Multiple sequence alignment - TraesCS3B01G168500

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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 TraesCS3B01G168500 chr3B 100.000 2369 0 0 1 2369 169349752 169347384 0.000000e+00 4375
1 TraesCS3B01G168500 chr3B 97.973 592 11 1 1 592 793124150 793124740 0.000000e+00 1026
2 TraesCS3B01G168500 chr3B 88.307 573 47 5 15 580 244628213 244627654 0.000000e+00 669
3 TraesCS3B01G168500 chr3B 84.444 225 27 4 550 772 736479910 736480128 5.130000e-52 215
4 TraesCS3B01G168500 chr3B 79.386 228 33 10 550 772 770735937 770736155 5.280000e-32 148
5 TraesCS3B01G168500 chr3A 99.489 1762 9 0 608 2369 721633092 721631331 0.000000e+00 3205
6 TraesCS3B01G168500 chr7B 99.323 1772 9 2 598 2369 721298087 721299855 0.000000e+00 3203
7 TraesCS3B01G168500 chr7B 87.435 573 52 5 15 580 158396880 158396321 1.990000e-180 641
8 TraesCS3B01G168500 chr2A 99.043 1776 17 0 594 2369 590787115 590785340 0.000000e+00 3186
9 TraesCS3B01G168500 chr2A 96.181 1571 45 7 812 2369 441097380 441098948 0.000000e+00 2555
10 TraesCS3B01G168500 chr2A 98.052 462 9 0 1 462 166787597 166787136 0.000000e+00 804
11 TraesCS3B01G168500 chr2A 96.694 121 4 0 460 580 166787033 166786913 3.990000e-48 202
12 TraesCS3B01G168500 chr6B 98.872 1773 19 1 598 2369 474539980 474541752 0.000000e+00 3162
13 TraesCS3B01G168500 chr6B 95.746 1575 49 8 812 2369 151876705 151878278 0.000000e+00 2521
14 TraesCS3B01G168500 chr6B 86.783 575 55 6 15 581 561640421 561639860 2.590000e-174 621
15 TraesCS3B01G168500 chr1A 98.694 1761 22 1 609 2369 335115469 335117228 0.000000e+00 3123
16 TraesCS3B01G168500 chr4A 96.411 1783 56 4 595 2369 540821706 540823488 0.000000e+00 2931
17 TraesCS3B01G168500 chr4A 95.630 595 15 3 1 593 552635618 552636203 0.000000e+00 944
18 TraesCS3B01G168500 chr6A 98.560 1528 20 2 598 2125 462594586 462593061 0.000000e+00 2699
19 TraesCS3B01G168500 chr4B 98.616 578 8 0 1 578 92923871 92924448 0.000000e+00 1024
20 TraesCS3B01G168500 chr5B 87.780 581 50 6 15 588 637444649 637444083 0.000000e+00 660
21 TraesCS3B01G168500 chr1B 87.304 575 50 11 15 580 326219241 326219801 9.240000e-179 636
22 TraesCS3B01G168500 chr6D 82.857 175 27 3 415 588 457067043 457066871 1.130000e-33 154


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 TraesCS3B01G168500 chr3B 169347384 169349752 2368 True 4375 4375 100.000 1 2369 1 chr3B.!!$R1 2368
1 TraesCS3B01G168500 chr3B 793124150 793124740 590 False 1026 1026 97.973 1 592 1 chr3B.!!$F3 591
2 TraesCS3B01G168500 chr3B 244627654 244628213 559 True 669 669 88.307 15 580 1 chr3B.!!$R2 565
3 TraesCS3B01G168500 chr3A 721631331 721633092 1761 True 3205 3205 99.489 608 2369 1 chr3A.!!$R1 1761
4 TraesCS3B01G168500 chr7B 721298087 721299855 1768 False 3203 3203 99.323 598 2369 1 chr7B.!!$F1 1771
5 TraesCS3B01G168500 chr7B 158396321 158396880 559 True 641 641 87.435 15 580 1 chr7B.!!$R1 565
6 TraesCS3B01G168500 chr2A 590785340 590787115 1775 True 3186 3186 99.043 594 2369 1 chr2A.!!$R1 1775
7 TraesCS3B01G168500 chr2A 441097380 441098948 1568 False 2555 2555 96.181 812 2369 1 chr2A.!!$F1 1557
8 TraesCS3B01G168500 chr2A 166786913 166787597 684 True 503 804 97.373 1 580 2 chr2A.!!$R2 579
9 TraesCS3B01G168500 chr6B 474539980 474541752 1772 False 3162 3162 98.872 598 2369 1 chr6B.!!$F2 1771
10 TraesCS3B01G168500 chr6B 151876705 151878278 1573 False 2521 2521 95.746 812 2369 1 chr6B.!!$F1 1557
11 TraesCS3B01G168500 chr6B 561639860 561640421 561 True 621 621 86.783 15 581 1 chr6B.!!$R1 566
12 TraesCS3B01G168500 chr1A 335115469 335117228 1759 False 3123 3123 98.694 609 2369 1 chr1A.!!$F1 1760
13 TraesCS3B01G168500 chr4A 540821706 540823488 1782 False 2931 2931 96.411 595 2369 1 chr4A.!!$F1 1774
14 TraesCS3B01G168500 chr4A 552635618 552636203 585 False 944 944 95.630 1 593 1 chr4A.!!$F2 592
15 TraesCS3B01G168500 chr6A 462593061 462594586 1525 True 2699 2699 98.560 598 2125 1 chr6A.!!$R1 1527
16 TraesCS3B01G168500 chr4B 92923871 92924448 577 False 1024 1024 98.616 1 578 1 chr4B.!!$F1 577
17 TraesCS3B01G168500 chr5B 637444083 637444649 566 True 660 660 87.780 15 588 1 chr5B.!!$R1 573
18 TraesCS3B01G168500 chr1B 326219241 326219801 560 False 636 636 87.304 15 580 1 chr1B.!!$F1 565

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
961 1085 0.336737 ACCCTCCGTCCAGATTCTCT 59.663 55.0 0.0 0.0 0.0 3.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2232 2372 2.084546 CACTTCCTTCGGTGGAAATCC 58.915 52.381 10.37 0.0 44.49 3.01 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
303 308 5.576447 AAATTACTTCCGGCCTAACAATG 57.424 39.130 0.00 0.0 0.00 2.82
413 422 9.657419 ATTGAATATGTGTCAATTTTTCTTCCC 57.343 29.630 0.00 0.0 41.82 3.97
433 442 3.670377 GCAACCACGGGCCTGTTC 61.670 66.667 16.73 0.0 0.00 3.18
484 598 3.022406 AGATAGTACCTCCGTGTGGAAC 58.978 50.000 0.00 0.0 45.87 3.62
510 628 3.920231 AGCATGTGAGCCAATTCTCTA 57.080 42.857 0.00 0.0 34.29 2.43
559 677 9.877178 TTAACATAATTTTTATCCCGTTGCAAT 57.123 25.926 0.59 0.0 0.00 3.56
585 703 5.046878 CACGGGCCATTGTCCTAGTATATAA 60.047 44.000 4.39 0.0 32.45 0.98
586 704 5.724854 ACGGGCCATTGTCCTAGTATATAAT 59.275 40.000 4.39 0.0 32.45 1.28
587 705 6.899075 ACGGGCCATTGTCCTAGTATATAATA 59.101 38.462 4.39 0.0 32.45 0.98
588 706 7.567622 ACGGGCCATTGTCCTAGTATATAATAT 59.432 37.037 4.39 0.0 32.45 1.28
589 707 9.085645 CGGGCCATTGTCCTAGTATATAATATA 57.914 37.037 4.39 0.0 32.45 0.86
961 1085 0.336737 ACCCTCCGTCCAGATTCTCT 59.663 55.000 0.00 0.0 0.00 3.10
1089 1213 3.017581 GCTGGGATCCACCACCCT 61.018 66.667 15.23 0.0 45.74 4.34
1332 1465 2.409570 GGAGGAACCCTAGCCATAAGT 58.590 52.381 0.00 0.0 31.76 2.24
2232 2372 6.325919 TGTAGTTGCAAATTTTACTGGAGG 57.674 37.500 4.05 0.0 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
303 308 4.109766 GGTATTTGCTTTGCCCGTTAATC 58.890 43.478 0.00 0.0 0.00 1.75
395 403 4.161189 TGCAAGGGAAGAAAAATTGACACA 59.839 37.500 0.00 0.0 0.00 3.72
413 422 3.673484 CAGGCCCGTGGTTGCAAG 61.673 66.667 0.00 0.0 0.00 4.01
484 598 5.717119 AGAATTGGCTCACATGCTTTTTAG 58.283 37.500 0.00 0.0 0.00 1.85
510 628 2.594592 GCACCGTGCCTTGGTTCT 60.595 61.111 12.80 0.0 37.72 3.01
559 677 2.535485 CTAGGACAATGGCCCGTGCA 62.535 60.000 0.00 0.0 40.13 4.57
624 742 0.792640 GACGACGTACGACCAGAAGA 59.207 55.000 24.41 0.0 45.77 2.87
1089 1213 6.114187 ACATGAAGAGAATGTGAGGTGTAA 57.886 37.500 0.00 0.0 36.89 2.41
1332 1465 1.826921 GGCGTCATCCGAGGAGGTA 60.827 63.158 3.61 0.0 41.99 3.08
2232 2372 2.084546 CACTTCCTTCGGTGGAAATCC 58.915 52.381 10.37 0.0 44.49 3.01


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

AutoCloner maintained by Alex Coulton.