Multiple sequence alignment - TraesCS2A01G172300

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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 TraesCS2A01G172300 chr2A 100.000 3227 0 0 1 3227 128482176 128485402 0.000000e+00 5960
1 TraesCS2A01G172300 chr2A 96.913 1166 33 3 2064 3227 419178724 419177560 0.000000e+00 1951
2 TraesCS2A01G172300 chr6A 97.547 1712 39 2 356 2064 561454825 561456536 0.000000e+00 2926
3 TraesCS2A01G172300 chr6A 97.019 1711 46 3 356 2064 561585811 561584104 0.000000e+00 2872
4 TraesCS2A01G172300 chr6A 96.281 1721 52 4 356 2064 561599045 561597325 0.000000e+00 2813
5 TraesCS2A01G172300 chr6A 97.429 1400 34 2 353 1750 16669145 16670544 0.000000e+00 2385
6 TraesCS2A01G172300 chr7A 97.136 1711 45 3 357 2064 16155319 16153610 0.000000e+00 2885
7 TraesCS2A01G172300 chr7A 95.733 1711 62 9 358 2064 488151252 488149549 0.000000e+00 2745
8 TraesCS2A01G172300 chr7A 95.377 1709 54 6 358 2064 488486095 488484410 0.000000e+00 2695
9 TraesCS2A01G172300 chr7A 96.835 1169 34 3 2061 3227 375446676 375445509 0.000000e+00 1951
10 TraesCS2A01G172300 chrUn 94.626 1712 73 5 355 2064 10231185 10229491 0.000000e+00 2634
11 TraesCS2A01G172300 chr1D 94.794 1383 49 6 680 2061 416512216 416513576 0.000000e+00 2134
12 TraesCS2A01G172300 chr4A 96.996 1165 32 3 2065 3227 7773606 7772443 0.000000e+00 1954
13 TraesCS2A01G172300 chr4A 96.824 1165 34 3 2065 3227 28268644 28267481 0.000000e+00 1943
14 TraesCS2A01G172300 chr5A 96.993 1164 29 5 2067 3227 564231777 564232937 0.000000e+00 1951
15 TraesCS2A01G172300 chr5A 96.824 1165 34 3 2065 3227 564224861 564226024 0.000000e+00 1943
16 TraesCS2A01G172300 chr3A 96.910 1165 33 3 2065 3227 353562883 353564046 0.000000e+00 1949
17 TraesCS2A01G172300 chr3A 96.824 1165 34 3 2065 3227 705357548 705356385 0.000000e+00 1943
18 TraesCS2A01G172300 chr3A 96.738 1165 35 3 2065 3227 594604271 594603108 0.000000e+00 1938
19 TraesCS2A01G172300 chr1A 95.675 1133 47 2 357 1488 565658026 565656895 0.000000e+00 1820
20 TraesCS2A01G172300 chr2B 86.957 299 24 10 64 353 176293067 176293359 4.020000e-84 322


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 TraesCS2A01G172300 chr2A 128482176 128485402 3226 False 5960 5960 100.000 1 3227 1 chr2A.!!$F1 3226
1 TraesCS2A01G172300 chr2A 419177560 419178724 1164 True 1951 1951 96.913 2064 3227 1 chr2A.!!$R1 1163
2 TraesCS2A01G172300 chr6A 561454825 561456536 1711 False 2926 2926 97.547 356 2064 1 chr6A.!!$F2 1708
3 TraesCS2A01G172300 chr6A 561584104 561585811 1707 True 2872 2872 97.019 356 2064 1 chr6A.!!$R1 1708
4 TraesCS2A01G172300 chr6A 561597325 561599045 1720 True 2813 2813 96.281 356 2064 1 chr6A.!!$R2 1708
5 TraesCS2A01G172300 chr6A 16669145 16670544 1399 False 2385 2385 97.429 353 1750 1 chr6A.!!$F1 1397
6 TraesCS2A01G172300 chr7A 16153610 16155319 1709 True 2885 2885 97.136 357 2064 1 chr7A.!!$R1 1707
7 TraesCS2A01G172300 chr7A 488149549 488151252 1703 True 2745 2745 95.733 358 2064 1 chr7A.!!$R3 1706
8 TraesCS2A01G172300 chr7A 488484410 488486095 1685 True 2695 2695 95.377 358 2064 1 chr7A.!!$R4 1706
9 TraesCS2A01G172300 chr7A 375445509 375446676 1167 True 1951 1951 96.835 2061 3227 1 chr7A.!!$R2 1166
10 TraesCS2A01G172300 chrUn 10229491 10231185 1694 True 2634 2634 94.626 355 2064 1 chrUn.!!$R1 1709
11 TraesCS2A01G172300 chr1D 416512216 416513576 1360 False 2134 2134 94.794 680 2061 1 chr1D.!!$F1 1381
12 TraesCS2A01G172300 chr4A 7772443 7773606 1163 True 1954 1954 96.996 2065 3227 1 chr4A.!!$R1 1162
13 TraesCS2A01G172300 chr4A 28267481 28268644 1163 True 1943 1943 96.824 2065 3227 1 chr4A.!!$R2 1162
14 TraesCS2A01G172300 chr5A 564231777 564232937 1160 False 1951 1951 96.993 2067 3227 1 chr5A.!!$F2 1160
15 TraesCS2A01G172300 chr5A 564224861 564226024 1163 False 1943 1943 96.824 2065 3227 1 chr5A.!!$F1 1162
16 TraesCS2A01G172300 chr3A 353562883 353564046 1163 False 1949 1949 96.910 2065 3227 1 chr3A.!!$F1 1162
17 TraesCS2A01G172300 chr3A 705356385 705357548 1163 True 1943 1943 96.824 2065 3227 1 chr3A.!!$R2 1162
18 TraesCS2A01G172300 chr3A 594603108 594604271 1163 True 1938 1938 96.738 2065 3227 1 chr3A.!!$R1 1162
19 TraesCS2A01G172300 chr1A 565656895 565658026 1131 True 1820 1820 95.675 357 1488 1 chr1A.!!$R1 1131


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
325 326 0.040058 ATCAAACCCATGCAGCCAGA 59.960 50.0 0.0 0.0 0.0 3.86 F
328 329 0.112995 AAACCCATGCAGCCAGAGAA 59.887 50.0 0.0 0.0 0.0 2.87 F
329 330 0.112995 AACCCATGCAGCCAGAGAAA 59.887 50.0 0.0 0.0 0.0 2.52 F
330 331 0.323178 ACCCATGCAGCCAGAGAAAG 60.323 55.0 0.0 0.0 0.0 2.62 F
340 341 0.392729 CCAGAGAAAGGGCTGCTGAG 60.393 60.0 0.0 0.0 0.0 3.35 F
341 342 0.392729 CAGAGAAAGGGCTGCTGAGG 60.393 60.0 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1731 1751 1.229209 TCCACACCCCTCTCCTGTC 60.229 63.158 0.0 0.0 0.00 3.51 R
1732 1752 1.229336 CTCCACACCCCTCTCCTGT 60.229 63.158 0.0 0.0 0.00 4.00 R
1847 1869 5.279056 CCTGTAGTTTCTTCTTCTCGTCCTT 60.279 44.000 0.0 0.0 0.00 3.36 R
1852 1877 5.630661 TCTCCTGTAGTTTCTTCTTCTCG 57.369 43.478 0.0 0.0 0.00 4.04 R
2159 2184 9.679661 TGTATTCACACATGTATTATGTTTCCT 57.320 29.630 0.0 0.0 0.00 3.36 R
2420 2446 1.043022 AGTGTTCCTCCGGTAAACGT 58.957 50.000 0.0 0.0 42.24 3.99 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)



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AutoCloner maintained by Alex Coulton.