Multiple sequence alignment - TraesCS7D01G242900

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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 TraesCS7D01G242900 chr7D 100.000 2646 0 0 1 2646 208642155 208639510 0 4887
1 TraesCS7D01G242900 chrUn 97.922 2647 54 1 1 2646 186201715 186204361 0 4582
2 TraesCS7D01G242900 chr1A 97.922 2647 51 3 1 2646 498684525 498687168 0 4580
3 TraesCS7D01G242900 chr7B 97.846 2646 56 1 1 2645 742996151 742993506 0 4569
4 TraesCS7D01G242900 chr7B 97.696 2647 59 2 1 2646 716872076 716874721 0 4549
5 TraesCS7D01G242900 chr5A 97.658 2647 61 1 1 2646 492862433 492859787 0 4543
6 TraesCS7D01G242900 chr4A 97.470 2648 64 3 1 2646 67603672 67601026 0 4516
7 TraesCS7D01G242900 chr2B 97.393 2647 68 1 1 2646 391167714 391165068 0 4505
8 TraesCS7D01G242900 chr3A 97.280 2647 71 1 1 2646 725803458 725800812 0 4488
9 TraesCS7D01G242900 chr4B 97.167 2647 72 3 1 2646 209306366 209303722 0 4470


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 TraesCS7D01G242900 chr7D 208639510 208642155 2645 True 4887 4887 100.000 1 2646 1 chr7D.!!$R1 2645
1 TraesCS7D01G242900 chrUn 186201715 186204361 2646 False 4582 4582 97.922 1 2646 1 chrUn.!!$F1 2645
2 TraesCS7D01G242900 chr1A 498684525 498687168 2643 False 4580 4580 97.922 1 2646 1 chr1A.!!$F1 2645
3 TraesCS7D01G242900 chr7B 742993506 742996151 2645 True 4569 4569 97.846 1 2645 1 chr7B.!!$R1 2644
4 TraesCS7D01G242900 chr7B 716872076 716874721 2645 False 4549 4549 97.696 1 2646 1 chr7B.!!$F1 2645
5 TraesCS7D01G242900 chr5A 492859787 492862433 2646 True 4543 4543 97.658 1 2646 1 chr5A.!!$R1 2645
6 TraesCS7D01G242900 chr4A 67601026 67603672 2646 True 4516 4516 97.470 1 2646 1 chr4A.!!$R1 2645
7 TraesCS7D01G242900 chr2B 391165068 391167714 2646 True 4505 4505 97.393 1 2646 1 chr2B.!!$R1 2645
8 TraesCS7D01G242900 chr3A 725800812 725803458 2646 True 4488 4488 97.280 1 2646 1 chr3A.!!$R1 2645
9 TraesCS7D01G242900 chr4B 209303722 209306366 2644 True 4470 4470 97.167 1 2646 1 chr4B.!!$R1 2645

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
514 516 1.210478 GCTTGGAAGGATAGAGTGCCA 59.79 52.381 0.0 0.0 0.0 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2407 2411 0.400213 ATCGACCAGCTTCCAACCAA 59.6 50.0 0.0 0.0 0.0 3.67 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
112 113 2.412112 GCAGCAGCAAGGCTATGC 59.588 61.111 10.35 10.35 43.68 3.14
126 127 3.084786 GGCTATGCCTCAGTCAAAGTTT 58.915 45.455 0.73 0.00 46.69 2.66
147 148 1.754226 GACAAGGGGCAAAACAGTTGA 59.246 47.619 0.00 0.00 0.00 3.18
203 204 3.445096 GCCAGTGCCATCATTAGAAAGTT 59.555 43.478 0.00 0.00 0.00 2.66
284 285 3.696051 GCAAGGATGTAAAGAATGAGGCA 59.304 43.478 0.00 0.00 0.00 4.75
357 358 4.939052 TCGAAAGAGGAAGAGAAGTTGT 57.061 40.909 0.00 0.00 34.84 3.32
404 405 5.105595 GCTAGAAACTCCAATGGCATTTTCT 60.106 40.000 21.32 21.32 0.00 2.52
514 516 1.210478 GCTTGGAAGGATAGAGTGCCA 59.790 52.381 0.00 0.00 0.00 4.92
588 590 3.257375 TCGAACGCCTGGCATACTAATAT 59.743 43.478 20.29 0.00 0.00 1.28
715 717 3.009143 TCTGCTCCTCCTAAAACCCTTTC 59.991 47.826 0.00 0.00 0.00 2.62
754 756 8.851876 AGATATAGATCTAAAGGGCCTAGAAGA 58.148 37.037 6.41 10.77 40.85 2.87
1293 1296 9.772605 TTTATATATTCCATTCCAGCCATTGAT 57.227 29.630 0.00 0.00 0.00 2.57
1360 1363 8.043710 CCAAGAAAGACCATATCAACTACTCTT 58.956 37.037 0.00 0.00 0.00 2.85
1398 1401 6.780457 AATCACGGAATTCAAATGGAAGAT 57.220 33.333 7.93 0.00 39.30 2.40
1748 1751 9.220906 TGATTATACCACATAGTTTAGGGAAGT 57.779 33.333 0.00 0.00 0.00 3.01
1801 1804 7.108841 AGATTATCGAAGCTTGTAACACCTA 57.891 36.000 2.10 0.00 0.00 3.08
1912 1915 3.699411 AATCCTATGCTCCATGCTCTC 57.301 47.619 0.00 0.00 43.37 3.20
1964 1967 1.691976 TGGCATAACCAGTATCTCCCG 59.308 52.381 0.00 0.00 46.36 5.14
2004 2007 7.161404 TGGATACCCATCTTTATCGATTCAAG 58.839 38.462 1.71 6.96 37.58 3.02
2027 2030 5.698545 AGGAAATGAATAAGTATCAGCGAGC 59.301 40.000 0.00 0.00 0.00 5.03
2028 2031 5.466728 GGAAATGAATAAGTATCAGCGAGCA 59.533 40.000 0.00 0.00 0.00 4.26
2250 2254 1.398692 GGTCCTTGCTTGTTCCAACA 58.601 50.000 0.00 0.00 37.08 3.33
2307 2311 5.705905 ACCAAAGGAAAGCAGATACAACTAC 59.294 40.000 0.00 0.00 0.00 2.73
2373 2377 3.187432 GCTTCCTTTGTAACAGCTCTGTC 59.813 47.826 2.68 0.00 44.13 3.51
2393 2397 2.099652 CTGGTCGTGGCTCACCTCAA 62.100 60.000 8.77 0.00 36.63 3.02
2407 2411 1.247567 CCTCAATGGACCAACGCTTT 58.752 50.000 0.00 0.00 38.35 3.51
2469 2473 0.604578 CACCTTTGCCAGTGGGATTG 59.395 55.000 12.15 3.87 35.59 2.67
2549 2553 1.405121 GCGTTCTACGGGGAGAATGTT 60.405 52.381 13.06 0.00 42.24 2.71
2602 2606 4.456535 TGAAACTGATCGGAAAAAGGACA 58.543 39.130 9.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 2.639839 CTCTCTCCAAAACTCCTTCCCA 59.360 50.000 0.00 0.00 0.00 4.37
126 127 1.480137 CAACTGTTTTGCCCCTTGTCA 59.520 47.619 0.00 0.00 0.00 3.58
147 148 7.348080 TCGACATGAACTTCTATTAGGACAT 57.652 36.000 0.00 0.00 0.00 3.06
203 204 1.816224 GGCTGAAACTAAAATGGCCGA 59.184 47.619 0.00 0.00 0.00 5.54
284 285 1.889530 GCGGGCCAGTCTGTTCTAGT 61.890 60.000 4.39 0.00 0.00 2.57
320 321 0.515564 TCGAAAAGTAGCAAAGCGGC 59.484 50.000 0.00 0.00 0.00 6.53
357 358 0.388134 GAGGCGCAGTCTCGTACAAA 60.388 55.000 10.83 0.00 40.46 2.83
404 405 6.147864 AGCTTCACTTTGCTTTCATTTACA 57.852 33.333 0.00 0.00 35.86 2.41
514 516 5.359009 CCTTCAATATGCCATCTTGTCTTGT 59.641 40.000 3.14 0.00 0.00 3.16
588 590 3.819564 AGTATTCAAGTATGCGGCTCA 57.180 42.857 0.00 0.00 0.00 4.26
754 756 2.418368 TTATTCGGTCCATGCTTGCT 57.582 45.000 0.00 0.00 0.00 3.91
937 939 6.704493 CCTGTGTTAGTAGTGCTAGTTTTTCA 59.296 38.462 0.00 0.00 0.00 2.69
1293 1296 4.745125 CAGTTCGAAAAGAGTGAGTTGCTA 59.255 41.667 0.00 0.00 0.00 3.49
1360 1363 5.924356 TCCGTGATTTATCCTGCTATTTGA 58.076 37.500 0.00 0.00 0.00 2.69
1398 1401 6.306987 AGGTTTGAATTGCCTTCTCTTTCTA 58.693 36.000 0.00 0.00 34.75 2.10
1458 1461 8.746052 TTGTTCTCTTGTTATTCTTTTCTGGA 57.254 30.769 0.00 0.00 0.00 3.86
1662 1665 0.613012 AAGGCCAGCTGGGTCATTTC 60.613 55.000 33.46 14.93 46.80 2.17
1748 1751 4.895668 ACTAACCCGAACTATGGTTTCA 57.104 40.909 0.00 0.00 42.09 2.69
1801 1804 4.941263 TGCGCTTTCCTAATGTGTTCTAAT 59.059 37.500 9.73 0.00 0.00 1.73
1912 1915 1.444212 CAAATGGAGCAAACCCGCG 60.444 57.895 0.00 0.00 36.85 6.46
1964 1967 3.244596 GGTATCCATGCCTCTTAGTTCCC 60.245 52.174 0.00 0.00 0.00 3.97
2004 2007 5.466728 TGCTCGCTGATACTTATTCATTTCC 59.533 40.000 0.00 0.00 0.00 3.13
2027 2030 4.250305 CCGGGCCCGTATTCCCTG 62.250 72.222 40.52 20.46 40.41 4.45
2028 2031 3.393743 TACCGGGCCCGTATTCCCT 62.394 63.158 40.52 16.67 40.41 4.20
2250 2254 5.233225 CACGTGATACATTCCTAGCATGAT 58.767 41.667 10.90 0.00 0.00 2.45
2307 2311 6.315714 TGGGAAATAGGACTAGGATCTGTAG 58.684 44.000 0.00 0.00 0.00 2.74
2373 2377 3.302347 GAGGTGAGCCACGACCAGG 62.302 68.421 0.00 0.00 34.83 4.45
2407 2411 0.400213 ATCGACCAGCTTCCAACCAA 59.600 50.000 0.00 0.00 0.00 3.67
2412 2416 2.184322 GCGATCGACCAGCTTCCA 59.816 61.111 21.57 0.00 0.00 3.53
2469 2473 3.723835 CGCATAGTACGAAAACCAACAGC 60.724 47.826 0.00 0.00 0.00 4.40
2522 2526 0.515564 CCCCGTAGAACGCTGTTTTG 59.484 55.000 0.00 0.00 40.91 2.44
2602 2606 6.962902 TCCCCTAATAAATGGGTGTTTTTGAT 59.037 34.615 0.00 0.00 41.82 2.57


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

AutoCloner maintained by Alex Coulton.