Multiple sequence alignment - TraesCS2A01G241900

Loading Multiple Alignment...

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 TraesCS2A01G241900 chr2A 100.000 2498 0 0 1 2498 335839269 335836772 0 4614
1 TraesCS2A01G241900 chr3D 97.378 2517 45 5 1 2498 589278903 589281417 0 4263
2 TraesCS2A01G241900 chr5D 97.023 2519 53 4 1 2498 6189581 6187064 0 4217
3 TraesCS2A01G241900 chr5D 96.902 2518 57 3 1 2498 503277585 503280101 0 4198
4 TraesCS2A01G241900 chr5D 96.071 2520 73 8 1 2498 432402856 432405371 0 4082
5 TraesCS2A01G241900 chr5D 97.608 2090 37 1 1 2077 503218859 503216770 0 3570
6 TraesCS2A01G241900 chr1A 97.023 2519 46 4 1 2498 554512889 554510379 0 4209
7 TraesCS2A01G241900 chr1D 96.665 2519 63 3 1 2498 254397468 254399986 0 4167
8 TraesCS2A01G241900 chr5A 95.992 2520 78 6 1 2498 607275041 607272523 0 4072
9 TraesCS2A01G241900 chr4A 94.818 2528 98 11 1 2498 309515771 309513247 0 3912
10 TraesCS2A01G241900 chrUn 97.657 2091 34 3 1 2077 93408990 93411079 0 3576
11 TraesCS2A01G241900 chrUn 97.418 2091 40 2 1 2077 216517961 216520051 0 3550
12 TraesCS2A01G241900 chrUn 96.881 1699 40 1 1 1686 372771012 372772710 0 2832
13 TraesCS2A01G241900 chrUn 96.898 677 14 2 1829 2498 239345464 239346140 0 1127
14 TraesCS2A01G241900 chr6D 97.561 2091 37 2 1 2077 168255567 168253477 0 3567
15 TraesCS2A01G241900 chr6D 95.979 1343 28 7 1179 2496 45519037 45517696 0 2158
16 TraesCS2A01G241900 chr3B 97.465 2091 38 3 1 2077 201527665 201525576 0 3554
17 TraesCS2A01G241900 chr2D 97.274 2091 43 2 1 2077 272793252 272795342 0 3533
18 TraesCS2A01G241900 chr2B 96.687 2113 49 5 1 2100 474909090 474906986 0 3494


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 TraesCS2A01G241900 chr2A 335836772 335839269 2497 True 4614 4614 100.000 1 2498 1 chr2A.!!$R1 2497
1 TraesCS2A01G241900 chr3D 589278903 589281417 2514 False 4263 4263 97.378 1 2498 1 chr3D.!!$F1 2497
2 TraesCS2A01G241900 chr5D 6187064 6189581 2517 True 4217 4217 97.023 1 2498 1 chr5D.!!$R1 2497
3 TraesCS2A01G241900 chr5D 503277585 503280101 2516 False 4198 4198 96.902 1 2498 1 chr5D.!!$F2 2497
4 TraesCS2A01G241900 chr5D 432402856 432405371 2515 False 4082 4082 96.071 1 2498 1 chr5D.!!$F1 2497
5 TraesCS2A01G241900 chr5D 503216770 503218859 2089 True 3570 3570 97.608 1 2077 1 chr5D.!!$R2 2076
6 TraesCS2A01G241900 chr1A 554510379 554512889 2510 True 4209 4209 97.023 1 2498 1 chr1A.!!$R1 2497
7 TraesCS2A01G241900 chr1D 254397468 254399986 2518 False 4167 4167 96.665 1 2498 1 chr1D.!!$F1 2497
8 TraesCS2A01G241900 chr5A 607272523 607275041 2518 True 4072 4072 95.992 1 2498 1 chr5A.!!$R1 2497
9 TraesCS2A01G241900 chr4A 309513247 309515771 2524 True 3912 3912 94.818 1 2498 1 chr4A.!!$R1 2497
10 TraesCS2A01G241900 chrUn 93408990 93411079 2089 False 3576 3576 97.657 1 2077 1 chrUn.!!$F1 2076
11 TraesCS2A01G241900 chrUn 216517961 216520051 2090 False 3550 3550 97.418 1 2077 1 chrUn.!!$F2 2076
12 TraesCS2A01G241900 chrUn 372771012 372772710 1698 False 2832 2832 96.881 1 1686 1 chrUn.!!$F4 1685
13 TraesCS2A01G241900 chrUn 239345464 239346140 676 False 1127 1127 96.898 1829 2498 1 chrUn.!!$F3 669
14 TraesCS2A01G241900 chr6D 168253477 168255567 2090 True 3567 3567 97.561 1 2077 1 chr6D.!!$R2 2076
15 TraesCS2A01G241900 chr6D 45517696 45519037 1341 True 2158 2158 95.979 1179 2496 1 chr6D.!!$R1 1317
16 TraesCS2A01G241900 chr3B 201525576 201527665 2089 True 3554 3554 97.465 1 2077 1 chr3B.!!$R1 2076
17 TraesCS2A01G241900 chr2D 272793252 272795342 2090 False 3533 3533 97.274 1 2077 1 chr2D.!!$F1 2076
18 TraesCS2A01G241900 chr2B 474906986 474909090 2104 True 3494 3494 96.687 1 2100 1 chr2B.!!$R1 2099

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
739 740 0.547553 TGGTAATTAAGACCCCCGGC 59.452 55.0 0.0 0.0 35.99 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1573 1581 2.513666 GAATCCACCATGCGCGGA 60.514 61.111 8.83 5.0 0.0 5.54 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
119 120 1.846712 TTGATCCATGGACGGCACCA 61.847 55.000 18.99 5.68 44.41 4.17
143 144 5.168647 TGTGGTAAAGGTCGTAATTCCAT 57.831 39.130 0.00 0.00 0.00 3.41
146 147 6.070653 TGTGGTAAAGGTCGTAATTCCATAGT 60.071 38.462 0.00 0.00 0.00 2.12
407 408 3.421844 GAAATGCCCTACCTTTGAGTGT 58.578 45.455 0.00 0.00 0.00 3.55
611 612 9.253832 AGAGATATGGTATAATGGAGAAGACAG 57.746 37.037 0.00 0.00 0.00 3.51
654 655 1.673009 CGGAAGCGCCCCTTGTTTA 60.673 57.895 2.29 0.00 32.78 2.01
739 740 0.547553 TGGTAATTAAGACCCCCGGC 59.452 55.000 0.00 0.00 35.99 6.13
747 748 2.361992 GACCCCCGGCGGAAAATT 60.362 61.111 30.79 6.33 0.00 1.82
754 755 1.437160 CGGCGGAAAATTGGGATGG 59.563 57.895 0.00 0.00 0.00 3.51
810 811 7.477494 TCGACGTAATTTCATAGAGTCATTCA 58.523 34.615 0.00 0.00 0.00 2.57
887 888 8.489676 AGGATGTAGAAGATCATAACATGAGT 57.510 34.615 0.00 0.00 43.53 3.41
978 979 5.720371 AGATCCATTTGTCTAGAGATCGG 57.280 43.478 10.21 3.55 36.19 4.18
1573 1581 0.725117 GCGAACGACGGGAATTGAAT 59.275 50.000 0.00 0.00 42.83 2.57
1974 2001 0.255033 GGGGGAATTCGTGCCTACTT 59.745 55.000 0.00 0.00 37.99 2.24
2119 2155 6.918892 TGTTGATATTGGGTATTTCTGTCG 57.081 37.500 0.00 0.00 0.00 4.35
2406 2449 0.675633 GCCAAGCAGCCAAGAAGAAA 59.324 50.000 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 0.601558 TCACTTGCCTGTCTACGGTC 59.398 55.000 0.00 0.00 0.00 4.79
119 120 5.562635 TGGAATTACGACCTTTACCACAAT 58.437 37.500 0.00 0.00 0.00 2.71
143 144 4.409718 TGCCTTGCGGTAATGATTACTA 57.590 40.909 14.34 0.38 36.39 1.82
146 147 5.222079 TCTATGCCTTGCGGTAATGATTA 57.778 39.130 0.00 0.00 0.00 1.75
240 241 3.912248 AGGGTCGTATTCTATGGTGACT 58.088 45.455 0.00 0.00 0.00 3.41
243 244 5.182570 TCGATTAGGGTCGTATTCTATGGTG 59.817 44.000 0.00 0.00 42.07 4.17
597 598 8.690203 TTCAAACAATTCTGTCTTCTCCATTA 57.310 30.769 0.00 0.00 33.45 1.90
598 599 7.587037 TTCAAACAATTCTGTCTTCTCCATT 57.413 32.000 0.00 0.00 33.45 3.16
611 612 2.458951 TGTGCGTGCTTCAAACAATTC 58.541 42.857 0.00 0.00 0.00 2.17
654 655 1.730851 AACCCGTCCTCCTCTCTTTT 58.269 50.000 0.00 0.00 0.00 2.27
739 740 0.746659 GGAGCCATCCCAATTTTCCG 59.253 55.000 0.00 0.00 40.03 4.30
754 755 5.867716 CACATATTATGGGTAACGTAGGAGC 59.132 44.000 8.48 0.00 37.60 4.70
810 811 7.876936 ATGTTCTTCATGTAGCATTCAGATT 57.123 32.000 0.00 0.00 35.19 2.40
853 854 6.916909 TGATCTTCTACATCCTAGGTCTCTT 58.083 40.000 9.08 0.00 0.00 2.85
887 888 2.951642 GGAATCCAAATCTGCCGAATCA 59.048 45.455 0.00 0.00 0.00 2.57
964 965 6.887002 AGATGTATATGCCGATCTCTAGACAA 59.113 38.462 0.00 0.00 0.00 3.18
978 979 7.971168 AGCATACGACTTTCTAGATGTATATGC 59.029 37.037 25.18 25.18 38.81 3.14
1287 1290 2.544685 CAACACTTAGATCCGGCTCTG 58.455 52.381 18.06 4.62 0.00 3.35
1415 1420 0.258774 AAGCGCAGGATAACCCCAAT 59.741 50.000 11.47 0.00 36.73 3.16
1573 1581 2.513666 GAATCCACCATGCGCGGA 60.514 61.111 8.83 5.00 0.00 5.54
1679 1703 5.048921 TGTCCAATATCTCGATCGAAGTACC 60.049 44.000 19.92 2.08 0.00 3.34
1974 2001 5.697473 TTTTCATAACTCGTGAAATGCCA 57.303 34.783 2.57 0.00 43.00 4.92
2336 2379 9.408069 CTTTAGGTATTAGTACTATGGCTTTCG 57.592 37.037 2.79 0.00 0.00 3.46
2406 2449 7.280205 AGTTTCAACAACTCTCGTTCTTTACAT 59.720 33.333 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.