Multiple sequence alignment - TraesCS1A01G133300

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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 TraesCS1A01G133300 chr1A 100.000 3272 0 0 1 3272 186719766 186716495 0.000000e+00 6043.0
1 TraesCS1A01G133300 chr7A 97.560 3279 71 4 1 3272 287640552 287637276 0.000000e+00 5603.0
2 TraesCS1A01G133300 chr7A 80.547 658 113 11 1839 2483 188027689 188028344 2.930000e-135 492.0
3 TraesCS1A01G133300 chr7A 97.701 87 2 0 2586 2672 83936106 83936192 2.030000e-32 150.0
4 TraesCS1A01G133300 chr7A 96.552 87 3 0 2586 2672 184126824 184126738 9.460000e-31 145.0
5 TraesCS1A01G133300 chr2B 91.356 1932 104 26 643 2546 491568818 491566922 0.000000e+00 2584.0
6 TraesCS1A01G133300 chr2B 94.243 608 27 5 2670 3272 491566842 491566238 0.000000e+00 922.0
7 TraesCS1A01G133300 chr2B 89.280 653 50 9 1 643 491569508 491568866 0.000000e+00 800.0
8 TraesCS1A01G133300 chr2B 87.349 166 19 2 1305 1469 520700647 520700811 4.310000e-44 189.0
9 TraesCS1A01G133300 chr5B 91.239 1929 111 28 643 2546 360595033 360596928 0.000000e+00 2573.0
10 TraesCS1A01G133300 chr5B 93.234 606 31 6 2670 3269 360597008 360597609 0.000000e+00 883.0
11 TraesCS1A01G133300 chr5B 87.595 661 54 16 1 643 360594335 360594985 0.000000e+00 741.0
12 TraesCS1A01G133300 chr5B 88.785 107 11 1 680 786 415050350 415050455 2.650000e-26 130.0
13 TraesCS1A01G133300 chr1B 91.564 1873 96 20 695 2560 282853953 282852136 0.000000e+00 2527.0
14 TraesCS1A01G133300 chr1B 90.575 626 36 10 2670 3272 282852068 282851443 0.000000e+00 808.0
15 TraesCS1A01G133300 chr1B 92.105 228 17 1 2670 2897 377095578 377095804 1.460000e-83 320.0
16 TraesCS1A01G133300 chr6A 94.362 1277 66 2 1201 2475 338193865 338192593 0.000000e+00 1954.0
17 TraesCS1A01G133300 chr6A 93.586 608 28 5 2670 3272 338192474 338191873 0.000000e+00 896.0
18 TraesCS1A01G133300 chr6A 89.120 625 58 10 1 615 338195348 338194724 0.000000e+00 769.0
19 TraesCS1A01G133300 chr6A 89.779 587 38 9 643 1208 338194667 338194082 0.000000e+00 732.0
20 TraesCS1A01G133300 chr6A 83.929 504 33 16 680 1146 127096076 127095584 3.880000e-119 438.0
21 TraesCS1A01G133300 chr3A 87.470 830 74 14 1684 2483 207242734 207241905 0.000000e+00 929.0
22 TraesCS1A01G133300 chr3A 94.775 555 24 3 2699 3248 521925818 521925264 0.000000e+00 859.0
23 TraesCS1A01G133300 chr3A 79.344 305 42 10 1839 2133 12610934 12610641 9.260000e-46 195.0
24 TraesCS1A01G133300 chr3A 93.204 103 5 2 2577 2678 296902716 296902817 2.030000e-32 150.0
25 TraesCS1A01G133300 chr3D 87.455 829 74 14 1684 2483 169887167 169886340 0.000000e+00 928.0
26 TraesCS1A01G133300 chr3D 87.234 94 11 1 550 643 157825364 157825456 4.470000e-19 106.0
27 TraesCS1A01G133300 chr3D 85.106 94 13 1 550 643 137630415 137630507 9.670000e-16 95.3
28 TraesCS1A01G133300 chr5A 85.827 635 59 16 793 1417 345359922 345359309 0.000000e+00 645.0
29 TraesCS1A01G133300 chr5A 86.170 94 12 1 550 643 294709029 294709121 2.080000e-17 100.0
30 TraesCS1A01G133300 chr7B 81.763 658 105 10 1839 2483 152052399 152051744 1.340000e-148 536.0
31 TraesCS1A01G133300 chr7B 92.241 232 17 1 2667 2897 399236370 399236601 8.750000e-86 327.0
32 TraesCS1A01G133300 chr7B 84.923 325 38 8 1146 1469 412610915 412611229 5.270000e-83 318.0
33 TraesCS1A01G133300 chr7B 84.615 325 39 7 1146 1469 13711900 13711586 2.450000e-81 313.0
34 TraesCS1A01G133300 chr2A 96.271 295 10 1 2670 2964 385699118 385699411 1.770000e-132 483.0
35 TraesCS1A01G133300 chr2A 93.651 315 13 4 2960 3269 385902123 385902435 6.390000e-127 464.0
36 TraesCS1A01G133300 chr2A 82.857 350 30 12 728 1048 431665891 431665543 1.490000e-73 287.0
37 TraesCS1A01G133300 chr6B 84.848 495 37 12 680 1146 191363713 191363229 6.390000e-127 464.0
38 TraesCS1A01G133300 chr6B 92.544 228 16 1 2670 2897 252385576 252385350 3.150000e-85 326.0
39 TraesCS1A01G133300 chr6B 94.681 94 4 1 2583 2676 617177202 617177294 9.460000e-31 145.0
40 TraesCS1A01G133300 chr6B 90.385 104 7 3 2569 2671 548134580 548134681 2.050000e-27 134.0
41 TraesCS1A01G133300 chr6B 85.106 94 13 1 550 643 195459354 195459446 9.670000e-16 95.3
42 TraesCS1A01G133300 chr6B 100.000 29 0 0 525 553 207933283 207933255 2.000000e-03 54.7
43 TraesCS1A01G133300 chr7D 90.801 337 15 3 643 964 546760659 546760324 1.390000e-118 436.0
44 TraesCS1A01G133300 chr7D 83.578 408 17 16 262 643 546761090 546760707 1.450000e-88 337.0
45 TraesCS1A01G133300 chr1D 93.537 294 13 4 2960 3248 456923923 456924215 1.800000e-117 433.0
46 TraesCS1A01G133300 chr1D 94.565 92 5 0 2873 2964 456918453 456918544 3.400000e-30 143.0
47 TraesCS1A01G133300 chr6D 87.293 362 27 7 793 1146 104965638 104965288 2.370000e-106 396.0
48 TraesCS1A01G133300 chr6D 94.624 93 4 1 2580 2671 6967927 6968019 3.400000e-30 143.0
49 TraesCS1A01G133300 chr6D 91.250 80 7 0 680 759 104966035 104965956 3.450000e-20 110.0
50 TraesCS1A01G133300 chr5D 83.754 357 28 12 721 1048 270486678 270487033 8.820000e-81 311.0
51 TraesCS1A01G133300 chr5D 85.106 94 13 1 550 643 270486538 270486630 9.670000e-16 95.3
52 TraesCS1A01G133300 chr3B 90.857 175 14 2 1 173 689925413 689925239 1.960000e-57 233.0
53 TraesCS1A01G133300 chr4D 97.701 87 2 0 2586 2672 481110365 481110279 2.030000e-32 150.0
54 TraesCS1A01G133300 chr4D 97.674 86 2 0 2586 2671 28237809 28237894 7.310000e-32 148.0
55 TraesCS1A01G133300 chr4D 90.667 75 7 0 566 640 280921253 280921327 2.080000e-17 100.0


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 TraesCS1A01G133300 chr1A 186716495 186719766 3271 True 6043.000000 6043 100.000000 1 3272 1 chr1A.!!$R1 3271
1 TraesCS1A01G133300 chr7A 287637276 287640552 3276 True 5603.000000 5603 97.560000 1 3272 1 chr7A.!!$R2 3271
2 TraesCS1A01G133300 chr7A 188027689 188028344 655 False 492.000000 492 80.547000 1839 2483 1 chr7A.!!$F2 644
3 TraesCS1A01G133300 chr2B 491566238 491569508 3270 True 1435.333333 2584 91.626333 1 3272 3 chr2B.!!$R1 3271
4 TraesCS1A01G133300 chr5B 360594335 360597609 3274 False 1399.000000 2573 90.689333 1 3269 3 chr5B.!!$F2 3268
5 TraesCS1A01G133300 chr1B 282851443 282853953 2510 True 1667.500000 2527 91.069500 695 3272 2 chr1B.!!$R1 2577
6 TraesCS1A01G133300 chr6A 338191873 338195348 3475 True 1087.750000 1954 91.711750 1 3272 4 chr6A.!!$R2 3271
7 TraesCS1A01G133300 chr3A 207241905 207242734 829 True 929.000000 929 87.470000 1684 2483 1 chr3A.!!$R2 799
8 TraesCS1A01G133300 chr3A 521925264 521925818 554 True 859.000000 859 94.775000 2699 3248 1 chr3A.!!$R3 549
9 TraesCS1A01G133300 chr3D 169886340 169887167 827 True 928.000000 928 87.455000 1684 2483 1 chr3D.!!$R1 799
10 TraesCS1A01G133300 chr5A 345359309 345359922 613 True 645.000000 645 85.827000 793 1417 1 chr5A.!!$R1 624
11 TraesCS1A01G133300 chr7B 152051744 152052399 655 True 536.000000 536 81.763000 1839 2483 1 chr7B.!!$R2 644
12 TraesCS1A01G133300 chr7D 546760324 546761090 766 True 386.500000 436 87.189500 262 964 2 chr7D.!!$R1 702
13 TraesCS1A01G133300 chr6D 104965288 104966035 747 True 253.000000 396 89.271500 680 1146 2 chr6D.!!$R1 466

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
45 46 0.603065 GCGAAAGAATTGCCCAACCT 59.397 50.0 0.00 0.0 0.0 3.50 F
246 247 2.105806 GAGATCCATGGCCTCCCGAC 62.106 65.0 18.02 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1732 2371 1.725641 CGCAAGGTCACAGATAAGCA 58.274 50.000 0.00 0.00 0.00 3.91 R
2404 3090 2.571757 CACCAATGCCTGCAGCTG 59.428 61.111 10.11 10.11 44.23 4.24 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
45 46 0.603065 GCGAAAGAATTGCCCAACCT 59.397 50.000 0.00 0.0 0.00 3.50
246 247 2.105806 GAGATCCATGGCCTCCCGAC 62.106 65.000 18.02 0.0 0.00 4.79
1173 1579 3.058914 GTGTGTGCTCCAGTGTTGATAAC 60.059 47.826 0.00 0.0 0.00 1.89
1372 2007 6.233434 TCTGTGAGCAAATTATCTTCACTGT 58.767 36.000 11.26 0.0 0.00 3.55
1732 2371 7.954666 AGGCAGTGTATACATTTTATTTGGT 57.045 32.000 9.18 0.0 0.00 3.67
2404 3090 8.080417 GGTTCCTAATTTAGTGTGAGGAAAAAC 58.920 37.037 5.39 0.0 45.48 2.43
2487 3173 2.489073 CCCACAAAACTTGAGGCCTACT 60.489 50.000 4.42 0.0 39.69 2.57
3195 3949 4.218417 CGGTTGGAAGAATGGAAAATCACT 59.782 41.667 0.00 0.0 0.00 3.41
3209 3963 2.496899 ATCACTTGGCTGTCGGATTT 57.503 45.000 0.00 0.0 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 1.066929 GGTTGGGCAATTCTTTCGCAT 60.067 47.619 0.00 0.00 0.00 4.73
246 247 0.805322 GACCTGAGCAGATGAGCACG 60.805 60.000 0.00 0.00 36.85 5.34
1634 2273 5.426504 CTCAAACATCTAGCACAAGAGGAT 58.573 41.667 2.94 0.00 31.81 3.24
1639 2278 5.455392 CAAACCTCAAACATCTAGCACAAG 58.545 41.667 0.00 0.00 0.00 3.16
1732 2371 1.725641 CGCAAGGTCACAGATAAGCA 58.274 50.000 0.00 0.00 0.00 3.91
2404 3090 2.571757 CACCAATGCCTGCAGCTG 59.428 61.111 10.11 10.11 44.23 4.24
2487 3173 1.323271 TTTGTTGGGCGCCTGTTCAA 61.323 50.000 28.56 19.01 0.00 2.69
3195 3949 0.881118 GCTTGAAATCCGACAGCCAA 59.119 50.000 0.00 0.00 0.00 4.52
3209 3963 1.105457 GCAATGCCCTATGTGCTTGA 58.895 50.000 0.00 0.00 34.13 3.02


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

AutoCloner maintained by Alex Coulton.