Multiple sequence alignment - TraesCS4B01G143000

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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 TraesCS4B01G143000 chr4B 100.000 3803 0 0 1 3803 189149787 189145985 0 7023
1 TraesCS4B01G143000 chr3B 98.502 3805 50 7 1 3803 642076068 642079867 0 6704
2 TraesCS4B01G143000 chr3B 98.476 3807 49 9 1 3803 542914468 542910667 0 6700
3 TraesCS4B01G143000 chr1B 98.502 3805 50 6 1 3803 167986966 167983167 0 6704
4 TraesCS4B01G143000 chr2A 98.397 3806 56 5 1 3803 740465334 740469137 0 6685
5 TraesCS4B01G143000 chr7A 98.318 3805 53 11 1 3803 708306945 708303150 0 6661
6 TraesCS4B01G143000 chr4A 98.293 3807 56 8 1 3803 24851514 24847713 0 6661
7 TraesCS4B01G143000 chr3A 98.293 3807 53 12 1 3803 591390323 591386525 0 6660
8 TraesCS4B01G143000 chr7B 98.266 3807 56 8 1 3803 74068426 74072226 0 6656
9 TraesCS4B01G143000 chr5A 98.240 3807 56 10 1 3803 400082544 400078745 0 6649


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 TraesCS4B01G143000 chr4B 189145985 189149787 3802 True 7023 7023 100.000 1 3803 1 chr4B.!!$R1 3802
1 TraesCS4B01G143000 chr3B 642076068 642079867 3799 False 6704 6704 98.502 1 3803 1 chr3B.!!$F1 3802
2 TraesCS4B01G143000 chr3B 542910667 542914468 3801 True 6700 6700 98.476 1 3803 1 chr3B.!!$R1 3802
3 TraesCS4B01G143000 chr1B 167983167 167986966 3799 True 6704 6704 98.502 1 3803 1 chr1B.!!$R1 3802
4 TraesCS4B01G143000 chr2A 740465334 740469137 3803 False 6685 6685 98.397 1 3803 1 chr2A.!!$F1 3802
5 TraesCS4B01G143000 chr7A 708303150 708306945 3795 True 6661 6661 98.318 1 3803 1 chr7A.!!$R1 3802
6 TraesCS4B01G143000 chr4A 24847713 24851514 3801 True 6661 6661 98.293 1 3803 1 chr4A.!!$R1 3802
7 TraesCS4B01G143000 chr3A 591386525 591390323 3798 True 6660 6660 98.293 1 3803 1 chr3A.!!$R1 3802
8 TraesCS4B01G143000 chr7B 74068426 74072226 3800 False 6656 6656 98.266 1 3803 1 chr7B.!!$F1 3802
9 TraesCS4B01G143000 chr5A 400078745 400082544 3799 True 6649 6649 98.240 1 3803 1 chr5A.!!$R1 3802

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
554 558 0.179020 TCAAGCTCACACACAAGGGG 60.179 55.000 0.0 0.0 0.0 4.79 F
1558 1571 3.826729 TGAGATCGAGGAAGAGTTGTTCA 59.173 43.478 0.0 0.0 0.0 3.18 F
2418 2434 0.595825 GCTGTCAAGGTTGTGCTTGC 60.596 55.000 0.0 0.0 0.0 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1758 1771 0.806241 AACGCAACGAAAACACTGGT 59.194 45.000 0.00 0.0 0.00 4.00 R
2637 2657 1.748329 AAGACGGAGCTGAGTGCACA 61.748 55.000 21.04 0.0 45.94 4.57 R
3663 3685 6.237942 GGATGATAACAGAAGAACATGTGACG 60.238 42.308 0.00 0.0 0.00 4.35 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
88 90 8.462016 GTTGAAGTAGTTGCCATTGAAATCTAT 58.538 33.333 0.00 0.00 0.00 1.98
127 129 2.017049 GTTGAAACTGCAGACTGTGGT 58.983 47.619 23.35 0.00 0.00 4.16
456 460 8.293867 GTGGCAACTAAACTACATGAACAAATA 58.706 33.333 0.00 0.00 37.61 1.40
554 558 0.179020 TCAAGCTCACACACAAGGGG 60.179 55.000 0.00 0.00 0.00 4.79
675 681 7.280652 ACCTCAAACATTCTTTTTCATTTGTGG 59.719 33.333 11.89 11.89 42.33 4.17
682 688 5.930837 TCTTTTTCATTTGTGGGACTTGT 57.069 34.783 0.00 0.00 0.00 3.16
713 722 8.641499 TTTTCTGAATTATTTGCGACAGTTTT 57.359 26.923 0.00 0.00 0.00 2.43
737 746 6.815089 TCAAACTTTGATAGTTGCCACAATT 58.185 32.000 0.00 0.00 46.34 2.32
1558 1571 3.826729 TGAGATCGAGGAAGAGTTGTTCA 59.173 43.478 0.00 0.00 0.00 3.18
1758 1771 5.059161 GTGAATGATCCATGCTTGCTACTA 58.941 41.667 0.00 0.00 0.00 1.82
2221 2235 6.471146 GTTGGATCATACATTATCCTGCTCT 58.529 40.000 0.00 0.00 41.94 4.09
2418 2434 0.595825 GCTGTCAAGGTTGTGCTTGC 60.596 55.000 0.00 0.00 0.00 4.01
2595 2614 2.173356 TGGCCAAGCATGCTATAGACTT 59.827 45.455 23.00 0.00 0.00 3.01
2637 2657 7.662669 CCTCAAAAATTTGAAAAGTGGATGGAT 59.337 33.333 9.63 0.00 45.61 3.41
2663 2683 0.902984 TCAGCTCCGTCTTGCCCTTA 60.903 55.000 0.00 0.00 0.00 2.69
2690 2710 8.274322 TGAGGTAATCAAAATGTCCACATCTAT 58.726 33.333 0.00 0.00 32.88 1.98
2769 2789 7.296660 TGTTTTTGTTGATGCTTCTTGTTTTG 58.703 30.769 0.88 0.00 0.00 2.44
2887 2908 3.295273 TGCCTCTGACAGCGACGT 61.295 61.111 0.00 0.00 0.00 4.34
3276 3297 8.985805 GGTTCGACTCTCAATTTTAGTTTTCTA 58.014 33.333 0.00 0.00 0.00 2.10
3663 3685 1.881973 TCAATGCAACTGGTCTGCTTC 59.118 47.619 0.00 0.00 40.59 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 90 5.405279 TCAACCCCAAAACTAGACTAGGTA 58.595 41.667 14.03 0.00 0.00 3.08
127 129 7.036829 CACATTCAATCATACTGCCAATTTCA 58.963 34.615 0.00 0.00 0.00 2.69
554 558 9.884636 ATTCATTTAGTAAAATTTAGTTGCCCC 57.115 29.630 0.00 0.00 32.87 5.80
573 577 7.557358 TGTATGTGGCAACTATCTCATTCATTT 59.443 33.333 0.00 0.00 37.61 2.32
713 722 5.843673 TTGTGGCAACTATCAAAGTTTGA 57.156 34.783 20.14 20.14 46.61 2.69
737 746 0.830444 AGTTCCGTCCAGTGCTACCA 60.830 55.000 0.00 0.00 0.00 3.25
1558 1571 1.616367 ACCCAGGAAACAAACGGGT 59.384 52.632 0.00 0.00 45.53 5.28
1758 1771 0.806241 AACGCAACGAAAACACTGGT 59.194 45.000 0.00 0.00 0.00 4.00
2418 2434 2.809861 ATCAGTTGCCCTGTCTGCGG 62.810 60.000 0.96 0.00 42.19 5.69
2487 2505 4.597404 TGTCAAATTTGTAAGCATGCCA 57.403 36.364 15.66 1.92 0.00 4.92
2595 2614 4.966787 GGCCCCCAAACACGCTGA 62.967 66.667 0.00 0.00 0.00 4.26
2637 2657 1.748329 AAGACGGAGCTGAGTGCACA 61.748 55.000 21.04 0.00 45.94 4.57
2663 2683 7.121382 AGATGTGGACATTTTGATTACCTCAT 58.879 34.615 0.00 0.00 36.57 2.90
2690 2710 1.815613 CATGTAATCCACGGCAAACCA 59.184 47.619 0.00 0.00 34.57 3.67
2887 2908 1.891919 GTGAACTGCCTCGCAACCA 60.892 57.895 0.00 0.00 38.41 3.67
3111 3132 1.878953 TCTTTCACTTTCTCCGGTGC 58.121 50.000 0.00 0.00 33.91 5.01
3276 3297 7.639113 TTGTTCCAAAGAAAAGATACACAGT 57.361 32.000 0.00 0.00 32.58 3.55
3663 3685 6.237942 GGATGATAACAGAAGAACATGTGACG 60.238 42.308 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.