Multiple sequence alignment - TraesCS5D01G549500

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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 TraesCS5D01G549500 chr5D 100.000 5182 0 0 1 5182 556549106 556543925 0.000000e+00 9570.0
1 TraesCS5D01G549500 chr5D 87.500 272 25 5 3470 3737 556533737 556533471 6.520000e-79 305.0
2 TraesCS5D01G549500 chr5D 93.846 130 8 0 4272 4401 500133472 500133601 4.090000e-46 196.0
3 TraesCS5D01G549500 chr5D 100.000 28 0 0 2325 2352 346884114 346884141 9.000000e-03 52.8
4 TraesCS5D01G549500 chrUn 86.113 1325 123 23 2896 4195 244921260 244919972 0.000000e+00 1371.0
5 TraesCS5D01G549500 chrUn 86.113 1325 123 23 2896 4195 285317277 285315989 0.000000e+00 1371.0
6 TraesCS5D01G549500 chrUn 86.157 1322 122 24 2896 4192 295399241 295400526 0.000000e+00 1371.0
7 TraesCS5D01G549500 chrUn 86.157 1322 122 24 2896 4192 306003443 306004728 0.000000e+00 1371.0
8 TraesCS5D01G549500 chrUn 86.032 988 57 36 1345 2307 244922573 244921642 0.000000e+00 985.0
9 TraesCS5D01G549500 chrUn 86.032 988 57 36 1345 2307 285318590 285317659 0.000000e+00 985.0
10 TraesCS5D01G549500 chrUn 86.009 679 80 14 2354 3024 244921659 244920988 0.000000e+00 713.0
11 TraesCS5D01G549500 chrUn 86.009 679 80 14 2354 3024 285317676 285317005 0.000000e+00 713.0
12 TraesCS5D01G549500 chrUn 86.380 558 63 12 2471 3021 295398959 295399510 9.600000e-167 597.0
13 TraesCS5D01G549500 chrUn 86.462 554 63 11 2474 3021 306003165 306003712 9.600000e-167 597.0
14 TraesCS5D01G549500 chrUn 83.468 496 61 12 2848 3343 244921260 244920786 4.760000e-120 442.0
15 TraesCS5D01G549500 chrUn 83.468 496 61 12 2848 3343 285317277 285316803 4.760000e-120 442.0
16 TraesCS5D01G549500 chrUn 83.570 493 60 12 2845 3337 295399238 295399709 4.760000e-120 442.0
17 TraesCS5D01G549500 chrUn 83.570 493 60 12 2845 3337 306003440 306003911 4.760000e-120 442.0
18 TraesCS5D01G549500 chrUn 77.338 631 75 35 466 1053 244923401 244922796 1.400000e-80 311.0
19 TraesCS5D01G549500 chrUn 77.338 631 75 35 466 1053 285319418 285318813 1.400000e-80 311.0
20 TraesCS5D01G549500 chrUn 83.529 340 38 6 3 341 244923814 244923492 8.430000e-78 302.0
21 TraesCS5D01G549500 chrUn 84.541 207 26 4 136 341 285319710 285319509 3.160000e-47 200.0
22 TraesCS5D01G549500 chrUn 93.333 135 9 0 4274 4408 293609603 293609469 3.160000e-47 200.0
23 TraesCS5D01G549500 chrUn 94.574 129 7 0 4274 4402 314565200 314565328 3.160000e-47 200.0
24 TraesCS5D01G549500 chr5B 87.608 1041 92 24 2797 3815 710237812 710238837 0.000000e+00 1173.0
25 TraesCS5D01G549500 chr5B 88.426 985 58 18 1342 2299 710236470 710237425 0.000000e+00 1136.0
26 TraesCS5D01G549500 chr5B 84.359 991 124 16 2376 3344 710237423 710238404 0.000000e+00 942.0
27 TraesCS5D01G549500 chr5B 90.671 343 25 3 3934 4276 710238863 710239198 2.850000e-122 449.0
28 TraesCS5D01G549500 chr5B 87.871 371 35 4 1 363 710234507 710234875 1.330000e-115 427.0
29 TraesCS5D01G549500 chr5B 85.538 325 21 8 495 815 710235231 710235533 3.010000e-82 316.0
30 TraesCS5D01G549500 chr5B 95.276 127 6 0 4275 4401 50519943 50520069 8.800000e-48 202.0
31 TraesCS5D01G549500 chr5B 95.522 67 3 0 401 467 710235178 710235244 1.970000e-19 108.0
32 TraesCS5D01G549500 chr6B 91.418 536 42 3 4649 5180 599981097 599981632 0.000000e+00 732.0
33 TraesCS5D01G549500 chr6B 91.541 532 41 3 4655 5182 26217740 26218271 0.000000e+00 730.0
34 TraesCS5D01G549500 chr6B 92.537 134 10 0 4275 4408 69718560 69718427 5.300000e-45 193.0
35 TraesCS5D01G549500 chr7D 91.337 531 42 3 4654 5180 478798823 478799353 0.000000e+00 723.0
36 TraesCS5D01G549500 chr7D 90.890 483 33 6 1477 1956 600610752 600611226 5.660000e-179 638.0
37 TraesCS5D01G549500 chr7D 89.936 467 37 5 1487 1951 600557165 600557623 1.240000e-165 593.0
38 TraesCS5D01G549500 chr2B 91.321 530 43 2 4654 5180 452910177 452910706 0.000000e+00 721.0
39 TraesCS5D01G549500 chr1B 91.182 533 41 6 4653 5180 594704026 594703495 0.000000e+00 719.0
40 TraesCS5D01G549500 chr1B 90.625 544 46 4 4641 5180 643024939 643025481 0.000000e+00 717.0
41 TraesCS5D01G549500 chr1B 94.531 128 7 0 4274 4401 464481748 464481621 1.140000e-46 198.0
42 TraesCS5D01G549500 chr4A 91.304 529 41 4 4656 5180 728114294 728114821 0.000000e+00 717.0
43 TraesCS5D01G549500 chr3B 91.149 531 43 3 4654 5180 465345740 465345210 0.000000e+00 717.0
44 TraesCS5D01G549500 chr3B 100.000 31 0 0 3825 3855 263260945 263260975 2.020000e-04 58.4
45 TraesCS5D01G549500 chr3B 96.970 33 1 0 2323 2355 493117283 493117251 7.250000e-04 56.5
46 TraesCS5D01G549500 chr7B 90.706 538 44 5 4649 5182 657535554 657536089 0.000000e+00 712.0
47 TraesCS5D01G549500 chr7B 93.382 136 9 0 4272 4407 637617925 637618060 8.800000e-48 202.0
48 TraesCS5D01G549500 chr5A 87.844 617 53 17 1349 1956 296997574 296998177 0.000000e+00 704.0
49 TraesCS5D01G549500 chr5A 85.784 612 57 15 1349 1956 689246624 689246039 5.700000e-174 621.0
50 TraesCS5D01G549500 chr5A 93.182 44 3 0 3819 3862 679658592 679658635 1.200000e-06 65.8
51 TraesCS5D01G549500 chr3A 85.784 612 56 15 1349 1956 148181001 148181585 2.050000e-173 619.0
52 TraesCS5D01G549500 chr3A 84.967 612 61 14 1349 1956 148257607 148258191 4.470000e-165 592.0
53 TraesCS5D01G549500 chr2D 95.276 127 6 0 4275 4401 58672253 58672127 8.800000e-48 202.0
54 TraesCS5D01G549500 chr2D 94.531 128 7 0 4274 4401 78576479 78576606 1.140000e-46 198.0
55 TraesCS5D01G549500 chr2D 90.909 110 10 0 3820 3929 102942674 102942565 1.160000e-31 148.0
56 TraesCS5D01G549500 chr2D 93.478 46 3 0 2307 2352 506797936 506797981 9.310000e-08 69.4
57 TraesCS5D01G549500 chr1A 79.208 101 19 2 3825 3924 171453440 171453341 9.310000e-08 69.4


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 TraesCS5D01G549500 chr5D 556543925 556549106 5181 True 9570.000000 9570 100.000000 1 5182 1 chr5D.!!$R2 5181
1 TraesCS5D01G549500 chrUn 295398959 295400526 1567 False 803.333333 1371 85.369000 2471 4192 3 chrUn.!!$F2 1721
2 TraesCS5D01G549500 chrUn 306003165 306004728 1563 False 803.333333 1371 85.396333 2474 4192 3 chrUn.!!$F3 1718
3 TraesCS5D01G549500 chrUn 244919972 244923814 3842 True 687.333333 1371 83.748167 3 4195 6 chrUn.!!$R2 4192
4 TraesCS5D01G549500 chrUn 285315989 285319710 3721 True 670.333333 1371 83.916833 136 4195 6 chrUn.!!$R3 4059
5 TraesCS5D01G549500 chr5B 710234507 710239198 4691 False 650.142857 1173 88.570714 1 4276 7 chr5B.!!$F2 4275
6 TraesCS5D01G549500 chr6B 599981097 599981632 535 False 732.000000 732 91.418000 4649 5180 1 chr6B.!!$F2 531
7 TraesCS5D01G549500 chr6B 26217740 26218271 531 False 730.000000 730 91.541000 4655 5182 1 chr6B.!!$F1 527
8 TraesCS5D01G549500 chr7D 478798823 478799353 530 False 723.000000 723 91.337000 4654 5180 1 chr7D.!!$F1 526
9 TraesCS5D01G549500 chr2B 452910177 452910706 529 False 721.000000 721 91.321000 4654 5180 1 chr2B.!!$F1 526
10 TraesCS5D01G549500 chr1B 594703495 594704026 531 True 719.000000 719 91.182000 4653 5180 1 chr1B.!!$R2 527
11 TraesCS5D01G549500 chr1B 643024939 643025481 542 False 717.000000 717 90.625000 4641 5180 1 chr1B.!!$F1 539
12 TraesCS5D01G549500 chr4A 728114294 728114821 527 False 717.000000 717 91.304000 4656 5180 1 chr4A.!!$F1 524
13 TraesCS5D01G549500 chr3B 465345210 465345740 530 True 717.000000 717 91.149000 4654 5180 1 chr3B.!!$R1 526
14 TraesCS5D01G549500 chr7B 657535554 657536089 535 False 712.000000 712 90.706000 4649 5182 1 chr7B.!!$F2 533
15 TraesCS5D01G549500 chr5A 296997574 296998177 603 False 704.000000 704 87.844000 1349 1956 1 chr5A.!!$F1 607
16 TraesCS5D01G549500 chr5A 689246039 689246624 585 True 621.000000 621 85.784000 1349 1956 1 chr5A.!!$R1 607
17 TraesCS5D01G549500 chr3A 148181001 148181585 584 False 619.000000 619 85.784000 1349 1956 1 chr3A.!!$F1 607
18 TraesCS5D01G549500 chr3A 148257607 148258191 584 False 592.000000 592 84.967000 1349 1956 1 chr3A.!!$F2 607


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
510 796 0.109342 CCTACTCATGGCATGGGTCC 59.891 60.0 34.75 0.0 40.83 4.46 F
1295 2357 0.033601 TTGAGCCCAACCAACTGTGT 60.034 50.0 0.00 0.0 0.00 3.72 F
1337 2399 0.034756 TGTATCAATCATCCCGCCGG 59.965 55.0 0.00 0.0 0.00 6.13 F
2833 4023 0.038618 GTTCATCCCACCCGCAAAAC 60.039 55.0 0.00 0.0 0.00 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1318 2380 0.034756 CCGGCGGGATGATTGATACA 59.965 55.0 20.56 0.0 34.06 2.29 R
2864 4054 0.038890 TGGTTTTGCCGATGGGATGA 59.961 50.0 0.00 0.0 41.21 2.92 R
2874 4064 0.251787 AGATGGGTCCTGGTTTTGCC 60.252 55.0 0.00 0.0 37.90 4.52 R
4467 5740 0.033642 GGCATAGAGTCGCCCCTTAC 59.966 60.0 0.00 0.0 42.82 2.34 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)



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AutoCloner maintained by Alex Coulton.