Multiple sequence alignment - TraesCS5D01G079100

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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 TraesCS5D01G079100 chr5D 100.000 2357 0 0 1 2357 79865255 79867611 0 4353
1 TraesCS5D01G079100 chr5D 93.260 2359 152 6 3 2357 197839898 197837543 0 3469
2 TraesCS5D01G079100 chr4D 96.185 2359 87 3 1 2357 483696359 483698716 0 3855
3 TraesCS5D01G079100 chr4D 95.589 2358 101 3 1 2357 135006221 135003866 0 3775
4 TraesCS5D01G079100 chr4D 94.744 2359 120 4 1 2357 241143245 241140889 0 3666
5 TraesCS5D01G079100 chr7D 96.976 1885 55 2 1 1883 579015578 579017462 0 3164
6 TraesCS5D01G079100 chr6B 94.695 2036 92 5 1 2027 53079007 53081035 0 3147
7 TraesCS5D01G079100 chr7A 96.575 1898 64 1 1 1897 563531481 563529584 0 3144
8 TraesCS5D01G079100 chr7A 97.189 498 14 0 1860 2357 4954288 4954785 0 843
9 TraesCS5D01G079100 chr3A 96.419 1899 66 2 1 1897 191855549 191857447 0 3129
10 TraesCS5D01G079100 chr1A 96.368 1900 66 3 1 1897 278506346 278508245 0 3123
11 TraesCS5D01G079100 chr1D 96.343 793 29 0 1565 2357 185763599 185764391 0 1304
12 TraesCS5D01G079100 chr5B 94.869 799 41 0 1559 2357 87747596 87748394 0 1249
13 TraesCS5D01G079100 chr3B 97.390 498 13 0 1860 2357 92194034 92194531 0 848
14 TraesCS5D01G079100 chr6A 97.189 498 14 0 1860 2357 289123072 289123569 0 843


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 TraesCS5D01G079100 chr5D 79865255 79867611 2356 False 4353 4353 100.000 1 2357 1 chr5D.!!$F1 2356
1 TraesCS5D01G079100 chr5D 197837543 197839898 2355 True 3469 3469 93.260 3 2357 1 chr5D.!!$R1 2354
2 TraesCS5D01G079100 chr4D 483696359 483698716 2357 False 3855 3855 96.185 1 2357 1 chr4D.!!$F1 2356
3 TraesCS5D01G079100 chr4D 135003866 135006221 2355 True 3775 3775 95.589 1 2357 1 chr4D.!!$R1 2356
4 TraesCS5D01G079100 chr4D 241140889 241143245 2356 True 3666 3666 94.744 1 2357 1 chr4D.!!$R2 2356
5 TraesCS5D01G079100 chr7D 579015578 579017462 1884 False 3164 3164 96.976 1 1883 1 chr7D.!!$F1 1882
6 TraesCS5D01G079100 chr6B 53079007 53081035 2028 False 3147 3147 94.695 1 2027 1 chr6B.!!$F1 2026
7 TraesCS5D01G079100 chr7A 563529584 563531481 1897 True 3144 3144 96.575 1 1897 1 chr7A.!!$R1 1896
8 TraesCS5D01G079100 chr3A 191855549 191857447 1898 False 3129 3129 96.419 1 1897 1 chr3A.!!$F1 1896
9 TraesCS5D01G079100 chr1A 278506346 278508245 1899 False 3123 3123 96.368 1 1897 1 chr1A.!!$F1 1896
10 TraesCS5D01G079100 chr1D 185763599 185764391 792 False 1304 1304 96.343 1565 2357 1 chr1D.!!$F1 792
11 TraesCS5D01G079100 chr5B 87747596 87748394 798 False 1249 1249 94.869 1559 2357 1 chr5B.!!$F1 798

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
177 178 0.108567 GTCTTCTCTCTTGGTCGGGC 60.109 60.0 0.0 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1978 1999 0.537188 ATACCGACAACAGCTCCCAG 59.463 55.0 0.0 0.0 0.0 4.45 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
66 67 3.760684 GGTTTAGAAGAGTCACGGTCCTA 59.239 47.826 0.00 0.00 0.00 2.94
101 102 4.560919 GCTTTTTCCCTTCTCGACTAGACA 60.561 45.833 0.00 0.00 32.51 3.41
134 135 1.361204 TTCCATTCAGGCAGGTGAGA 58.639 50.000 0.00 0.00 37.29 3.27
148 149 2.342648 GAGAAAGGGTGGCGTCGT 59.657 61.111 0.00 0.00 0.00 4.34
177 178 0.108567 GTCTTCTCTCTTGGTCGGGC 60.109 60.000 0.00 0.00 0.00 6.13
316 319 5.906113 TCTTGATAGAGTCTTTCTCGCTT 57.094 39.130 11.28 0.00 46.86 4.68
409 412 4.712829 TCCGATCAACAACTTGGAGGTATA 59.287 41.667 0.00 0.00 0.00 1.47
439 442 3.429410 GGCTTAAGGCATTGGTTTGCTAG 60.429 47.826 23.15 0.00 44.01 3.42
611 622 1.604604 CGCCCCTTTCTTGTTCTTGA 58.395 50.000 0.00 0.00 0.00 3.02
725 736 7.237263 AGGTAGGATGCTCATAGATGAAGAAAT 59.763 37.037 0.00 0.00 36.18 2.17
740 751 6.560253 TGAAGAAATGAGACTTTAGGCAAC 57.440 37.500 0.00 0.00 0.00 4.17
836 847 2.368439 AGCGCATCCATTTTCTTGCTA 58.632 42.857 11.47 0.00 32.97 3.49
915 926 2.363788 TCCTTCAGTGGTTCGAATCG 57.636 50.000 0.00 0.00 0.00 3.34
1060 1076 5.305585 TCAGTCCGCTAGTTTCTTTGATTT 58.694 37.500 0.00 0.00 0.00 2.17
1146 1162 1.486726 GAATGTGGTTCCGATCCCTCT 59.513 52.381 0.00 0.00 0.00 3.69
1243 1261 3.111484 ACCTTTTCTTTTCCTTGGGCAA 58.889 40.909 0.00 0.00 0.00 4.52
1294 1312 1.753073 CTTGGTCCATGATGGCCTTTC 59.247 52.381 20.41 1.19 37.47 2.62
1441 1459 4.655762 TGATTCGTCATGGTAGAGAAGG 57.344 45.455 0.00 0.00 0.00 3.46
1525 1545 0.857287 GTGTTTCGACGAGAACACCC 59.143 55.000 27.34 15.11 38.83 4.61
1570 1591 5.574443 ACGTAAGATAGCAAAAGTACGGTTC 59.426 40.000 12.02 0.00 38.82 3.62
1606 1627 6.604171 TGATATATTTGCTCACATTCCAGGT 58.396 36.000 0.00 0.00 0.00 4.00
1740 1761 5.896073 ATTCTGGATCGTAGAAAGGGAAT 57.104 39.130 13.08 0.00 43.58 3.01
1747 1768 8.123639 TGGATCGTAGAAAGGGAATATCTAAG 57.876 38.462 0.00 0.00 43.58 2.18
1756 1777 5.407407 AGGGAATATCTAAGTATGGTGCG 57.593 43.478 0.00 0.00 0.00 5.34
1854 1875 5.013599 CAGCTAGCTCCCTTTCCCTTATTAT 59.986 44.000 16.15 0.00 0.00 1.28
1918 1939 9.262358 CTTGACTTACTTAACTTACTGCTTTCT 57.738 33.333 0.00 0.00 0.00 2.52
1962 1983 3.505386 AGGTATACCTGCCTGATGAGAG 58.495 50.000 24.01 0.00 46.55 3.20
2092 2113 3.532641 ATTTCCCTTGCCAGACTTTCT 57.467 42.857 0.00 0.00 0.00 2.52
2150 2171 2.644798 ACCTAGCAACCTTCATTCCTGT 59.355 45.455 0.00 0.00 0.00 4.00
2209 2230 1.447489 CCGAGCAGCTCTTCCACTG 60.447 63.158 20.39 2.65 36.96 3.66
2283 2304 4.534500 TCCCAGTAAGCATTTCCTCTGTTA 59.466 41.667 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 4.691175 AGAAGTCCATTCTCGTCATGATG 58.309 43.478 8.74 8.74 45.50 3.07
66 67 1.229177 AAAAAGCCTGGCGGGGAAT 60.229 52.632 15.62 0.00 35.12 3.01
101 102 6.492772 GCCTGAATGGAATGAATATCTCCTTT 59.507 38.462 0.00 0.00 38.35 3.11
134 135 1.597027 CAAGACGACGCCACCCTTT 60.597 57.895 0.00 0.00 0.00 3.11
148 149 3.534357 AGAGAGAAGACAGGGTCAAGA 57.466 47.619 0.00 0.00 34.60 3.02
177 178 4.836825 TGAATGAGAAACTTAGCCTCCAG 58.163 43.478 0.00 0.00 0.00 3.86
297 300 7.860918 TTACTAAGCGAGAAAGACTCTATCA 57.139 36.000 0.00 0.00 42.92 2.15
316 319 2.789092 GCGCGCGTACTCTTCTTTACTA 60.789 50.000 32.35 0.00 0.00 1.82
348 351 0.321653 GTTGCCCGAAGATCCACTGT 60.322 55.000 0.00 0.00 0.00 3.55
439 442 8.803201 TGATACAATCTTCTTGTATGTCGATC 57.197 34.615 13.67 3.32 43.39 3.69
611 622 2.885266 TCTTCTTCGCTATAGACGCCAT 59.115 45.455 3.21 0.00 0.00 4.40
725 736 3.391296 AGAACCAGTTGCCTAAAGTCTCA 59.609 43.478 0.00 0.00 0.00 3.27
740 751 0.901124 AGCTGAGCTACCAGAACCAG 59.099 55.000 4.49 0.00 36.99 4.00
952 967 3.130160 CTTGCGGCTCTCCTTGCC 61.130 66.667 0.00 0.00 46.42 4.52
967 982 1.470890 CTTCGTTCTCTCGCTCTCCTT 59.529 52.381 0.00 0.00 0.00 3.36
1060 1076 1.487142 TGGAAAAGGAACACCGAGTGA 59.513 47.619 10.46 0.00 36.96 3.41
1221 1239 3.917300 TGCCCAAGGAAAAGAAAAGGTA 58.083 40.909 0.00 0.00 0.00 3.08
1294 1312 8.375608 AGAGATCCAATCGTCAAAATCAATAG 57.624 34.615 0.00 0.00 0.00 1.73
1441 1459 2.178273 GGTCCGTGCGCCATTTTC 59.822 61.111 4.18 0.00 0.00 2.29
1536 1556 5.171147 TGCTATCTTACGTAGAGCTGAAC 57.829 43.478 16.68 0.00 36.02 3.18
1570 1591 6.839033 AGCAAATATATCATGTCGATTGCTG 58.161 36.000 13.11 0.00 40.22 4.41
1606 1627 3.904800 TCCTGCGAATTATGACCTTCA 57.095 42.857 0.00 0.00 0.00 3.02
1699 1720 5.649395 CAGAATTCCTAGCAAATCCTTGACA 59.351 40.000 0.65 0.00 34.14 3.58
1740 1761 5.221382 GGTCTTTCCGCACCATACTTAGATA 60.221 44.000 0.00 0.00 32.33 1.98
1747 1768 2.973694 TAGGTCTTTCCGCACCATAC 57.026 50.000 0.00 0.00 41.99 2.39
1756 1777 7.067008 TCCATTCATTTCGATTTAGGTCTTTCC 59.933 37.037 0.00 0.00 0.00 3.13
1978 1999 0.537188 ATACCGACAACAGCTCCCAG 59.463 55.000 0.00 0.00 0.00 4.45
1988 2009 3.080300 AGAAATTGCCCATACCGACAA 57.920 42.857 0.00 0.00 0.00 3.18
2150 2171 4.588528 AGTAGCAAAGGCAAGATGGAAAAA 59.411 37.500 0.00 0.00 44.61 1.94
2209 2230 9.521503 GGAAGAGGTTTGATTGCTAATAAAATC 57.478 33.333 0.00 0.00 34.11 2.17
2283 2304 1.143073 GTCAGAGGTGGGAAACAAGGT 59.857 52.381 0.00 0.00 0.00 3.50


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

AutoCloner maintained by Alex Coulton.