Multiple sequence alignment - TraesCS6A01G069100

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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 TraesCS6A01G069100 chr6A 100.000 2570 0 0 1 2570 37417252 37419821 0 4747
1 TraesCS6A01G069100 chr6A 95.721 2594 56 13 4 2570 532336283 532333718 0 4124
2 TraesCS6A01G069100 chr6A 94.034 2598 88 21 1 2570 558828864 558831422 0 3877
3 TraesCS6A01G069100 chr6A 93.886 2061 69 19 1 2034 615748506 615750536 0 3055
4 TraesCS6A01G069100 chr6A 95.446 505 14 1 4 499 532336901 532336397 0 797
5 TraesCS6A01G069100 chr2A 95.146 2596 71 6 1 2570 721575205 721577771 0 4045
6 TraesCS6A01G069100 chr7A 94.725 2597 80 18 1 2570 704256975 704259541 0 3984
7 TraesCS6A01G069100 chr5A 94.686 2597 83 11 1 2570 509128657 509131225 0 3980
8 TraesCS6A01G069100 chr1A 94.181 2595 92 27 4 2570 376489650 376492213 0 3901
9 TraesCS6A01G069100 chr1A 96.550 2145 62 4 1 2135 549429803 549431945 0 3541
10 TraesCS6A01G069100 chr4A 94.256 2594 72 24 4 2570 37984814 37982271 0 3893
11 TraesCS6A01G069100 chr3A 92.799 2597 109 25 1 2570 741177932 741175387 0 3688
12 TraesCS6A01G069100 chr3A 94.479 1902 76 20 677 2569 721546638 721548519 0 2904
13 TraesCS6A01G069100 chr3D 95.680 1852 66 8 4 1843 374010825 374008976 0 2964
14 TraesCS6A01G069100 chr3D 88.949 742 47 23 1837 2570 580650377 580649663 0 883
15 TraesCS6A01G069100 chr2D 94.537 1922 84 8 1 1904 633747125 633749043 0 2948
16 TraesCS6A01G069100 chr5D 94.987 1855 78 8 1 1843 504761464 504763315 0 2896


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 TraesCS6A01G069100 chr6A 37417252 37419821 2569 False 4747.0 4747 100.0000 1 2570 1 chr6A.!!$F1 2569
1 TraesCS6A01G069100 chr6A 558828864 558831422 2558 False 3877.0 3877 94.0340 1 2570 1 chr6A.!!$F2 2569
2 TraesCS6A01G069100 chr6A 615748506 615750536 2030 False 3055.0 3055 93.8860 1 2034 1 chr6A.!!$F3 2033
3 TraesCS6A01G069100 chr6A 532333718 532336901 3183 True 2460.5 4124 95.5835 4 2570 2 chr6A.!!$R1 2566
4 TraesCS6A01G069100 chr2A 721575205 721577771 2566 False 4045.0 4045 95.1460 1 2570 1 chr2A.!!$F1 2569
5 TraesCS6A01G069100 chr7A 704256975 704259541 2566 False 3984.0 3984 94.7250 1 2570 1 chr7A.!!$F1 2569
6 TraesCS6A01G069100 chr5A 509128657 509131225 2568 False 3980.0 3980 94.6860 1 2570 1 chr5A.!!$F1 2569
7 TraesCS6A01G069100 chr1A 376489650 376492213 2563 False 3901.0 3901 94.1810 4 2570 1 chr1A.!!$F1 2566
8 TraesCS6A01G069100 chr1A 549429803 549431945 2142 False 3541.0 3541 96.5500 1 2135 1 chr1A.!!$F2 2134
9 TraesCS6A01G069100 chr4A 37982271 37984814 2543 True 3893.0 3893 94.2560 4 2570 1 chr4A.!!$R1 2566
10 TraesCS6A01G069100 chr3A 741175387 741177932 2545 True 3688.0 3688 92.7990 1 2570 1 chr3A.!!$R1 2569
11 TraesCS6A01G069100 chr3A 721546638 721548519 1881 False 2904.0 2904 94.4790 677 2569 1 chr3A.!!$F1 1892
12 TraesCS6A01G069100 chr3D 374008976 374010825 1849 True 2964.0 2964 95.6800 4 1843 1 chr3D.!!$R1 1839
13 TraesCS6A01G069100 chr3D 580649663 580650377 714 True 883.0 883 88.9490 1837 2570 1 chr3D.!!$R2 733
14 TraesCS6A01G069100 chr2D 633747125 633749043 1918 False 2948.0 2948 94.5370 1 1904 1 chr2D.!!$F1 1903
15 TraesCS6A01G069100 chr5D 504761464 504763315 1851 False 2896.0 2896 94.9870 1 1843 1 chr5D.!!$F1 1842

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
395 396 1.248785 CCGACGACTCCCCTCTCAAA 61.249 60.0 0.0 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2256 2995 0.250513 GTCGAGGGGCAGAAGAACAT 59.749 55.0 0.0 0.0 0.0 2.71 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
121 122 3.460868 GGGGCCCAAAATCGCTGG 61.461 66.667 26.86 0.00 0.00 4.85
395 396 1.248785 CCGACGACTCCCCTCTCAAA 61.249 60.000 0.00 0.00 0.00 2.69
451 461 3.674753 GGTTGAACATTTGCTCGATTTGG 59.325 43.478 0.00 0.00 0.00 3.28
499 1127 2.646930 CCAGCTACAATTGATGAGCCA 58.353 47.619 13.59 0.00 34.62 4.75
589 1217 1.683385 GCATTTGAGGGGATAAGCACC 59.317 52.381 0.00 0.00 41.99 5.01
1031 1661 1.251251 AGCCAGCATGAAAACAGGAC 58.749 50.000 0.00 0.00 39.69 3.85
1045 1675 4.101448 GGACGGCATGCCTGGAGT 62.101 66.667 33.07 23.46 0.00 3.85
1349 1981 6.773638 AGGAAAAGTTGAGCTCTGATAAGAA 58.226 36.000 16.19 0.00 0.00 2.52
1513 2145 2.330440 TGTTGAGCTCAAGACAGCAA 57.670 45.000 29.13 2.49 42.40 3.91
1573 2205 8.494433 AGGCTATTTGTGATGAGGACTAATTTA 58.506 33.333 0.00 0.00 0.00 1.40
1638 2271 7.213678 AGTAGCTATGAAGGAAAGCTGTAATC 58.786 38.462 6.33 0.00 45.83 1.75
1640 2273 7.366847 AGCTATGAAGGAAAGCTGTAATCTA 57.633 36.000 0.00 0.00 44.67 1.98
2008 2700 8.332464 CAAACTAACATACTGACGAAACTGAAA 58.668 33.333 0.00 0.00 0.00 2.69
2009 2701 8.603242 AACTAACATACTGACGAAACTGAAAT 57.397 30.769 0.00 0.00 0.00 2.17
2010 2702 8.603242 ACTAACATACTGACGAAACTGAAATT 57.397 30.769 0.00 0.00 0.00 1.82
2011 2703 9.052759 ACTAACATACTGACGAAACTGAAATTT 57.947 29.630 0.00 0.00 0.00 1.82
2012 2704 9.878599 CTAACATACTGACGAAACTGAAATTTT 57.121 29.630 0.00 0.00 0.00 1.82
2014 2706 9.659830 AACATACTGACGAAACTGAAATTTTAC 57.340 29.630 0.00 0.00 0.00 2.01
2015 2707 9.052759 ACATACTGACGAAACTGAAATTTTACT 57.947 29.630 0.00 0.00 0.00 2.24
2016 2708 9.878599 CATACTGACGAAACTGAAATTTTACTT 57.121 29.630 0.00 0.00 0.00 2.24
2018 2710 8.209917 ACTGACGAAACTGAAATTTTACTTCT 57.790 30.769 0.00 0.00 0.00 2.85
2019 2711 8.674607 ACTGACGAAACTGAAATTTTACTTCTT 58.325 29.630 0.00 0.00 0.00 2.52
2020 2712 9.159470 CTGACGAAACTGAAATTTTACTTCTTC 57.841 33.333 0.00 0.00 0.00 2.87
2021 2713 8.889717 TGACGAAACTGAAATTTTACTTCTTCT 58.110 29.630 0.00 0.00 0.00 2.85
2022 2714 9.159470 GACGAAACTGAAATTTTACTTCTTCTG 57.841 33.333 0.00 0.00 0.00 3.02
2023 2715 8.889717 ACGAAACTGAAATTTTACTTCTTCTGA 58.110 29.630 0.00 0.00 0.00 3.27
2024 2716 9.159470 CGAAACTGAAATTTTACTTCTTCTGAC 57.841 33.333 0.00 0.00 0.00 3.51
2025 2717 9.159470 GAAACTGAAATTTTACTTCTTCTGACG 57.841 33.333 0.00 0.00 0.00 4.35
2026 2718 8.433421 AACTGAAATTTTACTTCTTCTGACGA 57.567 30.769 0.00 0.00 0.00 4.20
2027 2719 8.433421 ACTGAAATTTTACTTCTTCTGACGAA 57.567 30.769 0.00 0.00 0.00 3.85
2028 2720 8.889717 ACTGAAATTTTACTTCTTCTGACGAAA 58.110 29.630 0.00 0.00 0.00 3.46
2029 2721 9.159470 CTGAAATTTTACTTCTTCTGACGAAAC 57.841 33.333 0.00 0.00 0.00 2.78
2030 2722 8.889717 TGAAATTTTACTTCTTCTGACGAAACT 58.110 29.630 0.00 0.00 0.00 2.66
2031 2723 9.159470 GAAATTTTACTTCTTCTGACGAAACTG 57.841 33.333 0.00 0.00 0.00 3.16
2225 2964 3.240134 GAGCTCTGGGTTGTCGGCA 62.240 63.158 6.43 0.00 0.00 5.69
2226 2965 2.045926 GCTCTGGGTTGTCGGCAT 60.046 61.111 0.00 0.00 0.00 4.40
2256 2995 4.209538 CAGCTTATCCACATCAATTGGGA 58.790 43.478 5.42 4.58 34.56 4.37
2419 3158 2.096248 GTCATCAGAGGACTCGGACTT 58.904 52.381 8.01 0.00 36.68 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
363 364 2.433604 AGTCGTCGGAGGAGATGTACTA 59.566 50.000 0.00 0.00 0.00 1.82
395 396 7.667219 ACAAATGAGGAATACAATGTTCTGACT 59.333 33.333 0.00 0.00 0.00 3.41
451 461 5.336744 TGAGAAATCCAACAAAAACGTGTC 58.663 37.500 0.00 0.00 0.00 3.67
499 1127 0.108615 CAGCAAGACCCTCGAACGAT 60.109 55.000 0.00 0.00 0.00 3.73
589 1217 2.009774 CAAGCAATGAACCTCCTACCG 58.990 52.381 0.00 0.00 0.00 4.02
907 1537 6.219473 CACAATTTGCAACACCCTACAATAA 58.781 36.000 0.00 0.00 0.00 1.40
1031 1661 0.179048 TGAATACTCCAGGCATGCCG 60.179 55.000 30.50 23.56 41.95 5.69
1045 1675 6.368791 GTGAGATTGTGTACAGTGCTTGAATA 59.631 38.462 0.00 0.00 0.00 1.75
1349 1981 6.150140 GTCAGCATAACAAATCTCCAAAGTCT 59.850 38.462 0.00 0.00 0.00 3.24
1513 2145 3.262915 AGCTTCCTCTTGTTGCTATCACT 59.737 43.478 0.00 0.00 31.71 3.41
1573 2205 2.156917 CACATGGTCAGACAGCAACAT 58.843 47.619 2.17 0.00 35.67 2.71
1653 2286 8.486210 TGCTACAGAAATAATAGAGTTCACCAT 58.514 33.333 0.00 0.00 34.49 3.55
1927 2619 7.394641 TGCAGCTACTATCTATGTTAGTATGCT 59.605 37.037 13.39 10.70 38.16 3.79
2008 2700 8.336080 GTTCAGTTTCGTCAGAAGAAGTAAAAT 58.664 33.333 0.00 0.00 37.70 1.82
2009 2701 7.548075 AGTTCAGTTTCGTCAGAAGAAGTAAAA 59.452 33.333 0.00 0.00 37.70 1.52
2010 2702 7.039882 AGTTCAGTTTCGTCAGAAGAAGTAAA 58.960 34.615 0.00 0.00 37.70 2.01
2011 2703 6.570692 AGTTCAGTTTCGTCAGAAGAAGTAA 58.429 36.000 0.00 0.00 37.70 2.24
2012 2704 6.145338 AGTTCAGTTTCGTCAGAAGAAGTA 57.855 37.500 0.00 0.00 37.70 2.24
2013 2705 5.012328 AGTTCAGTTTCGTCAGAAGAAGT 57.988 39.130 0.00 0.00 37.70 3.01
2014 2706 5.975410 AAGTTCAGTTTCGTCAGAAGAAG 57.025 39.130 0.00 0.00 37.70 2.85
2015 2707 6.737254 AAAAGTTCAGTTTCGTCAGAAGAA 57.263 33.333 0.00 0.00 37.70 2.52
2016 2708 6.594159 AGAAAAAGTTCAGTTTCGTCAGAAGA 59.406 34.615 0.00 0.00 38.50 2.87
2017 2709 6.776094 AGAAAAAGTTCAGTTTCGTCAGAAG 58.224 36.000 0.00 0.00 38.50 2.85
2018 2710 6.737254 AGAAAAAGTTCAGTTTCGTCAGAA 57.263 33.333 0.00 0.00 38.50 3.02
2019 2711 6.594159 AGAAGAAAAAGTTCAGTTTCGTCAGA 59.406 34.615 13.39 0.00 41.66 3.27
2020 2712 6.776094 AGAAGAAAAAGTTCAGTTTCGTCAG 58.224 36.000 13.39 0.00 41.66 3.51
2021 2713 6.737254 AGAAGAAAAAGTTCAGTTTCGTCA 57.263 33.333 13.39 0.00 41.66 4.35
2022 2714 7.426743 CAGAAGAAGAAAAAGTTCAGTTTCGTC 59.573 37.037 6.42 6.42 40.41 4.20
2023 2715 7.119262 TCAGAAGAAGAAAAAGTTCAGTTTCGT 59.881 33.333 0.00 0.00 38.50 3.85
2024 2716 7.426743 GTCAGAAGAAGAAAAAGTTCAGTTTCG 59.573 37.037 0.00 0.00 38.50 3.46
2025 2717 7.426743 CGTCAGAAGAAGAAAAAGTTCAGTTTC 59.573 37.037 0.00 0.00 36.09 2.78
2026 2718 7.119262 TCGTCAGAAGAAGAAAAAGTTCAGTTT 59.881 33.333 0.00 0.00 36.09 2.66
2027 2719 6.594159 TCGTCAGAAGAAGAAAAAGTTCAGTT 59.406 34.615 0.00 0.00 36.09 3.16
2028 2720 6.106673 TCGTCAGAAGAAGAAAAAGTTCAGT 58.893 36.000 0.00 0.00 36.09 3.41
2029 2721 6.589830 TCGTCAGAAGAAGAAAAAGTTCAG 57.410 37.500 0.00 0.00 36.09 3.02
2030 2722 6.978343 TTCGTCAGAAGAAGAAAAAGTTCA 57.022 33.333 0.00 0.00 38.91 3.18
2256 2995 0.250513 GTCGAGGGGCAGAAGAACAT 59.749 55.000 0.00 0.00 0.00 2.71
2294 3033 0.979709 AGCCTGATGTGCAGCTCCTA 60.980 55.000 0.00 0.00 43.50 2.94


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

AutoCloner maintained by Alex Coulton.