Multiple sequence alignment - TraesCS3D01G410900

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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 TraesCS3D01G410900 chr3D 100.000 2794 0 0 1 2794 523759660 523762453 0.000000e+00 5160.0
1 TraesCS3D01G410900 chr3D 96.825 63 2 0 1855 1917 213401318 213401380 3.810000e-19 106.0
2 TraesCS3D01G410900 chr6D 97.812 1920 36 6 1 1915 108464393 108466311 0.000000e+00 3308.0
3 TraesCS3D01G410900 chr6D 97.291 886 23 1 1909 2794 102377177 102378061 0.000000e+00 1502.0
4 TraesCS3D01G410900 chr2D 97.812 1920 36 5 1 1915 637321085 637319167 0.000000e+00 3308.0
5 TraesCS3D01G410900 chr2D 96.927 1920 56 3 1 1917 39496990 39498909 0.000000e+00 3216.0
6 TraesCS3D01G410900 chr2D 97.291 886 23 1 1909 2794 604410318 604409434 0.000000e+00 1502.0
7 TraesCS3D01G410900 chr5A 97.747 1864 37 4 1 1859 73031636 73033499 0.000000e+00 3205.0
8 TraesCS3D01G410900 chr1B 97.585 1863 41 4 1 1859 638749965 638748103 0.000000e+00 3188.0
9 TraesCS3D01G410900 chr7A 97.531 1863 38 6 1 1859 60106952 60105094 0.000000e+00 3179.0
10 TraesCS3D01G410900 chr7A 97.743 886 19 1 1909 2794 211226141 211227025 0.000000e+00 1524.0
11 TraesCS3D01G410900 chr6B 97.368 1862 46 3 1 1859 388367588 388365727 0.000000e+00 3164.0
12 TraesCS3D01G410900 chr3B 97.048 1863 51 4 1 1859 575754679 575752817 0.000000e+00 3133.0
13 TraesCS3D01G410900 chr2B 96.994 1863 52 4 1 1859 500714163 500716025 0.000000e+00 3127.0
14 TraesCS3D01G410900 chr7D 97.743 886 19 1 1909 2794 579021044 579021928 0.000000e+00 1524.0
15 TraesCS3D01G410900 chr6A 97.743 886 19 1 1909 2794 64683621 64682737 0.000000e+00 1524.0
16 TraesCS3D01G410900 chr3A 97.630 886 20 1 1909 2794 633125706 633126590 0.000000e+00 1519.0
17 TraesCS3D01G410900 chr7B 97.404 886 22 1 1909 2794 742962990 742962106 0.000000e+00 1507.0
18 TraesCS3D01G410900 chr4D 97.291 886 23 1 1909 2794 123252234 123253118 0.000000e+00 1502.0
19 TraesCS3D01G410900 chr4B 97.291 886 23 1 1909 2794 209137049 209137933 0.000000e+00 1502.0
20 TraesCS3D01G410900 chr5D 100.000 44 0 0 1874 1917 469489544 469489587 6.410000e-12 82.4


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 TraesCS3D01G410900 chr3D 523759660 523762453 2793 False 5160 5160 100.000 1 2794 1 chr3D.!!$F2 2793
1 TraesCS3D01G410900 chr6D 108464393 108466311 1918 False 3308 3308 97.812 1 1915 1 chr6D.!!$F2 1914
2 TraesCS3D01G410900 chr6D 102377177 102378061 884 False 1502 1502 97.291 1909 2794 1 chr6D.!!$F1 885
3 TraesCS3D01G410900 chr2D 637319167 637321085 1918 True 3308 3308 97.812 1 1915 1 chr2D.!!$R2 1914
4 TraesCS3D01G410900 chr2D 39496990 39498909 1919 False 3216 3216 96.927 1 1917 1 chr2D.!!$F1 1916
5 TraesCS3D01G410900 chr2D 604409434 604410318 884 True 1502 1502 97.291 1909 2794 1 chr2D.!!$R1 885
6 TraesCS3D01G410900 chr5A 73031636 73033499 1863 False 3205 3205 97.747 1 1859 1 chr5A.!!$F1 1858
7 TraesCS3D01G410900 chr1B 638748103 638749965 1862 True 3188 3188 97.585 1 1859 1 chr1B.!!$R1 1858
8 TraesCS3D01G410900 chr7A 60105094 60106952 1858 True 3179 3179 97.531 1 1859 1 chr7A.!!$R1 1858
9 TraesCS3D01G410900 chr7A 211226141 211227025 884 False 1524 1524 97.743 1909 2794 1 chr7A.!!$F1 885
10 TraesCS3D01G410900 chr6B 388365727 388367588 1861 True 3164 3164 97.368 1 1859 1 chr6B.!!$R1 1858
11 TraesCS3D01G410900 chr3B 575752817 575754679 1862 True 3133 3133 97.048 1 1859 1 chr3B.!!$R1 1858
12 TraesCS3D01G410900 chr2B 500714163 500716025 1862 False 3127 3127 96.994 1 1859 1 chr2B.!!$F1 1858
13 TraesCS3D01G410900 chr7D 579021044 579021928 884 False 1524 1524 97.743 1909 2794 1 chr7D.!!$F1 885
14 TraesCS3D01G410900 chr6A 64682737 64683621 884 True 1524 1524 97.743 1909 2794 1 chr6A.!!$R1 885
15 TraesCS3D01G410900 chr3A 633125706 633126590 884 False 1519 1519 97.630 1909 2794 1 chr3A.!!$F1 885
16 TraesCS3D01G410900 chr7B 742962106 742962990 884 True 1507 1507 97.404 1909 2794 1 chr7B.!!$R1 885
17 TraesCS3D01G410900 chr4D 123252234 123253118 884 False 1502 1502 97.291 1909 2794 1 chr4D.!!$F1 885
18 TraesCS3D01G410900 chr4B 209137049 209137933 884 False 1502 1502 97.291 1909 2794 1 chr4B.!!$F1 885

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
460 461 0.326713 TACCATCCGGATCCCAACCA 60.327 55.0 15.88 0.0 35.59 3.67 F
1185 1188 0.461163 CCATGTTCGTATGGTGGCGA 60.461 55.0 7.60 0.0 42.16 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1460 1466 0.179040 TCGTTTTTCCTTCCCTGCGT 60.179 50.0 0.0 0.0 0.0 5.24 R
2031 2038 1.367346 TGCAAGGGATGTAGGACCAA 58.633 50.0 0.0 0.0 0.0 3.67 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
242 243 3.318839 CCAAGAAAGAGTTCAATGGCACA 59.681 43.478 0.00 0.0 38.60 4.57
460 461 0.326713 TACCATCCGGATCCCAACCA 60.327 55.000 15.88 0.0 35.59 3.67
806 808 6.626302 ACCAATCAAAAACTTCTTCGTTTCA 58.374 32.000 0.00 0.0 36.16 2.69
906 908 9.997172 AATGAAAGAACTATCCCTTCCTATTTT 57.003 29.630 0.00 0.0 0.00 1.82
986 989 2.785540 GGGGGTTTACATACAACCGA 57.214 50.000 0.00 0.0 44.25 4.69
1087 1090 1.832167 GGAGCTTTGGCAACCACCA 60.832 57.895 0.00 0.0 41.70 4.17
1185 1188 0.461163 CCATGTTCGTATGGTGGCGA 60.461 55.000 7.60 0.0 42.16 5.54
1195 1198 3.305403 CGTATGGTGGCGAGATGTTCTAT 60.305 47.826 0.00 0.0 0.00 1.98
1363 1369 2.477245 GGAGGTATTTGCCCCCAAAAT 58.523 47.619 0.00 0.0 43.58 1.82
1393 1399 5.519808 GGGTTTTAGATCCTTGGGAAATCT 58.480 41.667 0.00 0.0 34.34 2.40
1430 1436 2.182516 ATTCTCCCTTCATCCGGAGT 57.817 50.000 11.34 0.0 45.12 3.85
1433 1439 0.905357 CTCCCTTCATCCGGAGTTGT 59.095 55.000 11.34 0.0 40.77 3.32
1460 1466 3.392285 ACTTGGGCTCATCATGCTATACA 59.608 43.478 0.00 0.0 0.00 2.29
1464 1470 2.407090 GCTCATCATGCTATACACGCA 58.593 47.619 0.00 0.0 42.25 5.24
1622 1629 2.137523 GCAACTGGCTTTCATGGTTTG 58.862 47.619 0.00 0.0 40.25 2.93
1623 1630 2.483538 GCAACTGGCTTTCATGGTTTGT 60.484 45.455 0.00 0.0 40.25 2.83
1742 1749 4.339247 GCATGGTACTGGCATTTTGTAGAT 59.661 41.667 0.00 0.0 0.00 1.98
1750 1757 4.148079 TGGCATTTTGTAGATGTGGTTCA 58.852 39.130 0.00 0.0 0.00 3.18
1872 1879 1.534697 GGGTAATTGGATCGCCCCA 59.465 57.895 0.00 0.0 33.40 4.96
1940 1947 2.746362 AGCTGCTTCCGAGAAATCTTTG 59.254 45.455 0.00 0.0 0.00 2.77
1947 1954 1.004277 CCGAGAAATCTTTGACCCCCA 59.996 52.381 0.00 0.0 0.00 4.96
2031 2038 6.761714 CACCGCTTAACTCCAATAATAGAACT 59.238 38.462 0.00 0.0 0.00 3.01
2038 2045 6.893020 ACTCCAATAATAGAACTTGGTCCT 57.107 37.500 0.00 0.0 40.28 3.85
2122 2129 6.319152 TCTCATTTCTTTTACGTGGTTTTGGA 59.681 34.615 0.00 0.0 0.00 3.53
2157 2164 2.432510 CTCTTTCCTCGGCTTCCTACAT 59.567 50.000 0.00 0.0 0.00 2.29
2464 2471 9.268268 TGAACCGGTATCTTTAGCATATAAAAG 57.732 33.333 8.00 0.0 34.65 2.27
2480 2487 8.181573 GCATATAAAAGATCCTTTGTTTGACGA 58.818 33.333 7.75 0.0 0.00 4.20
2518 2525 3.084786 CTGCTTCCTTCCTTTCCGATTT 58.915 45.455 0.00 0.0 0.00 2.17
2706 2713 3.619929 GGATTGCCAACTTGAATGAATGC 59.380 43.478 0.00 0.0 0.00 3.56
2718 2725 4.013050 TGAATGAATGCAATCCGGTTACA 58.987 39.130 0.00 0.0 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
242 243 6.146673 CGTGAAAATACCTCGGTTTCTTACTT 59.853 38.462 0.00 0.0 33.37 2.24
282 283 5.992217 AGAAATGCGAAAGAACTCAACTACT 59.008 36.000 0.00 0.0 0.00 2.57
451 452 3.181437 ACTCCGTTAGTTTTGGTTGGGAT 60.181 43.478 0.00 0.0 33.35 3.85
460 461 4.070009 GTTGGGATGACTCCGTTAGTTTT 58.930 43.478 0.00 0.0 43.11 2.43
537 538 1.235989 TGTCTGGGGAGACAGGTGT 59.764 57.895 0.69 0.0 43.09 4.16
806 808 0.402504 TTGGCGTGGGTTCTACCAAT 59.597 50.000 0.00 0.0 43.34 3.16
986 989 6.438425 AGATTCAATCATAAACCACTTTGCCT 59.562 34.615 0.00 0.0 0.00 4.75
1087 1090 3.711190 TGCATGTACATCACACCTCCTAT 59.289 43.478 5.07 0.0 40.86 2.57
1185 1188 5.344743 ACGTGGATTCACATAGAACATCT 57.655 39.130 4.68 0.0 43.79 2.90
1363 1369 4.571792 CCAAGGATCTAAAACCCCAATCCA 60.572 45.833 0.00 0.0 38.69 3.41
1393 1399 7.017531 GGGAGAATAGGGGTATTAAGAAGAGA 58.982 42.308 0.00 0.0 0.00 3.10
1430 1436 2.037902 TGATGAGCCCAAGTTACGACAA 59.962 45.455 0.00 0.0 0.00 3.18
1433 1439 2.905075 CATGATGAGCCCAAGTTACGA 58.095 47.619 0.00 0.0 0.00 3.43
1460 1466 0.179040 TCGTTTTTCCTTCCCTGCGT 60.179 50.000 0.00 0.0 0.00 5.24
1464 1470 1.143073 ACTGCTCGTTTTTCCTTCCCT 59.857 47.619 0.00 0.0 0.00 4.20
1742 1749 5.144100 ACAAATGGGAATAACTGAACCACA 58.856 37.500 0.00 0.0 33.42 4.17
1872 1879 1.806542 CGCTCATTAAACCACAGTGCT 59.193 47.619 0.00 0.0 0.00 4.40
1940 1947 0.750546 GAAGGGCGTAAATGGGGGTC 60.751 60.000 0.00 0.0 0.00 4.46
2031 2038 1.367346 TGCAAGGGATGTAGGACCAA 58.633 50.000 0.00 0.0 0.00 3.67
2038 2045 7.894753 TTCATTATCAAATGCAAGGGATGTA 57.105 32.000 0.00 0.0 41.96 2.29
2122 2129 7.442666 GCCGAGGAAAGAGATAATTGATAGTTT 59.557 37.037 0.00 0.0 0.00 2.66
2346 2353 7.376435 TCGCTCATAAAAGTGATTTTCATCA 57.624 32.000 0.00 0.0 37.05 3.07
2464 2471 3.127030 GGGATGTCGTCAAACAAAGGATC 59.873 47.826 0.00 0.0 31.81 3.36
2480 2487 1.488393 GCAGCTTTAGAGGAGGGATGT 59.512 52.381 0.00 0.0 0.00 3.06
2518 2525 2.889045 ACTTCTGCTCGTAACCACTACA 59.111 45.455 0.00 0.0 0.00 2.74
2585 2592 3.737355 GCATCTCGAACTAGTGGGTTACC 60.737 52.174 0.00 0.0 37.24 2.85
2588 2595 1.899814 TGCATCTCGAACTAGTGGGTT 59.100 47.619 0.00 0.0 0.00 4.11
2706 2713 2.419574 CCCCTACACTGTAACCGGATTG 60.420 54.545 9.46 0.0 0.00 2.67
2718 2725 8.568617 ACTCAATAATAAATCTCCCCTACACT 57.431 34.615 0.00 0.0 0.00 3.55


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

AutoCloner maintained by Alex Coulton.