Multiple sequence alignment - TraesCS2B01G534900

Loading Multiple Alignment...

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 TraesCS2B01G534900 chr2B 100.000 2848 0 0 1 2848 731068279 731071126 0 5260
1 TraesCS2B01G534900 chr2B 96.406 2866 83 4 1 2848 67283638 67280775 0 4704
2 TraesCS2B01G534900 chr2B 96.035 2724 78 13 154 2848 121622196 121619474 0 4405
3 TraesCS2B01G534900 chr7B 96.491 2878 70 8 1 2848 725464412 725461536 0 4726
4 TraesCS2B01G534900 chr7B 96.385 2877 74 3 2 2848 724305834 724302958 0 4710
5 TraesCS2B01G534900 chr3B 96.385 2877 74 3 1 2848 60550959 60548084 0 4710
6 TraesCS2B01G534900 chr3B 96.911 2622 67 4 1 2609 228483095 228480475 0 4381
7 TraesCS2B01G534900 chr3B 96.063 2616 79 7 1 2611 517876449 517873853 0 4239
8 TraesCS2B01G534900 chr1B 96.214 2879 71 10 1 2848 56407182 56410053 0 4678
9 TraesCS2B01G534900 chr1B 95.620 411 17 1 2438 2848 63662313 63662722 0 658
10 TraesCS2B01G534900 chr5B 97.066 2624 62 5 1 2611 209178205 209175584 0 4405
11 TraesCS2B01G534900 chr4A 96.724 2625 71 5 1 2611 691949137 691951760 0 4357
12 TraesCS2B01G534900 chr6B 96.298 2620 64 9 1 2589 26660136 26657519 0 4270
13 TraesCS2B01G534900 chrUn 93.878 980 31 12 1898 2848 34511107 34512086 0 1450
14 TraesCS2B01G534900 chrUn 93.878 980 31 12 1898 2848 301822865 301821886 0 1450
15 TraesCS2B01G534900 chrUn 93.878 980 31 12 1898 2848 315137690 315136711 0 1450
16 TraesCS2B01G534900 chrUn 93.878 980 31 12 1898 2848 322610473 322611452 0 1450
17 TraesCS2B01G534900 chrUn 93.878 980 31 12 1898 2848 338929195 338930174 0 1450


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 TraesCS2B01G534900 chr2B 731068279 731071126 2847 False 5260 5260 100.000 1 2848 1 chr2B.!!$F1 2847
1 TraesCS2B01G534900 chr2B 67280775 67283638 2863 True 4704 4704 96.406 1 2848 1 chr2B.!!$R1 2847
2 TraesCS2B01G534900 chr2B 121619474 121622196 2722 True 4405 4405 96.035 154 2848 1 chr2B.!!$R2 2694
3 TraesCS2B01G534900 chr7B 725461536 725464412 2876 True 4726 4726 96.491 1 2848 1 chr7B.!!$R2 2847
4 TraesCS2B01G534900 chr7B 724302958 724305834 2876 True 4710 4710 96.385 2 2848 1 chr7B.!!$R1 2846
5 TraesCS2B01G534900 chr3B 60548084 60550959 2875 True 4710 4710 96.385 1 2848 1 chr3B.!!$R1 2847
6 TraesCS2B01G534900 chr3B 228480475 228483095 2620 True 4381 4381 96.911 1 2609 1 chr3B.!!$R2 2608
7 TraesCS2B01G534900 chr3B 517873853 517876449 2596 True 4239 4239 96.063 1 2611 1 chr3B.!!$R3 2610
8 TraesCS2B01G534900 chr1B 56407182 56410053 2871 False 4678 4678 96.214 1 2848 1 chr1B.!!$F1 2847
9 TraesCS2B01G534900 chr5B 209175584 209178205 2621 True 4405 4405 97.066 1 2611 1 chr5B.!!$R1 2610
10 TraesCS2B01G534900 chr4A 691949137 691951760 2623 False 4357 4357 96.724 1 2611 1 chr4A.!!$F1 2610
11 TraesCS2B01G534900 chr6B 26657519 26660136 2617 True 4270 4270 96.298 1 2589 1 chr6B.!!$R1 2588
12 TraesCS2B01G534900 chrUn 34511107 34512086 979 False 1450 1450 93.878 1898 2848 1 chrUn.!!$F1 950
13 TraesCS2B01G534900 chrUn 301821886 301822865 979 True 1450 1450 93.878 1898 2848 1 chrUn.!!$R1 950
14 TraesCS2B01G534900 chrUn 315136711 315137690 979 True 1450 1450 93.878 1898 2848 1 chrUn.!!$R2 950
15 TraesCS2B01G534900 chrUn 322610473 322611452 979 False 1450 1450 93.878 1898 2848 1 chrUn.!!$F2 950
16 TraesCS2B01G534900 chrUn 338929195 338930174 979 False 1450 1450 93.878 1898 2848 1 chrUn.!!$F3 950

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
517 518 2.821969 GTCTGTCCATGCATTCCAAACT 59.178 45.455 0.0 0.0 0.0 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2434 2445 1.005805 ACAGGGCATGGACAAAGCATA 59.994 47.619 3.46 0.0 0.0 3.14 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
46 47 6.015180 TCCTTCATTGCTTGCTTGTTTCTATT 60.015 34.615 0.00 0.00 0.00 1.73
417 418 8.965819 TGCAATCTGAATAAGTTGGCTTAATTA 58.034 29.630 0.00 0.00 40.22 1.40
517 518 2.821969 GTCTGTCCATGCATTCCAAACT 59.178 45.455 0.00 0.00 0.00 2.66
543 544 7.894376 TCACCTAATAGTTACGTTTCCTTTG 57.106 36.000 0.00 0.00 0.00 2.77
716 717 5.011840 AGGTTCAAGAAGGTAGTGGAGTTAC 59.988 44.000 0.00 0.00 0.00 2.50
1109 1113 1.068333 GCAGAAAGCAAAGATGGCGAA 60.068 47.619 0.00 0.00 44.79 4.70
1344 1348 7.332213 TGTTGTCATCAATGAAGAAGAACAA 57.668 32.000 10.16 0.90 38.75 2.83
1913 1922 7.719483 TCTGCAGAAAAATTCAAAGAACAGAT 58.281 30.769 15.67 0.00 0.00 2.90
1915 1924 7.490840 TGCAGAAAAATTCAAAGAACAGATGA 58.509 30.769 0.00 0.00 0.00 2.92
1961 1970 3.556775 TGATACCGTAGCCGCAAATAAAC 59.443 43.478 0.00 0.00 0.00 2.01
1977 1986 6.128063 GCAAATAAACTCAGCATCAAGTCTCT 60.128 38.462 0.00 0.00 0.00 3.10
2113 2122 3.900966 AGTGCTAGATCATGCTGACAA 57.099 42.857 10.52 0.00 0.00 3.18
2221 2230 1.206610 ACAGCACACATTTTTGCCACA 59.793 42.857 0.00 0.00 39.75 4.17
2233 2244 4.385358 TTTTGCCACAGAGAACTTTTCC 57.615 40.909 0.00 0.00 0.00 3.13
2380 2391 2.390225 TGTTTAAGGCCACCCACAAT 57.610 45.000 5.01 0.00 0.00 2.71
2434 2445 7.066525 GTCAAGACTGCTATAGTAAGTCACTCT 59.933 40.741 26.31 12.45 42.28 3.24
2534 2574 3.992643 TCCATGCTTTGATGTTGTTTGG 58.007 40.909 0.00 0.00 0.00 3.28
2692 2732 5.086104 TGTTAGTCAGGAAGCCATCTTAC 57.914 43.478 0.00 0.00 33.17 2.34
2750 2790 6.604396 TCATATTGTTCCAATTGCATGTCTCT 59.396 34.615 0.00 0.00 0.00 3.10
2758 2798 3.550437 ATTGCATGTCTCTAGGTCACC 57.450 47.619 0.00 0.00 0.00 4.02
2760 2800 2.256306 TGCATGTCTCTAGGTCACCAA 58.744 47.619 0.00 0.00 0.00 3.67
2790 2830 9.725019 TCATCTTCTTGTATAGATTTTGTGTGT 57.275 29.630 0.00 0.00 31.54 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
246 247 0.963962 CTTGAGGTGGTGCTTGCAAT 59.036 50.000 0.00 0.00 0.00 3.56
384 385 7.431249 CCAACTTATTCAGATTGCAGCAATAT 58.569 34.615 20.90 15.29 33.90 1.28
417 418 1.349026 AGACTAACAGCACACAGGCAT 59.651 47.619 0.00 0.00 35.83 4.40
517 518 8.776470 CAAAGGAAACGTAACTATTAGGTGAAA 58.224 33.333 0.00 0.00 34.75 2.69
543 544 2.677337 GAGAGGCTCTTCTTTGCATGAC 59.323 50.000 19.80 0.00 0.00 3.06
716 717 3.912496 TGTACTCTGGGTCATCATTGG 57.088 47.619 0.00 0.00 0.00 3.16
1109 1113 1.613317 TTCCTGATGGTCCGTCGCAT 61.613 55.000 6.60 0.00 34.23 4.73
1913 1922 9.730705 AAAATACTTCTTCTTGATCTGATGTCA 57.269 29.630 0.00 0.00 0.00 3.58
1915 1924 9.730705 TCAAAATACTTCTTCTTGATCTGATGT 57.269 29.630 0.00 0.00 0.00 3.06
1961 1970 3.430098 GGTACCAGAGACTTGATGCTGAG 60.430 52.174 7.15 0.00 0.00 3.35
1977 1986 2.031870 CATCCGTCAGATCAGGTACCA 58.968 52.381 15.94 0.00 30.59 3.25
2221 2230 5.018374 AGGTCTCTAGGGAAAAGTTCTCT 57.982 43.478 0.00 0.00 44.35 3.10
2233 2244 4.202131 GGATCAAACGGTAAGGTCTCTAGG 60.202 50.000 0.00 0.00 0.00 3.02
2380 2391 2.552315 CGAAAACCCTTGCTTCTTGCTA 59.448 45.455 0.00 0.00 43.37 3.49
2392 2403 1.375326 GACTGGCTCCGAAAACCCT 59.625 57.895 0.00 0.00 0.00 4.34
2434 2445 1.005805 ACAGGGCATGGACAAAGCATA 59.994 47.619 3.46 0.00 0.00 3.14
2534 2574 6.073003 GCATGGAACTATAAGCATGGAACTAC 60.073 42.308 0.00 0.00 0.00 2.73
2692 2732 4.696479 AGCCTAGAATGGTGGTTCTATG 57.304 45.455 0.00 0.00 39.31 2.23
2750 2790 6.070021 ACAAGAAGATGATGATTGGTGACCTA 60.070 38.462 2.11 0.00 0.00 3.08
2790 2830 8.251383 TGGATTATTTGAAGTAACCAAACCAA 57.749 30.769 0.00 0.00 36.48 3.67


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

AutoCloner maintained by Alex Coulton.