Multiple sequence alignment - TraesCS3D01G212300

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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 TraesCS3D01G212300 chr3D 100.000 4103 0 0 1 4103 285004660 285008762 0 7577
1 TraesCS3D01G212300 chr3D 91.287 769 56 7 3338 4101 606795842 606795080 0 1038
2 TraesCS3D01G212300 chr3B 95.742 3382 67 19 1 3339 378210515 378207168 0 5376
3 TraesCS3D01G212300 chr3A 95.862 2513 79 12 840 3336 372457643 372460146 0 4041
4 TraesCS3D01G212300 chr3A 87.388 896 33 20 18 880 372456783 372457631 0 955
5 TraesCS3D01G212300 chr7D 96.489 769 24 3 3336 4103 528085014 528085780 0 1267
6 TraesCS3D01G212300 chr6D 96.340 765 26 2 3340 4103 389352727 389353490 0 1256
7 TraesCS3D01G212300 chr2D 96.104 770 29 1 3335 4103 555578981 555579750 0 1254
8 TraesCS3D01G212300 chr2D 91.591 773 56 8 3337 4102 174448904 174449674 0 1059
9 TraesCS3D01G212300 chr1B 94.057 774 42 4 3333 4103 33920561 33919789 0 1171
10 TraesCS3D01G212300 chr2B 94.133 767 42 3 3339 4103 682843278 682844043 0 1164
11 TraesCS3D01G212300 chr5B 93.872 767 44 3 3339 4103 612690610 612689845 0 1153
12 TraesCS3D01G212300 chr1D 90.921 771 63 5 3334 4099 457085878 457085110 0 1029


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 TraesCS3D01G212300 chr3D 285004660 285008762 4102 False 7577 7577 100.000 1 4103 1 chr3D.!!$F1 4102
1 TraesCS3D01G212300 chr3D 606795080 606795842 762 True 1038 1038 91.287 3338 4101 1 chr3D.!!$R1 763
2 TraesCS3D01G212300 chr3B 378207168 378210515 3347 True 5376 5376 95.742 1 3339 1 chr3B.!!$R1 3338
3 TraesCS3D01G212300 chr3A 372456783 372460146 3363 False 2498 4041 91.625 18 3336 2 chr3A.!!$F1 3318
4 TraesCS3D01G212300 chr7D 528085014 528085780 766 False 1267 1267 96.489 3336 4103 1 chr7D.!!$F1 767
5 TraesCS3D01G212300 chr6D 389352727 389353490 763 False 1256 1256 96.340 3340 4103 1 chr6D.!!$F1 763
6 TraesCS3D01G212300 chr2D 555578981 555579750 769 False 1254 1254 96.104 3335 4103 1 chr2D.!!$F2 768
7 TraesCS3D01G212300 chr2D 174448904 174449674 770 False 1059 1059 91.591 3337 4102 1 chr2D.!!$F1 765
8 TraesCS3D01G212300 chr1B 33919789 33920561 772 True 1171 1171 94.057 3333 4103 1 chr1B.!!$R1 770
9 TraesCS3D01G212300 chr2B 682843278 682844043 765 False 1164 1164 94.133 3339 4103 1 chr2B.!!$F1 764
10 TraesCS3D01G212300 chr5B 612689845 612690610 765 True 1153 1153 93.872 3339 4103 1 chr5B.!!$R1 764
11 TraesCS3D01G212300 chr1D 457085110 457085878 768 True 1029 1029 90.921 3334 4099 1 chr1D.!!$R1 765

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
922 1023 1.014044 CATTTTGCTGCTGCTGCCTG 61.014 55.000 25.44 14.84 40.48 4.85 F
1927 2039 1.079490 AGATGGTTGAGGTGGAGGAGA 59.921 52.381 0.00 0.00 0.00 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2117 2229 3.539604 GGGTGATTGATCTCTTCCACTG 58.460 50.0 0.0 0.0 0.00 3.66 R
3657 3778 1.346062 TGCAAGGAGACTGAGCTTCT 58.654 50.0 0.0 0.0 42.68 2.85 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
65 68 5.659440 TGTGGATTGGAAGGCTAAATTTC 57.341 39.130 0.00 0.00 0.00 2.17
391 407 2.662700 CAGACAATATACTCCGACGGC 58.337 52.381 9.66 0.00 0.00 5.68
393 409 2.891580 AGACAATATACTCCGACGGCAT 59.108 45.455 9.66 4.89 0.00 4.40
520 546 5.450688 GGATGCAACTACTACACTAGTCCTG 60.451 48.000 0.00 0.00 40.14 3.86
531 558 3.162666 CACTAGTCCTGGTGTACTTGGA 58.837 50.000 0.00 0.00 37.30 3.53
728 775 7.344441 CCGTTTTCTTCAACCAAAATCATTTC 58.656 34.615 0.00 0.00 0.00 2.17
770 817 1.600485 ACCGGACAAACAACTTAAGCG 59.400 47.619 9.46 0.00 0.00 4.68
775 822 4.084223 CGGACAAACAACTTAAGCGTGTAT 60.084 41.667 11.64 3.02 0.00 2.29
920 1021 1.740296 CCATTTTGCTGCTGCTGCC 60.740 57.895 25.44 10.66 40.48 4.85
921 1022 1.292223 CATTTTGCTGCTGCTGCCT 59.708 52.632 25.44 7.86 40.48 4.75
922 1023 1.014044 CATTTTGCTGCTGCTGCCTG 61.014 55.000 25.44 14.84 40.48 4.85
923 1024 2.781595 ATTTTGCTGCTGCTGCCTGC 62.782 55.000 25.44 18.74 40.48 4.85
924 1025 4.968766 TTGCTGCTGCTGCCTGCT 62.969 61.111 25.44 0.00 43.37 4.24
1221 1330 3.626924 AAGAGCGGCTGGGACGTT 61.627 61.111 7.50 0.00 35.91 3.99
1539 1651 4.450122 TGGCGCTCGTACGACGAC 62.450 66.667 30.43 29.10 46.73 4.34
1927 2039 1.079490 AGATGGTTGAGGTGGAGGAGA 59.921 52.381 0.00 0.00 0.00 3.71
2117 2229 5.187967 TGGAAGAAGTGGAGAAGGAGATTAC 59.812 44.000 0.00 0.00 0.00 1.89
2343 2455 2.518349 CACCACCACCACCACCAC 60.518 66.667 0.00 0.00 0.00 4.16
2968 3080 0.394080 GCTGCAGATCCAAGAAGGCT 60.394 55.000 20.43 0.00 37.29 4.58
3007 3119 0.976073 GGAGGACGGGGAGTTCATGA 60.976 60.000 0.00 0.00 0.00 3.07
3033 3145 1.137282 GGGTCCCTCTTCGAAGATGAC 59.863 57.143 30.88 30.88 35.73 3.06
3271 3390 8.066612 AGATTTGGTTCACTTTTCTTCTCAAA 57.933 30.769 0.00 0.00 0.00 2.69
3336 3455 3.201487 TGATTGCTTGTGGAGAGGATGAT 59.799 43.478 0.00 0.00 0.00 2.45
3539 3660 2.655364 CGCCGCGTCTTGATCGAT 60.655 61.111 4.92 0.00 0.00 3.59
3824 3945 0.041238 TCCAGAGAGGGGAACGACAT 59.959 55.000 0.00 0.00 38.24 3.06
3935 4059 1.448540 CGTTCCTGAAGCCTCGCAT 60.449 57.895 0.00 0.00 0.00 4.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
391 407 2.285220 GCAGTACAATGCACGGTCTATG 59.715 50.000 2.40 0.00 45.77 2.23
393 409 2.004583 GCAGTACAATGCACGGTCTA 57.995 50.000 2.40 0.00 45.77 2.59
520 546 1.345415 TCCTTCGGTTCCAAGTACACC 59.655 52.381 0.00 0.00 0.00 4.16
648 689 5.919141 GTCTATACTAGTGTAATGCGTTGGG 59.081 44.000 5.39 0.00 31.80 4.12
770 817 1.757699 GAGGTGAGGGGAGTGATACAC 59.242 57.143 0.00 0.00 34.10 2.90
775 822 1.229209 GGTGAGGTGAGGGGAGTGA 60.229 63.158 0.00 0.00 0.00 3.41
1221 1330 1.367471 CACGAGGCAGAGGTTGACA 59.633 57.895 0.00 0.00 37.23 3.58
1377 1489 3.827898 CTCGCCCAGACGTCCTCC 61.828 72.222 13.01 0.00 0.00 4.30
1530 1642 4.157958 AGCTCGGCGTCGTCGTAC 62.158 66.667 19.81 12.29 39.49 3.67
1539 1651 4.849329 GTCCGGTACAGCTCGGCG 62.849 72.222 0.00 0.00 45.31 6.46
1600 1712 3.125573 CGACGTCCTCCTGAGCGA 61.126 66.667 10.58 0.00 0.00 4.93
1660 1772 3.699894 CTGAGGCAGCGGTCTGGT 61.700 66.667 0.00 0.00 40.65 4.00
1701 1813 1.984570 CTTGGGGAGCCTCTCGACA 60.985 63.158 0.00 0.00 0.00 4.35
2117 2229 3.539604 GGGTGATTGATCTCTTCCACTG 58.460 50.000 0.00 0.00 0.00 3.66
2968 3080 4.429212 CGCCATGGTCACGGTCGA 62.429 66.667 14.67 0.00 0.00 4.20
3007 3119 1.879575 TCGAAGAGGGACCCAATGAT 58.120 50.000 14.60 0.00 0.00 2.45
3215 3334 7.576861 AAATACCTCAAATAACCCAATACCG 57.423 36.000 0.00 0.00 0.00 4.02
3657 3778 1.346062 TGCAAGGAGACTGAGCTTCT 58.654 50.000 0.00 0.00 42.68 2.85
3705 3826 2.817834 GCATGTTGGCGGCGTCTA 60.818 61.111 14.51 0.79 0.00 2.59
3863 3984 3.880047 ACGTCACGGATGAAAATCCTA 57.120 42.857 0.35 0.00 38.57 2.94


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

AutoCloner maintained by Alex Coulton.