Multiple sequence alignment - TraesCS2B01G269100

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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 TraesCS2B01G269100 chr2B 100.000 2264 0 0 1 2264 364338091 364335828 0.000000e+00 4181.0
1 TraesCS2B01G269100 chr5B 98.746 1515 11 4 751 2264 281832097 281830590 0.000000e+00 2686.0
2 TraesCS2B01G269100 chr5B 97.203 1573 26 7 704 2264 351468918 351467352 0.000000e+00 2645.0
3 TraesCS2B01G269100 chr5B 99.573 702 3 0 1 702 281833556 281832855 0.000000e+00 1280.0
4 TraesCS2B01G269100 chr5B 99.714 699 2 0 1 699 436475851 436476549 0.000000e+00 1280.0
5 TraesCS2B01G269100 chr7B 97.332 1574 22 7 704 2264 102653310 102654876 0.000000e+00 2656.0
6 TraesCS2B01G269100 chr7B 97.014 1574 27 7 704 2264 133431956 133430390 0.000000e+00 2628.0
7 TraesCS2B01G269100 chr7B 99.573 702 3 0 1 702 133433356 133432655 0.000000e+00 1280.0
8 TraesCS2B01G269100 chr4B 97.268 1574 23 7 704 2264 649623865 649625431 0.000000e+00 2651.0
9 TraesCS2B01G269100 chr4B 99.714 699 2 0 1 699 655790275 655790973 0.000000e+00 1280.0
10 TraesCS2B01G269100 chr4B 77.160 162 13 16 704 853 49106198 49106347 3.120000e-09 73.1
11 TraesCS2B01G269100 chr4B 76.101 159 14 15 704 850 402786619 402786473 6.750000e-06 62.1
12 TraesCS2B01G269100 chr5A 97.205 1574 24 7 704 2264 590566427 590567993 0.000000e+00 2645.0
13 TraesCS2B01G269100 chr4A 98.218 1515 19 4 751 2264 735293451 735294958 0.000000e+00 2641.0
14 TraesCS2B01G269100 chr2A 98.085 1514 23 4 751 2264 728934428 728935935 0.000000e+00 2630.0
15 TraesCS2B01G269100 chr2A 99.714 699 2 0 1 699 728932969 728933667 0.000000e+00 1280.0
16 TraesCS2B01G269100 chr2A 99.573 702 2 1 1 702 148615986 148615286 0.000000e+00 1279.0
17 TraesCS2B01G269100 chr7A 97.012 1573 28 8 704 2264 16005709 16007274 0.000000e+00 2627.0
18 TraesCS2B01G269100 chrUn 100.000 1086 0 0 207 1292 441532116 441533201 0.000000e+00 2006.0
19 TraesCS2B01G269100 chrUn 91.925 322 8 8 704 1013 418808795 418808480 3.450000e-118 435.0
20 TraesCS2B01G269100 chrUn 94.118 85 5 0 726 810 441532671 441532755 1.820000e-26 130.0
21 TraesCS2B01G269100 chrUn 82.292 96 5 10 751 846 134558317 134558234 3.120000e-09 73.1
22 TraesCS2B01G269100 chr1D 89.566 1083 72 14 704 1750 297551468 297550391 0.000000e+00 1336.0
23 TraesCS2B01G269100 chr1D 90.000 580 23 18 754 1310 490889415 490889982 0.000000e+00 717.0
24 TraesCS2B01G269100 chr6A 99.714 699 2 0 1 699 466678210 466678908 0.000000e+00 1280.0
25 TraesCS2B01G269100 chr3A 99.714 699 2 0 1 699 237052253 237052951 0.000000e+00 1280.0
26 TraesCS2B01G269100 chr6D 77.632 152 10 12 704 843 956902 957041 1.120000e-08 71.3


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 TraesCS2B01G269100 chr2B 364335828 364338091 2263 True 4181 4181 100.0000 1 2264 1 chr2B.!!$R1 2263
1 TraesCS2B01G269100 chr5B 351467352 351468918 1566 True 2645 2645 97.2030 704 2264 1 chr5B.!!$R1 1560
2 TraesCS2B01G269100 chr5B 281830590 281833556 2966 True 1983 2686 99.1595 1 2264 2 chr5B.!!$R2 2263
3 TraesCS2B01G269100 chr5B 436475851 436476549 698 False 1280 1280 99.7140 1 699 1 chr5B.!!$F1 698
4 TraesCS2B01G269100 chr7B 102653310 102654876 1566 False 2656 2656 97.3320 704 2264 1 chr7B.!!$F1 1560
5 TraesCS2B01G269100 chr7B 133430390 133433356 2966 True 1954 2628 98.2935 1 2264 2 chr7B.!!$R1 2263
6 TraesCS2B01G269100 chr4B 649623865 649625431 1566 False 2651 2651 97.2680 704 2264 1 chr4B.!!$F2 1560
7 TraesCS2B01G269100 chr4B 655790275 655790973 698 False 1280 1280 99.7140 1 699 1 chr4B.!!$F3 698
8 TraesCS2B01G269100 chr5A 590566427 590567993 1566 False 2645 2645 97.2050 704 2264 1 chr5A.!!$F1 1560
9 TraesCS2B01G269100 chr4A 735293451 735294958 1507 False 2641 2641 98.2180 751 2264 1 chr4A.!!$F1 1513
10 TraesCS2B01G269100 chr2A 728932969 728935935 2966 False 1955 2630 98.8995 1 2264 2 chr2A.!!$F1 2263
11 TraesCS2B01G269100 chr2A 148615286 148615986 700 True 1279 1279 99.5730 1 702 1 chr2A.!!$R1 701
12 TraesCS2B01G269100 chr7A 16005709 16007274 1565 False 2627 2627 97.0120 704 2264 1 chr7A.!!$F1 1560
13 TraesCS2B01G269100 chrUn 441532116 441533201 1085 False 1068 2006 97.0590 207 1292 2 chrUn.!!$F1 1085
14 TraesCS2B01G269100 chr1D 297550391 297551468 1077 True 1336 1336 89.5660 704 1750 1 chr1D.!!$R1 1046
15 TraesCS2B01G269100 chr1D 490889415 490889982 567 False 717 717 90.0000 754 1310 1 chr1D.!!$F1 556
16 TraesCS2B01G269100 chr6A 466678210 466678908 698 False 1280 1280 99.7140 1 699 1 chr6A.!!$F1 698
17 TraesCS2B01G269100 chr3A 237052253 237052951 698 False 1280 1280 99.7140 1 699 1 chr3A.!!$F1 698

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
35 36 0.87439 GAGGCGTTTCAGCATTGTCA 59.126 50.0 0.0 0.0 39.27 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1891 2640 0.107945 GGCCTGGTGTTTTTGCACAA 60.108 50.0 0.0 0.0 40.89 3.33 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
35 36 0.874390 GAGGCGTTTCAGCATTGTCA 59.126 50.000 0.00 0.0 39.27 3.58
721 1380 1.187087 GGTGCTAGAGGTGCTAGTGT 58.813 55.000 0.00 0.0 46.81 3.55
722 1381 1.550976 GGTGCTAGAGGTGCTAGTGTT 59.449 52.381 0.00 0.0 46.81 3.32
723 1382 2.417515 GGTGCTAGAGGTGCTAGTGTTC 60.418 54.545 0.00 0.0 46.81 3.18
724 1383 1.472878 TGCTAGAGGTGCTAGTGTTCG 59.527 52.381 0.00 0.0 46.81 3.95
725 1384 1.473278 GCTAGAGGTGCTAGTGTTCGT 59.527 52.381 0.00 0.0 46.81 3.85
726 1385 2.681848 GCTAGAGGTGCTAGTGTTCGTA 59.318 50.000 0.00 0.0 46.81 3.43
727 1386 3.242804 GCTAGAGGTGCTAGTGTTCGTAG 60.243 52.174 0.00 0.0 46.81 3.51
728 1387 3.069079 AGAGGTGCTAGTGTTCGTAGA 57.931 47.619 0.00 0.0 0.00 2.59
729 1388 3.011119 AGAGGTGCTAGTGTTCGTAGAG 58.989 50.000 0.00 0.0 38.43 2.43
730 1389 2.093106 AGGTGCTAGTGTTCGTAGAGG 58.907 52.381 0.00 0.0 38.43 3.69
731 1390 1.817447 GGTGCTAGTGTTCGTAGAGGT 59.183 52.381 0.00 0.0 38.43 3.85
732 1391 2.415625 GGTGCTAGTGTTCGTAGAGGTG 60.416 54.545 0.00 0.0 38.43 4.00
733 1392 1.201647 TGCTAGTGTTCGTAGAGGTGC 59.798 52.381 0.00 0.0 38.43 5.01
734 1393 1.473278 GCTAGTGTTCGTAGAGGTGCT 59.527 52.381 0.00 0.0 38.43 4.40
735 1394 2.681848 GCTAGTGTTCGTAGAGGTGCTA 59.318 50.000 0.00 0.0 38.43 3.49
739 1398 2.228343 GTGTTCGTAGAGGTGCTAGTGT 59.772 50.000 0.00 0.0 38.43 3.55
1533 2281 1.600916 GGGCACGCAAAGAGAAGGT 60.601 57.895 0.00 0.0 0.00 3.50
1891 2640 6.816140 TGCTAAGCAAAAACTTTAACAAGCTT 59.184 30.769 0.00 0.0 42.87 3.74
2215 2964 3.319198 GGAACCCTGGCGTCTGGA 61.319 66.667 15.35 0.0 34.32 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 3.511934 GCCATCTATAGACAAGACCGGAT 59.488 47.826 9.46 0.0 0.00 4.18
721 1380 2.161012 CGAACACTAGCACCTCTACGAA 59.839 50.000 0.00 0.0 0.00 3.85
722 1381 1.736126 CGAACACTAGCACCTCTACGA 59.264 52.381 0.00 0.0 0.00 3.43
723 1382 1.467734 ACGAACACTAGCACCTCTACG 59.532 52.381 0.00 0.0 0.00 3.51
724 1383 3.937706 TCTACGAACACTAGCACCTCTAC 59.062 47.826 0.00 0.0 0.00 2.59
725 1384 4.190001 CTCTACGAACACTAGCACCTCTA 58.810 47.826 0.00 0.0 0.00 2.43
726 1385 3.011119 CTCTACGAACACTAGCACCTCT 58.989 50.000 0.00 0.0 0.00 3.69
727 1386 2.097791 CCTCTACGAACACTAGCACCTC 59.902 54.545 0.00 0.0 0.00 3.85
728 1387 2.093106 CCTCTACGAACACTAGCACCT 58.907 52.381 0.00 0.0 0.00 4.00
729 1388 1.134560 CCCTCTACGAACACTAGCACC 59.865 57.143 0.00 0.0 0.00 5.01
730 1389 2.089980 TCCCTCTACGAACACTAGCAC 58.910 52.381 0.00 0.0 0.00 4.40
731 1390 2.366533 CTCCCTCTACGAACACTAGCA 58.633 52.381 0.00 0.0 0.00 3.49
732 1391 1.065851 GCTCCCTCTACGAACACTAGC 59.934 57.143 0.00 0.0 0.00 3.42
733 1392 2.097791 GTGCTCCCTCTACGAACACTAG 59.902 54.545 0.00 0.0 0.00 2.57
734 1393 2.089980 GTGCTCCCTCTACGAACACTA 58.910 52.381 0.00 0.0 0.00 2.74
735 1394 0.889306 GTGCTCCCTCTACGAACACT 59.111 55.000 0.00 0.0 0.00 3.55
739 1398 1.272490 CACTTGTGCTCCCTCTACGAA 59.728 52.381 0.00 0.0 0.00 3.85
1435 2183 1.043116 CCCGTGCATAGGACTCCTCA 61.043 60.000 12.15 0.0 34.61 3.86
1533 2281 0.891373 CCTCTCTTCTTGACGAGCCA 59.109 55.000 0.00 0.0 0.00 4.75
1891 2640 0.107945 GGCCTGGTGTTTTTGCACAA 60.108 50.000 0.00 0.0 40.89 3.33


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

AutoCloner maintained by Alex Coulton.