Multiple sequence alignment - TraesCS5D01G408700

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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 TraesCS5D01G408700 chr5D 100.000 2597 0 0 1 2597 473036335 473033739 0 4796
1 TraesCS5D01G408700 chr5D 97.468 1817 38 7 764 2578 421294668 421296478 0 3094
2 TraesCS5D01G408700 chr6D 97.760 2589 45 9 1 2578 449233528 449236114 0 4447
3 TraesCS5D01G408700 chr6D 96.915 2593 60 16 1 2578 418034098 418036685 0 4327
4 TraesCS5D01G408700 chr1D 97.527 2588 51 10 1 2578 155923078 155920494 0 4412
5 TraesCS5D01G408700 chr1D 96.895 773 16 5 1 769 33806299 33807067 0 1288
6 TraesCS5D01G408700 chr7D 97.450 2588 50 11 1 2578 440163763 440166344 0 4399
7 TraesCS5D01G408700 chr7D 96.946 2587 44 12 1 2578 403425131 403427691 0 4307
8 TraesCS5D01G408700 chr7D 96.023 2590 65 15 1 2578 590354634 590357197 0 4178
9 TraesCS5D01G408700 chr5A 94.050 2605 99 33 2 2579 598643344 598645919 0 3901
10 TraesCS5D01G408700 chr2D 97.577 1816 39 5 765 2578 43330494 43328682 0 3105
11 TraesCS5D01G408700 chr2D 97.801 773 11 3 1 769 14275003 14275773 0 1328
12 TraesCS5D01G408700 chr2D 97.552 776 10 6 1 769 43331070 43330297 0 1319


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 TraesCS5D01G408700 chr5D 473033739 473036335 2596 True 4796 4796 100.0000 1 2597 1 chr5D.!!$R1 2596
1 TraesCS5D01G408700 chr5D 421294668 421296478 1810 False 3094 3094 97.4680 764 2578 1 chr5D.!!$F1 1814
2 TraesCS5D01G408700 chr6D 449233528 449236114 2586 False 4447 4447 97.7600 1 2578 1 chr6D.!!$F2 2577
3 TraesCS5D01G408700 chr6D 418034098 418036685 2587 False 4327 4327 96.9150 1 2578 1 chr6D.!!$F1 2577
4 TraesCS5D01G408700 chr1D 155920494 155923078 2584 True 4412 4412 97.5270 1 2578 1 chr1D.!!$R1 2577
5 TraesCS5D01G408700 chr1D 33806299 33807067 768 False 1288 1288 96.8950 1 769 1 chr1D.!!$F1 768
6 TraesCS5D01G408700 chr7D 440163763 440166344 2581 False 4399 4399 97.4500 1 2578 1 chr7D.!!$F2 2577
7 TraesCS5D01G408700 chr7D 403425131 403427691 2560 False 4307 4307 96.9460 1 2578 1 chr7D.!!$F1 2577
8 TraesCS5D01G408700 chr7D 590354634 590357197 2563 False 4178 4178 96.0230 1 2578 1 chr7D.!!$F3 2577
9 TraesCS5D01G408700 chr5A 598643344 598645919 2575 False 3901 3901 94.0500 2 2579 1 chr5A.!!$F1 2577
10 TraesCS5D01G408700 chr2D 43328682 43331070 2388 True 2212 3105 97.5645 1 2578 2 chr2D.!!$R1 2577
11 TraesCS5D01G408700 chr2D 14275003 14275773 770 False 1328 1328 97.8010 1 769 1 chr2D.!!$F1 768

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
561 588 2.751259 ACAAATGAATCAGCGCATGTCT 59.249 40.909 11.47 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2496 3007 1.144057 CCTCCGCGTATGCTTTCCT 59.856 57.895 4.92 0.0 39.65 3.36 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
561 588 2.751259 ACAAATGAATCAGCGCATGTCT 59.249 40.909 11.47 0.00 0.00 3.41
719 755 6.238897 CCCAAACAAGTGTTTATAGTTGCTCA 60.239 38.462 9.01 0.00 45.54 4.26
1088 1521 2.056223 CCTTCTTGCATGCAGGGGG 61.056 63.158 27.32 23.71 0.00 5.40
1165 1598 8.136057 CAATGTTGGATCTAACACTACTCATC 57.864 38.462 24.81 0.00 42.74 2.92
1210 1643 1.507140 CCCACCTATGGTTGCTCCTA 58.493 55.000 0.00 0.00 45.66 2.94
1280 1713 1.102154 TCACAGCCACAACAACCTTG 58.898 50.000 0.00 0.00 0.00 3.61
1594 2027 3.163630 AGCAAACAAAATGTCGTGCTT 57.836 38.095 13.03 2.52 44.29 3.91
1668 2101 3.812053 GCAGATCATAACCATCCACTGAC 59.188 47.826 0.00 0.00 0.00 3.51
1679 2112 0.681733 TCCACTGACTGAGAAGCCAC 59.318 55.000 0.00 0.00 0.00 5.01
1680 2113 0.683973 CCACTGACTGAGAAGCCACT 59.316 55.000 0.00 0.00 0.00 4.00
1803 2236 7.012044 ACTCACATTGCGTTAAGTCTTTTTACT 59.988 33.333 0.00 0.00 0.00 2.24
1855 2312 3.450904 ACCTTGACCTGAGCCAACTATA 58.549 45.455 0.00 0.00 0.00 1.31
2571 3082 5.730550 ACCTCACGAACATGTACAATATGT 58.269 37.500 0.00 0.00 40.30 2.29
2579 3090 6.461386 CGAACATGTACAATATGTCGTTTGTG 59.539 38.462 0.00 0.00 37.77 3.33
2580 3091 6.795098 ACATGTACAATATGTCGTTTGTGT 57.205 33.333 0.00 0.00 36.75 3.72
2581 3092 7.197071 ACATGTACAATATGTCGTTTGTGTT 57.803 32.000 0.00 0.00 36.75 3.32
2582 3093 7.075121 ACATGTACAATATGTCGTTTGTGTTG 58.925 34.615 0.00 0.00 36.75 3.33
2583 3094 5.991568 TGTACAATATGTCGTTTGTGTTGG 58.008 37.500 0.00 0.00 36.75 3.77
2584 3095 4.497473 ACAATATGTCGTTTGTGTTGGG 57.503 40.909 0.00 0.00 34.87 4.12
2585 3096 3.254657 ACAATATGTCGTTTGTGTTGGGG 59.745 43.478 0.00 0.00 34.87 4.96
2586 3097 2.932855 TATGTCGTTTGTGTTGGGGA 57.067 45.000 0.00 0.00 0.00 4.81
2587 3098 2.286365 ATGTCGTTTGTGTTGGGGAT 57.714 45.000 0.00 0.00 0.00 3.85
2588 3099 1.600023 TGTCGTTTGTGTTGGGGATC 58.400 50.000 0.00 0.00 0.00 3.36
2589 3100 0.515564 GTCGTTTGTGTTGGGGATCG 59.484 55.000 0.00 0.00 0.00 3.69
2590 3101 0.107081 TCGTTTGTGTTGGGGATCGT 59.893 50.000 0.00 0.00 0.00 3.73
2591 3102 1.343789 TCGTTTGTGTTGGGGATCGTA 59.656 47.619 0.00 0.00 0.00 3.43
2592 3103 2.144730 CGTTTGTGTTGGGGATCGTAA 58.855 47.619 0.00 0.00 0.00 3.18
2593 3104 2.096119 CGTTTGTGTTGGGGATCGTAAC 60.096 50.000 0.00 0.00 0.00 2.50
2594 3105 2.879646 GTTTGTGTTGGGGATCGTAACA 59.120 45.455 4.54 4.54 32.39 2.41
2595 3106 2.465860 TGTGTTGGGGATCGTAACAG 57.534 50.000 7.91 0.00 35.24 3.16
2596 3107 1.972075 TGTGTTGGGGATCGTAACAGA 59.028 47.619 7.91 5.16 35.24 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
561 588 8.316640 ACAACAGCAAAGATTTGTTTTTACAA 57.683 26.923 7.12 0.00 40.24 2.41
1088 1521 4.984161 CCAATTGTTGATGTTCCTGTTCAC 59.016 41.667 4.43 0.00 0.00 3.18
1165 1598 1.635663 GCAACACGATTGTCCGGGAG 61.636 60.000 0.00 0.00 36.28 4.30
1210 1643 8.284792 ATGTGCCTCATGAACTAAAGCATTAGT 61.285 37.037 8.51 8.51 42.95 2.24
1280 1713 2.502510 CGAAGCGCATGCCAACAC 60.503 61.111 13.15 0.00 44.31 3.32
1463 1896 1.808411 TTTGCTCGATGAGGGAACAC 58.192 50.000 0.00 0.00 0.00 3.32
1594 2027 6.121776 TCTTTAAGCTTCACCACCATCTTA 57.878 37.500 0.00 0.00 0.00 2.10
1679 2112 2.618053 ACGGAGGTATTTCGAAAGCAG 58.382 47.619 16.80 6.45 0.00 4.24
1680 2113 2.754946 ACGGAGGTATTTCGAAAGCA 57.245 45.000 16.80 3.83 0.00 3.91
1803 2236 6.999950 TGCAGGAATAAGTAACAGTTCTGTA 58.000 36.000 5.87 0.00 0.00 2.74
2496 3007 1.144057 CCTCCGCGTATGCTTTCCT 59.856 57.895 4.92 0.00 39.65 3.36
2571 3082 0.107081 ACGATCCCCAACACAAACGA 59.893 50.000 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.