Multiple sequence alignment - TraesCS1A01G089000

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 TraesCS1A01G089000 chr1A 100.000 2303 0 0 1 2303 77263655 77265957 0 4253
1 TraesCS1A01G089000 chr1A 96.528 2304 57 4 1 2303 25270715 25268434 0 3790
2 TraesCS1A01G089000 chr1A 96.147 1635 45 6 1 1629 405515270 405513648 0 2654
3 TraesCS1A01G089000 chr6A 97.569 2304 55 1 1 2303 587986535 587984232 0 3943
4 TraesCS1A01G089000 chr5A 97.273 2310 56 2 1 2303 540624880 540622571 0 3910
5 TraesCS1A01G089000 chr3A 96.878 2306 46 9 1 2303 693613337 693611055 0 3836
6 TraesCS1A01G089000 chr4D 96.512 2322 55 8 1 2303 491381780 491384094 0 3816
7 TraesCS1A01G089000 chr1D 96.512 2322 55 8 1 2303 316243679 316241365 0 3816
8 TraesCS1A01G089000 chr2D 96.469 2322 55 9 1 2303 617341035 617343348 0 3808
9 TraesCS1A01G089000 chr2D 95.917 2327 63 10 1 2303 130078844 130076526 0 3742
10 TraesCS1A01G089000 chr3D 96.339 2322 58 9 1 2303 334424 336737 0 3792
11 TraesCS1A01G089000 chr3D 95.015 1023 25 13 1285 2303 610059709 610058709 0 1583
12 TraesCS1A01G089000 chr5D 95.736 2322 67 10 1 2303 78602643 78600335 0 3711
13 TraesCS1A01G089000 chr5D 95.513 2318 64 19 1 2303 552028755 552026463 0 3668
14 TraesCS1A01G089000 chr5D 96.880 1763 37 8 1 1753 555413826 555415580 0 2935
15 TraesCS1A01G089000 chr4A 95.209 2317 88 15 1 2303 731637059 731634752 0 3642
16 TraesCS1A01G089000 chr4A 94.260 2317 82 17 1 2303 478227422 478229701 0 3494
17 TraesCS1A01G089000 chr7A 97.837 1803 37 2 503 2303 70256082 70254280 0 3112


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 TraesCS1A01G089000 chr1A 77263655 77265957 2302 False 4253 4253 100.000 1 2303 1 chr1A.!!$F1 2302
1 TraesCS1A01G089000 chr1A 25268434 25270715 2281 True 3790 3790 96.528 1 2303 1 chr1A.!!$R1 2302
2 TraesCS1A01G089000 chr1A 405513648 405515270 1622 True 2654 2654 96.147 1 1629 1 chr1A.!!$R2 1628
3 TraesCS1A01G089000 chr6A 587984232 587986535 2303 True 3943 3943 97.569 1 2303 1 chr6A.!!$R1 2302
4 TraesCS1A01G089000 chr5A 540622571 540624880 2309 True 3910 3910 97.273 1 2303 1 chr5A.!!$R1 2302
5 TraesCS1A01G089000 chr3A 693611055 693613337 2282 True 3836 3836 96.878 1 2303 1 chr3A.!!$R1 2302
6 TraesCS1A01G089000 chr4D 491381780 491384094 2314 False 3816 3816 96.512 1 2303 1 chr4D.!!$F1 2302
7 TraesCS1A01G089000 chr1D 316241365 316243679 2314 True 3816 3816 96.512 1 2303 1 chr1D.!!$R1 2302
8 TraesCS1A01G089000 chr2D 617341035 617343348 2313 False 3808 3808 96.469 1 2303 1 chr2D.!!$F1 2302
9 TraesCS1A01G089000 chr2D 130076526 130078844 2318 True 3742 3742 95.917 1 2303 1 chr2D.!!$R1 2302
10 TraesCS1A01G089000 chr3D 334424 336737 2313 False 3792 3792 96.339 1 2303 1 chr3D.!!$F1 2302
11 TraesCS1A01G089000 chr3D 610058709 610059709 1000 True 1583 1583 95.015 1285 2303 1 chr3D.!!$R1 1018
12 TraesCS1A01G089000 chr5D 78600335 78602643 2308 True 3711 3711 95.736 1 2303 1 chr5D.!!$R1 2302
13 TraesCS1A01G089000 chr5D 552026463 552028755 2292 True 3668 3668 95.513 1 2303 1 chr5D.!!$R2 2302
14 TraesCS1A01G089000 chr5D 555413826 555415580 1754 False 2935 2935 96.880 1 1753 1 chr5D.!!$F1 1752
15 TraesCS1A01G089000 chr4A 731634752 731637059 2307 True 3642 3642 95.209 1 2303 1 chr4A.!!$R1 2302
16 TraesCS1A01G089000 chr4A 478227422 478229701 2279 False 3494 3494 94.260 1 2303 1 chr4A.!!$F1 2302
17 TraesCS1A01G089000 chr7A 70254280 70256082 1802 True 3112 3112 97.837 503 2303 1 chr7A.!!$R1 1800

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
814 859 2.284263 GCCTGTAATTCTGCAAAGGC 57.716 50.0 0.0 0.0 43.05 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2130 2212 0.324614 ATCGACATGTTGCTGTGGGA 59.675 50.0 8.34 0.0 0.0 4.37 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
70 76 7.482169 TCTCCTCTGCTTATGTTTCTTCTTA 57.518 36.000 0.00 0.0 0.00 2.10
119 125 3.276091 CGTGGCCGAACAGCAACA 61.276 61.111 0.00 0.0 36.40 3.33
141 147 4.303853 GTCGGACGATGATGACGG 57.696 61.111 0.00 0.0 34.93 4.79
526 556 8.866956 GGATTTGATTAGTTTGAATTTCTGCTG 58.133 33.333 0.00 0.0 0.00 4.41
814 859 2.284263 GCCTGTAATTCTGCAAAGGC 57.716 50.000 0.00 0.0 43.05 4.35
847 892 5.340322 AGCTCTGGGATATGTATCATGAGT 58.660 41.667 0.09 0.0 34.40 3.41
903 948 4.112634 TGGGATAGAGGTTGCAAAACTT 57.887 40.909 0.00 0.0 45.56 2.66
976 1021 7.950512 TGATGTGTCCAAGTTGTTTGATTATT 58.049 30.769 1.45 0.0 39.21 1.40
1039 1084 3.129988 GGCAATCAATGAACTGAAGGAGG 59.870 47.826 0.54 0.0 0.00 4.30
1133 1178 2.027745 GGTGCATCCTTCAGAGTCAAGA 60.028 50.000 0.00 0.0 0.00 3.02
1310 1355 1.003580 GATGGAGGAGTGAAGTGGCAA 59.996 52.381 0.00 0.0 0.00 4.52
1753 1806 8.153550 ACTTAAACTGACAGAACTGAATCTCAT 58.846 33.333 10.08 0.0 0.00 2.90
1891 1973 2.005960 GCTATGCGACCTGACCGTCT 62.006 60.000 0.00 0.0 0.00 4.18
2130 2212 3.863407 GAGTCCGCCTCCTTCATTT 57.137 52.632 0.00 0.0 33.79 2.32
2249 2331 1.827344 TCTTCTGATGCATCCACGAGT 59.173 47.619 23.67 0.0 0.00 4.18
2282 2364 4.529897 TGCTGTATCTCATGGCAATCTTT 58.470 39.130 0.00 0.0 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
119 125 1.092348 TCATCATCGTCCGACGTCTT 58.908 50.000 19.89 4.63 43.14 3.01
141 147 1.281899 GCTGAACTCGCTCATGTACC 58.718 55.000 0.00 0.00 0.00 3.34
526 556 6.047231 ACTAAACACTCTGTTTCCACTACAC 58.953 40.000 3.66 0.00 46.61 2.90
847 892 2.467880 CTGGGCTCTACCAAGGTTCTA 58.532 52.381 0.00 0.00 40.68 2.10
903 948 3.197333 CCAGAGAATCAAGCTCCTTCTGA 59.803 47.826 9.39 0.00 37.82 3.27
976 1021 7.140522 TGTCATGAGATTTGATTCCATCCTA 57.859 36.000 0.00 0.00 0.00 2.94
1039 1084 2.741517 GCTCCTCAAGTTGCTTCTTCTC 59.258 50.000 0.00 0.00 0.00 2.87
1133 1178 9.359653 CCTTCCTTCTGTTTTGGATTATATCAT 57.640 33.333 0.00 0.00 0.00 2.45
1151 1196 2.021208 GCTCCTTCATGGCCTTCCTTC 61.021 57.143 3.32 0.00 35.26 3.46
1310 1355 9.693739 CCTCATATATACTTACATCCAGAGAGT 57.306 37.037 0.00 0.00 0.00 3.24
1753 1806 2.942804 TCAGGGTGTTTGCAATCTCAA 58.057 42.857 0.00 0.00 0.00 3.02
1891 1973 2.435805 ACTCAAGTCAAGCAAGAGGTGA 59.564 45.455 0.00 0.00 0.00 4.02
2085 2167 1.987855 CTGGGCAGAGGGAACGGTA 60.988 63.158 0.00 0.00 0.00 4.02
2130 2212 0.324614 ATCGACATGTTGCTGTGGGA 59.675 50.000 8.34 0.00 0.00 4.37
2249 2331 0.740868 GATACAGCAGCGCACAAGGA 60.741 55.000 11.47 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.