Multiple sequence alignment - TraesCS2D01G463300

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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 TraesCS2D01G463300 chr2D 100.000 4855 0 0 1 4855 569138466 569133612 0.000000e+00 8966
1 TraesCS2D01G463300 chr2D 96.936 1958 45 5 1 1950 569108038 569106088 0.000000e+00 3269
2 TraesCS2D01G463300 chr2D 94.823 1835 69 7 1944 3760 569097554 569095728 0.000000e+00 2839
3 TraesCS2D01G463300 chr2D 95.266 866 31 5 3759 4615 569095681 569094817 0.000000e+00 1363
4 TraesCS2D01G463300 chr2D 89.956 229 21 2 4629 4855 596575605 596575833 1.320000e-75 294
5 TraesCS2D01G463300 chr2B 97.116 3780 85 4 1 3760 681741541 681737766 0.000000e+00 6355
6 TraesCS2D01G463300 chr2B 97.182 1100 26 4 3759 4855 681737719 681736622 0.000000e+00 1855
7 TraesCS2D01G463300 chr5A 78.196 1009 189 17 1002 1984 470076949 470077952 2.480000e-172 616
8 TraesCS2D01G463300 chr1B 89.407 236 23 2 4622 4855 645331169 645331404 3.670000e-76 296
9 TraesCS2D01G463300 chr1B 89.520 229 22 2 4629 4855 47627864 47628092 6.150000e-74 289
10 TraesCS2D01G463300 chr1D 88.646 229 25 1 4628 4855 106292444 106292672 1.330000e-70 278
11 TraesCS2D01G463300 chr1D 87.554 233 24 5 4626 4855 389331147 389330917 1.040000e-66 265
12 TraesCS2D01G463300 chr7D 88.596 228 24 2 4630 4855 610839256 610839483 4.790000e-70 276
13 TraesCS2D01G463300 chr4D 88.158 228 25 2 4630 4855 447333531 447333758 2.230000e-68 270
14 TraesCS2D01G463300 chr6A 88.106 227 25 2 4631 4855 602618790 602619016 8.010000e-68 268


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 TraesCS2D01G463300 chr2D 569133612 569138466 4854 True 8966 8966 100.0000 1 4855 1 chr2D.!!$R2 4854
1 TraesCS2D01G463300 chr2D 569106088 569108038 1950 True 3269 3269 96.9360 1 1950 1 chr2D.!!$R1 1949
2 TraesCS2D01G463300 chr2D 569094817 569097554 2737 True 2101 2839 95.0445 1944 4615 2 chr2D.!!$R3 2671
3 TraesCS2D01G463300 chr2B 681736622 681741541 4919 True 4105 6355 97.1490 1 4855 2 chr2B.!!$R1 4854
4 TraesCS2D01G463300 chr5A 470076949 470077952 1003 False 616 616 78.1960 1002 1984 1 chr5A.!!$F1 982

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
771 779 5.410355 AGGTCACGCTAGGTTGTTTATAA 57.590 39.130 0.00 0.0 0.00 0.98 F
1347 1363 4.878397 CCTGATGATTTACTCTGTGGTTCC 59.122 45.833 0.00 0.0 0.00 3.62 F
2314 2351 3.760684 GAGCCACATTCATCAAAAGGAGT 59.239 43.478 0.00 0.0 0.00 3.85 F
3123 3160 4.027674 TGCACCCATGTGTGTACTTATT 57.972 40.909 10.12 0.0 44.65 1.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1920 1954 0.473755 TCTGGCTCCAACTTTGCTCA 59.526 50.000 0.00 0.0 0.00 4.26 R
2945 2982 5.048013 GGTAACAAGCACAAGGAAGCTAAAT 60.048 40.000 0.00 0.0 40.90 1.40 R
3814 3917 1.686587 TGTCGTCACTGTGATTCTGGT 59.313 47.619 14.37 0.0 0.00 4.00 R
4709 4822 0.552848 CCATGACCCTAAGGCCACAT 59.447 55.000 5.01 0.0 36.11 3.21 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
278 280 8.630037 TCTTTAGTATGACGATGATTGCTCTAA 58.370 33.333 0.00 0.00 0.00 2.10
279 281 8.803201 TTTAGTATGACGATGATTGCTCTAAG 57.197 34.615 0.00 0.00 0.00 2.18
596 599 5.831702 ACTTACGTAGTTATCAGTCCAGG 57.168 43.478 0.00 0.00 37.78 4.45
611 614 6.785076 TCAGTCCAGGTATTTAACATTGGAA 58.215 36.000 3.20 0.00 41.98 3.53
770 778 6.720112 ATAGGTCACGCTAGGTTGTTTATA 57.280 37.500 0.00 0.00 0.00 0.98
771 779 5.410355 AGGTCACGCTAGGTTGTTTATAA 57.590 39.130 0.00 0.00 0.00 0.98
772 780 5.985911 AGGTCACGCTAGGTTGTTTATAAT 58.014 37.500 0.00 0.00 0.00 1.28
1019 1028 9.698309 CTATAGTATGCTTATTATGGATTCCGG 57.302 37.037 0.00 0.00 0.00 5.14
1347 1363 4.878397 CCTGATGATTTACTCTGTGGTTCC 59.122 45.833 0.00 0.00 0.00 3.62
1891 1925 7.093945 CCTGGCACAAAGTTATTTATGGTAAGT 60.094 37.037 0.00 0.00 38.70 2.24
2087 2124 8.709386 ATCGAGCCTATGATATTAAACATGAC 57.291 34.615 0.00 0.00 0.00 3.06
2314 2351 3.760684 GAGCCACATTCATCAAAAGGAGT 59.239 43.478 0.00 0.00 0.00 3.85
2448 2485 4.650734 TCTGGCATACAACTCAAACATCA 58.349 39.130 0.00 0.00 0.00 3.07
2453 2490 5.449588 GGCATACAACTCAAACATCATCTGG 60.450 44.000 0.00 0.00 0.00 3.86
2984 3021 7.064728 GTGCTTGTTACCACTTTCCTAATCTAG 59.935 40.741 0.00 0.00 0.00 2.43
2993 3030 9.939424 ACCACTTTCCTAATCTAGTCTATTAGT 57.061 33.333 8.21 0.00 35.87 2.24
3123 3160 4.027674 TGCACCCATGTGTGTACTTATT 57.972 40.909 10.12 0.00 44.65 1.40
3126 3163 6.004574 TGCACCCATGTGTGTACTTATTTTA 58.995 36.000 10.12 0.00 44.65 1.52
3374 3411 7.974675 TGCTACTTAGTTTAGCATTTCATCAC 58.025 34.615 5.79 0.00 45.57 3.06
3441 3478 5.336150 TGGTTTGCTTTGTGAAAGATGAA 57.664 34.783 0.16 0.00 41.02 2.57
3611 3648 4.625742 ACCTGAATCGATTGTAAACGTCAG 59.374 41.667 16.96 13.29 34.65 3.51
3626 3663 5.344743 AACGTCAGTGATACCATTCATCT 57.655 39.130 0.00 0.00 0.00 2.90
3710 3765 5.656416 TGCCTTCTTTTTCTCAGAAAAAGGA 59.344 36.000 36.13 31.31 43.66 3.36
3814 3917 8.661352 TCGAGTTCAAATGATGCTATTTCATA 57.339 30.769 0.00 0.00 33.52 2.15
3869 3972 5.212532 AGTCTTGAGAGCATATCATGACC 57.787 43.478 19.28 8.98 45.76 4.02
3901 4004 6.291648 AGCTTGATGAGATAGTTGTTCAGA 57.708 37.500 0.00 0.00 0.00 3.27
3984 4090 6.073765 CCGCATTACCTTCTATGTGTTATGTC 60.074 42.308 0.00 0.00 31.90 3.06
4042 4148 5.234757 TGTTTAGTGTGTGTGAACCGATTAC 59.765 40.000 0.00 0.00 0.00 1.89
4102 4208 1.305201 TGAAGTTGTGCCGACCTTTC 58.695 50.000 0.00 0.00 0.00 2.62
4133 4239 6.810911 ACTAACTCTAGCCACTATGAACATG 58.189 40.000 0.00 0.00 0.00 3.21
4634 4746 7.547019 CCAATATACATACGTACGTCTCTCCTA 59.453 40.741 26.53 5.60 0.00 2.94
4673 4785 2.041755 AGAAAAGGGGCTAGGGTTTCTG 59.958 50.000 0.00 0.00 37.20 3.02
4682 4794 0.838987 TAGGGTTTCTGCCTCCCGTT 60.839 55.000 0.00 0.00 45.27 4.44
4709 4822 2.761195 CGCCGATCTCCACGTCTCA 61.761 63.158 0.00 0.00 0.00 3.27
4732 4845 1.453928 GCCTTAGGGTCATGGGTGC 60.454 63.158 0.00 0.00 34.45 5.01
4780 4893 1.279271 GAGGGCTCTGCTTTTAGGTGA 59.721 52.381 0.00 0.00 0.00 4.02
4822 4935 7.489160 AGGGTTTGTGTTCTATTCAAAAAGAC 58.511 34.615 0.00 0.00 33.80 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
278 280 9.634021 GGAAAGGAATAAAATTACCAGATCTCT 57.366 33.333 0.00 0.00 0.00 3.10
279 281 9.408648 TGGAAAGGAATAAAATTACCAGATCTC 57.591 33.333 0.00 0.00 0.00 2.75
431 434 9.747898 AAGTCAGTTACCCATACAAATGAATAA 57.252 29.630 0.00 0.00 34.84 1.40
579 582 8.192774 TGTTAAATACCTGGACTGATAACTACG 58.807 37.037 0.00 0.00 0.00 3.51
1019 1028 1.889170 CCTTCTTTGAACCAGCTTCCC 59.111 52.381 0.00 0.00 0.00 3.97
1891 1925 2.104622 TGTCAAGTGTCCAGATCTGCAA 59.895 45.455 17.76 4.55 0.00 4.08
1920 1954 0.473755 TCTGGCTCCAACTTTGCTCA 59.526 50.000 0.00 0.00 0.00 4.26
2087 2124 1.079503 GCTAAAGCCTGACAACCTCG 58.920 55.000 0.00 0.00 34.31 4.63
2448 2485 6.931281 CACGTCATTTGATATACCTTCCAGAT 59.069 38.462 0.00 0.00 0.00 2.90
2453 2490 7.381408 TCGAATCACGTCATTTGATATACCTTC 59.619 37.037 0.00 0.00 43.13 3.46
2631 2668 6.820656 ACTGAAGTGCCAAGAGATATGTTAAG 59.179 38.462 0.00 0.00 0.00 1.85
2945 2982 5.048013 GGTAACAAGCACAAGGAAGCTAAAT 60.048 40.000 0.00 0.00 40.90 1.40
3123 3160 7.275341 GCAACTTGCACATGTAGCATAAATAAA 59.725 33.333 19.11 6.24 44.26 1.40
3126 3163 5.104374 GCAACTTGCACATGTAGCATAAAT 58.896 37.500 19.11 7.67 44.26 1.40
3204 3241 6.374565 AGTAGCTATTTCTCGTACGATGTT 57.625 37.500 19.87 6.88 0.00 2.71
3397 3434 6.714810 ACCAACAATGTATAAGCAAGAAGTGA 59.285 34.615 0.00 0.00 0.00 3.41
3652 3689 8.299570 AGGATGAATTCAACATGTCAAACTAAC 58.700 33.333 13.09 0.00 0.00 2.34
3757 3860 8.792633 CCACCTAAAACATGAGTAAAGATCAAA 58.207 33.333 0.00 0.00 0.00 2.69
3814 3917 1.686587 TGTCGTCACTGTGATTCTGGT 59.313 47.619 14.37 0.00 0.00 4.00
3869 3972 7.763172 ACTATCTCATCAAGCTAAAAAGACG 57.237 36.000 0.00 0.00 0.00 4.18
3901 4004 6.543735 AGGGTAAAGTAGCAAGAGTTTCAAT 58.456 36.000 0.00 0.00 0.00 2.57
4102 4208 3.381908 AGTGGCTAGAGTTAGTTCGGATG 59.618 47.826 0.00 0.00 0.00 3.51
4208 4315 4.947388 TCCATGCACTAAGGAATGTTTACC 59.053 41.667 0.00 0.00 0.00 2.85
4609 4721 7.361889 AGGAGAGACGTACGTATGTATATTG 57.638 40.000 21.75 0.00 32.11 1.90
4634 4746 1.068121 CTTGGAGGGGAGACAAAGGT 58.932 55.000 0.00 0.00 0.00 3.50
4693 4805 0.741326 ACATGAGACGTGGAGATCGG 59.259 55.000 0.00 0.00 0.00 4.18
4709 4822 0.552848 CCATGACCCTAAGGCCACAT 59.447 55.000 5.01 0.00 36.11 3.21
4758 4871 0.915364 CCTAAAAGCAGAGCCCTCCT 59.085 55.000 0.00 0.00 0.00 3.69
4770 4883 9.586435 AACAAAACTTGAAGAATCACCTAAAAG 57.414 29.630 0.00 0.00 34.61 2.27
4780 4893 7.763985 CACAAACCCTAACAAAACTTGAAGAAT 59.236 33.333 0.00 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.