Multiple sequence alignment - TraesCS5D01G105300

Loading Multiple Alignment...

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 TraesCS5D01G105300 chr5D 100.000 2369 0 0 1 2369 119255110 119252742 0 4375
1 TraesCS5D01G105300 chr5A 93.281 2411 84 40 1 2369 129277452 129275078 0 3483
2 TraesCS5D01G105300 chr5B 94.536 1830 53 20 551 2369 131715844 131714051 0 2782
3 TraesCS5D01G105300 chr5B 93.238 562 18 6 1 553 131716723 131716173 0 809


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 TraesCS5D01G105300 chr5D 119252742 119255110 2368 True 4375.0 4375 100.000 1 2369 1 chr5D.!!$R1 2368
1 TraesCS5D01G105300 chr5A 129275078 129277452 2374 True 3483.0 3483 93.281 1 2369 1 chr5A.!!$R1 2368
2 TraesCS5D01G105300 chr5B 131714051 131716723 2672 True 1795.5 2782 93.887 1 2369 2 chr5B.!!$R1 2368

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
49 50 0.169672 GCTGTCGAGGTTAGCACGTA 59.83 55.0 1.01 0.0 37.4 3.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1869 2232 0.179156 GCAACGATGTGCAAGGATGG 60.179 55.0 0.0 0.0 44.29 3.51 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
49 50 0.169672 GCTGTCGAGGTTAGCACGTA 59.830 55.000 1.01 0.00 37.40 3.57
78 79 8.041323 GGGAAAACTATAGATCAACAGAAGACA 58.959 37.037 6.78 0.00 0.00 3.41
259 263 7.571089 TGCACGTATAGTACAACTTTGTAAG 57.429 36.000 3.38 0.00 44.46 2.34
263 267 7.007725 CACGTATAGTACAACTTTGTAAGTCCG 59.992 40.741 3.38 5.89 44.46 4.79
273 277 1.447314 GTAAGTCCGCCGAACAGGG 60.447 63.158 0.00 0.00 41.48 4.45
360 364 3.803340 TCCCTCTCCTTTCCAATACACT 58.197 45.455 0.00 0.00 0.00 3.55
361 365 3.519510 TCCCTCTCCTTTCCAATACACTG 59.480 47.826 0.00 0.00 0.00 3.66
362 366 3.264450 CCCTCTCCTTTCCAATACACTGT 59.736 47.826 0.00 0.00 0.00 3.55
363 367 4.508662 CCTCTCCTTTCCAATACACTGTC 58.491 47.826 0.00 0.00 0.00 3.51
364 368 4.223923 CCTCTCCTTTCCAATACACTGTCT 59.776 45.833 0.00 0.00 0.00 3.41
365 369 5.422331 CCTCTCCTTTCCAATACACTGTCTA 59.578 44.000 0.00 0.00 0.00 2.59
366 370 6.406400 CCTCTCCTTTCCAATACACTGTCTAG 60.406 46.154 0.00 0.00 0.00 2.43
456 466 3.559238 AATTTAGCAAGCCAACAGACG 57.441 42.857 0.00 0.00 0.00 4.18
569 910 1.466856 TTAATCAGGCAGCAAGCTGG 58.533 50.000 22.20 7.26 43.77 4.85
650 991 2.510691 GCTGCACATGGCCATTGC 60.511 61.111 30.24 30.24 43.89 3.56
964 1321 1.819208 CGCGCATTCATTCCCTCCA 60.819 57.895 8.75 0.00 0.00 3.86
967 1324 1.450531 CGCATTCATTCCCTCCAGCC 61.451 60.000 0.00 0.00 0.00 4.85
968 1325 1.450531 GCATTCATTCCCTCCAGCCG 61.451 60.000 0.00 0.00 0.00 5.52
970 1327 1.925285 ATTCATTCCCTCCAGCCGCA 61.925 55.000 0.00 0.00 0.00 5.69
1035 1392 2.493973 CTCGTGCTGCTCCTCCTC 59.506 66.667 0.00 0.00 0.00 3.71
1411 1768 2.093075 AGAGATCACGTCCTCTCGGTTA 60.093 50.000 14.91 0.00 42.21 2.85
1514 1871 2.258013 GGTTGTTGCCGCTGCTGTA 61.258 57.895 0.70 0.00 38.71 2.74
1621 1981 5.473931 TCTTTCAAGACTGAATCCTCTTCG 58.526 41.667 0.00 0.00 41.22 3.79
1724 2084 5.949354 TGATTGGTGTCGGGAGAAAAATAAT 59.051 36.000 0.00 0.00 42.89 1.28
1771 2134 1.393603 TCAGGTGGATCTAGAGCGTG 58.606 55.000 1.16 2.95 0.00 5.34
1792 2155 2.515912 GAACCATCCGCAATTTTCGTC 58.484 47.619 0.00 0.00 0.00 4.20
1852 2215 1.072015 CATGATGGAGGAGGAAGAGCC 59.928 57.143 0.00 0.00 0.00 4.70
1871 2234 4.603131 AGCCATATTTTGCTCTTTCTCCA 58.397 39.130 0.00 0.00 30.33 3.86
1872 2235 5.206587 AGCCATATTTTGCTCTTTCTCCAT 58.793 37.500 0.00 0.00 30.33 3.41
2018 2386 1.750778 AGCCAATTCCATTTGCGTAGG 59.249 47.619 0.00 0.00 36.17 3.18
2024 2392 3.965379 TTCCATTTGCGTAGGACTACA 57.035 42.857 9.87 0.00 35.87 2.74
2025 2393 3.520290 TCCATTTGCGTAGGACTACAG 57.480 47.619 9.87 4.21 35.87 2.74
2026 2394 2.829720 TCCATTTGCGTAGGACTACAGT 59.170 45.455 9.87 0.00 35.87 3.55
2110 2482 3.997681 TCATTTCATTTCGCCAAGTACGA 59.002 39.130 0.00 0.00 37.86 3.43
2136 2508 7.831690 AGGAAAAGGGAGAAGATTGAGTAATTC 59.168 37.037 0.00 0.00 0.00 2.17
2143 2515 6.434018 AGAAGATTGAGTAATTCTTGCAGC 57.566 37.500 0.00 0.00 0.00 5.25
2178 2551 4.094887 GCGCAATTGAACCATTCTCTTCTA 59.905 41.667 10.34 0.00 0.00 2.10
2185 2558 5.668471 TGAACCATTCTCTTCTATGAGCTG 58.332 41.667 0.00 0.00 34.29 4.24
2197 2574 2.519771 ATGAGCTGCTGGGAAATGAA 57.480 45.000 7.01 0.00 0.00 2.57
2219 2596 1.739035 CGAGGTTGAGCTGCGGAATTA 60.739 52.381 0.00 0.00 0.00 1.40
2230 2607 3.209410 CTGCGGAATTAAGCCATTCTCT 58.791 45.455 0.00 0.00 34.12 3.10
2231 2608 3.206150 TGCGGAATTAAGCCATTCTCTC 58.794 45.455 2.66 0.00 34.12 3.20
2232 2609 2.550180 GCGGAATTAAGCCATTCTCTCC 59.450 50.000 1.99 0.00 34.12 3.71
2356 2736 3.279434 AGGAATAAATGCCGTGTCCTTC 58.721 45.455 0.00 0.00 31.31 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 7.979786 TCTGTTGATCTATAGTTTTCCCTCT 57.020 36.000 0.00 0.00 0.00 3.69
78 79 8.090250 TCAACATACTACGTGCTTACATTTTT 57.910 30.769 0.00 0.00 0.00 1.94
332 336 2.095461 GGAAAGGAGAGGGATGTTTGC 58.905 52.381 0.00 0.00 0.00 3.68
360 364 7.318141 CGAATTTTAAGGGTAGACACTAGACA 58.682 38.462 0.00 0.00 0.00 3.41
361 365 6.255237 GCGAATTTTAAGGGTAGACACTAGAC 59.745 42.308 0.00 0.00 0.00 2.59
362 366 6.154021 AGCGAATTTTAAGGGTAGACACTAGA 59.846 38.462 0.00 0.00 0.00 2.43
363 367 6.338937 AGCGAATTTTAAGGGTAGACACTAG 58.661 40.000 0.00 0.00 0.00 2.57
364 368 6.071221 TGAGCGAATTTTAAGGGTAGACACTA 60.071 38.462 0.00 0.00 0.00 2.74
365 369 5.161943 AGCGAATTTTAAGGGTAGACACT 57.838 39.130 0.00 0.00 0.00 3.55
366 370 4.933400 TGAGCGAATTTTAAGGGTAGACAC 59.067 41.667 0.00 0.00 0.00 3.67
569 910 3.063997 GGCATAATATGTCATAGGCGCAC 59.936 47.826 10.83 0.00 34.33 5.34
576 917 5.575218 CGTAACAGCGGCATAATATGTCATA 59.425 40.000 5.66 0.00 33.60 2.15
665 1006 0.743688 CATGTGACGAGGAGGAGGAG 59.256 60.000 0.00 0.00 0.00 3.69
1376 1733 4.899239 CTCTGGGCGCGGATGTCC 62.899 72.222 13.33 0.00 0.00 4.02
1377 1734 3.157217 ATCTCTGGGCGCGGATGTC 62.157 63.158 13.33 0.00 0.00 3.06
1378 1735 3.157217 GATCTCTGGGCGCGGATGT 62.157 63.158 13.33 4.69 0.00 3.06
1379 1736 2.356793 GATCTCTGGGCGCGGATG 60.357 66.667 13.33 7.62 0.00 3.51
1514 1871 3.723325 ACAAATGTCCCAATAGGCCAAT 58.277 40.909 5.01 0.00 34.51 3.16
1603 1960 3.244033 AGCGAAGAGGATTCAGTCTTG 57.756 47.619 5.50 1.45 33.04 3.02
1607 1964 3.450457 AGATGAAGCGAAGAGGATTCAGT 59.550 43.478 0.00 0.00 35.31 3.41
1608 1965 4.057406 AGATGAAGCGAAGAGGATTCAG 57.943 45.455 0.00 0.00 35.31 3.02
1611 1968 4.751767 AGAAGATGAAGCGAAGAGGATT 57.248 40.909 0.00 0.00 0.00 3.01
1724 2084 5.227908 CACAAGGAAAGCTCGTAGTAGAAA 58.772 41.667 0.00 0.00 0.00 2.52
1771 2134 1.201414 ACGAAAATTGCGGATGGTTCC 59.799 47.619 0.00 0.00 38.81 3.62
1792 2155 5.534278 TGGTGATAGCACTTCATCTCTAGAG 59.466 44.000 13.98 13.98 44.52 2.43
1852 2215 6.956202 AGGATGGAGAAAGAGCAAAATATG 57.044 37.500 0.00 0.00 0.00 1.78
1869 2232 0.179156 GCAACGATGTGCAAGGATGG 60.179 55.000 0.00 0.00 44.29 3.51
1870 2233 3.317608 GCAACGATGTGCAAGGATG 57.682 52.632 0.00 0.00 44.29 3.51
2110 2482 6.704056 TTACTCAATCTTCTCCCTTTTCCT 57.296 37.500 0.00 0.00 0.00 3.36
2136 2508 1.744368 AGCTCATGACCGCTGCAAG 60.744 57.895 8.56 0.00 34.69 4.01
2178 2551 2.519771 TTCATTTCCCAGCAGCTCAT 57.480 45.000 0.00 0.00 0.00 2.90
2185 2558 2.044123 ACCTCGATTCATTTCCCAGC 57.956 50.000 0.00 0.00 0.00 4.85
2197 2574 1.888436 TTCCGCAGCTCAACCTCGAT 61.888 55.000 0.00 0.00 0.00 3.59
2219 2596 0.545646 GCCTGAGGAGAGAATGGCTT 59.454 55.000 0.65 0.00 37.58 4.35
2230 2607 0.040351 ACAGTAGCTGAGCCTGAGGA 59.960 55.000 15.94 0.00 35.18 3.71
2231 2608 0.175302 CACAGTAGCTGAGCCTGAGG 59.825 60.000 15.94 0.00 35.18 3.86
2232 2609 1.180907 TCACAGTAGCTGAGCCTGAG 58.819 55.000 15.94 9.21 35.18 3.35


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

AutoCloner maintained by Alex Coulton.