Multiple sequence alignment - TraesCS3A01G354700

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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 TraesCS3A01G354700 chr3A 100.000 3092 0 0 1 3092 602681041 602684132 0 5710
1 TraesCS3A01G354700 chr3D 97.226 3100 71 6 1 3089 460413468 460416563 0 5234
2 TraesCS3A01G354700 chr3B 96.385 3098 82 17 1 3092 610492436 610495509 0 5073


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 TraesCS3A01G354700 chr3A 602681041 602684132 3091 False 5710 5710 100.000 1 3092 1 chr3A.!!$F1 3091
1 TraesCS3A01G354700 chr3D 460413468 460416563 3095 False 5234 5234 97.226 1 3089 1 chr3D.!!$F1 3088
2 TraesCS3A01G354700 chr3B 610492436 610495509 3073 False 5073 5073 96.385 1 3092 1 chr3B.!!$F1 3091

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
240 241 1.079875 CATGTTTTCAGGGCATGCGC 61.080 55.0 26.04 26.04 34.47 6.09 F
1302 1304 1.323271 AAAGGCTCCTCGAGATCGCA 61.323 55.0 15.71 0.00 39.60 5.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1569 1571 0.842635 CTGGATCCCCTGCTTTAGCT 59.157 55.0 9.90 0.00 42.66 3.32 R
2346 2353 1.812235 TGGACTTGCTACATGTGCAG 58.188 50.0 18.08 15.23 41.71 4.41 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
208 209 9.132521 GTTGACATGGAGATGAAATAAACAAAG 57.867 33.333 0.00 0.00 33.36 2.77
212 213 6.182039 TGGAGATGAAATAAACAAAGAGCG 57.818 37.500 0.00 0.00 0.00 5.03
240 241 1.079875 CATGTTTTCAGGGCATGCGC 61.080 55.000 26.04 26.04 34.47 6.09
277 278 3.802948 TTAAAAACCGCAAGCTTTGGA 57.197 38.095 19.01 0.00 0.00 3.53
310 311 7.715657 TGGTCAAGCATCAACAATATATTTCC 58.284 34.615 0.00 0.00 0.00 3.13
311 312 6.857964 GGTCAAGCATCAACAATATATTTCCG 59.142 38.462 0.00 0.00 0.00 4.30
445 446 6.166279 TGAATCTGAACACATTCCTACACTC 58.834 40.000 0.00 0.00 33.49 3.51
568 569 5.856126 TTGCGAGTCACTTATTGGTAAAG 57.144 39.130 0.00 0.00 0.00 1.85
923 925 3.751518 TCCTTGCACTTCCTTCCTAAAC 58.248 45.455 0.00 0.00 0.00 2.01
1097 1099 1.954528 CAGCTGCAAAGGTGGTCAG 59.045 57.895 0.00 0.00 34.04 3.51
1302 1304 1.323271 AAAGGCTCCTCGAGATCGCA 61.323 55.000 15.71 0.00 39.60 5.10
1569 1571 5.125417 GGCTTACCTCAAGACAATATTTGCA 59.875 40.000 0.00 0.00 42.49 4.08
1773 1775 5.600484 CCATAGGAGGTCATTCTCTAGTGTT 59.400 44.000 0.00 0.00 34.39 3.32
2071 2073 6.906659 TCTGAAGATGCAGAAGACATTTTTC 58.093 36.000 0.00 0.00 41.65 2.29
2338 2345 5.606348 ACCTTTCTCTGATCAGTATCCAC 57.394 43.478 21.92 0.00 0.00 4.02
2346 2353 5.847304 TCTGATCAGTATCCACATTACAGC 58.153 41.667 21.92 0.00 0.00 4.40
2510 2518 8.613060 TCTATCTATCTCCAAATGCACAAATC 57.387 34.615 0.00 0.00 0.00 2.17
2919 2927 1.478510 CTCATGGCTCTACGTCAACCT 59.521 52.381 0.00 0.00 0.00 3.50
2962 2970 5.836024 ACTATGTCAGGGACCTTGTTTAA 57.164 39.130 3.17 0.00 0.00 1.52
2982 2995 7.771361 TGTTTAAGAAATACAAGTCACTGGTGA 59.229 33.333 0.00 0.00 37.24 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 1.876156 CAGTGTCAACTTTGCCTCTCC 59.124 52.381 0.00 0.00 32.98 3.71
212 213 1.273327 CCTGAAAACATGGAGCAACCC 59.727 52.381 0.00 0.00 38.00 4.11
240 241 1.218844 TAAATTCGGAGGGGGAAGGG 58.781 55.000 0.00 0.00 0.00 3.95
252 253 4.965042 AAGCTTGCGGTTTTTAAATTCG 57.035 36.364 0.00 0.00 0.00 3.34
277 278 2.503331 TGATGCTTGACCAATTCACGT 58.497 42.857 0.00 0.00 32.26 4.49
445 446 2.888594 TCGTATTCTTTCGAGCAAGGG 58.111 47.619 0.00 0.00 0.00 3.95
923 925 0.962356 GGCAGAGATGGTGGTTGTGG 60.962 60.000 0.00 0.00 0.00 4.17
1302 1304 2.204059 AGGAGGCCCTTGTCAGCT 60.204 61.111 0.00 0.00 40.78 4.24
1569 1571 0.842635 CTGGATCCCCTGCTTTAGCT 59.157 55.000 9.90 0.00 42.66 3.32
1644 1646 2.450476 CCAAATGGGTTCTTCCTCCAG 58.550 52.381 0.00 0.00 33.68 3.86
1773 1775 9.699703 TTGTTTGATGACGAATATCGGATAATA 57.300 29.630 1.16 0.00 45.59 0.98
2071 2073 3.067106 ACTACCGTTGTCTGCAAATCTG 58.933 45.455 0.00 0.00 36.22 2.90
2144 2146 8.288208 GCATGTCTTTAGGAAACATATGATCAG 58.712 37.037 10.38 1.68 32.54 2.90
2338 2345 2.679336 TGCTACATGTGCAGCTGTAATG 59.321 45.455 18.88 17.58 38.63 1.90
2346 2353 1.812235 TGGACTTGCTACATGTGCAG 58.188 50.000 18.08 15.23 41.71 4.41
2558 2566 6.145535 CACAAGCTTTTGAGAGTATGTTTCC 58.854 40.000 6.78 0.00 0.00 3.13
2559 2567 6.634436 CACACAAGCTTTTGAGAGTATGTTTC 59.366 38.462 19.17 0.00 0.00 2.78
2851 2859 5.879223 ACAAGGATCAGCATTTAGAAGAGTG 59.121 40.000 0.00 0.00 0.00 3.51
2941 2949 6.049955 TCTTAAACAAGGTCCCTGACATAG 57.950 41.667 0.00 0.00 33.68 2.23
2942 2950 6.442541 TTCTTAAACAAGGTCCCTGACATA 57.557 37.500 0.00 0.00 33.68 2.29
2943 2951 4.993705 TCTTAAACAAGGTCCCTGACAT 57.006 40.909 0.00 0.00 33.68 3.06
2982 2995 3.005367 CCTTTCATGTTTTAAGTGCCCGT 59.995 43.478 0.00 0.00 0.00 5.28
3035 3048 5.512788 CACTACTGCTTTTTGTTTGTCACAG 59.487 40.000 0.00 0.00 36.48 3.66
3036 3049 5.398169 CACTACTGCTTTTTGTTTGTCACA 58.602 37.500 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.