Multiple sequence alignment - TraesCS5B01G545800

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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 TraesCS5B01G545800 chr5B 100.000 2519 0 0 1 2519 697910858 697908340 0 4652
1 TraesCS5B01G545800 chr5B 94.970 2525 117 8 1 2519 701869130 701866610 0 3951
2 TraesCS5B01G545800 chr3B 95.283 2523 109 9 1 2519 637643463 637640947 0 3991
3 TraesCS5B01G545800 chr3B 92.393 2537 143 27 1 2519 84776754 84774250 0 3570
4 TraesCS5B01G545800 chr3B 94.260 784 40 5 1 781 1649065 1649846 0 1194
5 TraesCS5B01G545800 chr3B 89.365 677 62 7 1 675 469810291 469809623 0 843
6 TraesCS5B01G545800 chrUn 94.931 2525 117 10 1 2519 8324586 8322067 0 3943
7 TraesCS5B01G545800 chr2B 94.618 2527 124 8 1 2519 731624896 731622374 0 3903
8 TraesCS5B01G545800 chr2B 90.264 986 81 15 1 981 739342529 739343504 0 1275
9 TraesCS5B01G545800 chr1B 94.618 2527 125 7 1 2519 603224523 603227046 0 3903
10 TraesCS5B01G545800 chr1B 95.958 2301 83 8 1 2294 39833635 39835932 0 3725
11 TraesCS5B01G545800 chr7B 92.956 2527 140 17 1 2519 465822595 465825091 0 3646
12 TraesCS5B01G545800 chr6B 92.815 2533 137 22 1 2519 257366250 257363749 0 3627


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 TraesCS5B01G545800 chr5B 697908340 697910858 2518 True 4652 4652 100.000 1 2519 1 chr5B.!!$R1 2518
1 TraesCS5B01G545800 chr5B 701866610 701869130 2520 True 3951 3951 94.970 1 2519 1 chr5B.!!$R2 2518
2 TraesCS5B01G545800 chr3B 637640947 637643463 2516 True 3991 3991 95.283 1 2519 1 chr3B.!!$R3 2518
3 TraesCS5B01G545800 chr3B 84774250 84776754 2504 True 3570 3570 92.393 1 2519 1 chr3B.!!$R1 2518
4 TraesCS5B01G545800 chr3B 1649065 1649846 781 False 1194 1194 94.260 1 781 1 chr3B.!!$F1 780
5 TraesCS5B01G545800 chr3B 469809623 469810291 668 True 843 843 89.365 1 675 1 chr3B.!!$R2 674
6 TraesCS5B01G545800 chrUn 8322067 8324586 2519 True 3943 3943 94.931 1 2519 1 chrUn.!!$R1 2518
7 TraesCS5B01G545800 chr2B 731622374 731624896 2522 True 3903 3903 94.618 1 2519 1 chr2B.!!$R1 2518
8 TraesCS5B01G545800 chr2B 739342529 739343504 975 False 1275 1275 90.264 1 981 1 chr2B.!!$F1 980
9 TraesCS5B01G545800 chr1B 603224523 603227046 2523 False 3903 3903 94.618 1 2519 1 chr1B.!!$F2 2518
10 TraesCS5B01G545800 chr1B 39833635 39835932 2297 False 3725 3725 95.958 1 2294 1 chr1B.!!$F1 2293
11 TraesCS5B01G545800 chr7B 465822595 465825091 2496 False 3646 3646 92.956 1 2519 1 chr7B.!!$F1 2518
12 TraesCS5B01G545800 chr6B 257363749 257366250 2501 True 3627 3627 92.815 1 2519 1 chr6B.!!$R1 2518

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
718 729 4.142138 TGGTTTTTGGCTGTTAAATCGTGT 60.142 37.5 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
1637 1655 0.106149 AAACCGACGCTCTTGGAACT 59.894 50.0 0.0 0.0 0.0 3.01 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
369 375 4.275689 TGCGAAACAGATGAACACATTTCT 59.724 37.500 0.00 0.00 0.00 2.52
647 656 4.406069 CTGTATGGATTTTGTGCGTTCTG 58.594 43.478 0.00 0.00 0.00 3.02
718 729 4.142138 TGGTTTTTGGCTGTTAAATCGTGT 60.142 37.500 0.00 0.00 0.00 4.49
865 878 8.547894 CACAAAGTTTAACTTAGCCCATTTTTC 58.452 33.333 10.97 0.00 37.47 2.29
1360 1377 1.272425 CCCCATGGTGTTTTCCTGCTA 60.272 52.381 11.73 0.00 0.00 3.49
1606 1624 2.959030 TGTAGCTGCTATACCTGGACTG 59.041 50.000 13.20 0.00 0.00 3.51
1637 1655 2.153039 CGAACTGATCGCAAGCACA 58.847 52.632 0.00 0.00 45.89 4.57
1795 1815 9.405587 TCACTTTAGTTTTCTTTCAGTTTTGTG 57.594 29.630 0.00 0.00 0.00 3.33
1876 1897 5.925969 CCTTAACTAGGCAACCACATTTTTG 59.074 40.000 0.00 0.00 37.17 2.44
2040 2061 3.780294 AGAGATAGTTGCATACCCACCAA 59.220 43.478 0.00 0.00 0.00 3.67
2044 2065 2.514803 AGTTGCATACCCACCAAGTTC 58.485 47.619 0.00 0.00 0.00 3.01
2049 2070 3.964031 TGCATACCCACCAAGTTCTTTTT 59.036 39.130 0.00 0.00 0.00 1.94
2165 2190 1.723542 GCAGTCTTGATCACGTCACAG 59.276 52.381 0.00 0.00 36.32 3.66
2277 2302 6.518493 TGTTCTAATATACGTGACCCCAATC 58.482 40.000 0.00 0.00 0.00 2.67
2309 2350 0.236711 CTCTTGGTGTGCGCAGAAAG 59.763 55.000 12.22 11.85 0.00 2.62
2463 2504 0.655733 CGTCCAAGCAGTTCACGTTT 59.344 50.000 0.00 0.00 0.00 3.60
2475 2516 2.619646 GTTCACGTTTAAGGGAAAGGCA 59.380 45.455 0.00 0.00 35.03 4.75
2513 2554 1.536676 CCCCACACACTTCCCAGTT 59.463 57.895 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
262 266 2.246091 AGCTCTTACCTCTGCTCCTT 57.754 50.000 0.00 0.00 0.00 3.36
325 329 4.736464 GCATTGGAAAAAGTCACGGAACTT 60.736 41.667 0.00 0.00 41.20 2.66
369 375 1.907807 GTGTGCCTGCATTGGGGAA 60.908 57.895 0.00 0.00 0.00 3.97
647 656 6.017933 CACATTCATCTCGCAACTTCTAAAC 58.982 40.000 0.00 0.00 0.00 2.01
718 729 0.690192 TGCTAGTGGCCTTGCTTACA 59.310 50.000 3.32 0.00 39.73 2.41
821 834 4.488126 TGTGTGACAGAAATTAGCAAGC 57.512 40.909 0.00 0.00 0.00 4.01
865 878 2.813908 GCGACCCTACAAGCACGG 60.814 66.667 0.00 0.00 0.00 4.94
1103 1120 1.071385 GCAGACCCCATATCCTGTGAG 59.929 57.143 0.00 0.00 0.00 3.51
1305 1322 2.173782 TGTGGTAGGAGCAAGGAAACAA 59.826 45.455 0.00 0.00 0.00 2.83
1435 1452 2.744202 CTGCGTTTTTATCACCTGCTCT 59.256 45.455 0.00 0.00 0.00 4.09
1527 1544 4.464008 AGATGAACAACAAGAGCAGGAAA 58.536 39.130 0.00 0.00 0.00 3.13
1574 1591 3.565764 AGCAGCTACATGAGGCAAATA 57.434 42.857 0.00 0.00 0.00 1.40
1606 1624 2.972625 TCAGTTCGTCCACATCCAATC 58.027 47.619 0.00 0.00 0.00 2.67
1637 1655 0.106149 AAACCGACGCTCTTGGAACT 59.894 50.000 0.00 0.00 0.00 3.01
1795 1815 4.219725 GCCTGACTTCTATATGACCTCCTC 59.780 50.000 0.00 0.00 0.00 3.71
1876 1897 3.402628 TCTGGTGAGTTGCTTAGGAAC 57.597 47.619 8.59 8.59 0.00 3.62
1961 1982 5.133941 TGTGTGGTTGCCTGAAAGTATAAA 58.866 37.500 0.00 0.00 0.00 1.40
2058 2082 5.893897 AAATGCAAACAAAGAAAAAGCCA 57.106 30.435 0.00 0.00 0.00 4.75
2060 2084 7.750014 TGAGAAAAATGCAAACAAAGAAAAAGC 59.250 29.630 0.00 0.00 0.00 3.51
2066 2090 6.397272 AGTGTGAGAAAAATGCAAACAAAGA 58.603 32.000 0.00 0.00 0.00 2.52
2067 2092 6.651755 AGTGTGAGAAAAATGCAAACAAAG 57.348 33.333 0.00 0.00 0.00 2.77
2165 2190 2.970974 GCCTTGCTGCCACGAACTC 61.971 63.158 0.00 0.00 0.00 3.01
2277 2302 3.282021 CACCAAGAGAGAGAGAGAGGAG 58.718 54.545 0.00 0.00 0.00 3.69
2309 2350 3.823304 ACCATCCTGACAAGCTTCTTTTC 59.177 43.478 0.00 0.00 0.00 2.29
2463 2504 1.375013 GCGTCGTGCCTTTCCCTTA 60.375 57.895 0.00 0.00 37.76 2.69
2475 2516 1.076533 GTCATTCACATCGGCGTCGT 61.077 55.000 10.18 1.93 37.69 4.34
2484 2525 0.776810 TGTGTGGGGGTCATTCACAT 59.223 50.000 0.00 0.00 42.34 3.21
2487 2528 0.850100 AAGTGTGTGGGGGTCATTCA 59.150 50.000 0.00 0.00 0.00 2.57
2488 2529 1.534729 GAAGTGTGTGGGGGTCATTC 58.465 55.000 0.00 0.00 0.00 2.67


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

AutoCloner maintained by Alex Coulton.