Multiple sequence alignment - TraesCS5A01G352400

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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 TraesCS5A01G352400 chr5A 100.000 2249 0 0 1 2249 554347236 554349484 0 4154
1 TraesCS5A01G352400 chr5A 96.750 1354 44 0 896 2249 560882915 560881562 0 2257
2 TraesCS5A01G352400 chr2A 96.209 1820 68 1 430 2249 94222242 94224060 0 2977
3 TraesCS5A01G352400 chr2A 96.493 1283 44 1 427 1709 65084948 65086229 0 2119
4 TraesCS5A01G352400 chr6A 95.996 1823 71 2 427 2249 508000995 508002815 0 2961
5 TraesCS5A01G352400 chr6A 95.573 655 26 2 427 1081 518952534 518953185 0 1046
6 TraesCS5A01G352400 chr3A 95.612 1823 70 5 427 2249 50435651 50437463 0 2915
7 TraesCS5A01G352400 chr1A 95.275 1820 71 5 430 2249 527083880 527082076 0 2870
8 TraesCS5A01G352400 chr7A 96.296 1539 55 2 430 1968 724636615 724638151 0 2525
9 TraesCS5A01G352400 chr6B 95.710 1352 54 3 901 2249 131761702 131760352 0 2172
10 TraesCS5A01G352400 chr6D 97.131 1220 30 2 427 1646 196358042 196359256 0 2054
11 TraesCS5A01G352400 chr1B 96.080 1046 39 2 1204 2249 552389898 552388855 0 1703
12 TraesCS5A01G352400 chr2D 97.191 890 25 0 1360 2249 464801694 464800805 0 1506
13 TraesCS5A01G352400 chr3B 97.000 800 23 1 1 799 61518335 61519134 0 1343


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 TraesCS5A01G352400 chr5A 554347236 554349484 2248 False 4154 4154 100.000 1 2249 1 chr5A.!!$F1 2248
1 TraesCS5A01G352400 chr5A 560881562 560882915 1353 True 2257 2257 96.750 896 2249 1 chr5A.!!$R1 1353
2 TraesCS5A01G352400 chr2A 94222242 94224060 1818 False 2977 2977 96.209 430 2249 1 chr2A.!!$F2 1819
3 TraesCS5A01G352400 chr2A 65084948 65086229 1281 False 2119 2119 96.493 427 1709 1 chr2A.!!$F1 1282
4 TraesCS5A01G352400 chr6A 508000995 508002815 1820 False 2961 2961 95.996 427 2249 1 chr6A.!!$F1 1822
5 TraesCS5A01G352400 chr6A 518952534 518953185 651 False 1046 1046 95.573 427 1081 1 chr6A.!!$F2 654
6 TraesCS5A01G352400 chr3A 50435651 50437463 1812 False 2915 2915 95.612 427 2249 1 chr3A.!!$F1 1822
7 TraesCS5A01G352400 chr1A 527082076 527083880 1804 True 2870 2870 95.275 430 2249 1 chr1A.!!$R1 1819
8 TraesCS5A01G352400 chr7A 724636615 724638151 1536 False 2525 2525 96.296 430 1968 1 chr7A.!!$F1 1538
9 TraesCS5A01G352400 chr6B 131760352 131761702 1350 True 2172 2172 95.710 901 2249 1 chr6B.!!$R1 1348
10 TraesCS5A01G352400 chr6D 196358042 196359256 1214 False 2054 2054 97.131 427 1646 1 chr6D.!!$F1 1219
11 TraesCS5A01G352400 chr1B 552388855 552389898 1043 True 1703 1703 96.080 1204 2249 1 chr1B.!!$R1 1045
12 TraesCS5A01G352400 chr2D 464800805 464801694 889 True 1506 1506 97.191 1360 2249 1 chr2D.!!$R1 889
13 TraesCS5A01G352400 chr3B 61518335 61519134 799 False 1343 1343 97.000 1 799 1 chr3B.!!$F1 798

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
591 592 0.527565 ACGTGCCATGGAAATTCTGC 59.472 50.0 18.4 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1394 1399 0.036732 AATGCAGGAACAGAAGGCGA 59.963 50.0 0.0 0.0 0.0 5.54 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
39 40 5.125578 GCTGGCTAGCTAACATTTTTAAGGT 59.874 40.000 15.78 0.0 46.57 3.50
67 68 3.249917 CACCGCAATAAATTGTTGGGTC 58.750 45.455 15.77 0.0 38.73 4.46
80 81 1.273327 GTTGGGTCAAATTCTGCCCTG 59.727 52.381 11.06 0.0 40.30 4.45
124 125 4.581309 ACTTCACTGATGATGAATGGGT 57.419 40.909 0.00 0.0 35.57 4.51
141 142 3.395639 TGGGTTGTAGATGTTGTCGTTC 58.604 45.455 0.00 0.0 0.00 3.95
197 198 7.377397 CGAGAATCATTTGAGTGCTACTAGTAC 59.623 40.741 0.00 0.0 33.17 2.73
198 199 7.197017 AGAATCATTTGAGTGCTACTAGTACG 58.803 38.462 0.00 0.0 35.89 3.67
238 239 1.204467 GCATTTTTGGATTCCTCGCCA 59.796 47.619 3.95 0.0 0.00 5.69
378 379 5.465935 TGTTTTCTTTTTGCTTCTGTTCGT 58.534 33.333 0.00 0.0 0.00 3.85
477 478 8.739039 CCAATTTGTGTATACCTTGATTCAGAA 58.261 33.333 0.00 0.0 0.00 3.02
591 592 0.527565 ACGTGCCATGGAAATTCTGC 59.472 50.000 18.40 0.0 0.00 4.26
914 916 7.561251 TGATCCCAGTTCTATTTCGTATTTGA 58.439 34.615 0.00 0.0 0.00 2.69
939 944 2.628178 CCGGTCTGATGGATTGCTACTA 59.372 50.000 0.00 0.0 0.00 1.82
955 960 3.429135 GCTACTACTGCTAGTTGGTGGTC 60.429 52.174 0.00 0.0 34.79 4.02
1122 1127 1.228367 ATGCATTGGGAGATCGGCC 60.228 57.895 0.00 0.0 0.00 6.13
1160 1165 2.889988 CATTGACGCCATCGCCGA 60.890 61.111 0.00 0.0 39.84 5.54
1179 1184 3.607370 GAACGGAGGTGGGTGCTCC 62.607 68.421 0.00 0.0 0.00 4.70
1394 1399 3.396685 AGCTTCCTCCTAGAGATGTGT 57.603 47.619 0.00 0.0 0.00 3.72
1416 1421 2.436417 GCCTTCTGTTCCTGCATTACA 58.564 47.619 0.00 0.0 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 3.005261 ACAATTTATTGCGGTGCACTGAA 59.995 39.130 29.83 17.44 41.38 3.02
67 68 4.774124 TCAGACTATCAGGGCAGAATTTG 58.226 43.478 0.00 0.00 0.00 2.32
80 81 7.727181 AGTAAATGGGTGTGTATCAGACTATC 58.273 38.462 0.00 0.00 0.00 2.08
141 142 1.087771 GCGAACCCTGGATAACACGG 61.088 60.000 0.00 0.00 0.00 4.94
197 198 2.097202 CACGAGCAAGAAAGAGACAACG 60.097 50.000 0.00 0.00 0.00 4.10
198 199 2.348966 GCACGAGCAAGAAAGAGACAAC 60.349 50.000 0.00 0.00 41.58 3.32
238 239 8.615878 TTTAGCACTTTACTAACACATGACAT 57.384 30.769 0.00 0.00 29.52 3.06
378 379 9.458374 GAAATTTTTCTACGGATGAGAAACAAA 57.542 29.630 0.00 0.00 41.46 2.83
667 668 9.847706 TTCAGAAGAATCGAATCTATATAGCAC 57.152 33.333 2.81 0.00 0.00 4.40
914 916 0.250038 CAATCCATCAGACCGGCGAT 60.250 55.000 9.30 0.00 0.00 4.58
939 944 1.003580 CCATGACCACCAACTAGCAGT 59.996 52.381 0.00 0.00 0.00 4.40
955 960 1.153489 CGTCTCTGTCCCTGCCATG 60.153 63.158 0.00 0.00 0.00 3.66
1160 1165 2.526873 AGCACCCACCTCCGTTCT 60.527 61.111 0.00 0.00 0.00 3.01
1179 1184 3.426426 CGGAACAGAGTAAGTCGAGAAGG 60.426 52.174 0.00 0.00 0.00 3.46
1394 1399 0.036732 AATGCAGGAACAGAAGGCGA 59.963 50.000 0.00 0.00 0.00 5.54
1416 1421 5.079643 ACTATTGCAGAAAGAATGGTGGTT 58.920 37.500 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.