Multiple sequence alignment - TraesCS5D01G251400

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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 TraesCS5D01G251400 chr5D 100.000 2549 0 0 1 2549 357076573 357074025 0.000000e+00 4708
1 TraesCS5D01G251400 chr5D 94.201 1966 79 12 606 2549 44511943 44513895 0.000000e+00 2966
2 TraesCS5D01G251400 chr5D 95.262 591 20 3 1 590 326744341 326744924 0.000000e+00 929
3 TraesCS5D01G251400 chr5D 94.949 594 25 3 1 590 14740658 14741250 0.000000e+00 926
4 TraesCS5D01G251400 chr5D 94.444 594 30 3 1 593 287811051 287810460 0.000000e+00 911
5 TraesCS5D01G251400 chrUn 94.289 1961 87 13 606 2546 20573301 20575256 0.000000e+00 2977
6 TraesCS5D01G251400 chrUn 94.545 1925 66 18 649 2549 43407879 43409788 0.000000e+00 2937
7 TraesCS5D01G251400 chrUn 93.939 594 25 7 1 592 79925721 79925137 0.000000e+00 887
8 TraesCS5D01G251400 chrUn 93.624 596 31 4 1 593 108948762 108948171 0.000000e+00 883
9 TraesCS5D01G251400 chr5A 94.097 1948 102 11 606 2549 28960259 28958321 0.000000e+00 2948
10 TraesCS5D01G251400 chr6D 93.947 1966 87 17 604 2549 12108139 12106186 0.000000e+00 2942
11 TraesCS5D01G251400 chr2B 93.884 1962 98 10 597 2549 485690844 485692792 0.000000e+00 2939
12 TraesCS5D01G251400 chr4D 93.842 1965 85 13 606 2549 78732769 78730820 0.000000e+00 2926
13 TraesCS5D01G251400 chr4B 93.510 1957 106 12 604 2549 251255859 251257805 0.000000e+00 2891
14 TraesCS5D01G251400 chr3B 93.493 1967 88 13 606 2549 370213881 370215830 0.000000e+00 2887
15 TraesCS5D01G251400 chr2D 92.476 1741 77 22 597 2311 498471653 498469941 0.000000e+00 2440
16 TraesCS5D01G251400 chr2A 91.175 1745 85 34 606 2311 775967962 775966248 0.000000e+00 2305
17 TraesCS5D01G251400 chr2A 92.226 1132 44 17 606 1700 6302711 6301587 0.000000e+00 1563
18 TraesCS5D01G251400 chr3D 96.128 594 18 4 1 593 526481732 526481143 0.000000e+00 965
19 TraesCS5D01G251400 chr1D 95.447 593 22 3 1 592 479342829 479342241 0.000000e+00 941
20 TraesCS5D01G251400 chr1D 92.623 366 19 4 606 971 17040736 17040379 1.050000e-143 520
21 TraesCS5D01G251400 chr3A 94.435 593 24 6 1 590 648679068 648679654 0.000000e+00 904
22 TraesCS5D01G251400 chr3A 92.412 369 21 5 606 971 683237673 683237309 1.050000e-143 520
23 TraesCS5D01G251400 chr7D 94.286 595 23 4 1 594 147576750 147576166 0.000000e+00 900
24 TraesCS5D01G251400 chr6A 91.599 369 22 5 604 971 203520914 203520554 3.790000e-138 501


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 TraesCS5D01G251400 chr5D 357074025 357076573 2548 True 4708 4708 100.000 1 2549 1 chr5D.!!$R2 2548
1 TraesCS5D01G251400 chr5D 44511943 44513895 1952 False 2966 2966 94.201 606 2549 1 chr5D.!!$F2 1943
2 TraesCS5D01G251400 chr5D 326744341 326744924 583 False 929 929 95.262 1 590 1 chr5D.!!$F3 589
3 TraesCS5D01G251400 chr5D 14740658 14741250 592 False 926 926 94.949 1 590 1 chr5D.!!$F1 589
4 TraesCS5D01G251400 chr5D 287810460 287811051 591 True 911 911 94.444 1 593 1 chr5D.!!$R1 592
5 TraesCS5D01G251400 chrUn 20573301 20575256 1955 False 2977 2977 94.289 606 2546 1 chrUn.!!$F1 1940
6 TraesCS5D01G251400 chrUn 43407879 43409788 1909 False 2937 2937 94.545 649 2549 1 chrUn.!!$F2 1900
7 TraesCS5D01G251400 chrUn 79925137 79925721 584 True 887 887 93.939 1 592 1 chrUn.!!$R1 591
8 TraesCS5D01G251400 chrUn 108948171 108948762 591 True 883 883 93.624 1 593 1 chrUn.!!$R2 592
9 TraesCS5D01G251400 chr5A 28958321 28960259 1938 True 2948 2948 94.097 606 2549 1 chr5A.!!$R1 1943
10 TraesCS5D01G251400 chr6D 12106186 12108139 1953 True 2942 2942 93.947 604 2549 1 chr6D.!!$R1 1945
11 TraesCS5D01G251400 chr2B 485690844 485692792 1948 False 2939 2939 93.884 597 2549 1 chr2B.!!$F1 1952
12 TraesCS5D01G251400 chr4D 78730820 78732769 1949 True 2926 2926 93.842 606 2549 1 chr4D.!!$R1 1943
13 TraesCS5D01G251400 chr4B 251255859 251257805 1946 False 2891 2891 93.510 604 2549 1 chr4B.!!$F1 1945
14 TraesCS5D01G251400 chr3B 370213881 370215830 1949 False 2887 2887 93.493 606 2549 1 chr3B.!!$F1 1943
15 TraesCS5D01G251400 chr2D 498469941 498471653 1712 True 2440 2440 92.476 597 2311 1 chr2D.!!$R1 1714
16 TraesCS5D01G251400 chr2A 775966248 775967962 1714 True 2305 2305 91.175 606 2311 1 chr2A.!!$R2 1705
17 TraesCS5D01G251400 chr2A 6301587 6302711 1124 True 1563 1563 92.226 606 1700 1 chr2A.!!$R1 1094
18 TraesCS5D01G251400 chr3D 526481143 526481732 589 True 965 965 96.128 1 593 1 chr3D.!!$R1 592
19 TraesCS5D01G251400 chr1D 479342241 479342829 588 True 941 941 95.447 1 592 1 chr1D.!!$R2 591
20 TraesCS5D01G251400 chr3A 648679068 648679654 586 False 904 904 94.435 1 590 1 chr3A.!!$F1 589
21 TraesCS5D01G251400 chr7D 147576166 147576750 584 True 900 900 94.286 1 594 1 chr7D.!!$R1 593

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
277 283 0.178929 ACGAAGGAGGAGTTCTGGGT 60.179 55.0 0.0 0.0 0.0 4.51 F
695 701 0.250597 GTTTTGCCCCTAGTCCGTGT 60.251 55.0 0.0 0.0 0.0 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1384 1444 1.006805 GCTCTCTGTCAGTGCGTGT 60.007 57.895 0.0 0.0 32.10 4.49 R
1774 1992 1.448540 CCTGCACTTGGCTCTACGG 60.449 63.158 0.0 0.0 45.15 4.02 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
161 162 1.316706 CGAAGAAGGAGGACGAGGCT 61.317 60.000 0.00 0.0 0.00 4.58
193 194 1.123928 GTGATCCCCATCGAGTCCTT 58.876 55.000 0.00 0.0 0.00 3.36
195 196 1.762957 TGATCCCCATCGAGTCCTTTC 59.237 52.381 0.00 0.0 0.00 2.62
197 198 1.144057 CCCCATCGAGTCCTTTCCG 59.856 63.158 0.00 0.0 0.00 4.30
198 199 1.327690 CCCCATCGAGTCCTTTCCGA 61.328 60.000 0.00 0.0 36.72 4.55
277 283 0.178929 ACGAAGGAGGAGTTCTGGGT 60.179 55.000 0.00 0.0 0.00 4.51
280 286 1.831652 AAGGAGGAGTTCTGGGTGCG 61.832 60.000 0.00 0.0 0.00 5.34
397 403 6.985188 TTGAACTATGTTGAATGGACTAGC 57.015 37.500 0.00 0.0 0.00 3.42
412 418 5.647589 TGGACTAGCAGTATGTCGTTTTAG 58.352 41.667 0.00 0.0 39.31 1.85
695 701 0.250597 GTTTTGCCCCTAGTCCGTGT 60.251 55.000 0.00 0.0 0.00 4.49
790 796 1.011333 GCGGCAAAGACGGCTAATTA 58.989 50.000 0.00 0.0 32.98 1.40
954 1013 4.858680 GGCGGTGGGAAGCTAGCC 62.859 72.222 12.13 0.0 37.61 3.93
1160 1220 1.351430 TACGTGTGCAGCGAGAATGC 61.351 55.000 16.16 0.0 44.11 3.56
1294 1354 4.012374 GGCCAAGACTCTGATGAATGAAA 58.988 43.478 0.00 0.0 0.00 2.69
1384 1444 1.573108 AGAAGAGATGGAGGGCGAAA 58.427 50.000 0.00 0.0 0.00 3.46
1527 1729 5.352016 GGTAATCGCACTGGTTGTAATGTTA 59.648 40.000 0.00 0.0 0.00 2.41
1774 1992 2.627699 TCTTTGTGGGCCAAATTCAGAC 59.372 45.455 8.40 0.0 42.02 3.51
1948 2169 4.519540 TTCCAGAGCCAAACAATTAAGC 57.480 40.909 0.00 0.0 0.00 3.09
1955 2178 7.363268 CCAGAGCCAAACAATTAAGCTTAGAAT 60.363 37.037 6.24 0.0 32.97 2.40
1956 2179 7.699812 CAGAGCCAAACAATTAAGCTTAGAATC 59.300 37.037 6.24 0.0 32.97 2.52
1957 2180 7.613411 AGAGCCAAACAATTAAGCTTAGAATCT 59.387 33.333 6.24 0.0 32.97 2.40
2192 2425 2.997897 GGTGCGACTGGGGACTCT 60.998 66.667 0.00 0.0 0.00 3.24
2193 2426 2.584391 GGTGCGACTGGGGACTCTT 61.584 63.158 0.00 0.0 0.00 2.85
2481 2724 7.878477 AATTTGCATGTTAGTTCATGACTTG 57.122 32.000 10.28 0.0 45.41 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
168 169 2.421739 GATGGGGATCACCGTCGG 59.578 66.667 20.44 10.48 41.60 4.79
193 194 2.291043 GCCCAGTCCTCCTTCGGAA 61.291 63.158 0.00 0.00 34.20 4.30
195 196 3.003173 TGCCCAGTCCTCCTTCGG 61.003 66.667 0.00 0.00 0.00 4.30
197 198 0.907230 AGTCTGCCCAGTCCTCCTTC 60.907 60.000 0.00 0.00 0.00 3.46
198 199 0.474660 AAGTCTGCCCAGTCCTCCTT 60.475 55.000 0.00 0.00 0.00 3.36
347 353 9.773328 ACATCAAATTCAACATAGTTTCATACG 57.227 29.630 0.00 0.00 0.00 3.06
412 418 8.040132 TGGTCCAAAATGATGATGTAAATTTCC 58.960 33.333 0.00 0.00 0.00 3.13
1160 1220 1.333619 CAATTGCCCCGATTCTTACCG 59.666 52.381 0.00 0.00 0.00 4.02
1384 1444 1.006805 GCTCTCTGTCAGTGCGTGT 60.007 57.895 0.00 0.00 32.10 4.49
1774 1992 1.448540 CCTGCACTTGGCTCTACGG 60.449 63.158 0.00 0.00 45.15 4.02
2142 2375 4.820716 TGCATTTTCCCACCTTCATTTTTG 59.179 37.500 0.00 0.00 0.00 2.44
2192 2425 3.697747 CCACGCGGTCCTGGGTAA 61.698 66.667 12.47 0.00 33.24 2.85
2213 2446 3.799755 GCAGCCCTAAACGCCACG 61.800 66.667 0.00 0.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.