Multiple sequence alignment - TraesCS2D01G216500

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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 TraesCS2D01G216500 chr2D 100.000 2639 0 0 1 2639 179287418 179284780 0 4874
1 TraesCS2D01G216500 chr2A 92.210 2118 78 26 1 2066 193735761 193733679 0 2916
2 TraesCS2D01G216500 chr2A 90.502 558 47 4 2086 2639 7799623 7800178 0 732
3 TraesCS2D01G216500 chr2B 88.635 1663 89 48 456 2088 236102315 236100723 0 1932
4 TraesCS2D01G216500 chr2B 92.986 556 34 3 2086 2639 707597808 707598360 0 806
5 TraesCS2D01G216500 chr2B 91.562 557 41 5 2086 2639 94869130 94868577 0 763
6 TraesCS2D01G216500 chr2B 92.324 469 27 4 1 460 236102819 236102351 0 658
7 TraesCS2D01G216500 chr6D 98.736 554 7 0 2086 2639 248021566 248021013 0 985
8 TraesCS2D01G216500 chr3D 97.834 554 11 1 2086 2639 415190122 415189570 0 955
9 TraesCS2D01G216500 chr3B 92.613 555 37 3 2086 2639 732849628 732850179 0 795
10 TraesCS2D01G216500 chr1A 91.055 559 43 4 2086 2639 547412894 547412338 0 749
11 TraesCS2D01G216500 chr5B 90.340 559 47 5 2086 2639 290032434 290031878 0 726
12 TraesCS2D01G216500 chr7A 89.910 555 49 3 2086 2639 89980862 89980314 0 708


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 TraesCS2D01G216500 chr2D 179284780 179287418 2638 True 4874 4874 100.0000 1 2639 1 chr2D.!!$R1 2638
1 TraesCS2D01G216500 chr2A 193733679 193735761 2082 True 2916 2916 92.2100 1 2066 1 chr2A.!!$R1 2065
2 TraesCS2D01G216500 chr2A 7799623 7800178 555 False 732 732 90.5020 2086 2639 1 chr2A.!!$F1 553
3 TraesCS2D01G216500 chr2B 236100723 236102819 2096 True 1295 1932 90.4795 1 2088 2 chr2B.!!$R2 2087
4 TraesCS2D01G216500 chr2B 707597808 707598360 552 False 806 806 92.9860 2086 2639 1 chr2B.!!$F1 553
5 TraesCS2D01G216500 chr2B 94868577 94869130 553 True 763 763 91.5620 2086 2639 1 chr2B.!!$R1 553
6 TraesCS2D01G216500 chr6D 248021013 248021566 553 True 985 985 98.7360 2086 2639 1 chr6D.!!$R1 553
7 TraesCS2D01G216500 chr3D 415189570 415190122 552 True 955 955 97.8340 2086 2639 1 chr3D.!!$R1 553
8 TraesCS2D01G216500 chr3B 732849628 732850179 551 False 795 795 92.6130 2086 2639 1 chr3B.!!$F1 553
9 TraesCS2D01G216500 chr1A 547412338 547412894 556 True 749 749 91.0550 2086 2639 1 chr1A.!!$R1 553
10 TraesCS2D01G216500 chr5B 290031878 290032434 556 True 726 726 90.3400 2086 2639 1 chr5B.!!$R1 553
11 TraesCS2D01G216500 chr7A 89980314 89980862 548 True 708 708 89.9100 2086 2639 1 chr7A.!!$R1 553

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
152 161 0.821711 TTTCCCTTGCCAACTGTCCG 60.822 55.000 0.0 0.0 0.00 4.79 F
629 706 1.006220 GGCCCAAACAAAAGCCTCG 60.006 57.895 0.0 0.0 42.34 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1326 1445 0.459489 GCACCACTTCCAAGCACAAA 59.541 50.0 0.0 0.0 0.00 2.83 R
1844 1969 0.937699 TGCGAGAACAGTACGTGTGC 60.938 55.0 0.0 0.0 40.26 4.57 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
105 113 7.015682 AGAGGGATTAACATGTACAGAGGTATG 59.984 40.741 0.00 0.00 0.00 2.39
152 161 0.821711 TTTCCCTTGCCAACTGTCCG 60.822 55.000 0.00 0.00 0.00 4.79
227 244 8.560903 ACTAGGGACTCCAAGATATTTTGAAAT 58.439 33.333 7.53 0.00 41.75 2.17
228 245 9.413734 CTAGGGACTCCAAGATATTTTGAAATT 57.586 33.333 7.53 0.00 41.75 1.82
289 306 1.071605 AGCGCACGAGATCTTTGTTC 58.928 50.000 11.47 0.00 0.00 3.18
341 364 6.480524 TCTGAATACAATACAACACACAGC 57.519 37.500 0.00 0.00 0.00 4.40
521 585 1.301009 GTAGCGAGCACATAGGCCC 60.301 63.158 0.00 0.00 0.00 5.80
526 590 1.302949 GAGCACATAGGCCCAACCA 59.697 57.895 0.00 0.00 43.14 3.67
529 593 1.315257 GCACATAGGCCCAACCAGTG 61.315 60.000 0.00 1.24 43.14 3.66
629 706 1.006220 GGCCCAAACAAAAGCCTCG 60.006 57.895 0.00 0.00 42.34 4.63
674 756 1.339929 GCGTCCAACAAAGTCCCAAAT 59.660 47.619 0.00 0.00 0.00 2.32
678 760 4.440802 CGTCCAACAAAGTCCCAAATTGAA 60.441 41.667 0.00 0.00 0.00 2.69
768 863 2.029964 GTCCGTTTCCCACTCGCA 59.970 61.111 0.00 0.00 0.00 5.10
777 872 3.046087 CCACTCGCACTGCACCAG 61.046 66.667 1.11 0.00 37.52 4.00
821 917 1.754745 CCCCACACACACTAGCACT 59.245 57.895 0.00 0.00 0.00 4.40
861 965 1.677576 CTCACGCCCGTATAAGTACCA 59.322 52.381 0.00 0.00 0.00 3.25
866 970 1.202452 GCCCGTATAAGTACCACGCTT 60.202 52.381 0.00 0.00 34.42 4.68
1173 1292 1.579429 CCGCCGGGAAAAAGACTTG 59.421 57.895 2.18 0.00 34.06 3.16
1278 1397 3.111939 CTGGACTCGGCCTACTCG 58.888 66.667 0.00 0.00 0.00 4.18
1296 1415 3.430497 TCCTCCTCCTCCTCCCGG 61.430 72.222 0.00 0.00 0.00 5.73
1326 1445 1.293683 GGTCCTCCTCCTCCTCCTCT 61.294 65.000 0.00 0.00 0.00 3.69
1350 1469 1.109323 GCTTGGAAGTGGTGCCAACT 61.109 55.000 0.00 0.00 39.14 3.16
1844 1969 0.960861 GGAAAGAGGAAAGTGCCGGG 60.961 60.000 2.18 0.00 0.00 5.73
1886 2013 0.108585 AATCATCTATTGCGGGCGGT 59.891 50.000 0.00 0.00 0.00 5.68
1964 2092 5.569441 CGATGGTGCGAGTATTTCTATACTG 59.431 44.000 2.74 0.00 45.43 2.74
2005 2133 1.927487 AGCTTGCAAATGATGGGTCA 58.073 45.000 0.00 0.00 39.04 4.02
2021 2149 2.037687 CATGGGGGCTTTCTGGCA 59.962 61.111 0.00 0.00 43.83 4.92
2025 2153 2.353610 GGGGGCTTTCTGGCATGTG 61.354 63.158 0.00 0.00 43.83 3.21
2120 2248 1.885887 GTGGTGCTTGAACTTGCCATA 59.114 47.619 0.00 0.00 0.00 2.74
2137 2265 3.531538 CCATAGATGTGCGGTTTAGTGT 58.468 45.455 0.00 0.00 0.00 3.55
2380 2522 5.422145 AGAAACTGACAATTTTGCTGCTTT 58.578 33.333 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 50 6.881065 TCATGTTGGAATAGGAGAAAAGACTG 59.119 38.462 0.00 0.00 0.00 3.51
105 113 5.642491 CCTAATAAAATCCTTACGGGCTAGC 59.358 44.000 6.04 6.04 34.39 3.42
152 161 6.316640 GGAGTAGAAAAGATTAACAAGAGGCC 59.683 42.308 0.00 0.00 0.00 5.19
227 244 1.003580 CCTGCCAGAGTGGAGCTTTAA 59.996 52.381 0.00 0.00 40.96 1.52
228 245 0.615331 CCTGCCAGAGTGGAGCTTTA 59.385 55.000 0.00 0.00 40.96 1.85
289 306 1.606224 GGCATTGTTTGGGTGAAGCTG 60.606 52.381 0.00 0.00 0.00 4.24
426 449 4.927782 TGAGGCCGTGTGGTGTGC 62.928 66.667 0.00 0.00 37.67 4.57
570 634 2.927580 TTGACCGGACGGACTCTGC 61.928 63.158 18.80 0.35 38.96 4.26
652 729 1.890510 GGGACTTTGTTGGACGCGT 60.891 57.895 13.85 13.85 0.00 6.01
653 730 1.440938 TTGGGACTTTGTTGGACGCG 61.441 55.000 3.53 3.53 0.00 6.01
654 731 0.741915 TTTGGGACTTTGTTGGACGC 59.258 50.000 0.00 0.00 0.00 5.19
655 732 3.067461 TCAATTTGGGACTTTGTTGGACG 59.933 43.478 0.00 0.00 0.00 4.79
768 863 2.519302 GTGGTTGGCTGGTGCAGT 60.519 61.111 0.00 0.00 41.91 4.40
821 917 1.469251 GCGTTACTGCTGCTAGTGCTA 60.469 52.381 12.80 0.00 40.48 3.49
861 965 2.338984 GTGTCCGTCTCCAAGCGT 59.661 61.111 0.00 0.00 0.00 5.07
866 970 3.371063 GCTCCGTGTCCGTCTCCA 61.371 66.667 0.00 0.00 0.00 3.86
907 1014 2.048597 CGTGTGTCGCCTGGCTTA 60.049 61.111 17.92 1.32 0.00 3.09
1278 1397 2.123640 CGGGAGGAGGAGGAGGAC 60.124 72.222 0.00 0.00 0.00 3.85
1296 1415 3.462678 GAGGACCGGGAGCAGGAC 61.463 72.222 6.32 0.00 0.00 3.85
1326 1445 0.459489 GCACCACTTCCAAGCACAAA 59.541 50.000 0.00 0.00 0.00 2.83
1524 1643 3.730761 GACGCAACCAGCAGGCTG 61.731 66.667 10.94 10.94 46.13 4.85
1844 1969 0.937699 TGCGAGAACAGTACGTGTGC 60.938 55.000 0.00 0.00 40.26 4.57
1886 2013 5.450826 GCAACATGCATGATGGAATCAGTTA 60.451 40.000 32.75 0.00 45.81 2.24
1915 2042 6.681865 GCAAAGTTTGGTTTCCACTAGCTAAA 60.682 38.462 17.11 0.00 30.78 1.85
1964 2092 3.221964 TCTAAAAGTTACTCGTCCGCC 57.778 47.619 0.00 0.00 0.00 6.13
2005 2133 1.382146 CATGCCAGAAAGCCCCCAT 60.382 57.895 0.00 0.00 0.00 4.00
2042 2170 9.807649 CTATGGAAATAAATTTCTTTCACCTGG 57.192 33.333 22.91 10.37 44.21 4.45
2072 2200 6.478016 GTGTATTTACCTCGATTGTAACCCTC 59.522 42.308 7.07 1.80 0.00 4.30
2120 2248 2.299013 TCAGACACTAAACCGCACATCT 59.701 45.455 0.00 0.00 0.00 2.90
2380 2522 3.065233 GCGCAAGGTTATGAATCATCACA 59.935 43.478 0.30 0.00 36.53 3.58


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

AutoCloner maintained by Alex Coulton.