Multiple sequence alignment - TraesCS3A01G485800

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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 TraesCS3A01G485800 chr3A 100.000 2690 0 0 1 2690 714595097 714597786 0.000000e+00 4968.0
1 TraesCS3A01G485800 chr3A 72.468 1264 242 79 581 1800 702421607 702420406 2.600000e-80 309.0
2 TraesCS3A01G485800 chr3A 88.106 227 22 5 510 732 699533357 699533582 5.710000e-67 265.0
3 TraesCS3A01G485800 chr3A 90.625 64 6 0 726 789 700441703 700441640 4.770000e-13 86.1
4 TraesCS3A01G485800 chr3D 91.064 1354 90 4 466 1799 579582863 579581521 0.000000e+00 1801.0
5 TraesCS3A01G485800 chr3D 92.554 1249 76 3 565 1799 579398533 579399778 0.000000e+00 1775.0
6 TraesCS3A01G485800 chr3D 85.112 759 64 19 1935 2682 579581304 579580584 0.000000e+00 730.0
7 TraesCS3A01G485800 chr3D 87.645 518 43 12 1935 2447 579399996 579400497 1.390000e-162 582.0
8 TraesCS3A01G485800 chr3D 92.344 209 14 2 2475 2682 579400493 579400700 2.020000e-76 296.0
9 TraesCS3A01G485800 chr3D 81.299 385 46 16 525 886 565641909 565642290 3.390000e-74 289.0
10 TraesCS3A01G485800 chr3D 74.290 634 133 25 1088 1702 568235447 568236069 9.620000e-60 241.0
11 TraesCS3A01G485800 chr3D 82.593 270 47 0 525 794 565830738 565831007 3.460000e-59 239.0
12 TraesCS3A01G485800 chr3D 74.843 477 78 29 2222 2673 569396125 569395666 7.650000e-41 178.0
13 TraesCS3A01G485800 chr3D 92.857 98 6 1 1783 1880 579399808 579399904 1.000000e-29 141.0
14 TraesCS3A01G485800 chr3D 77.477 222 38 6 1073 1291 567687178 567686966 3.640000e-24 122.0
15 TraesCS3A01G485800 chr3D 85.567 97 14 0 693 789 568136871 568136967 4.740000e-18 102.0
16 TraesCS3A01G485800 chr3D 75.385 195 30 12 136 317 579583233 579583044 7.980000e-11 78.7
17 TraesCS3A01G485800 chr3B 89.978 1357 101 9 466 1799 773746986 773748330 0.000000e+00 1720.0
18 TraesCS3A01G485800 chr3B 86.082 582 49 11 507 1077 773882827 773882267 4.960000e-167 597.0
19 TraesCS3A01G485800 chr3B 91.826 367 29 1 1433 1799 773882268 773881903 6.640000e-141 510.0
20 TraesCS3A01G485800 chr3B 93.438 320 18 2 1933 2249 773881696 773881377 3.130000e-129 472.0
21 TraesCS3A01G485800 chr3B 86.293 321 24 9 2246 2561 773881056 773880751 5.550000e-87 331.0
22 TraesCS3A01G485800 chr3B 72.703 1110 225 57 586 1664 756440294 756439232 1.570000e-77 300.0
23 TraesCS3A01G485800 chr3B 88.584 219 25 0 526 744 752973257 752973039 1.590000e-67 267.0
24 TraesCS3A01G485800 chr3B 83.513 279 38 6 523 800 684514005 684513734 1.240000e-63 254.0
25 TraesCS3A01G485800 chr3B 87.831 189 7 9 139 311 773883146 773882958 9.760000e-50 207.0
26 TraesCS3A01G485800 chr3B 74.833 449 98 11 1224 1663 754331007 754331449 3.540000e-44 189.0
27 TraesCS3A01G485800 chr3B 87.857 140 6 4 66 200 37739787 37739920 1.290000e-33 154.0
28 TraesCS3A01G485800 chr3B 97.368 76 2 0 326 401 773746862 773746937 2.170000e-26 130.0
29 TraesCS3A01G485800 chr3B 97.674 43 0 1 419 460 773746923 773746965 3.710000e-09 73.1
30 TraesCS3A01G485800 chr7A 74.857 525 107 22 1190 1702 41048137 41047626 5.830000e-52 215.0
31 TraesCS3A01G485800 chr7D 74.181 519 107 22 1190 1694 41601215 41600710 9.830000e-45 191.0
32 TraesCS3A01G485800 chr1B 89.209 139 5 5 66 200 670761337 670761205 5.960000e-37 165.0
33 TraesCS3A01G485800 chr4A 72.901 524 116 23 1190 1701 648794677 648794168 9.970000e-35 158.0
34 TraesCS3A01G485800 chr4A 77.778 270 24 19 65 321 714667310 714667064 1.680000e-27 134.0
35 TraesCS3A01G485800 chr4B 87.143 140 7 4 66 200 622342377 622342510 6.000000e-32 148.0
36 TraesCS3A01G485800 chr4B 84.800 125 6 6 65 177 430672208 430672085 2.190000e-21 113.0
37 TraesCS3A01G485800 chr2B 80.583 206 26 7 2382 2585 68197378 68197571 2.160000e-31 147.0
38 TraesCS3A01G485800 chr2B 79.630 162 24 6 1535 1690 773351349 773351507 1.020000e-19 108.0
39 TraesCS3A01G485800 chrUn 77.778 270 24 19 65 321 230759870 230759624 1.680000e-27 134.0
40 TraesCS3A01G485800 chr2D 89.888 89 6 2 2499 2584 43291232 43291320 7.870000e-21 111.0
41 TraesCS3A01G485800 chr1D 88.372 86 9 1 2483 2567 38282296 38282211 4.740000e-18 102.0
42 TraesCS3A01G485800 chr7B 85.567 97 13 1 2468 2563 750344698 750344794 1.700000e-17 100.0


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 TraesCS3A01G485800 chr3A 714595097 714597786 2689 False 4968.000000 4968 100.000000 1 2690 1 chr3A.!!$F2 2689
1 TraesCS3A01G485800 chr3A 702420406 702421607 1201 True 309.000000 309 72.468000 581 1800 1 chr3A.!!$R2 1219
2 TraesCS3A01G485800 chr3D 579580584 579583233 2649 True 869.900000 1801 83.853667 136 2682 3 chr3D.!!$R3 2546
3 TraesCS3A01G485800 chr3D 579398533 579400700 2167 False 698.500000 1775 91.350000 565 2682 4 chr3D.!!$F5 2117
4 TraesCS3A01G485800 chr3D 568235447 568236069 622 False 241.000000 241 74.290000 1088 1702 1 chr3D.!!$F4 614
5 TraesCS3A01G485800 chr3B 773746862 773748330 1468 False 641.033333 1720 95.006667 326 1799 3 chr3B.!!$F3 1473
6 TraesCS3A01G485800 chr3B 773880751 773883146 2395 True 423.400000 597 89.094000 139 2561 5 chr3B.!!$R4 2422
7 TraesCS3A01G485800 chr3B 756439232 756440294 1062 True 300.000000 300 72.703000 586 1664 1 chr3B.!!$R3 1078
8 TraesCS3A01G485800 chr7A 41047626 41048137 511 True 215.000000 215 74.857000 1190 1702 1 chr7A.!!$R1 512


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
296 325 0.457851 CGGTAGGGTTCAGAGCTGAG 59.542 60.0 0.00 0.0 41.13 3.35 F
1053 1193 0.037697 TGTTGATGTTCCGGGACTCG 60.038 55.0 15.59 0.0 38.88 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1155 1295 1.078848 GAATGTCAGCACCTCCGCT 60.079 57.895 0.0 0.0 45.21 5.52 R
2378 3016 1.337703 TGCAACCATGAAACAGTCAGC 59.662 47.619 0.0 0.0 40.43 4.26 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.