Multiple sequence alignment - TraesCS3B01G128200

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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 TraesCS3B01G128200 chr3B 100.000 2309 0 0 1 2309 106983578 106985886 0 4265
1 TraesCS3B01G128200 chr7D 97.931 1547 30 1 1 1545 23563080 23564626 0 2678
2 TraesCS3B01G128200 chr7D 97.736 1546 33 1 1 1544 135769091 135770636 0 2660
3 TraesCS3B01G128200 chr7D 97.670 1545 34 1 1 1543 400291678 400290134 0 2652
4 TraesCS3B01G128200 chr7D 97.540 1545 36 1 1 1543 135763964 135762420 0 2641
5 TraesCS3B01G128200 chr7D 97.479 1547 37 1 1 1545 14171013 14169467 0 2639
6 TraesCS3B01G128200 chr3D 97.674 1548 34 1 1 1546 564344206 564345753 0 2658
7 TraesCS3B01G128200 chr6D 97.539 1544 36 1 1 1542 402531209 402529666 0 2639
8 TraesCS3B01G128200 chr6D 97.346 1545 39 1 1 1543 392049941 392048397 0 2625
9 TraesCS3B01G128200 chr2D 97.303 1557 38 3 1 1554 70659370 70657815 0 2639
10 TraesCS3B01G128200 chr2B 92.708 768 56 0 1542 2309 689805140 689804373 0 1109
11 TraesCS3B01G128200 chr2B 92.198 769 59 1 1542 2309 450553709 450552941 0 1086
12 TraesCS3B01G128200 chr2B 92.057 768 61 0 1542 2309 151563281 151564048 0 1081
13 TraesCS3B01G128200 chr2B 91.525 767 65 0 1543 2309 170758122 170758888 0 1057
14 TraesCS3B01G128200 chr5B 92.257 762 56 3 1542 2303 617997951 617997193 0 1077
15 TraesCS3B01G128200 chr6B 91.938 769 60 2 1542 2309 661266923 661266156 0 1075
16 TraesCS3B01G128200 chr4B 91.927 768 62 0 1542 2309 101597080 101596313 0 1075
17 TraesCS3B01G128200 chr1B 91.797 768 63 0 1542 2309 645652107 645651340 0 1070
18 TraesCS3B01G128200 chr7B 91.547 769 64 1 1542 2309 100821963 100821195 0 1059


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 TraesCS3B01G128200 chr3B 106983578 106985886 2308 False 4265 4265 100.000 1 2309 1 chr3B.!!$F1 2308
1 TraesCS3B01G128200 chr7D 23563080 23564626 1546 False 2678 2678 97.931 1 1545 1 chr7D.!!$F1 1544
2 TraesCS3B01G128200 chr7D 135769091 135770636 1545 False 2660 2660 97.736 1 1544 1 chr7D.!!$F2 1543
3 TraesCS3B01G128200 chr7D 400290134 400291678 1544 True 2652 2652 97.670 1 1543 1 chr7D.!!$R3 1542
4 TraesCS3B01G128200 chr7D 135762420 135763964 1544 True 2641 2641 97.540 1 1543 1 chr7D.!!$R2 1542
5 TraesCS3B01G128200 chr7D 14169467 14171013 1546 True 2639 2639 97.479 1 1545 1 chr7D.!!$R1 1544
6 TraesCS3B01G128200 chr3D 564344206 564345753 1547 False 2658 2658 97.674 1 1546 1 chr3D.!!$F1 1545
7 TraesCS3B01G128200 chr6D 402529666 402531209 1543 True 2639 2639 97.539 1 1542 1 chr6D.!!$R2 1541
8 TraesCS3B01G128200 chr6D 392048397 392049941 1544 True 2625 2625 97.346 1 1543 1 chr6D.!!$R1 1542
9 TraesCS3B01G128200 chr2D 70657815 70659370 1555 True 2639 2639 97.303 1 1554 1 chr2D.!!$R1 1553
10 TraesCS3B01G128200 chr2B 689804373 689805140 767 True 1109 1109 92.708 1542 2309 1 chr2B.!!$R2 767
11 TraesCS3B01G128200 chr2B 450552941 450553709 768 True 1086 1086 92.198 1542 2309 1 chr2B.!!$R1 767
12 TraesCS3B01G128200 chr2B 151563281 151564048 767 False 1081 1081 92.057 1542 2309 1 chr2B.!!$F1 767
13 TraesCS3B01G128200 chr2B 170758122 170758888 766 False 1057 1057 91.525 1543 2309 1 chr2B.!!$F2 766
14 TraesCS3B01G128200 chr5B 617997193 617997951 758 True 1077 1077 92.257 1542 2303 1 chr5B.!!$R1 761
15 TraesCS3B01G128200 chr6B 661266156 661266923 767 True 1075 1075 91.938 1542 2309 1 chr6B.!!$R1 767
16 TraesCS3B01G128200 chr4B 101596313 101597080 767 True 1075 1075 91.927 1542 2309 1 chr4B.!!$R1 767
17 TraesCS3B01G128200 chr1B 645651340 645652107 767 True 1070 1070 91.797 1542 2309 1 chr1B.!!$R1 767
18 TraesCS3B01G128200 chr7B 100821195 100821963 768 True 1059 1059 91.547 1542 2309 1 chr7B.!!$R1 767

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
425 426 0.641783 GCGATGCAAAATCTTTGGCG 59.358 50.0 0.0 0.0 40.01 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1537 1540 0.251653 TCGAGTTGAGGTAGCAGGGT 60.252 55.0 0.0 0.0 0.0 4.34 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
278 279 9.643693 GATCATGTTCCAAAAATGACAGTTAAT 57.356 29.630 0.00 0.00 33.37 1.40
316 317 4.643334 TCGATGGGAGAGTCGAATAAAGAA 59.357 41.667 0.00 0.00 43.14 2.52
341 342 4.446994 TCAGGCTATCAGATATCAAGCG 57.553 45.455 5.32 0.00 33.96 4.68
382 383 7.449704 AGCATTACTGGAATTGAAGAGAACTTT 59.550 33.333 0.00 0.00 36.39 2.66
425 426 0.641783 GCGATGCAAAATCTTTGGCG 59.358 50.000 0.00 0.00 40.01 5.69
487 490 5.781210 TTGGCATGACATTTTGTTCACTA 57.219 34.783 0.00 0.00 0.00 2.74
617 620 5.355350 GCTTTGCAACTAGTCTGGATATTGT 59.645 40.000 0.00 0.00 0.00 2.71
664 667 3.949113 TGTACAACCTTTGTTTCCTGTCC 59.051 43.478 0.00 0.00 42.22 4.02
733 736 7.201350 GCAATGACGAAAATAACCAGAATGAAC 60.201 37.037 0.00 0.00 39.69 3.18
805 808 5.005394 GTGATGATTGATGTTGCAATTGCTC 59.995 40.000 29.37 21.65 38.53 4.26
829 832 7.371043 TCCCCTAACTACTAGATTTGAGGAAT 58.629 38.462 0.00 0.00 0.00 3.01
928 931 7.516198 AGAAGATGTTGCACTAATTTTGTCT 57.484 32.000 0.00 0.00 0.00 3.41
956 959 2.234661 TCACTCATGGTAAGTCAGCAGG 59.765 50.000 0.00 0.00 38.24 4.85
1029 1032 2.288334 GCCAAACACATTCATGTCAGCA 60.288 45.455 0.00 0.00 39.39 4.41
1334 1337 6.325028 TCACTAGAGGTTAGCATGCTATTTCT 59.675 38.462 27.35 26.54 0.00 2.52
1537 1540 3.206150 GCCTTCAAAATCATAGAGCCGA 58.794 45.455 0.00 0.00 0.00 5.54
1801 1804 4.141965 ATGATGACCGACGCGCCA 62.142 61.111 5.73 0.00 0.00 5.69
1841 1844 1.968310 GCCGGGCCAAATACAACAA 59.032 52.632 8.12 0.00 0.00 2.83
1843 1846 1.671556 GCCGGGCCAAATACAACAAAG 60.672 52.381 8.12 0.00 0.00 2.77
1988 1992 1.583556 TATGATGGCACCACAGACCT 58.416 50.000 0.00 0.00 0.00 3.85
2049 2054 0.891373 CCCGCGGAGATGATCTACAT 59.109 55.000 30.73 0.00 42.47 2.29
2117 2122 1.672881 GCTGAATAGCTTGCCGACAAT 59.327 47.619 0.00 0.00 46.57 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 3.561097 CCATTGTCATACCCTTGTCCACA 60.561 47.826 0.00 0.00 0.00 4.17
169 170 8.739972 CAACACCAAAGAAGGTAATAGCTTTAT 58.260 33.333 6.16 0.00 40.77 1.40
177 178 3.957497 TGCACAACACCAAAGAAGGTAAT 59.043 39.130 0.00 0.00 40.77 1.89
224 225 6.293135 GCAATAGCTGCCATCTTTTAGTAGAC 60.293 42.308 0.00 0.00 46.13 2.59
278 279 4.062293 CCCATCGAGTGTTACACAAAGAA 58.938 43.478 18.19 0.00 36.74 2.52
316 317 6.171921 GCTTGATATCTGATAGCCTGAACAT 58.828 40.000 10.16 0.00 0.00 2.71
341 342 3.850122 AATGCTTTTCTTAACTCGGGC 57.150 42.857 0.00 0.00 0.00 6.13
382 383 0.892755 AGTCTTGGCGTCATCGGTAA 59.107 50.000 0.00 0.00 37.56 2.85
425 426 3.542712 TCAAATTTCTCAAGTGCGCTC 57.457 42.857 9.73 4.74 0.00 5.03
487 490 6.714810 TGCAACTTCTTACTCACCATGTTTAT 59.285 34.615 0.00 0.00 0.00 1.40
617 620 5.533528 CCCATGTCAATTGCAATAGATCTCA 59.466 40.000 13.39 7.16 0.00 3.27
664 667 9.279904 CTGTCTTTTTCTAGTAATACGTCTCTG 57.720 37.037 0.00 0.00 0.00 3.35
733 736 0.381801 ACCTCACTTGCTTGCGTTTG 59.618 50.000 0.00 0.00 0.00 2.93
805 808 7.619512 ATTCCTCAAATCTAGTAGTTAGGGG 57.380 40.000 0.00 0.00 0.00 4.79
829 832 7.104939 CCAAATATGCTCCCAAATTTCTTCAA 58.895 34.615 0.00 0.00 0.00 2.69
836 839 6.625532 AGAAACCAAATATGCTCCCAAATT 57.374 33.333 0.00 0.00 0.00 1.82
928 931 6.371548 GCTGACTTACCATGAGTGAATTTGTA 59.628 38.462 0.00 0.00 0.00 2.41
956 959 6.693545 AGAAACGAAATCATCTAGATCGACAC 59.306 38.462 17.21 8.73 35.39 3.67
1522 1525 2.746472 GCAGGGTCGGCTCTATGATTTT 60.746 50.000 0.00 0.00 0.00 1.82
1537 1540 0.251653 TCGAGTTGAGGTAGCAGGGT 60.252 55.000 0.00 0.00 0.00 4.34
1620 1623 0.657368 GCTTGAACACCGCTTTGTCG 60.657 55.000 0.00 0.00 0.00 4.35
1785 1788 4.794439 CTGGCGCGTCGGTCATCA 62.794 66.667 12.39 0.00 0.00 3.07
1801 1804 4.694037 GCCGGACTTTTGTTTAGTGTATCT 59.306 41.667 5.05 0.00 0.00 1.98
1831 1834 9.545105 TTCAAATGATTCTGCTTTGTTGTATTT 57.455 25.926 0.00 0.00 32.89 1.40
1841 1844 3.254166 ACGCAGTTCAAATGATTCTGCTT 59.746 39.130 24.46 18.35 37.78 3.91
1843 1846 3.207474 ACGCAGTTCAAATGATTCTGC 57.793 42.857 20.83 20.83 37.78 4.26
1888 1891 4.109675 GCATAGGGGGTGTGCGGT 62.110 66.667 0.00 0.00 33.10 5.68
1988 1992 3.469008 AATCTTCAATCCATACCGCGA 57.531 42.857 8.23 0.00 0.00 5.87
2049 2054 2.481441 AGTGGGAGATACTTGATGGCA 58.519 47.619 0.00 0.00 0.00 4.92
2134 2139 2.622436 GAATGCGTCTGCTAGGTTCTT 58.378 47.619 0.00 0.00 43.34 2.52
2189 2195 3.106827 TGACTTAGGTCATCAGCATCCA 58.893 45.455 3.11 0.00 46.19 3.41


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

AutoCloner maintained by Alex Coulton.