Multiple sequence alignment - TraesCS6B01G207400

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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 TraesCS6B01G207400 chr6B 100.000 3375 0 0 1 3375 262474474 262471100 0.000000e+00 6233
1 TraesCS6B01G207400 chr6D 96.864 3412 67 13 1 3375 149473328 149469920 0.000000e+00 5672
2 TraesCS6B01G207400 chr6A 96.723 3418 69 11 1 3375 196784954 196788371 0.000000e+00 5651
3 TraesCS6B01G207400 chr2D 85.586 111 7 4 2032 2133 49178413 49178523 1.280000e-19 108


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 TraesCS6B01G207400 chr6B 262471100 262474474 3374 True 6233 6233 100.000 1 3375 1 chr6B.!!$R1 3374
1 TraesCS6B01G207400 chr6D 149469920 149473328 3408 True 5672 5672 96.864 1 3375 1 chr6D.!!$R1 3374
2 TraesCS6B01G207400 chr6A 196784954 196788371 3417 False 5651 5651 96.723 1 3375 1 chr6A.!!$F1 3374

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
525 546 1.005340 CCAGATTGCGAGTCTGCTTC 58.995 55.000 7.15 5.79 41.33 3.86 F
867 901 3.530535 TGTGATGGTATCATCCGTGTTG 58.469 45.455 13.46 0.00 46.92 3.33 F
1643 1687 0.179009 ATGTGCTGCTGGTTCACACT 60.179 50.000 0.00 0.00 42.59 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1643 1687 0.107831 CCACCTTTTGTCCGACTCCA 59.892 55.000 0.0 0.0 0.00 3.86 R
2033 2077 2.371841 TGCAACTACCAACAGAGGATGT 59.628 45.455 0.0 0.0 46.97 3.06 R
2579 2626 4.651503 AGAAAGAGACCTTTGACTCAGTGA 59.348 41.667 0.0 0.0 42.30 3.41 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
346 367 6.626623 GCATTGATTGATTAGCTGGTTGACTT 60.627 38.462 0.00 0.00 0.00 3.01
430 451 1.086067 ATCGTTCTGCTGTGCGGATG 61.086 55.000 1.70 0.00 43.86 3.51
525 546 1.005340 CCAGATTGCGAGTCTGCTTC 58.995 55.000 7.15 5.79 41.33 3.86
607 628 4.697514 TGATTACTTGCTGCAGAGGATAC 58.302 43.478 20.43 0.00 0.00 2.24
657 683 6.988580 TCAAGTATTCTCGTCCGACTATTCTA 59.011 38.462 0.00 0.00 0.00 2.10
867 901 3.530535 TGTGATGGTATCATCCGTGTTG 58.469 45.455 13.46 0.00 46.92 3.33
916 955 6.551385 ACTGCTTGACAAGTTTAGATCTTG 57.449 37.500 16.39 0.00 45.15 3.02
946 990 6.272318 TGTTTTTAAGAACACATTGGCTCAG 58.728 36.000 7.44 0.00 34.77 3.35
967 1011 9.974750 GCTCAGTTACTAAAATTTGTGATCTAC 57.025 33.333 0.00 0.00 0.00 2.59
1196 1240 4.733725 TTCTCCCCCGTCCCCAGG 62.734 72.222 0.00 0.00 0.00 4.45
1484 1528 8.774546 TGCCTGTTATGGAAATTATGGATAAA 57.225 30.769 0.00 0.00 0.00 1.40
1643 1687 0.179009 ATGTGCTGCTGGTTCACACT 60.179 50.000 0.00 0.00 42.59 3.55
1876 1920 5.219343 TGATGGATAAGGTAGATGCTGTG 57.781 43.478 0.00 0.00 0.00 3.66
2033 2077 6.777580 TCAAGATAGTGATACTGATAGTGCCA 59.222 38.462 0.00 0.00 0.00 4.92
2166 2213 4.777366 TGTATCTGGAACTGAATCACCTCA 59.223 41.667 0.00 0.00 40.32 3.86
2392 2439 9.712305 TCTAGATAGCCATTAAAAGTTATGAGC 57.288 33.333 0.00 0.00 0.00 4.26
2425 2472 8.417176 GCTTAGAATTTGTTTGTTATGTTGTCG 58.583 33.333 0.00 0.00 0.00 4.35
2579 2626 4.709886 ACTTTTCAGTACAACTTTTGCCCT 59.290 37.500 0.00 0.00 0.00 5.19
2615 2662 8.533569 AAGGTCTCTTTCTTTAATTGAACCAA 57.466 30.769 0.00 0.00 0.00 3.67
2724 2771 5.047872 TCTGCTACGTGGTTGTAATTGAGTA 60.048 40.000 0.00 0.00 0.00 2.59
2770 2817 5.693555 TCTGTTCTATTATTCTGCATGCTCG 59.306 40.000 20.33 10.19 0.00 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
252 272 3.714144 CCCCAGACTCTAGAAAGAAGGA 58.286 50.000 0.00 0.0 0.00 3.36
253 273 2.169561 GCCCCAGACTCTAGAAAGAAGG 59.830 54.545 0.00 0.0 0.00 3.46
430 451 6.391537 AGAAACAGATCGAAGAAACTAGGAC 58.608 40.000 0.00 0.0 43.58 3.85
546 567 0.104120 TATCGCCCACCAGATCAACG 59.896 55.000 0.00 0.0 0.00 4.10
615 636 3.057033 ACTTGACATGAGAAATTGCTGCC 60.057 43.478 0.00 0.0 0.00 4.85
657 683 7.215085 AGACGAACTGACTGGTTTAATTACTT 58.785 34.615 0.00 0.0 0.00 2.24
852 886 6.431198 AATAAACACAACACGGATGATACC 57.569 37.500 0.00 0.0 0.00 2.73
916 955 8.699749 GCCAATGTGTTCTTAAAAACAAGATAC 58.300 33.333 0.00 0.0 40.62 2.24
946 990 8.726988 TGCAGGTAGATCACAAATTTTAGTAAC 58.273 33.333 0.00 0.0 0.00 2.50
995 1039 2.111756 CTTTGCGGAATTTCATAGCGC 58.888 47.619 0.00 0.0 0.00 5.92
1017 1061 1.842381 GCAGTACCTCCACCTTGCCT 61.842 60.000 0.00 0.0 0.00 4.75
1196 1240 2.189521 CCCAGCATACCGGACCAC 59.810 66.667 9.46 0.0 0.00 4.16
1484 1528 4.559300 GCTGTGTCAACTGTTTGCCATAAT 60.559 41.667 0.00 0.0 32.17 1.28
1592 1636 5.186256 TCCTGAAAGTAATAACCATGGCA 57.814 39.130 13.04 0.0 0.00 4.92
1643 1687 0.107831 CCACCTTTTGTCCGACTCCA 59.892 55.000 0.00 0.0 0.00 3.86
2033 2077 2.371841 TGCAACTACCAACAGAGGATGT 59.628 45.455 0.00 0.0 46.97 3.06
2166 2213 3.309848 CCCCAGACCACCTTTAATTGGAT 60.310 47.826 5.51 0.0 36.28 3.41
2391 2438 4.686839 AACAAATTCTAAGCCTCTTCGC 57.313 40.909 0.00 0.0 0.00 4.70
2392 2439 6.002062 ACAAACAAATTCTAAGCCTCTTCG 57.998 37.500 0.00 0.0 0.00 3.79
2425 2472 9.694137 AATCCACTATTCTAAAGTAAGCGATAC 57.306 33.333 0.00 0.0 34.52 2.24
2579 2626 4.651503 AGAAAGAGACCTTTGACTCAGTGA 59.348 41.667 0.00 0.0 42.30 3.41
2724 2771 8.370182 ACAGAAATTTCATTGCCATCTTAAGTT 58.630 29.630 19.99 0.0 0.00 2.66
2770 2817 6.215845 ACTGAATACATGAAACTTGTTTGCC 58.784 36.000 0.00 0.0 0.00 4.52


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

AutoCloner maintained by Alex Coulton.