Multiple sequence alignment - TraesCS7D01G180400

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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 TraesCS7D01G180400 chr7D 100.000 3237 0 0 1 3237 133613473 133610237 0.000000e+00 5978.0
1 TraesCS7D01G180400 chr7D 99.444 3239 16 2 1 3237 133491025 133494263 0.000000e+00 5880.0
2 TraesCS7D01G180400 chr7D 93.683 1314 69 10 965 2273 133827095 133828399 0.000000e+00 1954.0
3 TraesCS7D01G180400 chr7D 93.458 107 6 1 2283 2389 133828445 133828550 1.200000e-34 158.0
4 TraesCS7D01G180400 chr7A 92.448 2304 133 23 1 2281 132412760 132410475 0.000000e+00 3253.0
5 TraesCS7D01G180400 chr7A 93.468 1332 67 9 965 2277 132618875 132620205 0.000000e+00 1960.0
6 TraesCS7D01G180400 chr7A 93.458 107 6 1 2283 2389 132620245 132620350 1.200000e-34 158.0
7 TraesCS7D01G180400 chr7B 93.610 1565 69 11 638 2189 94811397 94809851 0.000000e+00 2307.0
8 TraesCS7D01G180400 chr7B 93.797 1322 68 8 974 2285 95046571 95045254 0.000000e+00 1975.0
9 TraesCS7D01G180400 chr7B 86.124 418 52 5 367 782 94932979 94932566 2.290000e-121 446.0
10 TraesCS7D01G180400 chr7B 92.245 245 18 1 1023 1267 94922136 94921893 2.390000e-91 346.0
11 TraesCS7D01G180400 chr7B 87.500 248 28 3 1 247 186813795 186814040 1.900000e-72 283.0
12 TraesCS7D01G180400 chr7B 94.643 112 5 1 2278 2389 94808828 94808718 4.290000e-39 172.0
13 TraesCS7D01G180400 chr7B 96.923 65 2 0 2189 2253 94809322 94809258 3.410000e-20 110.0
14 TraesCS7D01G180400 chr7B 92.727 55 4 0 2419 2473 470243624 470243570 2.680000e-11 80.5
15 TraesCS7D01G180400 chrUn 99.830 1174 2 0 1175 2348 429907488 429906315 0.000000e+00 2158.0
16 TraesCS7D01G180400 chr2D 96.429 812 25 4 2428 3237 599214427 599215236 0.000000e+00 1336.0
17 TraesCS7D01G180400 chr2A 93.094 695 35 10 2551 3237 105546179 105546868 0.000000e+00 1005.0
18 TraesCS7D01G180400 chr2A 89.876 563 42 12 2685 3237 49424218 49424775 0.000000e+00 710.0
19 TraesCS7D01G180400 chr2A 93.388 121 8 0 2430 2550 44088429 44088309 2.570000e-41 180.0
20 TraesCS7D01G180400 chr6D 92.041 691 51 3 2550 3237 12662044 12661355 0.000000e+00 968.0
21 TraesCS7D01G180400 chr3A 87.956 822 70 16 2428 3237 651595074 651594270 0.000000e+00 942.0
22 TraesCS7D01G180400 chr3A 91.803 122 10 0 2429 2550 555406353 555406232 1.540000e-38 171.0
23 TraesCS7D01G180400 chr3A 77.700 287 55 7 1 286 466039021 466039299 2.000000e-37 167.0
24 TraesCS7D01G180400 chr4A 90.698 559 42 10 2683 3237 538896146 538896698 0.000000e+00 736.0
25 TraesCS7D01G180400 chr5B 90.214 562 43 9 2685 3237 517547561 517548119 0.000000e+00 723.0
26 TraesCS7D01G180400 chr5B 91.935 124 10 0 2427 2550 459417371 459417494 1.190000e-39 174.0
27 TraesCS7D01G180400 chr5B 90.833 120 11 0 2428 2547 655020121 655020002 9.290000e-36 161.0
28 TraesCS7D01G180400 chr5B 76.207 290 62 3 1 289 513378698 513378415 2.600000e-31 147.0
29 TraesCS7D01G180400 chr3B 90.214 562 41 11 2683 3237 776951198 776950644 0.000000e+00 721.0
30 TraesCS7D01G180400 chr6B 80.592 845 137 11 1238 2079 611500191 611501011 7.620000e-176 627.0
31 TraesCS7D01G180400 chr6B 89.706 68 2 4 2408 2473 229143716 229143780 7.440000e-12 82.4
32 TraesCS7D01G180400 chr6A 80.660 848 131 16 1238 2079 553055019 553055839 7.620000e-176 627.0
33 TraesCS7D01G180400 chr6A 89.565 115 11 1 2428 2542 615443851 615443964 9.360000e-31 145.0
34 TraesCS7D01G180400 chr5A 93.388 121 8 0 2430 2550 34693940 34693820 2.570000e-41 180.0
35 TraesCS7D01G180400 chr5A 91.304 69 6 0 2551 2619 38034190 38034258 9.560000e-16 95.3
36 TraesCS7D01G180400 chr2B 90.400 125 10 2 2427 2550 752853850 752853727 2.580000e-36 163.0
37 TraesCS7D01G180400 chr4D 89.516 124 9 3 2427 2550 464234653 464234534 1.560000e-33 154.0
38 TraesCS7D01G180400 chr3D 100.000 39 0 0 2389 2427 466382165 466382127 4.480000e-09 73.1


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 TraesCS7D01G180400 chr7D 133610237 133613473 3236 True 5978 5978 100.000000 1 3237 1 chr7D.!!$R1 3236
1 TraesCS7D01G180400 chr7D 133491025 133494263 3238 False 5880 5880 99.444000 1 3237 1 chr7D.!!$F1 3236
2 TraesCS7D01G180400 chr7D 133827095 133828550 1455 False 1056 1954 93.570500 965 2389 2 chr7D.!!$F2 1424
3 TraesCS7D01G180400 chr7A 132410475 132412760 2285 True 3253 3253 92.448000 1 2281 1 chr7A.!!$R1 2280
4 TraesCS7D01G180400 chr7A 132618875 132620350 1475 False 1059 1960 93.463000 965 2389 2 chr7A.!!$F1 1424
5 TraesCS7D01G180400 chr7B 95045254 95046571 1317 True 1975 1975 93.797000 974 2285 1 chr7B.!!$R3 1311
6 TraesCS7D01G180400 chr7B 94808718 94811397 2679 True 863 2307 95.058667 638 2389 3 chr7B.!!$R5 1751
7 TraesCS7D01G180400 chrUn 429906315 429907488 1173 True 2158 2158 99.830000 1175 2348 1 chrUn.!!$R1 1173
8 TraesCS7D01G180400 chr2D 599214427 599215236 809 False 1336 1336 96.429000 2428 3237 1 chr2D.!!$F1 809
9 TraesCS7D01G180400 chr2A 105546179 105546868 689 False 1005 1005 93.094000 2551 3237 1 chr2A.!!$F2 686
10 TraesCS7D01G180400 chr2A 49424218 49424775 557 False 710 710 89.876000 2685 3237 1 chr2A.!!$F1 552
11 TraesCS7D01G180400 chr6D 12661355 12662044 689 True 968 968 92.041000 2550 3237 1 chr6D.!!$R1 687
12 TraesCS7D01G180400 chr3A 651594270 651595074 804 True 942 942 87.956000 2428 3237 1 chr3A.!!$R2 809
13 TraesCS7D01G180400 chr4A 538896146 538896698 552 False 736 736 90.698000 2683 3237 1 chr4A.!!$F1 554
14 TraesCS7D01G180400 chr5B 517547561 517548119 558 False 723 723 90.214000 2685 3237 1 chr5B.!!$F2 552
15 TraesCS7D01G180400 chr3B 776950644 776951198 554 True 721 721 90.214000 2683 3237 1 chr3B.!!$R1 554
16 TraesCS7D01G180400 chr6B 611500191 611501011 820 False 627 627 80.592000 1238 2079 1 chr6B.!!$F2 841
17 TraesCS7D01G180400 chr6A 553055019 553055839 820 False 627 627 80.660000 1238 2079 1 chr6A.!!$F1 841

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
1072 1100 1.154016 CCGTACGAGACACAGGCAG 60.154 63.158 18.76 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2474 3504 0.595588 ATCGCAAACAACGCCAATGA 59.404 45.0 0.0 0.0 0.0 2.57 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
1072 1100 1.154016 CCGTACGAGACACAGGCAG 60.154 63.158 18.76 0.0 0.0 4.85
1698 1742 4.692475 GCCTACGTGTTGGCCGGT 62.692 66.667 13.49 0.0 44.0 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1072 1100 1.538512 GGGAAGAAGGTTTTGCGTACC 59.461 52.381 0.00 0.0 35.85 3.34
1698 1742 4.728102 CACTGCGTCGCCGGGTTA 62.728 66.667 15.88 0.0 33.68 2.85
2474 3504 0.595588 ATCGCAAACAACGCCAATGA 59.404 45.000 0.00 0.0 0.00 2.57


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

AutoCloner maintained by Alex Coulton.