Multiple sequence alignment - TraesCS5A01G509500

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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 TraesCS5A01G509500 chr5A 100.000 2549 0 0 1 2549 673648883 673646335 0.000000e+00 4708.0
1 TraesCS5A01G509500 chr5A 98.082 2555 41 7 1 2549 673631569 673629017 0.000000e+00 4440.0
2 TraesCS5A01G509500 chr1B 89.471 1757 171 7 796 2549 216514365 216516110 0.000000e+00 2207.0
3 TraesCS5A01G509500 chr6B 86.493 1762 215 13 796 2549 674971396 674969650 0.000000e+00 1914.0
4 TraesCS5A01G509500 chr6B 91.176 102 8 1 1 101 72434991 72435092 1.230000e-28 137.0
5 TraesCS5A01G509500 chr1A 84.025 1759 266 13 800 2549 361956704 361954952 0.000000e+00 1677.0
6 TraesCS5A01G509500 chr1A 80.472 466 48 20 84 509 239883154 239882692 1.470000e-82 316.0
7 TraesCS5A01G509500 chr7A 83.051 1770 268 25 796 2549 20393011 20391258 0.000000e+00 1578.0
8 TraesCS5A01G509500 chr1D 88.240 1199 130 9 796 1985 302906422 302905226 0.000000e+00 1423.0
9 TraesCS5A01G509500 chr1D 87.528 441 44 10 91 522 18984111 18983673 1.360000e-137 499.0
10 TraesCS5A01G509500 chr1D 88.000 350 28 5 249 584 90139818 90139469 3.950000e-108 401.0
11 TraesCS5A01G509500 chr1D 81.342 477 37 19 85 512 217293551 217293078 8.730000e-90 340.0
12 TraesCS5A01G509500 chr1D 84.062 320 21 13 294 584 46391308 46390990 5.370000e-72 281.0
13 TraesCS5A01G509500 chr1D 79.596 446 48 21 84 510 291101092 291101513 1.930000e-71 279.0
14 TraesCS5A01G509500 chr1D 87.500 176 20 2 336 509 49610054 49609879 4.300000e-48 202.0
15 TraesCS5A01G509500 chr3A 84.533 1403 206 10 814 2209 360862052 360860654 0.000000e+00 1378.0
16 TraesCS5A01G509500 chr3A 83.555 602 71 18 1 584 405998211 405998802 2.890000e-149 538.0
17 TraesCS5A01G509500 chr3A 81.919 542 49 16 84 585 600888750 600888218 1.820000e-111 412.0
18 TraesCS5A01G509500 chrUn 83.758 1373 210 10 1182 2549 292040319 292038955 0.000000e+00 1288.0
19 TraesCS5A01G509500 chrUn 85.129 464 39 10 84 518 63257476 63257938 5.000000e-122 448.0
20 TraesCS5A01G509500 chrUn 82.402 483 35 12 84 518 143922943 143922463 2.390000e-100 375.0
21 TraesCS5A01G509500 chrUn 81.838 468 41 20 84 510 97635804 97635340 1.120000e-93 353.0
22 TraesCS5A01G509500 chrUn 82.096 458 30 20 105 511 260712599 260712143 6.750000e-91 344.0
23 TraesCS5A01G509500 chrUn 89.455 275 23 4 249 518 29673910 29674183 2.430000e-90 342.0
24 TraesCS5A01G509500 chrUn 81.548 336 43 7 249 583 91336910 91336593 2.520000e-65 259.0
25 TraesCS5A01G509500 chr4A 83.758 1373 210 10 1182 2549 673133925 673132561 0.000000e+00 1288.0
26 TraesCS5A01G509500 chr4A 83.758 1373 210 10 1182 2549 673138563 673137199 0.000000e+00 1288.0
27 TraesCS5A01G509500 chr4A 84.112 535 67 12 1 522 42829950 42830479 3.790000e-138 501.0
28 TraesCS5A01G509500 chr6D 83.881 639 88 10 1920 2549 472210085 472209453 1.690000e-166 595.0
29 TraesCS5A01G509500 chr6D 88.222 450 41 9 84 522 77859793 77860241 6.250000e-146 527.0
30 TraesCS5A01G509500 chr6D 88.143 447 42 7 84 521 420194489 420194045 2.910000e-144 521.0
31 TraesCS5A01G509500 chr6D 83.512 467 45 14 79 518 357560318 357560779 8.490000e-110 407.0
32 TraesCS5A01G509500 chr6D 80.560 571 43 21 84 586 28284678 28284108 6.660000e-101 377.0
33 TraesCS5A01G509500 chr6D 81.267 363 40 13 249 584 311541993 311541632 4.180000e-68 268.0
34 TraesCS5A01G509500 chr6D 91.919 99 8 0 1 99 362224725 362224823 3.420000e-29 139.0
35 TraesCS5A01G509500 chr3D 86.347 542 50 17 1 522 533680962 533680425 1.020000e-158 569.0
36 TraesCS5A01G509500 chr3D 89.630 270 23 4 249 513 548483944 548484213 3.140000e-89 339.0
37 TraesCS5A01G509500 chr2B 85.164 519 53 16 84 589 732340567 732341074 6.290000e-141 510.0
38 TraesCS5A01G509500 chr7D 87.615 436 48 5 91 522 565669831 565669398 3.790000e-138 501.0
39 TraesCS5A01G509500 chr7D 89.170 277 23 4 249 518 40260948 40261224 3.140000e-89 339.0
40 TraesCS5A01G509500 chr7D 84.337 249 16 6 359 586 596677135 596676889 3.300000e-54 222.0
41 TraesCS5A01G509500 chr7D 92.857 98 7 0 3 100 423340061 423340158 2.640000e-30 143.0
42 TraesCS5A01G509500 chr4D 86.123 454 38 9 84 512 486344145 486344598 1.380000e-127 466.0
43 TraesCS5A01G509500 chr4D 80.759 369 37 12 249 583 401776023 401775655 9.050000e-65 257.0
44 TraesCS5A01G509500 chr4D 86.607 224 18 5 297 509 383876812 383876590 1.180000e-58 237.0
45 TraesCS5A01G509500 chr2A 84.069 521 41 18 105 584 603544872 603544353 4.970000e-127 464.0
46 TraesCS5A01G509500 chr2A 81.720 558 46 16 84 586 756135794 756135238 5.070000e-112 414.0
47 TraesCS5A01G509500 chr5D 83.213 554 40 21 84 584 454030063 454029510 2.310000e-125 459.0
48 TraesCS5A01G509500 chr6A 82.796 465 49 11 84 518 549246067 549245604 1.110000e-103 387.0
49 TraesCS5A01G509500 chr6A 82.270 282 29 10 249 510 558948604 558948884 9.180000e-55 224.0
50 TraesCS5A01G509500 chr6A 94.000 100 5 1 1 99 543536922 543537021 1.580000e-32 150.0
51 TraesCS5A01G509500 chr2D 79.599 549 61 26 85 585 580422257 580421712 1.880000e-91 346.0
52 TraesCS5A01G509500 chr4B 92.079 101 7 1 1 100 579899285 579899385 9.510000e-30 141.0
53 TraesCS5A01G509500 chr4B 87.952 83 7 3 518 598 667396433 667396514 7.510000e-16 95.3


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 TraesCS5A01G509500 chr5A 673646335 673648883 2548 True 4708 4708 100.000 1 2549 1 chr5A.!!$R2 2548
1 TraesCS5A01G509500 chr5A 673629017 673631569 2552 True 4440 4440 98.082 1 2549 1 chr5A.!!$R1 2548
2 TraesCS5A01G509500 chr1B 216514365 216516110 1745 False 2207 2207 89.471 796 2549 1 chr1B.!!$F1 1753
3 TraesCS5A01G509500 chr6B 674969650 674971396 1746 True 1914 1914 86.493 796 2549 1 chr6B.!!$R1 1753
4 TraesCS5A01G509500 chr1A 361954952 361956704 1752 True 1677 1677 84.025 800 2549 1 chr1A.!!$R2 1749
5 TraesCS5A01G509500 chr7A 20391258 20393011 1753 True 1578 1578 83.051 796 2549 1 chr7A.!!$R1 1753
6 TraesCS5A01G509500 chr1D 302905226 302906422 1196 True 1423 1423 88.240 796 1985 1 chr1D.!!$R6 1189
7 TraesCS5A01G509500 chr3A 360860654 360862052 1398 True 1378 1378 84.533 814 2209 1 chr3A.!!$R1 1395
8 TraesCS5A01G509500 chr3A 405998211 405998802 591 False 538 538 83.555 1 584 1 chr3A.!!$F1 583
9 TraesCS5A01G509500 chr3A 600888218 600888750 532 True 412 412 81.919 84 585 1 chr3A.!!$R2 501
10 TraesCS5A01G509500 chrUn 292038955 292040319 1364 True 1288 1288 83.758 1182 2549 1 chrUn.!!$R5 1367
11 TraesCS5A01G509500 chr4A 673132561 673138563 6002 True 1288 1288 83.758 1182 2549 2 chr4A.!!$R1 1367
12 TraesCS5A01G509500 chr4A 42829950 42830479 529 False 501 501 84.112 1 522 1 chr4A.!!$F1 521
13 TraesCS5A01G509500 chr6D 472209453 472210085 632 True 595 595 83.881 1920 2549 1 chr6D.!!$R4 629
14 TraesCS5A01G509500 chr6D 28284108 28284678 570 True 377 377 80.560 84 586 1 chr6D.!!$R1 502
15 TraesCS5A01G509500 chr3D 533680425 533680962 537 True 569 569 86.347 1 522 1 chr3D.!!$R1 521
16 TraesCS5A01G509500 chr2B 732340567 732341074 507 False 510 510 85.164 84 589 1 chr2B.!!$F1 505
17 TraesCS5A01G509500 chr2A 603544353 603544872 519 True 464 464 84.069 105 584 1 chr2A.!!$R1 479
18 TraesCS5A01G509500 chr2A 756135238 756135794 556 True 414 414 81.720 84 586 1 chr2A.!!$R2 502
19 TraesCS5A01G509500 chr5D 454029510 454030063 553 True 459 459 83.213 84 584 1 chr5D.!!$R1 500
20 TraesCS5A01G509500 chr2D 580421712 580422257 545 True 346 346 79.599 85 585 1 chr2D.!!$R1 500

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
889 988 0.843309 TCTTTGCTGGTGAACCCTCA 59.157 50.0 0.0 0.0 34.29 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2318 7075 4.735132 CGGCGGCACTCCTCGAAA 62.735 66.667 10.53 0.0 0.0 3.46 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
172 191 2.484889 GAGAGTCACGGTTTTGCTTCT 58.515 47.619 0.00 0.00 0.00 2.85
706 802 9.406113 AGTAGTCTAATCTACCGAGTACAAAAT 57.594 33.333 0.00 0.00 40.56 1.82
707 803 9.448294 GTAGTCTAATCTACCGAGTACAAAATG 57.552 37.037 0.00 0.00 34.99 2.32
715 811 4.253685 ACCGAGTACAAAATGTCTGGATG 58.746 43.478 0.00 0.00 0.00 3.51
825 921 1.000060 CGACAACCTAGGGTTTCGACA 60.000 52.381 27.69 0.00 44.33 4.35
889 988 0.843309 TCTTTGCTGGTGAACCCTCA 59.157 50.000 0.00 0.00 34.29 3.86
911 1010 1.306141 TCGGGCTGATCAAGGGAGT 60.306 57.895 0.00 0.00 0.00 3.85
1048 1158 2.282958 AGGGCAAGGAGACGACGA 60.283 61.111 0.00 0.00 0.00 4.20
1533 6283 3.878699 CAGCAGGCTTTTTGGTGAATTTT 59.121 39.130 0.00 0.00 44.54 1.82
1561 6311 5.308237 GGGTTAGGGTGAAGATAGACATCAT 59.692 44.000 0.00 0.00 33.21 2.45
2318 7075 4.537433 GCAGAATCGGCGGGCTCT 62.537 66.667 7.21 3.62 0.00 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.745975 CGAAAGCACAACCATACTTCTCA 59.254 43.478 0.00 0.00 0.00 3.27
172 191 1.436195 GCACAACCGTGACTCTTGCA 61.436 55.000 0.00 0.00 46.80 4.08
436 503 1.942657 CCGTGCATCCAAATCTCGAAT 59.057 47.619 0.00 0.00 0.00 3.34
518 588 1.334160 TCCCTAGTTGCGACAAGTCA 58.666 50.000 6.90 0.00 0.00 3.41
706 802 5.997746 CCTCAACTTTCTTTACATCCAGACA 59.002 40.000 0.00 0.00 0.00 3.41
707 803 5.998363 ACCTCAACTTTCTTTACATCCAGAC 59.002 40.000 0.00 0.00 0.00 3.51
715 811 6.694877 ACTTTCCACCTCAACTTTCTTTAC 57.305 37.500 0.00 0.00 0.00 2.01
889 988 1.333636 CCCTTGATCAGCCCGAGTCT 61.334 60.000 0.00 0.00 0.00 3.24
911 1010 2.652095 CGGTAAGGTCGCAGGGGAA 61.652 63.158 0.00 0.00 0.00 3.97
1048 1158 2.441750 TCAACTTGGCCAGTAGTTCCTT 59.558 45.455 18.13 0.00 32.94 3.36
1158 1268 1.148273 GGTCCTTGAGGTGTGCACA 59.852 57.895 17.42 17.42 36.34 4.57
1533 6283 1.961133 ATCTTCACCCTAACCCGGAA 58.039 50.000 0.73 0.00 0.00 4.30
1561 6311 8.655092 CAGTGACAAAACTCTTAATTTTTGCAA 58.345 29.630 0.00 0.00 43.54 4.08
1577 6328 4.410883 TCTCCCTTCTTACCAGTGACAAAA 59.589 41.667 0.00 0.00 0.00 2.44
2318 7075 4.735132 CGGCGGCACTCCTCGAAA 62.735 66.667 10.53 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.