Multiple sequence alignment - TraesCS3D01G289800

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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 TraesCS3D01G289800 chr3D 100.000 3389 0 0 1 3389 399840807 399837419 0 6259
1 TraesCS3D01G289800 chr3D 95.211 522 21 4 2871 3389 507104503 507105023 0 822
2 TraesCS3D01G289800 chr3D 95.019 522 22 4 2871 3389 360314041 360313521 0 817
3 TraesCS3D01G289800 chr3D 94.242 521 27 3 2871 3389 13643845 13643326 0 793
4 TraesCS3D01G289800 chr5D 97.704 2875 60 3 1 2870 562925174 562928047 0 4939
5 TraesCS3D01G289800 chr5D 94.646 523 23 5 2870 3389 357466281 357466801 0 806
6 TraesCS3D01G289800 chr5D 94.636 522 24 3 2870 3389 373581543 373581024 0 806
7 TraesCS3D01G289800 chr1A 97.670 2875 57 3 1 2870 94765603 94762734 0 4929
8 TraesCS3D01G289800 chr7A 97.565 2875 65 2 1 2870 211308107 211310981 0 4916
9 TraesCS3D01G289800 chr7A 97.113 2875 78 2 1 2870 563544632 563547506 0 4844
10 TraesCS3D01G289800 chr2D 97.530 2875 66 2 1 2870 200934935 200937809 0 4911
11 TraesCS3D01G289800 chr2D 96.902 2873 83 3 1 2868 604416906 604419777 0 4807
12 TraesCS3D01G289800 chr2D 94.778 517 26 1 2871 3386 45023185 45022669 0 804
13 TraesCS3D01G289800 chr2D 94.231 520 26 4 2871 3388 62272602 62272085 0 791
14 TraesCS3D01G289800 chr1D 97.530 2875 64 3 1 2870 185786577 185783705 0 4909
15 TraesCS3D01G289800 chr6D 97.861 2805 55 2 71 2870 458889921 458892725 0 4843
16 TraesCS3D01G289800 chr7D 96.765 2875 88 2 1 2870 307118245 307115371 0 4789
17 TraesCS3D01G289800 chr7D 94.061 522 27 4 2871 3389 22185372 22184852 0 789
18 TraesCS3D01G289800 chr4D 95.954 519 16 3 2871 3387 381725757 381726272 0 837


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 TraesCS3D01G289800 chr3D 399837419 399840807 3388 True 6259 6259 100.000 1 3389 1 chr3D.!!$R3 3388
1 TraesCS3D01G289800 chr3D 507104503 507105023 520 False 822 822 95.211 2871 3389 1 chr3D.!!$F1 518
2 TraesCS3D01G289800 chr3D 360313521 360314041 520 True 817 817 95.019 2871 3389 1 chr3D.!!$R2 518
3 TraesCS3D01G289800 chr3D 13643326 13643845 519 True 793 793 94.242 2871 3389 1 chr3D.!!$R1 518
4 TraesCS3D01G289800 chr5D 562925174 562928047 2873 False 4939 4939 97.704 1 2870 1 chr5D.!!$F2 2869
5 TraesCS3D01G289800 chr5D 357466281 357466801 520 False 806 806 94.646 2870 3389 1 chr5D.!!$F1 519
6 TraesCS3D01G289800 chr5D 373581024 373581543 519 True 806 806 94.636 2870 3389 1 chr5D.!!$R1 519
7 TraesCS3D01G289800 chr1A 94762734 94765603 2869 True 4929 4929 97.670 1 2870 1 chr1A.!!$R1 2869
8 TraesCS3D01G289800 chr7A 211308107 211310981 2874 False 4916 4916 97.565 1 2870 1 chr7A.!!$F1 2869
9 TraesCS3D01G289800 chr7A 563544632 563547506 2874 False 4844 4844 97.113 1 2870 1 chr7A.!!$F2 2869
10 TraesCS3D01G289800 chr2D 200934935 200937809 2874 False 4911 4911 97.530 1 2870 1 chr2D.!!$F1 2869
11 TraesCS3D01G289800 chr2D 604416906 604419777 2871 False 4807 4807 96.902 1 2868 1 chr2D.!!$F2 2867
12 TraesCS3D01G289800 chr2D 45022669 45023185 516 True 804 804 94.778 2871 3386 1 chr2D.!!$R1 515
13 TraesCS3D01G289800 chr2D 62272085 62272602 517 True 791 791 94.231 2871 3388 1 chr2D.!!$R2 517
14 TraesCS3D01G289800 chr1D 185783705 185786577 2872 True 4909 4909 97.530 1 2870 1 chr1D.!!$R1 2869
15 TraesCS3D01G289800 chr6D 458889921 458892725 2804 False 4843 4843 97.861 71 2870 1 chr6D.!!$F1 2799
16 TraesCS3D01G289800 chr7D 307115371 307118245 2874 True 4789 4789 96.765 1 2870 1 chr7D.!!$R2 2869
17 TraesCS3D01G289800 chr7D 22184852 22185372 520 True 789 789 94.061 2871 3389 1 chr7D.!!$R1 518
18 TraesCS3D01G289800 chr4D 381725757 381726272 515 False 837 837 95.954 2871 3387 1 chr4D.!!$F1 516

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
856 857 3.389329 AGAAGTGTTCTCTTTCTCCAGCA 59.611 43.478 0.00 0.00 34.07 4.41 F
1742 1749 2.182825 CTAACGCTTTCGAGCACGTAT 58.817 47.619 2.86 3.72 37.87 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1744 1751 0.536006 GCTCTATCAAAGGGCGCCAT 60.536 55.0 30.85 21.35 43.3 4.40 R
3162 3171 1.012486 CCCTGCGTCGGTAACTTCAC 61.012 60.0 0.00 0.00 0.0 3.18 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
35 36 6.709018 ATTGGCTTATACCACAATGTTACC 57.291 37.500 0.00 0.00 40.19 2.85
164 165 4.392921 AGACATGAGGTTCTTCATACCG 57.607 45.455 0.00 0.00 40.69 4.02
627 628 4.285517 TCTGCCTGTGAAAAGAAGAGAGAT 59.714 41.667 0.00 0.00 0.00 2.75
688 689 5.353123 TCAAGCAAAGACTGTTCGTAAGTTT 59.647 36.000 0.00 0.00 39.48 2.66
856 857 3.389329 AGAAGTGTTCTCTTTCTCCAGCA 59.611 43.478 0.00 0.00 34.07 4.41
946 947 4.279145 AGTCTAGTTTTCTCGCCCTATCA 58.721 43.478 0.00 0.00 0.00 2.15
1290 1291 4.524316 TGCAACAGCAAGCTGAATAATT 57.476 36.364 27.17 8.85 46.30 1.40
1327 1332 5.571285 AGGAAAGAAAGAATAGGGTTGTCC 58.429 41.667 0.00 0.00 0.00 4.02
1514 1519 2.291217 GCAAGGGGAATCAGAGAAAGGT 60.291 50.000 0.00 0.00 0.00 3.50
1587 1593 2.225041 CCCCCGGATCTACTAGTCATCA 60.225 54.545 0.73 0.00 0.00 3.07
1657 1664 3.522343 AGGAAGGAAAGGTATGTGGGTAC 59.478 47.826 0.00 0.00 0.00 3.34
1713 1720 6.876257 CACTAGAGAAAAGCAAGGACAAGTAT 59.124 38.462 0.00 0.00 0.00 2.12
1742 1749 2.182825 CTAACGCTTTCGAGCACGTAT 58.817 47.619 2.86 3.72 37.87 3.06
1744 1751 0.109458 ACGCTTTCGAGCACGTATGA 60.109 50.000 2.86 0.00 40.69 2.15
1751 1758 2.588877 AGCACGTATGATGGCGCC 60.589 61.111 22.73 22.73 0.00 6.53
1770 1777 3.369147 CGCCCTTTGATAGAGCATTATCG 59.631 47.826 0.00 0.00 33.63 2.92
1900 1907 2.816411 AGAAGGAATGTCGACCTACCA 58.184 47.619 14.12 0.00 35.25 3.25
2083 2090 7.333528 ACTCTTGACTATTGCTTGAAACAAA 57.666 32.000 0.00 0.00 0.00 2.83
2204 2211 2.646798 ACAAGGCTGAGGAAGGATTTCT 59.353 45.455 0.00 0.00 33.68 2.52
2289 2296 3.194968 GGAACAACTATGGAAGTCCTCGA 59.805 47.826 0.00 0.00 37.50 4.04
2478 2485 2.688507 AGCTGTACTGGAATGACAACG 58.311 47.619 1.65 0.00 0.00 4.10
2666 2673 5.461516 TGGGGACTACTACAACAGATAGA 57.538 43.478 0.00 0.00 0.00 1.98
2845 2852 3.695060 CCAGGAACGTCATCTACTACTGT 59.305 47.826 0.00 0.00 0.00 3.55
2967 2976 2.816087 GAGTGTTGTCTACGTACCCTCA 59.184 50.000 0.00 0.00 0.00 3.86
2978 2987 3.620488 ACGTACCCTCATAGACCGTAAA 58.380 45.455 0.00 0.00 0.00 2.01
3103 3112 0.038526 GTGACGTCCCACGAACTCAT 60.039 55.000 14.12 0.00 46.05 2.90
3115 3124 4.038522 CCACGAACTCATGATCCAGTAGAT 59.961 45.833 0.00 0.00 38.17 1.98
3162 3171 2.677003 GGCGTGATGACGGTGTTGG 61.677 63.158 6.88 0.00 46.20 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 3.423539 TTTGTCAAGGATCCTGTCAGG 57.576 47.619 17.02 13.21 36.46 3.86
164 165 5.416952 CCAATACTGGGAGAATGATTATGCC 59.583 44.000 3.20 3.20 39.30 4.40
627 628 4.103469 TGGACAGCCTTTCTTAAAGTGGTA 59.897 41.667 0.00 0.00 36.77 3.25
856 857 3.194005 TCCTGCGAGACTGTTCTTTTT 57.806 42.857 0.00 0.00 29.47 1.94
936 937 2.454336 TCCTTCTCTTGATAGGGCGA 57.546 50.000 0.00 0.00 0.00 5.54
1098 1099 1.339727 GGGCTGACGAATAACCAACCT 60.340 52.381 0.00 0.00 0.00 3.50
1327 1332 4.693283 TCTAATCCAAACAGCGTATCAGG 58.307 43.478 0.00 0.00 0.00 3.86
1514 1519 7.094677 CATGGTCATGATTGTTGACTAAACAGA 60.095 37.037 0.00 0.00 44.09 3.41
1612 1619 2.437085 TCAGGAATAGCCGACTCAGA 57.563 50.000 0.00 0.00 43.43 3.27
1637 1644 4.259356 GTGTACCCACATACCTTTCCTTC 58.741 47.826 0.00 0.00 41.44 3.46
1657 1664 8.396390 CCTTCATTCAATCTCTAACTCAATGTG 58.604 37.037 0.00 0.00 0.00 3.21
1713 1720 4.720090 CTCGAAAGCGTTAGTCAACTAGA 58.280 43.478 0.00 0.00 38.98 2.43
1742 1749 0.836606 TCTATCAAAGGGCGCCATCA 59.163 50.000 30.85 9.53 0.00 3.07
1744 1751 0.536006 GCTCTATCAAAGGGCGCCAT 60.536 55.000 30.85 21.35 43.30 4.40
1751 1758 6.073548 GGTTGTCGATAATGCTCTATCAAAGG 60.074 42.308 0.00 0.00 0.00 3.11
1770 1777 4.894784 TCATAGTTCACTTCAGGGTTGTC 58.105 43.478 0.00 0.00 0.00 3.18
1989 1996 4.819088 TGCACACAACAATAAAGACTGCTA 59.181 37.500 0.00 0.00 0.00 3.49
1991 1998 3.963665 TGCACACAACAATAAAGACTGC 58.036 40.909 0.00 0.00 0.00 4.40
2083 2090 3.550842 GCTTCTTTCCATTGCTTCAACGT 60.551 43.478 0.00 0.00 0.00 3.99
2204 2211 3.138884 TCAAGAGCATTGTGGCAGTAA 57.861 42.857 0.00 0.00 35.83 2.24
2289 2296 5.692613 TTTCCGTGAAATATTCGTTTGGT 57.307 34.783 0.00 0.00 0.00 3.67
2478 2485 7.084486 TGTATCGTGTACAGATTCTCATATGC 58.916 38.462 11.43 0.00 0.00 3.14
2666 2673 2.698274 GGTGGTTTGGTCCTTCAAATGT 59.302 45.455 0.00 0.00 38.64 2.71
2845 2852 3.315949 CGTCCCCCGGGAGTTTCA 61.316 66.667 26.32 0.00 46.16 2.69
2978 2987 2.397549 GCGTTGTAGTAACACTTCCGT 58.602 47.619 0.00 0.00 34.61 4.69
2990 2999 2.597305 GACTACATCAACCGCGTTGTAG 59.403 50.000 19.64 19.64 43.23 2.74
2991 3000 2.598589 GACTACATCAACCGCGTTGTA 58.401 47.619 16.97 10.48 43.23 2.41
3115 3124 1.452289 CGAAGCTCTCCCTCGAGGA 60.452 63.158 33.39 17.24 44.91 3.71
3117 3126 1.027255 TGACGAAGCTCTCCCTCGAG 61.027 60.000 11.49 5.13 37.48 4.04
3162 3171 1.012486 CCCTGCGTCGGTAACTTCAC 61.012 60.000 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.