Multiple sequence alignment - TraesCS4D01G055800

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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 TraesCS4D01G055800 chr4D 100.000 2321 0 0 1 2321 30903961 30906281 0 4287
1 TraesCS4D01G055800 chr5D 97.050 1661 45 4 1 1657 60521633 60519973 0 2793
2 TraesCS4D01G055800 chr5D 95.802 667 26 1 1655 2321 60519636 60518972 0 1075
3 TraesCS4D01G055800 chr6D 97.045 1658 48 1 1 1657 80673023 80671366 0 2789
4 TraesCS4D01G055800 chr2D 96.866 1659 49 3 1 1657 63681703 63683360 0 2772
5 TraesCS4D01G055800 chr2D 94.729 664 30 3 1655 2316 640875026 640874366 0 1027
6 TraesCS4D01G055800 chr7D 97.628 1602 35 3 58 1657 463977648 463979248 0 2745
7 TraesCS4D01G055800 chr5A 96.383 1659 57 3 1 1657 30143742 30145399 0 2728
8 TraesCS4D01G055800 chr5A 95.915 661 27 0 1655 2315 607301688 607302348 0 1072
9 TraesCS4D01G055800 chr3B 96.270 1662 55 7 1 1657 141753861 141755520 0 2719
10 TraesCS4D01G055800 chr3B 94.864 662 33 1 1655 2316 9254646 9253986 0 1033
11 TraesCS4D01G055800 chr3B 94.562 662 36 0 1655 2316 737834080 737833419 0 1024
12 TraesCS4D01G055800 chr7A 96.147 1661 60 3 1 1657 94445669 94444009 0 2710
13 TraesCS4D01G055800 chr7A 96.082 1659 61 3 1 1657 546231942 546233598 0 2700
14 TraesCS4D01G055800 chr3A 96.019 1658 62 4 1 1656 740090421 740088766 0 2693
15 TraesCS4D01G055800 chr3A 95.202 667 32 0 1655 2321 328924655 328925321 0 1055
16 TraesCS4D01G055800 chr3D 96.852 667 20 1 1655 2321 448308896 448308231 0 1114
17 TraesCS4D01G055800 chr3D 95.652 667 29 0 1655 2321 615068181 615068847 0 1072
18 TraesCS4D01G055800 chr5B 94.411 662 37 0 1655 2316 415772304 415771643 0 1018


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 TraesCS4D01G055800 chr4D 30903961 30906281 2320 False 4287 4287 100.000 1 2321 1 chr4D.!!$F1 2320
1 TraesCS4D01G055800 chr5D 60518972 60521633 2661 True 1934 2793 96.426 1 2321 2 chr5D.!!$R1 2320
2 TraesCS4D01G055800 chr6D 80671366 80673023 1657 True 2789 2789 97.045 1 1657 1 chr6D.!!$R1 1656
3 TraesCS4D01G055800 chr2D 63681703 63683360 1657 False 2772 2772 96.866 1 1657 1 chr2D.!!$F1 1656
4 TraesCS4D01G055800 chr2D 640874366 640875026 660 True 1027 1027 94.729 1655 2316 1 chr2D.!!$R1 661
5 TraesCS4D01G055800 chr7D 463977648 463979248 1600 False 2745 2745 97.628 58 1657 1 chr7D.!!$F1 1599
6 TraesCS4D01G055800 chr5A 30143742 30145399 1657 False 2728 2728 96.383 1 1657 1 chr5A.!!$F1 1656
7 TraesCS4D01G055800 chr5A 607301688 607302348 660 False 1072 1072 95.915 1655 2315 1 chr5A.!!$F2 660
8 TraesCS4D01G055800 chr3B 141753861 141755520 1659 False 2719 2719 96.270 1 1657 1 chr3B.!!$F1 1656
9 TraesCS4D01G055800 chr3B 9253986 9254646 660 True 1033 1033 94.864 1655 2316 1 chr3B.!!$R1 661
10 TraesCS4D01G055800 chr3B 737833419 737834080 661 True 1024 1024 94.562 1655 2316 1 chr3B.!!$R2 661
11 TraesCS4D01G055800 chr7A 94444009 94445669 1660 True 2710 2710 96.147 1 1657 1 chr7A.!!$R1 1656
12 TraesCS4D01G055800 chr7A 546231942 546233598 1656 False 2700 2700 96.082 1 1657 1 chr7A.!!$F1 1656
13 TraesCS4D01G055800 chr3A 740088766 740090421 1655 True 2693 2693 96.019 1 1656 1 chr3A.!!$R1 1655
14 TraesCS4D01G055800 chr3A 328924655 328925321 666 False 1055 1055 95.202 1655 2321 1 chr3A.!!$F1 666
15 TraesCS4D01G055800 chr3D 448308231 448308896 665 True 1114 1114 96.852 1655 2321 1 chr3D.!!$R1 666
16 TraesCS4D01G055800 chr3D 615068181 615068847 666 False 1072 1072 95.652 1655 2321 1 chr3D.!!$F1 666
17 TraesCS4D01G055800 chr5B 415771643 415772304 661 True 1018 1018 94.411 1655 2316 1 chr5B.!!$R1 661

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
848 850 0.034896 TGTTCTTGGACCCTCTTCGC 59.965 55.0 0.0 0.0 0.0 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2060 2411 1.105167 TCCGGATCCGCATCGTAGTT 61.105 55.0 29.12 0.0 38.24 2.24 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
337 339 1.640593 TTGAGAGGCCACAACCCACA 61.641 55.000 5.01 0.00 0.00 4.17
362 364 0.102481 CCCTGAAGTATGACCGTCGG 59.898 60.000 10.48 10.48 0.00 4.79
513 515 1.004044 ACCTTGCTCTTGGTGAGATGG 59.996 52.381 0.00 0.00 45.39 3.51
607 609 1.002134 CTGAGGGGTGGCGACAAAT 60.002 57.895 0.00 0.00 46.06 2.32
713 715 6.653320 TCTCGTGGCTACAAGAACATTTTTAT 59.347 34.615 0.00 0.00 34.72 1.40
755 757 0.537188 CGGCTGTTGTGGAGAGGTAT 59.463 55.000 0.00 0.00 0.00 2.73
804 806 1.409521 CCCAAGTGGTGTTTCCTGACA 60.410 52.381 0.00 0.00 37.07 3.58
848 850 0.034896 TGTTCTTGGACCCTCTTCGC 59.965 55.000 0.00 0.00 0.00 4.70
991 996 3.980646 GTACAAATGTGCAGTTGGACA 57.019 42.857 19.03 8.90 46.27 4.02
1080 1085 2.064581 GGAGCGTATCCCTGTGGGT 61.065 63.158 2.25 0.00 44.74 4.51
1156 1161 1.147191 AGGAGCGGTATCCCACTATCA 59.853 52.381 0.00 0.00 40.53 2.15
1278 1283 2.971660 TCAAATGCCTTGCCATCATG 57.028 45.000 0.00 0.00 34.76 3.07
1279 1284 1.134640 TCAAATGCCTTGCCATCATGC 60.135 47.619 0.00 0.00 34.76 4.06
1411 1418 0.317770 CATCTTTGGCGTGTGCGTTT 60.318 50.000 0.00 0.00 44.10 3.60
1532 1541 1.555075 AGTGTGGTGCTACATAGGTGG 59.445 52.381 0.00 0.00 32.43 4.61
1588 1598 8.744652 TGTACCACGGAAAAATGAAATTGATAT 58.255 29.630 0.00 0.00 36.10 1.63
1613 1623 6.040955 TCGATACTTCTCATGCTTTGTAGGAT 59.959 38.462 0.00 0.00 31.88 3.24
1930 2281 4.682787 CACGTGCTCAGTATAGAATGGAA 58.317 43.478 0.82 0.00 0.00 3.53
1934 2285 5.665459 GTGCTCAGTATAGAATGGAAGTGT 58.335 41.667 0.00 0.00 0.00 3.55
1942 2293 9.442047 CAGTATAGAATGGAAGTGTTTTCTTCT 57.558 33.333 6.44 0.00 42.19 2.85
2060 2411 3.772025 GGAAGATGAAGAGGAGGAGACAA 59.228 47.826 0.00 0.00 0.00 3.18
2189 2540 2.901192 TCAAGAACCATCCAACGTCCTA 59.099 45.455 0.00 0.00 0.00 2.94
2207 2558 2.237143 CCTAGATGGCAGAACACTCCAA 59.763 50.000 0.00 0.00 33.04 3.53
2238 2590 1.158007 AACAGGGGGAAGATGGTTGT 58.842 50.000 0.00 0.00 0.00 3.32
2316 2668 8.418597 TCTGGTGAACTAGAAATGTAGTTAGT 57.581 34.615 0.00 0.00 42.21 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 4.966850 ACAAAATCGTGTGAGAACTACG 57.033 40.909 0.00 0.00 39.04 3.51
307 309 2.097825 GGCCTCTCAACCGAAGTACTA 58.902 52.381 0.00 0.00 0.00 1.82
337 339 2.695666 CGGTCATACTTCAGGGACTCAT 59.304 50.000 0.00 0.00 34.60 2.90
362 364 7.709613 TCCATTCTTCTAAAATAAGGCTCGTAC 59.290 37.037 0.00 0.00 0.00 3.67
513 515 2.614057 CAATATCCTCCAAAGTGACGGC 59.386 50.000 0.00 0.00 0.00 5.68
607 609 0.616111 ACCAACCAAACCTGCAACCA 60.616 50.000 0.00 0.00 0.00 3.67
713 715 3.063526 GCACTCTCTGGGCACTCA 58.936 61.111 0.00 0.00 46.29 3.41
755 757 1.590591 TCCATAAGTAAGCCCTGGCA 58.409 50.000 11.38 0.00 44.88 4.92
804 806 4.008933 GGCTGTGTCTCCCGTGCT 62.009 66.667 0.00 0.00 0.00 4.40
848 850 4.021102 ACTCCACTTAACATCCCAGTTG 57.979 45.455 0.00 0.00 33.07 3.16
991 996 4.455606 GGCTTACTCCTCATACATGCTTT 58.544 43.478 0.00 0.00 0.00 3.51
992 997 3.493350 CGGCTTACTCCTCATACATGCTT 60.493 47.826 0.00 0.00 0.00 3.91
1080 1085 2.695359 GGAGCAATGGTCAAGTTACGA 58.305 47.619 14.70 0.00 0.00 3.43
1156 1161 1.203994 GACAGTAGCCCACGTGTATGT 59.796 52.381 15.65 9.22 0.00 2.29
1532 1541 4.819630 TCAACATGTGGTACAAGAAACTCC 59.180 41.667 0.00 0.00 44.16 3.85
1588 1598 5.359860 TCCTACAAAGCATGAGAAGTATCGA 59.640 40.000 0.00 0.00 0.00 3.59
1613 1623 1.723608 CTTGTTGTGTTGCCGGCTCA 61.724 55.000 29.70 22.99 0.00 4.26
1930 2281 2.158957 TGGACGAGCAGAAGAAAACACT 60.159 45.455 0.00 0.00 0.00 3.55
1934 2285 3.685139 AGATGGACGAGCAGAAGAAAA 57.315 42.857 0.00 0.00 0.00 2.29
1977 2328 1.809869 CTGGAAGATGGACGAGCGA 59.190 57.895 0.00 0.00 34.07 4.93
2060 2411 1.105167 TCCGGATCCGCATCGTAGTT 61.105 55.000 29.12 0.00 38.24 2.24
2120 2471 2.289694 GCTGAGAAGGTTGAGTTGGCTA 60.290 50.000 0.00 0.00 0.00 3.93
2189 2540 2.553904 CCTTTGGAGTGTTCTGCCATCT 60.554 50.000 0.00 0.00 0.00 2.90
2207 2558 1.677552 CCCTGTTGACGTAGCCCTT 59.322 57.895 0.00 0.00 0.00 3.95
2238 2590 4.336433 CACTTCACTTCTTGCCTCTTTTCA 59.664 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.