Multiple sequence alignment - TraesCS2D01G124000

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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 TraesCS2D01G124000 chr2D 100.000 2616 0 0 1 2616 72651074 72653689 0.000000e+00 4831
1 TraesCS2D01G124000 chr2D 97.973 2220 15 5 399 2616 72371017 72373208 0.000000e+00 3823
2 TraesCS2D01G124000 chr2D 97.103 1001 22 2 1 994 72627418 72628418 0.000000e+00 1681
3 TraesCS2D01G124000 chr2D 98.997 399 4 0 1 399 72370573 72370971 0.000000e+00 715
4 TraesCS2D01G124000 chr2A 97.911 1580 27 3 432 2006 71112250 71113828 0.000000e+00 2730
5 TraesCS2D01G124000 chr2A 97.054 611 18 0 2006 2616 71114239 71114849 0.000000e+00 1029
6 TraesCS2D01G124000 chr2A 89.073 723 67 8 1359 2074 71078583 71079300 0.000000e+00 887
7 TraesCS2D01G124000 chr2A 91.312 564 34 3 2068 2616 71210794 71211357 0.000000e+00 756
8 TraesCS2D01G124000 chr2A 91.135 564 35 3 2068 2616 71158034 71158597 0.000000e+00 750
9 TraesCS2D01G124000 chr2A 91.135 564 35 3 2068 2616 71312351 71312914 0.000000e+00 750
10 TraesCS2D01G124000 chr2A 92.437 476 35 1 699 1173 71073592 71074067 0.000000e+00 678
11 TraesCS2D01G124000 chr2A 92.698 315 16 2 2068 2375 71263423 71263737 5.140000e-122 448
12 TraesCS2D01G124000 chr2A 94.231 260 14 1 1 259 71110985 71111244 1.890000e-106 396
13 TraesCS2D01G124000 chr2A 96.552 145 5 0 448 592 71073466 71073610 9.360000e-60 241
14 TraesCS2D01G124000 chr2A 91.463 164 8 3 295 458 71072698 71072855 1.220000e-53 220
15 TraesCS2D01G124000 chr2A 84.571 175 5 6 1199 1361 71074543 71074707 1.250000e-33 154
16 TraesCS2D01G124000 chr2A 95.506 89 4 0 295 383 71111785 71111873 2.710000e-30 143
17 TraesCS2D01G124000 chr2B 95.974 1565 50 8 414 1969 109082333 109083893 0.000000e+00 2529
18 TraesCS2D01G124000 chr2B 96.690 1420 31 3 295 1712 109161482 109162887 0.000000e+00 2348
19 TraesCS2D01G124000 chr2B 96.200 1421 42 7 295 1712 109789050 109790461 0.000000e+00 2314
20 TraesCS2D01G124000 chr2B 93.982 914 34 4 1703 2616 109180351 109181243 0.000000e+00 1363
21 TraesCS2D01G124000 chr2B 96.329 790 28 1 1827 2616 109868846 109869634 0.000000e+00 1297
22 TraesCS2D01G124000 chr2B 94.099 644 29 2 1982 2616 109084098 109084741 0.000000e+00 970
23 TraesCS2D01G124000 chr2B 89.107 661 63 8 1260 1918 109357666 109358319 0.000000e+00 813
24 TraesCS2D01G124000 chr2B 88.024 501 45 9 295 788 109356715 109357207 1.750000e-161 579
25 TraesCS2D01G124000 chr2B 94.677 263 10 1 1 259 109075731 109075993 3.130000e-109 405
26 TraesCS2D01G124000 chr2B 94.483 145 8 0 984 1128 109357463 109357607 9.420000e-55 224
27 TraesCS2D01G124000 chr2B 97.087 103 3 0 295 397 109076570 109076672 9.620000e-40 174
28 TraesCS2D01G124000 chrUn 91.312 564 34 3 2068 2616 289659160 289659723 0.000000e+00 756
29 TraesCS2D01G124000 chr6B 80.231 865 128 31 782 1619 176969891 176969043 6.190000e-171 610
30 TraesCS2D01G124000 chr6D 83.878 490 67 9 772 1258 95787880 95788360 8.530000e-125 457
31 TraesCS2D01G124000 chr7A 93.050 259 18 0 1 259 421732581 421732839 1.900000e-101 379
32 TraesCS2D01G124000 chr1D 92.481 266 17 1 1 266 315546215 315546477 6.830000e-101 377
33 TraesCS2D01G124000 chr3D 92.188 256 20 0 1 256 365333466 365333211 1.910000e-96 363
34 TraesCS2D01G124000 chr1A 91.120 259 22 1 1 259 78545842 78546099 1.490000e-92 350
35 TraesCS2D01G124000 chr3B 90.189 265 23 1 2 266 592853206 592852945 2.490000e-90 342


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 TraesCS2D01G124000 chr2D 72651074 72653689 2615 False 4831.000000 4831 100.0000 1 2616 1 chr2D.!!$F2 2615
1 TraesCS2D01G124000 chr2D 72370573 72373208 2635 False 2269.000000 3823 98.4850 1 2616 2 chr2D.!!$F3 2615
2 TraesCS2D01G124000 chr2D 72627418 72628418 1000 False 1681.000000 1681 97.1030 1 994 1 chr2D.!!$F1 993
3 TraesCS2D01G124000 chr2A 71110985 71114849 3864 False 1074.500000 2730 96.1755 1 2616 4 chr2A.!!$F6 2615
4 TraesCS2D01G124000 chr2A 71210794 71211357 563 False 756.000000 756 91.3120 2068 2616 1 chr2A.!!$F2 548
5 TraesCS2D01G124000 chr2A 71158034 71158597 563 False 750.000000 750 91.1350 2068 2616 1 chr2A.!!$F1 548
6 TraesCS2D01G124000 chr2A 71312351 71312914 563 False 750.000000 750 91.1350 2068 2616 1 chr2A.!!$F4 548
7 TraesCS2D01G124000 chr2A 71072698 71079300 6602 False 436.000000 887 90.8192 295 2074 5 chr2A.!!$F5 1779
8 TraesCS2D01G124000 chr2B 109161482 109162887 1405 False 2348.000000 2348 96.6900 295 1712 1 chr2B.!!$F1 1417
9 TraesCS2D01G124000 chr2B 109789050 109790461 1411 False 2314.000000 2314 96.2000 295 1712 1 chr2B.!!$F3 1417
10 TraesCS2D01G124000 chr2B 109082333 109084741 2408 False 1749.500000 2529 95.0365 414 2616 2 chr2B.!!$F6 2202
11 TraesCS2D01G124000 chr2B 109180351 109181243 892 False 1363.000000 1363 93.9820 1703 2616 1 chr2B.!!$F2 913
12 TraesCS2D01G124000 chr2B 109868846 109869634 788 False 1297.000000 1297 96.3290 1827 2616 1 chr2B.!!$F4 789
13 TraesCS2D01G124000 chr2B 109356715 109358319 1604 False 538.666667 813 90.5380 295 1918 3 chr2B.!!$F7 1623
14 TraesCS2D01G124000 chr2B 109075731 109076672 941 False 289.500000 405 95.8820 1 397 2 chr2B.!!$F5 396
15 TraesCS2D01G124000 chrUn 289659160 289659723 563 False 756.000000 756 91.3120 2068 2616 1 chrUn.!!$F1 548
16 TraesCS2D01G124000 chr6B 176969043 176969891 848 True 610.000000 610 80.2310 782 1619 1 chr6B.!!$R1 837

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
184 190 5.246981 TCACCCAGATCTGTTCAAAGAAT 57.753 39.13 21.11 0.0 0.0 2.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2095 8645 1.330521 CCGGCGATGAAGGTTTACATG 59.669 52.381 9.3 0.0 0.0 3.21 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
184 190 5.246981 TCACCCAGATCTGTTCAAAGAAT 57.753 39.130 21.11 0.0 0.00 2.40
864 2405 9.831737 GGATGTGTGATGTCTATTTATTATTGC 57.168 33.333 0.00 0.0 0.00 3.56
2095 8645 6.817140 ACCGAAATCTGAATAGTTAGACAACC 59.183 38.462 0.00 0.0 35.05 3.77
2152 8702 6.264518 AGGTTCATTTCCTTTTACACGACATT 59.735 34.615 0.00 0.0 30.18 2.71
2202 8759 3.795688 AACTCACCACAGGATCAATGT 57.204 42.857 0.00 0.0 0.00 2.71
2371 8928 1.006337 CCCACCGGCAACAACATTG 60.006 57.895 0.00 0.0 0.00 2.82
2501 9058 2.661176 ACATCCCCCAGAACTCCTTA 57.339 50.000 0.00 0.0 0.00 2.69
2593 9166 6.931838 TGTACAGGAGGAACATAGTTAAGTG 58.068 40.000 0.00 0.0 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
184 190 2.492088 CGTACACCAGACTTGATGGAGA 59.508 50.000 0.0 0.0 40.51 3.71
647 2150 5.051240 GCTTTGATTTTTGTGTGAAGAGCTG 60.051 40.000 0.0 0.0 0.00 4.24
2095 8645 1.330521 CCGGCGATGAAGGTTTACATG 59.669 52.381 9.3 0.0 0.00 3.21
2152 8702 4.632688 GGCTTTAGTACCGTGCAAATTCTA 59.367 41.667 0.0 0.0 0.00 2.10
2202 8759 3.000041 CGTTGTGCTATGCTCCAGTAAA 59.000 45.455 0.0 0.0 0.00 2.01
2371 8928 4.977963 CGTTGGTGATAATTGGATCATTGC 59.022 41.667 0.0 0.0 38.11 3.56
2501 9058 0.036732 TCCGCAACCAGAAGCAGATT 59.963 50.000 0.0 0.0 0.00 2.40


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

AutoCloner maintained by Alex Coulton.