Multiple sequence alignment - TraesCS2B01G015300

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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 TraesCS2B01G015300 chr2B 100.000 6238 0 0 1 6238 7151370 7145133 0.000000e+00 11520
1 TraesCS2B01G015300 chr2B 99.596 5446 20 2 1 5444 7118810 7113365 0.000000e+00 9934
2 TraesCS2B01G015300 chr2B 99.431 5445 29 2 1 5444 7077128 7071685 0.000000e+00 9882
3 TraesCS2B01G015300 chr2B 98.753 5451 58 5 1 5444 454730531 454735978 0.000000e+00 9681
4 TraesCS2B01G015300 chr2B 94.467 5458 285 14 1 5444 6968627 6974081 0.000000e+00 8390
5 TraesCS2B01G015300 chr2B 98.584 4732 58 4 1 4726 454757221 454761949 0.000000e+00 8359
6 TraesCS2B01G015300 chr2B 94.137 5458 278 15 1 5444 6888217 6893646 0.000000e+00 8268
7 TraesCS2B01G015300 chr2B 99.089 4390 35 2 1060 5444 7037396 7033007 0.000000e+00 7880
8 TraesCS2B01G015300 chr2D 93.464 4590 260 28 284 4853 4036591 4041160 0.000000e+00 6778
9 TraesCS2B01G015300 chr2D 93.822 4063 213 24 809 4853 3985183 3989225 0.000000e+00 6078
10 TraesCS2B01G015300 chr2D 95.323 449 21 0 4996 5444 3989271 3989719 0.000000e+00 713
11 TraesCS2B01G015300 chr2D 95.323 449 21 0 4996 5444 4041206 4041654 0.000000e+00 713
12 TraesCS2B01G015300 chr2D 91.713 181 15 0 1 181 4036409 4036589 1.040000e-62 252
13 TraesCS2B01G015300 chr2D 90.055 181 18 0 1 181 3984422 3984602 1.050000e-57 235
14 TraesCS2B01G015300 chrUn 100.000 1325 0 0 318 1642 411497414 411496090 0.000000e+00 2447
15 TraesCS2B01G015300 chrUn 98.994 795 8 0 5444 6238 265904360 265903566 0.000000e+00 1424
16 TraesCS2B01G015300 chrUn 98.616 795 11 0 5444 6238 265897370 265896576 0.000000e+00 1408
17 TraesCS2B01G015300 chrUn 99.441 716 4 0 4729 5444 357090180 357089465 0.000000e+00 1301
18 TraesCS2B01G015300 chrUn 86.364 880 104 8 1 864 319763625 319764504 0.000000e+00 946
19 TraesCS2B01G015300 chrUn 98.073 519 7 1 1 519 362694272 362694787 0.000000e+00 900
20 TraesCS2B01G015300 chrUn 94.611 167 9 0 4902 5068 324495671 324495837 6.200000e-65 259
21 TraesCS2B01G015300 chrUn 94.611 167 9 0 4902 5068 332390706 332390540 6.200000e-65 259
22 TraesCS2B01G015300 chr1B 98.618 796 10 1 5444 6238 63149476 63150271 0.000000e+00 1408
23 TraesCS2B01G015300 chr1B 98.616 795 11 0 5444 6238 387227307 387228101 0.000000e+00 1408
24 TraesCS2B01G015300 chr1B 98.618 796 10 1 5444 6238 630621734 630620939 0.000000e+00 1408
25 TraesCS2B01G015300 chr1A 98.618 796 10 1 5444 6238 562275184 562274389 0.000000e+00 1408
26 TraesCS2B01G015300 chr5A 98.492 796 10 2 5445 6238 451933292 451934087 0.000000e+00 1402
27 TraesCS2B01G015300 chr3A 98.492 796 10 2 5444 6238 694209308 694210102 0.000000e+00 1402
28 TraesCS2B01G015300 chr7B 98.367 796 12 1 5444 6238 491119163 491118368 0.000000e+00 1397


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 TraesCS2B01G015300 chr2B 7145133 7151370 6237 True 11520 11520 100.000000 1 6238 1 chr2B.!!$R4 6237
1 TraesCS2B01G015300 chr2B 7113365 7118810 5445 True 9934 9934 99.596000 1 5444 1 chr2B.!!$R3 5443
2 TraesCS2B01G015300 chr2B 7071685 7077128 5443 True 9882 9882 99.431000 1 5444 1 chr2B.!!$R2 5443
3 TraesCS2B01G015300 chr2B 454730531 454735978 5447 False 9681 9681 98.753000 1 5444 1 chr2B.!!$F3 5443
4 TraesCS2B01G015300 chr2B 6968627 6974081 5454 False 8390 8390 94.467000 1 5444 1 chr2B.!!$F2 5443
5 TraesCS2B01G015300 chr2B 454757221 454761949 4728 False 8359 8359 98.584000 1 4726 1 chr2B.!!$F4 4725
6 TraesCS2B01G015300 chr2B 6888217 6893646 5429 False 8268 8268 94.137000 1 5444 1 chr2B.!!$F1 5443
7 TraesCS2B01G015300 chr2B 7033007 7037396 4389 True 7880 7880 99.089000 1060 5444 1 chr2B.!!$R1 4384
8 TraesCS2B01G015300 chr2D 4036409 4041654 5245 False 2581 6778 93.500000 1 5444 3 chr2D.!!$F2 5443
9 TraesCS2B01G015300 chr2D 3984422 3989719 5297 False 2342 6078 93.066667 1 5444 3 chr2D.!!$F1 5443
10 TraesCS2B01G015300 chrUn 411496090 411497414 1324 True 2447 2447 100.000000 318 1642 1 chrUn.!!$R5 1324
11 TraesCS2B01G015300 chrUn 265903566 265904360 794 True 1424 1424 98.994000 5444 6238 1 chrUn.!!$R2 794
12 TraesCS2B01G015300 chrUn 265896576 265897370 794 True 1408 1408 98.616000 5444 6238 1 chrUn.!!$R1 794
13 TraesCS2B01G015300 chrUn 357089465 357090180 715 True 1301 1301 99.441000 4729 5444 1 chrUn.!!$R4 715
14 TraesCS2B01G015300 chrUn 319763625 319764504 879 False 946 946 86.364000 1 864 1 chrUn.!!$F1 863
15 TraesCS2B01G015300 chrUn 362694272 362694787 515 False 900 900 98.073000 1 519 1 chrUn.!!$F3 518
16 TraesCS2B01G015300 chr1B 63149476 63150271 795 False 1408 1408 98.618000 5444 6238 1 chr1B.!!$F1 794
17 TraesCS2B01G015300 chr1B 387227307 387228101 794 False 1408 1408 98.616000 5444 6238 1 chr1B.!!$F2 794
18 TraesCS2B01G015300 chr1B 630620939 630621734 795 True 1408 1408 98.618000 5444 6238 1 chr1B.!!$R1 794
19 TraesCS2B01G015300 chr1A 562274389 562275184 795 True 1408 1408 98.618000 5444 6238 1 chr1A.!!$R1 794
20 TraesCS2B01G015300 chr5A 451933292 451934087 795 False 1402 1402 98.492000 5445 6238 1 chr5A.!!$F1 793
21 TraesCS2B01G015300 chr3A 694209308 694210102 794 False 1402 1402 98.492000 5444 6238 1 chr3A.!!$F1 794
22 TraesCS2B01G015300 chr7B 491118368 491119163 795 True 1397 1397 98.367000 5444 6238 1 chr7B.!!$R1 794

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
2179 2270 7.235606 ACAAAGCTATCTATATCCCAAGCTACA 59.764 37.037 0.0 0.0 39.29 2.74 F
2420 2513 0.816825 CTACTACTCCGGCCTACGCA 60.817 60.000 0.0 0.0 42.52 5.24 F
2910 3006 6.473778 CACTGGAGATACGAGTTGTTAGATTG 59.526 42.308 0.0 0.0 35.46 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3456 3556 2.910688 ATGTTGGTGTTCTCGTGACT 57.089 45.000 0.00 0.0 0.00 3.41 R
4617 4726 5.956068 TCGAACATCATGGAAAAATCACA 57.044 34.783 0.00 0.0 0.00 3.58 R
5308 5421 1.406539 CCCATCTTGAAGGCCAATTCG 59.593 52.381 5.01 0.0 33.68 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
2179 2270 7.235606 ACAAAGCTATCTATATCCCAAGCTACA 59.764 37.037 0.00 0.00 39.29 2.74
2420 2513 0.816825 CTACTACTCCGGCCTACGCA 60.817 60.000 0.00 0.00 42.52 5.24
2578 2671 9.610705 TCACTAGTCGACACTTCTTATAGTATT 57.389 33.333 19.50 0.00 33.62 1.89
2910 3006 6.473778 CACTGGAGATACGAGTTGTTAGATTG 59.526 42.308 0.00 0.00 35.46 2.67
3082 3181 6.577103 TGTTGTTTAAATCCAGCAATGACAA 58.423 32.000 0.00 0.00 0.00 3.18
3456 3556 7.112122 ACAATAGAAGCTCCATTGACAATGTA 58.888 34.615 23.27 9.98 37.18 2.29
4617 4726 5.296531 TCACAGTCATAAATATGTGCGCAAT 59.703 36.000 14.00 11.02 42.15 3.56
5336 5449 3.137360 GGCCTTCAAGATGGGATAAGAGT 59.863 47.826 0.00 0.00 0.00 3.24
5450 5563 3.669122 CGAACTACGATATAGCTGTTGGC 59.331 47.826 0.00 0.00 45.77 4.52
5578 5691 1.598132 CGATGACACGACGTAGAGGAT 59.402 52.381 0.00 0.00 35.09 3.24
5984 6099 2.422746 CCCCTCCAATCCTAGTCCAAT 58.577 52.381 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2179 2270 7.492344 CAGTTGCTTCTTTGTTTCATAGGTTTT 59.508 33.333 0.00 0.00 0.00 2.43
2910 3006 6.036191 TCGCCAAAACCAAAAATAGTTGAAAC 59.964 34.615 0.00 0.00 0.00 2.78
3082 3181 6.607019 TCCACTAAGGACATTTTTACCACTT 58.393 36.000 0.00 0.00 43.07 3.16
3456 3556 2.910688 ATGTTGGTGTTCTCGTGACT 57.089 45.000 0.00 0.00 0.00 3.41
4617 4726 5.956068 TCGAACATCATGGAAAAATCACA 57.044 34.783 0.00 0.00 0.00 3.58
5308 5421 1.406539 CCCATCTTGAAGGCCAATTCG 59.593 52.381 5.01 0.00 33.68 3.34
5336 5449 2.672996 GGCAGGAGAAAAGCGGCA 60.673 61.111 1.45 0.00 0.00 5.69
5578 5691 2.403259 TCGTGAAGACGTACGACTACA 58.597 47.619 24.41 13.28 46.20 2.74
5984 6099 0.938945 TCCCCTCCGAGGAATCCTAA 59.061 55.000 16.69 0.00 37.67 2.69


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

AutoCloner maintained by Alex Coulton.