Multiple sequence alignment - TraesCS1A01G318000

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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 TraesCS1A01G318000 chr1A 100.000 3144 0 0 1 3144 509494619 509491476 0.000000e+00 5806.0
1 TraesCS1A01G318000 chr1A 97.358 2271 38 14 28 2282 510184195 510186459 0.000000e+00 3842.0
2 TraesCS1A01G318000 chr1A 92.489 2463 122 33 732 3144 509703801 509701352 0.000000e+00 3465.0
3 TraesCS1A01G318000 chr1A 92.515 2445 136 27 732 3144 509777030 509774601 0.000000e+00 3458.0
4 TraesCS1A01G318000 chr1A 88.313 1814 168 26 1018 2794 509914760 509912954 0.000000e+00 2135.0
5 TraesCS1A01G318000 chr1A 91.103 1315 87 19 1018 2314 509719875 509718573 0.000000e+00 1753.0
6 TraesCS1A01G318000 chr1A 90.951 1315 89 19 1018 2314 509793255 509791953 0.000000e+00 1742.0
7 TraesCS1A01G318000 chr1A 100.000 46 0 0 3099 3144 519569766 519569811 5.590000e-13 86.1
8 TraesCS1A01G318000 chr1D 95.951 2297 68 17 3 2282 413060694 413062982 0.000000e+00 3703.0
9 TraesCS1A01G318000 chr1D 88.054 1850 154 35 990 2789 412642220 412644052 0.000000e+00 2130.0
10 TraesCS1A01G318000 chr1D 87.574 1859 155 37 990 2789 412746198 412748039 0.000000e+00 2089.0
11 TraesCS1A01G318000 chr1D 88.701 1655 123 33 990 2595 412763361 412765000 0.000000e+00 1962.0
12 TraesCS1A01G318000 chr1D 86.160 1185 118 28 990 2131 412507211 412508392 0.000000e+00 1238.0
13 TraesCS1A01G318000 chr1D 89.637 386 33 4 591 972 412897320 412897702 4.710000e-133 484.0
14 TraesCS1A01G318000 chr1D 88.101 395 34 8 591 972 412683614 412684008 1.030000e-124 457.0
15 TraesCS1A01G318000 chr1D 90.536 317 25 2 658 972 412814077 412814390 6.270000e-112 414.0
16 TraesCS1A01G318000 chr1D 100.000 46 0 0 3099 3144 7363900 7363855 5.590000e-13 86.1
17 TraesCS1A01G318000 chr1B 90.171 1872 119 34 732 2563 556297072 556298918 0.000000e+00 2377.0
18 TraesCS1A01G318000 chr1B 86.869 1980 179 46 732 2653 556251152 556253108 0.000000e+00 2141.0
19 TraesCS1A01G318000 chr1B 87.973 1613 124 41 738 2302 556064578 556062988 0.000000e+00 1840.0
20 TraesCS1A01G318000 chr1B 91.766 1008 52 18 618 1612 556965929 556966918 0.000000e+00 1373.0
21 TraesCS1A01G318000 chr1B 86.844 1163 113 24 999 2131 556108107 556109259 0.000000e+00 1264.0
22 TraesCS1A01G318000 chr1B 94.576 590 29 3 3 591 596471590 596471003 0.000000e+00 909.0
23 TraesCS1A01G318000 chr1B 87.618 743 57 18 997 1717 556969405 556970134 0.000000e+00 830.0
24 TraesCS1A01G318000 chr1B 90.667 525 34 11 2560 3084 556299259 556299768 0.000000e+00 684.0
25 TraesCS1A01G318000 chr1B 88.124 581 48 12 581 1151 556833740 556834309 0.000000e+00 671.0
26 TraesCS1A01G318000 chr1B 88.124 581 48 12 581 1151 556862161 556862730 0.000000e+00 671.0
27 TraesCS1A01G318000 chr1B 83.596 634 91 11 2456 3084 556267282 556267907 1.630000e-162 582.0
28 TraesCS1A01G318000 chr1B 82.629 639 93 17 2456 3084 556306829 556307459 1.650000e-152 549.0
29 TraesCS1A01G318000 chr1B 91.282 390 32 1 585 974 556968966 556969353 5.970000e-147 531.0
30 TraesCS1A01G318000 chr1B 84.211 513 49 17 2071 2556 556266339 556266846 1.320000e-128 470.0
31 TraesCS1A01G318000 chr1B 86.207 319 39 5 2478 2791 556968494 556968812 1.080000e-89 340.0
32 TraesCS1A01G318000 chr4B 88.189 1651 133 37 732 2338 633465802 633467434 0.000000e+00 1912.0
33 TraesCS1A01G318000 chr4B 87.719 1653 140 40 732 2338 633398670 633400305 0.000000e+00 1869.0
34 TraesCS1A01G318000 chr5B 92.424 594 42 3 3 594 377119100 377119692 0.000000e+00 845.0
35 TraesCS1A01G318000 chr5B 82.158 241 41 2 2849 3087 680927878 680927638 4.110000e-49 206.0
36 TraesCS1A01G318000 chr2B 91.405 605 41 8 3 599 229186524 229185923 0.000000e+00 819.0
37 TraesCS1A01G318000 chr2A 90.772 596 44 10 3 594 84363358 84362770 0.000000e+00 785.0
38 TraesCS1A01G318000 chr7D 91.207 580 46 3 3 581 520394548 520395123 0.000000e+00 784.0
39 TraesCS1A01G318000 chr6D 81.399 586 101 6 11 591 458604739 458605321 3.670000e-129 472.0
40 TraesCS1A01G318000 chrUn 80.737 597 107 7 1 592 111150075 111150668 2.860000e-125 459.0
41 TraesCS1A01G318000 chr4D 82.661 248 37 6 2852 3097 54281004 54280761 6.830000e-52 215.0
42 TraesCS1A01G318000 chr3A 83.122 237 38 2 2852 3087 220639465 220639230 6.830000e-52 215.0
43 TraesCS1A01G318000 chr3B 82.479 234 39 2 2852 3084 824291899 824292131 1.480000e-48 204.0
44 TraesCS1A01G318000 chr3D 100.000 46 0 0 3099 3144 8369495 8369540 5.590000e-13 86.1
45 TraesCS1A01G318000 chr3D 100.000 46 0 0 3099 3144 100292471 100292516 5.590000e-13 86.1
46 TraesCS1A01G318000 chr3D 100.000 46 0 0 3099 3144 601739170 601739215 5.590000e-13 86.1
47 TraesCS1A01G318000 chr3D 100.000 46 0 0 3099 3144 601741384 601741429 5.590000e-13 86.1
48 TraesCS1A01G318000 chr3D 100.000 46 0 0 3099 3144 601742491 601742536 5.590000e-13 86.1


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 TraesCS1A01G318000 chr1A 509491476 509494619 3143 True 5806.0 5806 100.00000 1 3144 1 chr1A.!!$R1 3143
1 TraesCS1A01G318000 chr1A 510184195 510186459 2264 False 3842.0 3842 97.35800 28 2282 1 chr1A.!!$F1 2254
2 TraesCS1A01G318000 chr1A 509701352 509703801 2449 True 3465.0 3465 92.48900 732 3144 1 chr1A.!!$R2 2412
3 TraesCS1A01G318000 chr1A 509774601 509777030 2429 True 3458.0 3458 92.51500 732 3144 1 chr1A.!!$R4 2412
4 TraesCS1A01G318000 chr1A 509912954 509914760 1806 True 2135.0 2135 88.31300 1018 2794 1 chr1A.!!$R6 1776
5 TraesCS1A01G318000 chr1A 509718573 509719875 1302 True 1753.0 1753 91.10300 1018 2314 1 chr1A.!!$R3 1296
6 TraesCS1A01G318000 chr1A 509791953 509793255 1302 True 1742.0 1742 90.95100 1018 2314 1 chr1A.!!$R5 1296
7 TraesCS1A01G318000 chr1D 413060694 413062982 2288 False 3703.0 3703 95.95100 3 2282 1 chr1D.!!$F8 2279
8 TraesCS1A01G318000 chr1D 412642220 412644052 1832 False 2130.0 2130 88.05400 990 2789 1 chr1D.!!$F2 1799
9 TraesCS1A01G318000 chr1D 412746198 412748039 1841 False 2089.0 2089 87.57400 990 2789 1 chr1D.!!$F4 1799
10 TraesCS1A01G318000 chr1D 412763361 412765000 1639 False 1962.0 1962 88.70100 990 2595 1 chr1D.!!$F5 1605
11 TraesCS1A01G318000 chr1D 412507211 412508392 1181 False 1238.0 1238 86.16000 990 2131 1 chr1D.!!$F1 1141
12 TraesCS1A01G318000 chr1B 556251152 556253108 1956 False 2141.0 2141 86.86900 732 2653 1 chr1B.!!$F2 1921
13 TraesCS1A01G318000 chr1B 556062988 556064578 1590 True 1840.0 1840 87.97300 738 2302 1 chr1B.!!$R1 1564
14 TraesCS1A01G318000 chr1B 556297072 556299768 2696 False 1530.5 2377 90.41900 732 3084 2 chr1B.!!$F7 2352
15 TraesCS1A01G318000 chr1B 556108107 556109259 1152 False 1264.0 1264 86.84400 999 2131 1 chr1B.!!$F1 1132
16 TraesCS1A01G318000 chr1B 596471003 596471590 587 True 909.0 909 94.57600 3 591 1 chr1B.!!$R2 588
17 TraesCS1A01G318000 chr1B 556965929 556970134 4205 False 768.5 1373 89.21825 585 2791 4 chr1B.!!$F8 2206
18 TraesCS1A01G318000 chr1B 556833740 556834309 569 False 671.0 671 88.12400 581 1151 1 chr1B.!!$F4 570
19 TraesCS1A01G318000 chr1B 556862161 556862730 569 False 671.0 671 88.12400 581 1151 1 chr1B.!!$F5 570
20 TraesCS1A01G318000 chr1B 556306829 556307459 630 False 549.0 549 82.62900 2456 3084 1 chr1B.!!$F3 628
21 TraesCS1A01G318000 chr1B 556266339 556267907 1568 False 526.0 582 83.90350 2071 3084 2 chr1B.!!$F6 1013
22 TraesCS1A01G318000 chr4B 633465802 633467434 1632 False 1912.0 1912 88.18900 732 2338 1 chr4B.!!$F2 1606
23 TraesCS1A01G318000 chr4B 633398670 633400305 1635 False 1869.0 1869 87.71900 732 2338 1 chr4B.!!$F1 1606
24 TraesCS1A01G318000 chr5B 377119100 377119692 592 False 845.0 845 92.42400 3 594 1 chr5B.!!$F1 591
25 TraesCS1A01G318000 chr2B 229185923 229186524 601 True 819.0 819 91.40500 3 599 1 chr2B.!!$R1 596
26 TraesCS1A01G318000 chr2A 84362770 84363358 588 True 785.0 785 90.77200 3 594 1 chr2A.!!$R1 591
27 TraesCS1A01G318000 chr7D 520394548 520395123 575 False 784.0 784 91.20700 3 581 1 chr7D.!!$F1 578
28 TraesCS1A01G318000 chr6D 458604739 458605321 582 False 472.0 472 81.39900 11 591 1 chr6D.!!$F1 580
29 TraesCS1A01G318000 chrUn 111150075 111150668 593 False 459.0 459 80.73700 1 592 1 chrUn.!!$F1 591

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
152 157 0.470766 TAAAGTTGCGAGTGTGGGGT 59.529 50.0 0.0 0.0 0.0 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2421 3145 9.066892 TGAAACATTATGATGCCCTAAGATAAC 57.933 33.333 0.0 0.0 36.72 1.89 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
152 157 0.470766 TAAAGTTGCGAGTGTGGGGT 59.529 50.000 0.00 0.0 0.0 4.95
1981 2508 3.459063 GACGGCGCCCTCCTTACT 61.459 66.667 23.46 0.0 0.0 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
152 157 6.718912 TGTCCACAATGGTTTCTGATAATCAA 59.281 34.615 0.0 0.0 39.03 2.57
2421 3145 9.066892 TGAAACATTATGATGCCCTAAGATAAC 57.933 33.333 0.0 0.0 36.72 1.89


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

AutoCloner maintained by Alex Coulton.