Multiple sequence alignment - TraesCS5D01G162900

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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 TraesCS5D01G162900 chr5D 100.000 4513 0 0 1 4513 254532854 254528342 0.000000e+00 8335.0
1 TraesCS5D01G162900 chr5D 97.209 4228 80 12 1 4203 551019607 551015393 0.000000e+00 7119.0
2 TraesCS5D01G162900 chr5D 97.037 135 4 0 3954 4088 199428927 199429061 1.260000e-55 228.0
3 TraesCS5D01G162900 chr7D 98.483 4086 35 4 1 4062 509913492 509909410 0.000000e+00 7177.0
4 TraesCS5D01G162900 chr7D 93.939 264 16 0 3691 3954 162188472 162188735 2.530000e-107 399.0
5 TraesCS5D01G162900 chr7D 99.429 175 1 0 4074 4248 509909450 509909276 7.290000e-83 318.0
6 TraesCS5D01G162900 chr7D 98.462 130 2 0 4074 4203 501018968 501018839 3.510000e-56 230.0
7 TraesCS5D01G162900 chr7D 95.726 117 5 0 3946 4062 501019044 501018928 5.960000e-44 189.0
8 TraesCS5D01G162900 chr4D 98.263 4087 34 9 1 4062 40831633 40835707 0.000000e+00 7119.0
9 TraesCS5D01G162900 chr4D 96.796 437 8 4 4076 4509 40835669 40836102 0.000000e+00 725.0
10 TraesCS5D01G162900 chr4D 82.569 218 25 13 4300 4509 10376307 10376519 3.590000e-41 180.0
11 TraesCS5D01G162900 chr7A 98.269 1849 28 3 923 2771 678171401 678169557 0.000000e+00 3234.0
12 TraesCS5D01G162900 chr7A 93.041 1322 41 4 2741 4062 678169557 678168287 0.000000e+00 1884.0
13 TraesCS5D01G162900 chr7A 96.923 130 4 0 4074 4203 678168327 678168198 7.600000e-53 219.0
14 TraesCS5D01G162900 chr7A 82.065 184 27 5 4330 4509 25888242 25888423 7.820000e-33 152.0
15 TraesCS5D01G162900 chr1B 97.458 1849 41 4 923 2771 154148262 154150104 0.000000e+00 3149.0
16 TraesCS5D01G162900 chr1B 93.527 1205 32 3 2741 3921 154150104 154151286 0.000000e+00 1751.0
17 TraesCS5D01G162900 chr1B 80.723 249 39 7 4268 4510 601175768 601176013 7.710000e-43 185.0
18 TraesCS5D01G162900 chr1B 92.982 114 8 0 3923 4036 154151259 154151372 2.790000e-37 167.0
19 TraesCS5D01G162900 chr1B 87.850 107 8 4 3 109 55535550 55535449 2.210000e-23 121.0
20 TraesCS5D01G162900 chr1B 90.741 54 3 2 4204 4256 416586759 416586811 2.250000e-08 71.3
21 TraesCS5D01G162900 chr2A 97.296 1849 44 5 923 2771 195113158 195115000 0.000000e+00 3133.0
22 TraesCS5D01G162900 chr2A 97.642 1569 32 4 1203 2771 721735602 721737165 0.000000e+00 2687.0
23 TraesCS5D01G162900 chr2A 91.159 1346 44 5 2741 4062 721737165 721738459 0.000000e+00 1757.0
24 TraesCS5D01G162900 chr2A 93.112 1205 37 3 2741 3921 195115000 195116182 0.000000e+00 1724.0
25 TraesCS5D01G162900 chr2A 96.711 304 4 2 923 1226 721735274 721735571 6.740000e-138 501.0
26 TraesCS5D01G162900 chr2A 94.615 130 7 0 4074 4203 721738419 721738548 7.660000e-48 202.0
27 TraesCS5D01G162900 chr2A 92.105 114 9 0 3923 4036 195116155 195116268 1.300000e-35 161.0
28 TraesCS5D01G162900 chr1A 96.647 1849 37 7 923 2771 14528458 14526635 0.000000e+00 3048.0
29 TraesCS5D01G162900 chr1A 93.361 1205 33 4 2741 3921 14526635 14525454 0.000000e+00 1738.0
30 TraesCS5D01G162900 chr1A 92.373 354 12 3 3356 3694 13765077 13764724 1.460000e-134 490.0
31 TraesCS5D01G162900 chr6D 97.513 563 12 1 1732 2294 39581154 39580594 0.000000e+00 961.0
32 TraesCS5D01G162900 chr6D 96.959 559 16 1 2622 3180 39577883 39577326 0.000000e+00 937.0
33 TraesCS5D01G162900 chr6D 96.418 335 10 1 2287 2619 39578443 39578109 6.600000e-153 551.0
34 TraesCS5D01G162900 chrUn 99.270 411 3 0 1309 1719 477629048 477629458 0.000000e+00 743.0
35 TraesCS5D01G162900 chrUn 90.625 160 9 2 4050 4203 214036591 214036750 1.650000e-49 207.0
36 TraesCS5D01G162900 chrUn 90.625 160 9 2 4050 4203 235654324 235654483 1.650000e-49 207.0
37 TraesCS5D01G162900 chrUn 90.625 160 9 2 4050 4203 253139828 253139669 1.650000e-49 207.0
38 TraesCS5D01G162900 chrUn 93.182 132 8 1 3957 4088 214036525 214036655 4.610000e-45 193.0
39 TraesCS5D01G162900 chrUn 93.182 132 8 1 3957 4088 235654258 235654388 4.610000e-45 193.0
40 TraesCS5D01G162900 chrUn 93.182 132 8 1 3957 4088 253139894 253139764 4.610000e-45 193.0
41 TraesCS5D01G162900 chrUn 88.785 107 7 4 3 109 315664031 315663930 4.740000e-25 126.0
42 TraesCS5D01G162900 chrUn 86.916 107 9 3 3 109 260014717 260014616 1.030000e-21 115.0
43 TraesCS5D01G162900 chrUn 86.916 107 9 3 3 109 262118917 262118816 1.030000e-21 115.0
44 TraesCS5D01G162900 chr1D 92.877 351 10 4 3359 3694 11620623 11620273 3.140000e-136 496.0
45 TraesCS5D01G162900 chr1D 93.561 264 17 0 3691 3954 202975768 202976031 1.180000e-105 394.0
46 TraesCS5D01G162900 chr1D 93.182 264 18 0 3691 3954 12258622 12258359 5.470000e-104 388.0
47 TraesCS5D01G162900 chr1D 81.377 247 34 11 4268 4509 36393988 36394227 1.660000e-44 191.0
48 TraesCS5D01G162900 chr1D 76.882 186 23 8 4296 4479 406729465 406729632 2.240000e-13 87.9
49 TraesCS5D01G162900 chr2B 91.200 250 13 5 4268 4510 37543048 37543295 9.360000e-87 331.0
50 TraesCS5D01G162900 chr2B 89.302 215 17 5 4300 4509 480140352 480140565 9.630000e-67 265.0
51 TraesCS5D01G162900 chr2B 89.302 215 17 5 4300 4509 480144054 480144267 9.630000e-67 265.0
52 TraesCS5D01G162900 chr2B 88.372 215 20 4 4299 4509 480156018 480156231 2.080000e-63 254.0
53 TraesCS5D01G162900 chr3A 97.312 186 5 0 803 988 365952930 365952745 2.620000e-82 316.0
54 TraesCS5D01G162900 chr3A 87.850 107 8 4 3 109 568015170 568015069 2.210000e-23 121.0
55 TraesCS5D01G162900 chr5B 90.741 108 9 1 1 108 557300164 557300270 4.710000e-30 143.0
56 TraesCS5D01G162900 chr3D 93.827 81 2 2 3280 3357 535396261 535396181 7.930000e-23 119.0
57 TraesCS5D01G162900 chr4A 75.688 218 29 13 4298 4509 17800227 17800426 2.240000e-13 87.9
58 TraesCS5D01G162900 chr6B 89.474 57 5 1 4201 4256 222004800 222004856 2.250000e-08 71.3
59 TraesCS5D01G162900 chr4B 85.294 68 7 3 4204 4271 629897719 629897655 2.910000e-07 67.6
60 TraesCS5D01G162900 chr4B 84.848 66 7 3 4206 4271 629891887 629891825 3.770000e-06 63.9
61 TraesCS5D01G162900 chr3B 88.462 52 5 1 4206 4256 786358929 786358980 1.360000e-05 62.1


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 TraesCS5D01G162900 chr5D 254528342 254532854 4512 True 8335.000000 8335 100.000000 1 4513 1 chr5D.!!$R1 4512
1 TraesCS5D01G162900 chr5D 551015393 551019607 4214 True 7119.000000 7119 97.209000 1 4203 1 chr5D.!!$R2 4202
2 TraesCS5D01G162900 chr7D 509909276 509913492 4216 True 3747.500000 7177 98.956000 1 4248 2 chr7D.!!$R2 4247
3 TraesCS5D01G162900 chr4D 40831633 40836102 4469 False 3922.000000 7119 97.529500 1 4509 2 chr4D.!!$F2 4508
4 TraesCS5D01G162900 chr7A 678168198 678171401 3203 True 1779.000000 3234 96.077667 923 4203 3 chr7A.!!$R1 3280
5 TraesCS5D01G162900 chr1B 154148262 154151372 3110 False 1689.000000 3149 94.655667 923 4036 3 chr1B.!!$F3 3113
6 TraesCS5D01G162900 chr2A 195113158 195116268 3110 False 1672.666667 3133 94.171000 923 4036 3 chr2A.!!$F1 3113
7 TraesCS5D01G162900 chr2A 721735274 721738548 3274 False 1286.750000 2687 95.031750 923 4203 4 chr2A.!!$F2 3280
8 TraesCS5D01G162900 chr1A 14525454 14528458 3004 True 2393.000000 3048 95.004000 923 3921 2 chr1A.!!$R2 2998
9 TraesCS5D01G162900 chr6D 39577326 39581154 3828 True 816.333333 961 96.963333 1732 3180 3 chr6D.!!$R1 1448
10 TraesCS5D01G162900 chr2B 480140352 480144267 3915 False 265.000000 265 89.302000 4300 4509 2 chr2B.!!$F3 209

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
146 147 2.046988 CTCGCCTCACACATGCCA 60.047 61.111 0.0 0.00 0.00 4.92 F
474 475 4.279922 CCTCGTTTTTAGGATGTTGGGTTT 59.720 41.667 0.0 0.00 36.08 3.27 F
1242 1293 4.530857 GCGCATCGGGCAGTACCT 62.531 66.667 0.3 0.00 45.17 3.08 F
2715 5151 1.802960 CAACTGTTGCTCCTGCTACTG 59.197 52.381 7.7 7.59 43.46 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1242 1293 6.529829 GCGCATATGTACCAGAAAATTCAAAA 59.470 34.615 0.3 0.00 0.00 2.44 R
2156 2209 7.118390 ACTGAATGAGTAGAAACATAAGTGTGC 59.882 37.037 0.0 0.00 33.64 4.57 R
2758 5224 0.037447 AGAGCAGGGGCAGAGAAAAC 59.963 55.000 0.0 0.00 44.61 2.43 R
4055 6624 1.437986 CGAGGTCCTAAAGGAGGCG 59.562 63.158 0.0 0.15 46.49 5.52 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
146 147 2.046988 CTCGCCTCACACATGCCA 60.047 61.111 0.00 0.00 0.00 4.92
474 475 4.279922 CCTCGTTTTTAGGATGTTGGGTTT 59.720 41.667 0.00 0.00 36.08 3.27
1088 1090 8.070171 GGTAATTCTCATCAACATTTCGTATGG 58.930 37.037 5.52 0.00 0.00 2.74
1242 1293 4.530857 GCGCATCGGGCAGTACCT 62.531 66.667 0.30 0.00 45.17 3.08
2156 2209 4.593206 TGGAATAGAGGGGCTACTACATTG 59.407 45.833 0.00 0.00 0.00 2.82
2509 4720 4.943705 TCAAAGTCTTCTCACCATAATGGC 59.056 41.667 0.00 0.00 42.67 4.40
2715 5151 1.802960 CAACTGTTGCTCCTGCTACTG 59.197 52.381 7.70 7.59 43.46 2.74
2918 5413 3.527253 TGATGGTTCATCCCCACATAAGT 59.473 43.478 5.57 0.00 39.87 2.24
3077 5573 2.178984 ACCACAGGAAATCCCTCCAAAA 59.821 45.455 0.00 0.00 45.60 2.44
3743 6312 6.013293 TCCGTCTCTCTATCCTGATCTGATTA 60.013 42.308 0.38 0.00 0.00 1.75
4263 6833 3.318539 GAGGTCGTGCGTGCGAGTA 62.319 63.158 3.87 0.00 41.85 2.59
4492 10771 6.071278 GCAGGTACCAAAATAAACCATGGTAA 60.071 38.462 20.12 10.29 46.76 2.85
4509 10788 7.125053 ACCATGGTAATTGGGACGAAAATAAAT 59.875 33.333 18.10 0.00 38.64 1.40
4510 10789 7.984617 CCATGGTAATTGGGACGAAAATAAATT 59.015 33.333 2.57 0.00 0.00 1.82
4511 10790 9.030301 CATGGTAATTGGGACGAAAATAAATTC 57.970 33.333 0.00 0.00 0.00 2.17
4512 10791 8.123639 TGGTAATTGGGACGAAAATAAATTCA 57.876 30.769 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
146 147 0.759346 GGCGATATGGTCTGGAAGGT 59.241 55.000 0.00 0.00 0.00 3.50
1242 1293 6.529829 GCGCATATGTACCAGAAAATTCAAAA 59.470 34.615 0.30 0.00 0.00 2.44
2156 2209 7.118390 ACTGAATGAGTAGAAACATAAGTGTGC 59.882 37.037 0.00 0.00 33.64 4.57
2509 4720 5.929697 ATGCACATGGTATTCAGTTATCG 57.070 39.130 0.00 0.00 0.00 2.92
2715 5151 7.497249 AGCTATTGATTGAAGTGACTGGTAATC 59.503 37.037 8.76 8.76 0.00 1.75
2757 5223 0.962855 GAGCAGGGGCAGAGAAAACC 60.963 60.000 0.00 0.00 44.61 3.27
2758 5224 0.037447 AGAGCAGGGGCAGAGAAAAC 59.963 55.000 0.00 0.00 44.61 2.43
2918 5413 0.911769 CCAGGGAGCATCAGGTACAA 59.088 55.000 0.00 0.00 36.25 2.41
3077 5573 4.828829 CGGGATTCACAGGTTAGTTTAGT 58.171 43.478 0.00 0.00 0.00 2.24
3522 6091 5.836898 TCTTGTACGGAATATACCACCAGAT 59.163 40.000 0.00 0.00 0.00 2.90
3743 6312 4.728772 AGAATCAGATCTGAGACGGAGAT 58.271 43.478 28.26 8.36 43.61 2.75
4030 6599 1.849977 GTCGAGGTCCTAAAGGAGGT 58.150 55.000 0.00 0.00 46.49 3.85
4055 6624 1.437986 CGAGGTCCTAAAGGAGGCG 59.562 63.158 0.00 0.15 46.49 5.52
4263 6833 1.808390 GCCCGCACGTACGAGAAAT 60.808 57.895 24.41 0.00 34.06 2.17


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

AutoCloner maintained by Alex Coulton.