Multiple sequence alignment - TraesCS5A01G260400

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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 TraesCS5A01G260400 chr5A 100.000 3107 0 0 1 3107 474327737 474324631 0.000000e+00 5738.0
1 TraesCS5A01G260400 chr5A 99.523 2932 13 1 176 3107 474195617 474192687 0.000000e+00 5336.0
2 TraesCS5A01G260400 chr5A 99.420 2932 8 2 176 3107 474062082 474059160 0.000000e+00 5312.0
3 TraesCS5A01G260400 chr5A 97.129 209 5 1 2899 3107 474383068 474382861 4.930000e-93 351.0
4 TraesCS5A01G260400 chr5A 98.246 171 2 1 1 170 474064065 474063895 6.510000e-77 298.0
5 TraesCS5A01G260400 chr5A 98.246 171 2 1 1 170 474197599 474197429 6.510000e-77 298.0
6 TraesCS5A01G260400 chr5A 78.056 360 67 8 1589 1945 474026204 474026554 1.880000e-52 217.0
7 TraesCS5A01G260400 chr5A 78.056 360 67 8 1589 1945 474159531 474159881 1.880000e-52 217.0
8 TraesCS5A01G260400 chr5A 78.056 360 67 8 1589 1945 474291839 474292189 1.880000e-52 217.0
9 TraesCS5A01G260400 chr5A 86.792 159 12 4 712 868 382336308 382336459 5.330000e-38 169.0
10 TraesCS5A01G260400 chr5A 94.643 56 2 1 16 70 621541254 621541199 5.520000e-13 86.1
11 TraesCS5A01G260400 chr5A 87.302 63 8 0 9 71 41431143 41431205 4.300000e-09 73.1
12 TraesCS5A01G260400 chr5D 93.482 2685 135 11 222 2900 371267307 371269957 0.000000e+00 3952.0
13 TraesCS5A01G260400 chr5D 96.159 1614 56 3 906 2514 371023184 371021572 0.000000e+00 2632.0
14 TraesCS5A01G260400 chr5D 76.441 399 80 12 1550 1940 52365589 52365981 1.460000e-48 204.0
15 TraesCS5A01G260400 chr5D 98.039 51 1 0 176 226 557197369 557197319 4.270000e-14 89.8
16 TraesCS5A01G260400 chr5D 97.959 49 1 0 176 224 329780555 329780603 5.520000e-13 86.1
17 TraesCS5A01G260400 chr5B 92.926 2700 138 14 222 2900 440533426 440536093 0.000000e+00 3879.0
18 TraesCS5A01G260400 chr5B 92.741 2700 141 14 222 2900 440513760 440516425 0.000000e+00 3849.0
19 TraesCS5A01G260400 chr5B 88.276 435 27 13 879 1293 441124340 441123910 1.660000e-137 499.0
20 TraesCS5A01G260400 chr5B 97.959 49 1 0 176 224 617706366 617706414 5.520000e-13 86.1
21 TraesCS5A01G260400 chrUn 96.042 960 26 2 222 1177 371166267 371167218 0.000000e+00 1552.0
22 TraesCS5A01G260400 chrUn 90.393 1093 63 12 1825 2900 272196412 272195345 0.000000e+00 1399.0
23 TraesCS5A01G260400 chrUn 90.830 807 51 8 1825 2622 465607523 465606731 0.000000e+00 1059.0
24 TraesCS5A01G260400 chr3A 86.864 472 43 7 222 688 701760485 701760942 7.690000e-141 510.0
25 TraesCS5A01G260400 chr7B 86.250 480 47 6 222 696 173302949 173303414 1.290000e-138 503.0
26 TraesCS5A01G260400 chr7B 95.918 49 2 0 22 70 530384892 530384844 2.570000e-11 80.5
27 TraesCS5A01G260400 chr7B 92.453 53 3 1 24 76 134530234 134530285 1.190000e-09 75.0
28 TraesCS5A01G260400 chr6D 87.648 421 37 5 272 691 460765586 460765180 2.800000e-130 475.0
29 TraesCS5A01G260400 chr6D 87.845 181 14 5 2889 3067 380043738 380043564 4.060000e-49 206.0
30 TraesCS5A01G260400 chr6D 85.535 159 14 4 712 868 73497393 73497242 1.150000e-34 158.0
31 TraesCS5A01G260400 chr1B 97.248 218 6 0 2890 3107 228760194 228760411 1.360000e-98 370.0
32 TraesCS5A01G260400 chr4A 96.789 218 7 0 2890 3107 552885199 552885416 6.330000e-97 364.0
33 TraesCS5A01G260400 chr4A 94.340 53 2 1 176 227 616838853 616838905 2.570000e-11 80.5
34 TraesCS5A01G260400 chr1D 88.950 181 14 5 2890 3067 372352893 372352716 5.220000e-53 219.0
35 TraesCS5A01G260400 chr7D 87.845 181 16 5 2889 3066 598673257 598673080 1.130000e-49 207.0
36 TraesCS5A01G260400 chr2D 87.778 180 14 6 2890 3067 32977652 32977825 1.460000e-48 204.0
37 TraesCS5A01G260400 chr2D 95.918 49 1 1 176 224 613442884 613442931 9.240000e-11 78.7
38 TraesCS5A01G260400 chr7A 82.278 158 21 4 712 868 539543828 539543677 2.510000e-26 130.0
39 TraesCS5A01G260400 chr6A 98.000 50 1 0 22 71 158316632 158316583 1.530000e-13 87.9
40 TraesCS5A01G260400 chr6A 97.917 48 1 0 177 224 82092540 82092587 1.990000e-12 84.2
41 TraesCS5A01G260400 chr3B 97.872 47 1 0 22 68 677764016 677763970 7.140000e-12 82.4
42 TraesCS5A01G260400 chr3B 95.918 49 2 0 23 71 452724649 452724697 2.570000e-11 80.5
43 TraesCS5A01G260400 chr3D 95.918 49 2 0 176 224 40010286 40010238 2.570000e-11 80.5


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 TraesCS5A01G260400 chr5A 474324631 474327737 3106 True 5738 5738 100.0000 1 3107 1 chr5A.!!$R1 3106
1 TraesCS5A01G260400 chr5A 474192687 474197599 4912 True 2817 5336 98.8845 1 3107 2 chr5A.!!$R5 3106
2 TraesCS5A01G260400 chr5A 474059160 474064065 4905 True 2805 5312 98.8330 1 3107 2 chr5A.!!$R4 3106
3 TraesCS5A01G260400 chr5D 371267307 371269957 2650 False 3952 3952 93.4820 222 2900 1 chr5D.!!$F3 2678
4 TraesCS5A01G260400 chr5D 371021572 371023184 1612 True 2632 2632 96.1590 906 2514 1 chr5D.!!$R1 1608
5 TraesCS5A01G260400 chr5B 440533426 440536093 2667 False 3879 3879 92.9260 222 2900 1 chr5B.!!$F2 2678
6 TraesCS5A01G260400 chr5B 440513760 440516425 2665 False 3849 3849 92.7410 222 2900 1 chr5B.!!$F1 2678
7 TraesCS5A01G260400 chrUn 371166267 371167218 951 False 1552 1552 96.0420 222 1177 1 chrUn.!!$F1 955
8 TraesCS5A01G260400 chrUn 272195345 272196412 1067 True 1399 1399 90.3930 1825 2900 1 chrUn.!!$R1 1075
9 TraesCS5A01G260400 chrUn 465606731 465607523 792 True 1059 1059 90.8300 1825 2622 1 chrUn.!!$R2 797

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
264 2077 1.085091 CATGTCTTGAGCTGCACTCC 58.915 55.0 1.02 0.7 45.61 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3086 4922 0.037734 ACGGCCGAGGGATTTTTCTT 59.962 50.0 35.9 0.0 0.0 2.52 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
35 36 7.313731 TGATAGGATCCAAATACTACTCCCTT 58.686 38.462 15.82 0.0 30.86 3.95
264 2077 1.085091 CATGTCTTGAGCTGCACTCC 58.915 55.000 1.02 0.7 45.61 3.85
3086 4922 1.704641 CCGATCCCATCTGTCTACCA 58.295 55.000 0.00 0.0 0.00 3.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
264 2077 2.276732 AAGTGGGTGAAGTGTGATGG 57.723 50.000 0.0 0.0 0.00 3.51
339 2152 3.827876 TGTTCCTGACGACACCACTAATA 59.172 43.478 0.0 0.0 0.00 0.98
918 2731 8.985805 GTTAGTACAGTAGCATTAACACTTGTT 58.014 33.333 0.0 0.0 41.73 2.83
3086 4922 0.037734 ACGGCCGAGGGATTTTTCTT 59.962 50.000 35.9 0.0 0.00 2.52


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

AutoCloner maintained by Alex Coulton.