Multiple sequence alignment - TraesCS4A01G016100

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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 TraesCS4A01G016100 chr4A 100.000 2321 0 0 1 2321 10535555 10533235 0.000000e+00 4287.0
1 TraesCS4A01G016100 chr5A 98.927 932 6 2 580 1507 353597517 353598448 0.000000e+00 1663.0
2 TraesCS4A01G016100 chr6B 98.499 933 10 2 579 1507 551036062 551035130 0.000000e+00 1642.0
3 TraesCS4A01G016100 chr4D 94.377 818 43 3 1506 2321 458680330 458681146 0.000000e+00 1253.0
4 TraesCS4A01G016100 chr4D 94.483 580 32 0 1 580 99724490 99725069 0.000000e+00 894.0
5 TraesCS4A01G016100 chr3A 92.244 851 60 3 661 1507 642168525 642169373 0.000000e+00 1201.0
6 TraesCS4A01G016100 chr3A 97.778 45 1 0 587 631 642168482 642168526 6.880000e-11 78.7
7 TraesCS4A01G016100 chr3D 90.920 815 70 4 1506 2318 82304791 82305603 0.000000e+00 1092.0
8 TraesCS4A01G016100 chr3D 90.146 822 69 10 1506 2321 75719092 75719907 0.000000e+00 1059.0
9 TraesCS4A01G016100 chr3D 89.866 819 78 5 1506 2321 43125457 43124641 0.000000e+00 1048.0
10 TraesCS4A01G016100 chr3D 94.483 580 32 0 1 580 142993141 142992562 0.000000e+00 894.0
11 TraesCS4A01G016100 chr3D 94.320 581 33 0 1 581 160598964 160598384 0.000000e+00 891.0
12 TraesCS4A01G016100 chr3D 94.037 587 33 2 1 587 346007731 346007147 0.000000e+00 889.0
13 TraesCS4A01G016100 chr5D 90.146 822 73 6 1506 2321 190119813 190120632 0.000000e+00 1062.0
14 TraesCS4A01G016100 chr5D 89.988 819 78 4 1506 2321 46520570 46521387 0.000000e+00 1055.0
15 TraesCS4A01G016100 chr5D 94.483 580 31 1 1 580 202668463 202667885 0.000000e+00 893.0
16 TraesCS4A01G016100 chr7D 89.988 819 75 6 1506 2321 181855183 181854369 0.000000e+00 1051.0
17 TraesCS4A01G016100 chr7D 89.878 820 78 5 1506 2321 417798150 417797332 0.000000e+00 1050.0
18 TraesCS4A01G016100 chr7D 94.483 580 30 2 1 580 501881301 501880724 0.000000e+00 893.0
19 TraesCS4A01G016100 chr3B 89.781 822 74 10 1506 2321 67129520 67128703 0.000000e+00 1044.0
20 TraesCS4A01G016100 chr3B 96.897 290 8 1 590 878 293752708 293752419 3.470000e-133 484.0
21 TraesCS4A01G016100 chr3B 83.140 172 15 8 1329 1493 169694146 169693982 6.680000e-31 145.0
22 TraesCS4A01G016100 chr1D 94.828 580 30 0 1 580 109621970 109621391 0.000000e+00 905.0
23 TraesCS4A01G016100 chr2D 94.655 580 31 0 1 580 539800350 539799771 0.000000e+00 900.0
24 TraesCS4A01G016100 chr1B 94.483 580 30 2 1 580 334867270 334866693 0.000000e+00 893.0


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 TraesCS4A01G016100 chr4A 10533235 10535555 2320 True 4287.00 4287 100.000 1 2321 1 chr4A.!!$R1 2320
1 TraesCS4A01G016100 chr5A 353597517 353598448 931 False 1663.00 1663 98.927 580 1507 1 chr5A.!!$F1 927
2 TraesCS4A01G016100 chr6B 551035130 551036062 932 True 1642.00 1642 98.499 579 1507 1 chr6B.!!$R1 928
3 TraesCS4A01G016100 chr4D 458680330 458681146 816 False 1253.00 1253 94.377 1506 2321 1 chr4D.!!$F2 815
4 TraesCS4A01G016100 chr4D 99724490 99725069 579 False 894.00 894 94.483 1 580 1 chr4D.!!$F1 579
5 TraesCS4A01G016100 chr3A 642168482 642169373 891 False 639.85 1201 95.011 587 1507 2 chr3A.!!$F1 920
6 TraesCS4A01G016100 chr3D 82304791 82305603 812 False 1092.00 1092 90.920 1506 2318 1 chr3D.!!$F2 812
7 TraesCS4A01G016100 chr3D 75719092 75719907 815 False 1059.00 1059 90.146 1506 2321 1 chr3D.!!$F1 815
8 TraesCS4A01G016100 chr3D 43124641 43125457 816 True 1048.00 1048 89.866 1506 2321 1 chr3D.!!$R1 815
9 TraesCS4A01G016100 chr3D 142992562 142993141 579 True 894.00 894 94.483 1 580 1 chr3D.!!$R2 579
10 TraesCS4A01G016100 chr3D 160598384 160598964 580 True 891.00 891 94.320 1 581 1 chr3D.!!$R3 580
11 TraesCS4A01G016100 chr3D 346007147 346007731 584 True 889.00 889 94.037 1 587 1 chr3D.!!$R4 586
12 TraesCS4A01G016100 chr5D 190119813 190120632 819 False 1062.00 1062 90.146 1506 2321 1 chr5D.!!$F2 815
13 TraesCS4A01G016100 chr5D 46520570 46521387 817 False 1055.00 1055 89.988 1506 2321 1 chr5D.!!$F1 815
14 TraesCS4A01G016100 chr5D 202667885 202668463 578 True 893.00 893 94.483 1 580 1 chr5D.!!$R1 579
15 TraesCS4A01G016100 chr7D 181854369 181855183 814 True 1051.00 1051 89.988 1506 2321 1 chr7D.!!$R1 815
16 TraesCS4A01G016100 chr7D 417797332 417798150 818 True 1050.00 1050 89.878 1506 2321 1 chr7D.!!$R2 815
17 TraesCS4A01G016100 chr7D 501880724 501881301 577 True 893.00 893 94.483 1 580 1 chr7D.!!$R3 579
18 TraesCS4A01G016100 chr3B 67128703 67129520 817 True 1044.00 1044 89.781 1506 2321 1 chr3B.!!$R1 815
19 TraesCS4A01G016100 chr1D 109621391 109621970 579 True 905.00 905 94.828 1 580 1 chr1D.!!$R1 579
20 TraesCS4A01G016100 chr2D 539799771 539800350 579 True 900.00 900 94.655 1 580 1 chr2D.!!$R1 579
21 TraesCS4A01G016100 chr1B 334866693 334867270 577 True 893.00 893 94.483 1 580 1 chr1B.!!$R1 579

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
512 513 1.45945 TTTGCCACTCCTTATTCCGC 58.541 50.0 0.0 0.0 0.0 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2011 2028 0.88649 AAGCGCTTGTTGGGAGACAG 60.886 55.0 24.4 0.0 0.0 3.51 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
331 332 9.770097 GACTCATATCATACAAGATTCTCCAAA 57.230 33.333 0.00 0.00 0.00 3.28
400 401 5.065731 AGTTACCGATAGACGAAGACGAAAT 59.934 40.000 0.00 0.00 45.77 2.17
414 415 2.104963 GACGAAATAGGGGATGCCTTCT 59.895 50.000 2.19 0.00 0.00 2.85
461 462 9.495572 CTCTTGGTTATCCTTGAATATTACCTC 57.504 37.037 0.00 0.00 34.23 3.85
511 512 2.159379 GCTTTTGCCACTCCTTATTCCG 60.159 50.000 0.00 0.00 40.15 4.30
512 513 1.459450 TTTGCCACTCCTTATTCCGC 58.541 50.000 0.00 0.00 0.00 5.54
567 568 6.024552 ACTTCACAACACAAAACTCAACAT 57.975 33.333 0.00 0.00 0.00 2.71
1255 1260 0.249405 CTCTGCTCAAGATCTCGCCC 60.249 60.000 0.00 0.00 33.29 6.13
1699 1707 9.956720 ACATAGAAAACAGAATCTGTCAAAAAG 57.043 29.630 17.02 7.12 44.62 2.27
1732 1740 8.189460 AGTTTGTAGTAATCTGGATAGTTCGAC 58.811 37.037 0.00 0.00 0.00 4.20
1860 1874 3.842925 TTCTGGGACTGGGCGCAAC 62.843 63.158 10.83 1.07 0.00 4.17
2011 2028 4.206477 ACAGCAAGGAAAAATATTGGGC 57.794 40.909 0.00 0.00 0.00 5.36
2082 2099 8.806177 TGATAATTTTAATGATGCTCACATGC 57.194 30.769 0.00 0.00 36.35 4.06
2237 2254 6.256539 GCAAAGGAGAAGAAAGAAACAAAAGG 59.743 38.462 0.00 0.00 0.00 3.11
2308 2325 8.223330 ACAGCCATATTTTCCTCTCTCATAATT 58.777 33.333 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
142 143 2.779755 TCTTTTTAGAGCATGGCGGA 57.220 45.000 0.00 0.00 0.00 5.54
195 196 9.890629 TCTATGTGCTTCACTTATATCTTTTGT 57.109 29.630 0.00 0.00 35.11 2.83
247 248 1.143073 ACACCTTTTGAGAGGGACACC 59.857 52.381 0.00 0.00 41.31 4.16
400 401 1.385915 CCCCAGAAGGCATCCCCTA 60.386 63.158 0.00 0.00 45.62 3.53
493 494 1.271652 TGCGGAATAAGGAGTGGCAAA 60.272 47.619 0.00 0.00 0.00 3.68
511 512 2.952310 GGGTAAGGATTTGATGGACTGC 59.048 50.000 0.00 0.00 0.00 4.40
512 513 4.235079 TGGGTAAGGATTTGATGGACTG 57.765 45.455 0.00 0.00 0.00 3.51
573 574 3.323403 CGGGAAGAGAGAGCCTTTATGAT 59.677 47.826 0.00 0.00 0.00 2.45
993 998 3.053291 GCGAACGCCATGGGTCAA 61.053 61.111 15.13 0.00 34.56 3.18
1081 1086 2.034558 CCGCATCCACAACAAAAGAAGT 59.965 45.455 0.00 0.00 0.00 3.01
1182 1187 4.889856 CGCACCGGATCCGCATCA 62.890 66.667 29.12 0.00 38.24 3.07
1699 1707 6.966021 TCCAGATTACTACAAACTGTTTTGC 58.034 36.000 2.41 0.00 45.32 3.68
1806 1816 9.414295 TCACAGAAGCATGATAAAATTTTGAAG 57.586 29.630 13.76 0.83 0.00 3.02
1838 1852 1.657751 GCGCCCAGTCCCAGAATTTC 61.658 60.000 0.00 0.00 0.00 2.17
1898 1912 1.972588 AGACCTTGGGATGGCTTACT 58.027 50.000 0.00 0.00 0.00 2.24
1945 1962 3.440522 GCCTCTGGTTAGATGTGGTTTTC 59.559 47.826 0.00 0.00 31.21 2.29
2011 2028 0.886490 AAGCGCTTGTTGGGAGACAG 60.886 55.000 24.40 0.00 0.00 3.51
2082 2099 8.077991 TCTCTTTGTGTTTCAATTGCTATCTTG 58.922 33.333 0.00 0.00 35.84 3.02
2237 2254 7.829378 ATTACCTCTCGTTATGTTGAGTTTC 57.171 36.000 0.00 0.00 33.88 2.78


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

AutoCloner maintained by Alex Coulton.