Multiple sequence alignment - TraesCS5D01G221500

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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 TraesCS5D01G221500 chr5D 100.000 2132 0 0 1 2132 329164368 329162237 0.000000e+00 3938
1 TraesCS5D01G221500 chr5D 98.102 2108 35 5 1 2104 560874662 560872556 0.000000e+00 3666
2 TraesCS5D01G221500 chr5D 97.286 2137 50 8 1 2132 6199088 6201221 0.000000e+00 3618
3 TraesCS5D01G221500 chr1D 97.520 2137 47 6 1 2132 254500192 254498057 0.000000e+00 3648
4 TraesCS5D01G221500 chr1D 92.364 2056 104 34 87 2132 244481977 244483989 0.000000e+00 2878
5 TraesCS5D01G221500 chr1A 96.393 2135 68 8 1 2132 168448379 168450507 0.000000e+00 3507
6 TraesCS5D01G221500 chr4D 96.253 2135 72 8 1 2131 19918686 19916556 0.000000e+00 3493
7 TraesCS5D01G221500 chr7A 94.525 2137 108 9 1 2132 352191832 352193964 0.000000e+00 3290
8 TraesCS5D01G221500 chr6B 96.479 1420 46 4 715 2132 22427421 22426004 0.000000e+00 2342
9 TraesCS5D01G221500 chr3B 97.454 1296 26 7 1 1291 201516873 201515580 0.000000e+00 2204
10 TraesCS5D01G221500 chr3B 94.970 676 31 3 1 675 524776891 524777564 0.000000e+00 1057
11 TraesCS5D01G221500 chr3D 97.832 1061 23 0 1072 2132 21905747 21904687 0.000000e+00 1832
12 TraesCS5D01G221500 chr7B 94.993 679 30 4 1 676 102631437 102632114 0.000000e+00 1062
13 TraesCS5D01G221500 chr2A 99.048 105 1 0 692 796 588453534 588453430 2.790000e-44 189


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 TraesCS5D01G221500 chr5D 329162237 329164368 2131 True 3938 3938 100.000 1 2132 1 chr5D.!!$R1 2131
1 TraesCS5D01G221500 chr5D 560872556 560874662 2106 True 3666 3666 98.102 1 2104 1 chr5D.!!$R2 2103
2 TraesCS5D01G221500 chr5D 6199088 6201221 2133 False 3618 3618 97.286 1 2132 1 chr5D.!!$F1 2131
3 TraesCS5D01G221500 chr1D 254498057 254500192 2135 True 3648 3648 97.520 1 2132 1 chr1D.!!$R1 2131
4 TraesCS5D01G221500 chr1D 244481977 244483989 2012 False 2878 2878 92.364 87 2132 1 chr1D.!!$F1 2045
5 TraesCS5D01G221500 chr1A 168448379 168450507 2128 False 3507 3507 96.393 1 2132 1 chr1A.!!$F1 2131
6 TraesCS5D01G221500 chr4D 19916556 19918686 2130 True 3493 3493 96.253 1 2131 1 chr4D.!!$R1 2130
7 TraesCS5D01G221500 chr7A 352191832 352193964 2132 False 3290 3290 94.525 1 2132 1 chr7A.!!$F1 2131
8 TraesCS5D01G221500 chr6B 22426004 22427421 1417 True 2342 2342 96.479 715 2132 1 chr6B.!!$R1 1417
9 TraesCS5D01G221500 chr3B 201515580 201516873 1293 True 2204 2204 97.454 1 1291 1 chr3B.!!$R1 1290
10 TraesCS5D01G221500 chr3B 524776891 524777564 673 False 1057 1057 94.970 1 675 1 chr3B.!!$F1 674
11 TraesCS5D01G221500 chr3D 21904687 21905747 1060 True 1832 1832 97.832 1072 2132 1 chr3D.!!$R1 1060
12 TraesCS5D01G221500 chr7B 102631437 102632114 677 False 1062 1062 94.993 1 676 1 chr7B.!!$F1 675

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
191 192 3.04639 GAGCCACGATGATTTAGTCTCG 58.954 50.0 0.0 0.0 35.23 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1638 1650 1.973812 GCAGCAGTCCAAGGGGTTC 60.974 63.158 0.0 0.0 34.93 3.62 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
146 147 6.586344 TGTTGAGATCCTATGAATCAGTTCC 58.414 40.000 0.00 0.00 33.26 3.62
191 192 3.046390 GAGCCACGATGATTTAGTCTCG 58.954 50.000 0.00 0.00 35.23 4.04
253 255 9.681692 CCGCTTGATAATCATTTATTGAATCAA 57.318 29.630 0.00 0.00 38.42 2.57
271 273 8.267620 TGAATCAATGTAATGACTCGACAAAT 57.732 30.769 0.00 0.00 28.40 2.32
272 274 8.390354 TGAATCAATGTAATGACTCGACAAATC 58.610 33.333 0.00 0.00 28.40 2.17
273 275 6.937457 ATCAATGTAATGACTCGACAAATCG 58.063 36.000 0.00 0.00 39.94 3.34
713 721 4.322101 CGTCCAGTAAAACGGAAGAATG 57.678 45.455 0.00 0.00 33.13 2.67
1245 1255 4.421948 TCTCGGAAGAAGATAGCGAAAAC 58.578 43.478 0.00 0.00 41.32 2.43
1267 1278 7.989416 AACAATTATCCCTAAAGTCGAAACA 57.011 32.000 0.00 0.00 0.00 2.83
1276 1287 6.548251 TCCCTAAAGTCGAAACAAAAAGGAAT 59.452 34.615 0.00 0.00 0.00 3.01
1496 1508 2.418746 CCTTGTAGTTGGATCTCCCACG 60.419 54.545 0.00 0.00 46.62 4.94
1606 1618 4.976116 CCAAATGTGTCCGAAAAAGAAGAC 59.024 41.667 0.00 0.00 0.00 3.01
1627 1639 2.821969 CCAAAGCAAAGGTAGCATGACT 59.178 45.455 0.00 0.00 0.00 3.41
1638 1650 4.929808 AGGTAGCATGACTAAAAGTGAACG 59.070 41.667 0.00 0.00 30.90 3.95
1657 1669 2.697147 GAACCCCTTGGACTGCTGCA 62.697 60.000 0.88 0.88 34.81 4.41
2023 2037 1.143684 GCCTGCTCTGAATAATCCCCA 59.856 52.381 0.00 0.00 0.00 4.96
2101 2115 9.959721 TTTAGACCAAGCTTCTGATAAACTAAT 57.040 29.630 0.00 0.00 0.00 1.73
2121 2135 8.514330 ACTAATATTTTCGGCTAAACCATTGA 57.486 30.769 0.00 0.00 39.03 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
191 192 2.628178 ACCCTTGCCTTTTGTTTAGCTC 59.372 45.455 0.00 0.00 0.00 4.09
271 273 7.574967 GCCCAAAAGACAAATATTTTCTCTCGA 60.575 37.037 0.00 0.00 26.55 4.04
272 274 6.528072 GCCCAAAAGACAAATATTTTCTCTCG 59.472 38.462 0.00 0.00 26.55 4.04
273 275 7.378181 TGCCCAAAAGACAAATATTTTCTCTC 58.622 34.615 0.00 0.00 26.55 3.20
275 277 7.961325 TTGCCCAAAAGACAAATATTTTCTC 57.039 32.000 0.00 0.00 26.55 2.87
276 278 7.772757 TGTTTGCCCAAAAGACAAATATTTTCT 59.227 29.630 0.00 2.96 35.87 2.52
277 279 7.924940 TGTTTGCCCAAAAGACAAATATTTTC 58.075 30.769 0.00 0.72 35.87 2.29
282 286 7.872113 ATTTTGTTTGCCCAAAAGACAAATA 57.128 28.000 9.15 0.00 44.80 1.40
284 288 6.385033 CAATTTTGTTTGCCCAAAAGACAAA 58.615 32.000 10.49 5.74 44.80 2.83
459 466 9.684448 TCTATCAAGATGATTCTAATTCGTCAC 57.316 33.333 0.00 0.00 38.26 3.67
803 812 6.796785 AACCCTTGAATTCAGAATAATGGG 57.203 37.500 19.22 19.22 37.08 4.00
1009 1018 2.280628 GGAGATGGCGACTAAAGTTGG 58.719 52.381 0.00 0.00 0.00 3.77
1245 1255 9.685828 TTTTTGTTTCGACTTTAGGGATAATTG 57.314 29.630 0.00 0.00 0.00 2.32
1267 1278 9.435688 GAAGCATTGGTTTATACATTCCTTTTT 57.564 29.630 2.14 0.00 0.00 1.94
1276 1287 8.995027 AATCTATGGAAGCATTGGTTTATACA 57.005 30.769 2.14 1.43 0.00 2.29
1606 1618 2.821969 AGTCATGCTACCTTTGCTTTGG 59.178 45.455 0.00 0.00 0.00 3.28
1627 1639 3.117963 TCCAAGGGGTTCGTTCACTTTTA 60.118 43.478 0.00 0.00 34.93 1.52
1638 1650 1.973812 GCAGCAGTCCAAGGGGTTC 60.974 63.158 0.00 0.00 34.93 3.62
2101 2115 8.514330 AGTTATCAATGGTTTAGCCGAAAATA 57.486 30.769 0.00 0.00 41.21 1.40


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

AutoCloner maintained by Alex Coulton.