Multiple sequence alignment - TraesCS3B01G225100

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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 TraesCS3B01G225100 chr3B 100.000 4263 0 0 1 4263 308394744 308399006 0.000000e+00 7873
1 TraesCS3B01G225100 chr3B 93.407 546 32 4 3 545 679987219 679987763 0.000000e+00 806
2 TraesCS3B01G225100 chr1B 98.065 3721 58 3 557 4263 670555768 670559488 0.000000e+00 6460
3 TraesCS3B01G225100 chr1B 97.404 886 22 1 3378 4263 555323385 555324269 0.000000e+00 1507
4 TraesCS3B01G225100 chr1B 97.119 486 13 1 3778 4263 146324319 146323835 0.000000e+00 819
5 TraesCS3B01G225100 chr2B 95.818 2128 87 2 2137 4263 262314701 262316827 0.000000e+00 3435
6 TraesCS3B01G225100 chr2B 98.595 1922 27 0 2342 4263 453184275 453186196 0.000000e+00 3400
7 TraesCS3B01G225100 chr5D 96.868 1788 56 0 2476 4263 484016476 484014689 0.000000e+00 2992
8 TraesCS3B01G225100 chr3D 96.860 1433 45 0 2831 4263 297889439 297890871 0.000000e+00 2398
9 TraesCS3B01G225100 chr3D 94.245 556 23 4 1 548 598645828 598645274 0.000000e+00 841
10 TraesCS3B01G225100 chr4B 97.263 548 12 3 1 548 564901143 564900599 0.000000e+00 926
11 TraesCS3B01G225100 chr6A 75.569 1932 422 37 1367 3257 52705288 52703366 0.000000e+00 907
12 TraesCS3B01G225100 chr6A 94.643 280 15 0 18 297 580956989 580957268 6.550000e-118 435
13 TraesCS3B01G225100 chr6A 93.254 252 14 3 300 548 581013045 581013296 6.730000e-98 368
14 TraesCS3B01G225100 chr7A 95.818 550 21 2 1 548 53686002 53685453 0.000000e+00 887
15 TraesCS3B01G225100 chr6B 75.751 1897 384 47 1373 3221 184805246 184807114 0.000000e+00 885
16 TraesCS3B01G225100 chr3A 77.256 1618 278 57 596 2158 82457692 82459274 0.000000e+00 867
17 TraesCS3B01G225100 chr3A 78.201 656 141 2 3607 4261 82460716 82461370 6.590000e-113 418
18 TraesCS3B01G225100 chr2D 95.091 550 24 3 1 548 448662119 448662667 0.000000e+00 863
19 TraesCS3B01G225100 chr7B 94.727 550 22 4 1 548 351906916 351906372 0.000000e+00 848
20 TraesCS3B01G225100 chr1A 75.302 1903 391 52 1371 3220 492001919 492000043 0.000000e+00 837
21 TraesCS3B01G225100 chr1D 93.571 560 19 7 1 548 7358003 7357449 0.000000e+00 819
22 TraesCS3B01G225100 chr7D 91.367 556 22 7 1 548 414483470 414484007 0.000000e+00 737
23 TraesCS3B01G225100 chr5B 97.862 421 9 0 3843 4263 436168049 436168469 0.000000e+00 728
24 TraesCS3B01G225100 chr2A 72.929 1895 440 63 1378 3230 547777948 547779811 1.320000e-164 590
25 TraesCS3B01G225100 chr6D 84.559 136 21 0 1820 1955 38451718 38451853 7.440000e-28 135


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 TraesCS3B01G225100 chr3B 308394744 308399006 4262 False 7873.0 7873 100.0000 1 4263 1 chr3B.!!$F1 4262
1 TraesCS3B01G225100 chr3B 679987219 679987763 544 False 806.0 806 93.4070 3 545 1 chr3B.!!$F2 542
2 TraesCS3B01G225100 chr1B 670555768 670559488 3720 False 6460.0 6460 98.0650 557 4263 1 chr1B.!!$F2 3706
3 TraesCS3B01G225100 chr1B 555323385 555324269 884 False 1507.0 1507 97.4040 3378 4263 1 chr1B.!!$F1 885
4 TraesCS3B01G225100 chr2B 262314701 262316827 2126 False 3435.0 3435 95.8180 2137 4263 1 chr2B.!!$F1 2126
5 TraesCS3B01G225100 chr2B 453184275 453186196 1921 False 3400.0 3400 98.5950 2342 4263 1 chr2B.!!$F2 1921
6 TraesCS3B01G225100 chr5D 484014689 484016476 1787 True 2992.0 2992 96.8680 2476 4263 1 chr5D.!!$R1 1787
7 TraesCS3B01G225100 chr3D 297889439 297890871 1432 False 2398.0 2398 96.8600 2831 4263 1 chr3D.!!$F1 1432
8 TraesCS3B01G225100 chr3D 598645274 598645828 554 True 841.0 841 94.2450 1 548 1 chr3D.!!$R1 547
9 TraesCS3B01G225100 chr4B 564900599 564901143 544 True 926.0 926 97.2630 1 548 1 chr4B.!!$R1 547
10 TraesCS3B01G225100 chr6A 52703366 52705288 1922 True 907.0 907 75.5690 1367 3257 1 chr6A.!!$R1 1890
11 TraesCS3B01G225100 chr7A 53685453 53686002 549 True 887.0 887 95.8180 1 548 1 chr7A.!!$R1 547
12 TraesCS3B01G225100 chr6B 184805246 184807114 1868 False 885.0 885 75.7510 1373 3221 1 chr6B.!!$F1 1848
13 TraesCS3B01G225100 chr3A 82457692 82461370 3678 False 642.5 867 77.7285 596 4261 2 chr3A.!!$F1 3665
14 TraesCS3B01G225100 chr2D 448662119 448662667 548 False 863.0 863 95.0910 1 548 1 chr2D.!!$F1 547
15 TraesCS3B01G225100 chr7B 351906372 351906916 544 True 848.0 848 94.7270 1 548 1 chr7B.!!$R1 547
16 TraesCS3B01G225100 chr1A 492000043 492001919 1876 True 837.0 837 75.3020 1371 3220 1 chr1A.!!$R1 1849
17 TraesCS3B01G225100 chr1D 7357449 7358003 554 True 819.0 819 93.5710 1 548 1 chr1D.!!$R1 547
18 TraesCS3B01G225100 chr7D 414483470 414484007 537 False 737.0 737 91.3670 1 548 1 chr7D.!!$F1 547
19 TraesCS3B01G225100 chr2A 547777948 547779811 1863 False 590.0 590 72.9290 1378 3230 1 chr2A.!!$F1 1852

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
71 72 1.633774 AGGACATCCACGTCTCACTT 58.366 50.000 0.00 0.00 38.89 3.16 F
620 646 2.204151 AGTAGCCCACCAGCCCTT 60.204 61.111 0.00 0.00 0.00 3.95 F
1964 2049 3.056328 GTGGTCAGCCGGCCTTTC 61.056 66.667 26.15 11.79 37.67 2.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1815 1894 4.406648 TCAATGTAGTCGATGGAGCATT 57.593 40.909 0.0 0.0 0.00 3.56 R
2372 2502 2.971452 GGAGCCGAGAAGAACCGT 59.029 61.111 0.0 0.0 0.00 4.83 R
3908 4207 0.179171 CACGTCGGTCGCTCTTACAT 60.179 55.000 0.0 0.0 44.19 2.29 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
71 72 1.633774 AGGACATCCACGTCTCACTT 58.366 50.000 0.00 0.00 38.89 3.16
160 162 6.859420 ACAACCTTATTTGGAAAAATGCAC 57.141 33.333 0.00 0.00 0.00 4.57
501 525 5.552870 ACACTTAGGAGATTGTTGTGACT 57.447 39.130 0.00 0.00 0.00 3.41
548 574 3.619483 CGACGCATAAGAAAACATGGGTA 59.381 43.478 0.00 0.00 45.17 3.69
549 575 4.493545 CGACGCATAAGAAAACATGGGTAC 60.494 45.833 0.00 0.00 45.17 3.34
550 576 4.585879 ACGCATAAGAAAACATGGGTACT 58.414 39.130 0.00 0.00 43.88 2.73
551 577 4.394920 ACGCATAAGAAAACATGGGTACTG 59.605 41.667 0.00 0.00 43.88 2.74
552 578 4.672409 GCATAAGAAAACATGGGTACTGC 58.328 43.478 0.00 0.00 0.00 4.40
553 579 4.440112 GCATAAGAAAACATGGGTACTGCC 60.440 45.833 0.00 0.00 0.00 4.85
554 580 3.525800 AAGAAAACATGGGTACTGCCT 57.474 42.857 0.00 0.00 37.43 4.75
555 581 3.525800 AGAAAACATGGGTACTGCCTT 57.474 42.857 0.00 0.00 37.43 4.35
620 646 2.204151 AGTAGCCCACCAGCCCTT 60.204 61.111 0.00 0.00 0.00 3.95
1885 1964 4.912395 GTGCTTGGGGTGTGGGCA 62.912 66.667 0.00 0.00 0.00 5.36
1964 2049 3.056328 GTGGTCAGCCGGCCTTTC 61.056 66.667 26.15 11.79 37.67 2.62
2422 2552 3.003763 GAGGAGGCCCGTGTCCTT 61.004 66.667 12.33 0.00 43.65 3.36
2966 3123 0.388520 CTCGATCCACAAGACACGCA 60.389 55.000 0.00 0.00 0.00 5.24
3338 3524 1.068352 AACTTCAGGGGGCTGGTCTT 61.068 55.000 0.00 0.00 0.00 3.01
3549 3780 6.045072 TCGTACAATTCTGGGTAAAGTGAT 57.955 37.500 0.00 0.00 0.00 3.06
3716 4014 1.929836 CTCTTCGTCTTGCCATGTAGC 59.070 52.381 0.00 0.00 0.00 3.58
3751 4049 6.980397 GGAGACAAAACTCAACAATGTTGATT 59.020 34.615 26.50 19.41 38.51 2.57
3769 4067 0.394938 TTAGTTCACGGCTGCCTTCA 59.605 50.000 17.92 0.00 0.00 3.02
3908 4207 1.451927 GCTTGTCCGCCATGATCCA 60.452 57.895 0.00 0.00 0.00 3.41
3972 4271 2.606519 CCCACCGACCCCTCTTGA 60.607 66.667 0.00 0.00 0.00 3.02
4018 4317 2.672996 GCCAGAAGCCGCCTTTGA 60.673 61.111 0.00 0.00 34.35 2.69
4135 4435 1.745115 GCCACGCTCCATAGTTGCA 60.745 57.895 0.00 0.00 0.00 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 6.769822 ACAGCTAGGGAAAGATGAAATACATG 59.230 38.462 0.00 0.00 39.56 3.21
71 72 9.859427 CCTGCAACAATCTCATTTTATTTTCTA 57.141 29.630 0.00 0.00 0.00 2.10
476 500 7.099764 AGTCACAACAATCTCCTAAGTGTATG 58.900 38.462 0.00 0.00 0.00 2.39
501 525 2.553028 GGTGAAGACTTTCATGGCTGGA 60.553 50.000 0.00 0.00 44.62 3.86
533 559 4.650972 AGGCAGTACCCATGTTTTCTTA 57.349 40.909 0.00 0.00 40.58 2.10
552 578 4.626081 CGGGGGCGAGCCATAAGG 62.626 72.222 16.65 0.00 37.98 2.69
553 579 4.626081 CCGGGGGCGAGCCATAAG 62.626 72.222 16.65 4.03 37.98 1.73
1815 1894 4.406648 TCAATGTAGTCGATGGAGCATT 57.593 40.909 0.00 0.00 0.00 3.56
1964 2049 4.813526 CTCCAGTCCGCGTCGACG 62.814 72.222 32.57 32.57 43.27 5.12
2372 2502 2.971452 GGAGCCGAGAAGAACCGT 59.029 61.111 0.00 0.00 0.00 4.83
2966 3123 1.151450 CCTTGGCACACCCTGAAGT 59.849 57.895 0.00 0.00 39.29 3.01
3084 3265 2.347490 GCTCCTTGAAGCGGTCCA 59.653 61.111 0.00 0.00 31.56 4.02
3549 3780 2.621055 ACATAGGCAAACGAAGCAACAA 59.379 40.909 0.00 0.00 0.00 2.83
3751 4049 0.613260 ATGAAGGCAGCCGTGAACTA 59.387 50.000 3.85 0.00 0.00 2.24
3769 4067 1.410850 CGGAGCCTATGTCCACCCAT 61.411 60.000 0.00 0.00 33.14 4.00
3908 4207 0.179171 CACGTCGGTCGCTCTTACAT 60.179 55.000 0.00 0.00 44.19 2.29
4135 4435 4.927049 TGGAGATGGATTTCTTTGAGCTT 58.073 39.130 0.00 0.00 0.00 3.74


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

AutoCloner maintained by Alex Coulton.