Multiple sequence alignment - TraesCS2B01G209900

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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 TraesCS2B01G209900 chr2B 100.000 2044 0 0 953 2996 192368143 192366100 0.000000e+00 3775
1 TraesCS2B01G209900 chr2B 100.000 463 0 0 1 463 192369095 192368633 0.000000e+00 856
2 TraesCS2B01G209900 chr2D 95.945 2047 66 7 953 2996 135309834 135307802 0.000000e+00 3304
3 TraesCS2B01G209900 chr2D 96.308 325 7 3 19 342 135310681 135310361 2.050000e-146 529
4 TraesCS2B01G209900 chr2A 95.259 2046 80 7 953 2996 143217421 143215391 0.000000e+00 3225
5 TraesCS2B01G209900 chr2A 89.440 464 19 3 1 463 143217902 143217468 2.610000e-155 558


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 TraesCS2B01G209900 chr2B 192366100 192369095 2995 True 2315.5 3775 100.0000 1 2996 2 chr2B.!!$R1 2995
1 TraesCS2B01G209900 chr2D 135307802 135310681 2879 True 1916.5 3304 96.1265 19 2996 2 chr2D.!!$R1 2977
2 TraesCS2B01G209900 chr2A 143215391 143217902 2511 True 1891.5 3225 92.3495 1 2996 2 chr2A.!!$R1 2995

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
359 362 0.178891 AAGCTTCTCCCTCCACTCCA 60.179 55.000 0.0 0.0 0.0 3.86 F
360 363 0.907230 AGCTTCTCCCTCCACTCCAC 60.907 60.000 0.0 0.0 0.0 4.02 F
362 365 1.229529 TTCTCCCTCCACTCCACCC 60.230 63.158 0.0 0.0 0.0 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1524 1886 0.530870 GCGGGTAGAGCATGGACTTC 60.531 60.000 0.0 0.0 34.19 3.01 R
1806 2168 1.045350 CCTCCCAGAGCCGAGATGAA 61.045 60.000 0.0 0.0 0.00 2.57 R
2089 2451 1.663702 GACACGACCACACCCTTCG 60.664 63.158 0.0 0.0 38.73 3.79 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
128 130 1.730064 CGAAACCAACCATACACGAGG 59.270 52.381 0.00 0.00 0.00 4.63
182 184 2.906897 GCCCCCACATGCCATACG 60.907 66.667 0.00 0.00 0.00 3.06
359 362 0.178891 AAGCTTCTCCCTCCACTCCA 60.179 55.000 0.00 0.00 0.00 3.86
360 363 0.907230 AGCTTCTCCCTCCACTCCAC 60.907 60.000 0.00 0.00 0.00 4.02
361 364 1.904990 GCTTCTCCCTCCACTCCACC 61.905 65.000 0.00 0.00 0.00 4.61
362 365 1.229529 TTCTCCCTCCACTCCACCC 60.230 63.158 0.00 0.00 0.00 4.61
363 366 2.689034 CTCCCTCCACTCCACCCC 60.689 72.222 0.00 0.00 0.00 4.95
364 367 4.348495 TCCCTCCACTCCACCCCC 62.348 72.222 0.00 0.00 0.00 5.40
365 368 4.675303 CCCTCCACTCCACCCCCA 62.675 72.222 0.00 0.00 0.00 4.96
366 369 3.330720 CCTCCACTCCACCCCCAC 61.331 72.222 0.00 0.00 0.00 4.61
367 370 3.330720 CTCCACTCCACCCCCACC 61.331 72.222 0.00 0.00 0.00 4.61
368 371 4.995058 TCCACTCCACCCCCACCC 62.995 72.222 0.00 0.00 0.00 4.61
1413 1775 3.151022 GCCGACCTCTCCCTCCTG 61.151 72.222 0.00 0.00 0.00 3.86
1521 1883 2.734591 GTCACCGTCTGCTCCACA 59.265 61.111 0.00 0.00 0.00 4.17
1524 1886 1.665916 CACCGTCTGCTCCACACTG 60.666 63.158 0.00 0.00 0.00 3.66
1806 2168 2.509964 GACCTTGAGTTATGGGGATGGT 59.490 50.000 0.00 0.00 0.00 3.55
1836 2198 2.286808 TGGGAGGGGCCATTGCTA 60.287 61.111 4.39 0.00 38.95 3.49
1884 2246 5.458041 TGATAGATTCGATGATGAGTGCA 57.542 39.130 0.00 0.00 0.00 4.57
1947 2309 3.394836 GAGGAGGGCGGCTCAGTT 61.395 66.667 9.56 0.00 0.00 3.16
1989 2351 2.935201 GGATGACAAGTCAGATGCAGTC 59.065 50.000 8.99 0.00 43.61 3.51
2013 2375 9.699703 GTCAGGTGATTAAGAAGATTATAGGTC 57.300 37.037 0.00 0.00 0.00 3.85
2069 2431 3.365472 GGAAATAAGTGAGGTGGGCAAT 58.635 45.455 0.00 0.00 0.00 3.56
2070 2432 3.131046 GGAAATAAGTGAGGTGGGCAATG 59.869 47.826 0.00 0.00 0.00 2.82
2071 2433 1.767759 ATAAGTGAGGTGGGCAATGC 58.232 50.000 0.00 0.00 0.00 3.56
2139 2502 0.043053 CGCTTAATGTGCACGATCGG 60.043 55.000 20.98 9.59 0.00 4.18
2153 2516 2.093711 ACGATCGGTTCATGTTCATGGA 60.094 45.455 20.98 1.46 0.00 3.41
2161 2524 5.048782 CGGTTCATGTTCATGGAGAAAGAAA 60.049 40.000 12.02 0.00 38.13 2.52
2266 2629 5.716703 TGGTGTATTCTTGATCTGTCTCAGA 59.283 40.000 1.92 1.92 44.99 3.27
2305 2668 4.622740 GGCAATGTGTGTAGCATTCTTTTC 59.377 41.667 0.00 0.00 34.68 2.29
2380 2743 7.887381 TCAACACATTTTTGGTTATACGGAAT 58.113 30.769 0.00 0.00 0.00 3.01
2443 2806 3.200483 TGATTCATGAATCTGCACTCGG 58.800 45.455 36.15 0.00 45.55 4.63
2453 2816 0.721718 CTGCACTCGGTCCGAATTTC 59.278 55.000 16.23 5.57 34.74 2.17
2471 2835 7.376072 CCGAATTTCTTTTACAGTGACTTCAAC 59.624 37.037 0.00 0.00 0.00 3.18
2533 2897 7.067372 ACATGGTAACCACATAAGACATGAATG 59.933 37.037 0.00 0.17 35.80 2.67
2611 2975 2.238144 ACAGATCACTGCCATGTAAGCT 59.762 45.455 0.00 0.00 46.95 3.74
2880 3244 9.098355 GCTGTTTTTATATGACAGATGTACTCA 57.902 33.333 12.31 0.00 42.54 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.142667 TGGGCAGACACTCATGAACAA 59.857 47.619 0.00 0.00 0.00 2.83
128 130 2.617274 GGTGAAGCTTCGTGGCACC 61.617 63.158 21.11 18.33 41.77 5.01
182 184 2.879813 TTTCCGGGCTTGCGGTATCC 62.880 60.000 0.00 0.00 0.00 2.59
192 195 2.346365 GGAGTTCGTTTCCGGGCT 59.654 61.111 0.00 0.00 33.95 5.19
380 383 4.397010 CAATGGGGTGGGGGTGGG 62.397 72.222 0.00 0.00 0.00 4.61
1521 1883 1.834263 GGGTAGAGCATGGACTTCAGT 59.166 52.381 0.00 0.00 0.00 3.41
1524 1886 0.530870 GCGGGTAGAGCATGGACTTC 60.531 60.000 0.00 0.00 34.19 3.01
1677 2039 3.381983 ATCAGCTGCACCGACCGA 61.382 61.111 9.47 0.00 0.00 4.69
1716 2078 4.809815 GGATACAAGAAAGATGAGCAGC 57.190 45.455 0.00 0.00 0.00 5.25
1806 2168 1.045350 CCTCCCAGAGCCGAGATGAA 61.045 60.000 0.00 0.00 0.00 2.57
1836 2198 5.661056 TCACGAAAGAGTACATGAGGATT 57.339 39.130 0.00 0.00 0.00 3.01
1947 2309 5.152934 TCCATCATCATCTCAATCTCCTCA 58.847 41.667 0.00 0.00 0.00 3.86
2013 2375 7.496529 TGAACAGATACACCTTGAGAAAAAG 57.503 36.000 0.00 0.00 0.00 2.27
2015 2377 9.739276 AATATGAACAGATACACCTTGAGAAAA 57.261 29.630 0.00 0.00 0.00 2.29
2089 2451 1.663702 GACACGACCACACCCTTCG 60.664 63.158 0.00 0.00 38.73 3.79
2139 2502 6.015940 AGGTTTCTTTCTCCATGAACATGAAC 60.016 38.462 15.21 8.98 41.20 3.18
2153 2516 5.859205 ATGACTGCAAAAGGTTTCTTTCT 57.141 34.783 0.00 0.00 41.92 2.52
2161 2524 1.693606 CCCCAAATGACTGCAAAAGGT 59.306 47.619 0.00 0.00 0.00 3.50
2266 2629 3.036429 GCCAGCCCTCGGATCACTT 62.036 63.158 0.00 0.00 0.00 3.16
2336 2699 3.750371 TGAGATGACAAAATTCCACCGT 58.250 40.909 0.00 0.00 0.00 4.83
2380 2743 8.426489 GGTACCTCAGTATTACAATATGTTCCA 58.574 37.037 4.06 0.00 0.00 3.53
2399 2762 3.444388 AGTTTCAGAGTCATCGGTACCTC 59.556 47.826 10.90 0.00 0.00 3.85
2443 2806 6.541111 AGTCACTGTAAAAGAAATTCGGAC 57.459 37.500 0.00 0.00 0.00 4.79
2453 2816 6.758886 AGACAGAGTTGAAGTCACTGTAAAAG 59.241 38.462 2.50 0.00 41.01 2.27
2502 2866 6.170506 GTCTTATGTGGTTACCATGTCTCAA 58.829 40.000 7.58 0.00 35.28 3.02
2550 2914 4.042187 ACTTCTGCAGTGGAAGAATAGGTT 59.958 41.667 18.16 0.00 38.04 3.50
2611 2975 2.373169 ACCATGTCTCAAGCTCAAAGGA 59.627 45.455 0.00 0.00 0.00 3.36
2817 3181 2.864931 CGCCTCGAGAAAGCATCGC 61.865 63.158 15.71 4.91 39.98 4.58
2880 3244 6.434340 GTGTTCCTGATCTAAGGTTGGAAAAT 59.566 38.462 0.00 0.00 38.58 1.82


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

AutoCloner maintained by Alex Coulton.