Multiple sequence alignment - TraesCS5B01G569200

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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 TraesCS5B01G569200 chr5B 100.000 2435 0 0 1 2435 711779393 711781827 0 4497
1 TraesCS5B01G569200 chr5B 92.986 2438 167 3 1 2435 135773056 135770620 0 3552
2 TraesCS5B01G569200 chr5B 92.942 2437 170 1 1 2435 135643952 135641516 0 3546
3 TraesCS5B01G569200 chr4B 95.729 2435 97 2 1 2435 669894260 669891833 0 3914
4 TraesCS5B01G569200 chr4B 93.317 2439 158 4 1 2435 8182049 8184486 0 3596
5 TraesCS5B01G569200 chr2B 94.463 2438 132 2 1 2435 776266260 776268697 0 3751
6 TraesCS5B01G569200 chr1A 94.094 2438 141 3 1 2435 575323263 575320826 0 3701
7 TraesCS5B01G569200 chr3B 93.437 2438 157 2 1 2435 791064457 791066894 0 3613
8 TraesCS5B01G569200 chr1B 93.399 2439 155 6 1 2435 37342058 37344494 0 3607
9 TraesCS5B01G569200 chr4A 92.825 2439 168 7 1 2435 740914308 740916743 0 3528


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 TraesCS5B01G569200 chr5B 711779393 711781827 2434 False 4497 4497 100.000 1 2435 1 chr5B.!!$F1 2434
1 TraesCS5B01G569200 chr5B 135770620 135773056 2436 True 3552 3552 92.986 1 2435 1 chr5B.!!$R2 2434
2 TraesCS5B01G569200 chr5B 135641516 135643952 2436 True 3546 3546 92.942 1 2435 1 chr5B.!!$R1 2434
3 TraesCS5B01G569200 chr4B 669891833 669894260 2427 True 3914 3914 95.729 1 2435 1 chr4B.!!$R1 2434
4 TraesCS5B01G569200 chr4B 8182049 8184486 2437 False 3596 3596 93.317 1 2435 1 chr4B.!!$F1 2434
5 TraesCS5B01G569200 chr2B 776266260 776268697 2437 False 3751 3751 94.463 1 2435 1 chr2B.!!$F1 2434
6 TraesCS5B01G569200 chr1A 575320826 575323263 2437 True 3701 3701 94.094 1 2435 1 chr1A.!!$R1 2434
7 TraesCS5B01G569200 chr3B 791064457 791066894 2437 False 3613 3613 93.437 1 2435 1 chr3B.!!$F1 2434
8 TraesCS5B01G569200 chr1B 37342058 37344494 2436 False 3607 3607 93.399 1 2435 1 chr1B.!!$F1 2434
9 TraesCS5B01G569200 chr4A 740914308 740916743 2435 False 3528 3528 92.825 1 2435 1 chr4A.!!$F1 2434

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
647 648 1.609783 GCTACAGGGGAAGCCACAT 59.39 57.895 0.0 0.0 32.4 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1461 1465 0.179 ACAATCCGGCTAGAAGGCAG 59.821 55.0 0.0 0.0 41.44 4.85 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
152 153 5.010012 ACGCTTGTGATCTTTTCAGGAAAAT 59.990 36.000 7.58 0.00 39.29 1.82
226 227 3.068881 CTCCAAAGCCAGGTCCGA 58.931 61.111 0.00 0.00 0.00 4.55
351 352 3.479269 CGCCGGACAGTTCTTCGC 61.479 66.667 5.05 0.00 0.00 4.70
504 505 2.359376 ATATATGCCAGTAGCCCCCA 57.641 50.000 0.00 0.00 42.71 4.96
580 581 7.707624 TCTTACAGAAAAGAATACCCGTCTA 57.292 36.000 0.00 0.00 32.59 2.59
647 648 1.609783 GCTACAGGGGAAGCCACAT 59.390 57.895 0.00 0.00 32.40 3.21
677 679 6.656693 CCCCTCTGGTAATATATGCTTCAAAG 59.343 42.308 0.00 0.00 0.00 2.77
958 961 6.705825 AGTGCTTGAACAAACTTTGAAAAAGT 59.294 30.769 8.55 0.00 0.00 2.66
991 994 5.009210 AGGAAGTCGACTAACAGAGATATGC 59.991 44.000 20.39 4.15 0.00 3.14
1085 1088 0.927537 CAACTGCACGAACGAGTTCA 59.072 50.000 15.20 0.00 39.46 3.18
1131 1134 2.160822 CCTTGTGGCCATCTATCTCG 57.839 55.000 9.72 0.00 0.00 4.04
1340 1343 1.816835 CCCTGTGAGCTTAGTGTACGA 59.183 52.381 0.00 0.00 0.00 3.43
1372 1375 0.393808 GGCCGCAAAGTATTCCCAGA 60.394 55.000 0.00 0.00 0.00 3.86
1539 1543 2.077687 GGACCCAATAGTCCGGAGTA 57.922 55.000 21.15 21.15 46.57 2.59
1739 1751 4.758251 TGCATGTCCGGACTGCGG 62.758 66.667 33.73 23.43 37.87 5.69
1808 1820 4.139859 TCAACTTTTAGTTCACCGACCA 57.860 40.909 0.00 0.00 36.03 4.02
1835 1847 4.281898 TCCCTTAAGAACGCTAGCTTTT 57.718 40.909 13.93 5.61 0.00 2.27
1863 1875 2.225394 ACCCAGTCTGAGGTACACATCT 60.225 50.000 10.34 0.00 33.52 2.90
1959 1971 3.185203 AGGAGCCAGGCAACCCAA 61.185 61.111 15.80 0.00 37.17 4.12
1988 2000 6.430451 GCCAAAACTTAAGTCATATCGATGG 58.570 40.000 8.95 9.40 33.49 3.51
2134 2146 3.973923 CGAACAATGCGCAGATGAA 57.026 47.368 26.91 0.00 0.00 2.57
2230 2243 3.835395 AGGAAGGAGACGAACTCAGAATT 59.165 43.478 13.89 5.45 46.54 2.17
2259 2272 2.826128 AGGCGTAGAATCTTCACAGACA 59.174 45.455 0.00 0.00 0.00 3.41
2279 2292 1.971167 GCTGCGTTCCATGGGTTCA 60.971 57.895 13.02 4.43 0.00 3.18
2280 2293 1.315257 GCTGCGTTCCATGGGTTCAT 61.315 55.000 13.02 0.00 0.00 2.57
2286 2299 2.280628 GTTCCATGGGTTCATCTCGAC 58.719 52.381 13.02 0.00 0.00 4.20
2340 2353 2.430367 GCCGGTCAGGACTTGGTT 59.570 61.111 1.90 0.00 45.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 4.324267 GGACTGCACTTCTTTTTAGCCTA 58.676 43.478 0.00 0.00 0.00 3.93
152 153 4.056125 CAGTCCGGTGAGCGCTCA 62.056 66.667 35.30 35.30 37.24 4.26
226 227 3.041940 CGTGTTCGCCTCCGCTTT 61.042 61.111 0.00 0.00 0.00 3.51
351 352 0.443869 CTTGGGAGAAACATGCGTCG 59.556 55.000 0.00 0.00 0.00 5.12
414 415 1.571955 TGGCTAGACCATCTTGAGCA 58.428 50.000 0.00 0.00 46.36 4.26
580 581 1.558756 CACTCTTCAAGCTCCTGGGAT 59.441 52.381 0.00 0.00 0.00 3.85
647 648 5.017431 AGCATATATTACCAGAGGGGGTCTA 59.983 44.000 0.00 0.00 42.42 2.59
677 679 4.092968 CCGCACTTCACAAACTACTTATCC 59.907 45.833 0.00 0.00 0.00 2.59
958 961 2.257371 CGACTTCCTCGCCGAACA 59.743 61.111 0.00 0.00 35.06 3.18
1085 1088 0.674895 GACGCCTTTCATCACCTGCT 60.675 55.000 0.00 0.00 0.00 4.24
1131 1134 3.752339 CCAAGGCTTTCGGGCAGC 61.752 66.667 0.00 0.00 43.56 5.25
1300 1303 0.266152 ATCTCCTTCCCATCGGGTCT 59.734 55.000 0.00 0.00 44.74 3.85
1340 1343 0.037590 TGCGGCCAATTCTACTTGGT 59.962 50.000 2.24 0.00 46.19 3.67
1372 1375 4.538746 GGCTGTCTAGTTTACAGTCCTT 57.461 45.455 10.72 0.00 42.47 3.36
1461 1465 0.179000 ACAATCCGGCTAGAAGGCAG 59.821 55.000 0.00 0.00 41.44 4.85
1510 1514 3.456277 GACTATTGGGTCCAGAGGTTGAT 59.544 47.826 0.00 0.00 0.00 2.57
1539 1543 1.362717 CGCGAGGGTATTCGGACAT 59.637 57.895 0.00 0.00 40.79 3.06
1739 1751 4.321527 CCCCAGATGTTTTTCTGCTCTTTC 60.322 45.833 0.00 0.00 41.50 2.62
1790 1802 7.094506 GGAATATTTGGTCGGTGAACTAAAAGT 60.095 37.037 0.00 0.00 34.00 2.66
1808 1820 6.592870 AGCTAGCGTTCTTAAGGGAATATTT 58.407 36.000 9.55 0.00 0.00 1.40
1835 1847 1.915266 CTCAGACTGGGTGGAGCCA 60.915 63.158 1.81 0.00 39.65 4.75
1840 1852 0.608640 GTGTACCTCAGACTGGGTGG 59.391 60.000 19.99 14.17 37.07 4.61
1863 1875 2.925706 TTACTGCCGGGTCAGCCA 60.926 61.111 15.44 4.53 37.59 4.75
1959 1971 6.128007 CGATATGACTTAAGTTTTGGCCAAGT 60.128 38.462 19.48 11.25 32.33 3.16
2134 2146 0.185901 TTCTTGCAGCCTTTGGAGGT 59.814 50.000 0.00 0.00 45.44 3.85
2253 2266 2.031163 GGAACGCAGCCTGTCTGT 59.969 61.111 0.00 0.00 44.66 3.41
2254 2267 1.376424 ATGGAACGCAGCCTGTCTG 60.376 57.895 0.00 0.00 45.62 3.51
2259 2272 3.210012 AACCCATGGAACGCAGCCT 62.210 57.895 15.22 0.00 0.00 4.58


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

AutoCloner maintained by Alex Coulton.