Multiple sequence alignment - TraesCS5D01G172600

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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 TraesCS5D01G172600 chr5D 100.000 2118 0 0 1 2118 269570038 269567921 0.000000e+00 3912
1 TraesCS5D01G172600 chr5D 96.450 2028 61 9 1 2021 193373545 193371522 0.000000e+00 3336
2 TraesCS5D01G172600 chr5D 96.444 2025 61 9 1 2021 191445151 191443134 0.000000e+00 3330
3 TraesCS5D01G172600 chr5D 100.000 86 0 0 2302 2387 269567737 269567652 2.460000e-35 159
4 TraesCS5D01G172600 chr5D 93.103 87 4 2 2302 2387 377327439 377327354 2.490000e-25 126
5 TraesCS5D01G172600 chr3D 97.189 2028 50 2 1 2021 521390526 521388499 0.000000e+00 3422
6 TraesCS5D01G172600 chr2D 96.937 2024 53 6 1 2021 485437803 485435786 0.000000e+00 3386
7 TraesCS5D01G172600 chr2D 95.349 86 4 0 2302 2387 309999612 309999527 1.150000e-28 137
8 TraesCS5D01G172600 chr2D 95.238 84 4 0 2302 2385 599336576 599336659 1.490000e-27 134
9 TraesCS5D01G172600 chr4D 96.686 2022 56 3 1 2021 38023637 38025648 0.000000e+00 3352
10 TraesCS5D01G172600 chr4D 96.642 2025 55 10 1 2021 299718317 299716302 0.000000e+00 3350
11 TraesCS5D01G172600 chr4D 96.538 2022 59 6 1 2021 358243144 358245155 0.000000e+00 3336
12 TraesCS5D01G172600 chr4D 96.252 2028 69 3 1 2021 276884637 276882610 0.000000e+00 3317
13 TraesCS5D01G172600 chr7D 96.637 2022 58 5 1 2021 194170598 194172610 0.000000e+00 3349
14 TraesCS5D01G172600 chr7D 96.512 86 2 1 2302 2387 194190197 194190281 8.900000e-30 141
15 TraesCS5D01G172600 chr7D 93.103 87 5 1 2302 2387 545865188 545865102 2.490000e-25 126
16 TraesCS5D01G172600 chr7D 93.023 86 4 2 2302 2387 396767007 396766924 8.960000e-25 124
17 TraesCS5D01G172600 chr1D 97.647 85 1 1 2302 2386 130650907 130650824 6.880000e-31 145
18 TraesCS5D01G172600 chr1D 93.103 87 4 2 2302 2386 130657606 130657520 2.490000e-25 126
19 TraesCS5D01G172600 chr6D 94.318 88 3 2 2302 2387 441499200 441499113 1.490000e-27 134


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 TraesCS5D01G172600 chr5D 269567652 269570038 2386 True 2035.5 3912 100.000 1 2387 2 chr5D.!!$R4 2386
1 TraesCS5D01G172600 chr5D 193371522 193373545 2023 True 3336.0 3336 96.450 1 2021 1 chr5D.!!$R2 2020
2 TraesCS5D01G172600 chr5D 191443134 191445151 2017 True 3330.0 3330 96.444 1 2021 1 chr5D.!!$R1 2020
3 TraesCS5D01G172600 chr3D 521388499 521390526 2027 True 3422.0 3422 97.189 1 2021 1 chr3D.!!$R1 2020
4 TraesCS5D01G172600 chr2D 485435786 485437803 2017 True 3386.0 3386 96.937 1 2021 1 chr2D.!!$R2 2020
5 TraesCS5D01G172600 chr4D 38023637 38025648 2011 False 3352.0 3352 96.686 1 2021 1 chr4D.!!$F1 2020
6 TraesCS5D01G172600 chr4D 299716302 299718317 2015 True 3350.0 3350 96.642 1 2021 1 chr4D.!!$R2 2020
7 TraesCS5D01G172600 chr4D 358243144 358245155 2011 False 3336.0 3336 96.538 1 2021 1 chr4D.!!$F2 2020
8 TraesCS5D01G172600 chr4D 276882610 276884637 2027 True 3317.0 3317 96.252 1 2021 1 chr4D.!!$R1 2020
9 TraesCS5D01G172600 chr7D 194170598 194172610 2012 False 3349.0 3349 96.637 1 2021 1 chr7D.!!$F1 2020

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
666 671 1.211703 TCTTTTAGGATGGCGGATGCA 59.788 47.619 0.0 0.0 45.35 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2032 2063 0.586802 GCGGCGGCTATTTAAAGAGG 59.413 55.0 9.78 0.0 35.83 3.69 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
348 352 5.723887 AGTTGATGGACTCACTTATCTTCCT 59.276 40.000 0.00 0.00 32.17 3.36
356 360 5.524535 ACTCACTTATCTTCCTAGCCTTCT 58.475 41.667 0.00 0.00 0.00 2.85
460 464 9.319143 GTGTGATTGCTACTCTGTTATAAATCT 57.681 33.333 0.00 0.00 0.00 2.40
666 671 1.211703 TCTTTTAGGATGGCGGATGCA 59.788 47.619 0.00 0.00 45.35 3.96
939 944 2.678336 GGGACGCATTGGAGAAGTTTAG 59.322 50.000 0.00 0.00 0.00 1.85
956 961 3.350219 TTAGCACAAGGAGCTTAAGGG 57.650 47.619 4.29 0.00 43.25 3.95
1008 1013 2.152830 GAGCAATGGGAGATGATCAGC 58.847 52.381 1.78 1.78 32.43 4.26
1033 1038 6.095860 CACCAAGAAGGATAGATCAATTGCAA 59.904 38.462 0.00 0.00 41.22 4.08
1134 1140 0.532573 TGACCAAGATCACGGAGCTC 59.467 55.000 4.71 4.71 0.00 4.09
1409 1415 7.820578 AGTAGACCACCATAATCAGTAGTAC 57.179 40.000 0.00 0.00 0.00 2.73
1480 1486 7.336931 AGTTAGATCGATTGTATGCCTTGTTTT 59.663 33.333 0.00 0.00 0.00 2.43
1532 1538 4.898861 TGTCTCATGTGCATATGGGTAGTA 59.101 41.667 21.20 0.90 30.45 1.82
1654 1661 1.738350 CTCAGTTGATTCAGCAGCAGG 59.262 52.381 3.25 0.00 0.00 4.85
1696 1712 1.846007 ACAGAACCAAGGCAACAACA 58.154 45.000 0.00 0.00 41.41 3.33
1697 1713 2.175202 ACAGAACCAAGGCAACAACAA 58.825 42.857 0.00 0.00 41.41 2.83
1698 1714 2.094234 ACAGAACCAAGGCAACAACAAC 60.094 45.455 0.00 0.00 41.41 3.32
1699 1715 2.094286 CAGAACCAAGGCAACAACAACA 60.094 45.455 0.00 0.00 41.41 3.33
1700 1716 2.564947 AGAACCAAGGCAACAACAACAA 59.435 40.909 0.00 0.00 41.41 2.83
1701 1717 3.197549 AGAACCAAGGCAACAACAACAAT 59.802 39.130 0.00 0.00 41.41 2.71
1816 1847 2.502142 TGTTGCAGATGATTGGCTCT 57.498 45.000 0.00 0.00 0.00 4.09
1876 1907 0.736053 TGCGGAAAGAGTGCGTTTTT 59.264 45.000 0.00 0.00 44.08 1.94
1903 1934 1.452651 CAGCTTGATGGACCCGCAT 60.453 57.895 0.00 0.00 0.00 4.73
1944 1975 2.111384 ACAGCCACACACCCTATAGAG 58.889 52.381 0.00 0.00 0.00 2.43
1966 1997 1.380302 GCCACATGGGACCAGTTCT 59.620 57.895 0.00 0.00 40.01 3.01
2024 2055 3.608432 GGCCATGAAGAAGCCACC 58.392 61.111 0.00 0.00 46.34 4.61
2025 2056 1.304381 GGCCATGAAGAAGCCACCA 60.304 57.895 0.00 0.00 46.34 4.17
2026 2057 1.598701 GGCCATGAAGAAGCCACCAC 61.599 60.000 0.00 0.00 46.34 4.16
2027 2058 0.895100 GCCATGAAGAAGCCACCACA 60.895 55.000 0.00 0.00 0.00 4.17
2028 2059 0.883833 CCATGAAGAAGCCACCACAC 59.116 55.000 0.00 0.00 0.00 3.82
2029 2060 0.883833 CATGAAGAAGCCACCACACC 59.116 55.000 0.00 0.00 0.00 4.16
2030 2061 0.251341 ATGAAGAAGCCACCACACCC 60.251 55.000 0.00 0.00 0.00 4.61
2031 2062 1.603739 GAAGAAGCCACCACACCCC 60.604 63.158 0.00 0.00 0.00 4.95
2032 2063 3.146828 AAGAAGCCACCACACCCCC 62.147 63.158 0.00 0.00 0.00 5.40
2048 2079 1.605753 CCCCCTCTTTAAATAGCCGC 58.394 55.000 0.00 0.00 0.00 6.53
2049 2080 1.605753 CCCCTCTTTAAATAGCCGCC 58.394 55.000 0.00 0.00 0.00 6.13
2050 2081 1.226746 CCCTCTTTAAATAGCCGCCG 58.773 55.000 0.00 0.00 0.00 6.46
2051 2082 0.586802 CCTCTTTAAATAGCCGCCGC 59.413 55.000 0.00 0.00 0.00 6.53
2052 2083 0.586802 CTCTTTAAATAGCCGCCGCC 59.413 55.000 0.00 0.00 34.57 6.13
2053 2084 1.155424 TCTTTAAATAGCCGCCGCCG 61.155 55.000 0.00 0.00 34.57 6.46
2054 2085 2.711185 CTTTAAATAGCCGCCGCCGC 62.711 60.000 0.00 0.00 34.57 6.53
2341 2372 3.902086 GGAGCCCGACGAGGTAGC 61.902 72.222 0.00 0.00 38.74 3.58
2342 2373 3.902086 GAGCCCGACGAGGTAGCC 61.902 72.222 0.00 0.00 38.74 3.93
2363 2394 4.622456 CGCCGTTGCCGCTGTTTT 62.622 61.111 0.00 0.00 0.00 2.43
2364 2395 2.279186 GCCGTTGCCGCTGTTTTT 60.279 55.556 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
356 360 6.841601 AGGCCATCTAATAAAGATAACAGCA 58.158 36.000 5.01 0.00 43.42 4.41
460 464 1.065851 TGACACGCACAGTACTCGAAA 59.934 47.619 9.21 0.00 0.00 3.46
666 671 3.030291 TGGTTGCATGAACTTGTTCCTT 58.970 40.909 10.51 0.00 34.66 3.36
939 944 2.357075 GTACCCTTAAGCTCCTTGTGC 58.643 52.381 0.00 0.00 0.00 4.57
956 961 4.142249 GCCCACAAATCTGGTAAATGGTAC 60.142 45.833 0.00 0.00 0.00 3.34
1008 1013 5.591472 TGCAATTGATCTATCCTTCTTGGTG 59.409 40.000 10.34 0.00 37.07 4.17
1033 1038 2.893489 GGTTTTGCTCCTGGATGAAAGT 59.107 45.455 0.00 0.00 0.00 2.66
1134 1140 2.732597 CGTAGCCTTGAGTTCTTCCTCG 60.733 54.545 0.00 0.00 34.04 4.63
1317 1323 7.095060 GCTTCATCAACAAAGTCATCTTCACTA 60.095 37.037 0.00 0.00 32.90 2.74
1654 1661 3.937706 ACTAGTGCTTGCATCAAGACATC 59.062 43.478 10.44 4.21 43.42 3.06
1696 1712 5.639931 GTGGGTTGTTGTTGTTGTTATTGTT 59.360 36.000 0.00 0.00 0.00 2.83
1697 1713 5.172205 GTGGGTTGTTGTTGTTGTTATTGT 58.828 37.500 0.00 0.00 0.00 2.71
1698 1714 4.568760 GGTGGGTTGTTGTTGTTGTTATTG 59.431 41.667 0.00 0.00 0.00 1.90
1699 1715 4.223032 TGGTGGGTTGTTGTTGTTGTTATT 59.777 37.500 0.00 0.00 0.00 1.40
1700 1716 3.769844 TGGTGGGTTGTTGTTGTTGTTAT 59.230 39.130 0.00 0.00 0.00 1.89
1701 1717 3.056749 GTGGTGGGTTGTTGTTGTTGTTA 60.057 43.478 0.00 0.00 0.00 2.41
1816 1847 2.031120 CAACTCCCTTCCAACTTTGCA 58.969 47.619 0.00 0.00 0.00 4.08
1876 1907 2.771435 CATCAAGCTGATGTGCGGA 58.229 52.632 14.42 0.00 46.80 5.54
1903 1934 4.227073 TGTGTAATTCTCCCACCATGATGA 59.773 41.667 0.00 0.00 0.00 2.92
1944 1975 1.377725 CTGGTCCCATGTGGCAGTC 60.378 63.158 0.00 0.00 0.00 3.51
1966 1997 2.073816 GGCAGTACGAAAAGCTTGCTA 58.926 47.619 0.00 0.00 0.00 3.49
2029 2060 1.605753 GCGGCTATTTAAAGAGGGGG 58.394 55.000 11.60 0.00 0.00 5.40
2030 2061 1.605753 GGCGGCTATTTAAAGAGGGG 58.394 55.000 11.60 0.00 0.00 4.79
2031 2062 1.226746 CGGCGGCTATTTAAAGAGGG 58.773 55.000 11.60 0.00 0.00 4.30
2032 2063 0.586802 GCGGCGGCTATTTAAAGAGG 59.413 55.000 9.78 0.00 35.83 3.69
2033 2064 0.586802 GGCGGCGGCTATTTAAAGAG 59.413 55.000 27.22 5.45 39.81 2.85
2034 2065 1.155424 CGGCGGCGGCTATTTAAAGA 61.155 55.000 30.65 0.00 39.81 2.52
2035 2066 1.278637 CGGCGGCGGCTATTTAAAG 59.721 57.895 30.65 9.12 39.81 1.85
2036 2067 2.825975 GCGGCGGCGGCTATTTAAA 61.826 57.895 33.02 0.00 39.81 1.52
2037 2068 3.273834 GCGGCGGCGGCTATTTAA 61.274 61.111 33.02 0.00 39.81 1.52
2324 2355 3.902086 GCTACCTCGTCGGGCTCC 61.902 72.222 0.00 0.00 36.97 4.70
2325 2356 3.902086 GGCTACCTCGTCGGGCTC 61.902 72.222 0.00 0.00 36.97 4.70


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

AutoCloner maintained by Alex Coulton.