Multiple sequence alignment - TraesCS5A01G362500

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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 TraesCS5A01G362500 chr5A 100.000 2548 0 0 1 2548 563443359 563445906 0.000000e+00 4706.0
1 TraesCS5A01G362500 chr5A 97.188 569 15 1 1 568 563541047 563541615 0.000000e+00 961.0
2 TraesCS5A01G362500 chr5A 96.309 569 19 2 1 568 563563206 563563773 0.000000e+00 933.0
3 TraesCS5A01G362500 chr7A 97.432 1986 43 4 569 2548 49208207 49210190 0.000000e+00 3378.0
4 TraesCS5A01G362500 chr7A 96.869 1980 47 5 572 2548 689996369 689994402 0.000000e+00 3299.0
5 TraesCS5A01G362500 chr7A 96.670 1982 49 6 571 2548 150203039 150201071 0.000000e+00 3278.0
6 TraesCS5A01G362500 chr7A 96.665 1649 41 4 902 2548 14472736 14471100 0.000000e+00 2728.0
7 TraesCS5A01G362500 chr7A 97.205 1145 26 3 571 1709 18189929 18191073 0.000000e+00 1932.0
8 TraesCS5A01G362500 chr2A 96.927 1985 54 7 566 2548 771778414 771780393 0.000000e+00 3321.0
9 TraesCS5A01G362500 chr2A 96.823 1983 43 6 569 2548 775967965 775966000 0.000000e+00 3295.0
10 TraesCS5A01G362500 chr2A 95.055 1982 52 23 571 2548 744582028 744583967 0.000000e+00 3075.0
11 TraesCS5A01G362500 chr2A 97.548 1142 24 2 572 1709 764220190 764221331 0.000000e+00 1951.0
12 TraesCS5A01G362500 chr2A 95.079 569 25 3 1 567 433377273 433377840 0.000000e+00 893.0
13 TraesCS5A01G362500 chr2A 93.345 571 35 3 1 568 214054027 214053457 0.000000e+00 841.0
14 TraesCS5A01G362500 chr1A 96.662 2007 51 9 552 2545 50511084 50513087 0.000000e+00 3321.0
15 TraesCS5A01G362500 chr3A 96.642 1995 40 7 565 2548 683237679 683235701 0.000000e+00 3288.0
16 TraesCS5A01G362500 chr3A 97.394 1151 26 2 563 1709 719846450 719847600 0.000000e+00 1956.0
17 TraesCS5A01G362500 chr3A 93.345 571 30 8 1 568 545299206 545299771 0.000000e+00 837.0
18 TraesCS5A01G362500 chr6A 95.541 1996 56 8 559 2548 203520925 203518957 0.000000e+00 3162.0
19 TraesCS5A01G362500 chr6A 93.380 574 33 5 1 571 371338296 371337725 0.000000e+00 845.0
20 TraesCS5A01G362500 chr4B 93.695 571 33 3 1 568 182286937 182287507 0.000000e+00 852.0
21 TraesCS5A01G362500 chr4B 92.845 573 38 3 1 571 312241924 312241353 0.000000e+00 828.0
22 TraesCS5A01G362500 chr6D 93.368 573 36 2 1 571 413277640 413277068 0.000000e+00 846.0
23 TraesCS5A01G362500 chr6D 90.767 574 50 3 1 571 38858324 38857751 0.000000e+00 763.0
24 TraesCS5A01G362500 chr6D 78.846 520 103 7 1 514 443552754 443553272 6.750000e-91 344.0
25 TraesCS5A01G362500 chr6D 79.046 482 93 8 39 514 443346939 443347418 8.790000e-85 324.0
26 TraesCS5A01G362500 chr6B 93.391 575 33 5 1 571 222676398 222675825 0.000000e+00 846.0
27 TraesCS5A01G362500 chr6B 92.348 575 37 6 1 571 151679293 151678722 0.000000e+00 811.0
28 TraesCS5A01G362500 chr5D 93.357 572 35 3 2 571 420459387 420458817 0.000000e+00 843.0
29 TraesCS5A01G362500 chr5D 88.636 572 60 5 1 568 273067974 273068544 0.000000e+00 691.0
30 TraesCS5A01G362500 chr4D 93.333 570 34 4 1 567 58940616 58941184 0.000000e+00 839.0
31 TraesCS5A01G362500 chr4D 92.469 571 40 3 3 571 127148925 127148356 0.000000e+00 813.0
32 TraesCS5A01G362500 chr3B 93.170 571 36 3 1 568 670760144 670760714 0.000000e+00 835.0
33 TraesCS5A01G362500 chr1B 92.105 570 40 5 1 567 611790400 611789833 0.000000e+00 798.0
34 TraesCS5A01G362500 chr7D 91.404 570 46 3 1 567 149106164 149106733 0.000000e+00 778.0
35 TraesCS5A01G362500 chr7D 90.941 574 49 3 1 571 232925761 232925188 0.000000e+00 769.0
36 TraesCS5A01G362500 chr3D 91.115 574 44 4 1 571 126364080 126363511 0.000000e+00 771.0
37 TraesCS5A01G362500 chr3D 90.418 574 52 3 1 571 87390850 87390277 0.000000e+00 752.0
38 TraesCS5A01G362500 chr2D 90.957 575 48 4 1 571 273018726 273018152 0.000000e+00 771.0
39 TraesCS5A01G362500 chrUn 89.373 574 51 6 1 571 92923445 92922879 0.000000e+00 713.0
40 TraesCS5A01G362500 chrUn 82.753 574 88 10 1 567 27750213 27749644 3.780000e-138 501.0
41 TraesCS5A01G362500 chr1D 88.281 512 54 6 60 568 174108654 174109162 2.170000e-170 608.0
42 TraesCS5A01G362500 chr1D 90.984 366 32 1 1 365 407809901 407809536 2.280000e-135 492.0
43 TraesCS5A01G362500 chr1D 97.297 37 1 0 1 37 192760292 192760328 2.120000e-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 TraesCS5A01G362500 chr5A 563443359 563445906 2547 False 4706 4706 100.000 1 2548 1 chr5A.!!$F1 2547
1 TraesCS5A01G362500 chr5A 563541047 563541615 568 False 961 961 97.188 1 568 1 chr5A.!!$F2 567
2 TraesCS5A01G362500 chr5A 563563206 563563773 567 False 933 933 96.309 1 568 1 chr5A.!!$F3 567
3 TraesCS5A01G362500 chr7A 49208207 49210190 1983 False 3378 3378 97.432 569 2548 1 chr7A.!!$F2 1979
4 TraesCS5A01G362500 chr7A 689994402 689996369 1967 True 3299 3299 96.869 572 2548 1 chr7A.!!$R3 1976
5 TraesCS5A01G362500 chr7A 150201071 150203039 1968 True 3278 3278 96.670 571 2548 1 chr7A.!!$R2 1977
6 TraesCS5A01G362500 chr7A 14471100 14472736 1636 True 2728 2728 96.665 902 2548 1 chr7A.!!$R1 1646
7 TraesCS5A01G362500 chr7A 18189929 18191073 1144 False 1932 1932 97.205 571 1709 1 chr7A.!!$F1 1138
8 TraesCS5A01G362500 chr2A 771778414 771780393 1979 False 3321 3321 96.927 566 2548 1 chr2A.!!$F4 1982
9 TraesCS5A01G362500 chr2A 775966000 775967965 1965 True 3295 3295 96.823 569 2548 1 chr2A.!!$R2 1979
10 TraesCS5A01G362500 chr2A 744582028 744583967 1939 False 3075 3075 95.055 571 2548 1 chr2A.!!$F2 1977
11 TraesCS5A01G362500 chr2A 764220190 764221331 1141 False 1951 1951 97.548 572 1709 1 chr2A.!!$F3 1137
12 TraesCS5A01G362500 chr2A 433377273 433377840 567 False 893 893 95.079 1 567 1 chr2A.!!$F1 566
13 TraesCS5A01G362500 chr2A 214053457 214054027 570 True 841 841 93.345 1 568 1 chr2A.!!$R1 567
14 TraesCS5A01G362500 chr1A 50511084 50513087 2003 False 3321 3321 96.662 552 2545 1 chr1A.!!$F1 1993
15 TraesCS5A01G362500 chr3A 683235701 683237679 1978 True 3288 3288 96.642 565 2548 1 chr3A.!!$R1 1983
16 TraesCS5A01G362500 chr3A 719846450 719847600 1150 False 1956 1956 97.394 563 1709 1 chr3A.!!$F2 1146
17 TraesCS5A01G362500 chr3A 545299206 545299771 565 False 837 837 93.345 1 568 1 chr3A.!!$F1 567
18 TraesCS5A01G362500 chr6A 203518957 203520925 1968 True 3162 3162 95.541 559 2548 1 chr6A.!!$R1 1989
19 TraesCS5A01G362500 chr6A 371337725 371338296 571 True 845 845 93.380 1 571 1 chr6A.!!$R2 570
20 TraesCS5A01G362500 chr4B 182286937 182287507 570 False 852 852 93.695 1 568 1 chr4B.!!$F1 567
21 TraesCS5A01G362500 chr4B 312241353 312241924 571 True 828 828 92.845 1 571 1 chr4B.!!$R1 570
22 TraesCS5A01G362500 chr6D 413277068 413277640 572 True 846 846 93.368 1 571 1 chr6D.!!$R2 570
23 TraesCS5A01G362500 chr6D 38857751 38858324 573 True 763 763 90.767 1 571 1 chr6D.!!$R1 570
24 TraesCS5A01G362500 chr6D 443552754 443553272 518 False 344 344 78.846 1 514 1 chr6D.!!$F2 513
25 TraesCS5A01G362500 chr6B 222675825 222676398 573 True 846 846 93.391 1 571 1 chr6B.!!$R2 570
26 TraesCS5A01G362500 chr6B 151678722 151679293 571 True 811 811 92.348 1 571 1 chr6B.!!$R1 570
27 TraesCS5A01G362500 chr5D 420458817 420459387 570 True 843 843 93.357 2 571 1 chr5D.!!$R1 569
28 TraesCS5A01G362500 chr5D 273067974 273068544 570 False 691 691 88.636 1 568 1 chr5D.!!$F1 567
29 TraesCS5A01G362500 chr4D 58940616 58941184 568 False 839 839 93.333 1 567 1 chr4D.!!$F1 566
30 TraesCS5A01G362500 chr4D 127148356 127148925 569 True 813 813 92.469 3 571 1 chr4D.!!$R1 568
31 TraesCS5A01G362500 chr3B 670760144 670760714 570 False 835 835 93.170 1 568 1 chr3B.!!$F1 567
32 TraesCS5A01G362500 chr1B 611789833 611790400 567 True 798 798 92.105 1 567 1 chr1B.!!$R1 566
33 TraesCS5A01G362500 chr7D 149106164 149106733 569 False 778 778 91.404 1 567 1 chr7D.!!$F1 566
34 TraesCS5A01G362500 chr7D 232925188 232925761 573 True 769 769 90.941 1 571 1 chr7D.!!$R1 570
35 TraesCS5A01G362500 chr3D 126363511 126364080 569 True 771 771 91.115 1 571 1 chr3D.!!$R2 570
36 TraesCS5A01G362500 chr3D 87390277 87390850 573 True 752 752 90.418 1 571 1 chr3D.!!$R1 570
37 TraesCS5A01G362500 chr2D 273018152 273018726 574 True 771 771 90.957 1 571 1 chr2D.!!$R1 570
38 TraesCS5A01G362500 chrUn 92922879 92923445 566 True 713 713 89.373 1 571 1 chrUn.!!$R2 570
39 TraesCS5A01G362500 chrUn 27749644 27750213 569 True 501 501 82.753 1 567 1 chrUn.!!$R1 566
40 TraesCS5A01G362500 chr1D 174108654 174109162 508 False 608 608 88.281 60 568 1 chr1D.!!$F1 508

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
548 560 0.244994 ACAGAGTAAGCAGACCGCAG 59.755 55.0 0.0 0.0 46.13 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2320 2375 2.096657 CACACGTGTCCAAACATTCACA 59.903 45.455 20.49 0.0 37.81 3.58 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
224 227 0.926155 CCAGCACGATCAATCTCACG 59.074 55.000 0.0 0.0 0.00 4.35
371 377 7.396339 ACCTTCATGTGTCTATTAGTGAGTGTA 59.604 37.037 0.0 0.0 0.00 2.90
546 558 0.737715 CCACAGAGTAAGCAGACCGC 60.738 60.000 0.0 0.0 42.91 5.68
548 560 0.244994 ACAGAGTAAGCAGACCGCAG 59.755 55.000 0.0 0.0 46.13 5.18
743 757 3.948719 GGTGGGACCAGGCGACAA 61.949 66.667 0.0 0.0 38.42 3.18
850 864 1.067776 GCTATATAAGCGGGCGACAGT 60.068 52.381 0.0 0.0 42.53 3.55
880 894 1.244697 ACGGTGACAGAGAGCACGAT 61.245 55.000 0.0 0.0 35.91 3.73
1136 1166 0.818296 CCGAGGAACCAGAATCGTCT 59.182 55.000 0.0 0.0 33.43 4.18
1237 1267 4.037923 GGTTGATCTGTTTGGTGTTCATGT 59.962 41.667 0.0 0.0 0.00 3.21
1738 1785 3.682696 TCAATGAAATGCAGCTCTCTGT 58.317 40.909 0.0 0.0 42.29 3.41
1750 1797 3.056250 CAGCTCTCTGTTCTGCCTTTCTA 60.056 47.826 0.0 0.0 35.61 2.10
2338 2393 2.612212 GACTGTGAATGTTTGGACACGT 59.388 45.455 0.0 0.0 38.91 4.49
2537 2592 3.795688 ATGAAACAGAGGGCTTCTCAA 57.204 42.857 0.0 0.0 44.81 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
224 227 7.548780 GGTTGGATATGATTATTGAGAGAGCTC 59.451 40.741 5.27 5.27 41.67 4.09
371 377 1.608717 GCACTCTCCCATGTCGGACT 61.609 60.000 9.88 0.00 36.56 3.85
421 432 3.432326 GGAAGTTATCTTGTCCGGCTGAT 60.432 47.826 0.00 0.00 33.64 2.90
743 757 5.234752 GGTCTGAATAAAATTGGCCGTTTT 58.765 37.500 18.90 18.90 33.67 2.43
865 879 2.420372 GTCACTATCGTGCTCTCTGTCA 59.580 50.000 0.00 0.00 40.99 3.58
880 894 1.002990 TCTCTCGCCGTGGTCACTA 60.003 57.895 0.00 0.00 0.00 2.74
1136 1166 0.663269 CTCGCTGCACACGTAGAACA 60.663 55.000 0.00 0.00 0.00 3.18
1237 1267 4.761739 CCAAAGAAAGAAGCATGTCACCTA 59.238 41.667 0.00 0.00 0.00 3.08
1709 1756 4.630069 AGCTGCATTTCATTGATCAAAAGC 59.370 37.500 13.09 10.48 0.00 3.51
1908 1958 7.346751 TCAATTAGCTTCCACAAAAAGTTCT 57.653 32.000 0.00 0.00 0.00 3.01
2179 2233 4.308458 CACGCGGTCCTGGGTTCA 62.308 66.667 12.47 0.00 32.02 3.18
2320 2375 2.096657 CACACGTGTCCAAACATTCACA 59.903 45.455 20.49 0.00 37.81 3.58
2338 2393 5.913137 AACAATGGAAAAACACTCTCACA 57.087 34.783 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.