Multiple sequence alignment - TraesCS2B01G351700

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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 TraesCS2B01G351700 chr2B 100.000 2600 0 0 1 2600 500712637 500715236 0 4802
1 TraesCS2B01G351700 chr2B 98.826 511 6 0 1 511 72612303 72611793 0 911
2 TraesCS2B01G351700 chr7A 98.538 2600 38 0 1 2600 60108478 60105879 0 4591
3 TraesCS2B01G351700 chr5A 98.500 2600 39 0 1 2600 73030110 73032709 0 4586
4 TraesCS2B01G351700 chr1B 98.346 2600 43 0 1 2600 638751491 638748892 0 4564
5 TraesCS2B01G351700 chr2D 97.658 2605 47 5 1 2600 637322608 637320013 0 4460
6 TraesCS2B01G351700 chr2D 96.737 2605 75 5 1 2597 189853477 189856079 0 4331
7 TraesCS2B01G351700 chr3D 97.428 2605 61 2 1 2600 523758129 523760732 0 4434
8 TraesCS2B01G351700 chr6B 97.154 2600 73 1 1 2600 388369113 388366515 0 4390
9 TraesCS2B01G351700 chr6B 96.043 2249 88 1 349 2596 588837820 588840068 0 3659
10 TraesCS2B01G351700 chrUn 98.527 2444 36 0 1 2444 273321782 273319339 0 4314
11 TraesCS2B01G351700 chr3B 98.246 570 10 0 1 570 575756166 575755597 0 998


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 TraesCS2B01G351700 chr2B 500712637 500715236 2599 False 4802 4802 100.000 1 2600 1 chr2B.!!$F1 2599
1 TraesCS2B01G351700 chr2B 72611793 72612303 510 True 911 911 98.826 1 511 1 chr2B.!!$R1 510
2 TraesCS2B01G351700 chr7A 60105879 60108478 2599 True 4591 4591 98.538 1 2600 1 chr7A.!!$R1 2599
3 TraesCS2B01G351700 chr5A 73030110 73032709 2599 False 4586 4586 98.500 1 2600 1 chr5A.!!$F1 2599
4 TraesCS2B01G351700 chr1B 638748892 638751491 2599 True 4564 4564 98.346 1 2600 1 chr1B.!!$R1 2599
5 TraesCS2B01G351700 chr2D 637320013 637322608 2595 True 4460 4460 97.658 1 2600 1 chr2D.!!$R1 2599
6 TraesCS2B01G351700 chr2D 189853477 189856079 2602 False 4331 4331 96.737 1 2597 1 chr2D.!!$F1 2596
7 TraesCS2B01G351700 chr3D 523758129 523760732 2603 False 4434 4434 97.428 1 2600 1 chr3D.!!$F1 2599
8 TraesCS2B01G351700 chr6B 388366515 388369113 2598 True 4390 4390 97.154 1 2600 1 chr6B.!!$R1 2599
9 TraesCS2B01G351700 chr6B 588837820 588840068 2248 False 3659 3659 96.043 349 2596 1 chr6B.!!$F1 2247
10 TraesCS2B01G351700 chrUn 273319339 273321782 2443 True 4314 4314 98.527 1 2444 1 chrUn.!!$R1 2443
11 TraesCS2B01G351700 chr3B 575755597 575756166 569 True 998 998 98.246 1 570 1 chr3B.!!$R1 569

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
843 858 1.661112 GAAATCAGTCGCTTCCCTTCG 59.339 52.381 0.0 0.0 0.0 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2222 2241 0.108585 GGAACAACCTCAGCACTCCA 59.891 55.0 0.0 0.0 35.41 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)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
403 409 2.068834 ATCGGTATCGGTGAAGTCCT 57.931 50.000 0.00 0.00 36.95 3.85
805 820 2.553028 GGAATTCCACAGGAGTCAAGCA 60.553 50.000 20.04 0.00 35.64 3.91
843 858 1.661112 GAAATCAGTCGCTTCCCTTCG 59.339 52.381 0.00 0.00 0.00 3.79
1000 1016 5.278266 CCTTTTTGAAGCGGATAGTTCACAA 60.278 40.000 0.00 0.00 32.40 3.33
1628 1644 3.663105 GGAGAAGCGACGAAATATACGAC 59.337 47.826 0.00 2.88 34.70 4.34
1646 1662 9.764363 ATATACGACATCACAAACATAGATTGT 57.236 29.630 0.00 0.00 41.50 2.71
1670 1686 5.237815 TCGCGGCTAAATATGAATTGAGAT 58.762 37.500 6.13 0.00 0.00 2.75
1703 1719 6.713276 TCTAATTTTGTAACCCGATCTTCCA 58.287 36.000 0.00 0.00 0.00 3.53
1726 1742 3.118445 TCTGATATGCGGGACAAACATCA 60.118 43.478 0.00 0.00 0.00 3.07
1860 1876 6.757897 TCATTTTTCGTGGATTAGCATCTT 57.242 33.333 0.00 0.00 0.00 2.40
1934 1950 5.940470 CCAATAGAACAAAGGTTAGCTCTGT 59.060 40.000 0.00 0.00 37.36 3.41
1947 1963 2.861462 GCTCTGTAGCTAGTCCACAG 57.139 55.000 7.18 7.18 45.85 3.66
1955 1971 1.078143 CTAGTCCACAGGCAAGGGC 60.078 63.158 0.00 0.00 40.13 5.19
2042 2058 1.271856 TGCTAACGGGACAGGAATCA 58.728 50.000 0.00 0.00 0.00 2.57
2136 2153 0.438830 GAAGATCACCGCGTGAACAC 59.561 55.000 13.81 9.37 45.96 3.32
2171 2188 0.032117 ATGTCACTCCCGAGGGATCA 60.032 55.000 11.86 9.16 43.66 2.92
2222 2241 4.456911 AGAATGATTGTTCATGTTCACGCT 59.543 37.500 0.00 0.00 41.83 5.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
403 409 7.942341 ACCACTCTACCACTTTAATTCAATGAA 59.058 33.333 0.00 0.00 0.00 2.57
414 420 3.326880 CCCACTTACCACTCTACCACTTT 59.673 47.826 0.00 0.00 0.00 2.66
805 820 7.449704 ACTGATTTCCAATTCTTCTTTGCTAGT 59.550 33.333 0.00 0.00 0.00 2.57
843 858 1.620819 TCTTCTGCTGACTTGAGTCCC 59.379 52.381 8.56 1.20 44.15 4.46
1029 1045 6.669125 TGAAAATGGAGTGGAAACATCATT 57.331 33.333 0.00 0.00 46.14 2.57
1489 1505 4.336433 CACATTGAACCCTCGAATATGCTT 59.664 41.667 0.00 0.00 0.00 3.91
1646 1662 5.053811 TCTCAATTCATATTTAGCCGCGAA 58.946 37.500 8.23 0.00 0.00 4.70
1670 1686 7.013464 TCGGGTTACAAAATTAGAAAGCTTTCA 59.987 33.333 34.39 19.54 39.61 2.69
1703 1719 3.558931 TGTTTGTCCCGCATATCAGAT 57.441 42.857 0.00 0.00 0.00 2.90
1726 1742 6.719370 TCTTGGCAACTTGGACAACTTATAAT 59.281 34.615 0.00 0.00 37.61 1.28
1808 1824 1.662517 TGCGAAAGAACTCAACTGCA 58.337 45.000 0.00 0.00 0.00 4.41
1860 1876 2.905415 ATGCCCATCAAAGAACCTCA 57.095 45.000 0.00 0.00 0.00 3.86
1934 1950 1.195115 CCTTGCCTGTGGACTAGCTA 58.805 55.000 0.00 0.00 0.00 3.32
1947 1963 1.926426 ATGGACCTACAGCCCTTGCC 61.926 60.000 0.00 0.00 38.69 4.52
1991 2007 1.276421 AGAGTTGGGATGACTCCGTTG 59.724 52.381 0.96 0.00 43.55 4.10
2042 2058 1.437547 AGTAGAGAGGTCCCCCACTTT 59.562 52.381 0.00 0.00 31.05 2.66
2062 2078 2.204034 TCTGGGGAGACAGGTGCA 59.796 61.111 0.00 0.00 38.98 4.57
2136 2153 6.241207 AGTGACATTCGTTACTTTGGATTG 57.759 37.500 0.00 0.00 38.76 2.67
2171 2188 8.530311 TGCAAAATTTCATGTATGATAGTGGTT 58.470 29.630 0.00 0.00 36.56 3.67
2222 2241 0.108585 GGAACAACCTCAGCACTCCA 59.891 55.000 0.00 0.00 35.41 3.86
2463 2483 4.385310 CCCATCCCCTAAAGTGGTAAAGAG 60.385 50.000 0.00 0.00 0.00 2.85
2499 2519 1.823797 TTGCCCCGGTTGTATGTAAC 58.176 50.000 0.00 0.00 0.00 2.50


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

AutoCloner maintained by Alex Coulton.