358609 327355599 0.000000e+00 4807
6 TraesCS2B01G089200 chr4B 94.498 3017 107 10 1 2993 402846983 402849964 0.000000e+00 4597
7 TraesCS2B01G089200 chr4B 95.842 962 39 1 1 961 500066763 500065802 0.000000e+00 1554
8 TraesCS2B01G089200 chr7B 93.792 2996 151 12 1 2993 81919849 81916886 0.000000e+00 4470
9 TraesCS2B01G089200 chr7B 95.850 2241 83 9 756 2993 111355893 111353660 0.000000e+00 3615
10 TraesCS2B01G089200 chr5B 95.874 2133 66 2 1 2132 450552114 450550003 0.000000e+00 3432
11 TraesCS2B01G089200 chr5A 90.428 2173 180 21 825 2993 538779669 538781817 0.000000e+00 2835
12 TraesCS2B01G089200 chr5A 85.340 382 49 4 1 381 700591239 700590864 3.620000e-104 388
13 TraesCS2B01G089200 chr5A 84.514 381 53 5 2 380 378599634 378600010 3.640000e-99 372
14 TraesCS2B01G089200 chr6A 90.395 2176 179 22 825 2993 60184449 60182297 0.000000e+00 2833
15 TraesCS2B01G089200 chr3B 90.244 2173 186 20 825 2993 706226450 706228600 0.000000e+00 2815


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 TraesCS2B01G089200 chr2B 50385689 50388681 2992 True 5528 5528 100.000 1 2993 1 chr2B.!!$R1 2992
1 TraesCS2B01G089200 chr2B 797505687 797508080 2393 True 3171 3171 90.674 1 2402 1 chr2B.!!$R2 2401
2 TraesCS2B01G089200 chr6B 616551288 616554298 3010 False 4819 4819 95.658 1 2993 1 chr6B.!!$F2 2992
3 TraesCS2B01G089200 chr6B 258480959 258483968 3009 False 4811 4811 95.625 1 2993 1 chr6B.!!$F1 2992
4 TraesCS2B01G089200 chr6B 526750562 526753578 3016 True 4785 4785 95.435 1 2993 1 chr6B.!!$R1 2992
5 TraesCS2B01G089200 chr4B 327355599 327358609 3010 True 4807 4807 95.593 1 2993 1 chr4B.!!$R1 2992
6 TraesCS2B01G089200 chr4B 402846983 402849964 2981 False 4597 4597 94.498 1 2993 1 chr4B.!!$F1 2992
7 TraesCS2B01G089200 chr4B 500065802 500066763 961 True 1554 1554 95.842 1 961 1 chr4B.!!$R2 960
8 TraesCS2B01G089200 chr7B 81916886 81919849 2963 True 4470 4470 93.792 1 2993 1 chr7B.!!$R1 2992
9 TraesCS2B01G089200 chr7B 111353660 111355893 2233 True 3615 3615 95.850 756 2993 1 chr7B.!!$R2 2237
10 TraesCS2B01G089200 chr5B 450550003 450552114 2111 True 3432 3432 95.874 1 2132 1 chr5B.!!$R1 2131
11 TraesCS2B01G089200 chr5A 538779669 538781817 2148 False 2835 2835 90.428 825 2993 1 chr5A.!!$F2 2168
12 TraesCS2B01G089200 chr6A 60182297 60184449 2152 True 2833 2833 90.395 825 2993 1 chr6A.!!$R1 2168
13 TraesCS2B01G089200 chr3B 706226450 706228600 2150 False 2815 2815 90.244 825 2993 1 chr3B.!!$F1 2168

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
27 28 0.178068 GCCTGTGGGAGAAGCGAATA 59.822 55.0 0.0 0.0 33.58 1.75 F
800 810 0.607489 ACTCCAGTTGCCATGTCTGC 60.607 55.0 0.0 0.0 0.00 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1220 1347 1.266718 GTTCGAACTTGCAGCATTGGA 59.733 47.619 20.97 0.0 0.0 3.53 R
2289 2454 0.392461 ATCGCCCACAACGCACTATT 60.392 50.000 0.00 0.0 0.0 1.73 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
27 28 0.178068 GCCTGTGGGAGAAGCGAATA 59.822 55.000 0.00 0.00 33.58 1.75
38 39 2.700897 AGAAGCGAATATACTGGGTGCT 59.299 45.455 0.00 0.00 0.00 4.40
82 83 2.551270 TCCCCTTTCTGCAGACTACAT 58.449 47.619 18.03 0.00 0.00 2.29
231 232 3.946201 ACCGCACTGAAGCAGCCT 61.946 61.111 0.00 0.00 34.37 4.58
411 415 6.404623 GCAGTTGCCATGTCTAATGAAATACA 60.405 38.462 0.00 0.00 34.31 2.29
417 421 7.176515 TGCCATGTCTAATGAAATACAGTTTGT 59.823 33.333 0.00 0.00 0.00 2.83
451 455 2.094597 GCTGCAGTTGCCATGTTCAATA 60.095 45.455 16.64 0.00 41.18 1.90
458 462 7.658982 TGCAGTTGCCATGTTCAATAAAAATTA 59.341 29.630 1.06 0.00 41.18 1.40
685 695 9.448438 TTGCTATGTTTACTCAAATGTAGATGT 57.552 29.630 0.00 0.00 0.00 3.06
800 810 0.607489 ACTCCAGTTGCCATGTCTGC 60.607 55.000 0.00 0.00 0.00 4.26
1220 1347 2.426024 TCGAGCAAGGCGAATACTACTT 59.574 45.455 0.00 0.00 34.45 2.24
1321 1448 1.360852 TGCCCCACCATTTCATAAGGT 59.639 47.619 0.00 0.00 35.65 3.50
1331 1458 3.358111 TTTCATAAGGTGGCGATGGAA 57.642 42.857 0.00 0.00 0.00 3.53
1372 1499 3.268603 CGCCGCAGACAACACACA 61.269 61.111 0.00 0.00 0.00 3.72
1468 1597 7.772292 AGAACTATGCTGAGCTAATTGATGAAA 59.228 33.333 5.83 0.00 0.00 2.69
1554 1683 5.413309 TTGAGGAGATCAAGAAGAGGAAC 57.587 43.478 0.00 0.00 43.09 3.62
1664 1793 1.299316 CAGCAAGCACACAAACCCG 60.299 57.895 0.00 0.00 0.00 5.28
1673 1802 1.378762 CACAAACCCGGGTCAGGAT 59.621 57.895 30.40 8.06 0.00 3.24
1685 1814 1.540367 TCAGGATCCCACCCCGTTT 60.540 57.895 8.55 0.00 0.00 3.60
1724 1853 4.717280 CCCCAGAGAGATAAGGTACAAGTT 59.283 45.833 0.00 0.00 0.00 2.66
1839 1969 5.045869 TGGACATTTTCTTCTGTACCCTAGG 60.046 44.000 0.06 0.06 0.00 3.02
1887 2028 5.422214 TTGGGAGAATAACTCTTGAGGAC 57.578 43.478 2.55 0.00 44.37 3.85
1972 2136 8.840321 ACTTAATCTGCCATGTTATGTGTATTC 58.160 33.333 0.00 0.00 0.00 1.75
2184 2349 3.069872 TGCTTGATCTGCCATGTTGTTTT 59.930 39.130 8.39 0.00 0.00 2.43
2212 2377 2.110578 TCTGCCATGTTAGCTCTGCTA 58.889 47.619 0.00 0.00 40.44 3.49
2282 2447 2.885266 TGGCAAATACCACGCAGTTTAA 59.115 40.909 0.00 0.00 41.61 1.52
2289 2454 6.380095 AATACCACGCAGTTTAAAGAAACA 57.620 33.333 3.60 0.00 46.30 2.83
2448 2617 2.128367 ACCGACAAAATGAAAACCGC 57.872 45.000 0.00 0.00 0.00 5.68
2652 2822 7.022384 AGAGAAACTACTAAATTGTCGACTCG 58.978 38.462 17.92 0.00 0.00 4.18
2839 3015 4.978099 TGATTTTCTTGACAGCTTCCTCT 58.022 39.130 0.00 0.00 0.00 3.69
2890 3066 7.708051 TGTTGAAATCTTTATTCGTCAACCAA 58.292 30.769 10.79 0.00 39.73 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 0.397254 AGTAGGCGAGCACCCAGTAT 60.397 55.000 0.00 0.0 0.00 2.12
82 83 4.143333 GAACCCCTCGCTGCGCTA 62.143 66.667 18.65 0.0 0.00 4.26
231 232 6.018588 CCATCGGTAAATACGTCAGCAATTTA 60.019 38.462 0.00 0.0 0.00 1.40
458 462 7.045416 TGTATCCGAGTAAGCATTGTAAACAT 58.955 34.615 0.00 0.0 0.00 2.71
1220 1347 1.266718 GTTCGAACTTGCAGCATTGGA 59.733 47.619 20.97 0.0 0.00 3.53
1321 1448 1.451207 CGTCCCAATTCCATCGCCA 60.451 57.895 0.00 0.0 0.00 5.69
1331 1458 2.126071 CGTCGTCAGCGTCCCAAT 60.126 61.111 0.00 0.0 39.49 3.16
1372 1499 1.968017 CATGCACAGCCAGAACCGT 60.968 57.895 0.00 0.0 0.00 4.83
1468 1597 1.341209 TGTCTCATCACTCTTGCACGT 59.659 47.619 0.00 0.0 0.00 4.49
1673 1802 1.377229 GTGATGAAACGGGGTGGGA 59.623 57.895 0.00 0.0 0.00 4.37
1685 1814 4.713946 GGCGACCCTTTGTGATGA 57.286 55.556 0.00 0.0 0.00 2.92
1724 1853 6.009589 TGTTTTGCTTGAATCTCCAATCCTA 58.990 36.000 0.00 0.0 0.00 2.94
1859 1995 8.588472 CCTCAAGAGTTATTCTCCCAAATTTTT 58.412 33.333 0.00 0.0 43.71 1.94
1860 1996 7.950124 TCCTCAAGAGTTATTCTCCCAAATTTT 59.050 33.333 0.00 0.0 43.71 1.82
1861 1997 7.394641 GTCCTCAAGAGTTATTCTCCCAAATTT 59.605 37.037 0.00 0.0 43.71 1.82
1887 2028 6.985117 TGAATTTTTCTTCCACTTCTGATGG 58.015 36.000 0.00 0.0 38.71 3.51
1972 2136 9.970395 ATTTAATACACATAACATGGCAGATTG 57.030 29.630 0.00 0.0 33.60 2.67
2184 2349 5.363868 AGAGCTAACATGGCAGATACAGTTA 59.636 40.000 0.00 0.0 0.00 2.24
2282 2447 3.004315 CCCACAACGCACTATTGTTTCTT 59.996 43.478 0.00 0.0 38.22 2.52
2289 2454 0.392461 ATCGCCCACAACGCACTATT 60.392 50.000 0.00 0.0 0.00 1.73
2448 2617 0.870307 CGGGTAGCGAAAGTCATCGG 60.870 60.000 0.00 0.0 42.93 4.18
2605 2775 7.067737 TCTCTAATATATGTGTGGACGTGAACA 59.932 37.037 0.00 0.0 0.00 3.18
2648 2818 1.366366 GTAGTGGTGGTGTGCGAGT 59.634 57.895 0.00 0.0 0.00 4.18
2652 2822 1.675552 ACTTTGTAGTGGTGGTGTGC 58.324 50.000 0.00 0.0 31.99 4.57
2839 3015 1.154282 CAGAGCACGCGAGTTCGTA 60.154 57.895 15.93 0.0 46.40 3.43


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

AutoCloner maintained by Alex Coulton.