Multiple sequence alignment - TraesCS3B01G385300

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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 TraesCS3B01G385300 chr3B 100.000 2596 0 0 1 2596 605446986 605444391 0.000000e+00 4795
1 TraesCS3B01G385300 chr3B 93.330 1964 94 17 1 1932 612313183 612315141 0.000000e+00 2867
2 TraesCS3B01G385300 chr3B 91.329 1061 91 1 874 1934 62530853 62529794 0.000000e+00 1448
3 TraesCS3B01G385300 chr3B 91.707 205 9 2 1945 2141 605482138 605481934 7.080000e-71 278
4 TraesCS3B01G385300 chr3B 83.553 152 15 6 586 735 235986750 235986893 1.620000e-27 134
5 TraesCS3B01G385300 chr1B 92.116 1966 99 26 1 1934 199669063 199667122 0.000000e+00 2721
6 TraesCS3B01G385300 chr1D 93.692 1712 96 7 248 1950 467476660 467474952 0.000000e+00 2553
7 TraesCS3B01G385300 chr7A 92.743 1061 72 4 874 1934 641403709 641402654 0.000000e+00 1528
8 TraesCS3B01G385300 chr4D 92.366 1061 74 4 874 1934 379508030 379506977 0.000000e+00 1504
9 TraesCS3B01G385300 chr4B 92.279 1062 79 3 874 1934 575618123 575617064 0.000000e+00 1504
10 TraesCS3B01G385300 chr1A 91.235 1061 88 2 874 1934 520787835 520788890 0.000000e+00 1439
11 TraesCS3B01G385300 chr1A 83.990 381 44 9 505 877 111797160 111796789 1.480000e-92 350
12 TraesCS3B01G385300 chr1A 95.745 94 4 0 783 876 543406891 543406984 4.470000e-33 152
13 TraesCS3B01G385300 chr1A 93.750 96 6 0 783 878 576164974 576165069 7.490000e-31 145
14 TraesCS3B01G385300 chr3A 91.454 1018 79 4 874 1889 170228793 170227782 0.000000e+00 1391
15 TraesCS3B01G385300 chr3A 97.285 663 16 1 1934 2594 600675417 600674755 0.000000e+00 1123
16 TraesCS3B01G385300 chr3D 94.622 595 25 4 2006 2594 458176119 458176712 0.000000e+00 915
17 TraesCS3B01G385300 chr3D 91.463 82 4 1 1945 2023 458176012 458176093 2.730000e-20 110
18 TraesCS3B01G385300 chr2A 92.241 580 27 3 539 1100 240853125 240853704 0.000000e+00 806
19 TraesCS3B01G385300 chr2A 86.207 435 27 15 139 541 240852569 240853002 8.530000e-120 440
20 TraesCS3B01G385300 chr2A 95.172 145 7 0 1 145 240827531 240827675 2.010000e-56 230
21 TraesCS3B01G385300 chr2A 82.550 149 17 5 586 732 726552473 726552332 3.510000e-24 122
22 TraesCS3B01G385300 chr6A 93.750 96 6 0 783 878 592411110 592411205 7.490000e-31 145
23 TraesCS3B01G385300 chr5A 93.750 96 6 0 783 878 688130819 688130914 7.490000e-31 145
24 TraesCS3B01G385300 chr4A 83.217 143 15 5 586 726 358821211 358821346 3.510000e-24 122


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 TraesCS3B01G385300 chr3B 605444391 605446986 2595 True 4795.0 4795 100.0000 1 2596 1 chr3B.!!$R2 2595
1 TraesCS3B01G385300 chr3B 612313183 612315141 1958 False 2867.0 2867 93.3300 1 1932 1 chr3B.!!$F2 1931
2 TraesCS3B01G385300 chr3B 62529794 62530853 1059 True 1448.0 1448 91.3290 874 1934 1 chr3B.!!$R1 1060
3 TraesCS3B01G385300 chr1B 199667122 199669063 1941 True 2721.0 2721 92.1160 1 1934 1 chr1B.!!$R1 1933
4 TraesCS3B01G385300 chr1D 467474952 467476660 1708 True 2553.0 2553 93.6920 248 1950 1 chr1D.!!$R1 1702
5 TraesCS3B01G385300 chr7A 641402654 641403709 1055 True 1528.0 1528 92.7430 874 1934 1 chr7A.!!$R1 1060
6 TraesCS3B01G385300 chr4D 379506977 379508030 1053 True 1504.0 1504 92.3660 874 1934 1 chr4D.!!$R1 1060
7 TraesCS3B01G385300 chr4B 575617064 575618123 1059 True 1504.0 1504 92.2790 874 1934 1 chr4B.!!$R1 1060
8 TraesCS3B01G385300 chr1A 520787835 520788890 1055 False 1439.0 1439 91.2350 874 1934 1 chr1A.!!$F1 1060
9 TraesCS3B01G385300 chr3A 170227782 170228793 1011 True 1391.0 1391 91.4540 874 1889 1 chr3A.!!$R1 1015
10 TraesCS3B01G385300 chr3A 600674755 600675417 662 True 1123.0 1123 97.2850 1934 2594 1 chr3A.!!$R2 660
11 TraesCS3B01G385300 chr3D 458176012 458176712 700 False 512.5 915 93.0425 1945 2594 2 chr3D.!!$F1 649
12 TraesCS3B01G385300 chr2A 240852569 240853704 1135 False 623.0 806 89.2240 139 1100 2 chr2A.!!$F2 961

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
284 309 1.1282 TCTTGTGGTGTGTAGGCAGT 58.872 50.0 0.0 0.0 0.0 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1819 1999 1.194781 AACACTCCCGCATCCTCTGT 61.195 55.0 0.0 0.0 0.0 3.41 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
178 179 2.094494 ACACCATTCACAGAGCTAGACG 60.094 50.000 0.00 0.00 0.00 4.18
284 309 1.128200 TCTTGTGGTGTGTAGGCAGT 58.872 50.000 0.00 0.00 0.00 4.40
497 531 8.978874 AATATGTGAATGCATTAGGAACTGTA 57.021 30.769 12.97 6.94 41.52 2.74
625 784 9.688592 ACTGCAGAGATTTTTATTTCTTTTCAG 57.311 29.630 23.35 0.00 0.00 3.02
836 1012 3.135348 TGGCATCTTTCTATCAGTGGAGG 59.865 47.826 0.00 0.00 0.00 4.30
837 1013 3.495806 GGCATCTTTCTATCAGTGGAGGG 60.496 52.174 0.00 0.00 0.00 4.30
861 1037 5.413499 CCTTGTTTTCAAATAGCAGGGATG 58.587 41.667 0.00 0.00 39.47 3.51
917 1093 6.072008 TGTGCTGTAACATTAATCAGTGCATT 60.072 34.615 0.00 0.00 0.00 3.56
985 1161 8.998814 TCATTTGAACATAATCTAACCCCTCTA 58.001 33.333 0.00 0.00 0.00 2.43
1149 1327 4.481930 TGACCAATCTTTGTTACTTGCG 57.518 40.909 0.00 0.00 0.00 4.85
1234 1412 1.450134 CACTATGCCTGCGCCAAGA 60.450 57.895 4.18 0.00 0.00 3.02
1399 1577 2.076100 CTTGCAGCGAGGATTGTTGTA 58.924 47.619 0.94 0.00 32.65 2.41
1414 1592 1.268352 GTTGTATCCAACCTGCGCAAA 59.732 47.619 13.05 0.00 44.25 3.68
1441 1619 2.588464 AGAAGTCCTTCTCGGAGACA 57.412 50.000 7.33 0.00 46.13 3.41
1473 1651 3.255725 CGCATGTTTCTGCCATGATTTT 58.744 40.909 4.66 0.00 41.78 1.82
1491 1669 5.701750 TGATTTTCTTCGGTTGGATTTCGTA 59.298 36.000 0.00 0.00 0.00 3.43
1498 1676 7.098477 TCTTCGGTTGGATTTCGTAGATTTAA 58.902 34.615 0.00 0.00 35.04 1.52
1525 1703 8.519526 GTGTTGAAAAATTATGGACTGTGGATA 58.480 33.333 0.00 0.00 0.00 2.59
1546 1724 4.772886 ACAGGATTAAGGACATGTACCC 57.227 45.455 3.84 0.00 29.45 3.69
1568 1746 2.423892 GCACTACAACGAGAGATCTGGA 59.576 50.000 0.00 0.00 0.00 3.86
1708 1888 8.650143 ACAAACTAAATGAAGATATGGTGGTT 57.350 30.769 0.00 0.00 0.00 3.67
1709 1889 8.739972 ACAAACTAAATGAAGATATGGTGGTTC 58.260 33.333 0.00 0.00 0.00 3.62
1819 1999 2.616842 GTGAGAAAAGACGGCTTCCAAA 59.383 45.455 2.63 0.00 31.82 3.28
1899 2079 2.237143 CACAATACTTGGCTCCCTCTCA 59.763 50.000 0.00 0.00 34.12 3.27
1907 2087 1.492993 GGCTCCCTCTCACCCTTTGT 61.493 60.000 0.00 0.00 0.00 2.83
2026 2252 9.436957 AGTACAATCACTCCTATGTTTTTACAG 57.563 33.333 0.00 0.00 0.00 2.74
2122 2356 2.977914 ACTTGACATCAGTTGATCGGG 58.022 47.619 0.00 0.00 31.21 5.14
2150 2384 2.098117 GCCTCATTTCTTCCACATTCCG 59.902 50.000 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
140 141 4.143543 TGGTGTCAATTTTCAGCTCATCA 58.856 39.130 9.27 0.00 33.89 3.07
178 179 5.065914 TCCCATGCTACATTCATAAGCTTC 58.934 41.667 0.00 0.00 37.16 3.86
225 226 6.720112 ATGGTTCATATAAGCAAGCACAAT 57.280 33.333 0.00 0.00 30.75 2.71
284 309 3.671008 ACCTTGTAACATACAGTCGCA 57.329 42.857 0.00 0.00 40.24 5.10
332 364 6.956202 AGTACTAACACCACGAGCTTATAT 57.044 37.500 0.00 0.00 0.00 0.86
334 366 6.038050 GTCTAGTACTAACACCACGAGCTTAT 59.962 42.308 3.76 0.00 0.00 1.73
381 414 7.626999 TGCAGTATAGTATACCCAAGGAATT 57.373 36.000 15.34 0.00 0.00 2.17
623 782 6.128580 GCATAAATAACAACCAAGGCAAACTG 60.129 38.462 0.00 0.00 0.00 3.16
625 784 5.121611 GGCATAAATAACAACCAAGGCAAAC 59.878 40.000 0.00 0.00 0.00 2.93
836 1012 3.588955 CCTGCTATTTGAAAACAAGGCC 58.411 45.455 0.00 0.00 0.00 5.19
837 1013 3.258123 TCCCTGCTATTTGAAAACAAGGC 59.742 43.478 0.00 0.00 0.00 4.35
917 1093 1.074084 TGATAGAAAACGTTGGGCCCA 59.926 47.619 24.45 24.45 0.00 5.36
1125 1302 5.746245 CGCAAGTAACAAAGATTGGTCAAAA 59.254 36.000 0.00 0.00 34.12 2.44
1399 1577 1.940752 GCATTTTTGCGCAGGTTGGAT 60.941 47.619 11.31 0.00 0.00 3.41
1441 1619 1.312371 AAACATGCGCCGTGGCTTAT 61.312 50.000 4.18 0.16 39.32 1.73
1473 1651 4.730949 ATCTACGAAATCCAACCGAAGA 57.269 40.909 0.00 0.00 0.00 2.87
1498 1676 6.549364 TCCACAGTCCATAATTTTTCAACACT 59.451 34.615 0.00 0.00 0.00 3.55
1525 1703 3.134081 CGGGTACATGTCCTTAATCCTGT 59.866 47.826 0.00 0.00 0.00 4.00
1546 1724 2.445316 CAGATCTCTCGTTGTAGTGCG 58.555 52.381 0.00 0.00 0.00 5.34
1568 1746 2.378038 TGAAAGCCACAAAGAAGCAGT 58.622 42.857 0.00 0.00 0.00 4.40
1708 1888 6.810182 GCTTTAAGTTGTACTATTGAGACCGA 59.190 38.462 0.00 0.00 0.00 4.69
1709 1889 6.035758 GGCTTTAAGTTGTACTATTGAGACCG 59.964 42.308 0.00 0.00 0.00 4.79
1745 1925 9.850628 TCAAGAGCAAATTTCAGAGAAAATATG 57.149 29.630 0.00 0.00 0.00 1.78
1792 1972 1.944430 GCCGTCTTTTCTCACCGGATT 60.944 52.381 9.46 0.00 41.08 3.01
1819 1999 1.194781 AACACTCCCGCATCCTCTGT 61.195 55.000 0.00 0.00 0.00 3.41
1899 2079 1.805428 GCGCCAATGACACAAAGGGT 61.805 55.000 0.00 0.00 0.00 4.34
1907 2087 1.270571 TGACTAGTTGCGCCAATGACA 60.271 47.619 4.18 0.00 0.00 3.58
2026 2252 1.370051 GTTTTGCCGGTTCTCGTGC 60.370 57.895 1.90 0.00 37.11 5.34
2077 2311 1.359475 GTGGCTCGATCGTAGGGAC 59.641 63.158 15.94 6.99 0.00 4.46
2122 2356 1.601430 GGAAGAAATGAGGCTGATCGC 59.399 52.381 0.00 1.55 38.13 4.58
2288 2522 3.058160 GCCATGGCGTTGCTCACT 61.058 61.111 23.48 0.00 0.00 3.41
2426 2660 2.872557 CGGCAGTACGAGTCCGAA 59.127 61.111 14.19 0.00 44.23 4.30


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

AutoCloner maintained by Alex Coulton.