Multiple sequence alignment - TraesCS1A01G047600

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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 TraesCS1A01G047600 chr1A 100.000 2438 0 0 1 2438 29700320 29697883 0 4503
1 TraesCS1A01G047600 chr2A 96.968 2441 66 5 1 2438 628425071 628422636 0 4091
2 TraesCS1A01G047600 chr2A 96.927 2441 67 6 1 2438 663122234 663124669 0 4085
3 TraesCS1A01G047600 chr2A 96.639 2440 73 7 1 2438 723285269 723282837 0 4043
4 TraesCS1A01G047600 chr2A 96.478 2442 71 6 1 2438 746668689 746671119 0 4019
5 TraesCS1A01G047600 chr2A 96.310 2439 81 7 1 2436 624542780 624540348 0 3997
6 TraesCS1A01G047600 chr2A 96.231 2441 82 8 1 2438 65305957 65303524 0 3989
7 TraesCS1A01G047600 chr2A 96.192 2442 84 7 1 2438 539821748 539819312 0 3986
8 TraesCS1A01G047600 chr4A 96.966 2439 69 4 1 2438 62476750 62474316 0 4089
9 TraesCS1A01G047600 chr6A 96.848 2443 69 5 1 2438 377062296 377059857 0 4078


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 TraesCS1A01G047600 chr1A 29697883 29700320 2437 True 4503 4503 100.000 1 2438 1 chr1A.!!$R1 2437
1 TraesCS1A01G047600 chr2A 628422636 628425071 2435 True 4091 4091 96.968 1 2438 1 chr2A.!!$R4 2437
2 TraesCS1A01G047600 chr2A 663122234 663124669 2435 False 4085 4085 96.927 1 2438 1 chr2A.!!$F1 2437
3 TraesCS1A01G047600 chr2A 723282837 723285269 2432 True 4043 4043 96.639 1 2438 1 chr2A.!!$R5 2437
4 TraesCS1A01G047600 chr2A 746668689 746671119 2430 False 4019 4019 96.478 1 2438 1 chr2A.!!$F2 2437
5 TraesCS1A01G047600 chr2A 624540348 624542780 2432 True 3997 3997 96.310 1 2436 1 chr2A.!!$R3 2435
6 TraesCS1A01G047600 chr2A 65303524 65305957 2433 True 3989 3989 96.231 1 2438 1 chr2A.!!$R1 2437
7 TraesCS1A01G047600 chr2A 539819312 539821748 2436 True 3986 3986 96.192 1 2438 1 chr2A.!!$R2 2437
8 TraesCS1A01G047600 chr4A 62474316 62476750 2434 True 4089 4089 96.966 1 2438 1 chr4A.!!$R1 2437
9 TraesCS1A01G047600 chr6A 377059857 377062296 2439 True 4078 4078 96.848 1 2438 1 chr6A.!!$R1 2437

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
223 224 0.895559 GGTGGAGGGGCAAACTTCTG 60.896 60.0 0.0 0.0 0.00 3.02 F
1341 1345 0.473755 ACATGGTGAGGAACTGTGCA 59.526 50.0 0.0 0.0 41.55 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1373 1377 1.087501 GGTTTCCACGAAGCTCATCC 58.912 55.0 0.0 0.0 0.00 3.51 R
2356 2373 0.407528 TTGGCCCACATTTCAGGCTA 59.592 50.0 0.0 0.0 46.31 3.93 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
223 224 0.895559 GGTGGAGGGGCAAACTTCTG 60.896 60.000 0.00 0.00 0.00 3.02
582 585 1.205055 GTCCCTTCCTCCAACCCTAG 58.795 60.000 0.00 0.00 0.00 3.02
598 601 4.055820 ACCCTAGGACCTCTAGATTCTGA 58.944 47.826 11.48 0.00 46.48 3.27
765 768 6.415867 CACAATGAGCTTAACAAAAGTGTCAG 59.584 38.462 0.00 0.00 36.80 3.51
949 953 4.289410 TCCCTGATGTCTGGAAATTGAGAA 59.711 41.667 7.43 0.00 37.15 2.87
1120 1124 6.049149 TGTATAGTTGCTAAACATCTCTGGC 58.951 40.000 0.00 0.00 38.88 4.85
1130 1134 0.754217 CATCTCTGGCCCCACATTGG 60.754 60.000 0.00 0.00 37.25 3.16
1265 1269 6.936900 TGCCTCTGGAAATATAGAAATGCTAC 59.063 38.462 0.00 0.00 0.00 3.58
1338 1342 2.057922 AGGAACATGGTGAGGAACTGT 58.942 47.619 0.00 0.00 41.55 3.55
1341 1345 0.473755 ACATGGTGAGGAACTGTGCA 59.526 50.000 0.00 0.00 41.55 4.57
1347 1351 2.887152 GGTGAGGAACTGTGCAATTCTT 59.113 45.455 0.00 0.00 41.55 2.52
1373 1377 1.726853 GGATCGGACAAGGACAAGTG 58.273 55.000 0.00 0.00 0.00 3.16
1425 1429 2.504367 CTCCAGAAACCGTTGGTGATT 58.496 47.619 0.00 0.00 35.34 2.57
1481 1485 4.719369 GACCCGTGCGCTCGTCTT 62.719 66.667 27.51 13.05 0.00 3.01
1581 1585 1.374252 CCGCTTGCTTACTGGTCGT 60.374 57.895 0.00 0.00 0.00 4.34
1790 1798 5.967674 GCTGTTGTATCAGAATATGTTGTGC 59.032 40.000 0.00 0.00 37.61 4.57
2029 2038 9.738832 GTGTACAAAAGCTTGGTAAGATTTAAA 57.261 29.630 11.56 0.00 45.50 1.52
2102 2112 6.619329 ATGCTCAGCCCCTTTTTATTTTTA 57.381 33.333 0.00 0.00 0.00 1.52
2356 2373 4.576216 TGAATACGTGCCACATTTTTGT 57.424 36.364 0.00 0.00 0.00 2.83
2359 2376 2.415697 ACGTGCCACATTTTTGTAGC 57.584 45.000 0.00 0.00 0.00 3.58
2386 2403 0.252197 GTGGGCCAATAGGTCGAAGT 59.748 55.000 8.40 0.00 41.80 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 60 4.228666 AGAGAGGAAGTCAGCTAACTCCTA 59.771 45.833 7.72 0.0 31.27 2.94
223 224 8.871629 TGAGGATCAATCTACCTCTATAAGAC 57.128 38.462 0.00 0.0 45.97 3.01
582 585 5.941555 TCCTTTTCAGAATCTAGAGGTCC 57.058 43.478 0.00 0.0 0.00 4.46
598 601 9.463443 GCGTGCATAATAGATTTTAATCCTTTT 57.537 29.630 0.00 0.0 36.04 2.27
622 625 5.446709 CATCTATAGCCAAATTTCACAGCG 58.553 41.667 0.00 0.0 0.00 5.18
765 768 1.670791 TTGACCGTCCCAAACTTCAC 58.329 50.000 0.00 0.0 0.00 3.18
815 818 3.195698 CCGGCTCGGCAGTAAAGC 61.196 66.667 0.56 0.0 41.17 3.51
949 953 9.147732 GAGAAATACATGAATTTTAGGGGGAAT 57.852 33.333 0.00 0.0 0.00 3.01
1130 1134 6.652900 GCCAATCTGACTAGAGAAATATTCCC 59.347 42.308 0.00 0.0 36.14 3.97
1265 1269 3.684788 CCAGGAGGTGTTACTGAAAATCG 59.315 47.826 0.00 0.0 34.21 3.34
1373 1377 1.087501 GGTTTCCACGAAGCTCATCC 58.912 55.000 0.00 0.0 0.00 3.51
1472 1476 3.953874 TCAGAGATCTTAAGACGAGCG 57.046 47.619 7.48 0.0 0.00 5.03
1481 1485 6.295745 GCCCATCATCTTCATCAGAGATCTTA 60.296 42.308 0.00 0.0 33.87 2.10
1770 1778 7.119116 ACGAAAGCACAACATATTCTGATACAA 59.881 33.333 0.00 0.0 0.00 2.41
1790 1798 3.365364 GGTTCCATTGCTGAGAACGAAAG 60.365 47.826 0.00 0.0 40.62 2.62
2067 2076 5.662657 AGGGGCTGAGCATTTTGTTATAAAT 59.337 36.000 6.82 0.0 0.00 1.40
2068 2077 5.022787 AGGGGCTGAGCATTTTGTTATAAA 58.977 37.500 6.82 0.0 0.00 1.40
2102 2112 2.102578 GTTGGGCCAGCAATGTTATCT 58.897 47.619 16.19 0.0 0.00 1.98
2211 2221 4.530857 GTAGCGTCCATGCGGCCT 62.531 66.667 0.00 0.0 40.67 5.19
2356 2373 0.407528 TTGGCCCACATTTCAGGCTA 59.592 50.000 0.00 0.0 46.31 3.93
2359 2376 2.034124 CCTATTGGCCCACATTTCAGG 58.966 52.381 0.00 0.0 0.00 3.86
2386 2403 4.566545 AATTGACAACGACTTGCATTGA 57.433 36.364 4.06 0.0 0.00 2.57


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

AutoCloner maintained by Alex Coulton.