Multiple sequence alignment - TraesCS6D01G260400

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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 TraesCS6D01G260400 chr6D 100.000 2348 0 0 1 2348 367879792 367877445 0.000000e+00 4337.0
1 TraesCS6D01G260400 chr6D 77.387 398 68 16 1956 2348 461385714 461386094 1.410000e-52 217.0
2 TraesCS6D01G260400 chr6D 78.512 242 43 6 1957 2194 49224540 49224304 1.450000e-32 150.0
3 TraesCS6D01G260400 chr5D 97.825 1701 35 2 1 1700 564670365 564672064 0.000000e+00 2935.0
4 TraesCS6D01G260400 chr5D 75.949 395 70 18 1957 2348 515796703 515797075 1.850000e-41 180.0
5 TraesCS6D01G260400 chr6A 95.123 1702 74 5 1 1701 183314311 183312618 0.000000e+00 2675.0
6 TraesCS6D01G260400 chr6A 94.765 1700 87 2 1 1700 183929683 183931380 0.000000e+00 2645.0
7 TraesCS6D01G260400 chr6A 90.168 1190 91 17 521 1700 22262078 22263251 0.000000e+00 1526.0
8 TraesCS6D01G260400 chr6A 93.354 632 42 0 1699 2330 508335635 508335004 0.000000e+00 935.0
9 TraesCS6D01G260400 chr7A 94.451 1676 90 3 27 1701 721643425 721641752 0.000000e+00 2577.0
10 TraesCS6D01G260400 chr7A 91.164 1709 136 10 3 1700 717769110 717767406 0.000000e+00 2305.0
11 TraesCS6D01G260400 chr1B 91.409 1711 125 18 3 1700 145446336 145444635 0.000000e+00 2326.0
12 TraesCS6D01G260400 chr5A 91.320 1705 136 11 1 1700 31278706 31280403 0.000000e+00 2318.0
13 TraesCS6D01G260400 chr5A 78.553 387 55 16 1963 2348 120744838 120744479 1.810000e-56 230.0
14 TraesCS6D01G260400 chr2B 83.652 1621 238 22 90 1700 748211381 748212984 0.000000e+00 1500.0
15 TraesCS6D01G260400 chr2B 79.149 235 42 5 1955 2187 489364336 489364107 3.120000e-34 156.0
16 TraesCS6D01G260400 chr6B 85.957 648 75 7 1699 2346 554121580 554122211 0.000000e+00 678.0
17 TraesCS6D01G260400 chr3A 89.298 299 27 4 1407 1700 621497549 621497847 1.020000e-98 370.0
18 TraesCS6D01G260400 chr3A 76.994 326 63 10 1986 2310 124217658 124217972 2.400000e-40 176.0
19 TraesCS6D01G260400 chr2D 78.740 381 60 11 1955 2332 45690439 45690801 3.900000e-58 235.0
20 TraesCS6D01G260400 chr2D 76.864 389 59 19 1963 2346 72341496 72341858 8.560000e-45 191.0
21 TraesCS6D01G260400 chr2D 85.263 95 8 4 2254 2348 640297244 640297156 2.480000e-15 93.5
22 TraesCS6D01G260400 chr7D 77.250 400 70 13 1951 2346 102584898 102584516 5.080000e-52 215.0
23 TraesCS6D01G260400 chr3D 77.157 394 72 11 1956 2348 275908882 275908506 1.830000e-51 213.0
24 TraesCS6D01G260400 chr4D 77.099 393 69 11 1955 2346 129756127 129755755 8.500000e-50 207.0
25 TraesCS6D01G260400 chr2A 75.819 397 73 18 1955 2347 502630248 502630625 1.850000e-41 180.0
26 TraesCS6D01G260400 chr7B 78.397 287 45 10 2058 2343 323835880 323836150 1.120000e-38 171.0
27 TraesCS6D01G260400 chr3B 84.615 91 8 3 2258 2348 685848524 685848608 4.160000e-13 86.1
28 TraesCS6D01G260400 chr4A 76.761 142 25 6 2205 2345 550079958 550080092 3.240000e-09 73.1


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 TraesCS6D01G260400 chr6D 367877445 367879792 2347 True 4337 4337 100.000 1 2348 1 chr6D.!!$R2 2347
1 TraesCS6D01G260400 chr5D 564670365 564672064 1699 False 2935 2935 97.825 1 1700 1 chr5D.!!$F2 1699
2 TraesCS6D01G260400 chr6A 183312618 183314311 1693 True 2675 2675 95.123 1 1701 1 chr6A.!!$R1 1700
3 TraesCS6D01G260400 chr6A 183929683 183931380 1697 False 2645 2645 94.765 1 1700 1 chr6A.!!$F2 1699
4 TraesCS6D01G260400 chr6A 22262078 22263251 1173 False 1526 1526 90.168 521 1700 1 chr6A.!!$F1 1179
5 TraesCS6D01G260400 chr6A 508335004 508335635 631 True 935 935 93.354 1699 2330 1 chr6A.!!$R2 631
6 TraesCS6D01G260400 chr7A 721641752 721643425 1673 True 2577 2577 94.451 27 1701 1 chr7A.!!$R2 1674
7 TraesCS6D01G260400 chr7A 717767406 717769110 1704 True 2305 2305 91.164 3 1700 1 chr7A.!!$R1 1697
8 TraesCS6D01G260400 chr1B 145444635 145446336 1701 True 2326 2326 91.409 3 1700 1 chr1B.!!$R1 1697
9 TraesCS6D01G260400 chr5A 31278706 31280403 1697 False 2318 2318 91.320 1 1700 1 chr5A.!!$F1 1699
10 TraesCS6D01G260400 chr2B 748211381 748212984 1603 False 1500 1500 83.652 90 1700 1 chr2B.!!$F1 1610
11 TraesCS6D01G260400 chr6B 554121580 554122211 631 False 678 678 85.957 1699 2346 1 chr6B.!!$F1 647

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
272 273 1.143889 CTCCAAGGATAAAGGAGGCCC 59.856 57.143 0.0 0.0 44.1 5.8 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2271 2295 0.388134 CCACCGAACGACCACTACTG 60.388 60.0 0.0 0.0 0.0 2.74 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
160 161 7.067008 TGTTTCTTCTCTCGAAAAAGGTGATTT 59.933 33.333 0.00 0.00 32.71 2.17
169 170 6.270064 TCGAAAAAGGTGATTTGGAAACTTC 58.730 36.000 0.00 0.00 0.00 3.01
272 273 1.143889 CTCCAAGGATAAAGGAGGCCC 59.856 57.143 0.00 0.00 44.10 5.80
349 350 3.913855 TTGGAAACACAGCAAGGGA 57.086 47.368 0.00 0.00 42.67 4.20
460 462 8.907885 GGAAGGCTATTATGAAAGTCAAAGAAT 58.092 33.333 0.00 0.00 0.00 2.40
1006 1015 0.394352 GGTTGCTAGGGTCATGTGGG 60.394 60.000 0.00 0.00 0.00 4.61
1251 1261 2.750657 GGCAGGTCTGATGAGGGGG 61.751 68.421 1.65 0.00 0.00 5.40
1405 1419 1.338105 CGTTTCCTCCTGAGTCATGCA 60.338 52.381 0.00 0.00 0.00 3.96
1416 1431 4.142665 CCTGAGTCATGCATTTCTCTGTTG 60.143 45.833 21.11 12.43 0.00 3.33
1510 1532 4.202111 GGTCAGCCTGTTAATTTTGTGTGT 60.202 41.667 0.00 0.00 0.00 3.72
1587 1609 1.881324 CGGGTGTTTATCGTGGGTTTT 59.119 47.619 0.00 0.00 0.00 2.43
1752 1776 1.488812 AGTTCCACTGTAGCCACACAA 59.511 47.619 0.00 0.00 0.00 3.33
1797 1821 0.670162 ACTGCTTGCAACGCTCAAAT 59.330 45.000 17.72 1.85 0.00 2.32
1943 1967 4.275689 TGCTGAAACAGGGCATAAATATCG 59.724 41.667 0.00 0.00 31.21 2.92
1958 1982 9.669353 GCATAAATATCGATCAACACAATCTTT 57.331 29.630 0.00 0.00 0.00 2.52
1973 1997 7.312899 ACACAATCTTTTTCGAGTTTGTCTTT 58.687 30.769 0.00 0.00 37.43 2.52
1983 2007 3.550233 CGAGTTTGTCTTTCGGACTCTGA 60.550 47.826 0.00 0.00 44.74 3.27
1984 2008 4.369182 GAGTTTGTCTTTCGGACTCTGAA 58.631 43.478 0.00 0.00 44.74 3.02
1999 2023 1.618837 TCTGAACCTCCTTGAGTTCGG 59.381 52.381 5.54 5.54 32.62 4.30
2036 2060 1.658717 CGAAGCTCCGGCGTAGATG 60.659 63.158 2.79 0.00 44.37 2.90
2126 2150 7.497249 GTGCTTCAGATCTATGTAAGGTTCAAT 59.503 37.037 0.00 0.00 0.00 2.57
2297 2321 2.164219 GTGGTCGTTCGGTGGTCTTATA 59.836 50.000 0.00 0.00 0.00 0.98
2304 2328 5.125900 TCGTTCGGTGGTCTTATAAATCTCA 59.874 40.000 0.00 0.00 0.00 3.27
2307 2331 7.516785 CGTTCGGTGGTCTTATAAATCTCAATG 60.517 40.741 0.00 0.00 0.00 2.82
2347 2371 8.810652 TTATGTTTGAAATGCTTTGTACTTCC 57.189 30.769 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
160 161 3.134574 ACGGTGCTTATGAAGTTTCCA 57.865 42.857 0.00 0.00 0.00 3.53
169 170 5.464965 AAGAATCGTTTACGGTGCTTATG 57.535 39.130 6.98 0.00 45.89 1.90
272 273 1.228124 TGCAAGTCTTTCACCCCCG 60.228 57.895 0.00 0.00 0.00 5.73
349 350 1.167851 CGAACAATGTCCTGCCACAT 58.832 50.000 0.00 0.00 38.74 3.21
1006 1015 1.203052 CAACATGCATCCAACAGTCCC 59.797 52.381 0.00 0.00 0.00 4.46
1251 1261 2.746362 CTCCATTGCTTCACAGTCTTCC 59.254 50.000 0.00 0.00 0.00 3.46
1405 1419 7.253422 CAAAAGATAATCCGCAACAGAGAAAT 58.747 34.615 0.00 0.00 0.00 2.17
1416 1431 4.438744 CCAGAACACCAAAAGATAATCCGC 60.439 45.833 0.00 0.00 0.00 5.54
1510 1532 4.525100 TGACACCAACATAGCTACTACACA 59.475 41.667 0.00 0.00 0.00 3.72
1587 1609 1.480954 GCGAGTTCAAGTATCCCTGGA 59.519 52.381 0.00 0.00 0.00 3.86
1752 1776 1.338973 TCCTACAGTTTCGCGTCTGTT 59.661 47.619 27.28 17.06 43.39 3.16
1920 1944 4.275689 CGATATTTATGCCCTGTTTCAGCA 59.724 41.667 0.00 0.00 41.50 4.41
1943 1967 7.432252 ACAAACTCGAAAAAGATTGTGTTGATC 59.568 33.333 0.00 0.00 39.78 2.92
1973 1997 1.203013 TCAAGGAGGTTCAGAGTCCGA 60.203 52.381 0.00 0.00 35.33 4.55
1983 2007 1.375326 GGCCGAACTCAAGGAGGTT 59.625 57.895 0.00 0.00 33.35 3.50
1984 2008 2.943978 CGGCCGAACTCAAGGAGGT 61.944 63.158 24.07 0.00 33.35 3.85
2020 2044 2.107141 GCATCTACGCCGGAGCTT 59.893 61.111 5.05 0.00 36.60 3.74
2126 2150 3.891586 GAAGCCGCAGTCGTCGTCA 62.892 63.158 0.00 0.00 0.00 4.35
2206 2230 1.156736 CGAAGCCAATTTGACCTCGT 58.843 50.000 0.00 0.00 0.00 4.18
2208 2232 1.534729 ACCGAAGCCAATTTGACCTC 58.465 50.000 0.00 0.00 0.00 3.85
2238 2262 3.106407 GCTGACGTGTCGCTGTCC 61.106 66.667 0.00 0.00 34.18 4.02
2271 2295 0.388134 CCACCGAACGACCACTACTG 60.388 60.000 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.