Multiple sequence alignment - TraesCS2B01G284000

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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 TraesCS2B01G284000 chr2B 100.000 2744 0 0 1 2744 391226252 391223509 0 5068
1 TraesCS2B01G284000 chr2B 97.414 2746 65 3 1 2744 391143796 391146537 0 4673
2 TraesCS2B01G284000 chr6B 98.471 2746 38 3 1 2744 596602867 596600124 0 4835
3 TraesCS2B01G284000 chr6B 98.111 2170 38 3 577 2744 715991505 715989337 0 3777
4 TraesCS2B01G284000 chr7A 98.325 2746 42 4 1 2744 638508674 638505931 0 4813
5 TraesCS2B01G284000 chr7A 98.288 2745 42 3 1 2744 708244618 708247358 0 4804
6 TraesCS2B01G284000 chrUn 98.325 2746 41 4 1 2744 171007277 171010019 0 4811
7 TraesCS2B01G284000 chr5B 97.961 2747 52 4 1 2744 567278986 567281731 0 4759
8 TraesCS2B01G284000 chr1B 97.743 2747 55 5 1 2744 672540215 672542957 0 4723
9 TraesCS2B01G284000 chr4B 97.413 2745 63 4 1 2744 495566957 495569694 0 4669


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 TraesCS2B01G284000 chr2B 391223509 391226252 2743 True 5068 5068 100.000 1 2744 1 chr2B.!!$R1 2743
1 TraesCS2B01G284000 chr2B 391143796 391146537 2741 False 4673 4673 97.414 1 2744 1 chr2B.!!$F1 2743
2 TraesCS2B01G284000 chr6B 596600124 596602867 2743 True 4835 4835 98.471 1 2744 1 chr6B.!!$R1 2743
3 TraesCS2B01G284000 chr6B 715989337 715991505 2168 True 3777 3777 98.111 577 2744 1 chr6B.!!$R2 2167
4 TraesCS2B01G284000 chr7A 638505931 638508674 2743 True 4813 4813 98.325 1 2744 1 chr7A.!!$R1 2743
5 TraesCS2B01G284000 chr7A 708244618 708247358 2740 False 4804 4804 98.288 1 2744 1 chr7A.!!$F1 2743
6 TraesCS2B01G284000 chrUn 171007277 171010019 2742 False 4811 4811 98.325 1 2744 1 chrUn.!!$F1 2743
7 TraesCS2B01G284000 chr5B 567278986 567281731 2745 False 4759 4759 97.961 1 2744 1 chr5B.!!$F1 2743
8 TraesCS2B01G284000 chr1B 672540215 672542957 2742 False 4723 4723 97.743 1 2744 1 chr1B.!!$F1 2743
9 TraesCS2B01G284000 chr4B 495566957 495569694 2737 False 4669 4669 97.413 1 2744 1 chr4B.!!$F1 2743

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
120 121 1.287146 ACTAGTGATAGGTGGTCCCGT 59.713 52.381 0.00 0.0 38.74 5.28 F
568 569 1.330655 CCCTAAGCCCAGCTTCTCGA 61.331 60.000 4.87 0.0 46.77 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1106 1111 2.737783 TGTACCGGATTTTTAGCACGTG 59.262 45.455 9.46 12.28 0.00 4.49 R
2407 2419 4.985538 AGTAAACAGGAGATTCCTTTGCA 58.014 39.130 0.00 0.00 46.91 4.08 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
120 121 1.287146 ACTAGTGATAGGTGGTCCCGT 59.713 52.381 0.00 0.00 38.74 5.28
289 290 4.346730 TCATACGGGAAAGTGAACTCCTA 58.653 43.478 0.00 0.00 31.88 2.94
476 477 2.427506 GATAATCATTCCGGTCCTGGC 58.572 52.381 0.00 0.00 0.00 4.85
568 569 1.330655 CCCTAAGCCCAGCTTCTCGA 61.331 60.000 4.87 0.00 46.77 4.04
589 590 2.821546 AGCTGCTATTGCGAAATACGA 58.178 42.857 0.00 0.00 45.77 3.43
671 672 2.632996 CCGGGCCTAGATTAGATGTTCA 59.367 50.000 0.84 0.00 0.00 3.18
778 783 6.331369 CTTCAACAGAAGCCCTTAAAATCA 57.669 37.500 0.00 0.00 33.07 2.57
781 786 5.774690 TCAACAGAAGCCCTTAAAATCATGT 59.225 36.000 0.00 0.00 0.00 3.21
1012 1017 3.390135 TCGACTTGAATGCGTCTTCTTT 58.610 40.909 0.00 0.00 0.00 2.52
1048 1053 2.196595 TCCATTTCAAGGGAGGACGAT 58.803 47.619 0.00 0.00 33.26 3.73
1106 1111 1.541588 GGTCTCTGGTTTGATGGTTGC 59.458 52.381 0.00 0.00 0.00 4.17
1238 1244 7.179338 CCCAGTAGTTCATATAGGAGCTATTGT 59.821 40.741 22.65 8.20 36.94 2.71
1403 1409 4.938575 TTCCATTACTACCAACCCACAT 57.061 40.909 0.00 0.00 0.00 3.21
1438 1444 5.773176 TCTCTGAGATATACGGTTTATGCCA 59.227 40.000 2.58 0.00 0.00 4.92
1633 1639 2.813354 GCCTTGGATTCTAGGAGCCATG 60.813 54.545 9.34 11.59 37.99 3.66
1740 1746 8.887036 ACAAAGAAACCTTTAAAATGTGGATC 57.113 30.769 0.00 0.00 32.94 3.36
1847 1853 0.772384 ATGGTAAACACGTTCCCCCA 59.228 50.000 0.00 0.00 0.00 4.96
2086 2096 0.252284 GGAAGAGTGGGTCAGAGGGA 60.252 60.000 0.00 0.00 0.00 4.20
2312 2324 1.064825 TTTCGGAAGGAGGAAGGCTT 58.935 50.000 0.00 0.00 0.00 4.35
2401 2413 3.885724 TTCTATTGTGTGCTCGATCCA 57.114 42.857 0.00 0.00 0.00 3.41
2407 2419 4.341366 TTGTGTGCTCGATCCATGATAT 57.659 40.909 0.00 0.00 0.00 1.63
2414 2426 3.126514 GCTCGATCCATGATATGCAAAGG 59.873 47.826 0.00 0.00 0.00 3.11
2613 2625 3.087031 CCAAACTTGGCATGACTCATCT 58.913 45.455 7.45 0.00 42.21 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
120 121 1.149101 ACCCTTCTCCAAAAGCTCCA 58.851 50.000 0.00 0.00 0.00 3.86
129 130 1.361543 ACACTAGGCTACCCTTCTCCA 59.638 52.381 0.00 0.00 42.87 3.86
568 569 3.001330 GTCGTATTTCGCAATAGCAGCTT 59.999 43.478 0.00 0.00 42.27 3.74
1012 1017 3.726557 ATGGAACTTGAATGCTGGAGA 57.273 42.857 0.00 0.00 0.00 3.71
1106 1111 2.737783 TGTACCGGATTTTTAGCACGTG 59.262 45.455 9.46 12.28 0.00 4.49
1238 1244 7.990314 TCATAACCATGAATAGGAATGAAACGA 59.010 33.333 0.00 0.00 38.25 3.85
1403 1409 7.548427 CCGTATATCTCAGAGAGGTCGTATTTA 59.452 40.741 6.24 0.00 0.00 1.40
1438 1444 5.796424 TTAGTCCAACTTCGTACCTTTCT 57.204 39.130 0.00 0.00 0.00 2.52
1633 1639 8.794335 AAAGGAGAAATAGTCCTGTTCATTAC 57.206 34.615 0.00 0.00 44.17 1.89
1740 1746 9.213799 GGAAAATCCTTATATTCTGAGCACTAG 57.786 37.037 0.00 0.00 32.53 2.57
1764 1770 5.590259 GTCTATCTTGCATTTTAAGCCAGGA 59.410 40.000 0.00 0.00 0.00 3.86
2086 2096 5.843421 AGAGAGGTATGCACTATGAAGGAAT 59.157 40.000 0.00 0.00 0.00 3.01
2312 2324 9.738832 TTCTACACGATATTCGATAATGAAACA 57.261 29.630 3.62 0.00 43.74 2.83
2401 2413 5.950023 ACAGGAGATTCCTTTGCATATCAT 58.050 37.500 0.00 0.00 46.91 2.45
2407 2419 4.985538 AGTAAACAGGAGATTCCTTTGCA 58.014 39.130 0.00 0.00 46.91 4.08
2613 2625 8.267620 AGGTAAGATCATGAATACAAGATGGA 57.732 34.615 0.00 0.00 35.11 3.41


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

AutoCloner maintained by Alex Coulton.