Multiple sequence alignment - TraesCS1A01G071600

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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 TraesCS1A01G071600 chr1A 100.000 2787 0 0 1 2787 54010363 54007577 0.000000e+00 5147
1 TraesCS1A01G071600 chr1A 97.670 1545 29 4 998 2541 109429631 109428093 0.000000e+00 2647
2 TraesCS1A01G071600 chr1A 94.948 970 32 5 1 970 109430792 109429840 0.000000e+00 1504
3 TraesCS1A01G071600 chr1A 100.000 242 0 0 2546 2787 109425714 109425473 5.480000e-122 448
4 TraesCS1A01G071600 chr6B 99.471 2459 11 2 1 2457 710146768 710149226 0.000000e+00 4468
5 TraesCS1A01G071600 chr6B 93.227 251 11 4 1891 2135 149616946 149616696 5.670000e-97 364
6 TraesCS1A01G071600 chr6A 99.222 2185 15 2 1 2183 514354620 514352436 0.000000e+00 3940
7 TraesCS1A01G071600 chr6A 99.228 1554 10 2 76 1627 514347560 514346007 0.000000e+00 2802
8 TraesCS1A01G071600 chr4A 97.604 1544 32 2 998 2541 76385223 76383685 0.000000e+00 2641
9 TraesCS1A01G071600 chr4A 94.845 970 31 6 1 970 76386381 76385431 0.000000e+00 1496
10 TraesCS1A01G071600 chr4A 90.438 502 28 6 1474 1972 420515787 420516271 0.000000e+00 643
11 TraesCS1A01G071600 chr4A 90.541 444 28 6 1711 2140 207970503 207970946 2.410000e-160 575
12 TraesCS1A01G071600 chr4A 91.549 355 24 4 2183 2532 207974380 207974733 4.170000e-133 484
13 TraesCS1A01G071600 chr4A 99.583 240 1 0 2546 2785 76381365 76381126 3.300000e-119 438
14 TraesCS1A01G071600 chr4A 97.107 242 6 1 2546 2787 702430892 702430652 9.290000e-110 407
15 TraesCS1A01G071600 chr4D 83.968 761 106 11 3 759 494290605 494289857 0.000000e+00 715
16 TraesCS1A01G071600 chr5B 90.438 502 28 4 1474 1972 163065997 163066481 0.000000e+00 643
17 TraesCS1A01G071600 chr5B 81.696 224 37 3 1307 1526 56317080 56316857 1.700000e-42 183
18 TraesCS1A01G071600 chr1B 90.438 502 28 4 1474 1972 558565925 558566409 0.000000e+00 643
19 TraesCS1A01G071600 chr1B 91.000 300 22 5 2194 2489 613031106 613031404 1.560000e-107 399
20 TraesCS1A01G071600 chr1B 93.227 251 11 4 1891 2135 613030663 613030913 5.670000e-97 364
21 TraesCS1A01G071600 chr1B 92.857 126 9 0 1350 1475 558565673 558565798 1.700000e-42 183
22 TraesCS1A01G071600 chr7A 92.774 429 26 4 1716 2140 9390870 9390443 1.420000e-172 616
23 TraesCS1A01G071600 chr7A 93.627 408 21 4 2135 2540 9390014 9389610 3.070000e-169 604
24 TraesCS1A01G071600 chr7B 92.308 429 28 4 1716 2140 607311027 607310600 3.070000e-169 604
25 TraesCS1A01G071600 chr7B 92.157 408 26 5 2135 2540 607310171 607309768 3.110000e-159 571
26 TraesCS1A01G071600 chr7B 92.163 319 19 1 1350 1662 607311344 607311026 1.970000e-121 446
27 TraesCS1A01G071600 chr2D 94.098 305 15 2 998 1302 242903620 242903319 7.030000e-126 460
28 TraesCS1A01G071600 chr3B 98.760 242 3 0 2546 2787 605647288 605647047 5.510000e-117 431
29 TraesCS1A01G071600 chr3B 95.816 239 10 0 2547 2785 255702200 255702438 1.210000e-103 387
30 TraesCS1A01G071600 chr4B 97.107 242 7 0 2546 2787 423393677 423393436 2.580000e-110 409
31 TraesCS1A01G071600 chr4B 91.000 300 22 5 2194 2489 70052214 70051916 1.560000e-107 399
32 TraesCS1A01G071600 chrUn 91.060 302 22 5 2192 2489 49429847 49429547 1.200000e-108 403
33 TraesCS1A01G071600 chrUn 93.200 250 12 4 1891 2135 49430287 49430038 2.040000e-96 363
34 TraesCS1A01G071600 chr2B 96.341 246 5 1 2546 2787 612671166 612671411 4.320000e-108 401
35 TraesCS1A01G071600 chr2B 93.776 241 15 0 2547 2787 213030242 213030002 2.040000e-96 363
36 TraesCS1A01G071600 chr2A 83.036 224 34 3 1307 1526 180217315 180217092 1.690000e-47 200


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 TraesCS1A01G071600 chr1A 54007577 54010363 2786 True 5147.000000 5147 100.000000 1 2787 1 chr1A.!!$R1 2786
1 TraesCS1A01G071600 chr1A 109425473 109430792 5319 True 1533.000000 2647 97.539333 1 2787 3 chr1A.!!$R2 2786
2 TraesCS1A01G071600 chr6B 710146768 710149226 2458 False 4468.000000 4468 99.471000 1 2457 1 chr6B.!!$F1 2456
3 TraesCS1A01G071600 chr6A 514352436 514354620 2184 True 3940.000000 3940 99.222000 1 2183 1 chr6A.!!$R2 2182
4 TraesCS1A01G071600 chr6A 514346007 514347560 1553 True 2802.000000 2802 99.228000 76 1627 1 chr6A.!!$R1 1551
5 TraesCS1A01G071600 chr4A 76381126 76386381 5255 True 1525.000000 2641 97.344000 1 2785 3 chr4A.!!$R2 2784
6 TraesCS1A01G071600 chr4A 207970503 207974733 4230 False 529.500000 575 91.045000 1711 2532 2 chr4A.!!$F2 821
7 TraesCS1A01G071600 chr4D 494289857 494290605 748 True 715.000000 715 83.968000 3 759 1 chr4D.!!$R1 756
8 TraesCS1A01G071600 chr1B 558565673 558566409 736 False 413.000000 643 91.647500 1350 1972 2 chr1B.!!$F1 622
9 TraesCS1A01G071600 chr1B 613030663 613031404 741 False 381.500000 399 92.113500 1891 2489 2 chr1B.!!$F2 598
10 TraesCS1A01G071600 chr7A 9389610 9390870 1260 True 610.000000 616 93.200500 1716 2540 2 chr7A.!!$R1 824
11 TraesCS1A01G071600 chr7B 607309768 607311344 1576 True 540.333333 604 92.209333 1350 2540 3 chr7B.!!$R1 1190
12 TraesCS1A01G071600 chrUn 49429547 49430287 740 True 383.000000 403 92.130000 1891 2489 2 chrUn.!!$R1 598

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
462 466 4.083271 GCTGTAGGTTTTGGATGTCAAGTC 60.083 45.833 0.0 0.0 36.62 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2314 6365 6.554334 TGTTATTCACCTTTGCTAGTGTTC 57.446 37.5 0.0 0.0 35.45 3.18 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
462 466 4.083271 GCTGTAGGTTTTGGATGTCAAGTC 60.083 45.833 0.00 0.0 36.62 3.01
719 724 8.092521 TCATGATCTGTCTCTTTGAAAAAGTC 57.907 34.615 0.00 0.0 0.00 3.01
2403 6455 8.102800 TGTTTGATATGACTGGCATGATATTC 57.897 34.615 6.18 0.0 37.87 1.75
2533 6585 9.329913 CGAAGAAAATGTTTTGTGAAGTATAGG 57.670 33.333 0.00 0.0 0.00 2.57
2534 6586 9.129209 GAAGAAAATGTTTTGTGAAGTATAGGC 57.871 33.333 0.00 0.0 0.00 3.93
2536 6588 8.860088 AGAAAATGTTTTGTGAAGTATAGGCTT 58.140 29.630 0.00 0.0 0.00 4.35
2539 6591 8.409358 AATGTTTTGTGAAGTATAGGCTTTCT 57.591 30.769 0.00 0.0 0.00 2.52
2540 6592 7.435068 TGTTTTGTGAAGTATAGGCTTTCTC 57.565 36.000 0.00 0.0 0.00 2.87
2541 6593 6.430000 TGTTTTGTGAAGTATAGGCTTTCTCC 59.570 38.462 0.00 0.0 0.00 3.71
2542 6594 4.755266 TGTGAAGTATAGGCTTTCTCCC 57.245 45.455 0.00 0.0 0.00 4.30
2543 6595 4.362677 TGTGAAGTATAGGCTTTCTCCCT 58.637 43.478 0.00 0.0 36.47 4.20
2544 6596 4.162320 TGTGAAGTATAGGCTTTCTCCCTG 59.838 45.833 0.00 0.0 33.88 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
462 466 5.070981 TCTCTTAATGGTCTGCCTATTCCAG 59.929 44.000 0.00 0.0 33.33 3.86
2314 6365 6.554334 TGTTATTCACCTTTGCTAGTGTTC 57.446 37.500 0.00 0.0 35.45 3.18
2533 6585 4.395231 GGTAATGTACAACAGGGAGAAAGC 59.605 45.833 0.00 0.0 0.00 3.51
2534 6586 4.630069 CGGTAATGTACAACAGGGAGAAAG 59.370 45.833 0.00 0.0 0.00 2.62
2536 6588 3.618019 GCGGTAATGTACAACAGGGAGAA 60.618 47.826 0.00 0.0 0.00 2.87
2539 6591 1.404449 CGCGGTAATGTACAACAGGGA 60.404 52.381 0.00 0.0 0.00 4.20
2540 6592 1.003851 CGCGGTAATGTACAACAGGG 58.996 55.000 0.00 0.0 0.00 4.45
2541 6593 0.372334 GCGCGGTAATGTACAACAGG 59.628 55.000 8.83 0.0 0.00 4.00
2542 6594 1.072391 TGCGCGGTAATGTACAACAG 58.928 50.000 8.83 0.0 0.00 3.16
2543 6595 0.791422 GTGCGCGGTAATGTACAACA 59.209 50.000 8.83 0.0 0.00 3.33
2544 6596 0.791422 TGTGCGCGGTAATGTACAAC 59.209 50.000 8.83 0.0 0.00 3.32


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

AutoCloner maintained by Alex Coulton.