Multiple sequence alignment - TraesCS5B01G216400

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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 TraesCS5B01G216400 chr5B 100.000 2459 0 0 1 2459 390402065 390404523 0.000000e+00 4542.0
1 TraesCS5B01G216400 chr5B 99.471 2459 13 0 1 2459 390522930 390525388 0.000000e+00 4470.0
2 TraesCS5B01G216400 chr5B 90.863 197 17 1 2099 2295 437687290 437687095 1.880000e-66 263.0
3 TraesCS5B01G216400 chr5B 84.848 132 16 2 2321 2448 472682776 472682645 1.980000e-26 130.0
4 TraesCS5B01G216400 chr5D 92.079 1313 55 23 520 1800 333978450 333979745 0.000000e+00 1803.0
5 TraesCS5B01G216400 chr5D 88.859 377 40 1 1 375 493140761 493140385 1.720000e-126 462.0
6 TraesCS5B01G216400 chr5D 85.897 156 14 4 1952 2107 333979865 333980012 2.530000e-35 159.0
7 TraesCS5B01G216400 chr5D 84.106 151 19 3 2313 2459 391906907 391906758 9.170000e-30 141.0
8 TraesCS5B01G216400 chr5D 87.000 100 12 1 1318 1417 287402078 287402176 7.190000e-21 111.0
9 TraesCS5B01G216400 chr5A 92.388 762 39 5 717 1471 435475522 435476271 0.000000e+00 1068.0
10 TraesCS5B01G216400 chr5A 87.349 332 21 5 1470 1800 435476299 435476610 6.460000e-96 361.0
11 TraesCS5B01G216400 chr5A 85.507 276 28 9 1000 1272 662064160 662063894 6.700000e-71 278.0
12 TraesCS5B01G216400 chr5A 86.574 216 11 7 520 717 435471741 435471956 3.180000e-54 222.0
13 TraesCS5B01G216400 chr5A 81.633 245 32 10 1097 1333 661666749 661666988 8.980000e-45 191.0
14 TraesCS5B01G216400 chr5A 83.333 156 18 4 1952 2107 435476759 435476906 1.190000e-28 137.0
15 TraesCS5B01G216400 chr5A 82.759 87 6 3 1891 1968 435476619 435476705 4.390000e-08 69.4
16 TraesCS5B01G216400 chrUn 100.000 442 0 0 767 1208 475903559 475903118 0.000000e+00 817.0
17 TraesCS5B01G216400 chrUn 94.054 185 11 0 2105 2289 52887539 52887723 5.180000e-72 281.0
18 TraesCS5B01G216400 chrUn 94.054 185 11 0 2105 2289 311299404 311299588 5.180000e-72 281.0
19 TraesCS5B01G216400 chrUn 94.054 185 11 0 2105 2289 311303305 311303489 5.180000e-72 281.0
20 TraesCS5B01G216400 chr7B 89.920 377 36 1 1 375 485470836 485471212 3.680000e-133 484.0
21 TraesCS5B01G216400 chr7B 88.360 378 42 2 1 376 657537291 657536914 1.040000e-123 453.0
22 TraesCS5B01G216400 chr7B 84.507 142 21 1 1318 1459 63582651 63582791 3.300000e-29 139.0
23 TraesCS5B01G216400 chr2A 89.125 377 39 1 1 375 25342451 25342827 3.700000e-128 468.0
24 TraesCS5B01G216400 chr2A 88.859 377 40 2 1 375 25336960 25337336 1.720000e-126 462.0
25 TraesCS5B01G216400 chr2A 83.562 146 18 3 2312 2453 672507638 672507781 5.520000e-27 132.0
26 TraesCS5B01G216400 chr1A 88.859 377 40 1 1 375 62486103 62486479 1.720000e-126 462.0
27 TraesCS5B01G216400 chr4D 88.594 377 41 1 1 375 403581411 403581787 8.010000e-125 457.0
28 TraesCS5B01G216400 chr4D 84.420 276 31 7 1000 1272 481338663 481338929 6.740000e-66 261.0
29 TraesCS5B01G216400 chr1D 88.564 376 41 1 2 375 474829517 474829892 2.880000e-124 455.0
30 TraesCS5B01G216400 chr4B 86.594 276 28 7 1000 1272 609575075 609575344 1.850000e-76 296.0
31 TraesCS5B01G216400 chr4B 89.189 148 12 4 1097 1241 610244401 610244255 5.400000e-42 182.0
32 TraesCS5B01G216400 chr4B 82.353 204 22 10 1034 1234 610098185 610097993 5.440000e-37 165.0
33 TraesCS5B01G216400 chr4B 78.947 133 23 3 2317 2444 653423671 653423539 4.360000e-13 86.1
34 TraesCS5B01G216400 chr3B 91.878 197 15 1 2099 2295 827034250 827034055 8.660000e-70 274.0
35 TraesCS5B01G216400 chr3B 91.878 197 15 1 2099 2295 827580302 827580107 8.660000e-70 274.0
36 TraesCS5B01G216400 chr7D 92.391 184 14 0 2106 2289 55191340 55191523 1.880000e-66 263.0
37 TraesCS5B01G216400 chr6A 92.308 182 14 0 2108 2289 61705493 61705312 2.430000e-65 259.0
38 TraesCS5B01G216400 chr6B 90.780 141 11 2 381 519 54656482 54656342 1.160000e-43 187.0
39 TraesCS5B01G216400 chr7A 84.066 182 23 6 1034 1215 718294751 718294576 1.170000e-38 171.0
40 TraesCS5B01G216400 chr3D 86.842 152 14 4 2312 2459 93254356 93254505 5.440000e-37 165.0
41 TraesCS5B01G216400 chr1B 90.476 126 8 4 390 512 29085735 29085859 1.960000e-36 163.0
42 TraesCS5B01G216400 chr1B 86.275 51 6 1 1823 1873 6540867 6540916 1.000000e-03 54.7
43 TraesCS5B01G216400 chr4A 88.550 131 9 5 390 516 11834704 11834832 1.180000e-33 154.0
44 TraesCS5B01G216400 chr4A 84.507 142 16 4 2312 2448 581272427 581272567 4.270000e-28 135.0
45 TraesCS5B01G216400 chr4A 84.397 141 15 5 2313 2448 692086315 692086453 5.520000e-27 132.0
46 TraesCS5B01G216400 chr3A 85.821 134 15 4 390 519 744678075 744678208 3.300000e-29 139.0
47 TraesCS5B01G216400 chr2B 85.000 140 17 3 2312 2448 797586564 797586702 3.300000e-29 139.0
48 TraesCS5B01G216400 chr2B 82.394 142 24 1 1318 1459 772711400 772711260 3.320000e-24 122.0


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 TraesCS5B01G216400 chr5B 390402065 390404523 2458 False 4542.00 4542 100.0000 1 2459 1 chr5B.!!$F1 2458
1 TraesCS5B01G216400 chr5B 390522930 390525388 2458 False 4470.00 4470 99.4710 1 2459 1 chr5B.!!$F2 2458
2 TraesCS5B01G216400 chr5D 333978450 333980012 1562 False 981.00 1803 88.9880 520 2107 2 chr5D.!!$F2 1587
3 TraesCS5B01G216400 chr5A 435471741 435476906 5165 False 371.48 1068 86.4806 520 2107 5 chr5A.!!$F2 1587
4 TraesCS5B01G216400 chrUn 311299404 311303489 4085 False 281.00 281 94.0540 2105 2289 2 chrUn.!!$F2 184

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
27 28 0.539986 GGTTTATGGGGAGCGTCTCA 59.46 55.0 8.71 0.0 31.08 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1484 5109 2.562912 CAGACATTGGCACACCGC 59.437 61.111 0.0 0.0 39.29 5.68 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
27 28 0.539986 GGTTTATGGGGAGCGTCTCA 59.460 55.000 8.71 0.00 31.08 3.27
335 336 1.594862 GCCATGCTTACTGCTTACTCG 59.405 52.381 0.00 0.00 43.37 4.18
765 4350 4.785453 CGGCCAGGTGCTCTTCCC 62.785 72.222 2.24 0.00 40.92 3.97
1484 5109 0.110056 CCGCTGCTAGCAGTTTGTTG 60.110 55.000 37.91 22.80 42.58 3.33
2231 9830 2.108168 CTATAGCCCGCTATAGCCCAA 58.892 52.381 23.85 1.08 46.26 4.12
2311 9910 7.782897 TGTTATAAGAGATATCACCTCAGGG 57.217 40.000 5.32 0.00 38.88 4.45
2315 9914 5.622346 AAGAGATATCACCTCAGGGTTTC 57.378 43.478 5.32 0.00 44.73 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 3.222354 GACCGGGAGCAGTCGTGTT 62.222 63.158 6.32 0.00 0.00 3.32
194 195 7.953158 ATACGAGTAAATGATGGATGAACAG 57.047 36.000 0.00 0.00 0.00 3.16
335 336 6.238130 GCACTTTTCCGATTAGACTAATCCAC 60.238 42.308 23.51 6.10 41.10 4.02
765 4350 0.460284 ATTTGCTACGTCTGGGCGAG 60.460 55.000 0.53 0.00 35.59 5.03
1484 5109 2.562912 CAGACATTGGCACACCGC 59.437 61.111 0.00 0.00 39.29 5.68
1699 5324 5.762711 TCAAGAAACTCGAAATCAATCACCA 59.237 36.000 0.00 0.00 0.00 4.17
2205 9804 0.323542 ATAGCGGGCTATAGCGAGGT 60.324 55.000 18.30 19.85 43.26 3.85
2231 9830 7.364970 CGGCAACCTTTAAAAACAGTTATAGT 58.635 34.615 0.00 0.00 0.00 2.12


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

AutoCloner maintained by Alex Coulton.