Multiple sequence alignment - TraesCS2B01G487200

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 TraesCS2B01G487200 chr2B 100.000 2264 0 0 1 2264 683727900 683730163 0.000000e+00 4181.0
1 TraesCS2B01G487200 chr2B 95.499 711 26 5 80 789 564984708 564985413 0.000000e+00 1131.0
2 TraesCS2B01G487200 chr2B 100.000 72 0 0 1 72 683744844 683744915 1.410000e-27 134.0
3 TraesCS2B01G487200 chr5A 99.184 1470 11 1 795 2264 559030696 559029228 0.000000e+00 2647.0
4 TraesCS2B01G487200 chr1A 99.048 1470 14 0 795 2264 554483274 554484743 0.000000e+00 2638.0
5 TraesCS2B01G487200 chr1A 98.438 128 1 1 72 199 309698333 309698459 8.140000e-55 224.0
6 TraesCS2B01G487200 chr5B 98.912 1470 16 0 795 2264 57513872 57512403 0.000000e+00 2627.0
7 TraesCS2B01G487200 chr5B 94.697 132 6 1 68 199 315302218 315302088 1.060000e-48 204.0
8 TraesCS2B01G487200 chr3A 98.503 1470 22 0 795 2264 105555707 105554238 0.000000e+00 2593.0
9 TraesCS2B01G487200 chr5D 99.098 1441 13 0 795 2235 299970737 299969297 0.000000e+00 2590.0
10 TraesCS2B01G487200 chr5D 98.435 1470 22 1 795 2264 503340695 503342163 0.000000e+00 2586.0
11 TraesCS2B01G487200 chr5D 98.231 1470 26 0 795 2264 6252023 6250554 0.000000e+00 2571.0
12 TraesCS2B01G487200 chrUn 98.435 1470 23 0 795 2264 261567440 261565971 0.000000e+00 2588.0
13 TraesCS2B01G487200 chrUn 95.968 496 18 1 297 792 470558455 470557962 0.000000e+00 804.0
14 TraesCS2B01G487200 chr1D 98.367 1470 24 0 795 2264 254460654 254462123 0.000000e+00 2582.0
15 TraesCS2B01G487200 chr7A 98.597 713 9 1 72 784 577489750 577490461 0.000000e+00 1260.0
16 TraesCS2B01G487200 chr7A 97.674 129 2 1 71 199 577691799 577691672 1.050000e-53 220.0
17 TraesCS2B01G487200 chr7D 95.113 532 25 1 254 785 488080090 488079560 0.000000e+00 837.0
18 TraesCS2B01G487200 chr7D 82.591 247 26 11 64 298 488103390 488103149 3.810000e-48 202.0
19 TraesCS2B01G487200 chr2A 94.403 536 30 0 254 789 606812243 606812778 0.000000e+00 824.0
20 TraesCS2B01G487200 chr2A 100.000 33 0 0 2232 2264 746954366 746954334 6.750000e-06 62.1
21 TraesCS2B01G487200 chr4D 94.559 533 27 2 254 785 252179065 252179596 0.000000e+00 822.0
22 TraesCS2B01G487200 chr4D 93.774 530 32 1 254 783 15089854 15090382 0.000000e+00 795.0
23 TraesCS2B01G487200 chr3B 96.573 496 15 1 297 792 809089577 809089084 0.000000e+00 821.0
24 TraesCS2B01G487200 chr3B 95.968 496 18 1 297 792 357688957 357688464 0.000000e+00 804.0
25 TraesCS2B01G487200 chr3B 88.024 167 14 6 72 238 809089715 809089555 2.290000e-45 193.0
26 TraesCS2B01G487200 chr6A 91.608 143 8 4 58 199 531546326 531546465 6.380000e-46 195.0
27 TraesCS2B01G487200 chr4A 87.135 171 16 6 68 238 584528067 584528231 2.970000e-44 189.0
28 TraesCS2B01G487200 chr2D 97.101 69 2 0 1 69 571869174 571869242 1.420000e-22 117.0
29 TraesCS2B01G487200 chr2D 100.000 34 0 0 1 34 571556220 571556253 1.880000e-06 63.9


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 TraesCS2B01G487200 chr2B 683727900 683730163 2263 False 4181 4181 100.0000 1 2264 1 chr2B.!!$F2 2263
1 TraesCS2B01G487200 chr2B 564984708 564985413 705 False 1131 1131 95.4990 80 789 1 chr2B.!!$F1 709
2 TraesCS2B01G487200 chr5A 559029228 559030696 1468 True 2647 2647 99.1840 795 2264 1 chr5A.!!$R1 1469
3 TraesCS2B01G487200 chr1A 554483274 554484743 1469 False 2638 2638 99.0480 795 2264 1 chr1A.!!$F2 1469
4 TraesCS2B01G487200 chr5B 57512403 57513872 1469 True 2627 2627 98.9120 795 2264 1 chr5B.!!$R1 1469
5 TraesCS2B01G487200 chr3A 105554238 105555707 1469 True 2593 2593 98.5030 795 2264 1 chr3A.!!$R1 1469
6 TraesCS2B01G487200 chr5D 299969297 299970737 1440 True 2590 2590 99.0980 795 2235 1 chr5D.!!$R2 1440
7 TraesCS2B01G487200 chr5D 503340695 503342163 1468 False 2586 2586 98.4350 795 2264 1 chr5D.!!$F1 1469
8 TraesCS2B01G487200 chr5D 6250554 6252023 1469 True 2571 2571 98.2310 795 2264 1 chr5D.!!$R1 1469
9 TraesCS2B01G487200 chrUn 261565971 261567440 1469 True 2588 2588 98.4350 795 2264 1 chrUn.!!$R1 1469
10 TraesCS2B01G487200 chr1D 254460654 254462123 1469 False 2582 2582 98.3670 795 2264 1 chr1D.!!$F1 1469
11 TraesCS2B01G487200 chr7A 577489750 577490461 711 False 1260 1260 98.5970 72 784 1 chr7A.!!$F1 712
12 TraesCS2B01G487200 chr7D 488079560 488080090 530 True 837 837 95.1130 254 785 1 chr7D.!!$R1 531
13 TraesCS2B01G487200 chr2A 606812243 606812778 535 False 824 824 94.4030 254 789 1 chr2A.!!$F1 535
14 TraesCS2B01G487200 chr4D 252179065 252179596 531 False 822 822 94.5590 254 785 1 chr4D.!!$F2 531
15 TraesCS2B01G487200 chr4D 15089854 15090382 528 False 795 795 93.7740 254 783 1 chr4D.!!$F1 529
16 TraesCS2B01G487200 chr3B 809089084 809089715 631 True 507 821 92.2985 72 792 2 chr3B.!!$R2 720

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
789 796 0.308376 GCAACGCACGGGTCTTTTTA 59.692 50.0 0.0 0.0 0.0 1.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1646 1653 1.13517 GTAAGCCTCACTCACGGGTAC 60.135 57.143 0.0 0.0 0.0 3.34 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
25 26 3.838565 TCAAAGTATCAAAGGGGTGCAA 58.161 40.909 0.0 0.0 0.00 4.08
26 27 4.415596 TCAAAGTATCAAAGGGGTGCAAT 58.584 39.130 0.0 0.0 0.00 3.56
27 28 4.837860 TCAAAGTATCAAAGGGGTGCAATT 59.162 37.500 0.0 0.0 0.00 2.32
28 29 5.306678 TCAAAGTATCAAAGGGGTGCAATTT 59.693 36.000 0.0 0.0 0.00 1.82
29 30 6.495181 TCAAAGTATCAAAGGGGTGCAATTTA 59.505 34.615 0.0 0.0 0.00 1.40
31 32 7.494922 AAGTATCAAAGGGGTGCAATTTAAT 57.505 32.000 0.0 0.0 0.00 1.40
32 33 8.602472 AAGTATCAAAGGGGTGCAATTTAATA 57.398 30.769 0.0 0.0 0.00 0.98
33 34 8.602472 AGTATCAAAGGGGTGCAATTTAATAA 57.398 30.769 0.0 0.0 0.00 1.40
34 35 9.041354 AGTATCAAAGGGGTGCAATTTAATAAA 57.959 29.630 0.0 0.0 0.00 1.40
35 36 9.660180 GTATCAAAGGGGTGCAATTTAATAAAA 57.340 29.630 0.0 0.0 0.00 1.52
137 139 4.143115 CGTCACAATACGCTTTCTTCACAT 60.143 41.667 0.0 0.0 35.87 3.21
473 475 6.276832 AGCTGTTGATAATGCTCAAATTGT 57.723 33.333 0.0 0.0 36.92 2.71
789 796 0.308376 GCAACGCACGGGTCTTTTTA 59.692 50.000 0.0 0.0 0.00 1.52
792 799 1.957668 ACGCACGGGTCTTTTTACTT 58.042 45.000 0.0 0.0 0.00 2.24
793 800 2.291365 ACGCACGGGTCTTTTTACTTT 58.709 42.857 0.0 0.0 0.00 2.66
797 804 5.008911 ACGCACGGGTCTTTTTACTTTATTT 59.991 36.000 0.0 0.0 0.00 1.40
1211 1218 6.711194 TGTTTGAATACCGAGTTACATTTCCA 59.289 34.615 0.0 0.0 0.00 3.53
1614 1621 4.290985 TGGGTTGATGATACAAGAGGGAAA 59.709 41.667 0.0 0.0 0.00 3.13
1696 1703 4.094887 CGTGTTGTAAATGCTCTGGCTAAT 59.905 41.667 0.0 0.0 39.59 1.73
1703 1710 7.973402 TGTAAATGCTCTGGCTAATCCTATTA 58.027 34.615 0.0 0.0 39.59 0.98
2130 2137 2.067459 CGCGAACGGCATACTTTAAC 57.933 50.000 0.0 0.0 43.84 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 5.192927 TGCACCCCTTTGATACTTTGATAG 58.807 41.667 0.00 0.00 0.00 2.08
2 3 5.186256 TGCACCCCTTTGATACTTTGATA 57.814 39.130 0.00 0.00 0.00 2.15
3 4 4.046286 TGCACCCCTTTGATACTTTGAT 57.954 40.909 0.00 0.00 0.00 2.57
4 5 3.517296 TGCACCCCTTTGATACTTTGA 57.483 42.857 0.00 0.00 0.00 2.69
5 6 4.806640 ATTGCACCCCTTTGATACTTTG 57.193 40.909 0.00 0.00 0.00 2.77
6 7 5.823861 AAATTGCACCCCTTTGATACTTT 57.176 34.783 0.00 0.00 0.00 2.66
7 8 6.926630 TTAAATTGCACCCCTTTGATACTT 57.073 33.333 0.00 0.00 0.00 2.24
8 9 8.602472 TTATTAAATTGCACCCCTTTGATACT 57.398 30.769 0.00 0.00 0.00 2.12
9 10 9.660180 TTTTATTAAATTGCACCCCTTTGATAC 57.340 29.630 0.00 0.00 0.00 2.24
68 69 9.862371 CCGTGCTTTATTATTAGTGAGAGATAT 57.138 33.333 0.00 0.00 0.00 1.63
69 70 9.074576 TCCGTGCTTTATTATTAGTGAGAGATA 57.925 33.333 0.00 0.00 0.00 1.98
70 71 7.952671 TCCGTGCTTTATTATTAGTGAGAGAT 58.047 34.615 0.00 0.00 0.00 2.75
77 78 6.362248 ACCCAATCCGTGCTTTATTATTAGT 58.638 36.000 0.00 0.00 0.00 2.24
137 139 8.444715 ACAAATCGTAAAAGCGTATTATGACAA 58.555 29.630 4.08 0.00 32.66 3.18
473 475 3.967332 ACTACTTTAACTTGGGCGCTA 57.033 42.857 7.64 0.00 0.00 4.26
789 796 7.449086 TCTTCCCGAACCAAACATAAATAAAGT 59.551 33.333 0.00 0.00 0.00 2.66
792 799 7.169591 TCTCTTCCCGAACCAAACATAAATAA 58.830 34.615 0.00 0.00 0.00 1.40
793 800 6.713276 TCTCTTCCCGAACCAAACATAAATA 58.287 36.000 0.00 0.00 0.00 1.40
797 804 4.224147 TGATCTCTTCCCGAACCAAACATA 59.776 41.667 0.00 0.00 0.00 2.29
1211 1218 5.234752 TGCCAATATTAGCACGAATCGTAT 58.765 37.500 8.35 2.72 38.32 3.06
1235 1242 1.690219 CCATTCCAGGGACCCGAGAG 61.690 65.000 4.40 0.00 0.00 3.20
1439 1446 2.248487 CACTTGAACTACGCGACCTAC 58.752 52.381 15.93 1.39 0.00 3.18
1614 1621 8.829612 CAATTCTTCCTGTTGCTTTTACAAAAT 58.170 29.630 0.00 0.00 0.00 1.82
1646 1653 1.135170 GTAAGCCTCACTCACGGGTAC 60.135 57.143 0.00 0.00 0.00 3.34
1696 1703 4.781775 TTCGCCTTTCCCATTAATAGGA 57.218 40.909 0.00 0.00 0.00 2.94
1703 1710 5.140454 AGCTATAATTTCGCCTTTCCCATT 58.860 37.500 0.00 0.00 0.00 3.16
2130 2137 8.350722 CCTGTTTGGAGAGATCATCATAAATTG 58.649 37.037 0.00 0.00 38.35 2.32


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

AutoCloner maintained by Alex Coulton.