Multiple sequence alignment - TraesCS1D01G197400

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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 TraesCS1D01G197400 chr1D 100.000 4221 0 0 1 4221 278511183 278515403 0.000000e+00 7795.0
1 TraesCS1D01G197400 chr1D 85.424 295 39 3 1719 2010 397213159 397212866 1.910000e-78 303.0
2 TraesCS1D01G197400 chr1B 93.896 2736 112 15 16 2699 378396066 378398798 0.000000e+00 4076.0
3 TraesCS1D01G197400 chr1B 92.438 1005 40 13 2743 3743 378398897 378399869 0.000000e+00 1402.0
4 TraesCS1D01G197400 chr1B 94.309 369 13 4 3738 4103 378399911 378400274 3.690000e-155 558.0
5 TraesCS1D01G197400 chr1B 83.392 283 32 10 1 273 432827627 432827350 9.060000e-62 248.0
6 TraesCS1D01G197400 chr1B 100.000 38 0 0 4184 4221 378400277 378400314 2.110000e-08 71.3
7 TraesCS1D01G197400 chr1A 92.565 1735 97 8 331 2036 350748775 350750506 0.000000e+00 2460.0
8 TraesCS1D01G197400 chr1A 94.036 1006 34 10 2743 3748 350751496 350752475 0.000000e+00 1502.0
9 TraesCS1D01G197400 chr1A 94.194 620 22 2 2080 2699 350750800 350751405 0.000000e+00 933.0
10 TraesCS1D01G197400 chr1A 95.405 370 13 4 3738 4103 350752500 350752869 1.690000e-163 586.0
11 TraesCS1D01G197400 chr1A 85.235 298 34 8 1719 2010 510700403 510700696 8.870000e-77 298.0
12 TraesCS1D01G197400 chr1A 86.022 279 29 8 4 273 403018305 403018582 1.480000e-74 291.0
13 TraesCS1D01G197400 chr1A 94.872 39 1 1 4184 4221 350752872 350752910 4.560000e-05 60.2
14 TraesCS1D01G197400 chr2B 86.622 299 34 5 1716 2010 494402008 494401712 4.070000e-85 326.0
15 TraesCS1D01G197400 chr7A 85.382 301 37 6 1715 2010 645255949 645255651 5.300000e-79 305.0
16 TraesCS1D01G197400 chr7A 82.143 112 18 2 358 468 360617657 360617547 1.250000e-15 95.3
17 TraesCS1D01G197400 chr3B 85.284 299 40 3 1716 2010 44638867 44639165 5.300000e-79 305.0
18 TraesCS1D01G197400 chr3D 84.950 299 41 3 1716 2010 469481226 469481524 2.470000e-77 300.0
19 TraesCS1D01G197400 chr3D 84.672 274 33 6 1 266 501747298 501747570 9.000000e-67 265.0
20 TraesCS1D01G197400 chr3D 82.374 278 35 8 4 273 439843054 439842783 3.280000e-56 230.0
21 TraesCS1D01G197400 chr6D 85.135 296 39 4 1719 2010 452576720 452576426 8.870000e-77 298.0
22 TraesCS1D01G197400 chr6D 100.000 86 0 0 4102 4187 79649841 79649926 4.370000e-35 159.0
23 TraesCS1D01G197400 chr5B 83.624 287 34 10 1 279 590584425 590584706 1.510000e-64 257.0
24 TraesCS1D01G197400 chr7D 83.871 279 34 5 4 273 614109038 614108762 5.420000e-64 255.0
25 TraesCS1D01G197400 chr7D 100.000 86 0 0 4102 4187 530797522 530797437 4.370000e-35 159.0
26 TraesCS1D01G197400 chr7D 81.905 105 15 3 358 460 311276542 311276440 7.520000e-13 86.1
27 TraesCS1D01G197400 chr5D 83.746 283 33 9 3 273 265522677 265522396 5.420000e-64 255.0
28 TraesCS1D01G197400 chr5D 100.000 86 0 0 4102 4187 6163847 6163762 4.370000e-35 159.0
29 TraesCS1D01G197400 chr5D 100.000 86 0 0 4102 4187 6261839 6261754 4.370000e-35 159.0
30 TraesCS1D01G197400 chr3A 82.734 278 39 6 4 273 736473866 736473590 5.450000e-59 239.0
31 TraesCS1D01G197400 chrUn 100.000 86 0 0 4102 4187 414537975 414537890 4.370000e-35 159.0
32 TraesCS1D01G197400 chr7B 100.000 86 0 0 4102 4187 137677930 137678015 4.370000e-35 159.0
33 TraesCS1D01G197400 chr4A 100.000 86 0 0 4102 4187 309455116 309455031 4.370000e-35 159.0
34 TraesCS1D01G197400 chr2D 100.000 86 0 0 4102 4187 135988594 135988679 4.370000e-35 159.0
35 TraesCS1D01G197400 chr2D 100.000 86 0 0 4102 4187 299147852 299147937 4.370000e-35 159.0


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 TraesCS1D01G197400 chr1D 278511183 278515403 4220 False 7795.000 7795 100.00000 1 4221 1 chr1D.!!$F1 4220
1 TraesCS1D01G197400 chr1B 378396066 378400314 4248 False 1526.825 4076 95.16075 16 4221 4 chr1B.!!$F1 4205
2 TraesCS1D01G197400 chr1A 350748775 350752910 4135 False 1108.240 2460 94.21440 331 4221 5 chr1A.!!$F3 3890


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
143 145 0.034767 CCTCAGAATTCCAGCTGCCA 60.035 55.0 8.66 0.00 32.27 4.92 F
389 392 0.038744 TCGACCCTCTAACCGGTTCT 59.961 55.0 26.16 2.77 30.56 3.01 F
1061 1088 0.187361 CTCCTACTCCTCTCCCCCAG 59.813 65.0 0.00 0.00 0.00 4.45 F
1579 1606 0.755686 CTGGATACTCCTGTGAGCCC 59.244 60.0 0.00 0.00 42.74 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2041 2086 2.502633 TGCTTTGGCAGAGCAACAA 58.497 47.368 28.10 6.96 46.35 2.83 R
2357 2658 2.166459 CCATTGACGAGAAGCAGGTCTA 59.834 50.000 0.00 0.00 0.00 2.59 R
2559 2862 0.035739 TTTGACGAAGGGGGCTACAC 59.964 55.000 0.00 0.00 0.00 2.90 R
3529 3891 0.253894 CCATGTCATGGTGCTCAGGA 59.746 55.000 21.98 0.00 45.54 3.86 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)



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AutoCloner maintained by Alex Coulton.