Multiple sequence alignment - TraesCS7B01G395800

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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 TraesCS7B01G395800 chr7B 100.000 3287 0 0 1 3287 662754028 662750742 0 6071
1 TraesCS7B01G395800 chr1A 98.986 2366 21 2 925 3287 554483987 554486352 0 4233
2 TraesCS7B01G395800 chr2B 98.943 2365 23 1 925 3287 683729407 683731771 0 4228
3 TraesCS7B01G395800 chr3A 98.604 2364 32 1 925 3287 105554994 105552631 0 4181
4 TraesCS7B01G395800 chr3A 97.859 934 16 3 1 931 105555952 105555020 0 1611
5 TraesCS7B01G395800 chr5D 98.308 2364 37 3 925 3287 6251310 6248949 0 4141
6 TraesCS7B01G395800 chr5D 98.223 2364 38 4 925 3287 503315468 503317828 0 4130
7 TraesCS7B01G395800 chr5D 97.122 2363 62 4 925 3287 432268317 432265961 0 3982
8 TraesCS7B01G395800 chr5D 98.075 935 13 3 1 931 299970983 299970050 0 1622
9 TraesCS7B01G395800 chr5D 97.540 935 16 5 1 931 503340450 503341381 0 1592
10 TraesCS7B01G395800 chr1D 97.805 2369 44 5 925 3287 254461367 254463733 0 4080
11 TraesCS7B01G395800 chr1D 97.294 2365 54 6 925 3287 51830000 51827644 0 4004
12 TraesCS7B01G395800 chr1D 97.216 934 17 5 1 931 254460414 254461341 0 1572
13 TraesCS7B01G395800 chr7A 96.743 2364 65 6 925 3287 537839447 537837095 0 3928
14 TraesCS7B01G395800 chr5A 98.077 936 11 4 1 931 559030943 559030010 0 1622
15 TraesCS7B01G395800 chrUn 97.968 935 14 3 1 931 386224624 386225557 0 1616
16 TraesCS7B01G395800 chrUn 97.433 935 18 4 1 931 261567685 261566753 0 1589
17 TraesCS7B01G395800 chr5B 97.968 935 14 3 1 931 57514118 57513185 0 1616
18 TraesCS7B01G395800 chr1B 97.953 928 15 2 1 924 633717976 633718903 0 1605


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 TraesCS7B01G395800 chr7B 662750742 662754028 3286 True 6071 6071 100.0000 1 3287 1 chr7B.!!$R1 3286
1 TraesCS7B01G395800 chr1A 554483987 554486352 2365 False 4233 4233 98.9860 925 3287 1 chr1A.!!$F1 2362
2 TraesCS7B01G395800 chr2B 683729407 683731771 2364 False 4228 4228 98.9430 925 3287 1 chr2B.!!$F1 2362
3 TraesCS7B01G395800 chr3A 105552631 105555952 3321 True 2896 4181 98.2315 1 3287 2 chr3A.!!$R1 3286
4 TraesCS7B01G395800 chr5D 6248949 6251310 2361 True 4141 4141 98.3080 925 3287 1 chr5D.!!$R1 2362
5 TraesCS7B01G395800 chr5D 503315468 503317828 2360 False 4130 4130 98.2230 925 3287 1 chr5D.!!$F1 2362
6 TraesCS7B01G395800 chr5D 432265961 432268317 2356 True 3982 3982 97.1220 925 3287 1 chr5D.!!$R3 2362
7 TraesCS7B01G395800 chr5D 299970050 299970983 933 True 1622 1622 98.0750 1 931 1 chr5D.!!$R2 930
8 TraesCS7B01G395800 chr5D 503340450 503341381 931 False 1592 1592 97.5400 1 931 1 chr5D.!!$F2 930
9 TraesCS7B01G395800 chr1D 51827644 51830000 2356 True 4004 4004 97.2940 925 3287 1 chr1D.!!$R1 2362
10 TraesCS7B01G395800 chr1D 254460414 254463733 3319 False 2826 4080 97.5105 1 3287 2 chr1D.!!$F1 3286
11 TraesCS7B01G395800 chr7A 537837095 537839447 2352 True 3928 3928 96.7430 925 3287 1 chr7A.!!$R1 2362
12 TraesCS7B01G395800 chr5A 559030010 559030943 933 True 1622 1622 98.0770 1 931 1 chr5A.!!$R1 930
13 TraesCS7B01G395800 chrUn 386224624 386225557 933 False 1616 1616 97.9680 1 931 1 chrUn.!!$F1 930
14 TraesCS7B01G395800 chrUn 261566753 261567685 932 True 1589 1589 97.4330 1 931 1 chrUn.!!$R1 930
15 TraesCS7B01G395800 chr5B 57513185 57514118 933 True 1616 1616 97.9680 1 931 1 chr5B.!!$R1 930
16 TraesCS7B01G395800 chr1B 633717976 633718903 927 False 1605 1605 97.9530 1 924 1 chr1B.!!$F1 923


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
824 834 1.006571 GCAACCCTTCGAGTCGACA 60.007 57.895 16.28 6.01 34.89 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2644 2692 1.067582 GATTCCCACTACCGGCTCG 59.932 63.158 0.0 0.0 0.0 5.03 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
400 410 4.321230 GGACCATTGAGCAACTCGAAAAAT 60.321 41.667 0.00 0.00 32.35 1.82
598 608 2.253513 CGACAGCGGGTTTTCCAAT 58.746 52.632 0.00 0.00 42.91 3.16
607 617 2.747135 CGGGTTTTCCAATAGGCCGTAT 60.747 50.000 0.00 0.00 42.91 3.06
694 704 1.507140 TATTGGCATTCTCGGGTCCT 58.493 50.000 0.00 0.00 0.00 3.85
824 834 1.006571 GCAACCCTTCGAGTCGACA 60.007 57.895 16.28 6.01 34.89 4.35
896 906 4.421131 AGGGATTGAGAATATAGGTCGCT 58.579 43.478 0.00 0.00 0.00 4.93
1458 1499 5.817296 CACTATTGTAGTAGCTGAAATGGCA 59.183 40.000 0.00 0.00 37.23 4.92
1976 2018 0.597568 TTTGCACAATTCGCCTCTGG 59.402 50.000 0.00 0.00 0.00 3.86
2724 2772 7.676947 ACCAAACTGCTCTATACTCTTAAACA 58.323 34.615 0.00 0.00 0.00 2.83
2926 2974 5.184287 CCCGGTAACAAACATTCATAAACCT 59.816 40.000 0.00 0.00 0.00 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
331 341 8.975663 TTTCGAATAGTACTCAAGATCCTCTA 57.024 34.615 0.00 0.0 0.00 2.43
369 379 0.105039 GCTCAATGGTCCCTCTACGG 59.895 60.000 0.00 0.0 0.00 4.02
598 608 2.973983 AGAGCTCCTTATACGGCCTA 57.026 50.000 10.93 0.0 0.00 3.93
607 617 4.864483 TCAGAGTTCCTAGAGCTCCTTA 57.136 45.455 10.93 0.0 40.05 2.69
824 834 6.250527 CGTTCGCGGAGAATTTTATGAATTTT 59.749 34.615 6.13 0.0 41.49 1.82
896 906 1.638589 CCCATCCCCCACTTGAACTAA 59.361 52.381 0.00 0.0 0.00 2.24
1370 1411 2.224161 GCTACGGAGGATGCTCTTTGAT 60.224 50.000 14.40 0.0 0.00 2.57
1458 1499 6.992715 GGTATTGTAATGTAGCAGGTGAATCT 59.007 38.462 0.00 0.0 0.00 2.40
1976 2018 7.582435 TGATTCTGACTTGTTTTATCGAGAC 57.418 36.000 0.00 0.0 0.00 3.36
2213 2255 3.578456 CCGCTTGCTCGGTGAATT 58.422 55.556 4.80 0.0 44.18 2.17
2644 2692 1.067582 GATTCCCACTACCGGCTCG 59.932 63.158 0.00 0.0 0.00 5.03
2724 2772 7.578458 TTTATCCACTAGTTACCCCTCTTTT 57.422 36.000 0.00 0.0 0.00 2.27
2808 2856 3.653835 GAGGAGCCCTCTTTACCATTT 57.346 47.619 12.53 0.0 46.41 2.32
2887 2935 0.893270 CCGGGTGCAACAAGATCCAA 60.893 55.000 3.06 0.0 39.98 3.53
2926 2974 2.605338 CCGGACACGTACTTCGAGAAAA 60.605 50.000 0.00 0.0 42.86 2.29
3138 3188 6.536941 GGAGAAGAAGCGACAGAAATTAGAAT 59.463 38.462 0.00 0.0 0.00 2.40
3151 3201 1.924731 TTCAGAGGGAGAAGAAGCGA 58.075 50.000 0.00 0.0 0.00 4.93



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

AutoCloner maintained by Alex Coulton.