Multiple sequence alignment - TraesCS6D01G395800

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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 TraesCS6D01G395800 chr6D 100.000 4659 0 0 1 4659 468171398 468166740 0.000000e+00 8604.0
1 TraesCS6D01G395800 chr6D 94.142 1468 84 1 2304 3769 468057626 468056159 0.000000e+00 2233.0
2 TraesCS6D01G395800 chr6D 87.941 1501 148 15 2646 4135 468147033 468145555 0.000000e+00 1738.0
3 TraesCS6D01G395800 chr6D 83.989 1880 220 42 458 2306 468059536 468057707 0.000000e+00 1729.0
4 TraesCS6D01G395800 chr6D 85.676 1508 183 21 458 1943 468098999 468097503 0.000000e+00 1557.0
5 TraesCS6D01G395800 chr6D 86.986 1337 151 13 2529 3857 468096754 468095433 0.000000e+00 1483.0
6 TraesCS6D01G395800 chr6D 79.001 1581 251 51 21 1547 468153307 468151754 0.000000e+00 1005.0
7 TraesCS6D01G395800 chr6D 89.877 326 30 1 75 397 468060785 468060460 2.590000e-112 416.0
8 TraesCS6D01G395800 chr6D 87.324 355 43 2 3 355 468185232 468184878 5.610000e-109 405.0
9 TraesCS6D01G395800 chr6D 91.213 239 18 2 1933 2168 468097485 468097247 5.820000e-84 322.0
10 TraesCS6D01G395800 chr6D 86.131 137 14 4 4207 4338 468145537 468145401 4.860000e-30 143.0
11 TraesCS6D01G395800 chr6B 91.593 2617 163 19 2053 4659 714341279 714338710 0.000000e+00 3561.0
12 TraesCS6D01G395800 chr6B 89.622 1137 111 4 2646 3776 714330687 714329552 0.000000e+00 1439.0
13 TraesCS6D01G395800 chr6B 94.570 884 36 4 706 1587 714342895 714342022 0.000000e+00 1356.0
14 TraesCS6D01G395800 chr6B 78.763 1601 267 56 4 1551 714336787 714335207 0.000000e+00 1005.0
15 TraesCS6D01G395800 chr6B 84.848 660 67 19 4004 4656 714327123 714326490 6.580000e-178 634.0
16 TraesCS6D01G395800 chr6B 83.705 448 49 13 1586 2014 714341899 714341457 7.260000e-108 401.0
17 TraesCS6D01G395800 chr6B 88.350 309 30 4 47 355 714410549 714410247 2.650000e-97 366.0
18 TraesCS6D01G395800 chr6B 97.279 147 3 1 3 148 714343041 714342895 1.000000e-61 248.0
19 TraesCS6D01G395800 chrUn 98.886 1795 17 1 2316 4110 346082032 346080241 0.000000e+00 3201.0
20 TraesCS6D01G395800 chrUn 96.141 1866 49 5 1 1863 210219627 210217782 0.000000e+00 3025.0
21 TraesCS6D01G395800 chrUn 88.389 1378 130 15 2646 4015 310899428 310900783 0.000000e+00 1631.0
22 TraesCS6D01G395800 chrUn 90.211 1042 86 9 2844 3875 79679518 79678483 0.000000e+00 1345.0
23 TraesCS6D01G395800 chrUn 78.879 1605 262 51 4 1548 216380871 216382458 0.000000e+00 1014.0
24 TraesCS6D01G395800 chrUn 97.263 548 15 0 4112 4659 311956088 311955541 0.000000e+00 929.0
25 TraesCS6D01G395800 chrUn 97.263 548 15 0 4112 4659 335694325 335694872 0.000000e+00 929.0
26 TraesCS6D01G395800 chrUn 86.761 355 36 5 3 355 75283660 75284005 7.310000e-103 385.0
27 TraesCS6D01G395800 chrUn 86.761 355 36 5 3 355 327314188 327313843 7.310000e-103 385.0
28 TraesCS6D01G395800 chrUn 87.821 312 32 4 44 355 211919524 211919829 1.230000e-95 361.0
29 TraesCS6D01G395800 chrUn 98.095 105 2 0 1865 1969 346082527 346082423 2.860000e-42 183.0
30 TraesCS6D01G395800 chrUn 90.323 62 5 1 4278 4338 467999904 467999965 3.860000e-11 80.5
31 TraesCS6D01G395800 chr6A 90.150 1137 108 4 2529 3663 614162943 614161809 0.000000e+00 1476.0
32 TraesCS6D01G395800 chr6A 82.997 1141 175 12 459 1587 614165291 614164158 0.000000e+00 1014.0
33 TraesCS6D01G395800 chr6A 85.273 421 51 6 3 415 614165825 614165408 1.550000e-114 424.0
34 TraesCS6D01G395800 chr6A 88.043 368 29 8 1586 1943 614164053 614163691 5.570000e-114 422.0
35 TraesCS6D01G395800 chr6A 90.717 237 20 1 1934 2168 614163673 614163437 9.730000e-82 315.0
36 TraesCS6D01G395800 chr6A 83.959 293 33 6 2208 2496 614163427 614163145 7.680000e-68 268.0
37 TraesCS6D01G395800 chr3D 84.524 84 11 2 963 1045 601499655 601499573 1.070000e-11 82.4


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 TraesCS6D01G395800 chr6D 468166740 468171398 4658 True 8604.000000 8604 100.000000 1 4659 1 chr6D.!!$R2 4658
1 TraesCS6D01G395800 chr6D 468056159 468060785 4626 True 1459.333333 2233 89.336000 75 3769 3 chr6D.!!$R4 3694
2 TraesCS6D01G395800 chr6D 468095433 468098999 3566 True 1120.666667 1557 87.958333 458 3857 3 chr6D.!!$R5 3399
3 TraesCS6D01G395800 chr6D 468151754 468153307 1553 True 1005.000000 1005 79.001000 21 1547 1 chr6D.!!$R1 1526
4 TraesCS6D01G395800 chr6D 468145401 468147033 1632 True 940.500000 1738 87.036000 2646 4338 2 chr6D.!!$R6 1692
5 TraesCS6D01G395800 chr6B 714335207 714343041 7834 True 1314.200000 3561 89.182000 3 4659 5 chr6B.!!$R3 4656
6 TraesCS6D01G395800 chr6B 714326490 714330687 4197 True 1036.500000 1439 87.235000 2646 4656 2 chr6B.!!$R2 2010
7 TraesCS6D01G395800 chrUn 210217782 210219627 1845 True 3025.000000 3025 96.141000 1 1863 1 chrUn.!!$R2 1862
8 TraesCS6D01G395800 chrUn 346080241 346082527 2286 True 1692.000000 3201 98.490500 1865 4110 2 chrUn.!!$R5 2245
9 TraesCS6D01G395800 chrUn 310899428 310900783 1355 False 1631.000000 1631 88.389000 2646 4015 1 chrUn.!!$F4 1369
10 TraesCS6D01G395800 chrUn 79678483 79679518 1035 True 1345.000000 1345 90.211000 2844 3875 1 chrUn.!!$R1 1031
11 TraesCS6D01G395800 chrUn 216380871 216382458 1587 False 1014.000000 1014 78.879000 4 1548 1 chrUn.!!$F3 1544
12 TraesCS6D01G395800 chrUn 311955541 311956088 547 True 929.000000 929 97.263000 4112 4659 1 chrUn.!!$R3 547
13 TraesCS6D01G395800 chrUn 335694325 335694872 547 False 929.000000 929 97.263000 4112 4659 1 chrUn.!!$F5 547
14 TraesCS6D01G395800 chr6A 614161809 614165825 4016 True 653.166667 1476 86.856500 3 3663 6 chr6A.!!$R1 3660

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
192 205 0.392595 TGCTGAGCAAGATGAGCAGG 60.393 55.000 3.81 0.0 36.54 4.85 F
1099 2020 0.106918 TCGATTTTTCCATCCCCCGG 60.107 55.000 0.00 0.0 0.00 5.73 F
1268 2189 0.968405 TGCCAAGGTGGAATTGAAGC 59.032 50.000 0.00 0.0 40.96 3.86 F
1390 2323 1.446792 CGATGAGTGCAAGCTCCGT 60.447 57.895 2.16 0.0 34.74 4.69 F
2386 3866 1.399727 CCACGCGGATGTCTTTGAAAC 60.400 52.381 12.47 0.0 0.00 2.78 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1474 2407 0.393820 AGGTTCCTTTTACGCCGTCA 59.606 50.000 0.0 0.0 0.00 4.35 R
2093 3407 0.877649 ATCCTATTCACAGCAGCGCG 60.878 55.000 0.0 0.0 0.00 6.86 R
2386 3866 1.145598 AGACATGAGCATGAGCCCG 59.854 57.895 16.7 0.0 43.56 6.13 R
2909 4572 3.589988 CACTAATCGGCTTCTTCACTGT 58.410 45.455 0.0 0.0 0.00 3.55 R
4236 8178 1.301423 GCGGTTTGTGGACAAGTACA 58.699 50.000 0.0 0.0 37.15 2.90 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
192 205 0.392595 TGCTGAGCAAGATGAGCAGG 60.393 55.000 3.81 0.00 36.54 4.85
982 1903 1.141881 CAATCCGTGCTCCTACGCT 59.858 57.895 0.00 0.00 42.44 5.07
1096 2017 5.845391 TTGTTATCGATTTTTCCATCCCC 57.155 39.130 1.71 0.00 0.00 4.81
1097 2018 4.211920 TGTTATCGATTTTTCCATCCCCC 58.788 43.478 1.71 0.00 0.00 5.40
1098 2019 1.981256 ATCGATTTTTCCATCCCCCG 58.019 50.000 0.00 0.00 0.00 5.73
1099 2020 0.106918 TCGATTTTTCCATCCCCCGG 60.107 55.000 0.00 0.00 0.00 5.73
1152 2073 1.596934 ACGGGACTATGCCTGTGTG 59.403 57.895 0.00 0.00 45.67 3.82
1186 2107 4.507756 GCTCATGTGTCAATGCGATTAGTA 59.492 41.667 0.00 0.00 0.00 1.82
1264 2185 1.559368 TGGATGCCAAGGTGGAATTG 58.441 50.000 0.00 0.00 35.37 2.32
1268 2189 0.968405 TGCCAAGGTGGAATTGAAGC 59.032 50.000 0.00 0.00 40.96 3.86
1390 2323 1.446792 CGATGAGTGCAAGCTCCGT 60.447 57.895 2.16 0.00 34.74 4.69
1474 2407 3.806949 TGTAAGCCAGGAATGAAAGGT 57.193 42.857 0.00 0.00 0.00 3.50
1649 2711 6.307031 TGTAGTTCGTGCATAATTGTGTTT 57.693 33.333 4.00 0.00 0.00 2.83
1685 2755 2.046023 CAGCATGCGTCCCCTCAA 60.046 61.111 13.01 0.00 0.00 3.02
1821 2925 3.278574 GTGGCAGGAATGCAACATACTA 58.721 45.455 2.89 0.00 38.55 1.82
2016 3296 7.471539 CGATATACCCAGAACTAAACTCATGGT 60.472 40.741 0.00 0.00 0.00 3.55
2037 3317 7.252612 TGGTTGTTTTCTAGATCTCCACATA 57.747 36.000 0.00 0.00 0.00 2.29
2093 3407 2.486592 AGCGTGGCAATGGTTTTAGTAC 59.513 45.455 0.00 0.00 0.00 2.73
2144 3460 9.601217 TTTTATTTATGAGACAGAAGGAGTAGC 57.399 33.333 0.00 0.00 0.00 3.58
2171 3487 5.005094 GGGTGTTTATTGTAGCAAGGTACA 58.995 41.667 7.94 7.94 0.00 2.90
2174 3490 7.337436 GGGTGTTTATTGTAGCAAGGTACAATA 59.663 37.037 27.70 27.70 46.93 1.90
2184 3500 9.976511 TGTAGCAAGGTACAATAAGTATATGAC 57.023 33.333 9.45 0.00 34.67 3.06
2267 3583 4.290093 TGGGTTCTACTCAGCTATCACAT 58.710 43.478 0.00 0.00 0.00 3.21
2386 3866 1.399727 CCACGCGGATGTCTTTGAAAC 60.400 52.381 12.47 0.00 0.00 2.78
2496 3977 5.700402 ATCCCTATGTACCATTGGATAGC 57.300 43.478 10.37 0.00 31.03 2.97
2894 4557 4.155280 GCGAAGTTTACAAGGGCATTCTTA 59.845 41.667 0.00 0.00 0.00 2.10
2909 4572 6.321181 GGGCATTCTTAATAATGAACCAGTCA 59.679 38.462 15.61 0.00 38.84 3.41
3609 5272 4.079615 TGTGGATCAAAGACCATGGATGAT 60.080 41.667 21.47 20.21 38.48 2.45
3669 5332 0.179225 AAGTCGTAATTTGCGCTGCG 60.179 50.000 19.17 19.17 0.00 5.18
4140 8082 2.676748 TCCAACTTCAGTTTGGGCAAT 58.323 42.857 1.39 0.00 35.83 3.56
4143 8085 3.007182 CCAACTTCAGTTTGGGCAATGAT 59.993 43.478 0.00 0.00 35.83 2.45
4236 8178 0.108377 TGCGACAATACTCGTGCCAT 60.108 50.000 0.00 0.00 35.99 4.40
4449 8398 3.420893 CCAGGTAATGTTCTGGCTGAAA 58.579 45.455 8.48 0.63 43.22 2.69
4605 8555 9.516546 TCGTCTAAGATAATTGAAGGAGCTATA 57.483 33.333 0.00 0.00 0.00 1.31
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
192 205 1.271597 ACCTGGAAGTGTGATTGGCTC 60.272 52.381 0.00 0.0 0.00 4.70
982 1903 2.118679 CATGACCTCTCCACCACCATA 58.881 52.381 0.00 0.0 0.00 2.74
1096 2017 0.748005 GTGGGACATGAACCATCCGG 60.748 60.000 14.45 0.0 44.52 5.14
1097 2018 2.780595 GTGGGACATGAACCATCCG 58.219 57.895 14.45 0.0 44.52 4.18
1264 2185 6.808704 GTCTGGATGTGGAAATTAAAAGCTTC 59.191 38.462 0.00 0.0 0.00 3.86
1268 2189 7.609532 AGAGAGTCTGGATGTGGAAATTAAAAG 59.390 37.037 0.00 0.0 0.00 2.27
1307 2230 9.726438 ATGGAGTTCCTATATAAACTTATGTGC 57.274 33.333 0.00 0.0 35.90 4.57
1390 2323 4.019411 TCAGTGGAGCAAGGATACAAATCA 60.019 41.667 0.00 0.0 41.41 2.57
1474 2407 0.393820 AGGTTCCTTTTACGCCGTCA 59.606 50.000 0.00 0.0 0.00 4.35
1522 2455 5.543507 ATTTGTGCTTACCCAAAATCACA 57.456 34.783 0.00 0.0 34.52 3.58
1685 2755 8.540388 TCTGCTAGTTATACTCAGGAATTTGTT 58.460 33.333 0.00 0.0 0.00 2.83
2016 3296 7.496346 ACCTATGTGGAGATCTAGAAAACAA 57.504 36.000 0.00 0.0 39.71 2.83
2093 3407 0.877649 ATCCTATTCACAGCAGCGCG 60.878 55.000 0.00 0.0 0.00 6.86
2144 3460 4.201910 CCTTGCTACAATAAACACCCATCG 60.202 45.833 0.00 0.0 0.00 3.84
2171 3487 9.159254 TCCACCATTCTGAGTCATATACTTATT 57.841 33.333 0.00 0.0 39.07 1.40
2174 3490 6.384015 TGTCCACCATTCTGAGTCATATACTT 59.616 38.462 0.00 0.0 39.07 2.24
2176 3492 6.040955 TCTGTCCACCATTCTGAGTCATATAC 59.959 42.308 0.00 0.0 0.00 1.47
2179 3495 4.352893 TCTGTCCACCATTCTGAGTCATA 58.647 43.478 0.00 0.0 0.00 2.15
2181 3497 2.564504 CTCTGTCCACCATTCTGAGTCA 59.435 50.000 0.00 0.0 0.00 3.41
2182 3498 2.828520 TCTCTGTCCACCATTCTGAGTC 59.171 50.000 0.00 0.0 0.00 3.36
2183 3499 2.894731 TCTCTGTCCACCATTCTGAGT 58.105 47.619 0.00 0.0 0.00 3.41
2184 3500 3.007290 TGTTCTCTGTCCACCATTCTGAG 59.993 47.826 0.00 0.0 0.00 3.35
2267 3583 1.541670 GGCTTTGTGTGAGGAACCGTA 60.542 52.381 0.00 0.0 0.00 4.02
2386 3866 1.145598 AGACATGAGCATGAGCCCG 59.854 57.895 16.70 0.0 43.56 6.13
2894 4557 6.533730 TCTTCACTGTGACTGGTTCATTATT 58.466 36.000 10.56 0.0 36.32 1.40
2909 4572 3.589988 CACTAATCGGCTTCTTCACTGT 58.410 45.455 0.00 0.0 0.00 3.55
4236 8178 1.301423 GCGGTTTGTGGACAAGTACA 58.699 50.000 0.00 0.0 37.15 2.90
4449 8398 4.414514 ACAAACTAAGGTCTTAACACCCCT 59.585 41.667 0.00 0.0 37.09 4.79


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

AutoCloner maintained by Alex Coulton.