Multiple sequence alignment - TraesCS3D01G254000

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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 TraesCS3D01G254000 chr3D 100.000 2953 0 0 1 2953 355632159 355629207 0 5454
1 TraesCS3D01G254000 chr3A 97.552 1593 34 4 1361 2953 474435679 474434092 0 2721
2 TraesCS3D01G254000 chr3A 98.463 1366 20 1 1 1366 474437164 474435800 0 2405
3 TraesCS3D01G254000 chr3B 95.940 1601 45 5 1354 2953 456554185 456552604 0 2579
4 TraesCS3D01G254000 chr3B 93.584 1356 64 12 1 1337 456555799 456554448 0 2001


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 TraesCS3D01G254000 chr3D 355629207 355632159 2952 True 5454 5454 100.0000 1 2953 1 chr3D.!!$R1 2952
1 TraesCS3D01G254000 chr3A 474434092 474437164 3072 True 2563 2721 98.0075 1 2953 2 chr3A.!!$R1 2952
2 TraesCS3D01G254000 chr3B 456552604 456555799 3195 True 2290 2579 94.7620 1 2953 2 chr3B.!!$R1 2952

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
434 435 0.850784 ACCCCACTTACTGTTGCCTT 59.149 50.000 0.0 0.0 0.0 4.35 F
1157 1172 3.543661 TCTTCCCCAGTATTTTACCCCA 58.456 45.455 0.0 0.0 0.0 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1542 1933 1.005340 GAGAATCTTCCTGCTGTGCG 58.995 55.000 0.0 0.0 0.0 5.34 R
2829 3220 1.214175 TGCAGACTTCTTTCCCAACCA 59.786 47.619 0.0 0.0 0.0 3.67 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
84 85 3.563808 TGTCAATTTGCAAAGCTAGTCGT 59.436 39.130 18.19 0.00 0.00 4.34
434 435 0.850784 ACCCCACTTACTGTTGCCTT 59.149 50.000 0.00 0.00 0.00 4.35
1157 1172 3.543661 TCTTCCCCAGTATTTTACCCCA 58.456 45.455 0.00 0.00 0.00 4.96
1233 1252 7.067494 GTGGTAGAAATTGATAATGCTGTTCCT 59.933 37.037 0.00 0.00 0.00 3.36
1398 1788 7.654022 TTCCTCTAACAATTGGTCACTTTTT 57.346 32.000 10.83 0.00 0.00 1.94
1478 1868 6.017400 ACAAATGCCAGACAAACAGAATAG 57.983 37.500 0.00 0.00 0.00 1.73
1517 1908 9.764870 CATTCTATGCTTAATTCCATGTATTCG 57.235 33.333 0.00 0.00 0.00 3.34
1542 1933 4.503741 TCTTTGTGTTCTAAATGCAGGC 57.496 40.909 0.00 0.00 0.00 4.85
1678 2069 4.081697 CGTACATATCCCTGCATATGACCA 60.082 45.833 6.97 0.00 38.54 4.02
1703 2094 7.490657 TGTGGAGGTATTACTACATGAAAGT 57.509 36.000 0.00 5.17 33.03 2.66
2412 2803 1.615392 AGCACACAAGCTTCCCATTTC 59.385 47.619 0.00 0.00 43.70 2.17
2523 2914 6.605594 ACGAAAGGGGATTTTTAAGCATGATA 59.394 34.615 0.00 0.00 0.00 2.15
2631 3022 7.233962 CCATTTCATCTGATTTTATCCCATGGA 59.766 37.037 15.22 0.00 35.55 3.41
2829 3220 2.414138 GTGTAAGTCAGCGGCGTAAATT 59.586 45.455 9.37 2.49 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 85 5.362717 CCTAACCACTCACATATCCACTGTA 59.637 44.000 0.00 0.00 0.00 2.74
434 435 1.841302 AACTGCTGAGCGAATGGGGA 61.841 55.000 0.00 0.00 0.00 4.81
1023 1038 1.134670 CCGCTAGCTGCTAAAGGAGTT 60.135 52.381 19.46 0.00 40.11 3.01
1115 1130 7.309194 GGAAGAACAAATAGCAAACACCATACT 60.309 37.037 0.00 0.00 0.00 2.12
1233 1252 3.596214 GCAGACCTTTATGAACTTCGGA 58.404 45.455 0.00 0.00 0.00 4.55
1430 1820 8.391106 GTCGATTTGAAGCATAAACTGTAGATT 58.609 33.333 0.00 0.00 0.00 2.40
1517 1908 5.687285 CCTGCATTTAGAACACAAAGAACAC 59.313 40.000 0.00 0.00 0.00 3.32
1542 1933 1.005340 GAGAATCTTCCTGCTGTGCG 58.995 55.000 0.00 0.00 0.00 5.34
1678 2069 7.987458 CACTTTCATGTAGTAATACCTCCACAT 59.013 37.037 0.00 0.00 0.00 3.21
2412 2803 5.870706 AGAGAAAGTGAGAAAAGTAAGGGG 58.129 41.667 0.00 0.00 0.00 4.79
2523 2914 3.543680 ATTTGCTAGCGTCATAGTGGT 57.456 42.857 10.77 0.00 0.00 4.16
2562 2953 9.415544 GACATGCTTTAGAAATTTCACATTCTT 57.584 29.630 19.99 0.27 37.16 2.52
2563 2954 8.579006 TGACATGCTTTAGAAATTTCACATTCT 58.421 29.630 19.99 0.65 39.19 2.40
2829 3220 1.214175 TGCAGACTTCTTTCCCAACCA 59.786 47.619 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.