Multiple sequence alignment - TraesCS5D01G221600

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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 TraesCS5D01G221600 chr5D 100.000 2684 0 0 1 2684 329191310 329193993 0.000000e+00 4957
1 TraesCS5D01G221600 chr5D 98.165 1689 30 1 997 2684 560874822 560876510 0.000000e+00 2946
2 TraesCS5D01G221600 chr5D 96.860 1688 31 5 997 2684 6198928 6197263 0.000000e+00 2804
3 TraesCS5D01G221600 chr1D 98.342 1689 27 1 997 2684 206075011 206073323 0.000000e+00 2963
4 TraesCS5D01G221600 chr1D 98.164 1688 31 0 997 2684 254500352 254502039 0.000000e+00 2946
5 TraesCS5D01G221600 chr1D 96.994 998 27 2 1 996 41841328 41840332 0.000000e+00 1674
6 TraesCS5D01G221600 chr1D 96.687 996 29 2 3 996 35929461 35928468 0.000000e+00 1653
7 TraesCS5D01G221600 chr3B 98.104 1688 32 0 997 2684 201517032 201518719 0.000000e+00 2940
8 TraesCS5D01G221600 chr6A 97.097 1688 45 1 997 2684 260130418 260128735 0.000000e+00 2843
9 TraesCS5D01G221600 chr7B 96.855 1685 52 1 997 2681 102631292 102629609 0.000000e+00 2817
10 TraesCS5D01G221600 chr4D 96.801 1688 49 2 997 2684 19918846 19920528 0.000000e+00 2813
11 TraesCS5D01G221600 chr7A 95.498 1688 70 3 997 2684 352191673 352189992 0.000000e+00 2691
12 TraesCS5D01G221600 chr2D 97.094 998 26 2 1 996 487064234 487063238 0.000000e+00 1679
13 TraesCS5D01G221600 chr2D 96.906 1002 28 2 1 1000 648406119 648405119 0.000000e+00 1676
14 TraesCS5D01G221600 chr6D 96.710 1003 29 3 1 1000 391293279 391294280 0.000000e+00 1666
15 TraesCS5D01G221600 chr6D 96.710 1003 28 4 1 1001 149294197 149293198 0.000000e+00 1664
16 TraesCS5D01G221600 chr6D 96.104 1001 35 3 1 999 464925636 464926634 0.000000e+00 1629
17 TraesCS5D01G221600 chr3D 96.697 999 29 2 1 997 590288526 590287530 0.000000e+00 1659
18 TraesCS5D01G221600 chrUn 96.293 998 33 3 1 996 157085617 157086612 0.000000e+00 1635
19 TraesCS5D01G221600 chr2A 94.483 145 8 0 997 1141 341916113 341916257 9.670000e-55 224


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 TraesCS5D01G221600 chr5D 329191310 329193993 2683 False 4957 4957 100.000 1 2684 1 chr5D.!!$F1 2683
1 TraesCS5D01G221600 chr5D 560874822 560876510 1688 False 2946 2946 98.165 997 2684 1 chr5D.!!$F2 1687
2 TraesCS5D01G221600 chr5D 6197263 6198928 1665 True 2804 2804 96.860 997 2684 1 chr5D.!!$R1 1687
3 TraesCS5D01G221600 chr1D 206073323 206075011 1688 True 2963 2963 98.342 997 2684 1 chr1D.!!$R3 1687
4 TraesCS5D01G221600 chr1D 254500352 254502039 1687 False 2946 2946 98.164 997 2684 1 chr1D.!!$F1 1687
5 TraesCS5D01G221600 chr1D 41840332 41841328 996 True 1674 1674 96.994 1 996 1 chr1D.!!$R2 995
6 TraesCS5D01G221600 chr1D 35928468 35929461 993 True 1653 1653 96.687 3 996 1 chr1D.!!$R1 993
7 TraesCS5D01G221600 chr3B 201517032 201518719 1687 False 2940 2940 98.104 997 2684 1 chr3B.!!$F1 1687
8 TraesCS5D01G221600 chr6A 260128735 260130418 1683 True 2843 2843 97.097 997 2684 1 chr6A.!!$R1 1687
9 TraesCS5D01G221600 chr7B 102629609 102631292 1683 True 2817 2817 96.855 997 2681 1 chr7B.!!$R1 1684
10 TraesCS5D01G221600 chr4D 19918846 19920528 1682 False 2813 2813 96.801 997 2684 1 chr4D.!!$F1 1687
11 TraesCS5D01G221600 chr7A 352189992 352191673 1681 True 2691 2691 95.498 997 2684 1 chr7A.!!$R1 1687
12 TraesCS5D01G221600 chr2D 487063238 487064234 996 True 1679 1679 97.094 1 996 1 chr2D.!!$R1 995
13 TraesCS5D01G221600 chr2D 648405119 648406119 1000 True 1676 1676 96.906 1 1000 1 chr2D.!!$R2 999
14 TraesCS5D01G221600 chr6D 391293279 391294280 1001 False 1666 1666 96.710 1 1000 1 chr6D.!!$F1 999
15 TraesCS5D01G221600 chr6D 149293198 149294197 999 True 1664 1664 96.710 1 1001 1 chr6D.!!$R1 1000
16 TraesCS5D01G221600 chr6D 464925636 464926634 998 False 1629 1629 96.104 1 999 1 chr6D.!!$F2 998
17 TraesCS5D01G221600 chr3D 590287530 590288526 996 True 1659 1659 96.697 1 997 1 chr3D.!!$R1 996
18 TraesCS5D01G221600 chrUn 157085617 157086612 995 False 1635 1635 96.293 1 996 1 chrUn.!!$F1 995

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
300 304 1.196127 GAGAGGGTTACGGCAAAAACG 59.804 52.381 0.0 0.0 37.36 3.6 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1945 2107 0.902531 GGATCCGGAGACACCTTTGA 59.097 55.0 11.34 0.0 36.31 2.69 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
300 304 1.196127 GAGAGGGTTACGGCAAAAACG 59.804 52.381 0.00 0.00 37.36 3.60
449 453 6.042143 TCAAAATGAACCTTTCAAAGCAGAC 58.958 36.000 0.00 0.00 43.95 3.51
500 504 6.315393 ACACACAAAAAGTCTGTAAAGATCGT 59.685 34.615 0.00 0.00 26.70 3.73
502 506 6.065153 CACAAAAAGTCTGTAAAGATCGTCG 58.935 40.000 0.00 0.00 0.00 5.12
513 517 1.771565 AGATCGTCGACCCCAACATA 58.228 50.000 10.58 0.00 0.00 2.29
629 634 4.511826 GGTCAAATTCTCTGTATAAGGGCG 59.488 45.833 0.00 0.00 0.00 6.13
652 657 6.457528 GCGTCTATTTTCATTTTGAGAGGAGG 60.458 42.308 0.00 0.00 0.00 4.30
865 870 1.553690 CCAGATGAACCGGGACCAGT 61.554 60.000 6.32 0.00 0.00 4.00
1001 1006 8.492415 TGCCCTGTTTTCTACTAGTGATATAT 57.508 34.615 5.39 0.00 0.00 0.86
1202 1208 4.186159 GCTACCGGTTTTGCTATGACTTA 58.814 43.478 15.04 0.00 0.00 2.24
1226 1232 0.602562 TACCGACCAACCGTTACAGG 59.397 55.000 0.00 0.00 37.30 4.00
1501 1508 4.819630 TCAAAATTGTGACAGGTGTACCTC 59.180 41.667 0.00 0.00 46.65 3.85
1523 1530 2.370849 ACGCCATTCCGGTAATAGGATT 59.629 45.455 0.00 0.00 37.65 3.01
1580 1587 1.547675 GGGCCAATCCACTTTGACTCA 60.548 52.381 4.39 0.00 36.21 3.41
1803 1965 7.551974 CACATGTCATTTGGATACTTCTCTTCT 59.448 37.037 0.00 0.00 37.61 2.85
1945 2107 6.040166 GGATCTGCCACATTAGAATTCACAAT 59.960 38.462 8.44 3.97 36.34 2.71
1960 2122 1.806542 CACAATCAAAGGTGTCTCCGG 59.193 52.381 0.00 0.00 41.99 5.14
2189 2351 2.892374 TCGTTGCATCGATTGTGATCT 58.108 42.857 15.58 0.00 34.85 2.75
2308 2470 4.487714 AGAAACTTGCGATATTGAGGGA 57.512 40.909 0.00 0.00 0.00 4.20
2400 2562 5.068987 GCCCACTTGGATATTGAGCATTTAA 59.931 40.000 0.00 0.00 37.39 1.52
2463 2625 9.588339 GGTGCAACTTCAGAAAAGAGAATCTGG 62.588 44.444 0.00 0.00 41.22 3.86
2637 2800 8.749354 GTTCACCTATCCCAATAACAAAGAAAT 58.251 33.333 0.00 0.00 0.00 2.17
2656 3208 7.565323 AGAAATCAGACTTAAATGATCCTGC 57.435 36.000 0.00 0.00 35.11 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 73 4.695217 TGAACACACAAAAAGTCAGGAC 57.305 40.909 0.00 0.00 0.00 3.85
367 371 9.323985 CAAGAAAATGAAATCCCTTTGTAACAA 57.676 29.630 0.00 0.00 0.00 2.83
437 441 6.206395 TCAAAATCAGTGTCTGCTTTGAAA 57.794 33.333 16.59 4.43 38.63 2.69
449 453 7.036829 TGAATATGCACCATTCAAAATCAGTG 58.963 34.615 18.56 0.00 38.98 3.66
616 621 6.474140 TGAAAATAGACGCCCTTATACAGA 57.526 37.500 0.00 0.00 0.00 3.41
629 634 7.607991 TGACCTCCTCTCAAAATGAAAATAGAC 59.392 37.037 0.00 0.00 0.00 2.59
652 657 0.687354 TCCCTCTCTGCCTTGTTGAC 59.313 55.000 0.00 0.00 0.00 3.18
706 711 0.458025 GAGTTTAGTCCCACCTCGCG 60.458 60.000 0.00 0.00 0.00 5.87
851 856 3.948719 GCCACTGGTCCCGGTTCA 61.949 66.667 0.00 0.00 32.44 3.18
1001 1006 0.032017 GAGTCCCCCTCTAAGAGCCA 60.032 60.000 0.00 0.00 37.22 4.75
1202 1208 3.509575 TGTAACGGTTGGTCGGTAGTAAT 59.490 43.478 3.07 0.00 32.61 1.89
1226 1232 1.324383 TTGAACCGAGGAAAAAGCCC 58.676 50.000 0.00 0.00 0.00 5.19
1329 1335 5.419542 AGATACACACGAAATACATGCAGT 58.580 37.500 0.00 0.00 0.00 4.40
1501 1508 1.069513 TCCTATTACCGGAATGGCGTG 59.930 52.381 9.46 0.00 43.94 5.34
1523 1530 4.186159 GCGTAATAACTCCACTAAAGGCA 58.814 43.478 0.00 0.00 0.00 4.75
1945 2107 0.902531 GGATCCGGAGACACCTTTGA 59.097 55.000 11.34 0.00 36.31 2.69
1960 2122 4.580580 GGGGACTTACATGTTGATTGGATC 59.419 45.833 2.30 0.00 0.00 3.36
2171 2333 2.096335 TGCAGATCACAATCGATGCAAC 59.904 45.455 0.00 0.00 39.06 4.17
2189 2351 7.987458 CCCTTCTTTTACTCTGATAGTATTGCA 59.013 37.037 0.00 0.00 40.41 4.08
2448 2610 8.470657 AAAAGCTTTACCAGATTCTCTTTTCT 57.529 30.769 13.10 0.00 27.99 2.52
2463 2625 5.701290 TGACTCTAGGCAAGAAAAGCTTTAC 59.299 40.000 13.10 0.06 33.60 2.01
2637 2800 8.267183 TCTTAATGCAGGATCATTTAAGTCTGA 58.733 33.333 11.50 0.00 37.75 3.27


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

AutoCloner maintained by Alex Coulton.