Multiple sequence alignment - TraesCS7A01G164800

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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 TraesCS7A01G164800 chr7A 100.000 2753 0 0 1 2753 120880628 120883380 0.000000e+00 5084
1 TraesCS7A01G164800 chrUn 98.440 2757 39 2 1 2753 186191237 186188481 0.000000e+00 4850
2 TraesCS7A01G164800 chrUn 98.634 2635 35 1 119 2753 86478354 86480987 0.000000e+00 4665
3 TraesCS7A01G164800 chr7B 98.440 2757 39 2 1 2753 743006241 743008997 0.000000e+00 4850
4 TraesCS7A01G164800 chr7D 98.296 2758 37 4 1 2753 579029915 579032667 0.000000e+00 4824
5 TraesCS7A01G164800 chr4B 97.896 2757 52 3 1 2753 209271131 209268377 0.000000e+00 4765
6 TraesCS7A01G164800 chr1D 97.858 2754 42 8 1 2753 212467672 212464935 0.000000e+00 4743
7 TraesCS7A01G164800 chr6D 97.423 2755 67 3 1 2753 369917828 369915076 0.000000e+00 4691
8 TraesCS7A01G164800 chr6D 97.315 2756 68 4 1 2753 283153942 283151190 0.000000e+00 4674
9 TraesCS7A01G164800 chr1A 98.596 2636 36 1 119 2753 112004608 112001973 0.000000e+00 4662
10 TraesCS7A01G164800 chr3B 92.715 151 2 5 1 146 730161722 730161868 2.780000e-50 209
11 TraesCS7A01G164800 chr3B 98.020 101 0 1 1 99 39816963 39817063 1.010000e-39 174


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 TraesCS7A01G164800 chr7A 120880628 120883380 2752 False 5084 5084 100.000 1 2753 1 chr7A.!!$F1 2752
1 TraesCS7A01G164800 chrUn 186188481 186191237 2756 True 4850 4850 98.440 1 2753 1 chrUn.!!$R1 2752
2 TraesCS7A01G164800 chrUn 86478354 86480987 2633 False 4665 4665 98.634 119 2753 1 chrUn.!!$F1 2634
3 TraesCS7A01G164800 chr7B 743006241 743008997 2756 False 4850 4850 98.440 1 2753 1 chr7B.!!$F1 2752
4 TraesCS7A01G164800 chr7D 579029915 579032667 2752 False 4824 4824 98.296 1 2753 1 chr7D.!!$F1 2752
5 TraesCS7A01G164800 chr4B 209268377 209271131 2754 True 4765 4765 97.896 1 2753 1 chr4B.!!$R1 2752
6 TraesCS7A01G164800 chr1D 212464935 212467672 2737 True 4743 4743 97.858 1 2753 1 chr1D.!!$R1 2752
7 TraesCS7A01G164800 chr6D 369915076 369917828 2752 True 4691 4691 97.423 1 2753 1 chr6D.!!$R2 2752
8 TraesCS7A01G164800 chr6D 283151190 283153942 2752 True 4674 4674 97.315 1 2753 1 chr6D.!!$R1 2752
9 TraesCS7A01G164800 chr1A 112001973 112004608 2635 True 4662 4662 98.596 119 2753 1 chr1A.!!$R1 2634

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
295 300 2.230508 TGCTTCTCCGTACTGATTCGTT 59.769 45.455 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2214 2226 0.969149 CCTCGTGGCAGCTATATCCA 59.031 55.0 0.0 0.0 0.0 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
295 300 2.230508 TGCTTCTCCGTACTGATTCGTT 59.769 45.455 0.00 0.00 0.00 3.85
760 765 3.641436 TGTGTGGTCTGTTCTAGTGACAT 59.359 43.478 2.92 0.00 32.84 3.06
794 799 6.549433 TTTATTATCACTTCCGGTACTGGT 57.451 37.500 20.40 2.53 0.00 4.00
820 825 6.127026 GGGGGCAATTACAATGTTATTAACCA 60.127 38.462 14.25 0.00 0.00 3.67
928 935 8.807118 GTCATCCAGAGGTGTATATTCTCATTA 58.193 37.037 0.00 0.00 0.00 1.90
1121 1128 2.028658 CCGCAGCTACCATGATCATAGT 60.029 50.000 8.15 10.09 0.00 2.12
1337 1344 8.561536 TTCCATTATGTACTTTCTATGGGAGA 57.438 34.615 12.93 0.00 34.64 3.71
1545 1552 1.134159 GCTGGATGGAATGCTCTGAGT 60.134 52.381 6.53 0.00 34.76 3.41
1730 1737 8.704849 TTTCATATTTTTGGAGAACTTCCTGA 57.295 30.769 0.00 0.00 46.92 3.86
1886 1898 1.358725 TATCGCCAACTGAACTGCGC 61.359 55.000 0.00 0.00 46.14 6.09
2075 2087 3.491964 CCATTTACGCTCATAGAACCCGA 60.492 47.826 0.00 0.00 0.00 5.14
2079 2091 2.618053 ACGCTCATAGAACCCGAAAAG 58.382 47.619 0.00 0.00 0.00 2.27
2214 2226 4.884668 TTAGAACACTTGGAATCCTCGT 57.115 40.909 0.00 0.00 0.00 4.18
2264 2276 9.768215 TTTCCCACTTAATAGATTCATTCCTTT 57.232 29.630 0.00 0.00 0.00 3.11
2498 2510 5.357314 CGGTAGAAGGTTCTCAGTAATCAGA 59.643 44.000 0.00 0.00 38.70 3.27
2636 2648 1.367346 TCAACCTGTGGGAATAGCCA 58.633 50.000 0.00 0.00 38.95 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 58 1.497161 ATTACTGAGCTACCCCGCTT 58.503 50.000 0.00 0.00 41.08 4.68
102 107 1.075536 GAGAAAAGAAAGAGGGGCCCA 59.924 52.381 27.72 0.00 0.00 5.36
295 300 1.222387 CGGGTCGGGCTAATTCCAA 59.778 57.895 0.00 0.00 0.00 3.53
747 752 7.482169 AAGTAGGAATGATGTCACTAGAACA 57.518 36.000 0.00 0.46 0.00 3.18
760 765 9.542462 CGGAAGTGATAATAAAAGTAGGAATGA 57.458 33.333 0.00 0.00 0.00 2.57
794 799 6.127026 GGTTAATAACATTGTAATTGCCCCCA 60.127 38.462 5.45 0.00 0.00 4.96
928 935 7.526041 TGACTAATAATACCAAATCCAGGCAT 58.474 34.615 0.00 0.00 0.00 4.40
1121 1128 2.079170 TTTGATTCCTGTGGGCACAA 57.921 45.000 0.00 0.00 41.33 3.33
1337 1344 4.688021 TCCAGCAAATAAAGCAAAAACGT 58.312 34.783 0.00 0.00 0.00 3.99
1545 1552 9.507329 ACTACGGATATATAAGAACCGAAACTA 57.493 33.333 19.84 7.73 45.31 2.24
1615 1622 3.559655 GCACATTTTTGGTTCTTTCCACC 59.440 43.478 0.00 0.00 37.20 4.61
1886 1898 3.568538 CAAGAAGGAATCGCTTTGGTTG 58.431 45.455 0.00 0.00 0.00 3.77
2079 2091 7.550196 TGGTCCTTAAACAACGGTATATTCTTC 59.450 37.037 0.00 0.00 0.00 2.87
2214 2226 0.969149 CCTCGTGGCAGCTATATCCA 59.031 55.000 0.00 0.00 0.00 3.41
2264 2276 1.184322 TACCCTCAACCGCCGTAACA 61.184 55.000 0.00 0.00 0.00 2.41
2515 2527 5.011840 ACCTTCTTAGGCGAAAAAGACTAGT 59.988 40.000 0.00 0.00 46.22 2.57
2636 2648 5.860648 TCTTTCTTTGGTAAGGAAGGGAT 57.139 39.130 6.19 0.00 44.14 3.85


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

AutoCloner maintained by Alex Coulton.