Multiple sequence alignment - TraesCS6B01G006100

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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 TraesCS6B01G006100 chr6B 100.000 5030 0 0 1 5030 4379577 4374548 0.000000e+00 9289
1 TraesCS6B01G006100 chr6B 97.747 2574 50 5 2463 5030 3836379 3838950 0.000000e+00 4425
2 TraesCS6B01G006100 chr6B 96.915 1880 50 5 1 1873 3834508 3836386 0.000000e+00 3144
3 TraesCS6B01G006100 chr6B 94.358 1347 65 3 224 1561 3799225 3800569 0.000000e+00 2056
4 TraesCS6B01G006100 chr6B 95.328 1220 48 6 1642 2858 3800566 3801779 0.000000e+00 1929
5 TraesCS6B01G006100 chr6B 78.388 583 80 23 1645 2190 664524243 664523670 2.240000e-88 337
6 TraesCS6B01G006100 chr6B 92.568 148 11 0 1 148 3799077 3799224 3.940000e-51 213
7 TraesCS6B01G006100 chr6B 82.273 220 28 6 338 547 85035111 85034893 4.000000e-41 180
8 TraesCS6B01G006100 chr6B 95.402 87 4 0 1559 1645 501671019 501670933 6.790000e-29 139
9 TraesCS6B01G006100 chr6D 93.712 3419 165 17 1643 5030 2134909 2138308 0.000000e+00 5077
10 TraesCS6B01G006100 chr6D 94.419 2652 122 14 2391 5030 4209764 4212401 0.000000e+00 4054
11 TraesCS6B01G006100 chr6D 92.500 1560 101 7 1 1550 2133347 2134900 0.000000e+00 2218
12 TraesCS6B01G006100 chr6D 91.899 1506 108 6 1 1495 4207541 4209043 0.000000e+00 2093
13 TraesCS6B01G006100 chr6D 91.840 723 41 14 1643 2363 4209057 4209763 0.000000e+00 992
14 TraesCS6B01G006100 chr6D 78.633 1624 252 46 1645 3213 439661556 439659973 0.000000e+00 989
15 TraesCS6B01G006100 chr6D 83.351 943 138 12 624 1556 439616067 439617000 0.000000e+00 854
16 TraesCS6B01G006100 chrUn 98.794 2488 27 3 1 2487 255513317 255515802 0.000000e+00 4425
17 TraesCS6B01G006100 chrUn 98.747 1995 22 2 3038 5030 355129168 355127175 0.000000e+00 3542
18 TraesCS6B01G006100 chrUn 98.411 1510 16 1 3529 5030 355695289 355693780 0.000000e+00 2649
19 TraesCS6B01G006100 chrUn 98.943 1230 12 1 1 1230 380679617 380680845 0.000000e+00 2198
20 TraesCS6B01G006100 chrUn 98.990 495 5 0 3038 3532 475068857 475068363 0.000000e+00 887
21 TraesCS6B01G006100 chrUn 99.101 445 3 1 1 445 408243422 408242979 0.000000e+00 798
22 TraesCS6B01G006100 chrUn 98.511 403 6 0 3529 3931 478404781 478405183 0.000000e+00 712
23 TraesCS6B01G006100 chrUn 99.692 325 1 0 4706 5030 343735835 343736159 3.350000e-166 595
24 TraesCS6B01G006100 chr6A 93.537 1176 68 3 3237 4404 772748 771573 0.000000e+00 1744
25 TraesCS6B01G006100 chr6A 94.071 1012 57 2 550 1561 775081 774073 0.000000e+00 1533
26 TraesCS6B01G006100 chr6A 92.022 727 41 10 1643 2364 774075 773361 0.000000e+00 1005
27 TraesCS6B01G006100 chr6A 95.270 592 24 3 2395 2984 773357 772768 0.000000e+00 935
28 TraesCS6B01G006100 chr6A 87.311 528 55 7 1 517 775994 775468 1.210000e-165 593
29 TraesCS6B01G006100 chr3D 80.311 772 123 18 4279 5029 368835544 368834781 1.580000e-154 556
30 TraesCS6B01G006100 chr1B 80.684 497 78 10 4547 5030 4074178 4074669 2.210000e-98 370
31 TraesCS6B01G006100 chr1B 95.402 87 4 0 1559 1645 420918159 420918073 6.790000e-29 139
32 TraesCS6B01G006100 chr1B 93.478 92 6 0 1556 1647 542139064 542139155 2.440000e-28 137
33 TraesCS6B01G006100 chr4D 81.356 413 73 3 4617 5029 503063828 503063420 2.900000e-87 333
34 TraesCS6B01G006100 chr1A 84.663 326 45 5 1 323 58345676 58345999 2.260000e-83 320
35 TraesCS6B01G006100 chr1D 78.962 366 59 11 4467 4822 92045423 92045780 3.030000e-57 233
36 TraesCS6B01G006100 chr5B 82.727 220 27 7 338 547 228620443 228620661 8.600000e-43 185
37 TraesCS6B01G006100 chr5B 76.279 215 40 7 4148 4352 711837891 711837678 2.480000e-18 104
38 TraesCS6B01G006100 chr7D 82.028 217 26 7 342 547 144588272 144588486 6.690000e-39 172
39 TraesCS6B01G006100 chr4B 81.364 220 30 8 338 547 622995004 622995222 8.660000e-38 169
40 TraesCS6B01G006100 chr2B 95.455 88 4 0 1559 1646 79359574 79359487 1.890000e-29 141
41 TraesCS6B01G006100 chr2B 95.402 87 4 0 1559 1645 81171484 81171398 6.790000e-29 139
42 TraesCS6B01G006100 chr3B 95.402 87 4 0 1559 1645 792892512 792892598 6.790000e-29 139
43 TraesCS6B01G006100 chr2A 91.837 98 7 1 1549 1645 227632601 227632698 8.780000e-28 135


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 TraesCS6B01G006100 chr6B 4374548 4379577 5029 True 9289.000000 9289 100.000000 1 5030 1 chr6B.!!$R1 5029
1 TraesCS6B01G006100 chr6B 3834508 3838950 4442 False 3784.500000 4425 97.331000 1 5030 2 chr6B.!!$F2 5029
2 TraesCS6B01G006100 chr6B 3799077 3801779 2702 False 1399.333333 2056 94.084667 1 2858 3 chr6B.!!$F1 2857
3 TraesCS6B01G006100 chr6B 664523670 664524243 573 True 337.000000 337 78.388000 1645 2190 1 chr6B.!!$R4 545
4 TraesCS6B01G006100 chr6D 2133347 2138308 4961 False 3647.500000 5077 93.106000 1 5030 2 chr6D.!!$F2 5029
5 TraesCS6B01G006100 chr6D 4207541 4212401 4860 False 2379.666667 4054 92.719333 1 5030 3 chr6D.!!$F3 5029
6 TraesCS6B01G006100 chr6D 439659973 439661556 1583 True 989.000000 989 78.633000 1645 3213 1 chr6D.!!$R1 1568
7 TraesCS6B01G006100 chr6D 439616067 439617000 933 False 854.000000 854 83.351000 624 1556 1 chr6D.!!$F1 932
8 TraesCS6B01G006100 chrUn 255513317 255515802 2485 False 4425.000000 4425 98.794000 1 2487 1 chrUn.!!$F1 2486
9 TraesCS6B01G006100 chrUn 355127175 355129168 1993 True 3542.000000 3542 98.747000 3038 5030 1 chrUn.!!$R1 1992
10 TraesCS6B01G006100 chrUn 355693780 355695289 1509 True 2649.000000 2649 98.411000 3529 5030 1 chrUn.!!$R2 1501
11 TraesCS6B01G006100 chrUn 380679617 380680845 1228 False 2198.000000 2198 98.943000 1 1230 1 chrUn.!!$F3 1229
12 TraesCS6B01G006100 chr6A 771573 775994 4421 True 1162.000000 1744 92.442200 1 4404 5 chr6A.!!$R1 4403
13 TraesCS6B01G006100 chr3D 368834781 368835544 763 True 556.000000 556 80.311000 4279 5029 1 chr3D.!!$R1 750

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
592 971 0.392595 GAGCGGACCCGGAAAGATTT 60.393 55.000 0.73 0.00 40.19 2.17 F
1205 1594 2.801077 TGGGGGCTAAAAAGTAGAGC 57.199 50.000 0.00 0.00 35.39 4.09 F
1996 2421 3.878160 AAGAAGCAGCCTAGACACTAC 57.122 47.619 0.00 0.00 0.00 2.73 F
2833 3281 3.495100 GGAGGAGAACAACACACTGACAT 60.495 47.826 0.00 0.00 0.00 3.06 F
3021 3478 5.003804 GGAACAAACCTCACAGTATGATGT 58.996 41.667 0.00 0.00 39.69 3.06 F
3731 4188 4.439974 GCCAAGTGCATTATTCGAATTCCA 60.440 41.667 17.19 5.86 40.77 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1458 1851 2.568062 TCAGTACGGTTTCAATAGCCCA 59.432 45.455 0.00 0.00 0.0 5.36 R
2833 3281 0.888736 CCGAACACCAGCACCAATCA 60.889 55.000 0.00 0.00 0.0 2.57 R
3107 3564 2.531771 TCCACGATAAACAGAGGGTGA 58.468 47.619 0.00 0.00 0.0 4.02 R
3731 4188 2.699954 CTGCGTCACCTTTGTTCCTAT 58.300 47.619 0.00 0.00 0.0 2.57 R
4015 4473 5.163405 TGAGTTCATGTCAGTAGGCCTTATC 60.163 44.000 12.58 1.81 0.0 1.75 R
4924 5479 5.483937 TGTACCATTAGTCCATGAGTTGAGT 59.516 40.000 0.00 0.00 0.0 3.41 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
592 971 0.392595 GAGCGGACCCGGAAAGATTT 60.393 55.000 0.73 0.00 40.19 2.17
1205 1594 2.801077 TGGGGGCTAAAAAGTAGAGC 57.199 50.000 0.00 0.00 35.39 4.09
1251 1641 4.517832 TGGAGATGTCTATGATTGCATTGC 59.482 41.667 0.46 0.46 35.94 3.56
1259 1649 5.913514 GTCTATGATTGCATTGCTGTGAATC 59.086 40.000 10.49 10.68 35.94 2.52
1306 1696 7.309990 CCATTATTGAAAGACCACAAAGTCCAT 60.310 37.037 0.00 0.00 37.49 3.41
1498 1891 8.271487 CGTACTGAACTAAGAACCTTTTTACAC 58.729 37.037 0.00 0.00 0.00 2.90
1996 2421 3.878160 AAGAAGCAGCCTAGACACTAC 57.122 47.619 0.00 0.00 0.00 2.73
2179 2618 5.304614 TGAAGGGCCTCATACTCTACAATAC 59.695 44.000 6.46 0.00 0.00 1.89
2472 2912 9.855021 GCAAAACAATGTAAGTAATATGAACCT 57.145 29.630 0.00 0.00 0.00 3.50
2653 3101 9.143155 TCAGGCTTATCTACACATACTATTCAA 57.857 33.333 0.00 0.00 0.00 2.69
2833 3281 3.495100 GGAGGAGAACAACACACTGACAT 60.495 47.826 0.00 0.00 0.00 3.06
3021 3478 5.003804 GGAACAAACCTCACAGTATGATGT 58.996 41.667 0.00 0.00 39.69 3.06
3559 4016 8.359060 ACTAGAAAGAATAAGATCACGATTGC 57.641 34.615 0.00 0.00 0.00 3.56
3731 4188 4.439974 GCCAAGTGCATTATTCGAATTCCA 60.440 41.667 17.19 5.86 40.77 3.53
4015 4473 6.001449 TCTTTTATGGTGGATTAGGGTCTG 57.999 41.667 0.00 0.00 0.00 3.51
4146 4605 0.546747 TAGCAGTAGTGTTGGGGCCT 60.547 55.000 0.84 0.00 0.00 5.19
4924 5479 6.830838 TGATATTTGCATGTATGTTACCACCA 59.169 34.615 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
555 934 2.437413 CTCCTCTTTACAACCTTGCCC 58.563 52.381 0.00 0.00 0.00 5.36
935 1324 7.825761 CCACCATATTTATATGCATCTGAGTGA 59.174 37.037 0.19 0.00 38.99 3.41
1051 1440 3.331889 ACATCTTTTCCTCTGGTCACCAT 59.668 43.478 0.00 0.00 30.82 3.55
1205 1594 6.089820 CCATCTTTCATCCGTTTTGATGTTTG 59.910 38.462 0.00 0.00 42.24 2.93
1458 1851 2.568062 TCAGTACGGTTTCAATAGCCCA 59.432 45.455 0.00 0.00 0.00 5.36
1613 2006 5.253330 TCTGTTCCAAAATAGATGACCCAC 58.747 41.667 0.00 0.00 28.72 4.61
2833 3281 0.888736 CCGAACACCAGCACCAATCA 60.889 55.000 0.00 0.00 0.00 2.57
2976 3426 9.639601 GTTCCAAGGTAAAAGGAAAATATGAAG 57.360 33.333 0.00 0.00 42.59 3.02
3021 3478 7.936496 TCAATGCATGACTTTTTGTATAGGA 57.064 32.000 0.00 0.00 31.50 2.94
3107 3564 2.531771 TCCACGATAAACAGAGGGTGA 58.468 47.619 0.00 0.00 0.00 4.02
3591 4048 6.238103 CGTCCTTAAATCAATATTGCGTGAGT 60.238 38.462 10.76 0.00 0.00 3.41
3731 4188 2.699954 CTGCGTCACCTTTGTTCCTAT 58.300 47.619 0.00 0.00 0.00 2.57
4015 4473 5.163405 TGAGTTCATGTCAGTAGGCCTTATC 60.163 44.000 12.58 1.81 0.00 1.75
4352 4818 6.700081 TGAGTTGTTATATCATTGCTACGGTC 59.300 38.462 0.00 0.00 0.00 4.79
4924 5479 5.483937 TGTACCATTAGTCCATGAGTTGAGT 59.516 40.000 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.