Multiple sequence alignment - TraesCS6A01G169000

Loading Multiple Alignment...

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 TraesCS6A01G169000 chr6A 100.000 2506 0 0 1 2506 176534599 176532094 0 4628
1 TraesCS6A01G169000 chr6A 95.671 2518 90 12 1 2506 484784651 484782141 0 4028
2 TraesCS6A01G169000 chr6A 94.625 614 25 3 1894 2506 357524783 357524177 0 944
3 TraesCS6A01G169000 chr4A 95.749 2517 92 8 1 2506 45631396 45633908 0 4041
4 TraesCS6A01G169000 chr4A 94.788 614 23 3 1894 2506 246821249 246820644 0 948
5 TraesCS6A01G169000 chr4A 94.625 614 26 2 1894 2506 9468754 9469361 0 944
6 TraesCS6A01G169000 chr7D 95.587 2538 77 9 1 2506 421675284 421677818 0 4034
7 TraesCS6A01G169000 chr2A 95.630 2517 94 9 1 2506 677262024 677264535 0 4024
8 TraesCS6A01G169000 chr2A 94.788 614 24 3 1894 2506 596740876 596740270 0 950
9 TraesCS6A01G169000 chr1D 95.358 2542 79 10 1 2506 361004141 361006679 0 4004
10 TraesCS6A01G169000 chr1D 95.309 2537 77 20 1 2504 10688676 10691203 0 3988
11 TraesCS6A01G169000 chr6D 94.843 2540 81 12 1 2506 397854470 397851947 0 3919
12 TraesCS6A01G169000 chr1A 94.756 2517 98 10 1 2506 519376701 519374208 0 3886
13 TraesCS6A01G169000 chr1A 95.277 614 21 3 1894 2506 517445084 517444478 0 966
14 TraesCS6A01G169000 chr5D 95.456 2377 71 11 1 2346 58009615 58007245 0 3757


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 TraesCS6A01G169000 chr6A 176532094 176534599 2505 True 4628 4628 100.000 1 2506 1 chr6A.!!$R1 2505
1 TraesCS6A01G169000 chr6A 484782141 484784651 2510 True 4028 4028 95.671 1 2506 1 chr6A.!!$R3 2505
2 TraesCS6A01G169000 chr6A 357524177 357524783 606 True 944 944 94.625 1894 2506 1 chr6A.!!$R2 612
3 TraesCS6A01G169000 chr4A 45631396 45633908 2512 False 4041 4041 95.749 1 2506 1 chr4A.!!$F2 2505
4 TraesCS6A01G169000 chr4A 246820644 246821249 605 True 948 948 94.788 1894 2506 1 chr4A.!!$R1 612
5 TraesCS6A01G169000 chr4A 9468754 9469361 607 False 944 944 94.625 1894 2506 1 chr4A.!!$F1 612
6 TraesCS6A01G169000 chr7D 421675284 421677818 2534 False 4034 4034 95.587 1 2506 1 chr7D.!!$F1 2505
7 TraesCS6A01G169000 chr2A 677262024 677264535 2511 False 4024 4024 95.630 1 2506 1 chr2A.!!$F1 2505
8 TraesCS6A01G169000 chr2A 596740270 596740876 606 True 950 950 94.788 1894 2506 1 chr2A.!!$R1 612
9 TraesCS6A01G169000 chr1D 361004141 361006679 2538 False 4004 4004 95.358 1 2506 1 chr1D.!!$F2 2505
10 TraesCS6A01G169000 chr1D 10688676 10691203 2527 False 3988 3988 95.309 1 2504 1 chr1D.!!$F1 2503
11 TraesCS6A01G169000 chr6D 397851947 397854470 2523 True 3919 3919 94.843 1 2506 1 chr6D.!!$R1 2505
12 TraesCS6A01G169000 chr1A 519374208 519376701 2493 True 3886 3886 94.756 1 2506 1 chr1A.!!$R2 2505
13 TraesCS6A01G169000 chr1A 517444478 517445084 606 True 966 966 95.277 1894 2506 1 chr1A.!!$R1 612
14 TraesCS6A01G169000 chr5D 58007245 58009615 2370 True 3757 3757 95.456 1 2346 1 chr5D.!!$R1 2345

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
962 1022 1.032657 ATGTCGACCTCCTCGTCAGG 61.033 60.0 14.12 0.0 42.48 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1774 1842 0.610174 TGGCAAGTGCGAGAGAGAAT 59.39 50.0 0.0 0.0 43.26 2.4 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
91 93 8.261522 AGTAAGTTCAGATCCTTCTTATTCACC 58.738 37.037 0.00 0.00 0.00 4.02
105 107 5.779771 TCTTATTCACCCCAAAATGAAGCTT 59.220 36.000 0.00 0.00 38.19 3.74
196 244 3.399330 ACGAACTCCGAACATGTTCATT 58.601 40.909 32.06 21.49 39.77 2.57
284 337 9.685276 TTTTCTCATAACCTTGTCACATATGAT 57.315 29.630 10.38 0.00 37.14 2.45
443 503 7.844493 TGGTAACTAGGTATCATAAACGGAT 57.156 36.000 0.00 0.00 37.61 4.18
617 677 3.292159 GCCAAACACCACCCGTCC 61.292 66.667 0.00 0.00 0.00 4.79
668 728 3.647590 TGATGCATCCTGATTGGCTACTA 59.352 43.478 23.67 0.00 35.26 1.82
696 756 3.258872 TCCTTCTCGGGTTTTTACGATCA 59.741 43.478 0.00 0.00 38.56 2.92
740 800 3.818210 TGTATTTTTCGCACATGACCACT 59.182 39.130 0.00 0.00 0.00 4.00
907 967 4.180057 CCATCTTCTCGTTCTTCTTCCTG 58.820 47.826 0.00 0.00 0.00 3.86
921 981 3.096852 TCTTCCTGTCGAGCAATTCCTA 58.903 45.455 0.00 0.00 0.00 2.94
962 1022 1.032657 ATGTCGACCTCCTCGTCAGG 61.033 60.000 14.12 0.00 42.48 3.86
1320 1387 0.734889 GTTCAATCTGCCCCATGACG 59.265 55.000 0.00 0.00 0.00 4.35
1470 1537 7.796054 TCTGATAGCTTTAGGAATACTTGCTT 58.204 34.615 0.00 0.00 33.39 3.91
1530 1598 2.353269 TGTTTGTCTACTGTTGTTGCCG 59.647 45.455 0.00 0.00 0.00 5.69
1531 1599 2.319136 TTGTCTACTGTTGTTGCCGT 57.681 45.000 0.00 0.00 0.00 5.68
1539 1607 3.011119 ACTGTTGTTGCCGTTGTTTAGA 58.989 40.909 0.00 0.00 0.00 2.10
1654 1722 3.069729 AGTTTCGGCAGAAGACAACTACT 59.930 43.478 0.00 0.00 37.70 2.57
1774 1842 9.159254 ACAAGGGATATACATCAAGTTCATCTA 57.841 33.333 0.00 0.00 32.32 1.98
1795 1863 0.037882 TCTCTCTCGCACTTGCCAAG 60.038 55.000 2.11 2.11 37.91 3.61
1807 1875 1.682854 CTTGCCAAGCTTTTGTCCTCA 59.317 47.619 0.00 0.00 0.00 3.86
1943 2015 6.621316 TGTTTAGGAACGATTGCTTTGTTA 57.379 33.333 0.00 0.00 38.65 2.41
2006 2079 6.239543 GCCCAATCTCTTCTATCTCATTGAGA 60.240 42.308 18.29 18.29 43.20 3.27
2032 2106 3.694043 TTTTGGCTTTCCTTTATGGGC 57.306 42.857 0.00 0.00 36.20 5.36
2197 2291 7.041372 TGACTAAAGCCAAACATCTCAAAGTAC 60.041 37.037 0.00 0.00 0.00 2.73
2448 2544 9.886132 CACATAACTTAACTTAGATAGGGTTGT 57.114 33.333 0.00 0.00 0.00 3.32
2486 2582 4.923893 TCTTACATATAACACGACACCGG 58.076 43.478 0.00 0.00 40.78 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
151 199 4.486529 AGAATAGGGAGAGAGGGTTTAGGA 59.513 45.833 0.00 0.00 0.00 2.94
196 244 4.284829 TCACACAAATGAGCTATCACCA 57.715 40.909 0.00 0.00 38.57 4.17
284 337 6.937465 TGTTGTAATTCTTGTACACATAGCCA 59.063 34.615 0.00 0.00 31.27 4.75
617 677 3.214123 CATGCCTGCCCCACATCG 61.214 66.667 0.00 0.00 0.00 3.84
668 728 1.129058 AAACCCGAGAAGGACAGTGT 58.871 50.000 0.00 0.00 45.00 3.55
696 756 5.957774 ACAATTTCATATGTAAAGTGGGGCT 59.042 36.000 21.13 7.47 36.50 5.19
740 800 6.169557 ACCAACTCTTAACACTGACATGTA 57.830 37.500 0.00 0.00 30.75 2.29
773 833 5.121811 TGCCACATTGTATTTTGCAGTTTT 58.878 33.333 0.00 0.00 0.00 2.43
857 917 4.583871 AGAAACAGAGGAATTGCTCGATT 58.416 39.130 19.75 15.13 0.00 3.34
907 967 5.220681 GGAAGAAACATAGGAATTGCTCGAC 60.221 44.000 1.37 0.00 0.00 4.20
1036 1096 1.864711 CTTCGAAGTCAACCGCTTCAA 59.135 47.619 17.24 0.13 41.61 2.69
1539 1607 8.031277 GCATTTGAGATAAACAGACTTGGATTT 58.969 33.333 0.00 0.00 0.00 2.17
1774 1842 0.610174 TGGCAAGTGCGAGAGAGAAT 59.390 50.000 0.00 0.00 43.26 2.40
1795 1863 2.612212 TGACGAACTTGAGGACAAAAGC 59.388 45.455 0.00 0.00 35.49 3.51
1807 1875 4.585955 TTCTAGCAGAACTGACGAACTT 57.414 40.909 5.97 0.00 0.00 2.66
1847 1916 1.475682 GCAGCTTGATTCTCTTTGGGG 59.524 52.381 0.00 0.00 0.00 4.96
2070 2144 5.484715 TGGTTCGCTAGGCATAATAATACC 58.515 41.667 0.00 0.00 0.00 2.73
2448 2544 4.730966 TGTAAGAACTTATGTTGCCCCAA 58.269 39.130 0.00 0.00 36.39 4.12
2450 2546 8.565416 GTTATATGTAAGAACTTATGTTGCCCC 58.435 37.037 0.00 0.00 36.39 5.80


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

AutoCloner maintained by Alex Coulton.