Multiple sequence alignment - TraesCS2A01G242000

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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 TraesCS2A01G242000 chr2A 100.000 3101 0 0 1 3101 335836878 335839978 0 5727
1 TraesCS2A01G242000 chr3D 97.436 3120 57 7 1 3101 589281311 589278196 0 5297
2 TraesCS2A01G242000 chr1A 97.213 3122 57 5 1 3101 554510485 554513597 0 5256
3 TraesCS2A01G242000 chr5D 97.085 3122 68 5 1 3101 6187170 6190289 0 5240
4 TraesCS2A01G242000 chr5D 96.988 3121 72 4 1 3101 503279995 503276877 0 5223
5 TraesCS2A01G242000 chr5D 96.093 3123 95 9 1 3101 432405265 432402148 0 5066
6 TraesCS2A01G242000 chr5D 97.678 2799 51 2 316 3101 503216770 503219567 0 4796
7 TraesCS2A01G242000 chr1D 96.925 3122 73 5 1 3101 254399880 254396761 0 5212
8 TraesCS2A01G242000 chr4B 95.328 3125 106 12 1 3101 308694712 308697820 0 4926
9 TraesCS2A01G242000 chr4A 95.145 3131 118 12 1 3101 309513353 309516479 0 4909
10 TraesCS2A01G242000 chrUn 97.679 2800 48 5 316 3101 93411079 93408283 0 4795
11 TraesCS2A01G242000 chrUn 97.357 2800 58 4 316 3101 216520051 216517254 0 4747
12 TraesCS2A01G242000 chrUn 97.023 571 10 2 1 564 239346034 239345464 0 953
13 TraesCS2A01G242000 chr3B 97.607 2800 51 4 316 3101 201525576 201528373 0 4785
14 TraesCS2A01G242000 chr6D 97.571 2800 53 3 316 3101 168253477 168256275 0 4780
15 TraesCS2A01G242000 chr6D 95.884 1239 25 7 1 1214 45517800 45519037 0 1982
16 TraesCS2A01G242000 chr2B 96.704 2822 71 6 293 3101 474906986 474909798 0 4676


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 TraesCS2A01G242000 chr2A 335836878 335839978 3100 False 5727 5727 100.000 1 3101 1 chr2A.!!$F1 3100
1 TraesCS2A01G242000 chr3D 589278196 589281311 3115 True 5297 5297 97.436 1 3101 1 chr3D.!!$R1 3100
2 TraesCS2A01G242000 chr1A 554510485 554513597 3112 False 5256 5256 97.213 1 3101 1 chr1A.!!$F1 3100
3 TraesCS2A01G242000 chr5D 6187170 6190289 3119 False 5240 5240 97.085 1 3101 1 chr5D.!!$F1 3100
4 TraesCS2A01G242000 chr5D 503276877 503279995 3118 True 5223 5223 96.988 1 3101 1 chr5D.!!$R2 3100
5 TraesCS2A01G242000 chr5D 432402148 432405265 3117 True 5066 5066 96.093 1 3101 1 chr5D.!!$R1 3100
6 TraesCS2A01G242000 chr5D 503216770 503219567 2797 False 4796 4796 97.678 316 3101 1 chr5D.!!$F2 2785
7 TraesCS2A01G242000 chr1D 254396761 254399880 3119 True 5212 5212 96.925 1 3101 1 chr1D.!!$R1 3100
8 TraesCS2A01G242000 chr4B 308694712 308697820 3108 False 4926 4926 95.328 1 3101 1 chr4B.!!$F1 3100
9 TraesCS2A01G242000 chr4A 309513353 309516479 3126 False 4909 4909 95.145 1 3101 1 chr4A.!!$F1 3100
10 TraesCS2A01G242000 chrUn 93408283 93411079 2796 True 4795 4795 97.679 316 3101 1 chrUn.!!$R1 2785
11 TraesCS2A01G242000 chrUn 216517254 216520051 2797 True 4747 4747 97.357 316 3101 1 chrUn.!!$R2 2785
12 TraesCS2A01G242000 chrUn 239345464 239346034 570 True 953 953 97.023 1 564 1 chrUn.!!$R3 563
13 TraesCS2A01G242000 chr3B 201525576 201528373 2797 False 4785 4785 97.607 316 3101 1 chr3B.!!$F1 2785
14 TraesCS2A01G242000 chr6D 168253477 168256275 2798 False 4780 4780 97.571 316 3101 1 chr6D.!!$F2 2785
15 TraesCS2A01G242000 chr6D 45517800 45519037 1237 False 1982 1982 95.884 1 1214 1 chr6D.!!$F1 1213
16 TraesCS2A01G242000 chr2B 474906986 474909798 2812 False 4676 4676 96.704 293 3101 1 chr2B.!!$F1 2808

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
976 1014 0.258774 AAGCGCAGGATAACCCCAAT 59.741 50.0 11.47 0.0 36.73 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2272 2315 1.846712 TTGATCCATGGACGGCACCA 61.847 55.0 18.99 5.68 44.41 4.17 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
55 56 9.408069 CTTTAGGTATTAGTACTATGGCTTTCG 57.592 37.037 2.79 0.00 0.00 3.46
417 433 5.697473 TTTTCATAACTCGTGAAATGCCA 57.303 34.783 2.57 0.00 43.00 4.92
712 733 5.048921 TGTCCAATATCTCGATCGAAGTACC 60.049 44.000 19.92 2.08 0.00 3.34
818 854 2.513666 GAATCCACCATGCGCGGA 60.514 61.111 8.83 5.00 0.00 5.54
976 1014 0.258774 AAGCGCAGGATAACCCCAAT 59.741 50.000 11.47 0.00 36.73 3.16
1104 1144 2.544685 CAACACTTAGATCCGGCTCTG 58.455 52.381 18.06 4.62 0.00 3.35
1413 1456 7.971168 AGCATACGACTTTCTAGATGTATATGC 59.029 37.037 25.18 25.18 38.81 3.14
1427 1470 6.887002 AGATGTATATGCCGATCTCTAGACAA 59.113 38.462 0.00 0.00 0.00 3.18
1504 1547 2.951642 GGAATCCAAATCTGCCGAATCA 59.048 45.455 0.00 0.00 0.00 2.57
1538 1581 6.916909 TGATCTTCTACATCCTAGGTCTCTT 58.083 40.000 9.08 0.00 0.00 2.85
1581 1624 7.876936 ATGTTCTTCATGTAGCATTCAGATT 57.123 32.000 0.00 0.00 35.19 2.40
1637 1680 5.867716 CACATATTATGGGTAACGTAGGAGC 59.132 44.000 8.48 0.00 37.60 4.70
1652 1695 0.746659 GGAGCCATCCCAATTTTCCG 59.253 55.000 0.00 0.00 40.03 4.30
1737 1780 1.730851 AACCCGTCCTCCTCTCTTTT 58.269 50.000 0.00 0.00 0.00 2.27
1780 1823 2.458951 TGTGCGTGCTTCAAACAATTC 58.541 42.857 0.00 0.00 0.00 2.17
1793 1836 7.587037 TTCAAACAATTCTGTCTTCTCCATT 57.413 32.000 0.00 0.00 33.45 3.16
1794 1837 8.690203 TTCAAACAATTCTGTCTTCTCCATTA 57.310 30.769 0.00 0.00 33.45 1.90
2148 2191 5.182570 TCGATTAGGGTCGTATTCTATGGTG 59.817 44.000 0.00 0.00 42.07 4.17
2151 2194 3.912248 AGGGTCGTATTCTATGGTGACT 58.088 45.455 0.00 0.00 0.00 3.41
2245 2288 5.222079 TCTATGCCTTGCGGTAATGATTA 57.778 39.130 0.00 0.00 0.00 1.75
2248 2291 4.409718 TGCCTTGCGGTAATGATTACTA 57.590 40.909 14.34 0.38 36.39 1.82
2272 2315 5.562635 TGGAATTACGACCTTTACCACAAT 58.437 37.500 0.00 0.00 0.00 2.71
2331 2374 0.601558 TCACTTGCCTGTCTACGGTC 59.398 55.000 0.00 0.00 0.00 4.79
2586 2630 6.272822 ACCCAATGCTTTATTTCTGTCTTC 57.727 37.500 0.00 0.00 0.00 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
272 279 6.918892 TGTTGATATTGGGTATTTCTGTCG 57.081 37.500 0.00 0.00 0.00 4.35
417 433 0.255033 GGGGGAATTCGTGCCTACTT 59.745 55.000 0.00 0.00 37.99 2.24
818 854 0.725117 GCGAACGACGGGAATTGAAT 59.275 50.000 0.00 0.00 42.83 2.57
1413 1456 5.720371 AGATCCATTTGTCTAGAGATCGG 57.280 43.478 10.21 3.55 36.19 4.18
1504 1547 8.489676 AGGATGTAGAAGATCATAACATGAGT 57.510 34.615 0.00 0.00 43.53 3.41
1581 1624 7.477494 TCGACGTAATTTCATAGAGTCATTCA 58.523 34.615 0.00 0.00 0.00 2.57
1637 1680 1.437160 CGGCGGAAAATTGGGATGG 59.563 57.895 0.00 0.00 0.00 3.51
1644 1687 2.361992 GACCCCCGGCGGAAAATT 60.362 61.111 30.79 6.33 0.00 1.82
1652 1695 0.547553 TGGTAATTAAGACCCCCGGC 59.452 55.000 0.00 0.00 35.99 6.13
1737 1780 1.673009 CGGAAGCGCCCCTTGTTTA 60.673 57.895 2.29 0.00 32.78 2.01
1780 1823 9.253832 AGAGATATGGTATAATGGAGAAGACAG 57.746 37.037 0.00 0.00 0.00 3.51
1984 2027 3.421844 GAAATGCCCTACCTTTGAGTGT 58.578 45.455 0.00 0.00 0.00 3.55
2245 2288 6.070653 TGTGGTAAAGGTCGTAATTCCATAGT 60.071 38.462 0.00 0.00 0.00 2.12
2248 2291 5.168647 TGTGGTAAAGGTCGTAATTCCAT 57.831 39.130 0.00 0.00 0.00 3.41
2272 2315 1.846712 TTGATCCATGGACGGCACCA 61.847 55.000 18.99 5.68 44.41 4.17
2522 2566 2.187958 AGGTGGTAGCTGTGAATAGCA 58.812 47.619 0.00 0.00 46.07 3.49
2668 2713 6.265422 GGGAAAGTCGATTTATGGATGGAATT 59.735 38.462 0.00 0.00 0.00 2.17
2771 2816 9.382275 CATCCATCATCCATACATAACGAATTA 57.618 33.333 0.00 0.00 0.00 1.40
3023 3068 5.642063 GGTGTTTTCATAGTCATCTCCGAAA 59.358 40.000 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.