Multiple sequence alignment - TraesCS3A01G409100

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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 TraesCS3A01G409100 chr3A 100.000 2321 0 0 1 2321 653826109 653823789 0 4287
1 TraesCS3A01G409100 chr7A 98.322 2324 34 3 1 2321 4959837 4962158 0 4071
2 TraesCS3A01G409100 chrUn 98.237 2325 30 4 1 2321 189392538 189394855 0 4056
3 TraesCS3A01G409100 chr5A 98.194 2325 31 4 1 2321 300072978 300075295 0 4050
4 TraesCS3A01G409100 chr2A 98.108 2325 33 4 1 2321 618279957 618277640 0 4039
5 TraesCS3A01G409100 chr6A 97.978 2324 36 5 1 2321 289128631 289130946 0 4021
6 TraesCS3A01G409100 chr7D 97.935 2325 37 4 1 2321 626698491 626696174 0 4017
7 TraesCS3A01G409100 chr7B 97.935 2325 37 5 1 2321 743086198 743088515 0 4017
8 TraesCS3A01G409100 chr4A 97.805 2323 45 3 1 2321 67587532 67585214 0 4002


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 TraesCS3A01G409100 chr3A 653823789 653826109 2320 True 4287 4287 100.000 1 2321 1 chr3A.!!$R1 2320
1 TraesCS3A01G409100 chr7A 4959837 4962158 2321 False 4071 4071 98.322 1 2321 1 chr7A.!!$F1 2320
2 TraesCS3A01G409100 chrUn 189392538 189394855 2317 False 4056 4056 98.237 1 2321 1 chrUn.!!$F1 2320
3 TraesCS3A01G409100 chr5A 300072978 300075295 2317 False 4050 4050 98.194 1 2321 1 chr5A.!!$F1 2320
4 TraesCS3A01G409100 chr2A 618277640 618279957 2317 True 4039 4039 98.108 1 2321 1 chr2A.!!$R1 2320
5 TraesCS3A01G409100 chr6A 289128631 289130946 2315 False 4021 4021 97.978 1 2321 1 chr6A.!!$F1 2320
6 TraesCS3A01G409100 chr7D 626696174 626698491 2317 True 4017 4017 97.935 1 2321 1 chr7D.!!$R1 2320
7 TraesCS3A01G409100 chr7B 743086198 743088515 2317 False 4017 4017 97.935 1 2321 1 chr7B.!!$F1 2320
8 TraesCS3A01G409100 chr4A 67585214 67587532 2318 True 4002 4002 97.805 1 2321 1 chr4A.!!$R1 2320

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
253 254 2.100252 TCATATCGGTCAGGAAACGACC 59.9 50.0 0.0 0.0 44.91 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1685 1696 0.179225 CCATTCGCTTCGTTCAACCG 60.179 55.0 0.0 0.0 0.0 4.44 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
142 143 3.011517 AGGGCGGGCATCTCACTT 61.012 61.111 3.27 0.0 0.00 3.16
253 254 2.100252 TCATATCGGTCAGGAAACGACC 59.900 50.000 0.00 0.0 44.91 4.79
344 345 4.937620 ACATTCGTAGCATTCATTGTCACT 59.062 37.500 0.00 0.0 0.00 3.41
892 895 2.365582 CCCTTTTTACCCATCGGACTG 58.634 52.381 0.00 0.0 0.00 3.51
1003 1007 2.989840 AGCGAGCGTAGATTCAATATGC 59.010 45.455 0.00 0.0 35.75 3.14
1045 1049 1.737838 TGCCTTATCACGAAAGCCAG 58.262 50.000 0.00 0.0 0.00 4.85
1099 1103 9.907819 TCCTGTTCCCTATAAATAAGGAGATTA 57.092 33.333 0.00 0.0 36.08 1.75
1245 1251 5.965922 TGTGATCTATTCTCGTGTCACATT 58.034 37.500 3.42 0.0 40.47 2.71
1255 1261 5.053811 TCTCGTGTCACATTGCTTTCTTTA 58.946 37.500 3.42 0.0 0.00 1.85
1329 1335 4.223477 AGCATTGTGGAATAGTGGCATTTT 59.777 37.500 0.00 0.0 0.00 1.82
1448 1454 1.810412 GCCAAACACGTCTCCTCAGTT 60.810 52.381 0.00 0.0 0.00 3.16
1463 1469 2.494073 CTCAGTTAAGGGTCTTCTCGCT 59.506 50.000 0.00 0.0 0.00 4.93
1513 1519 2.401583 TCGCTTAATGCATGTCACCT 57.598 45.000 0.00 0.0 43.06 4.00
1611 1622 8.086522 CCAATTTGATCAGAAGTGAGTTCATTT 58.913 33.333 15.09 0.0 37.67 2.32
1620 1631 8.735315 TCAGAAGTGAGTTCATTTTTGTTGTAA 58.265 29.630 2.50 0.0 37.67 2.41
1685 1696 3.181491 GCCGAGCTATCTATCCAGATCAC 60.181 52.174 0.00 0.0 40.81 3.06
2133 2146 0.881159 CCACGCGTTTTCCACCTACA 60.881 55.000 10.22 0.0 0.00 2.74
2287 2300 7.234187 CGAGAGCAGCATAATTGTTAGTTAA 57.766 36.000 0.00 0.0 0.00 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
133 134 5.170021 GGCTCTAGATATGCAAGTGAGATG 58.830 45.833 4.99 0.0 0.00 2.90
142 143 1.720781 TGCTGGGCTCTAGATATGCA 58.279 50.000 4.99 0.0 0.00 3.96
253 254 3.055819 TCCCGGAAAGAAGAAGAGTCATG 60.056 47.826 0.73 0.0 0.00 3.07
357 358 3.739300 TCGTACGGCTTCTTTTTCTTCTG 59.261 43.478 16.52 0.0 0.00 3.02
858 861 0.860457 AAAGGGGAAGCAGGAAAGGT 59.140 50.000 0.00 0.0 0.00 3.50
892 895 4.806247 CGTAGGAGATCAAAATGTGAGTCC 59.194 45.833 0.00 0.0 40.43 3.85
1003 1007 3.226346 TCCTTCGTTCGGTACAATCAG 57.774 47.619 0.00 0.0 0.00 2.90
1045 1049 4.210537 TGACTTCCTCAAACGAAACGAATC 59.789 41.667 0.00 0.0 0.00 2.52
1112 1118 2.846827 GGAAGAAGAGGGGATTTCTGGA 59.153 50.000 0.00 0.0 34.09 3.86
1113 1119 2.849318 AGGAAGAAGAGGGGATTTCTGG 59.151 50.000 0.00 0.0 34.09 3.86
1175 1181 3.569194 AGATCCGCTCTGAGTCTTCTA 57.431 47.619 6.53 0.0 31.12 2.10
1245 1251 4.927267 TGGAGGGAGAATAAAGAAAGCA 57.073 40.909 0.00 0.0 0.00 3.91
1255 1261 5.527026 AGTGAAGAAAATGGAGGGAGAAT 57.473 39.130 0.00 0.0 0.00 2.40
1329 1335 9.290988 TCACTAAGAACATTTTAGCCATTAACA 57.709 29.630 0.00 0.0 32.58 2.41
1395 1401 4.130118 CCGCTATGCTCCTATTCACTTTT 58.870 43.478 0.00 0.0 0.00 2.27
1448 1454 5.421056 TCTTATTTGAGCGAGAAGACCCTTA 59.579 40.000 0.00 0.0 0.00 2.69
1513 1519 1.153369 GCTGTATTGAGAGCGGGCA 60.153 57.895 0.00 0.0 31.42 5.36
1611 1622 5.103687 GGAAAGGTTTCGCTTTACAACAAA 58.896 37.500 0.00 0.0 38.06 2.83
1620 1631 2.650322 TGTCAAGGAAAGGTTTCGCTT 58.350 42.857 0.00 0.0 38.06 4.68
1685 1696 0.179225 CCATTCGCTTCGTTCAACCG 60.179 55.000 0.00 0.0 0.00 4.44
2133 2146 6.500049 AGGATATTTCGATGATTTCTCCCTCT 59.500 38.462 0.00 0.0 0.00 3.69
2287 2300 2.367378 CCCGTCCCCTCTTACCCT 59.633 66.667 0.00 0.0 0.00 4.34


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

AutoCloner maintained by Alex Coulton.