Multiple sequence alignment - TraesCS5B01G521400

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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 TraesCS5B01G521400 chr5B 100.000 2295 0 0 1 2295 683476612 683474318 0 4239
1 TraesCS5B01G521400 chr5B 96.709 2309 59 5 1 2295 538727037 538729342 0 3827
2 TraesCS5B01G521400 chr5B 96.405 2309 55 6 1 2295 42684468 42682174 0 3779
3 TraesCS5B01G521400 chr5B 96.090 2302 74 6 9 2295 511449591 511451891 0 3738
4 TraesCS5B01G521400 chr5B 95.862 2296 74 6 14 2295 427657201 427654913 0 3694
5 TraesCS5B01G521400 chr5B 95.669 2309 74 7 1 2295 419841065 419838769 0 3687
6 TraesCS5B01G521400 chr7B 96.884 2311 42 9 1 2295 679986321 679984025 0 3842
7 TraesCS5B01G521400 chr2B 96.232 2309 70 5 1 2295 215482686 215484991 0 3766
8 TraesCS5B01G521400 chr2B 96.035 2295 74 6 17 2295 152572079 152574372 0 3718
9 TraesCS5B01G521400 chr1B 95.853 2315 71 8 3 2295 331365106 331367417 0 3720
10 TraesCS5B01G521400 chr6B 95.455 2310 85 8 1 2295 624871085 624873389 0 3666
11 TraesCS5B01G521400 chr1D 94.957 2320 83 6 1 2295 467317329 467319639 0 3605
12 TraesCS5B01G521400 chr3B 96.606 1915 41 10 14 1914 478320273 478318369 0 3155
13 TraesCS5B01G521400 chr4B 95.449 1604 56 6 1 1590 581852350 581850750 0 2542
14 TraesCS5B01G521400 chr4B 95.783 1067 28 6 1 1053 457047817 457046754 0 1705


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 TraesCS5B01G521400 chr5B 683474318 683476612 2294 True 4239 4239 100.000 1 2295 1 chr5B.!!$R4 2294
1 TraesCS5B01G521400 chr5B 538727037 538729342 2305 False 3827 3827 96.709 1 2295 1 chr5B.!!$F2 2294
2 TraesCS5B01G521400 chr5B 42682174 42684468 2294 True 3779 3779 96.405 1 2295 1 chr5B.!!$R1 2294
3 TraesCS5B01G521400 chr5B 511449591 511451891 2300 False 3738 3738 96.090 9 2295 1 chr5B.!!$F1 2286
4 TraesCS5B01G521400 chr5B 427654913 427657201 2288 True 3694 3694 95.862 14 2295 1 chr5B.!!$R3 2281
5 TraesCS5B01G521400 chr5B 419838769 419841065 2296 True 3687 3687 95.669 1 2295 1 chr5B.!!$R2 2294
6 TraesCS5B01G521400 chr7B 679984025 679986321 2296 True 3842 3842 96.884 1 2295 1 chr7B.!!$R1 2294
7 TraesCS5B01G521400 chr2B 215482686 215484991 2305 False 3766 3766 96.232 1 2295 1 chr2B.!!$F2 2294
8 TraesCS5B01G521400 chr2B 152572079 152574372 2293 False 3718 3718 96.035 17 2295 1 chr2B.!!$F1 2278
9 TraesCS5B01G521400 chr1B 331365106 331367417 2311 False 3720 3720 95.853 3 2295 1 chr1B.!!$F1 2292
10 TraesCS5B01G521400 chr6B 624871085 624873389 2304 False 3666 3666 95.455 1 2295 1 chr6B.!!$F1 2294
11 TraesCS5B01G521400 chr1D 467317329 467319639 2310 False 3605 3605 94.957 1 2295 1 chr1D.!!$F1 2294
12 TraesCS5B01G521400 chr3B 478318369 478320273 1904 True 3155 3155 96.606 14 1914 1 chr3B.!!$R1 1900
13 TraesCS5B01G521400 chr4B 581850750 581852350 1600 True 2542 2542 95.449 1 1590 1 chr4B.!!$R2 1589
14 TraesCS5B01G521400 chr4B 457046754 457047817 1063 True 1705 1705 95.783 1 1053 1 chr4B.!!$R1 1052

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
701 734 0.535335 GCATACAAGGAGACGGTGGA 59.465 55.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1667 1702 1.134946 ACATCTTAAATGCGGCTTGCC 59.865 47.619 0.0 0.75 45.6 4.52 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
39 40 4.013050 CTCTCAAATCCTCTCCCAAAACC 58.987 47.826 0.00 0.0 0.00 3.27
403 422 6.202331 TCCTTGGATTAGTACTCATGGAAGA 58.798 40.000 12.08 0.0 32.75 2.87
498 531 1.683629 GGCAATATTGAACCGGACCCA 60.684 52.381 19.73 0.0 0.00 4.51
701 734 0.535335 GCATACAAGGAGACGGTGGA 59.465 55.000 0.00 0.0 0.00 4.02
709 742 1.697432 AGGAGACGGTGGACAAATCAA 59.303 47.619 0.00 0.0 0.00 2.57
720 753 4.016444 TGGACAAATCAATAGACAAGGCC 58.984 43.478 0.00 0.0 0.00 5.19
746 779 5.713025 TGAGTTATTTGCAATGAAGAAGGC 58.287 37.500 0.00 0.0 0.00 4.35
1045 1079 1.784062 GCATATGCATCGGACTCGC 59.216 57.895 22.84 0.0 41.59 5.03
1127 1162 4.020128 AGCTTTTGAGAAGGTATTCGGTCT 60.020 41.667 0.00 0.0 40.58 3.85
1128 1163 4.330347 GCTTTTGAGAAGGTATTCGGTCTC 59.670 45.833 0.00 0.0 40.58 3.36
1251 1286 4.637534 CGTGATTTGGGAGATGACAAGAAT 59.362 41.667 0.00 0.0 0.00 2.40
1252 1287 5.817296 CGTGATTTGGGAGATGACAAGAATA 59.183 40.000 0.00 0.0 0.00 1.75
1413 1448 6.929049 GTGAAGATGAAATATGTCCGTGGATA 59.071 38.462 0.00 0.0 0.00 2.59
1477 1512 1.835483 GAGCTGTGTGCCAACTCACG 61.835 60.000 0.00 0.0 42.02 4.35
1731 1766 4.202284 GCATACAACCGAATCCCTAGGTTA 60.202 45.833 8.29 0.0 45.52 2.85
1885 1920 1.439679 GGCTTTCGAACACTGTAGGG 58.560 55.000 0.00 0.0 0.00 3.53
1985 2020 2.600173 CCGGGTGTTGCCATTGGT 60.600 61.111 4.26 0.0 39.65 3.67
2202 2237 3.744660 GAACTTCTATAGGGCATGTGGG 58.255 50.000 0.00 0.0 0.00 4.61
2216 2251 1.145571 TGTGGGCTTAAGGAGTTGGT 58.854 50.000 4.29 0.0 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 4.855388 CGGACAAATTCTTCAGATTTGCAG 59.145 41.667 8.91 1.62 38.46 4.41
403 422 7.068702 TCCATCCCTATAAGCATTCAACATTT 58.931 34.615 0.00 0.00 0.00 2.32
498 531 3.430042 AACACCATGTCAAGCTCATCT 57.570 42.857 0.00 0.00 0.00 2.90
701 734 4.322057 AGGGCCTTGTCTATTGATTTGT 57.678 40.909 0.00 0.00 0.00 2.83
709 742 5.717119 AATAACTCAAGGGCCTTGTCTAT 57.283 39.130 37.83 28.35 41.66 1.98
720 753 6.810182 CCTTCTTCATTGCAAATAACTCAAGG 59.190 38.462 1.71 5.95 0.00 3.61
746 779 4.021719 AGTCCAAATGCAACCTTGAATCAG 60.022 41.667 7.83 0.00 0.00 2.90
1045 1079 1.588932 CGTCGGGACCATCGTCATG 60.589 63.158 0.00 0.00 41.13 3.07
1127 1162 4.097286 TGAACAATGTAGTCCGATGATCGA 59.903 41.667 17.52 0.00 43.74 3.59
1128 1163 4.359706 TGAACAATGTAGTCCGATGATCG 58.640 43.478 8.05 8.05 40.07 3.69
1251 1286 5.514500 ACTTAGACCCTTTTGCAATCCTA 57.486 39.130 0.00 0.00 0.00 2.94
1252 1287 4.388577 ACTTAGACCCTTTTGCAATCCT 57.611 40.909 0.00 0.00 0.00 3.24
1413 1448 1.968017 CCATGGTCTTGCACGCACT 60.968 57.895 2.57 0.00 0.00 4.40
1461 1496 1.089481 ACACGTGAGTTGGCACACAG 61.089 55.000 25.01 2.19 46.40 3.66
1477 1512 1.069596 CCCTTTTGCCTTGGCACAC 59.930 57.895 14.52 0.00 39.29 3.82
1667 1702 1.134946 ACATCTTAAATGCGGCTTGCC 59.865 47.619 0.00 0.75 45.60 4.52
1731 1766 2.480610 CGCGGCCATGGCTAACAAT 61.481 57.895 34.70 0.00 41.60 2.71
1985 2020 3.826157 CTCCACCTCAACCAAAGCAAATA 59.174 43.478 0.00 0.00 0.00 1.40
2202 2237 3.247006 TCATCGACCAACTCCTTAAGC 57.753 47.619 0.00 0.00 0.00 3.09
2216 2251 6.401394 AGACAACAATCTTGAAGATCATCGA 58.599 36.000 8.32 0.00 32.89 3.59


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

AutoCloner maintained by Alex Coulton.