Multiple sequence alignment - TraesCS1B01G065500

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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 TraesCS1B01G065500 chr1B 100.000 2624 0 0 1 2624 49798425 49801048 0 4846
1 TraesCS1B01G065500 chr1B 97.758 2632 51 6 1 2624 683734143 683731512 0 4527
2 TraesCS1B01G065500 chr1B 97.078 2635 64 7 1 2624 583536772 583534140 0 4427
3 TraesCS1B01G065500 chrUn 97.798 2634 48 5 1 2624 223706935 223704302 0 4534
4 TraesCS1B01G065500 chrUn 97.456 2634 57 7 1 2624 40085858 40088491 0 4484
5 TraesCS1B01G065500 chr2A 97.722 2634 49 6 1 2624 605912878 605910246 0 4521
6 TraesCS1B01G065500 chr7B 97.683 2633 52 6 1 2624 698140159 698142791 0 4516
7 TraesCS1B01G065500 chr5B 97.377 2631 61 7 1 2624 713082219 713079590 0 4470
8 TraesCS1B01G065500 chr3D 97.225 2631 60 7 1 2624 202649730 202652354 0 4442


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 TraesCS1B01G065500 chr1B 49798425 49801048 2623 False 4846 4846 100.000 1 2624 1 chr1B.!!$F1 2623
1 TraesCS1B01G065500 chr1B 683731512 683734143 2631 True 4527 4527 97.758 1 2624 1 chr1B.!!$R2 2623
2 TraesCS1B01G065500 chr1B 583534140 583536772 2632 True 4427 4427 97.078 1 2624 1 chr1B.!!$R1 2623
3 TraesCS1B01G065500 chrUn 223704302 223706935 2633 True 4534 4534 97.798 1 2624 1 chrUn.!!$R1 2623
4 TraesCS1B01G065500 chrUn 40085858 40088491 2633 False 4484 4484 97.456 1 2624 1 chrUn.!!$F1 2623
5 TraesCS1B01G065500 chr2A 605910246 605912878 2632 True 4521 4521 97.722 1 2624 1 chr2A.!!$R1 2623
6 TraesCS1B01G065500 chr7B 698140159 698142791 2632 False 4516 4516 97.683 1 2624 1 chr7B.!!$F1 2623
7 TraesCS1B01G065500 chr5B 713079590 713082219 2629 True 4470 4470 97.377 1 2624 1 chr5B.!!$R1 2623
8 TraesCS1B01G065500 chr3D 202649730 202652354 2624 False 4442 4442 97.225 1 2624 1 chr3D.!!$F1 2623

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
290 291 1.702491 GCGGATAACAACGGAGTGGC 61.702 60.0 0.0 0.0 45.0 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1973 1986 0.179018 GGTCAGCACTGGGTGTTTCT 60.179 55.0 0.0 0.0 43.0 2.52 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
113 114 8.837099 ATTATTCAAACCACAAAGGATCCATA 57.163 30.769 15.82 0.00 41.22 2.74
238 239 3.568007 TCCAATCAAAAACCAGACTTCCG 59.432 43.478 0.00 0.00 0.00 4.30
259 260 3.395054 AGATCCATCTCACTCAGACCA 57.605 47.619 0.00 0.00 32.26 4.02
290 291 1.702491 GCGGATAACAACGGAGTGGC 61.702 60.000 0.00 0.00 45.00 5.01
486 487 8.795341 CGTGACAACGGTATGATAATATGATAC 58.205 37.037 1.92 1.92 46.25 2.24
531 532 5.705400 AGAAGGAAATCCAAAAGGAACTCA 58.295 37.500 1.67 0.00 36.28 3.41
534 535 4.281941 AGGAAATCCAAAAGGAACTCAAGC 59.718 41.667 1.67 0.00 36.28 4.01
598 599 3.625649 AAAAGAGTCTCATGAGCTCCC 57.374 47.619 28.48 15.53 34.41 4.30
1318 1322 1.938625 TCGTTTCGTTCCCGTTCTTT 58.061 45.000 0.00 0.00 35.01 2.52
1396 1400 6.513393 CGGTCTGCTCTGTTTACAATTCTTTT 60.513 38.462 0.00 0.00 0.00 2.27
1423 1427 2.854777 CTCTTCTCTTTACCACGCGATG 59.145 50.000 15.93 7.49 0.00 3.84
1511 1515 5.769662 AGCAACAAAATGACAAGATGAGGTA 59.230 36.000 0.00 0.00 0.00 3.08
1554 1558 1.493446 AGAAGGGTCGAAGGTTTTGGT 59.507 47.619 0.00 0.00 0.00 3.67
1565 1569 3.141767 AGGTTTTGGTCCTGTAGCTTC 57.858 47.619 0.00 0.00 33.62 3.86
1641 1654 1.555075 TGAAGCTCTCGCCTTACCAAT 59.445 47.619 0.00 0.00 36.60 3.16
1737 1750 4.009675 GGAGTGTGCATCTTTATGTTGGA 58.990 43.478 0.00 0.00 35.38 3.53
1757 1770 0.384309 TGTTCTTCTGTCGTGCGACT 59.616 50.000 22.54 0.00 44.80 4.18
1811 1824 5.163195 GCCTCCTATTCTATTTGTTCAGGGA 60.163 44.000 0.00 0.00 0.00 4.20
1816 1829 2.274542 TCTATTTGTTCAGGGAGGGCA 58.725 47.619 0.00 0.00 0.00 5.36
1859 1872 1.227823 TATTCAATCCCGCCGCTGG 60.228 57.895 0.00 0.00 0.00 4.85
1973 1986 1.079819 GTGTAAGCCTCGCTGCTCA 60.080 57.895 0.00 0.00 41.80 4.26
2144 2158 2.821437 TCCAACCAACCCTTTTTGACA 58.179 42.857 0.00 0.00 0.00 3.58
2207 2221 4.980805 GTGAGCGCGGTGGGAACA 62.981 66.667 18.92 3.48 38.70 3.18
2327 2342 3.310860 GACTCGGTTCGGGGCACAT 62.311 63.158 0.00 0.00 34.24 3.21
2398 2413 2.203640 TGGTCTGGTGTCCGAGCT 60.204 61.111 0.00 0.00 0.00 4.09
2453 2468 2.615986 TCTATTAGCCGCCTATCCCA 57.384 50.000 0.00 0.00 0.00 4.37
2507 2522 0.963856 CAGCAAGCAAGGGATGAGCA 60.964 55.000 0.00 0.00 0.00 4.26
2555 2570 0.741915 TGCTGGGTCGGTTTGTTTTC 59.258 50.000 0.00 0.00 0.00 2.29
2556 2571 0.317519 GCTGGGTCGGTTTGTTTTCG 60.318 55.000 0.00 0.00 0.00 3.46
2599 2615 3.873801 GCTTCTTCACAAGCTTATCCCCA 60.874 47.826 0.00 0.00 44.71 4.96
2613 2629 2.478803 CCCCACCCCCTTTCCTGTT 61.479 63.158 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
113 114 5.011090 TCGAGAAGATTGGACGATGAAAT 57.989 39.130 0.00 0.00 0.00 2.17
259 260 6.255215 CGTTGTTATCCGCTACATTCAAAAT 58.745 36.000 0.00 0.00 0.00 1.82
531 532 1.210155 GCGATCGCACCAAAAGCTT 59.790 52.632 33.89 0.00 41.49 3.74
534 535 1.059369 CGAGCGATCGCACCAAAAG 59.941 57.895 38.60 17.49 44.88 2.27
659 661 4.733850 TGCGTCAGACACAATCTACTAAG 58.266 43.478 0.41 0.00 35.15 2.18
1063 1066 4.563140 ACCATTTCAATAGTACGGGTGT 57.437 40.909 0.00 0.00 0.00 4.16
1318 1322 8.052748 CCCCATGGATTCGATAATAAGGAAATA 58.947 37.037 15.22 0.00 0.00 1.40
1396 1400 4.082895 GCGTGGTAAAGAGAAGAGAGTACA 60.083 45.833 0.00 0.00 0.00 2.90
1423 1427 2.029844 GCTCACGCTTCACTGACCC 61.030 63.158 0.00 0.00 0.00 4.46
1737 1750 1.000163 AGTCGCACGACAGAAGAACAT 60.000 47.619 23.59 0.00 46.76 2.71
1757 1770 0.529773 GGTCGCACATAAGCCATCGA 60.530 55.000 0.00 0.00 0.00 3.59
1811 1824 1.548357 ATCAGAGTTCACGCTGCCCT 61.548 55.000 5.86 0.00 42.40 5.19
1816 1829 2.480416 GGATCGAATCAGAGTTCACGCT 60.480 50.000 0.00 0.00 0.00 5.07
1859 1872 2.777832 AAGGAGTCAACTGAGCATCC 57.222 50.000 0.00 0.00 0.00 3.51
1973 1986 0.179018 GGTCAGCACTGGGTGTTTCT 60.179 55.000 0.00 0.00 43.00 2.52
1996 2009 0.249280 TGCGCTTTCGTGTCTCTCAA 60.249 50.000 9.73 0.00 38.14 3.02
2256 2270 2.178580 CCAACACAACAATAGGGCCAT 58.821 47.619 6.18 0.00 0.00 4.40
2257 2271 1.626686 CCAACACAACAATAGGGCCA 58.373 50.000 6.18 0.00 0.00 5.36
2265 2280 1.682684 AACCCGGCCAACACAACAA 60.683 52.632 2.24 0.00 0.00 2.83
2316 2331 1.184431 TAGTTACGATGTGCCCCGAA 58.816 50.000 0.00 0.00 0.00 4.30
2327 2342 4.021229 TGGAATGGCTCTCTTAGTTACGA 58.979 43.478 0.00 0.00 0.00 3.43
2398 2413 1.244816 AGTCGTCGTCTGACCAATCA 58.755 50.000 1.55 0.00 42.37 2.57
2453 2468 7.791766 TCTTTCTATTCCATCCTAGTCCATTCT 59.208 37.037 0.00 0.00 0.00 2.40
2463 2478 3.132289 TCGCGTTCTTTCTATTCCATCCT 59.868 43.478 5.77 0.00 0.00 3.24
2599 2615 1.759236 GACGAACAGGAAAGGGGGT 59.241 57.895 0.00 0.00 0.00 4.95


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

AutoCloner maintained by Alex Coulton.