Multiple sequence alignment - TraesCS1D01G000700

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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 TraesCS1D01G000700 chr1D 100.000 2741 0 0 1 2741 211267 208527 0.000000e+00 5062.0
1 TraesCS1D01G000700 chr1D 93.373 166 11 0 2576 2741 122222 122057 2.110000e-61 246.0
2 TraesCS1D01G000700 chr1D 86.905 84 7 2 2527 2607 122313 122231 1.050000e-14 91.6
3 TraesCS1D01G000700 chr1A 93.314 1705 89 11 381 2075 4052548 4054237 0.000000e+00 2494.0
4 TraesCS1D01G000700 chr1A 86.636 651 43 17 2134 2741 4054234 4054883 0.000000e+00 680.0
5 TraesCS1D01G000700 chr1A 73.184 537 106 20 1211 1738 4049931 4050438 2.830000e-35 159.0
6 TraesCS1D01G000700 chr1B 92.221 1337 73 18 587 1909 5175116 5176435 0.000000e+00 1864.0
7 TraesCS1D01G000700 chr1B 85.082 858 52 20 1907 2741 5176692 5177496 0.000000e+00 806.0
8 TraesCS1D01G000700 chr1B 84.884 258 37 1 342 599 5174843 5175098 2.710000e-65 259.0
9 TraesCS1D01G000700 chr1B 97.222 36 1 0 2068 2103 112354572 112354607 8.200000e-06 62.1
10 TraesCS1D01G000700 chr7B 91.979 187 13 2 17 202 643480952 643481137 7.530000e-66 261.0
11 TraesCS1D01G000700 chr7B 97.222 36 1 0 2068 2103 485475450 485475415 8.200000e-06 62.1
12 TraesCS1D01G000700 chr7D 90.050 201 18 2 3 202 15771447 15771646 2.710000e-65 259.0
13 TraesCS1D01G000700 chr7D 89.340 197 16 4 4 199 400193098 400192906 2.730000e-60 243.0
14 TraesCS1D01G000700 chr4B 89.055 201 20 2 3 202 446767883 446767684 5.860000e-62 248.0
15 TraesCS1D01G000700 chr2B 87.273 220 21 6 1 218 702720795 702721009 7.580000e-61 244.0
16 TraesCS1D01G000700 chr2B 88.060 201 20 4 3 202 199405412 199405215 4.560000e-58 235.0
17 TraesCS1D01G000700 chr2A 88.557 201 20 3 3 202 762186985 762186787 9.810000e-60 241.0
18 TraesCS1D01G000700 chr6D 88.060 201 21 3 3 202 343124504 343124702 4.560000e-58 235.0
19 TraesCS1D01G000700 chr4D 88.060 201 21 3 3 202 447335185 447334987 4.560000e-58 235.0
20 TraesCS1D01G000700 chr6B 82.051 78 8 3 2067 2138 114836286 114836363 8.200000e-06 62.1
21 TraesCS1D01G000700 chr6B 97.222 36 1 0 2068 2103 267798658 267798623 8.200000e-06 62.1
22 TraesCS1D01G000700 chr2D 97.222 36 1 0 2068 2103 549418167 549418202 8.200000e-06 62.1
23 TraesCS1D01G000700 chrUn 92.857 42 2 1 2060 2101 110290435 110290475 2.950000e-05 60.2
24 TraesCS1D01G000700 chrUn 92.857 42 2 1 2060 2101 187683144 187683184 2.950000e-05 60.2
25 TraesCS1D01G000700 chrUn 92.857 42 2 1 2060 2101 307658760 307658720 2.950000e-05 60.2


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 TraesCS1D01G000700 chr1D 208527 211267 2740 True 5062.000000 5062 100.000000 1 2741 1 chr1D.!!$R1 2740
1 TraesCS1D01G000700 chr1A 4049931 4054883 4952 False 1111.000000 2494 84.378000 381 2741 3 chr1A.!!$F1 2360
2 TraesCS1D01G000700 chr1B 5174843 5177496 2653 False 976.333333 1864 87.395667 342 2741 3 chr1B.!!$F2 2399


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
322 323 0.322366 TGATGAAACGCCTGGATGCA 60.322 50.0 0.00 0.00 0.0 3.96 F
1329 3607 0.322456 TGGTAATGTGGGAGCAGTGC 60.322 55.0 7.13 7.13 0.0 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1480 3758 0.909610 TGGCTAGAACCCAGACCCTG 60.910 60.000 0.00 0.00 0.00 4.45 R
2304 4882 1.068055 GCAACCAATCAGAGTGGCTTG 60.068 52.381 17.11 18.64 40.02 4.01 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)



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AutoCloner maintained by Alex Coulton.