Multiple sequence alignment - TraesCS5A01G116600

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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 TraesCS5A01G116600 chr5A 100.000 2319 0 0 1 2319 238791595 238789277 0 4283
1 TraesCS5A01G116600 chr5A 98.264 1786 25 2 1 1785 300072979 300074759 0 3121
2 TraesCS5A01G116600 chr5A 97.353 529 14 0 1791 2319 169395371 169395899 0 900
3 TraesCS5A01G116600 chr5A 97.358 530 13 1 1791 2319 610021121 610021650 0 900
4 TraesCS5A01G116600 chr7A 98.487 1785 27 0 1 1785 4959838 4961622 0 3147
5 TraesCS5A01G116600 chr7A 97.736 530 11 1 1791 2319 443009303 443009832 0 911
6 TraesCS5A01G116600 chr7A 97.358 530 13 1 1791 2319 344568306 344568835 0 900
7 TraesCS5A01G116600 chrUn 98.264 1786 25 2 1 1785 189392539 189394319 0 3121
8 TraesCS5A01G116600 chr2A 98.155 1789 27 2 1 1788 618279956 618278173 0 3116
9 TraesCS5A01G116600 chr7D 98.099 1789 28 2 1 1788 626698490 626696707 0 3110
10 TraesCS5A01G116600 chr7D 97.987 1788 31 1 1 1788 203556345 203554563 0 3097
11 TraesCS5A01G116600 chr7B 98.152 1786 27 2 1 1785 743086199 743087979 0 3110
12 TraesCS5A01G116600 chr6A 98.151 1785 27 3 1 1785 289128632 289130410 0 3109
13 TraesCS5A01G116600 chr6A 97.363 531 12 2 1791 2319 356065621 356066151 0 902
14 TraesCS5A01G116600 chr4A 97.931 1788 34 3 1 1788 67587531 67585747 0 3094
15 TraesCS5A01G116600 chr3A 97.732 529 12 0 1791 2319 309311555 309311027 0 911
16 TraesCS5A01G116600 chr3A 97.547 530 12 1 1791 2319 370183848 370184377 0 905
17 TraesCS5A01G116600 chr1A 97.547 530 12 1 1791 2319 372508644 372509173 0 905
18 TraesCS5A01G116600 chr1A 97.363 531 12 2 1791 2319 88423709 88424239 0 902


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 TraesCS5A01G116600 chr5A 238789277 238791595 2318 True 4283 4283 100.000 1 2319 1 chr5A.!!$R1 2318
1 TraesCS5A01G116600 chr5A 300072979 300074759 1780 False 3121 3121 98.264 1 1785 1 chr5A.!!$F2 1784
2 TraesCS5A01G116600 chr5A 169395371 169395899 528 False 900 900 97.353 1791 2319 1 chr5A.!!$F1 528
3 TraesCS5A01G116600 chr5A 610021121 610021650 529 False 900 900 97.358 1791 2319 1 chr5A.!!$F3 528
4 TraesCS5A01G116600 chr7A 4959838 4961622 1784 False 3147 3147 98.487 1 1785 1 chr7A.!!$F1 1784
5 TraesCS5A01G116600 chr7A 443009303 443009832 529 False 911 911 97.736 1791 2319 1 chr7A.!!$F3 528
6 TraesCS5A01G116600 chr7A 344568306 344568835 529 False 900 900 97.358 1791 2319 1 chr7A.!!$F2 528
7 TraesCS5A01G116600 chrUn 189392539 189394319 1780 False 3121 3121 98.264 1 1785 1 chrUn.!!$F1 1784
8 TraesCS5A01G116600 chr2A 618278173 618279956 1783 True 3116 3116 98.155 1 1788 1 chr2A.!!$R1 1787
9 TraesCS5A01G116600 chr7D 626696707 626698490 1783 True 3110 3110 98.099 1 1788 1 chr7D.!!$R2 1787
10 TraesCS5A01G116600 chr7D 203554563 203556345 1782 True 3097 3097 97.987 1 1788 1 chr7D.!!$R1 1787
11 TraesCS5A01G116600 chr7B 743086199 743087979 1780 False 3110 3110 98.152 1 1785 1 chr7B.!!$F1 1784
12 TraesCS5A01G116600 chr6A 289128632 289130410 1778 False 3109 3109 98.151 1 1785 1 chr6A.!!$F1 1784
13 TraesCS5A01G116600 chr6A 356065621 356066151 530 False 902 902 97.363 1791 2319 1 chr6A.!!$F2 528
14 TraesCS5A01G116600 chr4A 67585747 67587531 1784 True 3094 3094 97.931 1 1788 1 chr4A.!!$R1 1787
15 TraesCS5A01G116600 chr3A 309311027 309311555 528 True 911 911 97.732 1791 2319 1 chr3A.!!$R1 528
16 TraesCS5A01G116600 chr3A 370183848 370184377 529 False 905 905 97.547 1791 2319 1 chr3A.!!$F1 528
17 TraesCS5A01G116600 chr1A 372508644 372509173 529 False 905 905 97.547 1791 2319 1 chr1A.!!$F2 528
18 TraesCS5A01G116600 chr1A 88423709 88424239 530 False 902 902 97.363 1791 2319 1 chr1A.!!$F1 528


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
539 541 2.233271 ACCCGACTCGTAACTTCAAGA 58.767 47.619 0.0 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1975 1990 0.827507 TTTGGCTGGTGGAAAGCTCC 60.828 55.0 0.0 0.0 42.81 4.7 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
33 34 3.069443 GCTTTGACAAGGGGTTTGATTCA 59.931 43.478 0.00 0.0 39.21 2.57
158 159 2.297315 CACTCGCATATCTAGAGCCCAA 59.703 50.000 0.00 0.0 35.56 4.12
270 271 5.848406 ACGACAATGACTCTTCTTCTTTCT 58.152 37.500 0.00 0.0 0.00 2.52
373 374 6.279513 TGACAAAAGAAGAAAAAGAAGCCA 57.720 33.333 0.00 0.0 0.00 4.75
539 541 2.233271 ACCCGACTCGTAACTTCAAGA 58.767 47.619 0.00 0.0 0.00 3.02
568 570 6.069331 CCATCCATCTCAATCCAAAATCTCT 58.931 40.000 0.00 0.0 0.00 3.10
1055 1058 2.679355 CGAAAGCCACATTCGTTTCA 57.321 45.000 0.82 0.0 43.41 2.69
1071 1074 5.063204 TCGTTTCATTTGAGGAAGTCACAT 58.937 37.500 0.00 0.0 33.71 3.21
1159 1162 1.282157 GCCCCTATCACAAGACCAAGT 59.718 52.381 0.00 0.0 0.00 3.16
1279 1282 5.046304 TCTCCCTCCATTTTCTTCACTACTG 60.046 44.000 0.00 0.0 0.00 2.74
1327 1330 4.223477 AGCATTGTGGAATAGTGGCATTTT 59.777 37.500 0.00 0.0 0.00 1.82
1427 1430 1.879372 GCATAGCGGCATCATCCAAGA 60.879 52.381 1.45 0.0 0.00 3.02
1437 1440 3.435327 GCATCATCCAAGACAAACACGTA 59.565 43.478 0.00 0.0 0.00 3.57
1565 1568 7.450014 TCTCTCACAAGACAGAGAAAGATTACT 59.550 37.037 0.00 0.0 41.82 2.24
1580 1588 8.277197 AGAAAGATTACTGATTCATCCAATCCA 58.723 33.333 9.60 0.0 40.44 3.41
1581 1589 8.827832 AAAGATTACTGATTCATCCAATCCAA 57.172 30.769 9.60 0.0 40.44 3.53
1582 1590 9.430399 AAAGATTACTGATTCATCCAATCCAAT 57.570 29.630 9.60 0.0 40.44 3.16
1583 1591 8.632906 AGATTACTGATTCATCCAATCCAATC 57.367 34.615 9.60 0.0 40.44 2.67
1584 1592 7.668886 AGATTACTGATTCATCCAATCCAATCC 59.331 37.037 9.60 0.0 40.44 3.01
1688 1701 6.159172 AGCTATCTATCCAGATCAGGGTTA 57.841 41.667 4.05 0.0 40.81 2.85
1785 1798 5.048153 TCGATGGCGATGTAAGATAGAAG 57.952 43.478 0.00 0.0 42.51 2.85
1788 1801 4.585955 TGGCGATGTAAGATAGAAGGAC 57.414 45.455 0.00 0.0 0.00 3.85
1789 1802 3.958147 TGGCGATGTAAGATAGAAGGACA 59.042 43.478 0.00 0.0 0.00 4.02
1953 1968 6.377912 TCCTTTGAAGTAGGGAAAAATTGGA 58.622 36.000 0.00 0.0 33.41 3.53
1975 1990 7.095910 TGGATTTATGCAAAACTGTAACCATG 58.904 34.615 0.00 0.0 0.00 3.66
2085 2102 2.978010 CCGTTTCGGGCTGCAACT 60.978 61.111 7.24 0.0 44.15 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 4.739793 AGAATGAATCAAACCCCTTGTCA 58.260 39.130 0.00 0.00 36.34 3.58
33 34 7.308435 CGACCTTATCTTTTTGCTCAAAGAAT 58.692 34.615 12.95 6.65 44.18 2.40
158 159 1.546476 GGTGTCGTTCAGGAGAGATGT 59.454 52.381 0.00 0.00 0.00 3.06
270 271 1.619363 AGGTGCCCATAGCTTCCCA 60.619 57.895 0.00 0.00 44.23 4.37
539 541 4.320546 TGGATTGAGATGGATGGTTGTT 57.679 40.909 0.00 0.00 0.00 2.83
568 570 2.354704 GGGTTTGGATCACAGACGATCA 60.355 50.000 0.00 0.00 43.07 2.92
1055 1058 4.202503 ACAGGACATGTGACTTCCTCAAAT 60.203 41.667 1.15 0.00 41.91 2.32
1071 1074 7.136885 TCTCCTTATTTATAGGGAACAGGACA 58.863 38.462 2.70 0.00 37.96 4.02
1279 1282 4.875544 TTGATTTATGTGTAGAAGCGGC 57.124 40.909 0.00 0.00 0.00 6.53
1327 1330 9.290988 TCACTAAGAACATTTTAGCCATTAACA 57.709 29.630 0.00 0.00 32.58 2.41
1427 1430 4.307432 CTTGACTGAGGATACGTGTTTGT 58.693 43.478 0.00 0.00 46.39 2.83
1437 1440 3.103742 GAGAAGACCCTTGACTGAGGAT 58.896 50.000 0.00 0.00 39.25 3.24
1565 1568 7.125963 TCAAATTGGATTGGATTGGATGAATCA 59.874 33.333 0.00 0.00 42.22 2.57
1580 1588 7.449395 TGAACTCACTTCTGATCAAATTGGATT 59.551 33.333 0.00 0.00 0.00 3.01
1581 1589 6.944290 TGAACTCACTTCTGATCAAATTGGAT 59.056 34.615 0.00 0.00 0.00 3.41
1582 1590 6.298361 TGAACTCACTTCTGATCAAATTGGA 58.702 36.000 0.00 0.00 0.00 3.53
1583 1591 6.564709 TGAACTCACTTCTGATCAAATTGG 57.435 37.500 0.00 0.00 0.00 3.16
1584 1592 8.080417 ACAATGAACTCACTTCTGATCAAATTG 58.920 33.333 0.00 0.00 0.00 2.32
1688 1701 2.607038 GGCTTTTCCATTCGCTTCGTTT 60.607 45.455 0.00 0.00 34.01 3.60
1785 1798 6.528321 TGAGATTCACATGATAATCCTGTCC 58.472 40.000 16.15 6.53 33.44 4.02
1788 1801 7.797038 TGTTGAGATTCACATGATAATCCTG 57.203 36.000 16.15 0.00 33.44 3.86
1789 1802 7.997223 ACATGTTGAGATTCACATGATAATCCT 59.003 33.333 17.05 8.00 37.72 3.24
1953 1968 7.238486 TCCATGGTTACAGTTTTGCATAAAT 57.762 32.000 12.58 0.00 0.00 1.40
1975 1990 0.827507 TTTGGCTGGTGGAAAGCTCC 60.828 55.000 0.00 0.00 42.81 4.70
2028 2043 3.535561 CTGGCAAGGTAACACATAGAGG 58.464 50.000 0.00 0.00 41.41 3.69
2085 2102 6.037720 TCGTCTGAAAAGTCTGCAACATTAAA 59.962 34.615 0.00 0.00 0.00 1.52



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

AutoCloner maintained by Alex Coulton.