Multiple sequence alignment - TraesCS2D01G585600

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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 TraesCS2D01G585600 chr2D 100.000 3131 0 0 1 3131 644529951 644526821 0 5782
1 TraesCS2D01G585600 chr2D 97.742 2436 53 1 696 3131 422069460 422071893 0 4193
2 TraesCS2D01G585600 chr2D 97.776 2428 49 1 704 3131 437672406 437669984 0 4180
3 TraesCS2D01G585600 chr2D 96.695 696 18 3 1 695 314087370 314086679 0 1153
4 TraesCS2D01G585600 chr6D 97.909 2439 49 2 694 3131 123792522 123790085 0 4220
5 TraesCS2D01G585600 chr6D 97.126 696 17 2 1 695 91534474 91533781 0 1171
6 TraesCS2D01G585600 chr7D 97.863 2433 48 3 699 3131 632615481 632613053 0 4202
7 TraesCS2D01G585600 chr7D 97.617 2434 51 2 699 3131 602036134 602033707 0 4167
8 TraesCS2D01G585600 chr7D 97.496 2436 59 2 696 3131 115055842 115058275 0 4159
9 TraesCS2D01G585600 chr7D 96.978 695 18 3 1 693 599749048 599748355 0 1164
10 TraesCS2D01G585600 chr7D 96.839 696 18 3 1 695 508362698 508362006 0 1160
11 TraesCS2D01G585600 chr7D 96.695 696 17 5 1 695 576597131 576596441 0 1153
12 TraesCS2D01G585600 chr1D 97.660 2436 51 1 696 3131 462971916 462974345 0 4178
13 TraesCS2D01G585600 chr1D 97.653 2429 57 0 703 3131 45267667 45270095 0 4170
14 TraesCS2D01G585600 chr1D 97.417 2439 57 1 693 3131 339309619 339312051 0 4150
15 TraesCS2D01G585600 chr1D 96.695 696 18 4 1 695 13391455 13392146 0 1153
16 TraesCS2D01G585600 chr1D 96.552 696 20 4 1 695 84318393 84319085 0 1149
17 TraesCS2D01G585600 chr1D 96.552 696 18 5 1 695 492349718 492350408 0 1147
18 TraesCS2D01G585600 chr4D 96.552 696 19 4 1 695 469738416 469737725 0 1147


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 TraesCS2D01G585600 chr2D 644526821 644529951 3130 True 5782 5782 100.000 1 3131 1 chr2D.!!$R3 3130
1 TraesCS2D01G585600 chr2D 422069460 422071893 2433 False 4193 4193 97.742 696 3131 1 chr2D.!!$F1 2435
2 TraesCS2D01G585600 chr2D 437669984 437672406 2422 True 4180 4180 97.776 704 3131 1 chr2D.!!$R2 2427
3 TraesCS2D01G585600 chr2D 314086679 314087370 691 True 1153 1153 96.695 1 695 1 chr2D.!!$R1 694
4 TraesCS2D01G585600 chr6D 123790085 123792522 2437 True 4220 4220 97.909 694 3131 1 chr6D.!!$R2 2437
5 TraesCS2D01G585600 chr6D 91533781 91534474 693 True 1171 1171 97.126 1 695 1 chr6D.!!$R1 694
6 TraesCS2D01G585600 chr7D 632613053 632615481 2428 True 4202 4202 97.863 699 3131 1 chr7D.!!$R5 2432
7 TraesCS2D01G585600 chr7D 602033707 602036134 2427 True 4167 4167 97.617 699 3131 1 chr7D.!!$R4 2432
8 TraesCS2D01G585600 chr7D 115055842 115058275 2433 False 4159 4159 97.496 696 3131 1 chr7D.!!$F1 2435
9 TraesCS2D01G585600 chr7D 599748355 599749048 693 True 1164 1164 96.978 1 693 1 chr7D.!!$R3 692
10 TraesCS2D01G585600 chr7D 508362006 508362698 692 True 1160 1160 96.839 1 695 1 chr7D.!!$R1 694
11 TraesCS2D01G585600 chr7D 576596441 576597131 690 True 1153 1153 96.695 1 695 1 chr7D.!!$R2 694
12 TraesCS2D01G585600 chr1D 462971916 462974345 2429 False 4178 4178 97.660 696 3131 1 chr1D.!!$F5 2435
13 TraesCS2D01G585600 chr1D 45267667 45270095 2428 False 4170 4170 97.653 703 3131 1 chr1D.!!$F2 2428
14 TraesCS2D01G585600 chr1D 339309619 339312051 2432 False 4150 4150 97.417 693 3131 1 chr1D.!!$F4 2438
15 TraesCS2D01G585600 chr1D 13391455 13392146 691 False 1153 1153 96.695 1 695 1 chr1D.!!$F1 694
16 TraesCS2D01G585600 chr1D 84318393 84319085 692 False 1149 1149 96.552 1 695 1 chr1D.!!$F3 694
17 TraesCS2D01G585600 chr1D 492349718 492350408 690 False 1147 1147 96.552 1 695 1 chr1D.!!$F6 694
18 TraesCS2D01G585600 chr4D 469737725 469738416 691 True 1147 1147 96.552 1 695 1 chr4D.!!$R1 694

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
468 476 0.894184 AAGAAGGAGGAGACGTCGCA 60.894 55.0 21.01 0.0 0.00 5.10 F
1591 1599 0.248458 CTTTGTCGCGCAACCACTTT 60.248 50.0 8.75 0.0 36.72 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2022 2039 1.743772 GCATCAATGTCTAGTGGCGGT 60.744 52.381 0.0 0.0 0.00 5.68 R
2676 2694 0.676466 CACCTGCATCCCGCTTTGTA 60.676 55.000 0.0 0.0 43.06 2.41 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
349 357 1.913762 CAACACCTCTCCTCCCCGT 60.914 63.158 0.00 0.00 0.00 5.28
468 476 0.894184 AAGAAGGAGGAGACGTCGCA 60.894 55.000 21.01 0.00 0.00 5.10
530 538 2.737359 GCACTCGGTCATCGGTGATTTA 60.737 50.000 0.00 0.00 40.18 1.40
531 539 3.517602 CACTCGGTCATCGGTGATTTAA 58.482 45.455 0.00 0.00 40.18 1.52
534 542 5.064707 CACTCGGTCATCGGTGATTTAAATT 59.935 40.000 0.00 0.00 40.18 1.82
710 718 4.106341 CCCCAACATATAAGTCCCTGGAAT 59.894 45.833 0.00 0.00 0.00 3.01
1029 1037 4.262036 GGAATTGTCAACAAGGAGTTTCCC 60.262 45.833 11.56 0.00 38.74 3.97
1066 1074 2.216898 GGCTGAACTATCTGTCATGGC 58.783 52.381 0.00 0.00 0.00 4.40
1126 1134 3.159347 GGGCGATCGGTAAGGGGT 61.159 66.667 18.30 0.00 0.00 4.95
1258 1266 1.228552 GCTTCTGGCCTTTGGACCA 60.229 57.895 3.32 0.00 34.27 4.02
1506 1514 2.589157 CCGCCAGGGGAACTACACA 61.589 63.158 4.70 0.00 0.00 3.72
1591 1599 0.248458 CTTTGTCGCGCAACCACTTT 60.248 50.000 8.75 0.00 36.72 2.66
1680 1688 2.363018 GGCAAGAAGAAGGGCCCC 60.363 66.667 21.43 3.37 40.55 5.80
1787 1804 0.678048 GAGCATTTCTCCCGCCAGTT 60.678 55.000 0.00 0.00 35.77 3.16
1920 1937 3.402681 GCTACTCCCCCTGCTGCA 61.403 66.667 0.88 0.88 0.00 4.41
2619 2637 4.537135 TTTGAGCTTTAGAGACATCCGT 57.463 40.909 0.00 0.00 0.00 4.69
2800 2818 3.188667 CCTCAAGACCGTTTTTAGAAGCC 59.811 47.826 0.00 0.00 0.00 4.35
2806 2824 3.756963 GACCGTTTTTAGAAGCCCTGAAT 59.243 43.478 0.00 0.00 0.00 2.57
2896 2914 5.260424 ACTCACATGGCCATAATGTTAACA 58.740 37.500 20.30 11.41 36.10 2.41
2917 2935 1.982226 TGAAGAACTTCCCGAATCCCA 59.018 47.619 11.30 0.00 38.77 4.37
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
70 71 2.765969 CCACTTCAGCCCATGGGT 59.234 61.111 31.58 15.87 37.65 4.51
468 476 0.386476 TTCAACACACGTACGGAGCT 59.614 50.000 21.06 0.00 0.00 4.09
530 538 2.478539 GGAGTCGTACTCGCCGTAATTT 60.479 50.000 8.33 0.00 45.96 1.82
531 539 1.064654 GGAGTCGTACTCGCCGTAATT 59.935 52.381 8.33 0.00 45.96 1.40
534 542 0.462581 ATGGAGTCGTACTCGCCGTA 60.463 55.000 8.33 0.00 45.96 4.02
648 656 5.659440 AAAATTTCCTACGCATCACCAAT 57.341 34.783 0.00 0.00 0.00 3.16
710 718 3.796178 GCATTTTCAGCGAAAACAGACAA 59.204 39.130 15.32 0.00 42.98 3.18
839 847 7.713507 TGCTAAACAATTAATCTACGGCAGTAT 59.286 33.333 0.00 0.00 31.58 2.12
895 903 9.974980 AAAGACGTTCCAATATTTAAAACATGT 57.025 25.926 0.00 0.00 0.00 3.21
1029 1037 2.046892 CCTGTCTGGGCCAACTCG 60.047 66.667 8.04 0.00 0.00 4.18
1056 1064 2.038813 TCCGAGGGCCATGACAGA 59.961 61.111 6.18 0.00 0.00 3.41
1258 1266 2.417719 CTCAAACCGCTGCTTAAGAGT 58.582 47.619 6.67 0.00 0.00 3.24
1282 1290 3.202906 GTGGCTTCACAGTGTACTTCAA 58.797 45.455 0.00 0.00 40.91 2.69
1322 1330 2.742372 CCGCAAACCTCAGACGGG 60.742 66.667 0.00 0.00 40.18 5.28
1506 1514 5.794894 ACGTCAATCAACTCTGAATACCTT 58.205 37.500 0.00 0.00 34.49 3.50
1591 1599 3.003173 CTGGCGAGAACTCCCCCA 61.003 66.667 3.50 6.04 0.00 4.96
1920 1937 2.446036 GGGGTCGCCTCTATGGGT 60.446 66.667 0.00 0.00 36.00 4.51
2022 2039 1.743772 GCATCAATGTCTAGTGGCGGT 60.744 52.381 0.00 0.00 0.00 5.68
2619 2637 3.018856 CTCAGCATGGAAACCATTAGCA 58.981 45.455 13.01 0.00 42.23 3.49
2676 2694 0.676466 CACCTGCATCCCGCTTTGTA 60.676 55.000 0.00 0.00 43.06 2.41
2896 2914 2.576191 TGGGATTCGGGAAGTTCTTCAT 59.424 45.455 13.44 0.04 0.00 2.57


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

AutoCloner maintained by Alex Coulton.