Multiple sequence alignment - TraesCS3A01G502600

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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 TraesCS3A01G502600 chr3A 100.000 2594 0 0 1 2594 725796715 725799308 0 4791
1 TraesCS3A01G502600 chr5A 98.305 2596 42 2 1 2594 19248878 19246283 0 4549
2 TraesCS3A01G502600 chr7D 98.304 2595 43 1 1 2594 381923967 381926561 0 4547
3 TraesCS3A01G502600 chr7D 98.151 2596 46 2 1 2594 382050044 382052639 0 4527
4 TraesCS3A01G502600 chr7D 98.150 2595 47 1 1 2594 203499965 203502559 0 4525
5 TraesCS3A01G502600 chr7D 97.962 2600 44 3 1 2594 381973801 381971205 0 4499
6 TraesCS3A01G502600 chr7B 97.996 2595 45 3 1 2594 716878814 716876226 0 4497
7 TraesCS3A01G502600 chr7B 97.612 2596 54 4 1 2594 742989412 742992001 0 4444
8 TraesCS3A01G502600 chr7A 97.803 2595 51 2 1 2594 60279279 60281868 0 4471
9 TraesCS3A01G502600 chr3B 96.495 2596 81 5 1 2594 797592968 797590381 0 4281


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 TraesCS3A01G502600 chr3A 725796715 725799308 2593 False 4791 4791 100.000 1 2594 1 chr3A.!!$F1 2593
1 TraesCS3A01G502600 chr5A 19246283 19248878 2595 True 4549 4549 98.305 1 2594 1 chr5A.!!$R1 2593
2 TraesCS3A01G502600 chr7D 381923967 381926561 2594 False 4547 4547 98.304 1 2594 1 chr7D.!!$F2 2593
3 TraesCS3A01G502600 chr7D 382050044 382052639 2595 False 4527 4527 98.151 1 2594 1 chr7D.!!$F3 2593
4 TraesCS3A01G502600 chr7D 203499965 203502559 2594 False 4525 4525 98.150 1 2594 1 chr7D.!!$F1 2593
5 TraesCS3A01G502600 chr7D 381971205 381973801 2596 True 4499 4499 97.962 1 2594 1 chr7D.!!$R1 2593
6 TraesCS3A01G502600 chr7B 716876226 716878814 2588 True 4497 4497 97.996 1 2594 1 chr7B.!!$R1 2593
7 TraesCS3A01G502600 chr7B 742989412 742992001 2589 False 4444 4444 97.612 1 2594 1 chr7B.!!$F1 2593
8 TraesCS3A01G502600 chr7A 60279279 60281868 2589 False 4471 4471 97.803 1 2594 1 chr7A.!!$F1 2593
9 TraesCS3A01G502600 chr3B 797590381 797592968 2587 True 4281 4281 96.495 1 2594 1 chr3B.!!$R1 2593

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
103 104 0.253044 CCCTTCCGAATGCTTCTCCA 59.747 55.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1988 1992 0.320508 GGACTTCGCCGTTCTTTCCT 60.321 55.0 0.0 0.0 0.0 3.36 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
103 104 0.253044 CCCTTCCGAATGCTTCTCCA 59.747 55.000 0.00 0.00 0.00 3.86
357 359 1.121378 GTAGCTAGGACCCCTCCAAC 58.879 60.000 0.00 0.00 39.39 3.77
497 499 4.929146 ACTAGCTGGGTAAGGAAAACAT 57.071 40.909 0.85 0.00 0.00 2.71
501 503 5.887214 AGCTGGGTAAGGAAAACATTTTT 57.113 34.783 0.00 0.00 0.00 1.94
531 533 9.132521 GATTGAGATGTCGATTTGTTTTTCATT 57.867 29.630 0.00 0.00 0.00 2.57
561 563 2.524394 GGCCGAGGGGATAGCAGA 60.524 66.667 0.00 0.00 34.06 4.26
592 594 1.507141 CTTTGCCTGCCGACGTTCTT 61.507 55.000 0.00 0.00 0.00 2.52
613 615 7.195818 TCTTATAAAGAATTCCGGCTCGGCT 62.196 44.000 0.65 0.00 39.83 5.52
730 732 2.380084 TCCACTTCAGATAACCACGC 57.620 50.000 0.00 0.00 0.00 5.34
812 814 3.243301 TGAGAGTGGAGTTACGTGAACAC 60.243 47.826 0.00 0.39 40.86 3.32
846 848 5.579119 GGAAAACAACTTTCATGTTCGGTTT 59.421 36.000 0.00 0.00 44.61 3.27
855 857 3.585862 TCATGTTCGGTTTAGAGAGCAC 58.414 45.455 0.00 0.00 30.79 4.40
1276 1280 4.991776 TGGTTTCTCATGTGGAACCATAA 58.008 39.130 28.95 12.87 34.36 1.90
1357 1361 3.769739 TCGCCATAGTTCCAGCATTAT 57.230 42.857 0.00 0.00 0.00 1.28
1485 1489 1.717194 CGTTAGCCGGCTTTTGTAGA 58.283 50.000 37.74 12.41 0.00 2.59
1713 1717 3.130516 GGTCGAGTCTGATACATCAACCA 59.869 47.826 0.00 0.00 36.18 3.67
1838 1842 1.263484 CGCGATCGTATACTGAGGTGT 59.737 52.381 17.81 0.00 0.00 4.16
1945 1949 3.453353 CCATCTCATTTGGGGCAGAAAAT 59.547 43.478 0.00 0.00 0.00 1.82
1987 1991 5.182380 TGATACAACCCTTTCCATTTTCGTC 59.818 40.000 0.00 0.00 0.00 4.20
1988 1992 3.292460 ACAACCCTTTCCATTTTCGTCA 58.708 40.909 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
103 104 2.231478 TCTTCGCGAGAACTTCAGGATT 59.769 45.455 9.59 0.00 46.92 3.01
357 359 3.129287 GGTGAACATAGGCTCAAACATGG 59.871 47.826 0.00 0.00 0.00 3.66
477 479 6.590234 AAAATGTTTTCCTTACCCAGCTAG 57.410 37.500 0.00 0.00 0.00 3.42
497 499 7.040478 ACAAATCGACATCTCAATCTCCAAAAA 60.040 33.333 0.00 0.00 0.00 1.94
501 503 5.089970 ACAAATCGACATCTCAATCTCCA 57.910 39.130 0.00 0.00 0.00 3.86
531 533 1.271379 CCTCGGCCTTCTTCCTTTTCA 60.271 52.381 0.00 0.00 0.00 2.69
613 615 1.896660 GTTGCCAGCACTTTCCCGA 60.897 57.895 0.00 0.00 0.00 5.14
677 679 0.108138 GTAGATGCCGAACCTGCTGT 60.108 55.000 0.00 0.00 0.00 4.40
790 792 2.953648 TGTTCACGTAACTCCACTCTCA 59.046 45.455 0.00 0.00 38.99 3.27
812 814 2.504367 AGTTGTTTTCCATCAGACGGG 58.496 47.619 0.00 0.00 0.00 5.28
846 848 4.038763 TCTCAACGAAAAAGGTGCTCTCTA 59.961 41.667 0.00 0.00 0.00 2.43
855 857 6.803154 AGGACTTATTCTCAACGAAAAAGG 57.197 37.500 0.00 0.00 34.79 3.11
1045 1049 3.004752 AGGCGCAATAGAAAGGAATGT 57.995 42.857 10.83 0.00 0.00 2.71
1276 1280 9.533831 ACCAATTAGTAGTGATTGAATTCCTTT 57.466 29.630 14.88 0.00 35.74 3.11
1357 1361 1.982660 TATTTGACACGGGTTTGCCA 58.017 45.000 0.00 0.00 36.17 4.92
1485 1489 4.857037 GCGGCGAAGAACAAATAGAATTTT 59.143 37.500 12.98 0.00 0.00 1.82
1551 1555 3.565482 CCCAACGACCTATAACGCTAGTA 59.435 47.826 0.00 0.00 0.00 1.82
1624 1628 2.125673 GCTACGTGTCCGGTGCAT 60.126 61.111 0.00 0.00 38.78 3.96
1713 1717 4.395625 TCGTACAAGGATATGGAGTCGAT 58.604 43.478 0.00 0.00 0.00 3.59
1838 1842 1.980784 TTCCAACAACCGACGGGGAA 61.981 55.000 20.00 17.17 39.97 3.97
1987 1991 0.790814 GACTTCGCCGTTCTTTCCTG 59.209 55.000 0.00 0.00 0.00 3.86
1988 1992 0.320508 GGACTTCGCCGTTCTTTCCT 60.321 55.000 0.00 0.00 0.00 3.36
2303 2307 1.300971 GCAGAGCCGTTTCATGAGCA 61.301 55.000 7.34 0.00 0.00 4.26
2467 2476 0.966179 GATTGAAGCCCCCAACGTTT 59.034 50.000 0.00 0.00 0.00 3.60


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

AutoCloner maintained by Alex Coulton.