Multiple sequence alignment - TraesCS5D01G341200

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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 TraesCS5D01G341200 chr5D 100.000 6981 0 0 1 6981 429360152 429353172 0.000000e+00 12892.0
1 TraesCS5D01G341200 chr5A 94.884 5141 189 43 729 5823 545217941 545212829 0.000000e+00 7969.0
2 TraesCS5D01G341200 chr5A 95.126 636 25 5 5802 6437 545212820 545212191 0.000000e+00 998.0
3 TraesCS5D01G341200 chr5A 89.441 483 25 14 281 739 545218635 545218155 2.810000e-163 586.0
4 TraesCS5D01G341200 chr5A 89.665 358 27 8 6626 6981 545212194 545211845 1.380000e-121 448.0
5 TraesCS5D01G341200 chr5A 89.524 210 16 5 6431 6638 397506073 397505868 1.930000e-65 261.0
6 TraesCS5D01G341200 chr5A 96.721 61 1 1 2608 2668 705520669 705520610 4.460000e-17 100.0
7 TraesCS5D01G341200 chr5B 95.052 3840 172 12 994 4824 518684863 518681033 0.000000e+00 6023.0
8 TraesCS5D01G341200 chr5B 93.988 998 33 14 4833 5829 518680962 518679991 0.000000e+00 1485.0
9 TraesCS5D01G341200 chr5B 88.126 1019 64 25 1 995 518685877 518684892 0.000000e+00 1158.0
10 TraesCS5D01G341200 chr5B 96.494 542 17 1 5814 6355 518679976 518679437 0.000000e+00 894.0
11 TraesCS5D01G341200 chr5B 88.154 363 29 5 6624 6981 518679390 518679037 3.010000e-113 420.0
12 TraesCS5D01G341200 chr5B 96.610 59 2 0 6374 6432 518679446 518679388 1.600000e-16 99.0
13 TraesCS5D01G341200 chr7D 93.548 186 8 4 6430 6614 44802275 44802093 2.480000e-69 274.0
14 TraesCS5D01G341200 chr4A 91.500 200 13 4 6431 6628 594365107 594364910 8.920000e-69 272.0
15 TraesCS5D01G341200 chr2D 93.048 187 11 2 6435 6621 101884248 101884064 8.920000e-69 272.0
16 TraesCS5D01G341200 chr2D 89.372 207 19 3 6420 6624 540163571 540163776 2.500000e-64 257.0
17 TraesCS5D01G341200 chr3A 91.795 195 15 1 6434 6628 78529649 78529456 3.210000e-68 270.0
18 TraesCS5D01G341200 chr3A 96.721 61 1 1 2608 2668 300788090 300788031 4.460000e-17 100.0
19 TraesCS5D01G341200 chr6A 90.955 199 15 3 6429 6625 494463089 494463286 1.490000e-66 265.0
20 TraesCS5D01G341200 chr3D 91.710 193 13 3 6436 6626 25294121 25293930 1.490000e-66 265.0
21 TraesCS5D01G341200 chr3D 96.721 61 1 1 2608 2668 168503528 168503587 4.460000e-17 100.0
22 TraesCS5D01G341200 chr1A 90.500 200 15 4 6435 6631 557897512 557897710 1.930000e-65 261.0
23 TraesCS5D01G341200 chr3B 84.264 197 19 11 2282 2468 28336118 28336312 1.550000e-41 182.0
24 TraesCS5D01G341200 chr2A 89.109 101 2 5 3768 3859 615291579 615291479 4.420000e-22 117.0
25 TraesCS5D01G341200 chr7B 96.721 61 1 1 2608 2668 215236735 215236794 4.460000e-17 100.0
26 TraesCS5D01G341200 chr7B 91.803 61 4 1 2608 2668 636396204 636396263 4.490000e-12 84.2
27 TraesCS5D01G341200 chr1D 96.721 61 1 1 2608 2668 46104206 46104147 4.460000e-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 TraesCS5D01G341200 chr5D 429353172 429360152 6980 True 12892.000000 12892 100.000000 1 6981 1 chr5D.!!$R1 6980
1 TraesCS5D01G341200 chr5A 545211845 545218635 6790 True 2500.250000 7969 92.279000 281 6981 4 chr5A.!!$R3 6700
2 TraesCS5D01G341200 chr5B 518679037 518685877 6840 True 1679.833333 6023 93.070667 1 6981 6 chr5B.!!$R1 6980


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
96 97 0.307760 GCTGAGACCAACCAAACACG 59.692 55.000 0.00 0.0 0.00 4.49 F
170 171 0.454196 TCGCATCGACCGAGAATTGA 59.546 50.000 5.97 0.0 0.00 2.57 F
321 332 0.456221 AATCCGTCTCACTGCGTAGG 59.544 55.000 5.26 0.0 0.00 3.18 F
2249 2557 0.030638 ACATTCAAAGGTGTGTGCGC 59.969 50.000 0.00 0.0 0.00 6.09 F
3345 3662 0.681733 AGCGTCTTGAGAAGGAAGCA 59.318 50.000 0.00 0.0 38.89 3.91 F
4598 4915 0.620556 CCAAGCATGTCCCTACCACT 59.379 55.000 0.00 0.0 0.00 4.00 F
5088 5468 3.119352 CCAACTTAGCTCATGAAAAGGCC 60.119 47.826 13.66 0.0 0.00 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2090 2389 0.385223 GAGCTGACAAAGTTGCTGCG 60.385 55.000 0.00 0.00 35.76 5.18 R
2216 2522 6.368516 ACCTTTGAATGTTGTTCTTTTGTGTG 59.631 34.615 0.00 0.00 0.00 3.82 R
2298 2606 4.584327 GCTTCAAAGCCTTAAGGTTCAA 57.416 40.909 22.55 9.65 46.20 2.69 R
3458 3775 0.035630 AGTGCCTGGATCAACAGAGC 60.036 55.000 0.00 0.93 40.97 4.09 R
4821 5139 0.105555 TTGGGAATGGGGATGCATCC 60.106 55.000 33.90 33.90 46.41 3.51 R
5842 6256 1.001633 TCTGGAGGTAAACACCGCTTC 59.998 52.381 0.00 0.00 34.28 3.86 R
6765 7218 1.203287 GCTCTGGTTTCATGCTTTCCC 59.797 52.381 0.00 0.00 0.00 3.97 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.