Multiple sequence alignment - TraesCS2B01G331300

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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 TraesCS2B01G331300 chr2B 100.000 2570 0 0 1 2570 474908947 474911516 0 4747
1 TraesCS2B01G331300 chr1A 98.140 2581 34 3 1 2570 554512746 554515323 0 4488
2 TraesCS2B01G331300 chr5D 97.947 2581 41 2 1 2570 503218716 503221295 0 4462
3 TraesCS2B01G331300 chr5D 97.365 2581 54 3 1 2570 6189438 6192015 0 4377
4 TraesCS2B01G331300 chr5D 97.696 2300 40 3 1 2288 503277728 503275430 0 3941
5 TraesCS2B01G331300 chr3B 97.947 2581 39 6 1 2570 201527522 201530099 0 4460
6 TraesCS2B01G331300 chr3B 98.312 2369 26 3 213 2570 101911885 101914250 0 4141
7 TraesCS2B01G331300 chr1D 97.714 2581 42 6 1 2570 254397611 254395037 0 4423
8 TraesCS2B01G331300 chr3A 97.598 2581 44 8 1 2570 672909509 672906936 0 4407
9 TraesCS2B01G331300 chr3A 96.499 457 3 2 2125 2570 164861427 164860973 0 743
10 TraesCS2B01G331300 chrUn 97.556 2578 48 4 4 2570 216518101 216515528 0 4397
11 TraesCS2B01G331300 chrUn 97.269 952 12 3 1630 2570 286266907 286267855 0 1602
12 TraesCS2B01G331300 chrUn 97.188 640 5 2 1942 2570 421834695 421835332 0 1070
13 TraesCS2B01G331300 chr6D 97.722 2327 41 2 1 2316 168255424 168257749 0 3993
14 TraesCS2B01G331300 chr3D 97.674 1333 17 3 1249 2570 589275209 589273880 0 2278


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 TraesCS2B01G331300 chr2B 474908947 474911516 2569 False 4747 4747 100.000 1 2570 1 chr2B.!!$F1 2569
1 TraesCS2B01G331300 chr1A 554512746 554515323 2577 False 4488 4488 98.140 1 2570 1 chr1A.!!$F1 2569
2 TraesCS2B01G331300 chr5D 503218716 503221295 2579 False 4462 4462 97.947 1 2570 1 chr5D.!!$F2 2569
3 TraesCS2B01G331300 chr5D 6189438 6192015 2577 False 4377 4377 97.365 1 2570 1 chr5D.!!$F1 2569
4 TraesCS2B01G331300 chr5D 503275430 503277728 2298 True 3941 3941 97.696 1 2288 1 chr5D.!!$R1 2287
5 TraesCS2B01G331300 chr3B 201527522 201530099 2577 False 4460 4460 97.947 1 2570 1 chr3B.!!$F2 2569
6 TraesCS2B01G331300 chr3B 101911885 101914250 2365 False 4141 4141 98.312 213 2570 1 chr3B.!!$F1 2357
7 TraesCS2B01G331300 chr1D 254395037 254397611 2574 True 4423 4423 97.714 1 2570 1 chr1D.!!$R1 2569
8 TraesCS2B01G331300 chr3A 672906936 672909509 2573 True 4407 4407 97.598 1 2570 1 chr3A.!!$R2 2569
9 TraesCS2B01G331300 chrUn 216515528 216518101 2573 True 4397 4397 97.556 4 2570 1 chrUn.!!$R1 2566
10 TraesCS2B01G331300 chrUn 286266907 286267855 948 False 1602 1602 97.269 1630 2570 1 chrUn.!!$F1 940
11 TraesCS2B01G331300 chrUn 421834695 421835332 637 False 1070 1070 97.188 1942 2570 1 chrUn.!!$F2 628
12 TraesCS2B01G331300 chr6D 168255424 168257749 2325 False 3993 3993 97.722 1 2316 1 chr6D.!!$F1 2315
13 TraesCS2B01G331300 chr3D 589273880 589275209 1329 True 2278 2278 97.674 1249 2570 1 chr3D.!!$R1 1321

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
814 817 1.216678 ACACCTCTCCAGATCCTCGAT 59.783 52.381 0.0 0.0 0.0 3.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1869 1874 6.923508 CGACTATTATCAACCTGACTGCAATA 59.076 38.462 0.0 0.0 0.0 1.9 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
190 192 5.952347 AGAAGTGGAATAGAATAACCCGT 57.048 39.130 0.00 0.00 0.00 5.28
231 233 4.765273 ACGTCTGTAATGCATTGTATGGA 58.235 39.130 22.27 9.66 34.26 3.41
241 243 5.372343 TGCATTGTATGGACCAGAATAGT 57.628 39.130 0.00 0.00 0.00 2.12
352 355 5.677319 TCTGTCTTAGTGAATCCCGATTT 57.323 39.130 0.00 0.00 0.00 2.17
779 782 3.744238 TCCGAGATGGCAAATATTCGA 57.256 42.857 0.00 0.00 37.80 3.71
803 806 5.983540 AGATGACTATGAAAACACCTCTCC 58.016 41.667 0.00 0.00 0.00 3.71
804 807 5.485353 AGATGACTATGAAAACACCTCTCCA 59.515 40.000 0.00 0.00 0.00 3.86
814 817 1.216678 ACACCTCTCCAGATCCTCGAT 59.783 52.381 0.00 0.00 0.00 3.59
1100 1103 2.233305 ACCTCGTGTGGGACTAATCT 57.767 50.000 0.00 0.00 0.00 2.40
1272 1277 6.349363 GGCTTCTTATTCCACAAGAACGAAAT 60.349 38.462 0.00 0.00 37.15 2.17
1280 1285 5.369833 TCCACAAGAACGAAATCACCTTTA 58.630 37.500 0.00 0.00 0.00 1.85
1680 1685 5.674525 TGGAACGAGCATGAAGAGATTAAT 58.325 37.500 0.00 0.00 0.00 1.40
1853 1858 1.001641 GGTGCTCTGGTGCAATCCT 60.002 57.895 0.00 0.00 45.12 3.24
1869 1874 5.242838 TGCAATCCTTTACCGACAGAAAAAT 59.757 36.000 0.00 0.00 0.00 1.82
2273 2289 1.422781 TCACCCGATCCGATAGTACCT 59.577 52.381 0.00 0.00 0.00 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
190 192 6.761242 CAGACGTATGATCATTACCCTTCAAA 59.239 38.462 14.65 0.00 0.00 2.69
241 243 6.958767 CCTGGAAAAGGTAGAAGAATAGGAA 58.041 40.000 0.00 0.00 41.74 3.36
779 782 6.013379 TGGAGAGGTGTTTTCATAGTCATCTT 60.013 38.462 0.00 0.00 0.00 2.40
803 806 5.840715 TCTCTCATTCAAATCGAGGATCTG 58.159 41.667 0.00 0.00 0.00 2.90
804 807 6.669125 ATCTCTCATTCAAATCGAGGATCT 57.331 37.500 0.00 0.00 0.00 2.75
814 817 6.157471 TGATCCCTCTCAATCTCTCATTCAAA 59.843 38.462 0.00 0.00 0.00 2.69
1100 1103 9.487790 GTTTTCCATGAGATGGTAAATGAAAAA 57.512 29.630 9.71 2.71 46.61 1.94
1280 1285 9.990868 AAAAACCCCTAGTATATGAAAGAATGT 57.009 29.630 0.00 0.00 0.00 2.71
1451 1456 7.987458 CCCAAGTTTGTCTATGAAGAGCTAATA 59.013 37.037 0.00 0.00 30.45 0.98
1680 1685 8.567285 AAAACTCAAAAGAGAAAGAAGTCTCA 57.433 30.769 5.10 0.00 45.55 3.27
1803 1808 9.814899 CTTCTAATAGGCCATGAACTATAGATG 57.185 37.037 5.01 0.00 30.13 2.90
1853 1858 7.041030 TGACTGCAATATTTTTCTGTCGGTAAA 60.041 33.333 0.00 0.00 32.41 2.01
1869 1874 6.923508 CGACTATTATCAACCTGACTGCAATA 59.076 38.462 0.00 0.00 0.00 1.90


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

AutoCloner maintained by Alex Coulton.