Multiple sequence alignment - TraesCS2B01G240300

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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 TraesCS2B01G240300 chr2B 100.000 3572 0 0 1 3572 244701373 244704944 0 6597
1 TraesCS2B01G240300 chr2B 98.280 3313 54 3 262 3572 244763245 244759934 0 5799
2 TraesCS2B01G240300 chr2B 95.760 3585 114 12 1 3572 424685064 424681505 0 5744
3 TraesCS2B01G240300 chr1B 96.260 3583 98 10 1 3572 95491994 95495551 0 5842
4 TraesCS2B01G240300 chr1B 96.119 3582 108 7 1 3572 530764171 530760611 0 5816
5 TraesCS2B01G240300 chr2A 96.147 3582 105 10 1 3572 374483629 374487187 0 5819
6 TraesCS2B01G240300 chr2A 96.066 3584 107 9 1 3572 628648261 628644700 0 5806
7 TraesCS2B01G240300 chr2A 96.039 3585 106 11 1 3572 628569757 628573318 0 5801
8 TraesCS2B01G240300 chr2A 95.841 3583 111 11 1 3572 161526823 161530378 0 5757
9 TraesCS2B01G240300 chr1A 96.011 3585 109 9 1 3572 409609185 409612748 0 5797
10 TraesCS2B01G240300 chr7D 96.978 3243 70 8 340 3572 474677238 474680462 0 5421
11 TraesCS2B01G240300 chr5B 95.822 2202 72 10 1373 3572 629227230 629225047 0 3539
12 TraesCS2B01G240300 chr6A 95.726 2176 71 6 1398 3572 610981354 610983508 0 3483
13 TraesCS2B01G240300 chr6A 96.674 1413 35 3 1 1401 610963205 610964617 0 2338
14 TraesCS2B01G240300 chr6A 96.601 1412 37 3 1 1401 610987687 610989098 0 2331
15 TraesCS2B01G240300 chr6A 96.530 1412 38 3 1 1401 611013773 611015184 0 2326
16 TraesCS2B01G240300 chr6B 96.822 1888 58 2 1 1887 615325516 615323630 0 3153
17 TraesCS2B01G240300 chr6B 97.400 1692 39 2 1882 3572 615318751 615317064 0 2876


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 TraesCS2B01G240300 chr2B 244701373 244704944 3571 False 6597 6597 100.000 1 3572 1 chr2B.!!$F1 3571
1 TraesCS2B01G240300 chr2B 244759934 244763245 3311 True 5799 5799 98.280 262 3572 1 chr2B.!!$R1 3310
2 TraesCS2B01G240300 chr2B 424681505 424685064 3559 True 5744 5744 95.760 1 3572 1 chr2B.!!$R2 3571
3 TraesCS2B01G240300 chr1B 95491994 95495551 3557 False 5842 5842 96.260 1 3572 1 chr1B.!!$F1 3571
4 TraesCS2B01G240300 chr1B 530760611 530764171 3560 True 5816 5816 96.119 1 3572 1 chr1B.!!$R1 3571
5 TraesCS2B01G240300 chr2A 374483629 374487187 3558 False 5819 5819 96.147 1 3572 1 chr2A.!!$F2 3571
6 TraesCS2B01G240300 chr2A 628644700 628648261 3561 True 5806 5806 96.066 1 3572 1 chr2A.!!$R1 3571
7 TraesCS2B01G240300 chr2A 628569757 628573318 3561 False 5801 5801 96.039 1 3572 1 chr2A.!!$F3 3571
8 TraesCS2B01G240300 chr2A 161526823 161530378 3555 False 5757 5757 95.841 1 3572 1 chr2A.!!$F1 3571
9 TraesCS2B01G240300 chr1A 409609185 409612748 3563 False 5797 5797 96.011 1 3572 1 chr1A.!!$F1 3571
10 TraesCS2B01G240300 chr7D 474677238 474680462 3224 False 5421 5421 96.978 340 3572 1 chr7D.!!$F1 3232
11 TraesCS2B01G240300 chr5B 629225047 629227230 2183 True 3539 3539 95.822 1373 3572 1 chr5B.!!$R1 2199
12 TraesCS2B01G240300 chr6A 610981354 610983508 2154 False 3483 3483 95.726 1398 3572 1 chr6A.!!$F2 2174
13 TraesCS2B01G240300 chr6A 610963205 610964617 1412 False 2338 2338 96.674 1 1401 1 chr6A.!!$F1 1400
14 TraesCS2B01G240300 chr6A 610987687 610989098 1411 False 2331 2331 96.601 1 1401 1 chr6A.!!$F3 1400
15 TraesCS2B01G240300 chr6A 611013773 611015184 1411 False 2326 2326 96.530 1 1401 1 chr6A.!!$F4 1400
16 TraesCS2B01G240300 chr6B 615323630 615325516 1886 True 3153 3153 96.822 1 1887 1 chr6B.!!$R2 1886
17 TraesCS2B01G240300 chr6B 615317064 615318751 1687 True 2876 2876 97.400 1882 3572 1 chr6B.!!$R1 1690

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
115 116 0.819259 GCATTTAGGATGGAGCCGCA 60.819 55.000 0.0 0.0 0.0 5.69 F
1815 1832 1.271325 ACTTGTTGCATGGGACGATCA 60.271 47.619 0.0 0.0 0.0 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2106 2123 1.836166 CCAGCTCCTCCAAGATTCTCA 59.164 52.381 0.0 0.0 0.0 3.27 R
3474 3512 0.182537 CTGGACCACAGGGACAACAA 59.817 55.000 0.0 0.0 43.7 2.83 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
44 45 4.621991 GTCATACATCATCGCTAACAGGT 58.378 43.478 0.00 0.0 0.00 4.00
59 60 6.128282 CGCTAACAGGTGAGATGTTTGTTAAT 60.128 38.462 0.00 0.0 41.08 1.40
115 116 0.819259 GCATTTAGGATGGAGCCGCA 60.819 55.000 0.00 0.0 0.00 5.69
285 286 3.513515 TGGGGATACTTTTCATTGGCAAC 59.486 43.478 0.00 0.0 0.00 4.17
371 373 4.828939 AGTCAAGTGCATCCAAAGATTCAA 59.171 37.500 0.00 0.0 26.94 2.69
374 376 5.477637 TCAAGTGCATCCAAAGATTCAATCA 59.522 36.000 0.00 0.0 26.94 2.57
379 381 5.655090 TGCATCCAAAGATTCAATCAGACAT 59.345 36.000 0.00 0.0 0.00 3.06
413 415 7.118496 TCCTTATTTTCAGGTTTTTGCTTCA 57.882 32.000 0.00 0.0 32.59 3.02
538 540 9.320295 TGTTCCCATAACAATTTTAGGAGAAAT 57.680 29.630 0.00 0.0 0.00 2.17
948 950 5.977489 TCGAATAGAGAACCAAGTCAAGA 57.023 39.130 0.00 0.0 0.00 3.02
1005 1007 4.467795 TCCGATCTGAAAAAGGAGATGAGT 59.532 41.667 0.00 0.0 0.00 3.41
1065 1067 5.304778 TGAATTTTGTCGATCTTCCTGACA 58.695 37.500 0.00 0.0 40.62 3.58
1813 1830 2.632377 CTACTTGTTGCATGGGACGAT 58.368 47.619 0.00 0.0 0.00 3.73
1815 1832 1.271325 ACTTGTTGCATGGGACGATCA 60.271 47.619 0.00 0.0 0.00 2.92
2101 2118 5.650703 TCATCACATTGCTCAACTCAATCAT 59.349 36.000 0.00 0.0 32.30 2.45
2106 2123 5.475909 ACATTGCTCAACTCAATCATGTCTT 59.524 36.000 0.00 0.0 32.30 3.01
2991 3021 8.243961 TGTTTTTCTCATTGTTTCCATTCCTA 57.756 30.769 0.00 0.0 0.00 2.94
3089 3119 0.541863 GAATGCTCCGGAAGAAGGGA 59.458 55.000 5.23 0.0 0.00 4.20
3137 3167 2.682856 GTGTGTGCTTTTCAGTGGAAGA 59.317 45.455 10.24 0.0 33.82 2.87
3402 3433 7.145985 GTCAGTGTTATTGTCACTTCAGTCTA 58.854 38.462 0.00 0.0 43.14 2.59
3474 3512 6.883217 ACTTCTGTTTGCATCTCTGTCAATAT 59.117 34.615 0.00 0.0 0.00 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 8.085909 TCGAGTAACTCATTAACAAACATCTCA 58.914 33.333 0.00 0.00 0.00 3.27
59 60 0.242825 CGTGCCCTTCGAGTAACTCA 59.757 55.000 0.00 0.00 0.00 3.41
285 286 7.122353 AGGGATGATGTCAAAGAAATTCTTCAG 59.878 37.037 8.86 5.38 35.27 3.02
371 373 9.917887 AAATAAGGAAAGAATCTCATGTCTGAT 57.082 29.630 0.00 0.00 0.00 2.90
374 376 9.745018 TGAAAATAAGGAAAGAATCTCATGTCT 57.255 29.630 0.00 0.00 0.00 3.41
379 381 8.940397 AACCTGAAAATAAGGAAAGAATCTCA 57.060 30.769 0.00 0.00 38.27 3.27
413 415 3.417069 TCGATGTGGATCAAAGTTGGT 57.583 42.857 0.00 0.00 0.00 3.67
538 540 2.418368 ATTTCTGAATGGTGCGGCTA 57.582 45.000 0.00 0.00 0.00 3.93
855 857 0.668096 CCCCGTTCGACGTGATTTCA 60.668 55.000 0.00 0.00 40.58 2.69
1052 1054 5.010516 AGGAATATCACTGTCAGGAAGATCG 59.989 44.000 4.53 0.00 0.00 3.69
1371 1387 4.482386 CGACCAGAGAAATAAAGTCACGA 58.518 43.478 0.00 0.00 0.00 4.35
2101 2118 3.055530 GCTCCTCCAAGATTCTCAAGACA 60.056 47.826 0.00 0.00 0.00 3.41
2106 2123 1.836166 CCAGCTCCTCCAAGATTCTCA 59.164 52.381 0.00 0.00 0.00 3.27
2156 2173 4.165758 CCCTTTCTCCTCCAAGATTCTCAT 59.834 45.833 0.00 0.00 0.00 2.90
2266 2283 3.652869 TCTTCTCCATTTCTTGAGGGTGT 59.347 43.478 0.00 0.00 0.00 4.16
3089 3119 2.281761 CAAGCCACGGCACCTTCT 60.282 61.111 11.35 0.00 44.88 2.85
3137 3167 8.552296 ACAAAACCCAGAGAATAGATATGAAGT 58.448 33.333 0.00 0.00 0.00 3.01
3402 3433 7.410120 TCTCATGTAGTAATGACACAGATGT 57.590 36.000 0.00 0.00 43.71 3.06
3453 3484 6.849502 ACAATATTGACAGAGATGCAAACAG 58.150 36.000 22.16 0.00 0.00 3.16
3454 3485 6.822667 ACAATATTGACAGAGATGCAAACA 57.177 33.333 22.16 0.00 0.00 2.83
3455 3486 7.086376 ACAACAATATTGACAGAGATGCAAAC 58.914 34.615 22.16 0.00 0.00 2.93
3456 3487 7.218228 ACAACAATATTGACAGAGATGCAAA 57.782 32.000 22.16 0.00 0.00 3.68
3457 3488 6.127925 GGACAACAATATTGACAGAGATGCAA 60.128 38.462 22.16 0.00 0.00 4.08
3458 3489 5.355071 GGACAACAATATTGACAGAGATGCA 59.645 40.000 22.16 0.00 0.00 3.96
3459 3490 5.220931 GGGACAACAATATTGACAGAGATGC 60.221 44.000 22.16 5.31 0.00 3.91
3474 3512 0.182537 CTGGACCACAGGGACAACAA 59.817 55.000 0.00 0.00 43.70 2.83


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

AutoCloner maintained by Alex Coulton.