Multiple sequence alignment - TraesCS5A01G343100

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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 TraesCS5A01G343100 chr5A 100.000 2426 0 0 1 2426 548227695 548225270 0.000000e+00 4481
1 TraesCS5A01G343100 chr5D 95.756 2427 77 10 1 2422 434330347 434332752 0.000000e+00 3888
2 TraesCS5A01G343100 chr5D 95.527 2057 54 9 1 2051 434383035 434381011 0.000000e+00 3254
3 TraesCS5A01G343100 chr5D 80.251 876 141 20 717 1573 435237356 435238218 4.400000e-177 630
4 TraesCS5A01G343100 chr5D 80.160 877 143 24 707 1573 434568967 434569822 5.690000e-176 627
5 TraesCS5A01G343100 chr5D 90.654 107 10 0 2316 2422 433992617 433992723 2.510000e-30 143
6 TraesCS5A01G343100 chr5D 88.393 112 8 2 1931 2042 433992508 433992614 1.960000e-26 130
7 TraesCS5A01G343100 chr5B 95.352 2431 68 9 1 2426 527041052 527038662 0.000000e+00 3821
8 TraesCS5A01G343100 chr5B 79.680 876 147 22 707 1573 527607516 527608369 9.600000e-169 603
9 TraesCS5A01G343100 chr5B 79.814 862 137 25 730 1573 527061063 527060221 5.780000e-166 593
10 TraesCS5A01G343100 chr5B 77.918 874 144 26 713 1573 527059201 527058364 1.300000e-137 499
11 TraesCS5A01G343100 chr5B 78.277 824 144 23 765 1569 528524503 528525310 4.660000e-137 497


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 TraesCS5A01G343100 chr5A 548225270 548227695 2425 True 4481 4481 100.000 1 2426 1 chr5A.!!$R1 2425
1 TraesCS5A01G343100 chr5D 434330347 434332752 2405 False 3888 3888 95.756 1 2422 1 chr5D.!!$F1 2421
2 TraesCS5A01G343100 chr5D 434381011 434383035 2024 True 3254 3254 95.527 1 2051 1 chr5D.!!$R1 2050
3 TraesCS5A01G343100 chr5D 435237356 435238218 862 False 630 630 80.251 717 1573 1 chr5D.!!$F3 856
4 TraesCS5A01G343100 chr5D 434568967 434569822 855 False 627 627 80.160 707 1573 1 chr5D.!!$F2 866
5 TraesCS5A01G343100 chr5B 527038662 527041052 2390 True 3821 3821 95.352 1 2426 1 chr5B.!!$R1 2425
6 TraesCS5A01G343100 chr5B 527607516 527608369 853 False 603 603 79.680 707 1573 1 chr5B.!!$F1 866
7 TraesCS5A01G343100 chr5B 527058364 527061063 2699 True 546 593 78.866 713 1573 2 chr5B.!!$R2 860
8 TraesCS5A01G343100 chr5B 528524503 528525310 807 False 497 497 78.277 765 1569 1 chr5B.!!$F2 804

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
409 416 2.125233 ACATGAGATGCTGGACTGGAT 58.875 47.619 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2067 2220 0.106708 TGCCTTCTCTGCACTTTCGT 59.893 50.0 0.0 0.0 32.85 3.85 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
146 149 2.224426 TGATGCACGGGAAACTAGTTGT 60.224 45.455 9.34 0.00 0.00 3.32
409 416 2.125233 ACATGAGATGCTGGACTGGAT 58.875 47.619 0.00 0.00 0.00 3.41
512 519 4.219725 TCCGACTGATCAACAACACATCTA 59.780 41.667 0.00 0.00 0.00 1.98
571 578 5.762179 ACAAGTTCCTGATCATTAGTCCA 57.238 39.130 0.00 0.00 0.00 4.02
581 588 6.207417 CCTGATCATTAGTCCAACACACTTTT 59.793 38.462 0.00 0.00 0.00 2.27
582 589 6.969366 TGATCATTAGTCCAACACACTTTTG 58.031 36.000 0.00 0.00 0.00 2.44
924 978 2.983229 ACCATCACTTCATCAGCTCAC 58.017 47.619 0.00 0.00 0.00 3.51
1010 1067 3.956199 CCAGAACCAACCATGATTAGCAT 59.044 43.478 0.00 0.00 37.85 3.79
1147 1205 2.006552 GCCACTGCATCATGTACACGA 61.007 52.381 0.00 0.00 37.47 4.35
1441 1499 3.822940 TCGTAACCCCTGAAAAACATGT 58.177 40.909 0.00 0.00 0.00 3.21
1481 1539 6.110033 TGTTGTCTTCTGCTTGTTGTAGTTA 58.890 36.000 0.00 0.00 0.00 2.24
1540 1598 7.011389 GGCAATAGGAAAAGGAAATTGTTATGC 59.989 37.037 0.00 0.00 31.65 3.14
1565 1623 3.994392 AGCTTTTTGATCATGCAAGCAAG 59.006 39.130 24.79 9.75 41.98 4.01
1752 1878 5.471116 GGCACAATCTATATGCAGTGATGAA 59.529 40.000 0.00 0.00 41.27 2.57
1977 2130 2.407090 TGCTCAATGAGAAGTGTGTCG 58.593 47.619 15.38 0.00 0.00 4.35
1988 2141 1.795768 AGTGTGTCGGTACTGCATTG 58.204 50.000 0.00 0.00 0.00 2.82
2042 2195 3.368843 GCAGCTAAATTCACAAACCATGC 59.631 43.478 0.00 0.00 0.00 4.06
2046 2199 6.867816 CAGCTAAATTCACAAACCATGCTTTA 59.132 34.615 0.00 0.00 0.00 1.85
2175 2332 4.275689 TGTGTTCCTTGCATCAACTAACTG 59.724 41.667 0.00 0.00 0.00 3.16
2181 2338 5.480422 TCCTTGCATCAACTAACTGAGTCTA 59.520 40.000 0.00 0.00 37.44 2.59
2183 2340 6.478344 CCTTGCATCAACTAACTGAGTCTATC 59.522 42.308 0.00 0.00 37.44 2.08
2286 2443 2.930826 AGACCATTGAACACCGAACT 57.069 45.000 0.00 0.00 0.00 3.01
2310 2467 3.760684 CTGAACCATTCTGGCTAGCTTTT 59.239 43.478 15.72 0.00 42.67 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
184 187 1.312815 GGCTGTTTCTGCTGAGTGTT 58.687 50.000 0.00 0.00 0.00 3.32
409 416 3.786656 GCTCCATGCATGTCTGGTA 57.213 52.632 24.58 2.94 42.31 3.25
571 578 4.929211 GCTGAAAGGAAACAAAAGTGTGTT 59.071 37.500 0.00 0.00 43.58 3.32
581 588 2.727123 TGACCAGCTGAAAGGAAACA 57.273 45.000 17.39 0.47 0.00 2.83
582 589 2.952310 ACTTGACCAGCTGAAAGGAAAC 59.048 45.455 17.39 0.00 0.00 2.78
924 978 1.898574 GTGCTCAGTTGGTGGTGGG 60.899 63.158 0.00 0.00 0.00 4.61
982 1039 2.983192 TCATGGTTGGTTCTGGGTCTTA 59.017 45.455 0.00 0.00 0.00 2.10
1010 1067 2.808202 GCCAGTTGAGCAAGTCTCTTCA 60.808 50.000 0.00 0.00 42.38 3.02
1329 1387 2.039480 AGAACTCAGCAATGCCTTCTCA 59.961 45.455 0.00 0.00 0.00 3.27
1441 1499 2.371841 ACAACATTAGGGTCTCTGCACA 59.628 45.455 0.00 0.00 0.00 4.57
1481 1539 9.357161 CTAACTCTCTTACACTATCCAGGTATT 57.643 37.037 0.00 0.00 0.00 1.89
1540 1598 4.212425 TGCTTGCATGATCAAAAAGCTTTG 59.788 37.500 27.02 1.54 42.87 2.77
1565 1623 3.455469 GCCCATGTCCCTGCTTGC 61.455 66.667 0.00 0.00 0.00 4.01
1653 1711 3.810310 AGTGCTAGATTGTACAGAGGC 57.190 47.619 0.00 0.00 0.00 4.70
1752 1878 5.604650 CCTTCTCAAGTTATATCCTGAGGGT 59.395 44.000 0.00 0.00 0.00 4.34
1892 2044 6.393990 TGCGCATTCAAATTTTAGGTAACAT 58.606 32.000 5.66 0.00 41.41 2.71
1977 2130 4.759782 AGACATGTACTCAATGCAGTACC 58.240 43.478 0.00 5.43 45.73 3.34
2067 2220 0.106708 TGCCTTCTCTGCACTTTCGT 59.893 50.000 0.00 0.00 32.85 3.85
2068 2221 2.918571 TGCCTTCTCTGCACTTTCG 58.081 52.632 0.00 0.00 32.85 3.46
2310 2467 1.407299 CGTCTTCTGATTGCCATGGGA 60.407 52.381 15.13 8.24 0.00 4.37


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

AutoCloner maintained by Alex Coulton.