Multiple sequence alignment - TraesCS3D01G298000

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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 TraesCS3D01G298000 chr3D 100.000 5298 0 0 1 5298 412085188 412090485 0.000000e+00 9784.0
1 TraesCS3D01G298000 chr3A 97.185 4761 98 14 3 4744 538017910 538013167 0.000000e+00 8017.0
2 TraesCS3D01G298000 chr3A 90.141 568 28 8 4735 5298 538013128 538012585 0.000000e+00 713.0
3 TraesCS3D01G298000 chr3B 96.390 4488 127 14 3 4477 539061667 539066132 0.000000e+00 7358.0
4 TraesCS3D01G298000 chr3B 91.681 565 27 10 4735 5298 539066492 539067037 0.000000e+00 765.0
5 TraesCS3D01G298000 chr3B 96.085 281 10 1 4465 4744 539066173 539066453 1.740000e-124 457.0
6 TraesCS3D01G298000 chr1A 93.478 46 1 2 5010 5053 529319073 529319118 3.420000e-07 67.6


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 TraesCS3D01G298000 chr3D 412085188 412090485 5297 False 9784 9784 100.000000 1 5298 1 chr3D.!!$F1 5297
1 TraesCS3D01G298000 chr3A 538012585 538017910 5325 True 4365 8017 93.663000 3 5298 2 chr3A.!!$R1 5295
2 TraesCS3D01G298000 chr3B 539061667 539067037 5370 False 2860 7358 94.718667 3 5298 3 chr3B.!!$F1 5295

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
80 81 0.102300 GCTCTCGAGGCTTCTCTTCC 59.898 60.000 13.56 0.00 35.43 3.46 F
804 821 0.308684 TTGTTTCTTCGCTGCTGCTG 59.691 50.000 14.03 0.77 36.97 4.41 F
1250 1279 1.091771 CGGCAGTTACCATCAGCCAG 61.092 60.000 0.00 0.00 45.47 4.85 F
1395 1424 1.534175 GGTAGTTCATCAGCGACTCCG 60.534 57.143 0.00 0.00 39.16 4.63 F
2233 2262 1.670406 GTGAGTGGCTGGTCTGCTG 60.670 63.158 0.24 0.00 0.00 4.41 F
3129 3158 2.090831 ACTCCTGGATGTCTGCCTATCT 60.091 50.000 0.00 0.00 0.00 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1383 1412 0.748367 TGCTAGTCGGAGTCGCTGAT 60.748 55.000 10.25 0.00 33.65 2.90 R
2196 2225 1.215423 ACAGGGCCTTTTCTTCTGTGT 59.785 47.619 1.32 0.00 37.31 3.72 R
2352 2381 1.363744 CACCATTCTTCACTCTCGGC 58.636 55.000 0.00 0.00 0.00 5.54 R
3292 3321 0.039165 GCAAGGCCACAAGTTAGTGC 60.039 55.000 5.01 0.00 38.18 4.40 R
3339 3368 1.612676 TCAACATTGCAGCTGCTTCT 58.387 45.000 36.61 19.64 42.66 2.85 R
4991 5125 1.160137 AAGATGCTTCGAGGTTGTGC 58.840 50.000 0.00 0.00 0.00 4.57 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
80 81 0.102300 GCTCTCGAGGCTTCTCTTCC 59.898 60.000 13.56 0.00 35.43 3.46
398 403 2.361230 GCTGGCCCAGGTTGTACC 60.361 66.667 13.78 0.00 38.99 3.34
430 441 1.805120 GCATCATCAAGCATGGGCAAC 60.805 52.381 0.00 0.00 44.61 4.17
550 567 3.879180 TTCCCTTTTCCTGCCGGCC 62.879 63.158 26.77 6.44 0.00 6.13
620 637 2.070028 GTTTTTCTCTCTCGTCCTGGC 58.930 52.381 0.00 0.00 0.00 4.85
724 741 2.808543 CGTTTTGTCCCTTCTCTCCAAG 59.191 50.000 0.00 0.00 0.00 3.61
778 795 2.780065 TGCTTTACTGCTGTTTGCTG 57.220 45.000 0.09 0.00 44.70 4.41
802 819 0.661483 GGTTGTTTCTTCGCTGCTGC 60.661 55.000 5.34 5.34 0.00 5.25
803 820 0.308993 GTTGTTTCTTCGCTGCTGCT 59.691 50.000 14.03 0.00 36.97 4.24
804 821 0.308684 TTGTTTCTTCGCTGCTGCTG 59.691 50.000 14.03 0.77 36.97 4.41
826 843 7.119997 GCTGTTGAATTACTCATACGTCATTC 58.880 38.462 0.00 0.00 32.78 2.67
921 938 9.211485 GAACAATTTCAAATCATGATGGACTTT 57.789 29.630 9.46 0.00 38.03 2.66
1185 1211 2.043752 TCCCCGACTGGTATCGCA 60.044 61.111 0.00 0.00 40.87 5.10
1231 1257 2.281345 ACACTCTGGTGCAGCAGC 60.281 61.111 35.36 18.07 46.57 5.25
1250 1279 1.091771 CGGCAGTTACCATCAGCCAG 61.092 60.000 0.00 0.00 45.47 4.85
1383 1412 1.562475 GGCCCATACCAAGGTAGTTCA 59.438 52.381 5.10 0.00 33.77 3.18
1395 1424 1.534175 GGTAGTTCATCAGCGACTCCG 60.534 57.143 0.00 0.00 39.16 4.63
2053 2082 2.471815 TCGGGTGAATAGGTGGAGAT 57.528 50.000 0.00 0.00 0.00 2.75
2196 2225 8.225603 AGAAGTATTTTGAGCTCAAGACAAAA 57.774 30.769 27.02 19.00 43.91 2.44
2233 2262 1.670406 GTGAGTGGCTGGTCTGCTG 60.670 63.158 0.24 0.00 0.00 4.41
2352 2381 3.506096 CTGCAGCATGGCCGACAG 61.506 66.667 0.00 0.00 35.86 3.51
3009 3038 2.685388 GGAGCTTCCAATTACTCCAAGC 59.315 50.000 3.07 0.00 46.57 4.01
3129 3158 2.090831 ACTCCTGGATGTCTGCCTATCT 60.091 50.000 0.00 0.00 0.00 1.98
3292 3321 2.266055 GGAGGAAGTGGTGGCGAG 59.734 66.667 0.00 0.00 0.00 5.03
3339 3368 2.117051 AGGATGCAGAGATCTGAAGCA 58.883 47.619 13.98 13.69 46.59 3.91
3792 3821 3.055530 CAGTTCAGTCAGAAGCCCAGTAT 60.056 47.826 0.00 0.00 36.78 2.12
4018 4047 2.955614 ACGTCCACCTTAGTTGATTCG 58.044 47.619 0.00 0.00 0.00 3.34
4189 4218 7.746703 ACCCTATCTTATTTCATCCCTGTTAC 58.253 38.462 0.00 0.00 0.00 2.50
4331 4360 3.951775 AGTTCTGTCCTGTCTGATGAC 57.048 47.619 0.00 0.00 43.20 3.06
4355 4384 4.990257 AGATGCCATGATTTTGTTCGAAG 58.010 39.130 0.00 0.00 0.00 3.79
4400 4430 2.889678 TCTGATGGGAGATGATGTCGAG 59.110 50.000 0.00 0.00 0.00 4.04
4447 4477 1.873591 GCCGTGTCTGTTGATTTGAGT 59.126 47.619 0.00 0.00 0.00 3.41
4662 4748 1.194547 AGCATTGTAGTTCGCACAACG 59.805 47.619 0.00 0.00 38.63 4.10
4682 4768 8.922676 CACAACGTAGTGACTGATATTAAACTT 58.077 33.333 0.00 0.00 45.00 2.66
4765 4899 3.195610 GGGGGCTGGAGAAACATAAAAAG 59.804 47.826 0.00 0.00 0.00 2.27
4766 4900 4.086457 GGGGCTGGAGAAACATAAAAAGA 58.914 43.478 0.00 0.00 0.00 2.52
4767 4901 4.711846 GGGGCTGGAGAAACATAAAAAGAT 59.288 41.667 0.00 0.00 0.00 2.40
4834 4968 9.573133 AACAACAATAGCATATAACTTTTGAGC 57.427 29.630 12.90 0.00 32.49 4.26
4937 5071 7.496346 TCCAGAAGACAAGAATTAGTACCAT 57.504 36.000 0.00 0.00 0.00 3.55
4938 5072 7.331026 TCCAGAAGACAAGAATTAGTACCATG 58.669 38.462 0.00 0.00 0.00 3.66
4964 5098 9.810231 GTGAATTTTGCATTAAAAGGTGTTATG 57.190 29.630 0.00 0.00 41.26 1.90
4991 5125 7.646526 CACATTCAACAATAATCTGCAGTATGG 59.353 37.037 14.67 5.41 35.86 2.74
5075 5212 7.549615 AGTAGTTGGACAAGAGTTTAACAAC 57.450 36.000 0.00 0.00 37.56 3.32
5080 5217 7.812669 AGTTGGACAAGAGTTTAACAACAAAAG 59.187 33.333 0.00 0.00 39.18 2.27
5081 5218 6.096695 TGGACAAGAGTTTAACAACAAAAGC 58.903 36.000 0.00 0.00 35.05 3.51
5134 5272 6.389830 TCATGATTTGACCCAAATATTCCG 57.610 37.500 5.06 0.00 43.05 4.30
5140 5278 2.092158 TGACCCAAATATTCCGCATCCA 60.092 45.455 0.00 0.00 0.00 3.41
5261 5399 0.038166 TCTTTGGCATGGTGAGTCCC 59.962 55.000 0.00 0.00 34.77 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.270986 GCCTCCACAACCCAGCAAG 61.271 63.158 0.00 0.00 0.00 4.01
3 4 2.203480 GCCTCCACAACCCAGCAA 60.203 61.111 0.00 0.00 0.00 3.91
5 6 4.643387 ACGCCTCCACAACCCAGC 62.643 66.667 0.00 0.00 0.00 4.85
6 7 2.358737 GACGCCTCCACAACCCAG 60.359 66.667 0.00 0.00 0.00 4.45
7 8 3.948719 GGACGCCTCCACAACCCA 61.949 66.667 0.00 0.00 36.42 4.51
398 403 0.933097 GATGATGCACAGCGTACCAG 59.067 55.000 0.00 0.00 0.00 4.00
430 441 2.951642 ACATAACATGCGAGAATTGGGG 59.048 45.455 0.00 0.00 0.00 4.96
575 592 9.678260 ACTTTCTCTAATTGCTTGATGATAAGT 57.322 29.630 0.00 0.00 0.00 2.24
620 637 1.355916 GGCTCAGCGAGTACTACGG 59.644 63.158 13.92 3.72 31.39 4.02
778 795 0.668535 AGCGAAGAAACAACCAAGCC 59.331 50.000 0.00 0.00 0.00 4.35
802 819 8.323854 CAGAATGACGTATGAGTAATTCAACAG 58.676 37.037 12.31 0.81 42.03 3.16
803 820 8.032451 TCAGAATGACGTATGAGTAATTCAACA 58.968 33.333 12.31 0.00 42.56 3.33
804 821 8.407457 TCAGAATGACGTATGAGTAATTCAAC 57.593 34.615 12.31 0.00 42.56 3.18
826 843 9.688592 GCTTGGGAATAATAATTTCTTCATCAG 57.311 33.333 0.00 0.00 0.00 2.90
921 938 6.222038 ACGGTATCTGCAGAAGATAGAAAA 57.778 37.500 22.50 0.00 46.40 2.29
1185 1211 6.884295 TGGAAAGAATATCACCGATTTTCAGT 59.116 34.615 9.01 0.00 34.21 3.41
1224 1250 3.804193 GGTAACTGCCGCTGCTGC 61.804 66.667 9.23 9.23 39.83 5.25
1231 1257 3.813596 GGCTGATGGTAACTGCCG 58.186 61.111 0.00 0.00 41.06 5.69
1250 1279 5.389935 GCATCGTCTAGCAATAACCTTATGC 60.390 44.000 0.00 0.00 0.00 3.14
1383 1412 0.748367 TGCTAGTCGGAGTCGCTGAT 60.748 55.000 10.25 0.00 33.65 2.90
1395 1424 5.120830 AGTTGAACGATCACAATTGCTAGTC 59.879 40.000 5.05 0.00 34.61 2.59
2053 2082 4.934797 ATTCATCTTTCTCCACCCTCAA 57.065 40.909 0.00 0.00 0.00 3.02
2196 2225 1.215423 ACAGGGCCTTTTCTTCTGTGT 59.785 47.619 1.32 0.00 37.31 3.72
2233 2262 7.475015 TCTGCATTTAGTTGCTCATAATTGTC 58.525 34.615 0.00 0.00 43.18 3.18
2352 2381 1.363744 CACCATTCTTCACTCTCGGC 58.636 55.000 0.00 0.00 0.00 5.54
3009 3038 1.581934 TCAACGTGTCAAGAAGCCTG 58.418 50.000 0.00 0.00 0.00 4.85
3129 3158 3.760151 GGCCATCTGCATGCTCAAATATA 59.240 43.478 20.33 0.00 43.89 0.86
3292 3321 0.039165 GCAAGGCCACAAGTTAGTGC 60.039 55.000 5.01 0.00 38.18 4.40
3339 3368 1.612676 TCAACATTGCAGCTGCTTCT 58.387 45.000 36.61 19.64 42.66 2.85
3792 3821 2.435805 CAGCTCCTGCCAAAGATAGGTA 59.564 50.000 0.00 0.00 40.80 3.08
4018 4047 5.810080 ATGGGTGAAGTCCTAAGCTATAC 57.190 43.478 0.00 0.00 0.00 1.47
4189 4218 2.424246 GGTAGAACCCTGAAGAGAGTCG 59.576 54.545 0.00 0.00 30.04 4.18
4234 4263 6.896021 TCTAGTAACAACAACAGAGTAGCT 57.104 37.500 0.00 0.00 0.00 3.32
4241 4270 9.909644 ACTAGTACAATCTAGTAACAACAACAG 57.090 33.333 0.00 0.00 45.71 3.16
4331 4360 4.735985 TCGAACAAAATCATGGCATCTTG 58.264 39.130 0.00 1.93 0.00 3.02
4355 4384 2.474816 GATTCTGTACCGGATCACAGC 58.525 52.381 22.46 11.07 41.58 4.40
4696 4782 8.398878 AGTAGGTTACTCTAGCATTCAGATAC 57.601 38.462 0.00 0.00 32.47 2.24
4714 4800 2.846950 AGGGCTCCATGTTAGTAGGTT 58.153 47.619 0.00 0.00 0.00 3.50
4937 5071 7.856145 AACACCTTTTAATGCAAAATTCACA 57.144 28.000 0.00 0.00 35.59 3.58
4938 5072 9.810231 CATAACACCTTTTAATGCAAAATTCAC 57.190 29.630 0.00 0.00 35.59 3.18
4991 5125 1.160137 AAGATGCTTCGAGGTTGTGC 58.840 50.000 0.00 0.00 0.00 4.57
5075 5212 8.947055 ATAACCTTGCAATAATTAGGCTTTTG 57.053 30.769 0.00 3.22 0.00 2.44
5080 5217 9.067986 AGAGTAATAACCTTGCAATAATTAGGC 57.932 33.333 0.00 5.24 0.00 3.93
5134 5272 5.320549 AGTCTTTTGATCATTGTGGATGC 57.679 39.130 0.00 0.00 35.64 3.91
5140 5278 5.075493 AGAGGCAAGTCTTTTGATCATTGT 58.925 37.500 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.