Multiple sequence alignment - TraesCS3D01G185300

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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 TraesCS3D01G185300 chr3D 100.000 4299 0 0 960 5258 170674917 170670619 0.000000e+00 7939
1 TraesCS3D01G185300 chr3D 100.000 646 0 0 1 646 170675876 170675231 0.000000e+00 1194
2 TraesCS3D01G185300 chr3A 96.403 4309 140 6 960 5258 208241090 208236787 0.000000e+00 7084
3 TraesCS3D01G185300 chr3A 97.063 647 15 2 1 646 208241801 208241158 0.000000e+00 1086
4 TraesCS3D01G185300 chr3B 95.763 4343 131 13 960 5258 246152608 246148275 0.000000e+00 6951
5 TraesCS3D01G185300 chr3B 93.972 647 8 7 1 646 246153294 246152678 0.000000e+00 950
6 TraesCS3D01G185300 chr6A 90.102 293 15 6 1 293 61705771 61706049 8.320000e-98 368


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 TraesCS3D01G185300 chr3D 170670619 170675876 5257 True 4566.5 7939 100.0000 1 5258 2 chr3D.!!$R1 5257
1 TraesCS3D01G185300 chr3A 208236787 208241801 5014 True 4085.0 7084 96.7330 1 5258 2 chr3A.!!$R1 5257
2 TraesCS3D01G185300 chr3B 246148275 246153294 5019 True 3950.5 6951 94.8675 1 5258 2 chr3B.!!$R1 5257

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
609 611 0.679640 TAAACCAAGCTCATGGGCCG 60.680 55.0 15.67 5.68 45.18 6.13 F
2298 2300 0.393077 TGGCGATAAAGGCTAGGCTC 59.607 55.0 20.50 6.23 37.59 4.70 F
4054 4065 0.109723 CCTCCACGGAAGTTCCCAAA 59.890 55.0 16.47 0.00 46.40 3.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2367 2369 0.394762 TGCAGGCATCATCCACCTTC 60.395 55.000 0.00 0.00 0.00 3.46 R
4060 4071 0.462225 CTCTCTGTCATGGGCTGCAG 60.462 60.000 10.11 10.11 33.16 4.41 R
5171 5218 2.373169 ACCAGCTCAACATCCAGAGAAA 59.627 45.455 0.00 0.00 33.74 2.52 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
42 43 2.621763 GACAGTGGCTGTTGTCCAG 58.378 57.895 3.16 0.00 45.44 3.86
561 563 4.039973 CCATTTACTAGAGTCGGCCCATTA 59.960 45.833 0.00 0.00 0.00 1.90
569 571 2.357952 GAGTCGGCCCATTATTGGAAAC 59.642 50.000 5.18 0.00 46.92 2.78
589 591 1.558756 CTGAGGCCCAAAGAGATCTGT 59.441 52.381 0.00 0.00 0.00 3.41
609 611 0.679640 TAAACCAAGCTCATGGGCCG 60.680 55.000 15.67 5.68 45.18 6.13
1488 1490 4.083862 GCGAGGGGGTGTCAGGTC 62.084 72.222 0.00 0.00 0.00 3.85
1508 1510 0.505655 GACGACCGTGTTTGTAGTGC 59.494 55.000 0.00 0.00 0.00 4.40
1628 1630 0.530650 ACACTGACTGCGGTTGTGAG 60.531 55.000 27.99 13.80 35.65 3.51
1688 1690 2.366916 AGCTGATAAGGGAGATGGAACG 59.633 50.000 0.00 0.00 0.00 3.95
1722 1724 3.641436 TGGGTGATGCGATGTTCTATAGT 59.359 43.478 0.00 0.00 0.00 2.12
1770 1772 0.890683 GCCTGTTGATGGAAGGGTTG 59.109 55.000 0.00 0.00 0.00 3.77
2083 2085 1.500736 AGGGGGATTTGGATAAGGCTG 59.499 52.381 0.00 0.00 0.00 4.85
2198 2200 2.635443 CCAAGGCCGCGGAAATGTT 61.635 57.895 33.48 10.82 0.00 2.71
2235 2237 7.935755 ACTGCTGATAATTTCACATATAGCACT 59.064 33.333 0.00 0.00 0.00 4.40
2257 2259 6.090358 CACTCTGTTACACGGTTACATTAAGG 59.910 42.308 0.00 0.00 0.00 2.69
2298 2300 0.393077 TGGCGATAAAGGCTAGGCTC 59.607 55.000 20.50 6.23 37.59 4.70
2481 2483 6.496565 TGATGTGTAAACTTGGGGATTTTGAT 59.503 34.615 0.00 0.00 0.00 2.57
2689 2691 5.234972 GCAAATTTCAAAGAAGGTGGTGAAG 59.765 40.000 0.00 0.00 31.98 3.02
2925 2927 5.347907 GGTCGTAGAACCATTGTTAAGTGAG 59.652 44.000 0.00 0.00 39.11 3.51
2937 2939 9.994432 CCATTGTTAAGTGAGTTCATTAAGATC 57.006 33.333 0.00 0.00 0.00 2.75
2979 2981 8.449397 CCTAGAATGATTAATATGCTGTCTTGC 58.551 37.037 0.00 0.00 0.00 4.01
3206 3208 5.200368 CTTTGCAAAGGTGGTTATCTTGT 57.800 39.130 28.12 0.00 32.40 3.16
3270 3272 6.666546 GGATTCATCCAACCATTATCATCCAT 59.333 38.462 0.51 0.00 46.38 3.41
3377 3379 9.778993 CATTCTTCCAACAATGATAACTTACAG 57.221 33.333 0.00 0.00 32.56 2.74
3487 3489 3.810941 CACTACCCGTGTTTACAACATGT 59.189 43.478 0.00 0.00 44.91 3.21
3545 3547 0.574454 GCGCTTGAGCTTATGTCTCG 59.426 55.000 0.00 0.00 39.32 4.04
3585 3587 3.270877 ACATCCGGATGCTTTTACACTC 58.729 45.455 38.44 0.00 42.39 3.51
3588 3590 0.373716 CGGATGCTTTTACACTCGGC 59.626 55.000 0.00 0.00 0.00 5.54
3598 3600 2.373540 TACACTCGGCGCAGTTATTT 57.626 45.000 10.83 0.00 0.00 1.40
3610 3612 3.663025 GCAGTTATTTGTGGGCATTGTT 58.337 40.909 0.00 0.00 0.00 2.83
3671 3673 5.376625 TGAATACCATTGTAAGGAGATGGC 58.623 41.667 1.70 0.00 43.25 4.40
3794 3796 8.745837 CAAACAAGTTGTTGAGCTAATAAACAG 58.254 33.333 21.53 0.00 40.14 3.16
3849 3851 1.397692 GCTCTTCTGTCTTCTGCATGC 59.602 52.381 11.82 11.82 0.00 4.06
3924 3926 5.506686 TGTCTGTATCCTCTTCAGATTCG 57.493 43.478 0.00 0.00 39.77 3.34
4054 4065 0.109723 CCTCCACGGAAGTTCCCAAA 59.890 55.000 16.47 0.00 46.40 3.28
4060 4071 0.310854 CGGAAGTTCCCAAAGCACAC 59.689 55.000 16.47 0.00 31.13 3.82
4088 4099 4.739137 GCCCATGACAGAGAGAACTGATAC 60.739 50.000 0.00 0.00 40.63 2.24
4100 4111 6.344500 AGAGAACTGATACTTTATGCACAGG 58.656 40.000 0.00 0.00 0.00 4.00
4164 4175 6.814146 GGAAGTCTTTCTATGACGACTTTGAT 59.186 38.462 5.17 0.00 44.23 2.57
4197 4208 1.064654 GCTATTGCTTCCCTTTGCTCG 59.935 52.381 0.00 0.00 36.03 5.03
4244 4255 3.777478 AGGCAATTGAAGCAATGATTCG 58.223 40.909 10.34 0.00 34.04 3.34
4305 4316 1.203287 GAAGTTCTTCTGGCCCATTGC 59.797 52.381 0.00 0.00 40.16 3.56
4327 4338 4.142534 GCATCATCTTCTGTAAGCAAAGCA 60.143 41.667 0.00 0.00 32.36 3.91
4339 4350 2.417719 AGCAAAGCAACTCTCGTAAGG 58.582 47.619 0.00 0.00 38.47 2.69
4364 4375 6.418101 ACACCATGTTCTTGCAGATATAACT 58.582 36.000 0.00 0.00 0.00 2.24
4385 4396 3.748083 TGAGGCTTCATAATGCATCCTC 58.252 45.455 17.35 17.35 38.95 3.71
4490 4506 3.904339 ACAGAAGATCTTGTACACTGGGT 59.096 43.478 14.00 0.00 0.00 4.51
4527 4543 1.609072 GGAAACCAGTGGCACTTCTTC 59.391 52.381 19.43 18.69 0.00 2.87
4529 4545 0.180406 AACCAGTGGCACTTCTTCGT 59.820 50.000 19.43 6.34 0.00 3.85
4596 4612 9.606631 GTAGTAAACTACTAGTAGAGCTACCAA 57.393 37.037 31.93 17.30 44.06 3.67
4708 4724 4.950050 AGTATATGCTCTTTGTTCCCTCG 58.050 43.478 0.00 0.00 0.00 4.63
4716 4732 4.628074 CTCTTTGTTCCCTCGTTGTCTTA 58.372 43.478 0.00 0.00 0.00 2.10
4748 4764 7.378966 TCACTTTCTAGCCCTATTCGAATATG 58.621 38.462 17.84 14.71 0.00 1.78
4758 4774 6.515035 GCCCTATTCGAATATGTTTCCTTTGG 60.515 42.308 17.84 11.08 0.00 3.28
4851 4875 3.084786 GCTAGTCTGCCTTTCCATTTGT 58.915 45.455 0.00 0.00 0.00 2.83
4882 4906 6.121590 ACAAATTTCTGAAAATGGCACCTTT 58.878 32.000 17.87 0.00 35.27 3.11
4933 4957 7.201478 CCTTGCTCTATACTTAGATTTATGCGC 60.201 40.741 0.00 0.00 33.98 6.09
4957 4981 6.541278 GCCCGTTTATTAGATGGTCTTTACTT 59.459 38.462 0.00 0.00 0.00 2.24
4993 5017 8.364894 ACTTTTAATTCAATTGGGTGAGGTTAC 58.635 33.333 5.42 0.00 0.00 2.50
5006 5030 4.470304 GGTGAGGTTACCCAGAACTATCTT 59.530 45.833 0.00 0.00 34.56 2.40
5013 5037 4.559862 ACCCAGAACTATCTTGGAACTG 57.440 45.455 3.23 0.00 40.22 3.16
5035 5059 6.428159 ACTGACTGGTTTCAGATAAACATGAC 59.572 38.462 0.00 0.00 45.19 3.06
5041 5065 9.612620 CTGGTTTCAGATAAACATGACTAAAAC 57.387 33.333 0.00 0.15 43.49 2.43
5042 5066 9.126151 TGGTTTCAGATAAACATGACTAAAACA 57.874 29.630 0.00 0.00 32.04 2.83
5171 5218 0.771127 TGCCTTAGTTTGCTCCCAGT 59.229 50.000 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 1.087501 GGGATGGTTTCTGAAGCGTC 58.912 55.000 0.00 0.00 44.61 5.19
561 563 2.158325 TCTTTGGGCCTCAGTTTCCAAT 60.158 45.455 4.53 0.00 38.81 3.16
569 571 1.558756 ACAGATCTCTTTGGGCCTCAG 59.441 52.381 4.53 0.00 0.00 3.35
589 591 1.555967 GGCCCATGAGCTTGGTTTAA 58.444 50.000 0.00 0.00 34.77 1.52
609 611 7.254590 GCTCACTTGTATTTGAGTCATGGTATC 60.255 40.741 0.00 0.00 41.24 2.24
618 620 3.258372 TCCGAGCTCACTTGTATTTGAGT 59.742 43.478 15.40 0.00 41.24 3.41
1488 1490 0.774098 CACTACAAACACGGTCGTCG 59.226 55.000 0.00 0.00 45.88 5.12
1508 1510 2.910199 TGGAGAAGCCAGAAATGATCG 58.090 47.619 0.00 0.00 43.33 3.69
1628 1630 2.747855 CCTGCCTCCCGAGCAAAC 60.748 66.667 0.00 0.00 40.35 2.93
1688 1690 2.815589 GCATCACCCACCATATCCTTCC 60.816 54.545 0.00 0.00 0.00 3.46
2198 2200 7.446931 TGAAATTATCAGCAGTAACACCTTCAA 59.553 33.333 0.00 0.00 33.04 2.69
2235 2237 6.343716 TCCTTAATGTAACCGTGTAACAGA 57.656 37.500 0.00 0.00 35.74 3.41
2257 2259 1.101331 ACACCGGTCGTATCCTCTTC 58.899 55.000 2.59 0.00 0.00 2.87
2298 2300 1.478510 AGTGCAATCCCACTACTCTCG 59.521 52.381 0.00 0.00 43.86 4.04
2367 2369 0.394762 TGCAGGCATCATCCACCTTC 60.395 55.000 0.00 0.00 0.00 3.46
2481 2483 3.569194 TCAAACAACTCAACTGCCCTA 57.431 42.857 0.00 0.00 0.00 3.53
2689 2691 5.699839 ACGAATGAAATTTAGCACACCTTC 58.300 37.500 0.00 0.00 36.07 3.46
2925 2927 3.005155 GCAGGCCATGGATCTTAATGAAC 59.995 47.826 18.40 0.00 0.00 3.18
2979 2981 0.607489 CACCCTTCTTGCTGAGGTGG 60.607 60.000 0.00 4.33 43.47 4.61
3206 3208 4.350368 TCACACAAGTCTAATGCCTTCA 57.650 40.909 0.00 0.00 0.00 3.02
3270 3272 5.116180 CACAAACCACTGAGAACAGAGTTA 58.884 41.667 0.00 0.00 46.03 2.24
3545 3547 6.374578 GGATGTAGACAAAGCTTCTCAAAAC 58.625 40.000 0.00 0.00 0.00 2.43
3585 3587 1.136565 CCCACAAATAACTGCGCCG 59.863 57.895 4.18 0.00 0.00 6.46
3588 3590 2.261345 CAATGCCCACAAATAACTGCG 58.739 47.619 0.00 0.00 0.00 5.18
3598 3600 2.114616 ACCTTTCAAACAATGCCCACA 58.885 42.857 0.00 0.00 0.00 4.17
3610 3612 2.945008 CAGCTTCAGTGTCACCTTTCAA 59.055 45.455 0.00 0.00 0.00 2.69
3671 3673 6.543430 TCATAAATCCAACAAAATCTGGGG 57.457 37.500 0.00 0.00 33.19 4.96
3794 3796 4.439057 TGTTTCAACCTCATATCCTACGC 58.561 43.478 0.00 0.00 0.00 4.42
3849 3851 1.957177 TCATCGATCTTCCCTTCCTCG 59.043 52.381 0.00 0.00 0.00 4.63
3924 3926 7.982354 AGCTGACCAAGTGTATTAGAACTATTC 59.018 37.037 0.00 0.00 0.00 1.75
4054 4065 2.675423 CATGGGCTGCAGTGTGCT 60.675 61.111 16.64 0.00 45.31 4.40
4060 4071 0.462225 CTCTCTGTCATGGGCTGCAG 60.462 60.000 10.11 10.11 33.16 4.41
4065 4076 1.552337 TCAGTTCTCTCTGTCATGGGC 59.448 52.381 0.00 0.00 36.85 5.36
4088 4099 8.554528 CAGTATTATCACTTCCTGTGCATAAAG 58.445 37.037 0.00 0.00 45.81 1.85
4164 4175 7.182749 AGGGAAGCAATAGCAGGATAATATGTA 59.817 37.037 0.00 0.00 45.49 2.29
4197 4208 1.955683 GCCTTAACCAGCTCCCCTTTC 60.956 57.143 0.00 0.00 0.00 2.62
4244 4255 5.278808 GGTCACCAAACTTAACCAGAATTCC 60.279 44.000 0.65 0.00 0.00 3.01
4305 4316 5.556355 TGCTTTGCTTACAGAAGATGATG 57.444 39.130 0.00 0.00 34.25 3.07
4327 4338 2.897969 ACATGGTGTCCTTACGAGAGTT 59.102 45.455 0.00 0.00 46.40 3.01
4364 4375 3.748083 GAGGATGCATTATGAAGCCTCA 58.252 45.455 27.48 1.80 40.05 3.86
4385 4396 9.507280 ACAGAATGCATATTAACAAAATTCTCG 57.493 29.630 0.00 0.00 42.53 4.04
4490 4506 2.568546 TCCTCCTTTCTCATGCCCTA 57.431 50.000 0.00 0.00 0.00 3.53
4623 4639 2.948979 TGTTTGCACCATTTTCTCTCGT 59.051 40.909 0.00 0.00 0.00 4.18
4687 4703 4.694339 ACGAGGGAACAAAGAGCATATAC 58.306 43.478 0.00 0.00 0.00 1.47
4716 4732 9.057089 CGAATAGGGCTAGAAAGTGAAAATAAT 57.943 33.333 0.00 0.00 0.00 1.28
4748 4764 6.986231 ACATTGTCAAAGATTCCAAAGGAAAC 59.014 34.615 2.16 0.13 45.41 2.78
4758 4774 7.972277 AGTGCATCATTACATTGTCAAAGATTC 59.028 33.333 0.00 0.00 0.00 2.52
4851 4875 6.518200 GCCATTTTCAGAAATTTGTACAGGGA 60.518 38.462 0.00 0.00 33.25 4.20
4882 4906 7.120579 GGGTGATTGTGTTCAGTTCATATGTAA 59.879 37.037 1.90 0.00 0.00 2.41
4933 4957 8.502105 AAAGTAAAGACCATCTAATAAACGGG 57.498 34.615 0.00 0.00 0.00 5.28
4993 5017 4.223923 AGTCAGTTCCAAGATAGTTCTGGG 59.776 45.833 0.00 0.00 43.73 4.45
4997 5021 5.153950 ACCAGTCAGTTCCAAGATAGTTC 57.846 43.478 0.00 0.00 0.00 3.01
5006 5030 5.560722 TTATCTGAAACCAGTCAGTTCCA 57.439 39.130 2.38 0.00 44.56 3.53
5013 5037 8.547967 TTAGTCATGTTTATCTGAAACCAGTC 57.452 34.615 0.00 0.00 33.49 3.51
5049 5073 5.924475 AAATGACACGTAGGTTTCTTGAG 57.076 39.130 3.62 0.00 0.00 3.02
5132 5179 6.290605 AGGCATTTCATAAACTGTTTGCTTT 58.709 32.000 15.69 0.68 0.00 3.51
5139 5186 6.868339 GCAAACTAAGGCATTTCATAAACTGT 59.132 34.615 0.00 0.00 0.00 3.55
5171 5218 2.373169 ACCAGCTCAACATCCAGAGAAA 59.627 45.455 0.00 0.00 33.74 2.52


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

AutoCloner maintained by Alex Coulton.