Multiple sequence alignment - TraesCS4D01G315700

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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 TraesCS4D01G315700 chr4D 100.000 2813 0 0 1 2813 481172131 481174943 0.000000e+00 5195.0
1 TraesCS4D01G315700 chr4B 86.708 978 74 18 1784 2734 609504743 609505691 0.000000e+00 1035.0
2 TraesCS4D01G315700 chr4B 86.397 963 76 31 1 943 609502383 609503310 0.000000e+00 1002.0
3 TraesCS4D01G315700 chr4B 84.158 202 27 3 981 1177 609503319 609503520 1.030000e-44 191.0
4 TraesCS4D01G315700 chr4B 93.333 75 5 0 2739 2813 609505775 609505849 8.240000e-21 111.0
5 TraesCS4D01G315700 chr5A 89.157 415 25 4 627 1037 662334121 662333723 1.500000e-137 499.0
6 TraesCS4D01G315700 chr5A 88.272 324 28 5 319 632 662334515 662334192 2.050000e-101 379.0
7 TraesCS4D01G315700 chr5A 90.941 287 12 7 1 280 662334796 662334517 9.510000e-100 374.0
8 TraesCS4D01G315700 chr5A 91.139 237 15 2 2455 2686 662332261 662332026 1.630000e-82 316.0
9 TraesCS4D01G315700 chr5A 85.526 152 10 5 1088 1227 662333713 662333562 6.280000e-32 148.0
10 TraesCS4D01G315700 chr5A 98.649 74 1 0 1251 1324 662333487 662333414 6.320000e-27 132.0
11 TraesCS4D01G315700 chr5A 91.304 92 8 0 2722 2813 662332032 662331941 2.940000e-25 126.0
12 TraesCS4D01G315700 chr5A 87.838 74 6 1 2255 2325 662332403 662332330 1.800000e-12 84.2
13 TraesCS4D01G315700 chr2D 85.024 414 50 3 1387 1788 37246004 37246417 7.250000e-111 411.0
14 TraesCS4D01G315700 chr2A 86.686 338 45 0 1387 1724 42026843 42026506 2.650000e-100 375.0
15 TraesCS4D01G315700 chr2A 72.770 426 78 27 1223 1633 131711568 131711970 2.960000e-20 110.0
16 TraesCS4D01G315700 chr2A 90.476 42 4 0 2225 2266 712054193 712054152 3.910000e-04 56.5
17 TraesCS4D01G315700 chr2B 80.000 410 72 6 1387 1788 64807580 64807173 7.620000e-76 294.0
18 TraesCS4D01G315700 chr2B 92.424 132 10 0 1224 1355 64863939 64863808 3.700000e-44 189.0
19 TraesCS4D01G315700 chr1A 77.426 505 75 26 1226 1713 11530587 11531069 5.970000e-67 265.0
20 TraesCS4D01G315700 chr1A 81.319 91 16 1 2171 2261 419033839 419033928 3.890000e-09 73.1
21 TraesCS4D01G315700 chr1A 93.478 46 2 1 2217 2262 331272235 331272191 1.810000e-07 67.6
22 TraesCS4D01G315700 chr4A 80.347 173 31 2 1224 1394 742751305 742751476 8.180000e-26 128.0
23 TraesCS4D01G315700 chr4A 79.769 173 32 2 1224 1394 743383886 743384057 3.810000e-24 122.0
24 TraesCS4D01G315700 chr7D 84.127 126 20 0 1224 1349 2052555 2052680 3.810000e-24 122.0
25 TraesCS4D01G315700 chrUn 78.824 170 36 0 1225 1394 265076215 265076046 6.370000e-22 115.0
26 TraesCS4D01G315700 chr1D 82.418 91 15 1 2171 2261 325484579 325484490 8.350000e-11 78.7
27 TraesCS4D01G315700 chr1D 90.385 52 5 0 2209 2260 53260562 53260511 5.030000e-08 69.4
28 TraesCS4D01G315700 chr3B 93.750 48 3 0 2190 2237 756662939 756662986 3.890000e-09 73.1
29 TraesCS4D01G315700 chr1B 81.319 91 16 1 2171 2261 437599791 437599702 3.890000e-09 73.1
30 TraesCS4D01G315700 chr1B 93.478 46 2 1 2217 2262 355408309 355408265 1.810000e-07 67.6
31 TraesCS4D01G315700 chr3D 81.481 81 12 3 2172 2251 454901709 454901787 2.340000e-06 63.9


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 TraesCS4D01G315700 chr4D 481172131 481174943 2812 False 5195.000 5195 100.00000 1 2813 1 chr4D.!!$F1 2812
1 TraesCS4D01G315700 chr4B 609502383 609505849 3466 False 584.750 1035 87.64900 1 2813 4 chr4B.!!$F1 2812
2 TraesCS4D01G315700 chr5A 662331941 662334796 2855 True 257.275 499 90.35325 1 2813 8 chr5A.!!$R1 2812


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
739 842 0.179084 TGCATACGGCTAGGCTCAAC 60.179 55.0 15.11 0.77 45.15 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2431 3486 0.039618 GAATGGCAGTGGGGAAGGAA 59.96 55.0 0.0 0.0 0.0 3.36 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.