Multiple sequence alignment - TraesCS2B01G017500

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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 TraesCS2B01G017500 chr2B 100.000 3668 0 0 1 3668 8173790 8177457 0.000000e+00 6774.0
1 TraesCS2B01G017500 chr2B 99.035 2902 27 1 1 2901 8009177 8012078 0.000000e+00 5203.0
2 TraesCS2B01G017500 chr2B 97.501 2001 50 0 211 2211 7963063 7965063 0.000000e+00 3419.0
3 TraesCS2B01G017500 chr2B 97.101 2001 58 0 211 2211 8131828 8133828 0.000000e+00 3374.0
4 TraesCS2B01G017500 chr2B 89.895 1999 150 32 828 2809 30981881 30983844 0.000000e+00 2525.0
5 TraesCS2B01G017500 chr2B 99.092 771 7 0 2898 3668 8012595 8013365 0.000000e+00 1386.0
6 TraesCS2B01G017500 chr2B 88.742 151 8 2 2898 3039 756551045 756551195 3.760000e-40 176.0
7 TraesCS2B01G017500 chr2B 78.832 274 33 11 258 522 8597802 8597545 1.050000e-35 161.0
8 TraesCS2B01G017500 chr2B 97.727 44 0 1 2254 2297 8133874 8133832 1.410000e-09 75.0
9 TraesCS2B01G017500 chr2B 100.000 37 0 0 3467 3503 68580389 68580353 6.570000e-08 69.4
10 TraesCS2B01G017500 chr2B 97.297 37 1 0 3467 3503 417782010 417782046 3.060000e-06 63.9
11 TraesCS2B01G017500 chr2B 97.059 34 1 0 3529 3562 783934990 783935023 1.420000e-04 58.4
12 TraesCS2B01G017500 chr2A 90.215 1860 113 23 988 2808 2274750 2272921 0.000000e+00 2362.0
13 TraesCS2B01G017500 chr2A 84.932 365 36 12 2898 3250 491535690 491536047 5.830000e-93 351.0
14 TraesCS2B01G017500 chr2A 86.500 200 18 6 17 212 683834947 683834753 1.030000e-50 211.0
15 TraesCS2B01G017500 chr2A 92.063 126 7 3 90 212 689429269 689429144 1.350000e-39 174.0
16 TraesCS2B01G017500 chr2A 90.164 61 5 1 517 577 640708114 640708055 1.090000e-10 78.7
17 TraesCS2B01G017500 chr2A 89.831 59 6 0 525 583 384888813 384888871 3.930000e-10 76.8
18 TraesCS2B01G017500 chr7B 87.500 488 45 9 2898 3372 662927929 662928413 1.930000e-152 549.0
19 TraesCS2B01G017500 chr7B 92.749 331 21 2 3341 3668 662928464 662928794 3.310000e-130 475.0
20 TraesCS2B01G017500 chr7B 86.667 345 31 9 2898 3228 717271778 717272121 5.790000e-98 368.0
21 TraesCS2B01G017500 chr7B 85.163 337 37 9 2900 3223 244743958 244744294 2.110000e-87 333.0
22 TraesCS2B01G017500 chr7B 82.192 219 23 8 1 212 525193306 525193515 1.350000e-39 174.0
23 TraesCS2B01G017500 chr7B 80.672 119 10 8 2232 2348 374530281 374530388 3.040000e-11 80.5
24 TraesCS2B01G017500 chr7B 94.118 51 2 1 3462 3512 134035398 134035349 3.930000e-10 76.8
25 TraesCS2B01G017500 chr7B 90.566 53 4 1 2828 2880 105829427 105829376 6.570000e-08 69.4
26 TraesCS2B01G017500 chr4B 88.166 338 26 7 2898 3224 629960865 629960531 1.240000e-104 390.0
27 TraesCS2B01G017500 chr3D 88.060 335 29 4 2898 3221 447637742 447637408 1.600000e-103 387.0
28 TraesCS2B01G017500 chr3D 95.935 123 5 0 90 212 601178839 601178961 2.230000e-47 200.0
29 TraesCS2B01G017500 chr5B 86.501 363 34 8 2898 3250 264885927 264885570 5.750000e-103 385.0
30 TraesCS2B01G017500 chr5B 91.339 127 7 3 1 123 453383665 453383791 1.750000e-38 171.0
31 TraesCS2B01G017500 chr5B 87.417 151 10 2 2898 3039 281370075 281369925 8.150000e-37 165.0
32 TraesCS2B01G017500 chr1B 87.574 338 28 7 2898 3224 65288217 65288551 2.670000e-101 379.0
33 TraesCS2B01G017500 chr1B 92.683 123 7 1 92 212 662378316 662378194 3.760000e-40 176.0
34 TraesCS2B01G017500 chr1B 100.000 37 0 0 3467 3503 31150655 31150619 6.570000e-08 69.4
35 TraesCS2B01G017500 chr1B 97.297 37 1 0 3467 3503 560224110 560224074 3.060000e-06 63.9
36 TraesCS2B01G017500 chr1B 92.683 41 2 1 3523 3562 649387750 649387790 1.420000e-04 58.4
37 TraesCS2B01G017500 chr1A 85.873 361 37 6 2900 3250 518746430 518746074 4.470000e-99 372.0
38 TraesCS2B01G017500 chr6A 85.552 353 40 8 2900 3250 573144229 573144572 3.480000e-95 359.0
39 TraesCS2B01G017500 chr6A 93.333 120 6 2 90 208 66000406 66000288 3.760000e-40 176.0
40 TraesCS2B01G017500 chr6A 75.660 341 66 11 2168 2504 50408437 50408110 1.760000e-33 154.0
41 TraesCS2B01G017500 chr6A 75.660 341 66 11 2168 2504 50465032 50464705 1.760000e-33 154.0
42 TraesCS2B01G017500 chr6A 75.595 336 65 11 2173 2504 50865022 50864700 2.280000e-32 150.0
43 TraesCS2B01G017500 chr6B 87.432 183 15 7 33 212 61365808 61365985 1.730000e-48 204.0
44 TraesCS2B01G017500 chr6B 93.750 112 7 0 3153 3264 695480018 695480129 6.300000e-38 169.0
45 TraesCS2B01G017500 chr6B 92.920 113 6 2 3153 3264 76111806 76111917 2.930000e-36 163.0
46 TraesCS2B01G017500 chr6B 82.963 135 11 5 3518 3640 77456090 77456224 1.080000e-20 111.0
47 TraesCS2B01G017500 chr6B 94.737 38 2 0 3280 3317 76112243 76112280 3.960000e-05 60.2
48 TraesCS2B01G017500 chr4A 87.417 151 10 2 2898 3039 717726729 717726579 8.150000e-37 165.0
49 TraesCS2B01G017500 chr4A 87.417 151 10 2 2898 3039 733354592 733354442 8.150000e-37 165.0
50 TraesCS2B01G017500 chr4A 82.418 182 22 9 37 212 20351987 20351810 2.280000e-32 150.0
51 TraesCS2B01G017500 chr4A 90.741 54 5 0 2827 2880 707665165 707665218 5.080000e-09 73.1
52 TraesCS2B01G017500 chr2D 87.417 151 9 3 2898 3039 638306427 638306576 8.150000e-37 165.0
53 TraesCS2B01G017500 chr1D 86.713 143 14 3 2898 3039 363855896 363855758 1.760000e-33 154.0
54 TraesCS2B01G017500 chrUn 75.710 317 65 9 2168 2482 114234842 114235148 8.210000e-32 148.0
55 TraesCS2B01G017500 chr7D 98.592 71 1 0 3568 3638 452139202 452139272 3.850000e-25 126.0
56 TraesCS2B01G017500 chr7D 98.592 71 1 0 3568 3638 598520791 598520861 3.850000e-25 126.0
57 TraesCS2B01G017500 chr7D 81.513 119 9 9 2232 2348 379091508 379091615 6.530000e-13 86.1
58 TraesCS2B01G017500 chr7D 90.769 65 4 2 2817 2880 590865555 590865618 6.530000e-13 86.1
59 TraesCS2B01G017500 chr7D 92.683 41 3 0 3280 3320 68918278 68918238 3.960000e-05 60.2
60 TraesCS2B01G017500 chr7A 81.513 119 9 9 2232 2348 427558266 427558373 6.530000e-13 86.1
61 TraesCS2B01G017500 chr7A 89.655 58 6 0 526 583 86232221 86232278 1.410000e-09 75.0
62 TraesCS2B01G017500 chr3B 88.060 67 7 1 517 583 457002082 457002017 1.090000e-10 78.7
63 TraesCS2B01G017500 chr3B 97.297 37 1 0 3467 3503 43606904 43606940 3.060000e-06 63.9
64 TraesCS2B01G017500 chr6D 100.000 40 0 0 3599 3638 361415203 361415242 1.410000e-09 75.0
65 TraesCS2B01G017500 chr5D 93.878 49 2 1 3455 3503 485356657 485356704 5.080000e-09 73.1
66 TraesCS2B01G017500 chr5D 87.931 58 7 0 526 583 216833508 216833451 6.570000e-08 69.4
67 TraesCS2B01G017500 chr5A 87.719 57 7 0 527 583 379890261 379890205 2.360000e-07 67.6


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 TraesCS2B01G017500 chr2B 8173790 8177457 3667 False 6774.0 6774 100.0000 1 3668 1 chr2B.!!$F3 3667
1 TraesCS2B01G017500 chr2B 7963063 7965063 2000 False 3419.0 3419 97.5010 211 2211 1 chr2B.!!$F1 2000
2 TraesCS2B01G017500 chr2B 8131828 8133828 2000 False 3374.0 3374 97.1010 211 2211 1 chr2B.!!$F2 2000
3 TraesCS2B01G017500 chr2B 8009177 8013365 4188 False 3294.5 5203 99.0635 1 3668 2 chr2B.!!$F8 3667
4 TraesCS2B01G017500 chr2B 30981881 30983844 1963 False 2525.0 2525 89.8950 828 2809 1 chr2B.!!$F4 1981
5 TraesCS2B01G017500 chr2A 2272921 2274750 1829 True 2362.0 2362 90.2150 988 2808 1 chr2A.!!$R1 1820
6 TraesCS2B01G017500 chr7B 662927929 662928794 865 False 512.0 549 90.1245 2898 3668 2 chr7B.!!$F5 770

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
903 905 0.467384 CACCTAGCAGATGACCCTGG 59.533 60.0 0.0 0.0 34.82 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2839 2926 1.071699 TGGCTCCTATTTATCGGGTGC 59.928 52.381 0.0 0.0 38.44 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
44 45 6.416415 GGAGAATATACGTGGGAGAGAGATA 58.584 44.000 0.00 0.0 0.00 1.98
138 140 3.128349 CGTAATAATTCGGTCCCACCAG 58.872 50.000 0.00 0.0 38.47 4.00
140 142 3.277142 AATAATTCGGTCCCACCAGAC 57.723 47.619 0.00 0.0 38.47 3.51
144 146 0.971386 TTCGGTCCCACCAGACTAAC 59.029 55.000 0.00 0.0 38.47 2.34
164 166 5.554822 AACGGCTCGCAAAATCTAATTAA 57.445 34.783 0.00 0.0 0.00 1.40
746 748 1.343069 GAGTGGTGGTCAAGAGAGGT 58.657 55.000 0.00 0.0 0.00 3.85
864 866 7.406104 AGAAGATATAAGGATAATGTTGGGGC 58.594 38.462 0.00 0.0 0.00 5.80
903 905 0.467384 CACCTAGCAGATGACCCTGG 59.533 60.000 0.00 0.0 34.82 4.45
954 969 9.271828 GAACAAGAATTTGGGTCACAATTTAAT 57.728 29.630 0.00 0.0 39.21 1.40
1989 2004 3.352338 AACATCCGACGCGAGGTCC 62.352 63.158 15.93 0.0 42.99 4.46
2803 2890 2.605837 TTGCCGAGTACAAGAACACA 57.394 45.000 0.00 0.0 0.00 3.72
2839 2926 0.250081 GCCGAGAGCCCTATGAAAGG 60.250 60.000 0.00 0.0 46.09 3.11
3151 3767 3.553437 CTTGGACTGTCGCCGTCGT 62.553 63.158 1.07 0.0 36.96 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 4.201122 CTCCCATGGCCCAGCTCC 62.201 72.222 6.09 0.0 0.00 4.70
135 137 0.669318 TTTGCGAGCCGTTAGTCTGG 60.669 55.000 0.00 0.0 0.00 3.86
138 140 2.000447 AGATTTTGCGAGCCGTTAGTC 59.000 47.619 0.00 0.0 0.00 2.59
140 142 4.795970 ATTAGATTTTGCGAGCCGTTAG 57.204 40.909 0.00 0.0 0.00 2.34
144 146 3.960002 CGTTAATTAGATTTTGCGAGCCG 59.040 43.478 0.00 0.0 0.00 5.52
164 166 4.351127 AGACTCCCTAGAAATTACCACGT 58.649 43.478 0.00 0.0 0.00 4.49
574 576 3.565214 TGGGAAGTCGGGCAGCAA 61.565 61.111 0.00 0.0 0.00 3.91
923 925 4.216472 GTGACCCAAATTCTTGTTCCTCTC 59.784 45.833 0.00 0.0 0.00 3.20
1696 1711 0.607489 GAGGAAAAGCTCAGCCTGCA 60.607 55.000 6.00 0.0 0.00 4.41
2718 2804 3.968096 CGTGTTGTGCTTGTTCACTTATG 59.032 43.478 0.00 0.0 37.81 1.90
2803 2890 1.337071 CGGCATACGTACTGTGATCCT 59.663 52.381 0.00 0.0 37.93 3.24
2839 2926 1.071699 TGGCTCCTATTTATCGGGTGC 59.928 52.381 0.00 0.0 38.44 5.01
3392 4092 2.033141 ACTCCAGCAGCAACGCAT 59.967 55.556 0.00 0.0 0.00 4.73


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

AutoCloner maintained by Alex Coulton.