Multiple sequence alignment - TraesCS6B01G232700

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 TraesCS6B01G232700 chr6B 100.000 2579 0 0 1 2579 388166991 388164413 0 4763
1 TraesCS6B01G232700 chr6B 97.173 2582 68 4 2 2579 388359045 388356465 0 4359
2 TraesCS6B01G232700 chr2B 96.978 2581 73 4 2 2579 751961810 751959232 0 4329
3 TraesCS6B01G232700 chr2B 95.446 1669 37 9 908 2576 112852577 112854206 0 2625
4 TraesCS6B01G232700 chr7B 96.819 2578 78 4 2 2576 531994930 531997506 0 4303
5 TraesCS6B01G232700 chr3A 96.476 2582 84 6 2 2579 718994176 718991598 0 4257
6 TraesCS6B01G232700 chr3B 95.587 2583 107 6 2 2579 575746127 575743547 0 4132
7 TraesCS6B01G232700 chr7A 97.142 2344 61 6 237 2579 708264393 708262055 0 3952
8 TraesCS6B01G232700 chr4B 95.604 2275 91 5 302 2576 547038351 547040616 0 3639
9 TraesCS6B01G232700 chr5D 95.766 2220 85 7 358 2576 244894244 244896455 0 3570
10 TraesCS6B01G232700 chr5D 95.311 2026 84 8 2 2022 79846321 79844302 0 3205


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 TraesCS6B01G232700 chr6B 388164413 388166991 2578 True 4763 4763 100.000 1 2579 1 chr6B.!!$R1 2578
1 TraesCS6B01G232700 chr6B 388356465 388359045 2580 True 4359 4359 97.173 2 2579 1 chr6B.!!$R2 2577
2 TraesCS6B01G232700 chr2B 751959232 751961810 2578 True 4329 4329 96.978 2 2579 1 chr2B.!!$R1 2577
3 TraesCS6B01G232700 chr2B 112852577 112854206 1629 False 2625 2625 95.446 908 2576 1 chr2B.!!$F1 1668
4 TraesCS6B01G232700 chr7B 531994930 531997506 2576 False 4303 4303 96.819 2 2576 1 chr7B.!!$F1 2574
5 TraesCS6B01G232700 chr3A 718991598 718994176 2578 True 4257 4257 96.476 2 2579 1 chr3A.!!$R1 2577
6 TraesCS6B01G232700 chr3B 575743547 575746127 2580 True 4132 4132 95.587 2 2579 1 chr3B.!!$R1 2577
7 TraesCS6B01G232700 chr7A 708262055 708264393 2338 True 3952 3952 97.142 237 2579 1 chr7A.!!$R1 2342
8 TraesCS6B01G232700 chr4B 547038351 547040616 2265 False 3639 3639 95.604 302 2576 1 chr4B.!!$F1 2274
9 TraesCS6B01G232700 chr5D 244894244 244896455 2211 False 3570 3570 95.766 358 2576 1 chr5D.!!$F1 2218
10 TraesCS6B01G232700 chr5D 79844302 79846321 2019 True 3205 3205 95.311 2 2022 1 chr5D.!!$R1 2020

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
671 676 0.527113 TTTGGCATGAGAACCGCATG 59.473 50.0 0.0 6.36 42.85 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2486 2499 0.973632 TGGGCGAGCTTTCTTCACTA 59.026 50.0 0.0 0.0 0.0 2.74 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
298 302 4.947883 TGATCGATCCCTCTATTATGGGT 58.052 43.478 22.31 0.00 43.74 4.51
414 418 5.548056 ACTCTTCTTTCATCCTCCTTACCAA 59.452 40.000 0.00 0.00 0.00 3.67
507 511 1.066215 AGCTACCAATGCACATCACGA 60.066 47.619 0.00 0.00 0.00 4.35
519 523 3.484649 GCACATCACGATGAAATCATTGC 59.515 43.478 13.83 7.29 45.97 3.56
669 674 1.243342 CCTTTGGCATGAGAACCGCA 61.243 55.000 0.00 0.00 0.00 5.69
671 676 0.527113 TTTGGCATGAGAACCGCATG 59.473 50.000 0.00 6.36 42.85 4.06
764 769 8.570096 TGAAATCGTCGAATTTCGTATAGAAT 57.430 30.769 17.61 4.97 44.85 2.40
780 785 8.533657 TCGTATAGAATGAAAAGGAACCACTTA 58.466 33.333 0.00 0.00 0.00 2.24
1393 1399 4.428615 TGCCGAAACCTAAATGTAAAGC 57.571 40.909 0.00 0.00 0.00 3.51
1412 1418 3.490348 AGCCAGCAACACTTCTAAATGT 58.510 40.909 0.00 0.00 0.00 2.71
1440 1446 2.813474 CGCCGCATCCGTCTTCAA 60.813 61.111 0.00 0.00 0.00 2.69
1519 1525 6.253083 GTCTACGTTCAAAGCTTCTACCATAC 59.747 42.308 0.00 0.00 0.00 2.39
1535 1541 7.058525 TCTACCATACACCTAATTCGAGAAGA 58.941 38.462 0.00 0.00 0.00 2.87
1649 1658 6.038271 GCGGATCCAATACACATAAGACTTTT 59.962 38.462 13.41 0.00 0.00 2.27
1804 1815 6.665248 CCTCCATTTTAGGTTTTTCTCAGGAT 59.335 38.462 0.00 0.00 0.00 3.24
1814 1825 8.341892 AGGTTTTTCTCAGGATAGAATTTCAC 57.658 34.615 0.00 0.00 35.48 3.18
1837 1848 4.499183 GAAGTCATATCGGCCAGATAAGG 58.501 47.826 17.34 13.58 44.27 2.69
2126 2138 0.395312 ACCGTCCGGACTTGAAACAT 59.605 50.000 30.92 5.59 38.96 2.71
2426 2439 2.218603 GGAAGAGGAAAACGACAGCAA 58.781 47.619 0.00 0.00 0.00 3.91
2486 2499 4.298332 GTTTGAGCGTTGGTTTTGATGAT 58.702 39.130 0.00 0.00 0.00 2.45
2526 2539 1.856802 AAGACGTACGTGGAACCAAC 58.143 50.000 28.16 8.58 0.00 3.77
2576 2589 3.763897 GAGAACTGGGTGCATTGGTAAAT 59.236 43.478 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
261 265 5.008415 GGATCGATCATCACATTCTGCTTTT 59.992 40.000 25.93 0.00 32.33 2.27
298 302 9.969001 AGTAGAGGCTTTGGTATAAACATAAAA 57.031 29.630 0.00 0.00 0.00 1.52
414 418 2.650322 TCTGAACCAGGAAAAGCGTTT 58.350 42.857 0.00 0.00 31.51 3.60
463 467 4.394920 TCAAGACGAAGGCATTTTCCATAC 59.605 41.667 0.00 0.00 0.00 2.39
669 674 5.408604 GCATTAGTTACATTAGCGTAGGCAT 59.591 40.000 10.48 0.00 43.41 4.40
671 676 4.748102 TGCATTAGTTACATTAGCGTAGGC 59.252 41.667 0.00 0.00 40.37 3.93
764 769 9.807921 AAAGAGAATATAAGTGGTTCCTTTTCA 57.192 29.630 0.00 0.00 0.00 2.69
826 831 1.887242 GCAGCAATGATACCGCCGA 60.887 57.895 0.00 0.00 0.00 5.54
929 934 1.705873 AGGAGACTGGTCTTGACGTT 58.294 50.000 4.67 0.00 40.61 3.99
939 944 4.889995 ACTTTTGAAAGGAAAGGAGACTGG 59.110 41.667 8.23 0.00 39.79 4.00
1393 1399 4.516698 AGTGACATTTAGAAGTGTTGCTGG 59.483 41.667 0.00 0.00 0.00 4.85
1412 1418 2.852495 GATGCGGCGGGAAGAAGTGA 62.852 60.000 9.78 0.00 0.00 3.41
1440 1446 6.153000 AGTGAAAACCTGTGACTATATCGTCT 59.847 38.462 8.66 0.00 35.00 4.18
1519 1525 7.484975 ACTATCAAGTCTTCTCGAATTAGGTG 58.515 38.462 0.00 0.00 0.00 4.00
1616 1624 2.139118 GTATTGGATCCGCTCTTCTGC 58.861 52.381 7.39 0.00 0.00 4.26
1804 1815 5.690409 GCCGATATGACTTCGTGAAATTCTA 59.310 40.000 0.00 0.00 34.85 2.10
1814 1825 2.732412 ATCTGGCCGATATGACTTCG 57.268 50.000 8.11 0.00 36.38 3.79
1837 1848 3.386768 TCAATATGGAGCCGTTAGAGC 57.613 47.619 0.00 0.00 0.00 4.09
1904 1916 3.258372 TGACTCTGCTGATACCGAGTTTT 59.742 43.478 0.00 0.00 36.90 2.43
2449 2462 1.202604 TCAAACCGAAGCTTTCCGAGT 60.203 47.619 8.97 3.19 0.00 4.18
2486 2499 0.973632 TGGGCGAGCTTTCTTCACTA 59.026 50.000 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.