Multiple sequence alignment - TraesCS3D01G054500

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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 TraesCS3D01G054500 chr3D 100.000 2951 0 0 1 2951 22369199 22366249 0.000000e+00 5450.0
1 TraesCS3D01G054500 chr3D 85.443 158 14 7 2248 2398 22366487 22366332 3.940000e-34 156.0
2 TraesCS3D01G054500 chr3D 85.443 158 14 7 2713 2868 22366952 22366802 3.940000e-34 156.0
3 TraesCS3D01G054500 chr3D 100.000 35 0 0 1547 1581 22367599 22367565 6.830000e-07 65.8
4 TraesCS3D01G054500 chr3D 100.000 35 0 0 1601 1635 22367653 22367619 6.830000e-07 65.8
5 TraesCS3D01G054500 chr3B 93.936 3018 101 24 1 2951 39905282 39908284 0.000000e+00 4484.0
6 TraesCS3D01G054500 chr3B 84.615 156 14 8 2244 2391 39908041 39908194 2.370000e-31 147.0
7 TraesCS3D01G054500 chr3B 100.000 35 0 0 1601 1635 39906822 39906856 6.830000e-07 65.8
8 TraesCS3D01G054500 chr3A 93.435 3016 115 28 1 2951 32120341 32117344 0.000000e+00 4396.0
9 TraesCS3D01G054500 chr3A 85.443 158 14 7 2244 2394 32117586 32117431 3.940000e-34 156.0
10 TraesCS3D01G054500 chr3A 78.788 231 37 9 2641 2868 32118138 32117917 8.520000e-31 145.0
11 TraesCS3D01G054500 chr3A 100.000 35 0 0 1547 1581 32118714 32118680 6.830000e-07 65.8
12 TraesCS3D01G054500 chr3A 100.000 35 0 0 1601 1635 32118795 32118761 6.830000e-07 65.8
13 TraesCS3D01G054500 chrUn 100.000 80 0 0 2872 2951 478489749 478489828 6.590000e-32 148.0


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 TraesCS3D01G054500 chr3D 22366249 22369199 2950 True 1178.72 5450 94.177200 1 2951 5 chr3D.!!$R1 2950
1 TraesCS3D01G054500 chr3B 39905282 39908284 3002 False 1565.60 4484 92.850333 1 2951 3 chr3B.!!$F1 2950
2 TraesCS3D01G054500 chr3A 32117344 32120341 2997 True 965.72 4396 91.533200 1 2951 5 chr3A.!!$R1 2950

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
59 60 0.825010 GCAGCCCTGACATTATGGGG 60.825 60.0 0.00 0.0 41.19 4.96 F
73 74 1.560505 ATGGGGTTCAACATTCAGCC 58.439 50.0 0.00 0.0 0.00 4.85 F
1592 1597 0.539051 GATGTCCTGGTAGCAGCAGT 59.461 55.0 16.62 2.0 41.84 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1197 1202 0.331278 AACCATCTGAAATGCCCGGA 59.669 50.000 0.73 0.0 0.00 5.14 R
1846 1878 1.070445 CGACATCATCTGGAGGGCC 59.930 63.158 0.00 0.0 29.14 5.80 R
2870 2971 1.079503 GATCACCAAAGACTCGCCAC 58.920 55.000 0.00 0.0 0.00 5.01 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
27 28 5.234757 TGACAGATTTTTGCAACATTTCAGC 59.765 36.000 0.00 0.00 0.00 4.26
36 37 4.239304 TGCAACATTTCAGCAGCATTAAG 58.761 39.130 0.00 0.00 33.75 1.85
59 60 0.825010 GCAGCCCTGACATTATGGGG 60.825 60.000 0.00 0.00 41.19 4.96
73 74 1.560505 ATGGGGTTCAACATTCAGCC 58.439 50.000 0.00 0.00 0.00 4.85
159 160 7.885714 CGAATTTACATTGCGATACAACAAAAC 59.114 33.333 0.00 0.00 42.27 2.43
246 250 8.145122 AGAACATATAAAAGACGGATCCTTCTC 58.855 37.037 20.29 6.99 0.00 2.87
734 739 9.542462 AATTTAACTAAAAGGAGGAGTTTTTGC 57.458 29.630 0.00 0.00 35.17 3.68
1592 1597 0.539051 GATGTCCTGGTAGCAGCAGT 59.461 55.000 16.62 2.00 41.84 4.40
1846 1878 5.738118 AGGTCTCGAAGAATTAGACGTAG 57.262 43.478 0.00 0.00 40.44 3.51
1890 1922 0.787183 GAGTTGTCGCAGCTGAGTTC 59.213 55.000 20.43 12.62 0.00 3.01
1905 1937 4.781071 CTGAGTTCAAGCTGTTTGATGAC 58.219 43.478 7.77 4.61 44.90 3.06
1907 1939 3.466836 AGTTCAAGCTGTTTGATGACGA 58.533 40.909 7.77 0.00 44.90 4.20
1916 1948 4.435253 GCTGTTTGATGACGATGTTCTCAG 60.435 45.833 0.00 0.00 0.00 3.35
2025 2057 7.005062 ACACATCATATTTAGAGAACGCAAC 57.995 36.000 0.00 0.00 0.00 4.17
2086 2127 4.142227 ACTGTACCGACATAGGCAAGTAAG 60.142 45.833 0.00 0.00 34.24 2.34
2232 2302 9.886132 AATAATTCGGAAGACACAAGTATACTT 57.114 29.630 12.50 12.50 41.84 2.24
2543 2616 9.434559 GACAAGTAAAACTGTTCAGTCAAATAC 57.565 33.333 5.91 7.35 0.00 1.89
2544 2617 8.952278 ACAAGTAAAACTGTTCAGTCAAATACA 58.048 29.630 5.91 0.00 0.00 2.29
2545 2618 9.950680 CAAGTAAAACTGTTCAGTCAAATACAT 57.049 29.630 5.91 0.00 0.00 2.29
2573 2671 7.224557 ACACACTAATCAAAATTCAAAAGTGCC 59.775 33.333 0.00 0.00 33.72 5.01
2579 2677 5.540911 TCAAAATTCAAAAGTGCCATCTCC 58.459 37.500 0.00 0.00 0.00 3.71
2584 2682 2.038426 TCAAAAGTGCCATCTCCGAGAA 59.962 45.455 1.27 0.00 0.00 2.87
2659 2759 2.229784 CCATGGAGAACCTGTTTGCTTC 59.770 50.000 5.56 0.00 37.04 3.86
2864 2965 2.956132 TGGCTCACCCTTGATTTCAAA 58.044 42.857 0.00 0.00 35.15 2.69
2870 2971 5.766222 CTCACCCTTGATTTCAAAGAGTTG 58.234 41.667 0.00 0.00 35.15 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 1.133976 AGGGCTGCTACCTTAATGCTG 60.134 52.381 0.00 0.00 33.64 4.41
36 37 2.498167 CATAATGTCAGGGCTGCTACC 58.502 52.381 0.00 0.00 0.00 3.18
59 60 3.427233 GCTCATCTGGCTGAATGTTGAAC 60.427 47.826 0.00 0.00 0.00 3.18
159 160 1.600957 CACTGGCTGAACTGTGTTGAG 59.399 52.381 0.00 0.00 36.10 3.02
201 202 5.007626 TGTTCTTTCTTCGACCAGTTCATTG 59.992 40.000 0.00 0.00 0.00 2.82
476 481 1.321743 GACAGCATCGACATTGACGAC 59.678 52.381 13.08 2.65 42.37 4.34
725 730 6.551736 TCAGTTTAGTGAACAGCAAAAACTC 58.448 36.000 0.17 0.00 40.34 3.01
852 857 4.225942 AGATCCAGCCTCAATAGTTTGTCA 59.774 41.667 0.00 0.00 34.32 3.58
1197 1202 0.331278 AACCATCTGAAATGCCCGGA 59.669 50.000 0.73 0.00 0.00 5.14
1846 1878 1.070445 CGACATCATCTGGAGGGCC 59.930 63.158 0.00 0.00 29.14 5.80
1890 1922 3.818961 ACATCGTCATCAAACAGCTTG 57.181 42.857 0.00 0.00 36.25 4.01
1905 1937 2.669924 CACACATCCACTGAGAACATCG 59.330 50.000 0.00 0.00 0.00 3.84
1907 1939 2.373169 ACCACACATCCACTGAGAACAT 59.627 45.455 0.00 0.00 0.00 2.71
1916 1948 2.489329 CCATCAAGAACCACACATCCAC 59.511 50.000 0.00 0.00 0.00 4.02
2015 2047 2.322830 GGGGTTCCGTTGCGTTCTC 61.323 63.158 0.00 0.00 0.00 2.87
2025 2057 3.951663 AGAATCTAGTTTTGGGGTTCCG 58.048 45.455 0.00 0.00 35.24 4.30
2086 2127 7.615582 TTTGTGATGTATTGGACTGAAGATC 57.384 36.000 0.00 0.00 0.00 2.75
2138 2204 5.791666 TGTCTCATAGCTTCATCATGGATC 58.208 41.667 0.00 0.00 0.00 3.36
2188 2254 9.090692 CGAATTATTTTGGATTTTCAAGCAGAT 57.909 29.630 0.00 0.00 0.00 2.90
2232 2302 6.208402 TCTGTACACCACTTTTACGGTATACA 59.792 38.462 5.01 0.00 41.65 2.29
2429 2501 7.391388 TCTAGGTTTTTGGGTAAACTTCCTA 57.609 36.000 0.00 0.00 37.96 2.94
2430 2502 6.270219 TCTAGGTTTTTGGGTAAACTTCCT 57.730 37.500 0.00 0.00 37.96 3.36
2433 2505 9.516546 CTAGAATCTAGGTTTTTGGGTAAACTT 57.483 33.333 9.38 0.00 37.96 2.66
2494 2567 8.105829 TGTCTATATTTTTACGGGGTTGGTAAA 58.894 33.333 0.00 0.00 37.89 2.01
2496 2569 7.192852 TGTCTATATTTTTACGGGGTTGGTA 57.807 36.000 0.00 0.00 0.00 3.25
2497 2570 6.064735 TGTCTATATTTTTACGGGGTTGGT 57.935 37.500 0.00 0.00 0.00 3.67
2498 2571 6.600427 ACTTGTCTATATTTTTACGGGGTTGG 59.400 38.462 0.00 0.00 0.00 3.77
2499 2572 7.619964 ACTTGTCTATATTTTTACGGGGTTG 57.380 36.000 0.00 0.00 0.00 3.77
2500 2573 9.737844 TTTACTTGTCTATATTTTTACGGGGTT 57.262 29.630 0.00 0.00 0.00 4.11
2501 2574 9.737844 TTTTACTTGTCTATATTTTTACGGGGT 57.262 29.630 0.00 0.00 0.00 4.95
2502 2575 9.992910 GTTTTACTTGTCTATATTTTTACGGGG 57.007 33.333 0.00 0.00 0.00 5.73
2546 2619 9.243637 GCACTTTTGAATTTTGATTAGTGTGTA 57.756 29.630 0.00 0.00 35.42 2.90
2548 2621 7.224362 TGGCACTTTTGAATTTTGATTAGTGTG 59.776 33.333 0.00 0.00 35.42 3.82
2549 2622 7.271511 TGGCACTTTTGAATTTTGATTAGTGT 58.728 30.769 0.00 0.00 35.42 3.55
2556 2654 5.540911 GGAGATGGCACTTTTGAATTTTGA 58.459 37.500 0.00 0.00 0.00 2.69
2562 2660 2.038426 TCTCGGAGATGGCACTTTTGAA 59.962 45.455 2.97 0.00 33.89 2.69
2647 2747 1.425066 TGGATCTGGAAGCAAACAGGT 59.575 47.619 0.00 0.00 35.47 4.00
2710 2810 5.268118 TCTAGCTGAATCTGTACACCATG 57.732 43.478 0.00 0.00 0.00 3.66
2711 2811 5.600069 TGATCTAGCTGAATCTGTACACCAT 59.400 40.000 0.00 0.00 0.00 3.55
2754 2854 7.201848 CCACATAATTCACAAACCTGCTATCAT 60.202 37.037 0.00 0.00 0.00 2.45
2811 2911 8.714179 CATGACGTTACTTGGTTTATACAAGAA 58.286 33.333 11.65 0.50 46.27 2.52
2864 2965 1.541233 CCAAAGACTCGCCACAACTCT 60.541 52.381 0.00 0.00 0.00 3.24
2870 2971 1.079503 GATCACCAAAGACTCGCCAC 58.920 55.000 0.00 0.00 0.00 5.01


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

AutoCloner maintained by Alex Coulton.