Multiple sequence alignment - TraesCS6B01G233300

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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 TraesCS6B01G233300 chr6B 100.000 2597 0 0 1 2597 388359022 388356426 0 4796
1 TraesCS6B01G233300 chr6B 97.113 2598 70 4 1 2597 388166967 388164374 0 4377
2 TraesCS6B01G233300 chr2B 97.381 2596 61 2 1 2596 751961787 751959199 0 4410
3 TraesCS6B01G233300 chr2B 95.152 1712 43 10 886 2597 112852576 112854247 0 2665
4 TraesCS6B01G233300 chr7B 97.112 2597 74 1 1 2597 531994953 531997548 0 4379
5 TraesCS6B01G233300 chr3A 96.767 2598 80 4 1 2597 718994153 718991559 0 4329
6 TraesCS6B01G233300 chr3B 95.845 2599 104 3 1 2597 575746104 575743508 0 4198
7 TraesCS6B01G233300 chr7A 97.566 2383 52 3 216 2597 708264393 708262016 0 4074
8 TraesCS6B01G233300 chr4B 96.029 2317 83 6 281 2597 547038351 547040658 0 3760
9 TraesCS6B01G233300 chr5D 95.798 2261 88 5 337 2597 244894244 244896497 0 3642
10 TraesCS6B01G233300 chr5D 95.657 2003 79 5 1 2001 79846298 79844302 0 3210


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 TraesCS6B01G233300 chr6B 388356426 388359022 2596 True 4796 4796 100.000 1 2597 1 chr6B.!!$R2 2596
1 TraesCS6B01G233300 chr6B 388164374 388166967 2593 True 4377 4377 97.113 1 2597 1 chr6B.!!$R1 2596
2 TraesCS6B01G233300 chr2B 751959199 751961787 2588 True 4410 4410 97.381 1 2596 1 chr2B.!!$R1 2595
3 TraesCS6B01G233300 chr2B 112852576 112854247 1671 False 2665 2665 95.152 886 2597 1 chr2B.!!$F1 1711
4 TraesCS6B01G233300 chr7B 531994953 531997548 2595 False 4379 4379 97.112 1 2597 1 chr7B.!!$F1 2596
5 TraesCS6B01G233300 chr3A 718991559 718994153 2594 True 4329 4329 96.767 1 2597 1 chr3A.!!$R1 2596
6 TraesCS6B01G233300 chr3B 575743508 575746104 2596 True 4198 4198 95.845 1 2597 1 chr3B.!!$R1 2596
7 TraesCS6B01G233300 chr7A 708262016 708264393 2377 True 4074 4074 97.566 216 2597 1 chr7A.!!$R1 2381
8 TraesCS6B01G233300 chr4B 547038351 547040658 2307 False 3760 3760 96.029 281 2597 1 chr4B.!!$F1 2316
9 TraesCS6B01G233300 chr5D 244894244 244896497 2253 False 3642 3642 95.798 337 2597 1 chr5D.!!$F1 2260
10 TraesCS6B01G233300 chr5D 79844302 79846298 1996 True 3210 3210 95.657 1 2001 1 chr5D.!!$R1 2000

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
125 126 1.131638 ATTAGAGGGCAAGCGATGGA 58.868 50.000 0.0 0.0 0.00 3.41 F
663 665 1.656569 CGCCTACCTACGCTAACGC 60.657 63.158 0.0 0.0 45.53 4.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1334 1337 2.161410 CGGCATAACAAAGCTTGCACTA 59.839 45.455 0.0 0.0 36.82 2.74 R
2431 2439 0.951558 GCTCAAACCGAAGCTTTCCA 59.048 50.000 0.0 0.0 0.00 3.53 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
99 100 1.136356 CATTGTGTATGCGCCGCAA 59.864 52.632 18.69 9.41 43.62 4.85
125 126 1.131638 ATTAGAGGGCAAGCGATGGA 58.868 50.000 0.00 0.00 0.00 3.41
663 665 1.656569 CGCCTACCTACGCTAACGC 60.657 63.158 0.00 0.00 45.53 4.84
868 870 6.028146 TGTGCAATGCTTATGTGAAATCTT 57.972 33.333 6.82 0.00 0.00 2.40
978 980 6.139679 TGAAAAAGATGGAGTTACCTGGAT 57.860 37.500 0.00 0.00 39.86 3.41
1411 1414 2.187946 CTTCTTCCCGCCGCATCT 59.812 61.111 0.00 0.00 0.00 2.90
1533 1536 7.444703 AGAAGGCTTGATAGTCCTAAGAAAT 57.555 36.000 3.46 0.00 30.72 2.17
1721 1726 0.824182 CTAGGAGGGCCGTCTACCAG 60.824 65.000 23.90 12.21 39.96 4.00
1742 1748 3.454082 AGAAGATAGAGTTTGAGCCTGGG 59.546 47.826 0.00 0.00 0.00 4.45
1903 1910 2.197577 GAAACTCGGTATCAGCAGAGC 58.802 52.381 0.00 0.00 34.31 4.09
1983 1990 2.293399 CCCTCAAAGCGCTAACAAAGTT 59.707 45.455 12.05 0.00 0.00 2.66
2178 2185 1.609072 GGCACTCACTTCCTTTGGAAC 59.391 52.381 0.00 0.00 36.71 3.62
2220 2227 2.742053 CTCGTTCCGTTGACCATCAAAT 59.258 45.455 0.00 0.00 38.22 2.32
2431 2439 7.862873 GCTAAAGTGAGAAATAAACAACTGCTT 59.137 33.333 0.00 0.00 0.00 3.91
2517 2526 5.245075 ACGTGGAACCAATGATACCAAAAAT 59.755 36.000 0.00 0.00 32.32 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
190 191 1.933021 AGGTGGAATGGACTACGTGA 58.067 50.000 0.00 0.0 0.00 4.35
663 665 1.667236 TCCGCCATCTGCATTAGTTG 58.333 50.000 0.00 0.0 41.33 3.16
868 870 7.804129 CCAACGAAACGAATAAGTTTTGGATTA 59.196 33.333 12.64 0.0 45.26 1.75
1334 1337 2.161410 CGGCATAACAAAGCTTGCACTA 59.839 45.455 0.00 0.0 36.82 2.74
1411 1414 5.190677 TGTGACTATATCGTCCTGAAGACA 58.809 41.667 5.03 0.0 46.69 3.41
1712 1717 6.438259 TCAAACTCTATCTTCTGGTAGACG 57.562 41.667 0.00 0.0 0.00 4.18
1721 1726 3.432890 CCCCAGGCTCAAACTCTATCTTC 60.433 52.174 0.00 0.0 0.00 2.87
1947 1954 4.640771 TTGAGGGCTTCACTATGTTCTT 57.359 40.909 0.00 0.0 34.94 2.52
1983 1990 9.675464 TCTTTTTGGAAAACTTCTCTACTTACA 57.325 29.630 0.00 0.0 0.00 2.41
2178 2185 5.163814 CGAGTAGAGAAGAAAAATGCCCTTG 60.164 44.000 0.00 0.0 0.00 3.61
2431 2439 0.951558 GCTCAAACCGAAGCTTTCCA 59.048 50.000 0.00 0.0 0.00 3.53
2517 2526 7.348274 ACCCAGTTCTCCTCATATTTGATTCTA 59.652 37.037 0.00 0.0 0.00 2.10


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

AutoCloner maintained by Alex Coulton.