Multiple sequence alignment - TraesCS6B01G400100

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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 TraesCS6B01G400100 chr6B 100.000 2261 0 0 310 2570 675570294 675572554 0.000000 4176.0
1 TraesCS6B01G400100 chr6B 100.000 32 0 0 1 32 675569985 675570016 0.000028 60.2
2 TraesCS6B01G400100 chr1A 98.186 2260 37 2 312 2570 491377764 491380020 0.000000 3943.0
3 TraesCS6B01G400100 chr1A 100.000 32 0 0 1 32 491377700 491377731 0.000028 60.2
4 TraesCS6B01G400100 chr2A 98.099 2262 37 4 312 2570 41620090 41617832 0.000000 3934.0
5 TraesCS6B01G400100 chr2A 100.000 32 0 0 1 32 41620154 41620123 0.000028 60.2
6 TraesCS6B01G400100 chr5A 97.832 2260 42 5 314 2570 522984869 522987124 0.000000 3895.0
7 TraesCS6B01G400100 chr5A 98.146 1888 32 3 686 2570 480140682 480138795 0.000000 3290.0
8 TraesCS6B01G400100 chr2B 97.746 2263 43 6 312 2570 721362373 721360115 0.000000 3890.0
9 TraesCS6B01G400100 chr2B 100.000 32 0 0 1 32 70808026 70808057 0.000028 60.2
10 TraesCS6B01G400100 chr2B 100.000 32 0 0 1 32 726990116 726990147 0.000028 60.2
11 TraesCS6B01G400100 chr2B 100.000 32 0 0 1 32 767302994 767302963 0.000028 60.2
12 TraesCS6B01G400100 chr2B 100.000 32 0 0 1 32 775142727 775142758 0.000028 60.2
13 TraesCS6B01G400100 chr1B 97.700 2261 45 5 314 2570 636803889 636806146 0.000000 3880.0
14 TraesCS6B01G400100 chr1B 96.979 662 17 1 312 973 659750631 659751289 0.000000 1109.0
15 TraesCS6B01G400100 chr1B 100.000 32 0 0 1 32 659750567 659750598 0.000028 60.2
16 TraesCS6B01G400100 chr5B 98.031 2235 38 4 339 2570 375732632 375730401 0.000000 3879.0
17 TraesCS6B01G400100 chr5B 97.656 2261 48 3 312 2570 606865444 606863187 0.000000 3877.0
18 TraesCS6B01G400100 chr5B 97.302 2261 55 4 312 2570 503878170 503880426 0.000000 3832.0
19 TraesCS6B01G400100 chr7B 100.000 32 0 0 1 32 513247825 513247856 0.000028 60.2
20 TraesCS6B01G400100 chr2D 100.000 32 0 0 1 32 91167655 91167686 0.000028 60.2


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 TraesCS6B01G400100 chr6B 675569985 675572554 2569 False 2118.1 4176 100.0000 1 2570 2 chr6B.!!$F1 2569
1 TraesCS6B01G400100 chr1A 491377700 491380020 2320 False 2001.6 3943 99.0930 1 2570 2 chr1A.!!$F1 2569
2 TraesCS6B01G400100 chr2A 41617832 41620154 2322 True 1997.1 3934 99.0495 1 2570 2 chr2A.!!$R1 2569
3 TraesCS6B01G400100 chr5A 522984869 522987124 2255 False 3895.0 3895 97.8320 314 2570 1 chr5A.!!$F1 2256
4 TraesCS6B01G400100 chr5A 480138795 480140682 1887 True 3290.0 3290 98.1460 686 2570 1 chr5A.!!$R1 1884
5 TraesCS6B01G400100 chr2B 721360115 721362373 2258 True 3890.0 3890 97.7460 312 2570 1 chr2B.!!$R1 2258
6 TraesCS6B01G400100 chr1B 636803889 636806146 2257 False 3880.0 3880 97.7000 314 2570 1 chr1B.!!$F1 2256
7 TraesCS6B01G400100 chr1B 659750567 659751289 722 False 584.6 1109 98.4895 1 973 2 chr1B.!!$F2 972
8 TraesCS6B01G400100 chr5B 375730401 375732632 2231 True 3879.0 3879 98.0310 339 2570 1 chr5B.!!$R1 2231
9 TraesCS6B01G400100 chr5B 606863187 606865444 2257 True 3877.0 3877 97.6560 312 2570 1 chr5B.!!$R2 2258
10 TraesCS6B01G400100 chr5B 503878170 503880426 2256 False 3832.0 3832 97.3020 312 2570 1 chr5B.!!$F1 2258

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
680 681 1.000521 TGGGCTGATTCCTTGCAGG 60.001 57.895 0.0 0.0 36.46 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2093 2100 3.165875 AGAGTTCTTCATCGTCCAAGGA 58.834 45.455 0.0 0.0 0.0 3.36 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
643 644 3.181501 CCGATGCGGTGTGTTAATTTCAT 60.182 43.478 0.00 0.00 42.73 2.57
680 681 1.000521 TGGGCTGATTCCTTGCAGG 60.001 57.895 0.00 0.00 36.46 4.85
857 858 4.441634 CCGACACTACAGGGATCCTAAAAG 60.442 50.000 12.58 7.38 29.64 2.27
1137 1139 4.798574 AGGTGACGAATTTTTCAGATTGC 58.201 39.130 0.00 0.00 0.00 3.56
1196 1198 4.381411 GAAGATCCTGCCGTAGCTATTTT 58.619 43.478 0.00 0.00 40.80 1.82
1899 1905 9.189156 CATTTTCTTTCCCTCCACTAATTATCA 57.811 33.333 0.00 0.00 0.00 2.15
2093 2100 4.202202 CCTTCGAGGATGCAGAACTCTTAT 60.202 45.833 11.70 0.00 37.67 1.73
2318 2325 1.922447 TCCACCTTGCATCCAACCTAT 59.078 47.619 0.00 0.00 0.00 2.57
2434 2441 3.967326 TGAGATCGTCCCATGGAACTATT 59.033 43.478 15.22 0.00 31.38 1.73
2505 2512 4.884668 TCCCAGAGTGAAAACTACGATT 57.115 40.909 0.00 0.00 0.00 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
442 443 4.694233 ACCGAGCAGCACCAGCAG 62.694 66.667 0.00 0.00 45.49 4.24
443 444 4.254709 AACCGAGCAGCACCAGCA 62.255 61.111 0.00 0.00 45.49 4.41
634 635 2.722094 ACAGCGAGCCCATGAAATTAA 58.278 42.857 0.00 0.00 0.00 1.40
643 644 2.518112 TTTGCAACAGCGAGCCCA 60.518 55.556 0.00 0.00 0.00 5.36
680 681 0.674895 GGTCACACTGCAGATCCACC 60.675 60.000 23.35 16.27 0.00 4.61
808 809 0.883833 AGAACCAAAAGCAGGCATCG 59.116 50.000 0.00 0.00 0.00 3.84
857 858 2.104963 ACAGAGGAAATTAGGCGGGATC 59.895 50.000 0.00 0.00 0.00 3.36
1137 1139 5.292589 GCATATGAAAAACTTCATGCCCAAG 59.707 40.000 6.97 0.00 41.38 3.61
1158 1160 3.213206 TCTTCCTCATAATTGGCGCAT 57.787 42.857 10.83 0.00 0.00 4.73
1196 1198 1.376543 CGGAGGCTTGTCGTACTCTA 58.623 55.000 0.00 0.00 0.00 2.43
1347 1350 1.738365 CGAATCTCAGTCACTGCCCAG 60.738 57.143 0.00 0.00 0.00 4.45
1899 1905 5.621197 TTTATAGTTGTTGCACGATGCTT 57.379 34.783 10.54 0.00 45.31 3.91
2093 2100 3.165875 AGAGTTCTTCATCGTCCAAGGA 58.834 45.455 0.00 0.00 0.00 3.36
2318 2325 4.828939 TGAGGAGGTACGTAAAGAACTTCA 59.171 41.667 0.00 0.00 0.00 3.02
2434 2441 4.408921 ACCGATTTCAGGATGGACAATAGA 59.591 41.667 0.00 0.00 36.16 1.98
2490 2497 8.842358 TTATCCTTTCAATCGTAGTTTTCACT 57.158 30.769 0.00 0.00 36.99 3.41
2505 2512 4.653801 TCGAGATGTCCCATTATCCTTTCA 59.346 41.667 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.