Multiple sequence alignment - TraesCS6B01G227600

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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 TraesCS6B01G227600 chr6B 100.000 3545 0 0 1 3545 353552242 353548698 0 6547
1 TraesCS6B01G227600 chr6B 97.226 2451 64 4 1 2448 319457334 319459783 0 4146
2 TraesCS6B01G227600 chr4A 97.098 3549 97 4 1 3545 713792488 713788942 0 5978
3 TraesCS6B01G227600 chr2B 97.099 3551 94 7 1 3545 19851981 19855528 0 5978
4 TraesCS6B01G227600 chr2B 94.154 3575 149 29 4 3545 655694281 655690734 0 5389
5 TraesCS6B01G227600 chr2B 97.455 2161 53 1 1 2159 512426262 512424102 0 3685
6 TraesCS6B01G227600 chr2B 97.068 1330 36 3 2218 3545 658222502 658221174 0 2237
7 TraesCS6B01G227600 chr4B 97.131 3311 87 7 1 3306 603291277 603287970 0 5581
8 TraesCS6B01G227600 chr4B 94.052 3581 151 25 1 3545 15516595 15520149 0 5376
9 TraesCS6B01G227600 chr3B 93.661 3581 162 27 1 3545 60566605 60570156 0 5295
10 TraesCS6B01G227600 chr7B 96.511 2207 71 5 1 2204 599829324 599831527 0 3644
11 TraesCS6B01G227600 chr7B 97.070 1331 36 3 2218 3545 180026082 180024752 0 2239
12 TraesCS6B01G227600 chr7B 97.070 1331 35 4 2218 3545 693176173 693177502 0 2239


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 TraesCS6B01G227600 chr6B 353548698 353552242 3544 True 6547 6547 100.000 1 3545 1 chr6B.!!$R1 3544
1 TraesCS6B01G227600 chr6B 319457334 319459783 2449 False 4146 4146 97.226 1 2448 1 chr6B.!!$F1 2447
2 TraesCS6B01G227600 chr4A 713788942 713792488 3546 True 5978 5978 97.098 1 3545 1 chr4A.!!$R1 3544
3 TraesCS6B01G227600 chr2B 19851981 19855528 3547 False 5978 5978 97.099 1 3545 1 chr2B.!!$F1 3544
4 TraesCS6B01G227600 chr2B 655690734 655694281 3547 True 5389 5389 94.154 4 3545 1 chr2B.!!$R2 3541
5 TraesCS6B01G227600 chr2B 512424102 512426262 2160 True 3685 3685 97.455 1 2159 1 chr2B.!!$R1 2158
6 TraesCS6B01G227600 chr2B 658221174 658222502 1328 True 2237 2237 97.068 2218 3545 1 chr2B.!!$R3 1327
7 TraesCS6B01G227600 chr4B 603287970 603291277 3307 True 5581 5581 97.131 1 3306 1 chr4B.!!$R1 3305
8 TraesCS6B01G227600 chr4B 15516595 15520149 3554 False 5376 5376 94.052 1 3545 1 chr4B.!!$F1 3544
9 TraesCS6B01G227600 chr3B 60566605 60570156 3551 False 5295 5295 93.661 1 3545 1 chr3B.!!$F1 3544
10 TraesCS6B01G227600 chr7B 599829324 599831527 2203 False 3644 3644 96.511 1 2204 1 chr7B.!!$F1 2203
11 TraesCS6B01G227600 chr7B 180024752 180026082 1330 True 2239 2239 97.070 2218 3545 1 chr7B.!!$R1 1327
12 TraesCS6B01G227600 chr7B 693176173 693177502 1329 False 2239 2239 97.070 2218 3545 1 chr7B.!!$F2 1327

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
902 948 0.107831 GTGTGCTTGGGTAGGTGTGA 59.892 55.0 0.0 0.0 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2646 2705 1.243902 GCACCATCGACCCAGAAAAA 58.756 50.0 0.0 0.0 0.0 1.94 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
240 246 0.233848 CAGCGGCGAAACGTTACTTT 59.766 50.000 12.98 0.00 35.98 2.66
514 526 2.871637 GCTTGCTTCCCCAAAATCAACC 60.872 50.000 0.00 0.00 0.00 3.77
697 715 4.261572 CCTGATTATATGGTTTGGGTTGCG 60.262 45.833 0.00 0.00 0.00 4.85
740 784 6.125719 TGCCTGGTTATGTTCAATTGCTATA 58.874 36.000 0.00 0.00 0.00 1.31
761 805 2.346766 TGTGAATCTGGTGTGCTTGT 57.653 45.000 0.00 0.00 0.00 3.16
902 948 0.107831 GTGTGCTTGGGTAGGTGTGA 59.892 55.000 0.00 0.00 0.00 3.58
946 992 1.635487 TGCTACTTGCTTCCATCCCTT 59.365 47.619 0.00 0.00 43.37 3.95
981 1027 8.303876 TGCTTTACTTTTTCCCATATTCTCAAC 58.696 33.333 0.00 0.00 0.00 3.18
1007 1053 3.405823 AAACAGGTTGGCAATGATTGG 57.594 42.857 1.92 0.00 0.00 3.16
1296 1345 1.001520 GTTGGTAATGGTTTGGGTGCC 59.998 52.381 0.00 0.00 0.00 5.01
1324 1373 2.936919 TGATGAAGCTTGGTCACAGT 57.063 45.000 2.10 0.00 0.00 3.55
1411 1460 1.923356 TTCCTTGCAGATGGGGTTTC 58.077 50.000 3.24 0.00 0.00 2.78
1510 1559 2.743664 CGAAAGCCTGATGTTGATGACA 59.256 45.455 0.00 0.00 43.71 3.58
1511 1560 3.189080 CGAAAGCCTGATGTTGATGACAA 59.811 43.478 0.00 0.00 42.62 3.18
1688 1737 7.617041 AAGCTAAGATGATTGTGAAGGTAAC 57.383 36.000 0.00 0.00 0.00 2.50
1913 1962 4.090819 TGGACATGCCTACTAGTTGTGTA 58.909 43.478 0.00 0.00 37.63 2.90
2081 2131 5.750524 TGCTGGACTTGCCTAATATTTACA 58.249 37.500 0.00 0.00 37.63 2.41
2225 2275 0.482446 TGGATGGGGTCAACTTGCTT 59.518 50.000 0.00 0.00 0.00 3.91
2266 2317 4.813697 CCCCTGGTTTGTTTTGTGTATTTG 59.186 41.667 0.00 0.00 0.00 2.32
2267 2318 4.272261 CCCTGGTTTGTTTTGTGTATTTGC 59.728 41.667 0.00 0.00 0.00 3.68
2329 2380 2.811410 AGCTTCATGAATTGCCCAAGA 58.189 42.857 8.96 0.00 0.00 3.02
2542 2595 7.542025 GCTCTTGAACAAGGATGATACAAAAT 58.458 34.615 13.46 0.00 38.88 1.82
2646 2705 3.652869 TGAGGAAGACAGGGTTGAGAATT 59.347 43.478 0.00 0.00 0.00 2.17
2680 2739 2.979676 TGCAGCAAGGAAGGCGTG 60.980 61.111 0.00 0.00 36.08 5.34
2682 2741 2.979676 CAGCAAGGAAGGCGTGCA 60.980 61.111 0.00 0.00 36.08 4.57
2783 2845 1.484038 GGATTAACAGGCATGGGCAA 58.516 50.000 2.31 0.00 43.71 4.52
2846 2908 4.737054 CGTCAAGCTTTGATTGGCTATTT 58.263 39.130 0.00 0.00 42.47 1.40
2939 3001 7.370383 TGGCACAGTCAATTAAAAAGATCTTC 58.630 34.615 8.78 0.00 0.00 2.87
2957 3019 1.070786 CCCTACAAGTGTGCACCGT 59.929 57.895 15.69 8.85 0.00 4.83
3293 3355 5.005682 GTCCATTTTGAACTTTGTGAAGCAC 59.994 40.000 0.00 0.00 36.29 4.40
3399 3461 5.899547 TCATCTTACCCAATAGAGAAGCAGA 59.100 40.000 0.00 0.00 0.00 4.26
3400 3462 6.556495 TCATCTTACCCAATAGAGAAGCAGAT 59.444 38.462 0.00 0.00 0.00 2.90
3467 3529 7.062749 TGAGTTTCAGTTGACTACAAGGTAT 57.937 36.000 0.00 0.00 36.64 2.73
3474 3536 7.903145 TCAGTTGACTACAAGGTATAATGTGT 58.097 34.615 0.00 0.00 36.64 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
514 526 4.505922 TGTTTTTCTTAAATGCAGGCAACG 59.494 37.500 0.00 0.00 46.39 4.10
740 784 3.005050 CACAAGCACACCAGATTCACAAT 59.995 43.478 0.00 0.00 0.00 2.71
761 805 2.335752 CAAGCAAACAACACAGCAACA 58.664 42.857 0.00 0.00 0.00 3.33
902 948 6.039717 CACAGTAAATACAGGCAAGCCAATAT 59.960 38.462 14.40 7.50 38.92 1.28
946 992 5.348164 GGAAAAAGTAAAGCAAGTCAGCAA 58.652 37.500 0.00 0.00 36.85 3.91
981 1027 7.299586 CAATCATTGCCAACCTGTTTTATTTG 58.700 34.615 0.00 0.00 0.00 2.32
1007 1053 2.019984 CAGCTGGTTCCTCATTTAGGC 58.980 52.381 5.57 0.00 46.10 3.93
1050 1096 4.344359 TCCAGTAGCATGTTGTGTACAA 57.656 40.909 0.00 0.00 40.89 2.41
1249 1297 1.079197 CGGTATCACCTGCAGCACA 60.079 57.895 8.66 0.00 35.66 4.57
1296 1345 4.990257 ACCAAGCTTCATCATCATTTTCG 58.010 39.130 0.00 0.00 0.00 3.46
1324 1373 1.550130 CCCACGTAAGGCTCCTTGGA 61.550 60.000 11.25 0.00 46.39 3.53
1434 1483 7.475299 TCAACTCCCCAGTTTTAATATCCTTT 58.525 34.615 0.00 0.00 41.24 3.11
1443 1492 7.342284 TGTTGTTTTATCAACTCCCCAGTTTTA 59.658 33.333 10.18 0.00 45.26 1.52
1479 1528 4.819630 ACATCAGGCTTTCGAAACTTGTTA 59.180 37.500 6.47 0.00 0.00 2.41
1510 1559 2.540383 GGGAATCTTTTCTGCCCCTTT 58.460 47.619 0.00 0.00 32.50 3.11
1511 1560 1.616994 CGGGAATCTTTTCTGCCCCTT 60.617 52.381 0.00 0.00 35.30 3.95
1576 1625 7.114754 TCATCATCAAGAAAGACAATAGCCTT 58.885 34.615 0.00 0.00 0.00 4.35
1654 1703 2.489329 TCATCTTAGCTTTGCAACCAGC 59.511 45.455 14.09 14.09 45.96 4.85
1688 1737 0.179026 CACCTCCCATCTGCCATCTG 60.179 60.000 0.00 0.00 0.00 2.90
1913 1962 6.948309 AGTAACTTGTTGATGGGCTAAGAAAT 59.052 34.615 0.00 0.00 0.00 2.17
2266 2317 2.177950 CTCAGGCAACACATGAGGC 58.822 57.895 0.00 0.00 37.41 4.70
2542 2595 6.211584 GCAACTGTCTCTATCATATCCCCTTA 59.788 42.308 0.00 0.00 0.00 2.69
2646 2705 1.243902 GCACCATCGACCCAGAAAAA 58.756 50.000 0.00 0.00 0.00 1.94
2680 2739 9.175312 AGATACAATCATGATAAGATTCCATGC 57.825 33.333 9.04 0.00 37.99 4.06
2682 2741 9.902684 GGAGATACAATCATGATAAGATTCCAT 57.097 33.333 9.04 0.00 33.64 3.41
2760 2822 1.756538 CCCATGCCTGTTAATCCCAAC 59.243 52.381 0.00 0.00 0.00 3.77
2783 2845 2.104967 CCACAGCCCAACATGAATGAT 58.895 47.619 0.00 0.00 0.00 2.45
2846 2908 2.746279 TTGCCTCAAGGAAGGTTTCA 57.254 45.000 0.00 0.00 38.79 2.69
2939 3001 0.534203 AACGGTGCACACTTGTAGGG 60.534 55.000 20.43 0.00 0.00 3.53
3191 3253 3.897239 TGACTGCAAGAAAGGGAAGAAA 58.103 40.909 0.00 0.00 37.43 2.52
3293 3355 8.950210 AGTATGTGTGTTTGGATTTTCTGATAG 58.050 33.333 0.00 0.00 0.00 2.08
3399 3461 5.046014 AGTCCCTAGTATACGATCCGTACAT 60.046 44.000 1.08 0.00 45.07 2.29
3400 3462 4.284490 AGTCCCTAGTATACGATCCGTACA 59.716 45.833 1.08 0.00 45.07 2.90
3467 3529 1.002544 TCACCATGCGGTCACACATTA 59.997 47.619 0.00 0.00 44.71 1.90
3474 3536 1.336440 CAAGTTTTCACCATGCGGTCA 59.664 47.619 0.00 0.00 44.71 4.02


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

AutoCloner maintained by Alex Coulton.