Multiple sequence alignment - TraesCS1A01G245200

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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 TraesCS1A01G245200 chr1A 100.000 2417 0 0 1 2417 434045757 434048173 0 4464
1 TraesCS1A01G245200 chr3A 96.649 2417 75 4 1 2417 468235779 468233369 0 4010
2 TraesCS1A01G245200 chr3A 93.254 2446 121 22 1 2417 543424662 543427092 0 3563
3 TraesCS1A01G245200 chr2A 94.310 2443 99 20 1 2417 743396725 743394297 0 3705
4 TraesCS1A01G245200 chr4A 94.176 2438 107 18 1 2417 402279441 402281864 0 3683
5 TraesCS1A01G245200 chr7D 94.113 2446 101 20 1 2417 32519311 32516880 0 3679
6 TraesCS1A01G245200 chr7D 93.947 2445 106 20 1 2417 625869580 625872010 0 3657
7 TraesCS1A01G245200 chr7D 93.868 2446 107 15 1 2417 485662819 485660388 0 3646
8 TraesCS1A01G245200 chr5D 93.908 2446 106 23 1 2417 182585500 182583069 0 3651
9 TraesCS1A01G245200 chr6A 93.888 2438 113 22 1 2417 343409405 343406983 0 3644
10 TraesCS1A01G245200 chr6D 94.041 1997 81 9 1 1970 62080477 62078492 0 2994


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 TraesCS1A01G245200 chr1A 434045757 434048173 2416 False 4464 4464 100.000 1 2417 1 chr1A.!!$F1 2416
1 TraesCS1A01G245200 chr3A 468233369 468235779 2410 True 4010 4010 96.649 1 2417 1 chr3A.!!$R1 2416
2 TraesCS1A01G245200 chr3A 543424662 543427092 2430 False 3563 3563 93.254 1 2417 1 chr3A.!!$F1 2416
3 TraesCS1A01G245200 chr2A 743394297 743396725 2428 True 3705 3705 94.310 1 2417 1 chr2A.!!$R1 2416
4 TraesCS1A01G245200 chr4A 402279441 402281864 2423 False 3683 3683 94.176 1 2417 1 chr4A.!!$F1 2416
5 TraesCS1A01G245200 chr7D 32516880 32519311 2431 True 3679 3679 94.113 1 2417 1 chr7D.!!$R1 2416
6 TraesCS1A01G245200 chr7D 625869580 625872010 2430 False 3657 3657 93.947 1 2417 1 chr7D.!!$F1 2416
7 TraesCS1A01G245200 chr7D 485660388 485662819 2431 True 3646 3646 93.868 1 2417 1 chr7D.!!$R2 2416
8 TraesCS1A01G245200 chr5D 182583069 182585500 2431 True 3651 3651 93.908 1 2417 1 chr5D.!!$R1 2416
9 TraesCS1A01G245200 chr6A 343406983 343409405 2422 True 3644 3644 93.888 1 2417 1 chr6A.!!$R1 2416
10 TraesCS1A01G245200 chr6D 62078492 62080477 1985 True 2994 2994 94.041 1 1970 1 chr6D.!!$R1 1969

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
894 943 0.036294 AGAGGGTTAACTTGGAGCGC 60.036 55.0 0.0 0.0 0.0 5.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1802 1860 2.503356 CAAGACTAGGAAGCCCATGAGT 59.497 50.0 0.0 0.0 33.88 3.41 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
199 200 3.169355 ACGCCGATAACCGTAAGAAAT 57.831 42.857 0.00 0.00 43.02 2.17
318 319 3.890756 TGGTGTCATGTTTCAAGCATCTT 59.109 39.130 0.00 0.00 0.00 2.40
353 354 5.437060 ACTTGCAGAGAAACTTGGAAACTA 58.563 37.500 3.37 0.00 0.00 2.24
376 377 4.163839 AGAGAAGAGCCAGATTGTATTGCT 59.836 41.667 0.00 0.00 34.40 3.91
377 378 4.450053 AGAAGAGCCAGATTGTATTGCTC 58.550 43.478 0.00 0.00 46.74 4.26
591 596 7.822161 ATTGATGCTGCACCTATAATTGTTA 57.178 32.000 3.57 0.00 0.00 2.41
646 676 8.533569 AGGTTAAAATCAAAGAAACTGAAGGA 57.466 30.769 0.00 0.00 0.00 3.36
718 748 3.890756 ACACTTTGGAATGCAAGTCATCA 59.109 39.130 0.00 0.00 33.40 3.07
745 775 0.599204 GTGGGTACGGATACATGGCG 60.599 60.000 0.00 0.00 32.40 5.69
762 792 2.494073 TGGCGAAAACTTCAACTGGTTT 59.506 40.909 0.00 0.00 37.26 3.27
768 798 6.346999 GCGAAAACTTCAACTGGTTTTGAAAA 60.347 34.615 8.24 0.00 43.29 2.29
773 803 9.549078 AAACTTCAACTGGTTTTGAAAAGTTTA 57.451 25.926 11.35 0.00 43.29 2.01
880 929 1.334869 GTGCAAACACACAAGAGAGGG 59.665 52.381 0.00 0.00 46.61 4.30
894 943 0.036294 AGAGGGTTAACTTGGAGCGC 60.036 55.000 0.00 0.00 0.00 5.92
1029 1079 6.463995 AAGTTTGTAGAATTGAGCCAACAA 57.536 33.333 0.00 0.00 0.00 2.83
1125 1175 7.659799 TGCTAAAAGTGCACTTCTATTTACAGA 59.340 33.333 31.20 7.09 34.61 3.41
1224 1274 0.322008 GACTCCAGGTTCAAGGCCAG 60.322 60.000 5.01 0.00 0.00 4.85
1377 1432 8.436046 AATTAGCTAGCTGATTCTTCTCTTTG 57.564 34.615 27.68 0.00 27.91 2.77
1444 1502 4.040461 GGAATATGTGCTAGCTAGGGACAA 59.960 45.833 22.10 10.83 38.41 3.18
1592 1650 1.751351 CCTTCGCTGATGAGTCCACTA 59.249 52.381 0.00 0.00 0.00 2.74
1619 1677 1.683938 CCCATGCAGAATCTCTTGCCA 60.684 52.381 0.00 0.00 0.00 4.92
1642 1700 1.569072 GATATGGGGGTTGTGAGGGTT 59.431 52.381 0.00 0.00 0.00 4.11
1802 1860 0.315886 TCGCTCGGCAAACTCTGTTA 59.684 50.000 0.00 0.00 0.00 2.41
1814 1878 3.618690 ACTCTGTTACTCATGGGCTTC 57.381 47.619 0.00 0.00 0.00 3.86
2171 2242 3.774766 TGCAGGATCCAAAGAACTAGCTA 59.225 43.478 15.82 0.00 0.00 3.32
2179 2250 4.707448 TCCAAAGAACTAGCTAGACTGGAG 59.293 45.833 27.45 15.92 0.00 3.86
2399 2471 2.009774 CCACATGCTAGCACCACTAAC 58.990 52.381 22.07 0.00 0.00 2.34
2413 2485 6.940298 AGCACCACTAACAAATATAGTGTTGT 59.060 34.615 12.71 4.67 45.63 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.559698 TCTGGTTGCAAATCTTCCGA 57.440 45.000 0.00 0.00 0.00 4.55
116 117 4.373156 AACCAGTGAGACTAGCCATTTT 57.627 40.909 0.00 0.00 0.00 1.82
166 167 2.669569 GGCGTTCTTCTGGCTGCA 60.670 61.111 0.50 0.00 0.00 4.41
199 200 8.038351 TGATCCGATTATGTGTTTTGTCTTCTA 58.962 33.333 0.00 0.00 0.00 2.10
353 354 4.163839 AGCAATACAATCTGGCTCTTCTCT 59.836 41.667 0.00 0.00 0.00 3.10
417 421 4.378459 CGTAAACTTTCTGGGAATCTGTGC 60.378 45.833 0.00 0.00 0.00 4.57
521 525 5.301551 ACAAGAATAACACAGTCCAATGCAA 59.698 36.000 0.00 0.00 0.00 4.08
591 596 7.124573 AGTGCTTTTTCCTAAAAATGGAAGT 57.875 32.000 0.00 0.00 43.48 3.01
607 613 7.781056 TGATTTTAACCTCTTCAAGTGCTTTT 58.219 30.769 0.00 0.00 0.00 2.27
745 775 8.083462 ACTTTTCAAAACCAGTTGAAGTTTTC 57.917 30.769 0.00 0.00 45.62 2.29
768 798 9.906660 CTTGCTCTTCGATCTAGATATTAAACT 57.093 33.333 4.89 0.00 0.00 2.66
773 803 6.588719 AGCTTGCTCTTCGATCTAGATATT 57.411 37.500 4.89 0.00 0.00 1.28
880 929 1.132640 CAGCGCGCTCCAAGTTAAC 59.867 57.895 34.28 0.00 0.00 2.01
894 943 2.985809 CTCAAGTTGTTCTCTCTCAGCG 59.014 50.000 2.11 0.00 0.00 5.18
1125 1175 1.207329 GTCAACCCTCTTCGTAGGCAT 59.793 52.381 0.00 0.00 35.09 4.40
1224 1274 2.533129 GCGCATTTGAAGAAATAGCAGC 59.467 45.455 0.30 0.00 35.81 5.25
1377 1432 0.385029 TGCAGCAACAACACATGGTC 59.615 50.000 0.00 0.00 0.00 4.02
1619 1677 1.846439 CCTCACAACCCCCATATCAGT 59.154 52.381 0.00 0.00 0.00 3.41
1696 1754 4.730487 GCATGGGCTGACAAGTCT 57.270 55.556 1.53 0.00 36.96 3.24
1802 1860 2.503356 CAAGACTAGGAAGCCCATGAGT 59.497 50.000 0.00 0.00 33.88 3.41
1814 1878 6.183360 GGTTCTAACATCCTACCAAGACTAGG 60.183 46.154 0.00 0.00 33.16 3.02
2011 2077 4.823989 GCAAGCATGTAACTAAGGGATCAT 59.176 41.667 0.00 0.00 0.00 2.45
2074 2140 5.276440 ACAATTATTCCAGCCCCATTGTAA 58.724 37.500 0.00 0.00 33.99 2.41
2075 2141 4.877773 ACAATTATTCCAGCCCCATTGTA 58.122 39.130 0.00 0.00 33.99 2.41
2179 2250 5.128008 AGACTAAACTGCCCTTGATCTAGAC 59.872 44.000 5.68 0.00 0.00 2.59
2189 2260 2.633481 ACTTCGAAGACTAAACTGCCCT 59.367 45.455 31.08 0.99 34.32 5.19


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

AutoCloner maintained by Alex Coulton.