Multiple sequence alignment - TraesCS3D01G250600

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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 TraesCS3D01G250600 chr3D 100.000 7641 0 0 1 7641 350828374 350820734 0.000000e+00 14111.0
1 TraesCS3D01G250600 chr3A 96.957 6670 134 30 995 7641 468588494 468581871 0.000000e+00 11129.0
2 TraesCS3D01G250600 chr3A 94.251 974 20 18 1 949 468589724 468588762 0.000000e+00 1456.0
3 TraesCS3D01G250600 chr3B 95.679 4629 121 33 1 4609 449288609 449284040 0.000000e+00 7367.0
4 TraesCS3D01G250600 chr3B 94.073 1721 72 14 5713 7426 449282756 449281059 0.000000e+00 2586.0
5 TraesCS3D01G250600 chr3B 95.141 885 32 7 4826 5709 449283797 449282923 0.000000e+00 1386.0
6 TraesCS3D01G250600 chr3B 95.302 149 5 1 4681 4827 449284039 449283891 1.280000e-57 235.0
7 TraesCS3D01G250600 chr5D 97.297 37 1 0 5442 5478 337898750 337898714 6.400000e-06 63.9


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 TraesCS3D01G250600 chr3D 350820734 350828374 7640 True 14111.0 14111 100.00000 1 7641 1 chr3D.!!$R1 7640
1 TraesCS3D01G250600 chr3A 468581871 468589724 7853 True 6292.5 11129 95.60400 1 7641 2 chr3A.!!$R1 7640
2 TraesCS3D01G250600 chr3B 449281059 449288609 7550 True 2893.5 7367 95.04875 1 7426 4 chr3B.!!$R1 7425

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
591 600 3.524759 CGCGCGTCGTGTCTTCTC 61.525 66.667 24.19 0.0 32.40 2.87 F
1701 1956 0.457851 AGAAGACCTTCCTCATCGCG 59.542 55.000 0.00 0.0 40.33 5.87 F
2641 2902 0.531090 CACGTCCACTCCAACCGAAA 60.531 55.000 0.00 0.0 0.00 3.46 F
2881 3142 1.570813 TAACAGCTGAATCCATCGCG 58.429 50.000 23.35 0.0 34.29 5.87 F
3537 3798 1.598882 TGATAAACACGCTGTGCCAA 58.401 45.000 8.31 0.0 36.98 4.52 F
3693 3954 2.487762 TGGAATGAAGATTGTTGCCGTC 59.512 45.455 0.00 0.0 0.00 4.79 F
4586 4857 2.954989 TCACTGCACTTTGTTATGCCAA 59.045 40.909 0.00 0.0 41.33 4.52 F
5634 6003 0.321298 GGCAAAGCGTCTGGAGGTAA 60.321 55.000 0.00 0.0 0.00 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1746 2001 0.457166 CGTTGATGTCGAAGCCGGTA 60.457 55.000 1.9 0.0 36.24 4.02 R
2700 2961 0.692476 CCAAGGTGGTGGTCTCATCA 59.308 55.000 0.0 0.0 33.63 3.07 R
3693 3954 2.107950 TACCTTTGGCATCAGTTCCG 57.892 50.000 0.0 0.0 0.00 4.30 R
4611 4882 2.514458 ATAACACTTGAAGGGGGCAG 57.486 50.000 0.0 0.0 0.00 4.85 R
4972 5340 3.131400 GCTTGTCAACCCAACCTGTAAAA 59.869 43.478 0.0 0.0 0.00 1.52 R
5319 5687 4.708726 AGCACTCAACATTAAAGCCATC 57.291 40.909 0.0 0.0 0.00 3.51 R
6374 6910 1.888215 ATGGCTTAGTCCATGCATCG 58.112 50.000 0.0 0.0 44.72 3.84 R
7437 7986 1.291877 ACGTTTGTCAGCCGCATCTC 61.292 55.000 0.0 0.0 0.00 2.75 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
591 600 3.524759 CGCGCGTCGTGTCTTCTC 61.525 66.667 24.19 0.00 32.40 2.87
592 601 3.524759 GCGCGTCGTGTCTTCTCG 61.525 66.667 8.43 0.00 0.00 4.04
1701 1956 0.457851 AGAAGACCTTCCTCATCGCG 59.542 55.000 0.00 0.00 40.33 5.87
1746 2001 4.074526 ATCTGCCAGACGCGTGCT 62.075 61.111 20.70 11.30 42.08 4.40
2279 2534 1.687123 GTGCTACCTGATACGGATGGT 59.313 52.381 0.00 0.00 36.66 3.55
2595 2856 1.349282 GTCGACGCAAACACGGTTT 59.651 52.632 0.00 0.00 37.37 3.27
2624 2885 3.503748 AGCTAATTTCTGCTGTGTTCCAC 59.496 43.478 0.00 0.00 38.21 4.02
2625 2886 3.667960 GCTAATTTCTGCTGTGTTCCACG 60.668 47.826 0.00 0.00 37.14 4.94
2626 2887 1.967319 ATTTCTGCTGTGTTCCACGT 58.033 45.000 0.00 0.00 37.14 4.49
2627 2888 1.295792 TTTCTGCTGTGTTCCACGTC 58.704 50.000 0.00 0.00 37.14 4.34
2628 2889 0.531974 TTCTGCTGTGTTCCACGTCC 60.532 55.000 0.00 0.00 37.14 4.79
2629 2890 1.227527 CTGCTGTGTTCCACGTCCA 60.228 57.895 0.00 0.00 37.14 4.02
2641 2902 0.531090 CACGTCCACTCCAACCGAAA 60.531 55.000 0.00 0.00 0.00 3.46
2670 2931 5.063438 TCTGAGTTTCGAGCATTAATTTCGG 59.937 40.000 15.38 2.82 35.21 4.30
2700 2961 7.066284 GTGATATTGTAGATCACTGTTGCCTTT 59.934 37.037 8.22 0.00 46.42 3.11
2863 3124 2.158871 ACAACGCTTTCAGGTGGACTTA 60.159 45.455 0.00 0.00 0.00 2.24
2881 3142 1.570813 TAACAGCTGAATCCATCGCG 58.429 50.000 23.35 0.00 34.29 5.87
3497 3758 2.236146 TGCTGGACTGATGGTTATTCGT 59.764 45.455 0.00 0.00 0.00 3.85
3535 3796 1.737236 TCATGATAAACACGCTGTGCC 59.263 47.619 8.31 0.00 36.98 5.01
3537 3798 1.598882 TGATAAACACGCTGTGCCAA 58.401 45.000 8.31 0.00 36.98 4.52
3572 3833 6.281848 TGTTTAGCACTCTTTGTTTACGAG 57.718 37.500 0.00 0.00 0.00 4.18
3693 3954 2.487762 TGGAATGAAGATTGTTGCCGTC 59.512 45.455 0.00 0.00 0.00 4.79
3790 4053 5.658634 TCTGCTCTGATGGTACTGTTTCTAT 59.341 40.000 0.00 0.00 0.00 1.98
3811 4074 8.016301 TCTATGCTCTGTCAATATGAGAGTTT 57.984 34.615 4.68 0.00 38.72 2.66
4024 4290 6.016276 CAGGGCTAGAAATTACCGCATTAATT 60.016 38.462 0.00 0.00 33.84 1.40
4028 4294 8.228464 GGCTAGAAATTACCGCATTAATTAGAC 58.772 37.037 0.00 0.00 32.44 2.59
4029 4295 8.770828 GCTAGAAATTACCGCATTAATTAGACA 58.229 33.333 0.00 0.00 32.44 3.41
4123 4389 6.747414 TGGAAGCATGTTATAGTATCCAGT 57.253 37.500 0.00 0.00 32.29 4.00
4197 4464 6.547510 AGACAACTGCTTCATAGAACCTTTTT 59.452 34.615 0.00 0.00 0.00 1.94
4202 4469 5.136828 TGCTTCATAGAACCTTTTTGTGGA 58.863 37.500 0.00 0.00 0.00 4.02
4586 4857 2.954989 TCACTGCACTTTGTTATGCCAA 59.045 40.909 0.00 0.00 41.33 4.52
4611 4882 6.985188 TTGTCTACTTGATCCTTATGCAAC 57.015 37.500 0.00 0.00 0.00 4.17
4659 4930 8.481314 ACTAATATATGATGTATGCTGGTCCAG 58.519 37.037 15.15 15.15 34.12 3.86
5240 5608 3.352648 AGCTTTATATTTGGTGGCGTGT 58.647 40.909 0.00 0.00 0.00 4.49
5319 5687 5.798434 TGATGATGTGTTAACTACTCGAACG 59.202 40.000 7.22 0.00 0.00 3.95
5338 5706 4.685169 ACGATGGCTTTAATGTTGAGTG 57.315 40.909 0.00 0.00 0.00 3.51
5400 5769 8.850454 TGTCTTTTCTCGTTTCATTTAAAAGG 57.150 30.769 0.00 0.00 35.60 3.11
5478 5847 1.132527 TCCCTCTCCCTGAGAAAACCA 60.133 52.381 0.00 0.00 45.39 3.67
5634 6003 0.321298 GGCAAAGCGTCTGGAGGTAA 60.321 55.000 0.00 0.00 0.00 2.85
5650 6019 7.987458 TCTGGAGGTAATTGATGTTACTCATTC 59.013 37.037 0.00 0.00 36.83 2.67
5856 6389 4.342092 GGTGCCTTGTGCTTTATCCATATT 59.658 41.667 0.00 0.00 42.00 1.28
6030 6563 5.945784 TGAAAGCAAGGTAAGCATGTCTAAT 59.054 36.000 0.00 0.00 0.00 1.73
6039 6572 7.275920 AGGTAAGCATGTCTAATTCAACCTAG 58.724 38.462 0.00 0.00 32.02 3.02
6047 6580 5.932303 TGTCTAATTCAACCTAGTGCTTGTC 59.068 40.000 0.00 0.00 0.00 3.18
6377 6913 1.528824 CCAACTCCTGATGGGCGAT 59.471 57.895 0.00 0.00 33.12 4.58
6771 7307 1.704628 TCCTCAAATGCCACCTTCTCA 59.295 47.619 0.00 0.00 0.00 3.27
7017 7563 0.746659 AAGGCCAACAACTGCTCAAC 59.253 50.000 5.01 0.00 0.00 3.18
7370 7918 4.808364 GCTAAAATCACACAAAGCACCAAA 59.192 37.500 0.00 0.00 0.00 3.28
7371 7919 5.466393 GCTAAAATCACACAAAGCACCAAAT 59.534 36.000 0.00 0.00 0.00 2.32
7601 8150 7.509546 ACTAATTATGGTTAGGGTGATCACAG 58.490 38.462 26.47 12.36 36.27 3.66
7604 8153 2.902608 TGGTTAGGGTGATCACAGAGT 58.097 47.619 26.47 10.40 0.00 3.24
7616 8165 1.598130 ACAGAGTTTGCCTCGGTGC 60.598 57.895 0.00 0.00 45.35 5.01
7638 8187 3.495806 CCAAAGGCAACAAAATTAGGGCA 60.496 43.478 0.00 0.00 41.41 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
109 111 2.050350 CCAACCTCCGTCCGCTCTA 61.050 63.158 0.00 0.00 0.00 2.43
111 113 3.692406 ACCAACCTCCGTCCGCTC 61.692 66.667 0.00 0.00 0.00 5.03
584 593 3.066233 GCGGGAGGGACGAGAAGAC 62.066 68.421 0.00 0.00 0.00 3.01
590 599 4.501285 ATCGAGCGGGAGGGACGA 62.501 66.667 0.00 0.00 37.39 4.20
591 600 3.967335 GATCGAGCGGGAGGGACG 61.967 72.222 0.00 0.00 0.00 4.79
592 601 3.607661 GGATCGAGCGGGAGGGAC 61.608 72.222 0.00 0.00 0.00 4.46
952 985 3.889692 CGGGGATGGATGGGGTGG 61.890 72.222 0.00 0.00 0.00 4.61
993 1026 3.869272 GCGCGCTCCATTGGACTG 61.869 66.667 26.67 0.00 0.00 3.51
1665 1920 4.991687 GTCTTCTTCTTGGACTTGACGATT 59.008 41.667 0.00 0.00 0.00 3.34
1746 2001 0.457166 CGTTGATGTCGAAGCCGGTA 60.457 55.000 1.90 0.00 36.24 4.02
2203 2458 0.470833 CAATTTGGTGGGTGGGTGGA 60.471 55.000 0.00 0.00 0.00 4.02
2212 2467 3.129287 GTCACTATCAGGCAATTTGGTGG 59.871 47.826 0.00 0.00 0.00 4.61
2279 2534 1.847798 ATGCTCGGCCACTAACCCAA 61.848 55.000 2.24 0.00 0.00 4.12
2619 2880 1.448497 GGTTGGAGTGGACGTGGAA 59.552 57.895 0.00 0.00 0.00 3.53
2624 2885 2.373540 TATTTCGGTTGGAGTGGACG 57.626 50.000 0.00 0.00 0.00 4.79
2625 2886 4.941873 AGAATTATTTCGGTTGGAGTGGAC 59.058 41.667 0.00 0.00 36.93 4.02
2626 2887 4.941263 CAGAATTATTTCGGTTGGAGTGGA 59.059 41.667 0.00 0.00 36.93 4.02
2627 2888 4.941263 TCAGAATTATTTCGGTTGGAGTGG 59.059 41.667 0.00 0.00 36.93 4.00
2628 2889 5.643777 ACTCAGAATTATTTCGGTTGGAGTG 59.356 40.000 0.00 0.00 36.93 3.51
2629 2890 5.805728 ACTCAGAATTATTTCGGTTGGAGT 58.194 37.500 0.00 0.00 36.93 3.85
2691 2952 2.229792 GTGGTCTCATCAAAGGCAACA 58.770 47.619 0.00 0.00 41.41 3.33
2700 2961 0.692476 CCAAGGTGGTGGTCTCATCA 59.308 55.000 0.00 0.00 33.63 3.07
2863 3124 1.709147 GCGCGATGGATTCAGCTGTT 61.709 55.000 12.10 2.24 0.00 3.16
3693 3954 2.107950 TACCTTTGGCATCAGTTCCG 57.892 50.000 0.00 0.00 0.00 4.30
3790 4053 7.708322 GTGATAAACTCTCATATTGACAGAGCA 59.292 37.037 0.00 0.00 0.00 4.26
3811 4074 3.814842 CACTGAGGTTGCAACTTGTGATA 59.185 43.478 27.64 7.99 0.00 2.15
3924 4189 8.079211 AGACAGTGAAAGTATCCTAATTGCTA 57.921 34.615 0.00 0.00 0.00 3.49
3936 4201 8.445275 TGCAAGAAAATAAGACAGTGAAAGTA 57.555 30.769 0.00 0.00 0.00 2.24
3943 4208 5.767168 AGAAGCTGCAAGAAAATAAGACAGT 59.233 36.000 1.02 0.00 34.07 3.55
3944 4209 6.251655 AGAAGCTGCAAGAAAATAAGACAG 57.748 37.500 1.02 0.00 34.07 3.51
3945 4210 7.744087 TTAGAAGCTGCAAGAAAATAAGACA 57.256 32.000 1.02 0.00 34.07 3.41
3946 4211 8.672815 AGATTAGAAGCTGCAAGAAAATAAGAC 58.327 33.333 1.02 0.00 34.07 3.01
3947 4212 8.798859 AGATTAGAAGCTGCAAGAAAATAAGA 57.201 30.769 1.02 0.00 34.07 2.10
4123 4389 4.755629 CCAATTTCCATGCAATTTGTGTGA 59.244 37.500 0.00 0.00 0.00 3.58
4197 4464 9.638239 GTCAATTAATTCAAATAGCTTTCCACA 57.362 29.630 0.00 0.00 0.00 4.17
4586 4857 7.831193 AGTTGCATAAGGATCAAGTAGACAAAT 59.169 33.333 0.00 0.00 0.00 2.32
4611 4882 2.514458 ATAACACTTGAAGGGGGCAG 57.486 50.000 0.00 0.00 0.00 4.85
4961 5329 7.398829 ACCCAACCTGTAAAAACAAGAAAAAT 58.601 30.769 0.00 0.00 0.00 1.82
4967 5335 5.106442 GTCAACCCAACCTGTAAAAACAAG 58.894 41.667 0.00 0.00 0.00 3.16
4968 5336 4.527038 TGTCAACCCAACCTGTAAAAACAA 59.473 37.500 0.00 0.00 0.00 2.83
4969 5337 4.087182 TGTCAACCCAACCTGTAAAAACA 58.913 39.130 0.00 0.00 0.00 2.83
4970 5338 4.722361 TGTCAACCCAACCTGTAAAAAC 57.278 40.909 0.00 0.00 0.00 2.43
4971 5339 4.382147 GCTTGTCAACCCAACCTGTAAAAA 60.382 41.667 0.00 0.00 0.00 1.94
4972 5340 3.131400 GCTTGTCAACCCAACCTGTAAAA 59.869 43.478 0.00 0.00 0.00 1.52
5240 5608 9.554724 GCAAAATGAAATAATACAAAGAGACGA 57.445 29.630 0.00 0.00 0.00 4.20
5319 5687 4.708726 AGCACTCAACATTAAAGCCATC 57.291 40.909 0.00 0.00 0.00 3.51
5400 5769 6.857777 AGTCTGATAATGTAGCTGCATTTC 57.142 37.500 30.87 25.16 39.50 2.17
5573 5942 4.762956 AGCAATCTTTGAAGCTTCAGTC 57.237 40.909 27.02 12.94 38.61 3.51
5634 6003 5.351465 GTGTGACCGAATGAGTAACATCAAT 59.649 40.000 0.00 0.00 38.38 2.57
5718 6251 4.469657 TGGGTAGTGTTTCTGCAGATTTT 58.530 39.130 19.04 4.70 0.00 1.82
5856 6389 6.373005 TTCCAAGATCCAGTCAGTGAATTA 57.627 37.500 0.00 0.00 0.00 1.40
6047 6580 2.025441 CCAACGGTTGGTGCAACG 59.975 61.111 27.87 4.40 44.36 4.10
6374 6910 1.888215 ATGGCTTAGTCCATGCATCG 58.112 50.000 0.00 0.00 44.72 3.84
6520 7056 6.462500 TGGCAAGAGCATAAGAGAGATTATC 58.538 40.000 0.00 0.00 44.61 1.75
6601 7137 2.190488 CTTCCTCTGCCACCTGGGAC 62.190 65.000 0.00 0.00 40.01 4.46
7017 7563 5.277538 GGCAGGCTGATAATTTAACTCTTCG 60.278 44.000 20.86 0.00 0.00 3.79
7437 7986 1.291877 ACGTTTGTCAGCCGCATCTC 61.292 55.000 0.00 0.00 0.00 2.75
7616 8165 3.073678 GCCCTAATTTTGTTGCCTTTGG 58.926 45.455 0.00 0.00 0.00 3.28


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

AutoCloner maintained by Alex Coulton.