Multiple sequence alignment - TraesCS7A01G103600

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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 TraesCS7A01G103600 chr7A 100.000 3346 0 0 1 3346 63385411 63382066 0.000000e+00 6180.0
1 TraesCS7A01G103600 chr7A 91.966 585 47 0 1414 1998 63378416 63379000 0.000000e+00 821.0
2 TraesCS7A01G103600 chr7A 89.590 586 58 1 1415 1997 31592096 31592681 0.000000e+00 741.0
3 TraesCS7A01G103600 chr7A 85.642 397 40 11 1012 1393 63377965 63378359 5.200000e-108 401.0
4 TraesCS7A01G103600 chr7A 100.000 30 0 0 3239 3268 430757427 430757398 4.660000e-04 56.5
5 TraesCS7A01G103600 chr7D 92.965 1322 56 14 864 2160 58843443 58842134 0.000000e+00 1892.0
6 TraesCS7A01G103600 chr7D 92.637 584 43 0 1414 1997 58829830 58830413 0.000000e+00 841.0
7 TraesCS7A01G103600 chr7D 87.563 595 62 3 1415 1997 31119637 31120231 0.000000e+00 678.0
8 TraesCS7A01G103600 chr7D 86.395 588 48 14 2 581 58846171 58845608 6.140000e-172 614.0
9 TraesCS7A01G103600 chr7D 93.069 303 13 6 559 860 58843790 58843495 1.430000e-118 436.0
10 TraesCS7A01G103600 chr7D 85.219 433 31 13 2400 2805 58834627 58834201 6.680000e-112 414.0
11 TraesCS7A01G103600 chr7D 80.916 524 57 24 2730 3228 58832679 58832174 1.130000e-99 374.0
12 TraesCS7A01G103600 chr7D 84.615 364 28 16 1022 1360 58829385 58829745 1.490000e-88 337.0
13 TraesCS7A01G103600 chr7D 89.370 254 12 3 2146 2384 58842116 58841863 4.190000e-79 305.0
14 TraesCS7A01G103600 chr7D 85.345 116 16 1 2271 2385 58833551 58833436 5.860000e-23 119.0
15 TraesCS7A01G103600 chr7D 96.970 33 1 0 798 830 58829011 58829043 4.660000e-04 56.5
16 TraesCS7A01G103600 chr4A 90.470 808 44 14 1413 2199 675955098 675954303 0.000000e+00 1035.0
17 TraesCS7A01G103600 chr4A 93.857 586 36 0 1413 1998 675932608 675933193 0.000000e+00 883.0
18 TraesCS7A01G103600 chr4A 84.161 846 74 28 2540 3345 675951468 675950643 0.000000e+00 765.0
19 TraesCS7A01G103600 chr4A 89.273 550 36 9 873 1401 675955694 675955147 0.000000e+00 667.0
20 TraesCS7A01G103600 chr4A 83.184 446 53 14 2791 3228 675960241 675959810 4.050000e-104 388.0
21 TraesCS7A01G103600 chr4A 80.906 508 76 14 16 516 675957460 675956967 6.770000e-102 381.0
22 TraesCS7A01G103600 chr4A 85.759 323 19 18 534 852 675956065 675955766 1.940000e-82 316.0
23 TraesCS7A01G103600 chr4A 89.712 243 19 2 1124 1360 675932278 675932520 4.190000e-79 305.0
24 TraesCS7A01G103600 chr4A 88.793 116 9 4 2271 2385 675962239 675962127 4.500000e-29 139.0
25 TraesCS7A01G103600 chr4A 84.211 114 17 1 2271 2383 675961229 675961116 3.530000e-20 110.0
26 TraesCS7A01G103600 chr5B 87.100 876 93 13 1140 1997 27813040 27813913 0.000000e+00 974.0
27 TraesCS7A01G103600 chr5B 95.122 41 1 1 3241 3280 34747227 34747267 2.790000e-06 63.9
28 TraesCS7A01G103600 chr5D 86.740 905 80 20 1140 2010 37201806 37202704 0.000000e+00 970.0
29 TraesCS7A01G103600 chr5D 78.673 211 29 9 3 207 539864803 539864603 3.500000e-25 126.0
30 TraesCS7A01G103600 chr2D 88.608 158 16 2 55 211 391105433 391105277 1.230000e-44 191.0
31 TraesCS7A01G103600 chr2D 81.340 209 27 10 4 204 59656562 59656358 3.460000e-35 159.0
32 TraesCS7A01G103600 chr6D 81.019 216 24 12 2 207 81104660 81104452 4.470000e-34 156.0
33 TraesCS7A01G103600 chr6D 90.000 50 5 0 3222 3271 89164064 89164015 7.750000e-07 65.8
34 TraesCS7A01G103600 chr2A 81.714 175 22 9 16 182 535338690 535338862 1.620000e-28 137.0
35 TraesCS7A01G103600 chr1A 80.000 205 23 15 2 196 553948674 553948478 5.820000e-28 135.0
36 TraesCS7A01G103600 chr3A 78.818 203 36 5 17 212 745890286 745890084 2.710000e-26 130.0
37 TraesCS7A01G103600 chr4B 82.400 125 17 4 2594 2714 38366513 38366390 1.640000e-18 104.0
38 TraesCS7A01G103600 chr6B 90.000 50 5 0 3218 3267 661073187 661073236 7.750000e-07 65.8


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 TraesCS7A01G103600 chr7A 63382066 63385411 3345 True 6180.000000 6180 100.000000 1 3346 1 chr7A.!!$R1 3345
1 TraesCS7A01G103600 chr7A 31592096 31592681 585 False 741.000000 741 89.590000 1415 1997 1 chr7A.!!$F1 582
2 TraesCS7A01G103600 chr7A 63377965 63379000 1035 False 611.000000 821 88.804000 1012 1998 2 chr7A.!!$F2 986
3 TraesCS7A01G103600 chr7D 58841863 58846171 4308 True 811.750000 1892 90.449750 2 2384 4 chr7D.!!$R2 2382
4 TraesCS7A01G103600 chr7D 31119637 31120231 594 False 678.000000 678 87.563000 1415 1997 1 chr7D.!!$F1 582
5 TraesCS7A01G103600 chr7D 58829011 58830413 1402 False 411.500000 841 91.407333 798 1997 3 chr7D.!!$F2 1199
6 TraesCS7A01G103600 chr7D 58832174 58834627 2453 True 302.333333 414 83.826667 2271 3228 3 chr7D.!!$R1 957
7 TraesCS7A01G103600 chr4A 675932278 675933193 915 False 594.000000 883 91.784500 1124 1998 2 chr4A.!!$F1 874
8 TraesCS7A01G103600 chr4A 675950643 675962239 11596 True 475.125000 1035 85.844625 16 3345 8 chr4A.!!$R1 3329
9 TraesCS7A01G103600 chr5B 27813040 27813913 873 False 974.000000 974 87.100000 1140 1997 1 chr5B.!!$F1 857
10 TraesCS7A01G103600 chr5D 37201806 37202704 898 False 970.000000 970 86.740000 1140 2010 1 chr5D.!!$F1 870


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
233 5006 0.091678 GCAATGACAATTTGCACGCG 59.908 50.000 3.53 3.53 46.78 6.01 F
234 5007 0.091678 CAATGACAATTTGCACGCGC 59.908 50.000 5.73 0.00 39.24 6.86 F
256 5029 0.387622 GCGCACACAGACAAATGCAT 60.388 50.000 0.30 0.00 37.97 3.96 F
2045 9849 1.002576 TGCGTGCTCATTGTTGTTCTG 60.003 47.619 0.00 0.00 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1272 8991 0.324460 ACTGGCCGTAGAGGTAGCTT 60.324 55.000 0.0 0.0 43.70 3.74 R
2158 10004 1.053424 TTTGTACCTGGCCGAGACTT 58.947 50.000 0.0 0.0 0.00 3.01 R
2196 10042 1.998315 CAAGAGTCAATCGACAGCCAG 59.002 52.381 0.0 0.0 45.23 4.85 R
3198 14954 2.249309 CACGTCGGCACAAGCAAG 59.751 61.111 0.0 0.0 44.61 4.01 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.