Multiple sequence alignment - TraesCS2B01G454700

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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 TraesCS2B01G454700 chr2B 100.000 2264 0 0 1 2264 649657461 649655198 0.000000e+00 4181
1 TraesCS2B01G454700 chr2B 92.063 1726 111 14 1 1702 579908099 579909822 0.000000e+00 2405
2 TraesCS2B01G454700 chr3B 96.614 1713 46 2 1 1702 40993586 40991875 0.000000e+00 2832
3 TraesCS2B01G454700 chr3B 92.601 446 31 2 1699 2143 40991586 40991142 6.820000e-180 640
4 TraesCS2B01G454700 chr3B 94.344 389 20 2 1697 2084 40991517 40991130 1.500000e-166 595
5 TraesCS2B01G454700 chr3B 91.415 431 35 2 1714 2143 40991642 40991213 6.960000e-165 590
6 TraesCS2B01G454700 chr3B 97.899 238 5 0 2027 2264 40989655 40989418 1.620000e-111 412
7 TraesCS2B01G454700 chr4B 95.918 1715 57 5 1 1702 664037784 664036070 0.000000e+00 2767
8 TraesCS2B01G454700 chr4B 92.416 567 43 0 1698 2264 664035661 664035095 0.000000e+00 809
9 TraesCS2B01G454700 chr7D 95.346 1719 57 5 1 1702 16799697 16797985 0.000000e+00 2710
10 TraesCS2B01G454700 chr7D 84.238 571 82 5 1697 2263 16797666 16797100 1.180000e-152 549
11 TraesCS2B01G454700 chr4A 95.116 1720 65 6 1 1702 514407630 514405912 0.000000e+00 2693
12 TraesCS2B01G454700 chr6A 93.310 1719 98 6 1 1702 387215226 387216944 0.000000e+00 2521
13 TraesCS2B01G454700 chr5B 93.198 1720 98 5 1 1702 426532757 426534475 0.000000e+00 2510
14 TraesCS2B01G454700 chr5B 92.903 1719 104 4 1 1702 658084097 658085814 0.000000e+00 2483
15 TraesCS2B01G454700 chr5B 92.521 1551 104 7 1 1539 16010569 16012119 0.000000e+00 2211
16 TraesCS2B01G454700 chr5B 95.325 877 30 1 837 1702 35438901 35439777 0.000000e+00 1382
17 TraesCS2B01G454700 chr5B 90.685 569 50 3 1697 2264 35439973 35440539 0.000000e+00 754
18 TraesCS2B01G454700 chr1A 92.696 1109 56 7 617 1702 480958738 480959844 0.000000e+00 1576
19 TraesCS2B01G454700 chr7A 95.214 982 35 2 732 1702 130557907 130558887 0.000000e+00 1543
20 TraesCS2B01G454700 chr7A 87.324 568 72 0 1697 2264 595030212 595029645 0.000000e+00 651
21 TraesCS2B01G454700 chr7A 85.811 444 63 0 1700 2143 595030422 595029979 2.630000e-129 472
22 TraesCS2B01G454700 chr6B 89.474 570 56 4 1697 2264 425597951 425598518 0.000000e+00 717
23 TraesCS2B01G454700 chr6B 94.010 384 12 2 1330 1702 425597321 425597704 2.520000e-159 571
24 TraesCS2B01G454700 chr1D 87.992 533 61 3 1734 2264 490890569 490891100 5.310000e-176 627
25 TraesCS2B01G454700 chr7B 86.041 437 61 0 1697 2133 34280348 34279912 9.470000e-129 470


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 TraesCS2B01G454700 chr2B 649655198 649657461 2263 True 4181.0 4181 100.0000 1 2264 1 chr2B.!!$R1 2263
1 TraesCS2B01G454700 chr2B 579908099 579909822 1723 False 2405.0 2405 92.0630 1 1702 1 chr2B.!!$F1 1701
2 TraesCS2B01G454700 chr3B 40989418 40993586 4168 True 1013.8 2832 94.5746 1 2264 5 chr3B.!!$R1 2263
3 TraesCS2B01G454700 chr4B 664035095 664037784 2689 True 1788.0 2767 94.1670 1 2264 2 chr4B.!!$R1 2263
4 TraesCS2B01G454700 chr7D 16797100 16799697 2597 True 1629.5 2710 89.7920 1 2263 2 chr7D.!!$R1 2262
5 TraesCS2B01G454700 chr4A 514405912 514407630 1718 True 2693.0 2693 95.1160 1 1702 1 chr4A.!!$R1 1701
6 TraesCS2B01G454700 chr6A 387215226 387216944 1718 False 2521.0 2521 93.3100 1 1702 1 chr6A.!!$F1 1701
7 TraesCS2B01G454700 chr5B 426532757 426534475 1718 False 2510.0 2510 93.1980 1 1702 1 chr5B.!!$F2 1701
8 TraesCS2B01G454700 chr5B 658084097 658085814 1717 False 2483.0 2483 92.9030 1 1702 1 chr5B.!!$F3 1701
9 TraesCS2B01G454700 chr5B 16010569 16012119 1550 False 2211.0 2211 92.5210 1 1539 1 chr5B.!!$F1 1538
10 TraesCS2B01G454700 chr5B 35438901 35440539 1638 False 1068.0 1382 93.0050 837 2264 2 chr5B.!!$F4 1427
11 TraesCS2B01G454700 chr1A 480958738 480959844 1106 False 1576.0 1576 92.6960 617 1702 1 chr1A.!!$F1 1085
12 TraesCS2B01G454700 chr7A 130557907 130558887 980 False 1543.0 1543 95.2140 732 1702 1 chr7A.!!$F1 970
13 TraesCS2B01G454700 chr7A 595029645 595030422 777 True 561.5 651 86.5675 1697 2264 2 chr7A.!!$R1 567
14 TraesCS2B01G454700 chr6B 425597321 425598518 1197 False 644.0 717 91.7420 1330 2264 2 chr6B.!!$F1 934
15 TraesCS2B01G454700 chr1D 490890569 490891100 531 False 627.0 627 87.9920 1734 2264 1 chr1D.!!$F1 530

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
635 637 0.190069 AGAGGTGGTAGTGGTGGTCA 59.81 55.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1498 1617 0.532573 CCCTCTCTTGCTCACGCTTA 59.467 55.0 0.0 0.0 36.97 3.09 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
71 72 1.590525 GTGGCACAACACGAGACGA 60.591 57.895 13.86 0.00 44.16 4.20
180 181 1.431440 GCATTTGATAACGGCGGCA 59.569 52.632 13.24 0.28 0.00 5.69
384 385 5.646215 AGAAGGAGAACTAAGAGGTTCAGA 58.354 41.667 9.50 0.00 45.52 3.27
468 469 2.703007 GGAGGCTCCTGACACTATCAAT 59.297 50.000 26.44 0.00 36.69 2.57
513 515 1.068402 CACAATGAGCGGACATGCAAA 60.068 47.619 0.00 0.00 37.31 3.68
530 532 7.929159 ACATGCAAAAATAGGAAAACCAAAAG 58.071 30.769 0.00 0.00 0.00 2.27
635 637 0.190069 AGAGGTGGTAGTGGTGGTCA 59.810 55.000 0.00 0.00 0.00 4.02
675 714 0.680280 GAGGTGGTGGTCGAGCTAGA 60.680 60.000 16.64 0.00 30.83 2.43
762 873 0.681564 CTAGAGGTGGTGGTCGAGCT 60.682 60.000 16.64 0.00 33.17 4.09
797 908 1.122019 GGTGGTGGTGGTCAGAGAGT 61.122 60.000 0.00 0.00 0.00 3.24
848 959 5.177696 GTCGTAGAGGAATGGTTGATAATGC 59.822 44.000 0.00 0.00 36.95 3.56
867 978 3.340034 TGCATCGACCTTCGGTTATTTT 58.660 40.909 0.00 0.00 40.88 1.82
1391 1510 3.576982 TCACGAGGTACCAAAAGATGTCT 59.423 43.478 15.94 0.00 0.00 3.41
1498 1617 3.007398 AGAAGGAGAAGAACGAGCACAAT 59.993 43.478 0.00 0.00 0.00 2.71
1544 1663 1.633774 AGAGAAGGAGGCTCGTCAAA 58.366 50.000 10.54 0.00 37.46 2.69
1698 1840 9.906660 TTGTTTAATGTATGAACTTGTCATTCC 57.093 29.630 0.00 0.00 45.13 3.01
1820 2442 1.542375 ACCCAGATGCCAAGGTCCT 60.542 57.895 0.00 0.00 0.00 3.85
1831 2453 2.895424 AAGGTCCTTGGCGTCTGGG 61.895 63.158 2.38 0.00 0.00 4.45
1857 2479 5.189180 AGTATCCAGAGAGCATTTTTCCAC 58.811 41.667 0.00 0.00 0.00 4.02
1876 2498 3.432046 CCACTTTGGAAATTTGCACACCT 60.432 43.478 12.36 0.00 40.96 4.00
1971 2807 1.041447 GCTAAGGTCCCTGGCGTCTA 61.041 60.000 0.00 0.00 0.00 2.59
2037 2873 3.637273 GACGCCAAGGTCCCTGGT 61.637 66.667 8.38 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 72 3.514706 TGCAGCACCACCATATTGAAAAT 59.485 39.130 0.00 0.00 0.00 1.82
180 181 3.418684 ACAGGTATGTTTCTCGCCTTT 57.581 42.857 0.00 0.00 35.63 3.11
220 221 2.439409 CACATGGAACTCTTGCATCCA 58.561 47.619 8.38 8.38 46.60 3.41
384 385 1.701847 GCCAGGTCATCCATATCACCT 59.298 52.381 0.00 0.00 40.05 4.00
468 469 3.345607 TTCACCGCACACCCCACAA 62.346 57.895 0.00 0.00 0.00 3.33
530 532 3.626217 ACCTCCACGACTTGTTTTTCTTC 59.374 43.478 0.00 0.00 0.00 2.87
635 637 5.381757 CTCTAGCACTTGTACTCCCTCTAT 58.618 45.833 0.00 0.00 0.00 1.98
675 714 1.072331 CCACCACCTCTAGCACTTGTT 59.928 52.381 0.00 0.00 0.00 2.83
762 873 1.550524 CCACCTCTAGCACTTGTGCTA 59.449 52.381 27.11 27.11 44.28 3.49
773 884 0.898320 CTGACCACCACCACCTCTAG 59.102 60.000 0.00 0.00 0.00 2.43
783 894 1.618837 GTGCTTACTCTCTGACCACCA 59.381 52.381 0.00 0.00 0.00 4.17
797 908 2.028112 CCACCTCTAGCACTTGTGCTTA 60.028 50.000 29.37 18.28 43.52 3.09
867 978 7.921041 ACTAGATCAACCATCTGGATTAAGA 57.079 36.000 2.55 0.00 41.66 2.10
950 1063 6.591448 CACAAGACATAAAGAGAGTACATGCA 59.409 38.462 0.00 0.00 0.00 3.96
1086 1199 1.472376 GGCACATCCTTCTCCTTCTCG 60.472 57.143 0.00 0.00 0.00 4.04
1391 1510 5.892119 AGTAATCTCGATGTTGGTCCTCTTA 59.108 40.000 0.00 0.00 0.00 2.10
1498 1617 0.532573 CCCTCTCTTGCTCACGCTTA 59.467 55.000 0.00 0.00 36.97 3.09
1698 1840 4.279169 TCCAAACTGGAAAAATGCTCTCTG 59.721 41.667 0.00 0.00 45.00 3.35
1820 2442 1.483415 GGATACTAACCCAGACGCCAA 59.517 52.381 0.00 0.00 0.00 4.52
1831 2453 6.823689 TGGAAAAATGCTCTCTGGATACTAAC 59.176 38.462 0.00 0.00 37.61 2.34
1857 2479 5.222631 GTCTAGGTGTGCAAATTTCCAAAG 58.777 41.667 0.00 0.00 0.00 2.77
1876 2498 1.987855 CCAGGGACCTTGGCGTCTA 60.988 63.158 10.14 0.00 33.07 2.59
1898 2592 4.737855 TGCTCTCTGGATACTAAACCAC 57.262 45.455 0.00 0.00 37.61 4.16
2005 2841 0.878416 GCGTCTGGGTGTGCAAATTA 59.122 50.000 0.00 0.00 0.00 1.40
2084 4523 2.847234 ACCTTGGCGTCTGGGTGA 60.847 61.111 3.86 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.