Multiple sequence alignment - TraesCS3B01G512700

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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 TraesCS3B01G512700 chr3B 100.000 2606 0 0 1 2606 756180395 756183000 0.000000e+00 4813.0
1 TraesCS3B01G512700 chr3B 87.437 995 71 16 665 1611 755043752 755042764 0.000000e+00 1096.0
2 TraesCS3B01G512700 chr3B 86.659 817 74 18 1599 2398 755042746 755041948 0.000000e+00 872.0
3 TraesCS3B01G512700 chr3B 84.412 417 28 12 734 1113 756135564 756135980 2.450000e-100 375.0
4 TraesCS3B01G512700 chr3B 84.286 350 36 11 130 478 755049730 755049399 9.000000e-85 324.0
5 TraesCS3B01G512700 chr3B 85.027 187 27 1 2410 2595 754983634 754983448 3.420000e-44 189.0
6 TraesCS3B01G512700 chr3B 88.235 68 8 0 2264 2331 756182593 756182660 5.980000e-12 82.4
7 TraesCS3B01G512700 chrUn 96.236 1966 63 5 651 2606 41100133 41102097 0.000000e+00 3210.0
8 TraesCS3B01G512700 chrUn 99.452 1277 3 4 1 1275 389811756 389810482 0.000000e+00 2316.0
9 TraesCS3B01G512700 chrUn 99.614 518 1 1 1 518 289010631 289010115 0.000000e+00 944.0
10 TraesCS3B01G512700 chrUn 83.607 427 34 19 723 1113 324345885 324346311 4.100000e-98 368.0
11 TraesCS3B01G512700 chr3D 88.474 1605 124 32 805 2364 567215467 567217055 0.000000e+00 1882.0
12 TraesCS3B01G512700 chr3D 88.095 1134 99 20 1278 2386 569547394 569546272 0.000000e+00 1314.0
13 TraesCS3B01G512700 chr3D 91.159 328 12 7 945 1263 569549301 569548982 1.850000e-116 429.0
14 TraesCS3B01G512700 chr3D 78.006 632 103 24 130 746 567214844 567215454 5.300000e-97 364.0
15 TraesCS3B01G512700 chr3D 88.106 227 19 6 2385 2606 569546208 569545985 1.990000e-66 263.0
16 TraesCS3B01G512700 chr3D 86.631 187 24 1 2410 2595 567222148 567222334 3.400000e-49 206.0
17 TraesCS3B01G512700 chr3D 81.673 251 38 7 123 369 526190024 526189778 4.400000e-48 202.0
18 TraesCS3B01G512700 chr3D 76.808 401 60 24 123 514 481519882 481519506 7.360000e-46 195.0
19 TraesCS3B01G512700 chr3D 84.444 90 8 3 443 530 463675096 463675011 1.660000e-12 84.2
20 TraesCS3B01G512700 chr3D 95.455 44 2 0 487 530 8725371 8725414 1.290000e-08 71.3
21 TraesCS3B01G512700 chr3A 93.492 630 26 3 994 1611 700576601 700575975 0.000000e+00 922.0
22 TraesCS3B01G512700 chr3A 90.547 677 51 6 945 1611 701863970 701863297 0.000000e+00 883.0
23 TraesCS3B01G512700 chr3A 91.413 559 37 9 1837 2386 700575772 700575216 0.000000e+00 756.0
24 TraesCS3B01G512700 chr3A 91.473 387 26 5 1845 2230 701863004 701862624 2.300000e-145 525.0
25 TraesCS3B01G512700 chr3A 87.023 262 18 9 1596 1851 701863283 701863032 5.490000e-72 281.0
26 TraesCS3B01G512700 chr3A 88.987 227 20 3 2385 2606 701862225 701861999 2.550000e-70 276.0
27 TraesCS3B01G512700 chr3A 93.023 172 5 5 2222 2386 701862442 701862271 7.200000e-61 244.0
28 TraesCS3B01G512700 chr3A 90.066 151 7 5 1596 1738 700575961 700575811 3.420000e-44 189.0
29 TraesCS3B01G512700 chr3A 87.975 158 19 0 738 895 701864638 701864481 1.230000e-43 187.0
30 TraesCS3B01G512700 chr3A 82.990 194 29 2 723 912 700577032 700576839 3.450000e-39 172.0
31 TraesCS3B01G512700 chr3A 88.235 68 8 0 2264 2331 700575410 700575343 5.980000e-12 82.4
32 TraesCS3B01G512700 chr2B 85.219 778 58 32 1614 2372 726561928 726562667 0.000000e+00 747.0
33 TraesCS3B01G512700 chr2B 76.879 173 28 10 20 189 747314989 747315152 1.280000e-13 87.9
34 TraesCS3B01G512700 chr7B 84.923 776 59 30 1617 2372 611463201 611462464 0.000000e+00 732.0
35 TraesCS3B01G512700 chr7B 79.126 206 31 10 2 202 59082268 59082070 5.850000e-27 132.0
36 TraesCS3B01G512700 chr7B 78.571 154 25 7 52 202 585879396 585879248 7.680000e-16 95.3
37 TraesCS3B01G512700 chr5B 84.923 776 59 31 1617 2372 619015323 619014586 0.000000e+00 732.0
38 TraesCS3B01G512700 chr5B 75.132 189 37 10 19 202 525435840 525436023 2.150000e-11 80.5
39 TraesCS3B01G512700 chr4D 79.114 316 47 15 128 439 386496760 386496460 1.580000e-47 200.0
40 TraesCS3B01G512700 chr6B 77.143 315 54 15 130 439 719989838 719989537 1.600000e-37 167.0
41 TraesCS3B01G512700 chr6B 92.683 41 2 1 475 515 720045539 720045578 1.010000e-04 58.4
42 TraesCS3B01G512700 chr5A 76.161 323 64 11 123 440 678295668 678295982 9.650000e-35 158.0
43 TraesCS3B01G512700 chr2A 80.500 200 27 8 2 200 768053786 768053598 2.700000e-30 143.0
44 TraesCS3B01G512700 chr1D 78.977 176 30 6 16 187 399327402 399327574 2.120000e-21 113.0
45 TraesCS3B01G512700 chr5D 83.529 85 12 2 822 906 399841558 399841476 7.730000e-11 78.7
46 TraesCS3B01G512700 chr5D 100.000 29 0 0 487 515 520656266 520656238 1.000000e-03 54.7
47 TraesCS3B01G512700 chr7D 78.070 114 21 4 40 151 630683521 630683632 4.650000e-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 TraesCS3B01G512700 chr3B 756180395 756183000 2605 False 2447.700000 4813 94.1175 1 2606 2 chr3B.!!$F2 2605
1 TraesCS3B01G512700 chr3B 755041948 755043752 1804 True 984.000000 1096 87.0480 665 2398 2 chr3B.!!$R3 1733
2 TraesCS3B01G512700 chrUn 41100133 41102097 1964 False 3210.000000 3210 96.2360 651 2606 1 chrUn.!!$F1 1955
3 TraesCS3B01G512700 chrUn 389810482 389811756 1274 True 2316.000000 2316 99.4520 1 1275 1 chrUn.!!$R2 1274
4 TraesCS3B01G512700 chrUn 289010115 289010631 516 True 944.000000 944 99.6140 1 518 1 chrUn.!!$R1 517
5 TraesCS3B01G512700 chr3D 567214844 567217055 2211 False 1123.000000 1882 83.2400 130 2364 2 chr3D.!!$F3 2234
6 TraesCS3B01G512700 chr3D 569545985 569549301 3316 True 668.666667 1314 89.1200 945 2606 3 chr3D.!!$R4 1661
7 TraesCS3B01G512700 chr3A 700575216 700577032 1816 True 424.280000 922 89.2392 723 2386 5 chr3A.!!$R1 1663
8 TraesCS3B01G512700 chr3A 701861999 701864638 2639 True 399.333333 883 89.8380 738 2606 6 chr3A.!!$R2 1868
9 TraesCS3B01G512700 chr2B 726561928 726562667 739 False 747.000000 747 85.2190 1614 2372 1 chr2B.!!$F1 758
10 TraesCS3B01G512700 chr7B 611462464 611463201 737 True 732.000000 732 84.9230 1617 2372 1 chr7B.!!$R3 755
11 TraesCS3B01G512700 chr5B 619014586 619015323 737 True 732.000000 732 84.9230 1617 2372 1 chr5B.!!$R1 755

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
602 620 5.989477 TCAAGAAGACTGACTCAAAAAGGA 58.011 37.5 0.0 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2444 5052 1.657751 GAATGCCGAGACAAAGCCCC 61.658 60.0 0.0 0.0 0.0 5.8 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
281 282 9.458727 AGAATAAGCATATCATAGTGGGATTTG 57.541 33.333 0.00 0.00 0.00 2.32
602 620 5.989477 TCAAGAAGACTGACTCAAAAAGGA 58.011 37.500 0.00 0.00 0.00 3.36
1429 3687 2.701780 CCTCAGCTGTACGGCGACT 61.702 63.158 20.70 0.61 37.29 4.18
1503 3761 1.592400 CGGTCACTGTTCTCGGCCTA 61.592 60.000 0.00 0.00 0.00 3.93
1745 4041 9.981114 TCTGCGATAATAGAAATTTGTCATCTA 57.019 29.630 0.00 0.00 0.00 1.98
1878 4217 1.673920 GTTCCAAGTTCCAACTCGCAA 59.326 47.619 0.00 0.00 38.57 4.85
1883 4222 3.314080 CCAAGTTCCAACTCGCAAGTTTA 59.686 43.478 0.00 0.00 43.28 2.01
1910 4249 3.254166 ACACCTAAAGCATGAGCAACAAG 59.746 43.478 0.00 0.00 45.49 3.16
1922 4261 7.015877 GCATGAGCAACAAGTAACTAAAGTAC 58.984 38.462 0.00 0.00 41.58 2.73
1923 4262 7.307751 GCATGAGCAACAAGTAACTAAAGTACA 60.308 37.037 0.00 0.00 41.58 2.90
1924 4263 8.721478 CATGAGCAACAAGTAACTAAAGTACAT 58.279 33.333 0.00 0.00 0.00 2.29
1925 4264 9.938280 ATGAGCAACAAGTAACTAAAGTACATA 57.062 29.630 0.00 0.00 0.00 2.29
1931 4274 9.748708 AACAAGTAACTAAAGTACATACGAACA 57.251 29.630 0.00 0.00 0.00 3.18
1939 4282 5.401531 AAGTACATACGAACAGGTCACAT 57.598 39.130 0.00 0.00 0.00 3.21
1990 4334 8.839310 ACATGAGGTTGTAGATATTAATCTGC 57.161 34.615 0.00 0.00 42.60 4.26
2171 4516 5.123979 CCAACTAAAAGGTTGCTAGGTGATC 59.876 44.000 0.00 0.00 43.48 2.92
2212 4557 4.009675 TGAGACTATTTTGGTGATGTGCC 58.990 43.478 0.00 0.00 0.00 5.01
2272 4807 0.515564 CACCGGTTAGTTTTGGCGAG 59.484 55.000 2.97 0.00 0.00 5.03
2372 4914 5.900865 TCAGAAACATGCAGCAATATCAA 57.099 34.783 0.00 0.00 0.00 2.57
2427 5034 2.399448 GGTTAACAAACAATGTGGGCG 58.601 47.619 8.10 0.00 42.99 6.13
2444 5052 2.159517 GGGCGACTGAAGTTATTTGCAG 60.160 50.000 0.00 0.00 34.65 4.41
2540 5151 5.323371 TGCCAAAACCTAAGATATTGTGC 57.677 39.130 0.00 0.00 0.00 4.57
2570 5181 6.445357 TGCACTGTCGAGTAGATATTAACA 57.555 37.500 3.79 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1491 3749 2.579878 CCTGAGTAGGCCGAGAACA 58.420 57.895 0.00 0.0 37.25 3.18
1764 4060 6.154192 TGTTCAGAGAGAGATAGCACTCAAAT 59.846 38.462 8.15 0.0 39.14 2.32
1878 4217 7.575720 GCTCATGCTTTAGGTGTTCATTAAACT 60.576 37.037 0.00 0.0 36.12 2.66
1883 4222 4.081406 TGCTCATGCTTTAGGTGTTCATT 58.919 39.130 0.00 0.0 40.48 2.57
1910 4249 8.023128 TGACCTGTTCGTATGTACTTTAGTTAC 58.977 37.037 0.00 0.0 0.00 2.50
1922 4261 6.754675 TGTACATTATGTGACCTGTTCGTATG 59.245 38.462 8.26 0.0 0.00 2.39
1923 4262 6.869695 TGTACATTATGTGACCTGTTCGTAT 58.130 36.000 8.26 0.0 0.00 3.06
1924 4263 6.270156 TGTACATTATGTGACCTGTTCGTA 57.730 37.500 8.26 0.0 0.00 3.43
1925 4264 5.142061 TGTACATTATGTGACCTGTTCGT 57.858 39.130 8.26 0.0 0.00 3.85
1931 4274 7.093333 TGACTCTTCATGTACATTATGTGACCT 60.093 37.037 5.37 0.0 0.00 3.85
1939 4282 7.836842 TGCTAACTGACTCTTCATGTACATTA 58.163 34.615 5.37 0.0 0.00 1.90
1990 4334 7.389803 TTGTTTGGTCACAAGATACATATGG 57.610 36.000 7.80 0.0 37.97 2.74
2061 4405 2.022129 CGCAGTCGAAGGTCACACC 61.022 63.158 0.00 0.0 36.74 4.16
2171 4516 4.698780 TCTCATTTTGCTTCCTCATCTGTG 59.301 41.667 0.00 0.0 0.00 3.66
2212 4557 4.105486 TCTACATTTTCATCTGCGACTCG 58.895 43.478 0.00 0.0 0.00 4.18
2272 4807 3.988379 TTTCATCTGCAACTCAACACC 57.012 42.857 0.00 0.0 0.00 4.16
2372 4914 2.936202 ACTTGTGATTCACTGCAGGTT 58.064 42.857 19.93 0.0 35.11 3.50
2427 5034 2.164422 GCCCCTGCAAATAACTTCAGTC 59.836 50.000 0.00 0.0 37.47 3.51
2444 5052 1.657751 GAATGCCGAGACAAAGCCCC 61.658 60.000 0.00 0.0 0.00 5.80
2517 5128 5.421693 TGCACAATATCTTAGGTTTTGGCAT 59.578 36.000 7.36 0.0 0.00 4.40
2540 5151 4.237724 TCTACTCGACAGTGCAAAGATTG 58.762 43.478 0.00 0.0 33.62 2.67
2570 5181 7.600752 GCTTCACTGAATTTAGTAGAAGTCACT 59.399 37.037 25.40 0.0 37.70 3.41


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

AutoCloner maintained by Alex Coulton.