Multiple sequence alignment - TraesCS1A01G368900

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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 TraesCS1A01G368900 chr1A 100.000 2446 0 0 1 2446 546518495 546520940 0.000000e+00 4518
1 TraesCS1A01G368900 chr7D 90.628 1910 124 28 585 2446 127375812 127377714 0.000000e+00 2484
2 TraesCS1A01G368900 chr7D 88.914 1786 142 32 585 2326 58131750 58129977 0.000000e+00 2150
3 TraesCS1A01G368900 chr7D 94.810 578 27 3 7 583 155825999 155825424 0.000000e+00 898
4 TraesCS1A01G368900 chr5D 90.110 1911 134 30 585 2446 42206483 42208387 0.000000e+00 2431
5 TraesCS1A01G368900 chr5D 95.156 578 25 2 7 583 556601888 556601313 0.000000e+00 909
6 TraesCS1A01G368900 chr5D 94.819 579 26 2 7 583 367216353 367215777 0.000000e+00 900
7 TraesCS1A01G368900 chr5D 94.965 576 25 3 7 581 553944381 553943809 0.000000e+00 900
8 TraesCS1A01G368900 chr2D 89.644 1912 141 32 585 2446 639485011 639483107 0.000000e+00 2381
9 TraesCS1A01G368900 chr2D 88.778 1907 153 37 585 2443 345251460 345253353 0.000000e+00 2279
10 TraesCS1A01G368900 chr2D 94.674 582 26 3 1 581 128993384 128993961 0.000000e+00 898
11 TraesCS1A01G368900 chr2D 94.058 589 31 4 1 587 9110767 9111353 0.000000e+00 891
12 TraesCS1A01G368900 chr2D 78.095 735 135 15 890 1604 37276725 37275997 2.230000e-120 442
13 TraesCS1A01G368900 chr1D 89.523 1909 143 31 585 2443 182580742 182582643 0.000000e+00 2364
14 TraesCS1A01G368900 chr1D 89.203 1908 151 29 585 2443 71287179 71289080 0.000000e+00 2331
15 TraesCS1A01G368900 chr2A 98.050 1333 23 3 1116 2446 32113979 32115310 0.000000e+00 2314
16 TraesCS1A01G368900 chr2A 96.833 442 11 1 582 1020 32113532 32113973 0.000000e+00 736
17 TraesCS1A01G368900 chr6B 94.692 584 28 2 1 583 65232261 65232842 0.000000e+00 904
18 TraesCS1A01G368900 chr4D 94.369 586 29 2 1 583 30760216 30760800 0.000000e+00 896
19 TraesCS1A01G368900 chr4D 94.783 575 28 1 7 581 8587175 8586603 0.000000e+00 894
20 TraesCS1A01G368900 chr3A 85.526 152 20 2 588 738 503709843 503709693 9.050000e-35 158


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 TraesCS1A01G368900 chr1A 546518495 546520940 2445 False 4518 4518 100.0000 1 2446 1 chr1A.!!$F1 2445
1 TraesCS1A01G368900 chr7D 127375812 127377714 1902 False 2484 2484 90.6280 585 2446 1 chr7D.!!$F1 1861
2 TraesCS1A01G368900 chr7D 58129977 58131750 1773 True 2150 2150 88.9140 585 2326 1 chr7D.!!$R1 1741
3 TraesCS1A01G368900 chr7D 155825424 155825999 575 True 898 898 94.8100 7 583 1 chr7D.!!$R2 576
4 TraesCS1A01G368900 chr5D 42206483 42208387 1904 False 2431 2431 90.1100 585 2446 1 chr5D.!!$F1 1861
5 TraesCS1A01G368900 chr5D 556601313 556601888 575 True 909 909 95.1560 7 583 1 chr5D.!!$R3 576
6 TraesCS1A01G368900 chr5D 367215777 367216353 576 True 900 900 94.8190 7 583 1 chr5D.!!$R1 576
7 TraesCS1A01G368900 chr5D 553943809 553944381 572 True 900 900 94.9650 7 581 1 chr5D.!!$R2 574
8 TraesCS1A01G368900 chr2D 639483107 639485011 1904 True 2381 2381 89.6440 585 2446 1 chr2D.!!$R2 1861
9 TraesCS1A01G368900 chr2D 345251460 345253353 1893 False 2279 2279 88.7780 585 2443 1 chr2D.!!$F3 1858
10 TraesCS1A01G368900 chr2D 128993384 128993961 577 False 898 898 94.6740 1 581 1 chr2D.!!$F2 580
11 TraesCS1A01G368900 chr2D 9110767 9111353 586 False 891 891 94.0580 1 587 1 chr2D.!!$F1 586
12 TraesCS1A01G368900 chr2D 37275997 37276725 728 True 442 442 78.0950 890 1604 1 chr2D.!!$R1 714
13 TraesCS1A01G368900 chr1D 182580742 182582643 1901 False 2364 2364 89.5230 585 2443 1 chr1D.!!$F2 1858
14 TraesCS1A01G368900 chr1D 71287179 71289080 1901 False 2331 2331 89.2030 585 2443 1 chr1D.!!$F1 1858
15 TraesCS1A01G368900 chr2A 32113532 32115310 1778 False 1525 2314 97.4415 582 2446 2 chr2A.!!$F1 1864
16 TraesCS1A01G368900 chr6B 65232261 65232842 581 False 904 904 94.6920 1 583 1 chr6B.!!$F1 582
17 TraesCS1A01G368900 chr4D 30760216 30760800 584 False 896 896 94.3690 1 583 1 chr4D.!!$F1 582
18 TraesCS1A01G368900 chr4D 8586603 8587175 572 True 894 894 94.7830 7 581 1 chr4D.!!$R1 574

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
120 121 0.111253 CCACCTTGGTGAGCCTCTTT 59.889 55.0 20.27 0.0 35.27 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1566 1595 0.478072 AGGACAACATCTGCCACCAA 59.522 50.0 0.0 0.0 0.0 3.67 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
30 31 8.340618 TCATTTTTCTCAAGATTTGTCTAGGG 57.659 34.615 0.00 0.0 0.00 3.53
120 121 0.111253 CCACCTTGGTGAGCCTCTTT 59.889 55.000 20.27 0.0 35.27 2.52
263 268 3.827898 CGGCCCTCGTCCTGTCTC 61.828 72.222 0.00 0.0 0.00 3.36
337 342 6.942532 AGTGTTTATGACAATTATGCCGAT 57.057 33.333 0.00 0.0 40.65 4.18
349 354 4.787381 TTATGCCGATAAACGTGACATG 57.213 40.909 0.00 0.0 40.78 3.21
350 355 1.364721 TGCCGATAAACGTGACATGG 58.635 50.000 0.00 0.0 40.78 3.66
557 566 5.039333 GCAATGCGCTTGAAGATTAGAAAT 58.961 37.500 19.38 0.0 36.97 2.17
971 984 3.695830 TCTTCTAGGTCGCACCAAATT 57.304 42.857 7.86 0.0 41.95 1.82
1500 1529 2.027024 GTGTGACAGTCGCCGACA 59.973 61.111 20.65 0.0 34.60 4.35
1796 1850 4.890158 ATGAATGATGATGCCTACGGTA 57.110 40.909 0.00 0.0 0.00 4.02
1838 1892 3.703001 TCCTGTCAGAATGGGAGTTTC 57.297 47.619 0.00 0.0 36.16 2.78
1873 1929 9.333497 GCTTTTCAGCATTAATTTCATTTTTCC 57.667 29.630 0.00 0.0 46.49 3.13
1891 1947 7.637631 TTTTTCCTTTTTGCATTTTAAGCCT 57.362 28.000 0.00 0.0 0.00 4.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 7.944554 ACCCTAGACAAATCTTGAGAAAAATGA 59.055 33.333 0.00 0.00 36.29 2.57
12 13 4.565652 GCCAACCCTAGACAAATCTTGAGA 60.566 45.833 0.00 0.00 36.29 3.27
30 31 2.358247 ACATGACGGACCGCCAAC 60.358 61.111 15.39 3.91 0.00 3.77
106 107 6.814954 AGATAAGATAAAGAGGCTCACCAA 57.185 37.500 18.26 0.00 39.06 3.67
359 366 7.496346 TTCTGGTTCACATAACTCCTAGATT 57.504 36.000 0.00 0.00 0.00 2.40
369 377 5.048364 CGGTTGGAATTTCTGGTTCACATAA 60.048 40.000 0.00 0.00 0.00 1.90
735 744 3.194968 ACACCGTGAAATCCTCGTCTAAT 59.805 43.478 5.28 0.00 0.00 1.73
971 984 2.724672 ACCTAGGGATCTATCTGCTCCA 59.275 50.000 14.81 0.00 32.81 3.86
1090 1116 2.206750 GCACTTGTAGAAACACCGACA 58.793 47.619 0.00 0.00 34.61 4.35
1094 1120 0.872388 CCGGCACTTGTAGAAACACC 59.128 55.000 0.00 0.00 34.61 4.16
1096 1122 2.623878 TTCCGGCACTTGTAGAAACA 57.376 45.000 0.00 0.00 0.00 2.83
1500 1529 2.671070 CAGGTTGATGGAGGCGGT 59.329 61.111 0.00 0.00 0.00 5.68
1566 1595 0.478072 AGGACAACATCTGCCACCAA 59.522 50.000 0.00 0.00 0.00 3.67
1838 1892 1.800805 TGCTGAAAAGCCTTCTCTCG 58.199 50.000 0.00 0.00 0.00 4.04
1863 1917 9.513727 GCTTAAAATGCAAAAAGGAAAAATGAA 57.486 25.926 0.00 0.00 0.00 2.57
1873 1929 9.518906 AAAAATCAAGGCTTAAAATGCAAAAAG 57.481 25.926 0.00 0.00 0.00 2.27
1891 1947 2.487762 CACGCCAGCTCCTAAAAATCAA 59.512 45.455 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.