Multiple sequence alignment - TraesCS6D01G108500

Loading Multiple Alignment...

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 TraesCS6D01G108500 chr6D 100.000 6170 0 0 1 6170 73062644 73068813 0.000000e+00 11394
1 TraesCS6D01G108500 chr6A 98.617 5135 71 0 1 5135 89586684 89591818 0.000000e+00 9090
2 TraesCS6D01G108500 chr6A 96.957 986 18 3 5187 6170 89592184 89593159 0.000000e+00 1644
3 TraesCS6D01G108500 chr6A 100.000 56 0 0 5132 5187 89592074 89592129 3.040000e-18 104
4 TraesCS6D01G108500 chr6B 97.956 5187 103 1 1 5187 147576486 147581669 0.000000e+00 8988
5 TraesCS6D01G108500 chr6B 97.160 986 17 2 5187 6170 147581724 147582700 0.000000e+00 1655


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 TraesCS6D01G108500 chr6D 73062644 73068813 6169 False 11394.000000 11394 100.000000 1 6170 1 chr6D.!!$F1 6169
1 TraesCS6D01G108500 chr6A 89586684 89593159 6475 False 3612.666667 9090 98.524667 1 6170 3 chr6A.!!$F1 6169
2 TraesCS6D01G108500 chr6B 147576486 147582700 6214 False 5321.500000 8988 97.558000 1 6170 2 chr6B.!!$F1 6169

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
945 946 1.242076 CTTTGCAGTCACTGAAGGGG 58.758 55.000 9.70 0.0 32.44 4.79 F
1250 1251 1.531423 AAGTCTGAAGTGCAGCATGG 58.469 50.000 0.00 0.0 44.52 3.66 F
1767 1768 4.287067 TCCTTACAGGAGTTTCTGCTCAAT 59.713 41.667 0.00 0.0 40.06 2.57 F
3236 3237 3.161866 GGATAACTTGGCTGGGAAACAA 58.838 45.455 0.00 0.0 0.00 2.83 F
3610 3611 0.036105 TGTGCTGCAGGATGGTAGTG 60.036 55.000 17.12 0.0 35.86 2.74 F
3666 3667 0.110486 GCTTGGGGGAACTGTTGAGA 59.890 55.000 0.00 0.0 0.00 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2480 2481 3.381045 TGAAGCTCAGTACGTGAAGTTG 58.619 45.455 0.00 0.00 33.60 3.16 R
3236 3237 4.422073 TCATGCTCGACCTCCAATAATT 57.578 40.909 0.00 0.00 0.00 1.40 R
3610 3611 4.303086 CACCAGATGGAATTTCAGCATC 57.697 45.455 4.50 7.27 38.94 3.91 R
4917 4918 0.250684 TGGCAAGGCGATGTGAAAGA 60.251 50.000 0.00 0.00 0.00 2.52 R
5098 5099 4.095410 TGAAGCAACAAAACACACTGAG 57.905 40.909 0.00 0.00 0.00 3.35 R
5494 5811 6.914757 GGAATATGAGTATTCTGCAAAAGTGC 59.085 38.462 7.78 0.00 44.62 4.40 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
36 37 8.218488 ACTGTTAAGGGAGAACTTGAACTAATT 58.782 33.333 0.00 0.00 32.02 1.40
443 444 5.440207 AATTGCAGGGCTTTATTGGAAAT 57.560 34.783 0.00 0.00 0.00 2.17
603 604 3.763097 TTGCATCTTTCATACGCCAAG 57.237 42.857 0.00 0.00 0.00 3.61
722 723 8.548721 CAGTTCCGATATTTACCAATCTGTAAC 58.451 37.037 0.00 0.00 30.73 2.50
792 793 5.964758 ACAGTTGTGTGTCAAAAACATGAT 58.035 33.333 0.00 0.00 40.80 2.45
945 946 1.242076 CTTTGCAGTCACTGAAGGGG 58.758 55.000 9.70 0.00 32.44 4.79
1250 1251 1.531423 AAGTCTGAAGTGCAGCATGG 58.469 50.000 0.00 0.00 44.52 3.66
1650 1651 5.049818 GTCTGCTCAAAGCGATAATGCTAAT 60.050 40.000 0.00 0.00 46.60 1.73
1761 1762 7.331026 TGTATGATTCCTTACAGGAGTTTCTG 58.669 38.462 0.00 0.00 46.73 3.02
1767 1768 4.287067 TCCTTACAGGAGTTTCTGCTCAAT 59.713 41.667 0.00 0.00 40.06 2.57
2259 2260 6.976925 AGAAACTTGAAAATGCAGTTGAAGAG 59.023 34.615 19.94 10.58 0.00 2.85
3236 3237 3.161866 GGATAACTTGGCTGGGAAACAA 58.838 45.455 0.00 0.00 0.00 2.83
3610 3611 0.036105 TGTGCTGCAGGATGGTAGTG 60.036 55.000 17.12 0.00 35.86 2.74
3654 3655 1.073025 TGCTGTACTGTGCTTGGGG 59.927 57.895 1.46 0.00 0.00 4.96
3666 3667 0.110486 GCTTGGGGGAACTGTTGAGA 59.890 55.000 0.00 0.00 0.00 3.27
3787 3788 3.733380 CGCTTCTACATCAGAGACTGGTG 60.733 52.174 9.99 9.99 46.89 4.17
3803 3804 3.648067 ACTGGTGGAGATGACAAAGAGAA 59.352 43.478 0.00 0.00 0.00 2.87
3890 3891 1.279152 CGTGATGAAGCAGCTGAGAG 58.721 55.000 20.43 0.00 0.00 3.20
3920 3921 1.834263 ACTAATGCTGGAGGTGGAGAC 59.166 52.381 0.00 0.00 0.00 3.36
4008 4009 5.181245 GCTTGTGCTTGAACTGGAATTAGTA 59.819 40.000 0.00 0.00 36.03 1.82
4026 4027 4.056092 AGTAAGTAAGCAGCGGGATAAC 57.944 45.455 0.00 0.00 0.00 1.89
4074 4075 0.820226 AGTTAGAGCATGCTCGCAGA 59.180 50.000 35.50 22.16 46.90 4.26
4247 4248 1.209504 AGAATTAGCGGGTAAGCAGCA 59.790 47.619 5.82 0.00 40.15 4.41
4317 4318 8.592809 ACTTCACTGAGAGAGAAACTGAATATT 58.407 33.333 0.00 0.00 0.00 1.28
4479 4480 2.396590 TGGGCCGATTAACTGAGAAC 57.603 50.000 0.00 0.00 0.00 3.01
4548 4549 4.085357 TGCTTTGAGTACAGTGGACATT 57.915 40.909 8.55 0.00 0.00 2.71
4576 4577 6.642540 TCGAGAATTTGATACAGATCCAATCG 59.357 38.462 0.00 0.00 28.54 3.34
4732 4733 4.058817 CGATAACCTGCAGGAGGAATTAC 58.941 47.826 39.19 17.48 46.33 1.89
4917 4918 5.247110 TCAACTAAGAGAGGTCTGCTTTGAT 59.753 40.000 0.00 0.00 31.37 2.57
4947 4948 2.338015 CCTTGCCAGCGCATTCAGT 61.338 57.895 11.47 0.00 46.67 3.41
5098 5099 7.122204 ACAAGGTAAATTTAGGCTACCAATGTC 59.878 37.037 9.25 0.00 38.04 3.06
5262 5577 6.775629 TGGAAATGAGGCTTGTACTAAGTTTT 59.224 34.615 0.00 0.00 0.00 2.43
5421 5736 4.605640 AAATTGTTGGTGCTAATGTGCT 57.394 36.364 0.00 0.00 0.00 4.40
5426 5741 7.587037 ATTGTTGGTGCTAATGTGCTATATT 57.413 32.000 0.00 0.00 0.00 1.28
5440 5755 8.854614 ATGTGCTATATTAGATTTTGGGAGTC 57.145 34.615 0.00 0.00 0.00 3.36
5495 5812 3.410508 TGATTTCAATTTGGCCCTTTGC 58.589 40.909 0.00 0.00 40.16 3.68
5496 5813 3.181447 TGATTTCAATTTGGCCCTTTGCA 60.181 39.130 0.00 0.00 43.89 4.08
5497 5814 2.252976 TTCAATTTGGCCCTTTGCAC 57.747 45.000 0.00 0.00 43.89 4.57
5498 5815 1.422531 TCAATTTGGCCCTTTGCACT 58.577 45.000 0.00 0.00 43.89 4.40
5678 5995 6.238184 GGTTTTTCAATTGACCAGAAAGCAAG 60.238 38.462 7.89 0.00 33.35 4.01
5708 6025 3.503748 GCTGAAGTTATGTCCAACTTGCT 59.496 43.478 6.00 0.00 46.23 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 1.768275 TCCTGTTTCTGAGAAGCCACA 59.232 47.619 6.58 2.59 0.00 4.17
443 444 6.312399 ACTCAACATTATCTTTTTGCGACA 57.688 33.333 0.00 0.00 0.00 4.35
483 484 2.679355 TGTTTGCTTCCGATTCAACG 57.321 45.000 0.00 0.00 0.00 4.10
603 604 3.287312 TGCAACTCAAGCTGTTTATGC 57.713 42.857 7.01 7.01 0.00 3.14
792 793 2.824546 GATGAGGCCAGGCGATGA 59.175 61.111 5.01 0.00 0.00 2.92
945 946 3.873952 CACCTTTAGCAACCTCTAGATGC 59.126 47.826 8.48 8.48 40.34 3.91
1250 1251 0.948141 AGTGCGCTGTCTTTCTGCTC 60.948 55.000 9.73 0.00 38.56 4.26
1539 1540 1.301716 GAGACCTTCGCTTGCACCA 60.302 57.895 0.00 0.00 0.00 4.17
1761 1762 3.836949 TGAATTTCCAAGCGAATTGAGC 58.163 40.909 2.66 0.00 41.83 4.26
1767 1768 4.379813 GCTTCATCTGAATTTCCAAGCGAA 60.380 41.667 0.00 0.00 33.01 4.70
2480 2481 3.381045 TGAAGCTCAGTACGTGAAGTTG 58.619 45.455 0.00 0.00 33.60 3.16
3236 3237 4.422073 TCATGCTCGACCTCCAATAATT 57.578 40.909 0.00 0.00 0.00 1.40
3610 3611 4.303086 CACCAGATGGAATTTCAGCATC 57.697 45.455 4.50 7.27 38.94 3.91
3654 3655 7.148137 TGGTCTAAAACTTTTCTCAACAGTTCC 60.148 37.037 0.00 0.00 30.22 3.62
3787 3788 6.634805 TCAGTACATTCTCTTTGTCATCTCC 58.365 40.000 0.00 0.00 0.00 3.71
3890 3891 1.873591 CCAGCATTAGTAATCGTGCCC 59.126 52.381 3.82 0.00 38.31 5.36
4008 4009 1.838077 AGGTTATCCCGCTGCTTACTT 59.162 47.619 0.00 0.00 38.74 2.24
4026 4027 5.182760 ACTCTGATTTAGCTTTTCTTGCAGG 59.817 40.000 0.00 0.00 0.00 4.85
4150 4151 2.094752 GCCGGTTTATTTGAGCATGTGT 60.095 45.455 1.90 0.00 0.00 3.72
4247 4248 2.773087 AGCTTCTCTTGCAGATCATCCT 59.227 45.455 0.00 0.00 0.00 3.24
4317 4318 2.586425 CCTTTCCCTTTTCTGACAGCA 58.414 47.619 0.00 0.00 0.00 4.41
4479 4480 5.554636 GTTGTATCATGCAAGTTCTTCTCG 58.445 41.667 0.00 0.00 0.00 4.04
4548 4549 5.163416 TGGATCTGTATCAAATTCTCGAGCA 60.163 40.000 7.81 0.00 33.41 4.26
4732 4733 0.321122 AGTGCGGCTTCTTCCTTGAG 60.321 55.000 0.00 0.00 0.00 3.02
4917 4918 0.250684 TGGCAAGGCGATGTGAAAGA 60.251 50.000 0.00 0.00 0.00 2.52
4947 4948 5.957771 AGCTGATAAGGTCCACATCTTTA 57.042 39.130 0.00 0.00 0.00 1.85
5071 5072 8.110908 ACATTGGTAGCCTAAATTTACCTTGTA 58.889 33.333 8.23 0.00 38.12 2.41
5072 5073 6.951778 ACATTGGTAGCCTAAATTTACCTTGT 59.048 34.615 8.23 8.63 38.12 3.16
5098 5099 4.095410 TGAAGCAACAAAACACACTGAG 57.905 40.909 0.00 0.00 0.00 3.35
5262 5577 8.992073 CGATCATAAAGAAATATGACATGGTGA 58.008 33.333 0.00 0.00 43.17 4.02
5426 5741 7.617225 TGAAAGAATACGACTCCCAAAATCTA 58.383 34.615 0.00 0.00 0.00 1.98
5492 5809 7.970061 GAATATGAGTATTCTGCAAAAGTGCAA 59.030 33.333 2.66 0.00 44.91 4.08
5493 5810 7.475015 GAATATGAGTATTCTGCAAAAGTGCA 58.525 34.615 0.89 0.89 45.24 4.57
5494 5811 6.914757 GGAATATGAGTATTCTGCAAAAGTGC 59.085 38.462 7.78 0.00 44.62 4.40
5495 5812 7.988737 TGGAATATGAGTATTCTGCAAAAGTG 58.011 34.615 7.78 0.00 43.68 3.16
5496 5813 8.579850 TTGGAATATGAGTATTCTGCAAAAGT 57.420 30.769 7.78 0.00 43.68 2.66
5498 5815 9.806203 CATTTGGAATATGAGTATTCTGCAAAA 57.194 29.630 12.33 0.00 43.68 2.44
5678 5995 5.967088 TGGACATAACTTCAGCTAACTCTC 58.033 41.667 0.00 0.00 0.00 3.20
5708 6025 7.521423 CGTTATTTTGGGAAGTGAATCTGTTCA 60.521 37.037 0.00 0.00 41.89 3.18
5845 6162 6.091986 CCTTCAATCTCAGAAACTGAACTAGC 59.908 42.308 0.00 0.00 40.18 3.42


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

AutoCloner maintained by Alex Coulton.