Multiple sequence alignment - TraesCS5D01G087100

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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 TraesCS5D01G087100 chr5D 100.000 2902 0 0 1 2902 92293466 92296367 0 5360
1 TraesCS5D01G087100 chr5D 96.031 2923 78 10 1 2900 437728864 437725957 0 4721
2 TraesCS5D01G087100 chr5D 95.501 2334 74 8 592 2900 51585563 51583236 0 3699
3 TraesCS5D01G087100 chr5D 96.384 636 23 0 1 636 51586237 51585602 0 1048
4 TraesCS5D01G087100 chr1D 95.204 2961 83 15 1 2902 152625638 152628598 0 4626
5 TraesCS5D01G087100 chr1D 95.849 530 11 3 2373 2902 152482806 152483324 0 846
6 TraesCS5D01G087100 chr7D 94.533 2945 95 18 1 2900 107242438 107239515 0 4486
7 TraesCS5D01G087100 chr7D 96.535 1010 24 5 1 1010 509206230 509205232 0 1661
8 TraesCS5D01G087100 chr5A 94.439 2931 105 20 4 2900 40241892 40238986 0 4457
9 TraesCS5D01G087100 chr5A 94.989 2714 71 13 101 2791 562123425 562120754 0 4198
10 TraesCS5D01G087100 chr5A 94.935 2231 63 9 592 2791 687969706 687971917 0 3448
11 TraesCS5D01G087100 chr3B 94.025 2929 97 23 1 2900 823896287 823893408 0 4368
12 TraesCS5D01G087100 chr6A 95.027 2212 50 9 604 2791 553572477 553570302 0 3421
13 TraesCS5D01G087100 chr2D 94.313 1987 69 18 1 1958 104542276 104540305 0 3003
14 TraesCS5D01G087100 chr2D 95.200 1771 56 10 1 1748 165663552 165665316 0 2772
15 TraesCS5D01G087100 chr2D 94.139 836 41 7 3 835 67032693 67033523 0 1266
16 TraesCS5D01G087100 chr2B 93.620 1928 58 13 998 2902 32110226 32112111 0 2819
17 TraesCS5D01G087100 chr2B 93.915 1627 55 9 1280 2902 559330218 559328632 0 2416
18 TraesCS5D01G087100 chr2A 94.827 1759 49 4 1056 2791 5148332 5150071 0 2706
19 TraesCS5D01G087100 chr7A 94.295 1595 49 13 101 1672 626868516 626870091 0 2403
20 TraesCS5D01G087100 chr5B 94.793 1498 62 6 1414 2902 163625275 163623785 0 2320


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 TraesCS5D01G087100 chr5D 92293466 92296367 2901 False 5360.0 5360 100.0000 1 2902 1 chr5D.!!$F1 2901
1 TraesCS5D01G087100 chr5D 437725957 437728864 2907 True 4721.0 4721 96.0310 1 2900 1 chr5D.!!$R1 2899
2 TraesCS5D01G087100 chr5D 51583236 51586237 3001 True 2373.5 3699 95.9425 1 2900 2 chr5D.!!$R2 2899
3 TraesCS5D01G087100 chr1D 152625638 152628598 2960 False 4626.0 4626 95.2040 1 2902 1 chr1D.!!$F2 2901
4 TraesCS5D01G087100 chr1D 152482806 152483324 518 False 846.0 846 95.8490 2373 2902 1 chr1D.!!$F1 529
5 TraesCS5D01G087100 chr7D 107239515 107242438 2923 True 4486.0 4486 94.5330 1 2900 1 chr7D.!!$R1 2899
6 TraesCS5D01G087100 chr7D 509205232 509206230 998 True 1661.0 1661 96.5350 1 1010 1 chr7D.!!$R2 1009
7 TraesCS5D01G087100 chr5A 40238986 40241892 2906 True 4457.0 4457 94.4390 4 2900 1 chr5A.!!$R1 2896
8 TraesCS5D01G087100 chr5A 562120754 562123425 2671 True 4198.0 4198 94.9890 101 2791 1 chr5A.!!$R2 2690
9 TraesCS5D01G087100 chr5A 687969706 687971917 2211 False 3448.0 3448 94.9350 592 2791 1 chr5A.!!$F1 2199
10 TraesCS5D01G087100 chr3B 823893408 823896287 2879 True 4368.0 4368 94.0250 1 2900 1 chr3B.!!$R1 2899
11 TraesCS5D01G087100 chr6A 553570302 553572477 2175 True 3421.0 3421 95.0270 604 2791 1 chr6A.!!$R1 2187
12 TraesCS5D01G087100 chr2D 104540305 104542276 1971 True 3003.0 3003 94.3130 1 1958 1 chr2D.!!$R1 1957
13 TraesCS5D01G087100 chr2D 165663552 165665316 1764 False 2772.0 2772 95.2000 1 1748 1 chr2D.!!$F2 1747
14 TraesCS5D01G087100 chr2D 67032693 67033523 830 False 1266.0 1266 94.1390 3 835 1 chr2D.!!$F1 832
15 TraesCS5D01G087100 chr2B 32110226 32112111 1885 False 2819.0 2819 93.6200 998 2902 1 chr2B.!!$F1 1904
16 TraesCS5D01G087100 chr2B 559328632 559330218 1586 True 2416.0 2416 93.9150 1280 2902 1 chr2B.!!$R1 1622
17 TraesCS5D01G087100 chr2A 5148332 5150071 1739 False 2706.0 2706 94.8270 1056 2791 1 chr2A.!!$F1 1735
18 TraesCS5D01G087100 chr7A 626868516 626870091 1575 False 2403.0 2403 94.2950 101 1672 1 chr7A.!!$F1 1571
19 TraesCS5D01G087100 chr5B 163623785 163625275 1490 True 2320.0 2320 94.7930 1414 2902 1 chr5B.!!$R1 1488

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
406 411 1.003928 TGCATCAGGAACTCTGCATGT 59.996 47.619 0.00 0.00 45.46 3.21 F
1293 1519 0.106569 CCATCACCTTGGGCATGCTA 60.107 55.000 18.92 4.21 32.80 3.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1363 1589 1.668151 GGCGAGCGTCCTTGAAGTT 60.668 57.895 0.0 0.0 0.0 2.66 R
2657 2944 7.308450 AGCAGTATTTAGATTGGCAGAGATA 57.692 36.000 0.0 0.0 0.0 1.98 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
72 73 9.212593 TGCTTATCCTTGGTATCTATATGCATA 57.787 33.333 9.27 9.27 31.91 3.14
406 411 1.003928 TGCATCAGGAACTCTGCATGT 59.996 47.619 0.00 0.00 45.46 3.21
615 733 2.223900 TGCTATGCTGCTACTGCTACTG 60.224 50.000 0.00 0.00 40.48 2.74
621 739 2.797792 GCTGCTACTGCTACTGCTACTG 60.798 54.545 0.00 0.00 40.48 2.74
763 930 5.136828 TGTCAAAGCTGGGTTCAATTCTTA 58.863 37.500 0.00 0.00 0.00 2.10
1246 1472 5.512060 GGAGCTATTCCATGCACTGAATCTA 60.512 44.000 14.05 0.59 46.01 1.98
1293 1519 0.106569 CCATCACCTTGGGCATGCTA 60.107 55.000 18.92 4.21 32.80 3.49
1363 1589 0.820226 CCTCACGCTCATCTTCCTCA 59.180 55.000 0.00 0.00 0.00 3.86
1412 1638 5.046591 TCGAGAAGGTAATTGTCTGTCCATT 60.047 40.000 0.00 0.00 0.00 3.16
1487 1713 2.118679 ACTACCATGGTGCTGATGCTA 58.881 47.619 28.17 2.56 40.48 3.49
1622 1848 9.021807 TGCTAACACAGAGAGTATTTACTACTT 57.978 33.333 0.00 0.00 40.88 2.24
1977 2231 2.949644 TCGTCGACACTATCATCCACAT 59.050 45.455 17.16 0.00 0.00 3.21
2125 2379 1.689959 GCAATGTGTTGTAGTGCAGC 58.310 50.000 0.00 0.00 38.83 5.25
2388 2645 1.267121 TTGGTCTCAGCCCTGACTAC 58.733 55.000 0.00 0.00 35.46 2.73
2459 2727 4.377897 CCTGACTACCGAAGTTTTTGTCT 58.622 43.478 0.00 0.00 39.07 3.41
2843 3137 1.815866 GCTGCGGCCCAACAATAAT 59.184 52.632 6.12 0.00 0.00 1.28
2879 3173 2.203394 CTTGGCCCATGATCCCGG 60.203 66.667 0.00 0.00 0.00 5.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 73 3.706086 AGAAAGCCTGAAACACAAATGGT 59.294 39.130 0.00 0.00 0.00 3.55
148 149 6.960542 AGGCCTACTATAGCATAACAGGTAAT 59.039 38.462 1.29 0.00 0.00 1.89
156 157 6.740944 TGAACAAGGCCTACTATAGCATAA 57.259 37.500 5.16 0.00 0.00 1.90
309 313 1.028330 ACCATGTGCAGGCTTCATCG 61.028 55.000 0.00 0.00 0.00 3.84
383 388 1.901833 TGCAGAGTTCCTGATGCACTA 59.098 47.619 0.00 0.00 45.78 2.74
406 411 3.490439 TGATGAGACAAAGGACAGCAA 57.510 42.857 0.00 0.00 0.00 3.91
484 490 5.221185 GCAGATGGATGATTAGCAAACATGT 60.221 40.000 0.00 0.00 30.21 3.21
603 721 1.407258 AGCAGTAGCAGTAGCAGTAGC 59.593 52.381 0.00 0.00 45.49 3.58
604 722 3.880490 AGTAGCAGTAGCAGTAGCAGTAG 59.120 47.826 0.00 0.00 45.49 2.57
605 723 3.628032 CAGTAGCAGTAGCAGTAGCAGTA 59.372 47.826 0.00 0.00 45.49 2.74
615 733 1.407258 AGCAGTAGCAGTAGCAGTAGC 59.593 52.381 0.00 0.00 45.49 3.58
621 739 1.661341 AATGCAGCAGTAGCAGTAGC 58.339 50.000 0.00 0.00 46.36 3.58
763 930 6.330250 AGAGTGGAAAGTACCATATATTGCCT 59.670 38.462 0.00 0.00 42.17 4.75
1363 1589 1.668151 GGCGAGCGTCCTTGAAGTT 60.668 57.895 0.00 0.00 0.00 2.66
1412 1638 4.743151 CACAACTTAGTTAACTGCAGACGA 59.257 41.667 23.35 1.16 0.00 4.20
1622 1848 3.305539 GCATGCAAAATCTCTGTGTTGGA 60.306 43.478 14.21 0.00 0.00 3.53
2459 2727 9.230122 TCTCATATTTCTATGCAACTTCAACAA 57.770 29.630 0.00 0.00 35.64 2.83
2564 2849 8.635765 ACAAAGGGCCATGTATAATACAATAG 57.364 34.615 12.67 0.00 42.76 1.73
2598 2883 8.530311 CCAGATCACATAATACAAGCTCTATCT 58.470 37.037 0.00 0.00 0.00 1.98
2656 2943 7.739825 AGCAGTATTTAGATTGGCAGAGATAA 58.260 34.615 0.00 0.00 0.00 1.75
2657 2944 7.308450 AGCAGTATTTAGATTGGCAGAGATA 57.692 36.000 0.00 0.00 0.00 1.98


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

AutoCloner maintained by Alex Coulton.