Multiple sequence alignment - TraesCS4A01G429600

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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 TraesCS4A01G429600 chr4A 100.000 2832 0 0 1 2832 700451459 700448628 0 5230
1 TraesCS4A01G429600 chr3B 98.024 2834 44 4 1 2832 797655906 797658729 0 4913
2 TraesCS4A01G429600 chr3B 97.354 2834 63 4 1 2832 545458777 545455954 0 4807
3 TraesCS4A01G429600 chr7B 97.495 2834 59 8 1 2832 666318610 666321433 0 4830
4 TraesCS4A01G429600 chr2B 97.459 2834 65 3 1 2832 607650280 607653108 0 4828
5 TraesCS4A01G429600 chr2B 97.319 2835 64 5 1 2832 50540670 50543495 0 4804
6 TraesCS4A01G429600 chr2B 97.214 2836 72 4 1 2832 752110252 752113084 0 4793
7 TraesCS4A01G429600 chr2B 97.212 2834 70 3 1 2832 84048753 84051579 0 4787
8 TraesCS4A01G429600 chr6B 97.320 2836 64 8 1 2832 227425608 227422781 0 4806
9 TraesCS4A01G429600 chr4B 97.248 2834 69 6 1 2832 490008560 490005734 0 4793


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 TraesCS4A01G429600 chr4A 700448628 700451459 2831 True 5230 5230 100.000 1 2832 1 chr4A.!!$R1 2831
1 TraesCS4A01G429600 chr3B 797655906 797658729 2823 False 4913 4913 98.024 1 2832 1 chr3B.!!$F1 2831
2 TraesCS4A01G429600 chr3B 545455954 545458777 2823 True 4807 4807 97.354 1 2832 1 chr3B.!!$R1 2831
3 TraesCS4A01G429600 chr7B 666318610 666321433 2823 False 4830 4830 97.495 1 2832 1 chr7B.!!$F1 2831
4 TraesCS4A01G429600 chr2B 607650280 607653108 2828 False 4828 4828 97.459 1 2832 1 chr2B.!!$F3 2831
5 TraesCS4A01G429600 chr2B 50540670 50543495 2825 False 4804 4804 97.319 1 2832 1 chr2B.!!$F1 2831
6 TraesCS4A01G429600 chr2B 752110252 752113084 2832 False 4793 4793 97.214 1 2832 1 chr2B.!!$F4 2831
7 TraesCS4A01G429600 chr2B 84048753 84051579 2826 False 4787 4787 97.212 1 2832 1 chr2B.!!$F2 2831
8 TraesCS4A01G429600 chr6B 227422781 227425608 2827 True 4806 4806 97.320 1 2832 1 chr6B.!!$R1 2831
9 TraesCS4A01G429600 chr4B 490005734 490008560 2826 True 4793 4793 97.248 1 2832 1 chr4B.!!$R1 2831

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
727 728 3.242870 GCTGCTGTTATGCCTGTATTCAC 60.243 47.826 0.0 0.0 0.0 3.18 F
1235 1239 0.467384 CTGATGGGTGAAGATCCGCT 59.533 55.000 0.0 0.0 0.0 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1554 1558 0.469917 GCTGCTGCTCCCATTACCTA 59.530 55.000 8.53 0.0 36.03 3.08 R
2087 2091 5.502079 ACCTATAGGAGATCTGACATACCG 58.498 45.833 26.01 0.0 38.94 4.02 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
177 178 5.240183 GCTGCTATCTTATTCCAAGATGCAA 59.760 40.000 17.00 8.14 38.73 4.08
398 399 4.613437 AGGGCATCTGTTGGTTCATTAAT 58.387 39.130 0.00 0.00 0.00 1.40
430 431 3.278574 TCTGCATATTTCAGGTTTCCGG 58.721 45.455 0.00 0.00 32.63 5.14
727 728 3.242870 GCTGCTGTTATGCCTGTATTCAC 60.243 47.826 0.00 0.00 0.00 3.18
728 729 4.194640 CTGCTGTTATGCCTGTATTCACT 58.805 43.478 0.00 0.00 0.00 3.41
729 730 3.940852 TGCTGTTATGCCTGTATTCACTG 59.059 43.478 0.00 0.00 0.00 3.66
967 970 7.392953 TGCATGTTTTATGATCTGTTGTAAGGA 59.607 33.333 0.00 0.00 0.00 3.36
1064 1067 2.003301 GTTGGATGCTTCCGAGTTCTC 58.997 52.381 13.54 0.00 45.89 2.87
1235 1239 0.467384 CTGATGGGTGAAGATCCGCT 59.533 55.000 0.00 0.00 0.00 5.52
1328 1332 1.003118 GGGCCACATGTACTTGTCTCA 59.997 52.381 11.23 0.00 0.00 3.27
1331 1335 3.599343 GCCACATGTACTTGTCTCATGA 58.401 45.455 11.23 0.00 40.64 3.07
1389 1393 3.181410 TGGGGTACTTCCTTCTCTTCAGA 60.181 47.826 0.00 0.00 36.25 3.27
1400 1404 1.326852 TCTCTTCAGATACGACGACGC 59.673 52.381 7.30 0.00 43.96 5.19
1554 1558 3.006752 ACGGTCATTGTTGCATTTTGGAT 59.993 39.130 0.00 0.00 0.00 3.41
1745 1749 0.325016 TGAGGATGAGGAGCTGCAGA 60.325 55.000 20.43 0.00 0.00 4.26
2087 2091 3.565482 TGCATGAGAACTGAACTTTGTCC 59.435 43.478 0.00 0.00 0.00 4.02
2114 2118 8.110908 GGTATGTCAGATCTCCTATAGGTTAGT 58.889 40.741 18.51 3.80 36.34 2.24
2450 2463 8.525290 AGCTCCAAAATAACTTATGTTAGCAT 57.475 30.769 7.24 0.00 41.33 3.79
2631 2644 8.246180 ACTTATGTTAGCACAAAATGATCAAGG 58.754 33.333 0.00 0.00 36.16 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
177 178 8.230472 AGAACATGTCAGTTTGAGAGAAAATT 57.770 30.769 0.00 0.0 0.00 1.82
398 399 8.049117 ACCTGAAATATGCAGATGTTAGAAAGA 58.951 33.333 4.91 0.0 35.39 2.52
430 431 4.202430 TGAACTTCACTTCCTTTACCTCCC 60.202 45.833 0.00 0.0 0.00 4.30
967 970 5.130145 AGCAGCAGAAGAGACCAATTAGTAT 59.870 40.000 0.00 0.0 0.00 2.12
1041 1044 0.976641 ACTCGGAAGCATCCAACTCA 59.023 50.000 8.98 0.0 46.97 3.41
1064 1067 5.163364 ACTGAAGCCTCAAGTATGATAGTGG 60.163 44.000 0.00 0.0 34.37 4.00
1235 1239 4.332543 CCTGTCGCAGCTTCACATTATTTA 59.667 41.667 1.84 0.0 0.00 1.40
1328 1332 2.761208 CGGTAGAACTTCTCCCACTCAT 59.239 50.000 1.65 0.0 0.00 2.90
1331 1335 1.893801 CACGGTAGAACTTCTCCCACT 59.106 52.381 1.65 0.0 0.00 4.00
1389 1393 4.118995 TTGGCGGCGTCGTCGTAT 62.119 61.111 21.48 0.0 45.11 3.06
1400 1404 2.108514 ACGATGAGCATGTTGGCGG 61.109 57.895 0.00 0.0 39.27 6.13
1483 1487 5.816955 ATGTAGAGGAATAAGAAGAGGCC 57.183 43.478 0.00 0.0 0.00 5.19
1554 1558 0.469917 GCTGCTGCTCCCATTACCTA 59.530 55.000 8.53 0.0 36.03 3.08
1745 1749 0.820891 GCCTGATGCCCATCGTCATT 60.821 55.000 4.02 0.0 39.78 2.57
1800 1804 1.303561 GCCACCACCATCTCTTGCA 60.304 57.895 0.00 0.0 0.00 4.08
1829 1833 2.392662 CTCAGCCACCTCCATCTCTTA 58.607 52.381 0.00 0.0 0.00 2.10
1984 1988 1.626356 GCAGTGGAGGCAGTGGGATA 61.626 60.000 0.00 0.0 0.00 2.59
2087 2091 5.502079 ACCTATAGGAGATCTGACATACCG 58.498 45.833 26.01 0.0 38.94 4.02


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

AutoCloner maintained by Alex Coulton.