Multiple sequence alignment - TraesCS2A01G239600

Loading Multiple Alignment...

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 TraesCS2A01G239600 chr2A 100.000 2255 0 0 1 2255 332946112 332943858 0.000000e+00 4165
1 TraesCS2A01G239600 chr1D 97.883 2267 35 4 1 2255 141314962 141312697 0.000000e+00 3908
2 TraesCS2A01G239600 chr7B 97.707 2268 39 3 1 2255 644465616 644467883 0.000000e+00 3888
3 TraesCS2A01G239600 chr3A 97.574 2267 43 3 1 2255 633109427 633111693 0.000000e+00 3871
4 TraesCS2A01G239600 chr7A 97.530 2267 44 3 1 2255 60150114 60147848 0.000000e+00 3866
5 TraesCS2A01G239600 chr1B 97.353 2267 48 3 1 2255 672477334 672479600 0.000000e+00 3843
6 TraesCS2A01G239600 chr1B 97.266 2268 48 5 1 2255 638702493 638700227 0.000000e+00 3832
7 TraesCS2A01G239600 chr4B 97.352 2266 49 2 1 2255 209079344 209077079 0.000000e+00 3842
8 TraesCS2A01G239600 chr6B 97.221 2267 51 3 1 2255 306997817 306995551 0.000000e+00 3827
9 TraesCS2A01G239600 chr2B 96.781 2268 55 6 1 2255 391114663 391112401 0.000000e+00 3768
10 TraesCS2A01G239600 chrUn 97.557 1269 20 2 1 1258 251407340 251406072 0.000000e+00 2161
11 TraesCS2A01G239600 chrUn 97.478 1269 21 2 1 1258 189409256 189410524 0.000000e+00 2156
12 TraesCS2A01G239600 chrUn 97.007 902 16 2 1 891 453904533 453903632 0.000000e+00 1506
13 TraesCS2A01G239600 chrUn 98.596 285 4 0 1 285 345807314 345807598 2.580000e-139 505
14 TraesCS2A01G239600 chr7D 97.397 1268 23 1 1 1258 626681066 626679799 0.000000e+00 2150
15 TraesCS2A01G239600 chr7D 97.256 656 8 1 1 646 382066839 382067494 0.000000e+00 1103


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 TraesCS2A01G239600 chr2A 332943858 332946112 2254 True 4165 4165 100.000 1 2255 1 chr2A.!!$R1 2254
1 TraesCS2A01G239600 chr1D 141312697 141314962 2265 True 3908 3908 97.883 1 2255 1 chr1D.!!$R1 2254
2 TraesCS2A01G239600 chr7B 644465616 644467883 2267 False 3888 3888 97.707 1 2255 1 chr7B.!!$F1 2254
3 TraesCS2A01G239600 chr3A 633109427 633111693 2266 False 3871 3871 97.574 1 2255 1 chr3A.!!$F1 2254
4 TraesCS2A01G239600 chr7A 60147848 60150114 2266 True 3866 3866 97.530 1 2255 1 chr7A.!!$R1 2254
5 TraesCS2A01G239600 chr1B 672477334 672479600 2266 False 3843 3843 97.353 1 2255 1 chr1B.!!$F1 2254
6 TraesCS2A01G239600 chr1B 638700227 638702493 2266 True 3832 3832 97.266 1 2255 1 chr1B.!!$R1 2254
7 TraesCS2A01G239600 chr4B 209077079 209079344 2265 True 3842 3842 97.352 1 2255 1 chr4B.!!$R1 2254
8 TraesCS2A01G239600 chr6B 306995551 306997817 2266 True 3827 3827 97.221 1 2255 1 chr6B.!!$R1 2254
9 TraesCS2A01G239600 chr2B 391112401 391114663 2262 True 3768 3768 96.781 1 2255 1 chr2B.!!$R1 2254
10 TraesCS2A01G239600 chrUn 251406072 251407340 1268 True 2161 2161 97.557 1 1258 1 chrUn.!!$R1 1257
11 TraesCS2A01G239600 chrUn 189409256 189410524 1268 False 2156 2156 97.478 1 1258 1 chrUn.!!$F1 1257
12 TraesCS2A01G239600 chrUn 453903632 453904533 901 True 1506 1506 97.007 1 891 1 chrUn.!!$R2 890
13 TraesCS2A01G239600 chr7D 626679799 626681066 1267 True 2150 2150 97.397 1 1258 1 chr7D.!!$R1 1257
14 TraesCS2A01G239600 chr7D 382066839 382067494 655 False 1103 1103 97.256 1 646 1 chr7D.!!$F1 645

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
321 332 2.533266 TGCTTTCGCTTGACTCTTCT 57.467 45.000 0.00 0.00 36.97 2.85 F
458 469 3.119495 AGCAGTTATTTGAAATGACGGGC 60.119 43.478 17.83 17.83 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1213 1227 0.892063 GCGGCCCAAAAATGGTAAGA 59.108 50.000 0.0 0.0 0.0 2.10 R
1767 1783 2.126307 GCTCGCTCAGTTCGCTCA 60.126 61.111 0.0 0.0 0.0 4.26 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
86 87 4.721776 AGATAGGGGTTTGCTATTCTCACA 59.278 41.667 0.00 0.00 0.00 3.58
268 269 4.083324 CGCAGGAGCAAAAAGAGTGAAATA 60.083 41.667 0.00 0.00 42.27 1.40
321 332 2.533266 TGCTTTCGCTTGACTCTTCT 57.467 45.000 0.00 0.00 36.97 2.85
448 459 7.450074 TCAAAGAGTAAGGAGCAGTTATTTGA 58.550 34.615 0.00 0.00 32.32 2.69
458 469 3.119495 AGCAGTTATTTGAAATGACGGGC 60.119 43.478 17.83 17.83 0.00 6.13
677 688 7.321745 AGTTAGCCAGTCATAGCAATTTAAC 57.678 36.000 0.00 0.00 0.00 2.01
747 758 3.370103 CGGGTAGGCTTTGAGGAACATTA 60.370 47.826 0.00 0.00 0.00 1.90
911 925 3.254411 TGCCGCTTGTGTGAATTTCATTA 59.746 39.130 1.78 0.00 0.00 1.90
1189 1203 3.791245 AGGATTTCGCAAAACTTTTGCA 58.209 36.364 29.67 18.33 45.14 4.08
1234 1249 2.096248 CTTACCATTTTTGGGCCGCTA 58.904 47.619 0.00 0.00 0.00 4.26
1375 1390 4.453478 GGCTTTAGGTACGCTTTAGTTTGT 59.547 41.667 0.00 0.00 0.00 2.83
1400 1415 9.209175 GTAATCATTAAAGATATGCTCGACCTT 57.791 33.333 0.00 0.00 0.00 3.50
1444 1459 6.341316 TCGTACGTACCTTCTACTATCAACT 58.659 40.000 19.67 0.00 0.00 3.16
1462 1477 6.412362 TCAACTAGATGAGATAGGGCTTTC 57.588 41.667 0.00 0.00 0.00 2.62
1605 1620 2.496070 TCAGTGATAGTTCGGAACCAGG 59.504 50.000 16.84 4.58 0.00 4.45
1730 1746 3.489398 CGCGCTACTCTTCCTTTATGAGT 60.489 47.826 5.56 0.00 43.18 3.41
1767 1783 6.870971 GATCTACTGATCTAAGAACTCCGT 57.129 41.667 0.00 0.00 44.19 4.69
1791 1807 0.174389 GAACTGAGCGAGCCATGAGA 59.826 55.000 0.00 0.00 0.00 3.27
1880 1896 1.065126 GGTCCAAACCTGCTGAGCTAT 60.065 52.381 5.83 0.00 42.80 2.97
1989 2006 6.154706 GTGATGGGACTACTTCCTTAAAGAGA 59.845 42.308 0.00 0.00 45.09 3.10
2059 2077 1.793414 AAAAACAGGCTTTGCTCCCT 58.207 45.000 0.00 0.00 0.00 4.20
2107 2126 2.608752 GGTCGAAGTTTAGACCGCTCAA 60.609 50.000 13.44 0.00 46.08 3.02
2108 2127 2.662156 GTCGAAGTTTAGACCGCTCAAG 59.338 50.000 0.00 0.00 0.00 3.02
2157 2176 4.081142 TGAAAGAGGCGATCAGAATGGTAA 60.081 41.667 0.00 0.00 36.16 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 3.904717 AGATAGGTCCACGAGTTGAGAT 58.095 45.455 0.00 0.00 0.00 2.75
86 87 9.605951 AATGGGGTAAATAAATATGAGCAATCT 57.394 29.630 0.00 0.00 0.00 2.40
268 269 0.546988 AAGAGGGGGCTTACGTCCTT 60.547 55.000 0.00 0.00 34.49 3.36
448 459 1.001393 ACCAATCCGCCCGTCATTT 60.001 52.632 0.00 0.00 0.00 2.32
458 469 0.674581 TTGCAGCTCTGACCAATCCG 60.675 55.000 0.29 0.00 0.00 4.18
657 668 6.889198 TCTAGTTAAATTGCTATGACTGGCT 58.111 36.000 0.00 0.00 0.00 4.75
677 688 2.386661 TCCCGAAGCAAGCTTTCTAG 57.613 50.000 8.91 0.00 36.26 2.43
765 776 6.450545 GCACAATAGACATATCTGCTCAGTA 58.549 40.000 0.00 0.00 36.29 2.74
855 869 5.472820 GCAGAGAATGGAGAAGGGAAATATG 59.527 44.000 0.00 0.00 0.00 1.78
911 925 2.766651 ACACACGGGACCCACAGT 60.767 61.111 12.15 2.21 0.00 3.55
1213 1227 0.892063 GCGGCCCAAAAATGGTAAGA 59.108 50.000 0.00 0.00 0.00 2.10
1234 1249 6.263754 AGGTTCAGGAAATGGAAATGGTAAT 58.736 36.000 0.00 0.00 0.00 1.89
1375 1390 9.208022 CAAGGTCGAGCATATCTTTAATGATTA 57.792 33.333 18.15 0.00 0.00 1.75
1400 1415 5.924356 ACGATGATACCATGGACATAAACA 58.076 37.500 21.47 8.65 33.43 2.83
1444 1459 5.667626 ACCTTTGAAAGCCCTATCTCATCTA 59.332 40.000 0.00 0.00 0.00 1.98
1462 1477 2.896685 AGGAGACTGACTCTGACCTTTG 59.103 50.000 7.06 0.00 44.37 2.77
1730 1746 6.755542 TCAGTAGATCTGGATAGAGTCTCA 57.244 41.667 5.18 0.00 43.76 3.27
1767 1783 2.126307 GCTCGCTCAGTTCGCTCA 60.126 61.111 0.00 0.00 0.00 4.26
1880 1896 8.630278 CGAGATCTCGTAAAGGAAAAATTAGA 57.370 34.615 32.23 0.00 46.99 2.10
2157 2176 2.547218 CGGGATCGTAAATGGATTCGGT 60.547 50.000 0.00 0.00 0.00 4.69


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

AutoCloner maintained by Alex Coulton.