Multiple sequence alignment - TraesCS6A01G208600

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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 TraesCS6A01G208600 chr6A 100.000 2243 0 0 1 2243 375860759 375858517 0 4143
1 TraesCS6A01G208600 chr6A 96.301 2244 82 1 1 2243 155857299 155859542 0 3683
2 TraesCS6A01G208600 chr4B 96.704 2245 71 3 1 2243 209242557 209244800 0 3733
3 TraesCS6A01G208600 chr3B 96.481 2245 76 3 1 2243 483333212 483335455 0 3705
4 TraesCS6A01G208600 chr3B 95.948 2246 87 3 1 2243 575839742 575837498 0 3640
5 TraesCS6A01G208600 chr2A 96.437 2245 78 2 1 2243 750453591 750451347 0 3701
6 TraesCS6A01G208600 chr2A 97.246 1307 35 1 1 1306 755480549 755481855 0 2213
7 TraesCS6A01G208600 chr4A 95.856 2244 92 1 1 2243 350172240 350174483 0 3627
8 TraesCS6A01G208600 chr3A 95.396 2020 80 6 235 2243 230228527 230226510 0 3203
9 TraesCS6A01G208600 chr7A 97.169 1307 36 1 1 1306 60084936 60086242 0 2207
10 TraesCS6A01G208600 chr7D 97.895 1045 20 2 1201 2243 626650505 626651549 0 1807
11 TraesCS6A01G208600 chr2D 97.799 1045 21 2 1201 2243 635067377 635066333 0 1801
12 TraesCS6A01G208600 chr6B 92.424 726 51 4 1055 1778 401858416 401859139 0 1033


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 TraesCS6A01G208600 chr6A 375858517 375860759 2242 True 4143 4143 100.000 1 2243 1 chr6A.!!$R1 2242
1 TraesCS6A01G208600 chr6A 155857299 155859542 2243 False 3683 3683 96.301 1 2243 1 chr6A.!!$F1 2242
2 TraesCS6A01G208600 chr4B 209242557 209244800 2243 False 3733 3733 96.704 1 2243 1 chr4B.!!$F1 2242
3 TraesCS6A01G208600 chr3B 483333212 483335455 2243 False 3705 3705 96.481 1 2243 1 chr3B.!!$F1 2242
4 TraesCS6A01G208600 chr3B 575837498 575839742 2244 True 3640 3640 95.948 1 2243 1 chr3B.!!$R1 2242
5 TraesCS6A01G208600 chr2A 750451347 750453591 2244 True 3701 3701 96.437 1 2243 1 chr2A.!!$R1 2242
6 TraesCS6A01G208600 chr2A 755480549 755481855 1306 False 2213 2213 97.246 1 1306 1 chr2A.!!$F1 1305
7 TraesCS6A01G208600 chr4A 350172240 350174483 2243 False 3627 3627 95.856 1 2243 1 chr4A.!!$F1 2242
8 TraesCS6A01G208600 chr3A 230226510 230228527 2017 True 3203 3203 95.396 235 2243 1 chr3A.!!$R1 2008
9 TraesCS6A01G208600 chr7A 60084936 60086242 1306 False 2207 2207 97.169 1 1306 1 chr7A.!!$F1 1305
10 TraesCS6A01G208600 chr7D 626650505 626651549 1044 False 1807 1807 97.895 1201 2243 1 chr7D.!!$F1 1042
11 TraesCS6A01G208600 chr2D 635066333 635067377 1044 True 1801 1801 97.799 1201 2243 1 chr2D.!!$R1 1042
12 TraesCS6A01G208600 chr6B 401858416 401859139 723 False 1033 1033 92.424 1055 1778 1 chr6B.!!$F1 723

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
574 576 1.138266 GCCCCTTACTCGCAGATGTAA 59.862 52.381 0.0 0.0 33.89 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1565 1572 0.902984 GGAAAAACAGGCCCCGGATT 60.903 55.0 0.73 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
106 108 6.510317 GCTCTTTTATCGCAGAATTAGACCAC 60.510 42.308 0.00 0.00 43.58 4.16
395 397 3.132824 TGTGATCGAATGCCACTAGACAT 59.867 43.478 0.00 0.00 0.00 3.06
574 576 1.138266 GCCCCTTACTCGCAGATGTAA 59.862 52.381 0.00 0.00 33.89 2.41
589 591 5.182001 GCAGATGTAAGAAGAAGGCTTTTCA 59.818 40.000 18.02 2.85 33.61 2.69
618 620 5.589831 ACTGAACCCCAATAGGCTATTTTT 58.410 37.500 16.95 8.16 0.00 1.94
678 682 1.804151 CTTGCGTAAACCAAGCTGCTA 59.196 47.619 0.90 0.00 34.00 3.49
679 683 2.107950 TGCGTAAACCAAGCTGCTAT 57.892 45.000 0.90 0.00 32.19 2.97
690 694 2.697751 CAAGCTGCTATGAGTCTACCCT 59.302 50.000 0.90 0.00 0.00 4.34
898 902 5.746721 GTCCGCATAACCCAATATTTGAAAC 59.253 40.000 0.00 0.00 0.00 2.78
1034 1038 3.494398 GCTAAATCAATAGGTGCCGGAGA 60.494 47.826 5.05 0.00 0.00 3.71
1053 1057 4.521943 GAGATGCTACAATTGCTTTAGCG 58.478 43.478 17.07 0.00 45.83 4.26
1089 1093 2.992124 TTGGAAACGTCCTCAGTTCA 57.008 45.000 0.00 0.00 45.22 3.18
1186 1190 4.022416 TCACCGAAGCTATTGCATTGTTTT 60.022 37.500 1.12 0.00 42.74 2.43
1565 1572 3.220110 AGGCGAGACATAAGTTATCGGA 58.780 45.455 5.93 0.00 37.58 4.55
1586 1594 2.203567 CGGGGCCTGTTTTTCCCA 60.204 61.111 3.48 0.00 41.85 4.37
1658 1666 4.751600 CAGAAAGTTTTGGAAAATGGAGCC 59.248 41.667 0.00 0.00 0.00 4.70
1690 1698 3.635836 ACTACTTTGGTCCCTAGCGATAC 59.364 47.826 0.00 0.00 0.00 2.24
1871 1879 1.328680 GTATCGTTGCTGCATCACCAG 59.671 52.381 1.84 0.00 35.93 4.00
1944 1952 3.181476 CCAGTTGCTTAGTGGTTTGCTTT 60.181 43.478 5.41 0.00 41.70 3.51
1950 1958 3.628017 CTTAGTGGTTTGCTTTTCGGTG 58.372 45.455 0.00 0.00 0.00 4.94
2065 2073 3.565307 GGCCTACAATCCATGGAAATCA 58.435 45.455 20.67 3.90 0.00 2.57
2091 2099 3.107601 TCCGATCACTGGGAAAGAAGAT 58.892 45.455 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
106 108 4.374399 ACGGATAAGCCAACGTTAATAGG 58.626 43.478 0.00 0.00 35.90 2.57
300 302 6.084326 AGTGGTTCATATTGTGGTTGTTTC 57.916 37.500 0.00 0.00 0.00 2.78
346 348 6.055588 AGCCGTTGACAGTAGCATAAATTAT 58.944 36.000 0.00 0.00 0.00 1.28
348 350 4.261801 AGCCGTTGACAGTAGCATAAATT 58.738 39.130 0.00 0.00 0.00 1.82
358 360 0.464036 TCACAGAAGCCGTTGACAGT 59.536 50.000 0.00 0.00 0.00 3.55
414 416 7.232941 TCAGGATTACTAGTACTTAGAATGGCC 59.767 40.741 0.00 0.00 33.39 5.36
589 591 0.402504 TATTGGGGTTCAGTTGGCGT 59.597 50.000 0.00 0.00 0.00 5.68
659 663 1.885560 TAGCAGCTTGGTTTACGCAA 58.114 45.000 0.00 0.00 0.00 4.85
678 682 2.848678 TGTGGCTAGGGTAGACTCAT 57.151 50.000 0.00 0.00 32.75 2.90
679 683 2.457598 CTTGTGGCTAGGGTAGACTCA 58.542 52.381 0.00 0.00 35.66 3.41
690 694 2.124996 AGCTCCCCCTTGTGGCTA 59.875 61.111 0.00 0.00 0.00 3.93
787 791 9.645128 ATGTGGATTGAAAATCATCAGGTATAA 57.355 29.630 2.66 0.00 0.00 0.98
822 826 5.009631 TGCAAGGCTTGTCACATAGTAAAT 58.990 37.500 26.71 0.00 0.00 1.40
827 831 3.921119 TTTGCAAGGCTTGTCACATAG 57.079 42.857 26.71 0.79 0.00 2.23
898 902 1.152881 GGGCCTGCACCTCCATAAG 60.153 63.158 0.84 0.00 0.00 1.73
1034 1038 2.358898 CCCGCTAAAGCAATTGTAGCAT 59.641 45.455 20.33 3.10 40.23 3.79
1053 1057 0.811616 CAATACCGACAGCAGCTCCC 60.812 60.000 0.00 0.00 0.00 4.30
1089 1093 0.381801 GCGCCACGGAATGAATCAAT 59.618 50.000 0.00 0.00 0.00 2.57
1186 1190 1.009997 AGAAAGGCCATCATTGGGGA 58.990 50.000 5.01 0.00 43.84 4.81
1255 1261 9.990360 TTTACATCTGTAACTACATTCTCACAA 57.010 29.630 2.33 0.00 39.92 3.33
1565 1572 0.902984 GGAAAAACAGGCCCCGGATT 60.903 55.000 0.73 0.00 0.00 3.01
1627 1635 9.403110 CATTTTCCAAAACTTTCTGTCTCATAG 57.597 33.333 0.00 0.00 0.00 2.23
1658 1666 3.365969 GGACCAAAGTAGTGAAAATGGCG 60.366 47.826 0.00 0.00 0.00 5.69
1662 1670 5.254115 GCTAGGGACCAAAGTAGTGAAAAT 58.746 41.667 0.00 0.00 0.00 1.82
1690 1698 7.379529 CACTTTCCATGTTAGTTTAAGCAACAG 59.620 37.037 10.96 5.84 37.93 3.16
1871 1879 3.426292 GGAAAAGCAAGTCAGGAATACGC 60.426 47.826 0.00 0.00 0.00 4.42
1944 1952 1.700739 ACCTTGATTGGGTACACCGAA 59.299 47.619 0.00 0.00 44.64 4.30
2065 2073 4.030913 TCTTTCCCAGTGATCGGAATAGT 58.969 43.478 1.24 0.00 37.96 2.12


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

AutoCloner maintained by Alex Coulton.