Multiple sequence alignment - TraesCS6D01G200700

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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 TraesCS6D01G200700 chr6D 100.000 2351 0 0 1 2351 283186522 283188872 0 4342
1 TraesCS6D01G200700 chrUn 98.257 2352 38 3 1 2351 257943222 257945571 0 4113
2 TraesCS6D01G200700 chrUn 98.087 2352 37 6 1 2351 233526158 233523814 0 4087
3 TraesCS6D01G200700 chr4D 97.959 2352 46 2 1 2351 123688071 123690421 0 4076
4 TraesCS6D01G200700 chr2D 97.832 2352 48 3 1 2351 637309595 637307246 0 4058
5 TraesCS6D01G200700 chr2D 97.408 2353 52 7 1 2351 306151997 306154342 0 3999
6 TraesCS6D01G200700 chr4B 96.939 2352 63 7 1 2351 495538664 495536321 0 3936
7 TraesCS6D01G200700 chr7D 96.896 2352 68 5 1 2351 307088607 307090954 0 3934
8 TraesCS6D01G200700 chr6B 97.511 2290 50 5 63 2351 128890812 128888529 0 3906
9 TraesCS6D01G200700 chr2A 96.474 2354 78 5 1 2351 444302028 444304379 0 3882


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 TraesCS6D01G200700 chr6D 283186522 283188872 2350 False 4342 4342 100.000 1 2351 1 chr6D.!!$F1 2350
1 TraesCS6D01G200700 chrUn 257943222 257945571 2349 False 4113 4113 98.257 1 2351 1 chrUn.!!$F1 2350
2 TraesCS6D01G200700 chrUn 233523814 233526158 2344 True 4087 4087 98.087 1 2351 1 chrUn.!!$R1 2350
3 TraesCS6D01G200700 chr4D 123688071 123690421 2350 False 4076 4076 97.959 1 2351 1 chr4D.!!$F1 2350
4 TraesCS6D01G200700 chr2D 637307246 637309595 2349 True 4058 4058 97.832 1 2351 1 chr2D.!!$R1 2350
5 TraesCS6D01G200700 chr2D 306151997 306154342 2345 False 3999 3999 97.408 1 2351 1 chr2D.!!$F1 2350
6 TraesCS6D01G200700 chr4B 495536321 495538664 2343 True 3936 3936 96.939 1 2351 1 chr4B.!!$R1 2350
7 TraesCS6D01G200700 chr7D 307088607 307090954 2347 False 3934 3934 96.896 1 2351 1 chr7D.!!$F1 2350
8 TraesCS6D01G200700 chr6B 128888529 128890812 2283 True 3906 3906 97.511 63 2351 1 chr6B.!!$R1 2288
9 TraesCS6D01G200700 chr2A 444302028 444304379 2351 False 3882 3882 96.474 1 2351 1 chr2A.!!$F1 2350

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
176 177 2.290641 GCTGATCACTGTCGTTTTGGTT 59.709 45.455 0.0 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2133 2139 0.539986 GGTAAGCGGACCATGGAAGA 59.46 55.0 21.47 0.0 39.51 2.87 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
54 55 2.417379 GCTGTAAGTGCTCCGAATCAGA 60.417 50.000 0.00 0.00 35.30 3.27
159 160 5.882000 ACAAATGCAGTCTTGTATATGCTGA 59.118 36.000 9.24 0.00 39.42 4.26
176 177 2.290641 GCTGATCACTGTCGTTTTGGTT 59.709 45.455 0.00 0.00 0.00 3.67
419 421 7.446625 AGCTTCATAGTGACAAGTCATTTTCTT 59.553 33.333 6.15 0.00 42.18 2.52
482 485 4.084013 ACGATCGTTGGATTTCAAAGACAC 60.084 41.667 16.60 0.00 44.23 3.67
881 886 2.541466 CCGAAGATTCTAGGGGGCTAT 58.459 52.381 0.00 0.00 0.00 2.97
937 942 4.035208 GGGTACTCAAGATATTGCGTTTGG 59.965 45.833 0.45 0.00 0.00 3.28
1055 1060 4.083110 CGATGAACAAGTCAGAATTGCCTT 60.083 41.667 10.55 0.00 40.43 4.35
1116 1121 6.379386 TCAGCTTCGTTATCGATTAGGTATG 58.621 40.000 1.71 0.00 45.65 2.39
1234 1239 0.532573 GGGAGAACGAGCAGACATCA 59.467 55.000 0.00 0.00 0.00 3.07
1286 1291 5.297776 GTGGAATTCGTCATCAAGATGGATT 59.702 40.000 9.96 6.07 42.90 3.01
1369 1374 3.660865 TGAAAGAAGGCTACCGAAAGAC 58.339 45.455 0.00 0.00 0.00 3.01
1449 1454 5.482006 TGGTACTTGTCTGATCAATCACAG 58.518 41.667 0.00 0.00 35.72 3.66
1478 1483 9.796120 TTCATTAGTTCACTTGATTTTTCGTTT 57.204 25.926 0.00 0.00 0.00 3.60
1546 1551 2.673523 GCCACTCCATGTCTGGCT 59.326 61.111 15.13 0.00 42.80 4.75
1647 1652 3.049206 GCTTCACTATCGCTCATGACTC 58.951 50.000 0.00 0.00 0.00 3.36
1650 1655 2.683362 TCACTATCGCTCATGACTCGTT 59.317 45.455 11.09 6.87 0.00 3.85
1657 1662 2.987149 CGCTCATGACTCGTTGTAGTTT 59.013 45.455 0.00 0.00 0.00 2.66
1733 1738 5.441718 TCCTGAATGCCTCTTTCTTGTAT 57.558 39.130 0.00 0.00 0.00 2.29
1799 1804 1.447838 CCAACGCACGCTAGATGGT 60.448 57.895 0.00 0.00 0.00 3.55
1859 1864 3.075005 TAGCTTCCGCGCCCTTCT 61.075 61.111 0.00 0.00 42.32 2.85
2118 2124 3.942829 TGCTGTTTTCTATCAGTCCCAG 58.057 45.455 0.00 0.00 34.57 4.45
2133 2139 1.843376 CCAGGCGGATACTCCCCAT 60.843 63.158 0.00 0.00 44.96 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
159 160 4.712122 AAACAACCAAAACGACAGTGAT 57.288 36.364 0.00 0.0 0.00 3.06
358 360 3.524380 ACCCTGGGGATTACGAAATAACA 59.476 43.478 18.88 0.0 38.96 2.41
419 421 8.415950 TGGAAAATGAAAGAGCCAAAGTAATA 57.584 30.769 0.00 0.0 0.00 0.98
531 534 7.180408 TCAAGGAGTACTAAGAAAGGTGCTAAT 59.820 37.037 0.00 0.0 0.00 1.73
937 942 4.287766 ACAATCTACACCTCTCCAAACC 57.712 45.455 0.00 0.0 0.00 3.27
1055 1060 6.573289 CGGTCCAATTCCATCCATTTTTGTTA 60.573 38.462 0.00 0.0 0.00 2.41
1116 1121 5.188434 TCATTCATCTTGATGTTCCCACTC 58.812 41.667 10.01 0.0 0.00 3.51
1332 1337 7.090173 CCTTCTTTCATTTCCGAATTTGCTTA 58.910 34.615 0.00 0.0 0.00 3.09
1449 1454 8.682016 CGAAAAATCAAGTGAACTAATGAACAC 58.318 33.333 0.00 0.0 0.00 3.32
1478 1483 3.678056 AGTAAGCGGTTCAAGACATCA 57.322 42.857 1.59 0.0 0.00 3.07
1546 1551 0.889638 AGTGAGCGAGACCAAGACGA 60.890 55.000 0.00 0.0 0.00 4.20
1647 1652 9.488124 GACTACTACATAGAGAAAACTACAACG 57.512 37.037 0.00 0.0 34.65 4.10
1650 1655 7.201679 GCCGACTACTACATAGAGAAAACTACA 60.202 40.741 0.00 0.0 34.65 2.74
1657 1662 4.434545 AGGCCGACTACTACATAGAGAA 57.565 45.455 0.00 0.0 34.65 2.87
1859 1864 2.892215 TCACATCAATTGAAGCAGGCAA 59.108 40.909 13.09 0.0 0.00 4.52
2133 2139 0.539986 GGTAAGCGGACCATGGAAGA 59.460 55.000 21.47 0.0 39.51 2.87
2217 2223 2.415962 ATCCTCTGTCACCCCCACCA 62.416 60.000 0.00 0.0 0.00 4.17


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

AutoCloner maintained by Alex Coulton.