Multiple sequence alignment - TraesCS2D01G033900

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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 TraesCS2D01G033900 chr2D 100.000 2633 0 0 1 2633 13130525 13127893 0.000000e+00 4863.0
1 TraesCS2D01G033900 chr2A 96.696 2603 56 10 39 2633 15154675 15152095 0.000000e+00 4303.0
2 TraesCS2D01G033900 chr2A 79.191 173 21 8 1828 2000 413390266 413390109 3.580000e-19 106.0
3 TraesCS2D01G033900 chr5D 82.243 214 25 8 1798 2008 456746895 456746692 3.480000e-39 172.0
4 TraesCS2D01G033900 chr5A 92.105 38 3 0 1821 1858 461263722 461263759 1.000000e-03 54.7


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 TraesCS2D01G033900 chr2D 13127893 13130525 2632 True 4863 4863 100.000 1 2633 1 chr2D.!!$R1 2632
1 TraesCS2D01G033900 chr2A 15152095 15154675 2580 True 4303 4303 96.696 39 2633 1 chr2A.!!$R1 2594

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
277 278 0.453282 CAGCGGTCTGTGCAAAATCG 60.453 55.0 0.0 0.0 35.61 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2028 2037 0.920763 AATCCATGTCTGAGGGGGCA 60.921 55.0 0.0 0.0 0.0 5.36 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
17 18 4.313819 CTTTCCGGTTGTAGCCCC 57.686 61.111 0.00 0.00 0.00 5.80
18 19 1.743995 CTTTCCGGTTGTAGCCCCG 60.744 63.158 0.00 0.00 43.82 5.73
23 24 4.484872 GGTTGTAGCCCCGAGCCC 62.485 72.222 0.00 0.00 45.47 5.19
24 25 3.712907 GTTGTAGCCCCGAGCCCA 61.713 66.667 0.00 0.00 45.47 5.36
25 26 2.931105 TTGTAGCCCCGAGCCCAA 60.931 61.111 0.00 0.00 45.47 4.12
26 27 2.966732 TTGTAGCCCCGAGCCCAAG 61.967 63.158 0.00 0.00 45.47 3.61
27 28 4.176752 GTAGCCCCGAGCCCAAGG 62.177 72.222 0.00 0.00 45.47 3.61
81 82 7.171848 CGCTAGATATAAGGACGATATAGCTGT 59.828 40.741 0.00 0.00 37.94 4.40
103 104 1.994467 CGACATCGCTTGAGCAGAC 59.006 57.895 3.65 0.00 42.21 3.51
128 129 3.584294 GGGGTAGTAGCAGATTAAGGGA 58.416 50.000 1.13 0.00 0.00 4.20
239 240 3.620821 GCTGTAGGAAGAAGCTGAATGAC 59.379 47.826 0.00 0.00 34.05 3.06
277 278 0.453282 CAGCGGTCTGTGCAAAATCG 60.453 55.000 0.00 0.00 35.61 3.34
318 319 5.743636 TGGGTTACTGTTAAATAGTCGGT 57.256 39.130 0.00 0.00 0.00 4.69
464 465 7.379529 GGGATATATGTTGTGCTTTTGATTTCG 59.620 37.037 0.00 0.00 0.00 3.46
605 606 6.821031 ATGGCTGTACCGTGTTTTAATAAA 57.179 33.333 0.00 0.00 43.94 1.40
705 706 1.293498 CTCGTCCTTGGTGGTCCAG 59.707 63.158 0.00 0.00 45.22 3.86
721 722 1.202371 TCCAGCCGTCGTGTATGATTC 60.202 52.381 0.00 0.00 0.00 2.52
933 942 4.119862 TGTGAAGAAGAGAGAAACAACGG 58.880 43.478 0.00 0.00 0.00 4.44
1125 1134 2.283676 ACATCCGACGTCCCTGGT 60.284 61.111 10.58 0.66 0.00 4.00
1404 1413 4.033776 CATGGCACGGACACCCCT 62.034 66.667 0.00 0.00 0.00 4.79
1468 1477 1.219393 GACAGCTCCCAGCACTACC 59.781 63.158 0.00 0.00 45.56 3.18
1670 1679 7.242079 CAGGTCGTCCGTATACTCTATATTTG 58.758 42.308 0.56 0.00 39.05 2.32
1671 1680 7.118825 CAGGTCGTCCGTATACTCTATATTTGA 59.881 40.741 0.56 0.00 39.05 2.69
1695 1704 0.107410 GTTGTGGTGTGTGTCCTCCA 60.107 55.000 0.00 0.00 0.00 3.86
1861 1870 6.480320 CCTAACTATTGCACATCTAAGTGACC 59.520 42.308 0.00 0.00 42.05 4.02
1873 1882 7.121759 CACATCTAAGTGACCCAATCTCAAAAT 59.878 37.037 0.00 0.00 42.05 1.82
1885 1894 9.093458 ACCCAATCTCAAAATAGAAAGACAAAT 57.907 29.630 0.00 0.00 0.00 2.32
1919 1928 9.715121 ACAAAAGAAAATACATGCATGAATCTT 57.285 25.926 32.75 25.00 0.00 2.40
1922 1931 7.766219 AGAAAATACATGCATGAATCTTTGC 57.234 32.000 32.75 20.80 39.33 3.68
1938 1947 9.932207 TGAATCTTTGCTTAAAATGAATGACAT 57.068 25.926 0.00 0.00 41.45 3.06
1940 1949 7.585286 TCTTTGCTTAAAATGAATGACATGC 57.415 32.000 0.00 0.00 39.39 4.06
1941 1950 7.153315 TCTTTGCTTAAAATGAATGACATGCA 58.847 30.769 0.00 0.00 39.39 3.96
1966 1975 9.494479 CATGTGTCTTAAATGTGCAATACTTAG 57.506 33.333 0.00 0.00 0.00 2.18
1968 1977 7.880713 TGTGTCTTAAATGTGCAATACTTAGGA 59.119 33.333 0.00 0.00 0.00 2.94
2015 2024 8.687301 CAAAACTGATTAACAAAATACACCGTC 58.313 33.333 0.00 0.00 0.00 4.79
2042 2051 0.779997 AAAGTTGCCCCCTCAGACAT 59.220 50.000 0.00 0.00 0.00 3.06
2167 2176 0.398381 GCCCAAGGCCCCATATTTGA 60.398 55.000 0.00 0.00 44.06 2.69
2183 2192 0.478072 TTGAGAGGGGTGCACACATT 59.522 50.000 22.94 8.43 0.00 2.71
2250 2259 0.767375 TGGTTCCTGAAAGCTGCTCT 59.233 50.000 1.00 0.00 36.31 4.09
2276 2285 5.788450 AGTCATGCTACAAGATATAGGCAC 58.212 41.667 0.00 0.00 32.52 5.01
2392 2401 8.833231 TTGTTTGTACCTTCTAGAAAGAGATG 57.167 34.615 8.10 0.00 31.96 2.90
2412 2421 0.890996 GTGGACTCAGTGGGGCTTTG 60.891 60.000 0.00 0.00 0.00 2.77
2444 2453 3.364764 GCAAGTGATTCACTCAACTCTGC 60.365 47.826 19.23 18.59 44.62 4.26
2466 2475 2.047061 CCCTAGTGCCCTACTGCAATA 58.953 52.381 0.00 0.00 44.11 1.90
2507 2516 3.725600 GCATGCAACATTCGAAAATTGCC 60.726 43.478 30.98 19.78 45.45 4.52
2514 2523 5.088680 ACATTCGAAAATTGCCATTGGAT 57.911 34.783 6.95 0.00 0.00 3.41
2551 2560 9.249457 TCTACTAGCAGATGAACAATTTATTCG 57.751 33.333 0.00 0.00 0.00 3.34
2552 2561 9.249457 CTACTAGCAGATGAACAATTTATTCGA 57.751 33.333 0.00 0.00 0.00 3.71
2553 2562 8.136057 ACTAGCAGATGAACAATTTATTCGAG 57.864 34.615 0.00 0.00 0.00 4.04
2554 2563 6.992063 AGCAGATGAACAATTTATTCGAGT 57.008 33.333 0.00 0.00 0.00 4.18
2555 2564 9.249457 CTAGCAGATGAACAATTTATTCGAGTA 57.751 33.333 0.00 0.00 0.00 2.59
2556 2565 8.668510 AGCAGATGAACAATTTATTCGAGTAT 57.331 30.769 0.00 0.00 0.00 2.12
2557 2566 9.764363 AGCAGATGAACAATTTATTCGAGTATA 57.236 29.630 0.00 0.00 0.00 1.47
2607 2616 8.366401 TGAAATTTTTGGACATCAAAGATGCTA 58.634 29.630 6.90 0.00 45.00 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.743995 CGGGGCTACAACCGGAAAG 60.744 63.158 9.46 0.00 46.08 2.62
1 2 2.348243 CGGGGCTACAACCGGAAA 59.652 61.111 9.46 0.00 46.08 3.13
6 7 4.484872 GGGCTCGGGGCTACAACC 62.485 72.222 9.45 0.00 41.46 3.77
7 8 3.262448 TTGGGCTCGGGGCTACAAC 62.262 63.158 9.45 0.00 41.46 3.32
8 9 2.931105 TTGGGCTCGGGGCTACAA 60.931 61.111 9.45 2.04 41.46 2.41
9 10 3.399181 CTTGGGCTCGGGGCTACA 61.399 66.667 9.45 0.00 41.46 2.74
10 11 4.176752 CCTTGGGCTCGGGGCTAC 62.177 72.222 9.45 0.00 41.46 3.58
20 21 3.134127 GTCATCCACGCCTTGGGC 61.134 66.667 0.00 0.00 46.92 5.36
21 22 1.746615 CTGTCATCCACGCCTTGGG 60.747 63.158 0.00 0.00 46.92 4.12
23 24 1.746615 CCCTGTCATCCACGCCTTG 60.747 63.158 0.00 0.00 0.00 3.61
24 25 2.671070 CCCTGTCATCCACGCCTT 59.329 61.111 0.00 0.00 0.00 4.35
25 26 4.101448 GCCCTGTCATCCACGCCT 62.101 66.667 0.00 0.00 0.00 5.52
26 27 4.101448 AGCCCTGTCATCCACGCC 62.101 66.667 0.00 0.00 0.00 5.68
27 28 2.512515 GAGCCCTGTCATCCACGC 60.513 66.667 0.00 0.00 0.00 5.34
28 29 2.202797 CGAGCCCTGTCATCCACG 60.203 66.667 0.00 0.00 0.00 4.94
29 30 2.512515 GCGAGCCCTGTCATCCAC 60.513 66.667 0.00 0.00 0.00 4.02
30 31 3.785859 GGCGAGCCCTGTCATCCA 61.786 66.667 1.97 0.00 0.00 3.41
31 32 3.329542 TTGGCGAGCCCTGTCATCC 62.330 63.158 12.05 0.00 34.56 3.51
32 33 1.817099 CTTGGCGAGCCCTGTCATC 60.817 63.158 12.05 0.00 34.56 2.92
33 34 2.270205 CTTGGCGAGCCCTGTCAT 59.730 61.111 12.05 0.00 34.56 3.06
34 35 2.922503 TCTTGGCGAGCCCTGTCA 60.923 61.111 12.05 0.00 34.56 3.58
35 36 2.435059 GTCTTGGCGAGCCCTGTC 60.435 66.667 12.05 0.00 34.56 3.51
36 37 2.925170 AGTCTTGGCGAGCCCTGT 60.925 61.111 12.05 0.00 34.56 4.00
37 38 2.435586 CAGTCTTGGCGAGCCCTG 60.436 66.667 12.05 7.61 34.56 4.45
92 93 4.785453 CCCCGGGTCTGCTCAAGC 62.785 72.222 21.85 0.00 42.50 4.01
103 104 0.763223 AATCTGCTACTACCCCCGGG 60.763 60.000 15.80 15.80 42.03 5.73
118 119 1.135960 GCTGCCTCCTCCCTTAATCT 58.864 55.000 0.00 0.00 0.00 2.40
128 129 2.669849 CTGCTCAAGCTGCCTCCT 59.330 61.111 3.32 0.00 42.66 3.69
239 240 3.489738 GCTGGGTTGAAATCCAATGATCG 60.490 47.826 0.00 0.00 37.08 3.69
277 278 7.454260 AACCCATGAAGAGTTAGTTTCATTC 57.546 36.000 0.00 0.00 40.93 2.67
318 319 9.337396 CATGCTAACTAAAACATATTAGTGGGA 57.663 33.333 0.86 0.52 43.52 4.37
566 567 6.101650 ACAGCCATAGATCGATGTTCATAA 57.898 37.500 13.86 0.00 0.00 1.90
577 578 3.454371 AACACGGTACAGCCATAGATC 57.546 47.619 0.00 0.00 36.97 2.75
578 579 3.906720 AAACACGGTACAGCCATAGAT 57.093 42.857 0.00 0.00 36.97 1.98
579 580 3.688694 AAAACACGGTACAGCCATAGA 57.311 42.857 0.00 0.00 36.97 1.98
580 581 7.542534 TTATTAAAACACGGTACAGCCATAG 57.457 36.000 0.00 0.00 36.97 2.23
605 606 4.736307 GCCGTTTCTAAACACGTTCATTTT 59.264 37.500 6.41 0.00 38.81 1.82
705 706 0.928229 GGTGAATCATACACGACGGC 59.072 55.000 0.00 0.00 38.90 5.68
721 722 4.885413 TGAAAATGAAAGAATGGCTGGTG 58.115 39.130 0.00 0.00 0.00 4.17
837 846 1.155889 TTCGCGACGACACTAACCTA 58.844 50.000 9.15 0.00 34.89 3.08
1404 1413 6.761242 GCACATATAAGTACACCTCAATCACA 59.239 38.462 0.00 0.00 0.00 3.58
1670 1679 2.159435 GGACACACACCACAACTGTTTC 60.159 50.000 0.00 0.00 0.00 2.78
1671 1680 1.816224 GGACACACACCACAACTGTTT 59.184 47.619 0.00 0.00 0.00 2.83
1695 1704 5.404066 GTGCAAATACGGTAGCAAAACAAAT 59.596 36.000 2.59 0.00 38.91 2.32
1800 1809 3.138653 TGCCCTACAAAGACCCTTTGTTA 59.861 43.478 24.30 12.83 42.10 2.41
1836 1845 6.480320 GGTCACTTAGATGTGCAATAGTTAGG 59.520 42.308 0.00 0.00 37.81 2.69
1841 1850 4.769688 TGGGTCACTTAGATGTGCAATAG 58.230 43.478 0.00 0.00 37.81 1.73
1905 1914 7.820386 TCATTTTAAGCAAAGATTCATGCATGT 59.180 29.630 25.43 8.12 44.95 3.21
1912 1921 9.932207 ATGTCATTCATTTTAAGCAAAGATTCA 57.068 25.926 0.00 0.00 32.08 2.57
1919 1928 6.874664 ACATGCATGTCATTCATTTTAAGCAA 59.125 30.769 26.61 0.00 35.87 3.91
1922 1931 7.821595 ACACATGCATGTCATTCATTTTAAG 57.178 32.000 29.23 15.21 39.39 1.85
1938 1947 4.581077 TTGCACATTTAAGACACATGCA 57.419 36.364 0.00 0.00 39.68 3.96
1939 1948 6.324819 AGTATTGCACATTTAAGACACATGC 58.675 36.000 0.00 0.00 0.00 4.06
1940 1949 9.494479 CTAAGTATTGCACATTTAAGACACATG 57.506 33.333 0.00 0.00 0.00 3.21
1941 1950 8.677300 CCTAAGTATTGCACATTTAAGACACAT 58.323 33.333 0.00 0.00 0.00 3.21
2025 2034 1.687612 CATGTCTGAGGGGGCAACT 59.312 57.895 0.00 0.00 0.00 3.16
2028 2037 0.920763 AATCCATGTCTGAGGGGGCA 60.921 55.000 0.00 0.00 0.00 5.36
2042 2051 5.551233 CCTACAACAAGTCTCTTGAATCCA 58.449 41.667 15.04 0.00 0.00 3.41
2167 2176 1.271926 GGTTAATGTGTGCACCCCTCT 60.272 52.381 15.69 0.00 0.00 3.69
2183 2192 3.520317 ACAATGTCGGTTATCCTGGGTTA 59.480 43.478 0.00 0.00 0.00 2.85
2276 2285 5.902681 TGGTTAACTAGATCCAACGATCAG 58.097 41.667 5.42 1.81 46.42 2.90
2392 2401 2.069165 AAAGCCCCACTGAGTCCACC 62.069 60.000 0.00 0.00 0.00 4.61
2412 2421 4.397417 AGTGAATCACTTGCCTAATCTTGC 59.603 41.667 10.56 0.00 42.59 4.01
2444 2453 2.815308 CAGTAGGGCACTAGGGCG 59.185 66.667 11.67 0.00 44.56 6.13
2466 2475 5.352569 GCATGCACTACTATCAAGTGAAAGT 59.647 40.000 14.21 0.00 45.89 2.66
2486 2495 3.432592 TGGCAATTTTCGAATGTTGCATG 59.567 39.130 31.49 14.59 46.46 4.06
2507 2516 1.202734 AGATGTGCTCGGGATCCAATG 60.203 52.381 15.23 2.55 0.00 2.82
2514 2523 1.319541 GCTAGTAGATGTGCTCGGGA 58.680 55.000 0.00 0.00 0.00 5.14
2567 2576 9.835389 TCCAAAAATTTCAGACTGATTTGATTT 57.165 25.926 22.34 15.59 29.04 2.17
2575 2584 6.957920 TGATGTCCAAAAATTTCAGACTGA 57.042 33.333 0.00 0.00 0.00 3.41
2578 2587 8.706035 CATCTTTGATGTCCAAAAATTTCAGAC 58.294 33.333 0.00 0.00 43.50 3.51
2582 2591 7.662604 AGCATCTTTGATGTCCAAAAATTTC 57.337 32.000 8.98 0.00 43.50 2.17
2586 2595 6.265196 ACAGTAGCATCTTTGATGTCCAAAAA 59.735 34.615 8.98 0.00 43.50 1.94


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

AutoCloner maintained by Alex Coulton.