Multiple sequence alignment - TraesCS2B01G429000

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 TraesCS2B01G429000 chr2B 100.000 2907 0 0 1 2907 616459236 616462142 0.000000e+00 5369
1 TraesCS2B01G429000 chr2B 92.481 1463 85 11 445 1897 63131876 63130429 0.000000e+00 2069
2 TraesCS2B01G429000 chr6D 98.042 2911 50 4 1 2906 433250792 433253700 0.000000e+00 5053
3 TraesCS2B01G429000 chr6D 97.837 2912 57 4 1 2906 32039174 32036263 0.000000e+00 5024
4 TraesCS2B01G429000 chr6D 97.248 1381 36 1 71 1449 420713332 420714712 0.000000e+00 2338
5 TraesCS2B01G429000 chr6D 96.198 868 27 4 1508 2369 420714702 420715569 0.000000e+00 1415
6 TraesCS2B01G429000 chr2A 96.681 2621 66 10 295 2906 605004802 605002194 0.000000e+00 4338
7 TraesCS2B01G429000 chr2A 90.159 315 29 2 2592 2906 364416095 364416407 2.700000e-110 409
8 TraesCS2B01G429000 chr5A 96.684 2141 52 9 295 2426 539077469 539075339 0.000000e+00 3542
9 TraesCS2B01G429000 chr5A 92.392 1919 100 16 1 1897 139476947 139475053 0.000000e+00 2693
10 TraesCS2B01G429000 chr5A 91.901 605 42 4 2001 2601 139472297 139471696 0.000000e+00 839
11 TraesCS2B01G429000 chr4B 93.073 1920 89 21 1 1897 74348680 74350578 0.000000e+00 2769
12 TraesCS2B01G429000 chr4D 92.500 1920 95 17 1 1897 403008888 403010781 0.000000e+00 2702
13 TraesCS2B01G429000 chr4D 90.997 311 27 1 2597 2906 403014224 403014534 4.480000e-113 418
14 TraesCS2B01G429000 chr2D 92.392 1919 97 18 1 1897 644817658 644819549 0.000000e+00 2689
15 TraesCS2B01G429000 chr2D 92.244 606 39 5 2001 2601 644822341 644822943 0.000000e+00 852
16 TraesCS2B01G429000 chr2D 91.318 311 26 1 2597 2906 644823081 644823391 9.630000e-115 424
17 TraesCS2B01G429000 chr7D 92.236 1919 98 19 1 1897 29571829 29569940 0.000000e+00 2671
18 TraesCS2B01G429000 chr7D 92.586 607 36 6 2001 2601 29567148 29566545 0.000000e+00 863
19 TraesCS2B01G429000 chr7D 90.997 311 27 1 2597 2906 29566407 29566097 4.480000e-113 418
20 TraesCS2B01G429000 chr1D 91.662 1919 109 19 1 1897 187808364 187810253 0.000000e+00 2610
21 TraesCS2B01G429000 chr1D 91.749 606 42 5 2001 2601 187813044 187813646 0.000000e+00 835
22 TraesCS2B01G429000 chr1D 91.640 311 25 1 2597 2906 187813784 187814094 2.070000e-116 429
23 TraesCS2B01G429000 chr6A 92.550 1490 75 14 1 1470 615073953 615072480 0.000000e+00 2104
24 TraesCS2B01G429000 chr6A 90.675 311 28 1 2597 2906 615068809 615068499 2.080000e-111 412


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 TraesCS2B01G429000 chr2B 616459236 616462142 2906 False 5369.000000 5369 100.000000 1 2907 1 chr2B.!!$F1 2906
1 TraesCS2B01G429000 chr2B 63130429 63131876 1447 True 2069.000000 2069 92.481000 445 1897 1 chr2B.!!$R1 1452
2 TraesCS2B01G429000 chr6D 433250792 433253700 2908 False 5053.000000 5053 98.042000 1 2906 1 chr6D.!!$F1 2905
3 TraesCS2B01G429000 chr6D 32036263 32039174 2911 True 5024.000000 5024 97.837000 1 2906 1 chr6D.!!$R1 2905
4 TraesCS2B01G429000 chr6D 420713332 420715569 2237 False 1876.500000 2338 96.723000 71 2369 2 chr6D.!!$F2 2298
5 TraesCS2B01G429000 chr2A 605002194 605004802 2608 True 4338.000000 4338 96.681000 295 2906 1 chr2A.!!$R1 2611
6 TraesCS2B01G429000 chr5A 539075339 539077469 2130 True 3542.000000 3542 96.684000 295 2426 1 chr5A.!!$R1 2131
7 TraesCS2B01G429000 chr5A 139471696 139476947 5251 True 1766.000000 2693 92.146500 1 2601 2 chr5A.!!$R2 2600
8 TraesCS2B01G429000 chr4B 74348680 74350578 1898 False 2769.000000 2769 93.073000 1 1897 1 chr4B.!!$F1 1896
9 TraesCS2B01G429000 chr4D 403008888 403014534 5646 False 1560.000000 2702 91.748500 1 2906 2 chr4D.!!$F1 2905
10 TraesCS2B01G429000 chr2D 644817658 644823391 5733 False 1321.666667 2689 91.984667 1 2906 3 chr2D.!!$F1 2905
11 TraesCS2B01G429000 chr7D 29566097 29571829 5732 True 1317.333333 2671 91.939667 1 2906 3 chr7D.!!$R1 2905
12 TraesCS2B01G429000 chr1D 187808364 187814094 5730 False 1291.333333 2610 91.683667 1 2906 3 chr1D.!!$F1 2905
13 TraesCS2B01G429000 chr6A 615068499 615073953 5454 True 1258.000000 2104 91.612500 1 2906 2 chr6A.!!$R1 2905

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
462 481 0.307760 CCACGCCGATAATTTCCTGC 59.692 55.000 0.00 0.0 0.00 4.85 F
1116 1149 1.552337 GCCTCTTGAGAGACCACATGA 59.448 52.381 9.55 0.0 44.74 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1640 1690 1.382629 CCGAGGAACCCCATTTGGT 59.617 57.895 0.0 0.0 41.55 3.67 R
1964 3659 5.806654 ATGTGTTGGGTCTTGCTTTATTT 57.193 34.783 0.0 0.0 0.00 1.40 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
271 278 0.742635 TGTCTCTGTTGCAACGCACA 60.743 50.000 23.79 18.75 38.71 4.57
403 422 6.907961 TCTCCAGTAAGCAGTATACTAGGAA 58.092 40.000 4.74 0.00 33.84 3.36
462 481 0.307760 CCACGCCGATAATTTCCTGC 59.692 55.000 0.00 0.00 0.00 4.85
625 645 6.536941 GGACTTTACATGGTTTCTTGCAAAAA 59.463 34.615 0.00 1.75 0.00 1.94
626 648 7.226523 GGACTTTACATGGTTTCTTGCAAAAAT 59.773 33.333 0.00 0.00 0.00 1.82
890 923 6.713762 TTTCTTCATTCAGTTTCATGTGGT 57.286 33.333 0.00 0.00 0.00 4.16
1116 1149 1.552337 GCCTCTTGAGAGACCACATGA 59.448 52.381 9.55 0.00 44.74 3.07
1295 1330 2.496871 CACAAGTCTCAGAGAGGCAGAT 59.503 50.000 0.00 0.00 36.65 2.90
1702 1758 0.739813 GACACCGACACATACTGGGC 60.740 60.000 0.00 0.00 0.00 5.36
1759 1816 1.599071 TGCGCGATCCATTCATTCTTC 59.401 47.619 12.10 0.00 0.00 2.87
1790 1851 4.402793 TCCTTCCTTATTCCTCTCAACTCG 59.597 45.833 0.00 0.00 0.00 4.18
1964 3659 1.480789 TGGTCGATGGTAGCTTGCTA 58.519 50.000 0.00 0.00 0.00 3.49
2217 5014 5.772672 TCCTTGAGAATCTACTAGATGAGGC 59.227 44.000 0.00 0.00 34.65 4.70
2516 5317 1.382629 GGGGCCTGTCCAAGCTTTA 59.617 57.895 0.84 0.00 36.21 1.85
2584 5386 5.909477 TCTAAATGGTTAGGTATGTGTCGG 58.091 41.667 0.00 0.00 37.83 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
160 167 4.442707 ACATATATGCCCATCTCCCTTCT 58.557 43.478 12.79 0.00 0.00 2.85
247 254 2.411547 GCGTTGCAACAGAGACATACAC 60.412 50.000 28.01 0.00 0.00 2.90
403 422 9.783081 AAATTTTCCTAGAGCACAAATTCAAAT 57.217 25.926 0.00 0.00 0.00 2.32
626 648 9.638239 GAGCCATGTGAGTCAATTTTAATTTTA 57.362 29.630 0.00 0.00 0.00 1.52
631 653 5.000591 TCGAGCCATGTGAGTCAATTTTAA 58.999 37.500 0.00 0.00 0.00 1.52
638 671 0.969149 AACTCGAGCCATGTGAGTCA 59.031 50.000 13.61 0.00 41.88 3.41
866 899 7.111247 ACCACATGAAACTGAATGAAGAAAA 57.889 32.000 0.00 0.00 0.00 2.29
890 923 1.138036 CGTCCTCCACGCGTCATTA 59.862 57.895 9.86 0.00 42.87 1.90
1116 1149 1.134175 CAAAAACTGCCACCAGAACGT 59.866 47.619 0.00 0.00 41.77 3.99
1295 1330 6.755141 GTGGTTATTCTGAATAGTTGTCGCTA 59.245 38.462 9.81 0.00 0.00 4.26
1549 1590 2.047179 GTCACGAAGCCCTGTCCC 60.047 66.667 0.00 0.00 0.00 4.46
1640 1690 1.382629 CCGAGGAACCCCATTTGGT 59.617 57.895 0.00 0.00 41.55 3.67
1702 1758 3.988976 TCTCTCTGGTTGGAAATGGAG 57.011 47.619 0.00 0.00 0.00 3.86
1759 1816 4.781934 AGGAATAAGGAAGGATCAAACGG 58.218 43.478 0.00 0.00 0.00 4.44
1964 3659 5.806654 ATGTGTTGGGTCTTGCTTTATTT 57.193 34.783 0.00 0.00 0.00 1.40
2374 5174 6.448207 TCATTCGTGATCATAAATGGCAAA 57.552 33.333 22.62 9.18 31.53 3.68
2516 5317 9.951866 ATTTTAACATTCCCCCATCTACTATTT 57.048 29.630 0.00 0.00 0.00 1.40
2584 5386 6.122277 TCATCCCATGAAAGAATACAGGTTC 58.878 40.000 0.00 0.00 36.11 3.62
2813 5760 6.509656 ACTGATTGCATATCAAATTTCGCAT 58.490 32.000 11.14 0.00 38.34 4.73


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

AutoCloner maintained by Alex Coulton.