Multiple sequence alignment - TraesCS5D01G202100

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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 TraesCS5D01G202100 chr5D 100.000 5413 0 0 1 5413 306564360 306569772 0.000000e+00 9997
1 TraesCS5D01G202100 chr5B 94.766 5235 166 32 1 5153 351699829 351705037 0.000000e+00 8050
2 TraesCS5D01G202100 chr5B 82.836 268 32 9 5155 5413 351705069 351705331 1.520000e-55 228
3 TraesCS5D01G202100 chr5A 96.815 3674 60 19 160 3794 390735396 390731741 0.000000e+00 6083
4 TraesCS5D01G202100 chr5A 97.738 1503 30 2 3914 5413 390731402 390729901 0.000000e+00 2584
5 TraesCS5D01G202100 chr5A 92.329 717 43 10 1 709 390749157 390748445 0.000000e+00 1009
6 TraesCS5D01G202100 chr5A 92.500 200 14 1 1 199 390735593 390735394 8.870000e-73 285


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 TraesCS5D01G202100 chr5D 306564360 306569772 5412 False 9997 9997 100.000000 1 5413 1 chr5D.!!$F1 5412
1 TraesCS5D01G202100 chr5B 351699829 351705331 5502 False 4139 8050 88.801000 1 5413 2 chr5B.!!$F1 5412
2 TraesCS5D01G202100 chr5A 390729901 390735593 5692 True 2984 6083 95.684333 1 5413 3 chr5A.!!$R2 5412
3 TraesCS5D01G202100 chr5A 390748445 390749157 712 True 1009 1009 92.329000 1 709 1 chr5A.!!$R1 708

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
138 142 1.269448 GGTTGACGTGCAATTGACCAT 59.731 47.619 10.34 0.0 39.03 3.55 F
1791 1882 0.031994 CGTTTCCCCTTTGGCTTGTG 59.968 55.000 0.00 0.0 0.00 3.33 F
1792 1883 1.408969 GTTTCCCCTTTGGCTTGTGA 58.591 50.000 0.00 0.0 0.00 3.58 F
1794 1885 1.923356 TTCCCCTTTGGCTTGTGATC 58.077 50.000 0.00 0.0 0.00 2.92 F
2380 2491 3.339141 TGTTACACACACTTGCAGTCAA 58.661 40.909 0.00 0.0 0.00 3.18 F
4085 4442 1.301423 TGTGGTTGAAACGTGCCTAC 58.699 50.000 0.00 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1793 1884 0.472471 AACCGGCAAGACCAGAAAGA 59.528 50.000 0.00 0.00 39.03 2.52 R
2707 2818 1.417517 TCTGTGATGTTGTGGTCTGCT 59.582 47.619 0.00 0.00 0.00 4.24 R
2767 2878 2.449464 CTTCTCATGGCCATGGTCAAA 58.551 47.619 38.81 26.19 39.24 2.69 R
3803 3941 8.428852 AGACAACAAAATTTATATAATGCCCCC 58.571 33.333 0.00 0.00 0.00 5.40 R
4285 4642 1.694696 GAAGAGGAACCTGGACACAGT 59.305 52.381 0.00 0.00 43.36 3.55 R
5311 5716 0.713883 CGCAAACTGCAGGTACGTAG 59.286 55.000 19.93 1.16 45.36 3.51 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
62 65 2.418197 GCACGCATTCCTTAGTAGTCCA 60.418 50.000 0.00 0.00 0.00 4.02
71 74 3.901844 TCCTTAGTAGTCCAAGCAACAGT 59.098 43.478 0.00 0.00 0.00 3.55
81 84 5.102313 GTCCAAGCAACAGTTAAATATGCC 58.898 41.667 8.66 0.00 37.73 4.40
83 86 4.864247 CCAAGCAACAGTTAAATATGCCAC 59.136 41.667 8.66 0.00 37.73 5.01
138 142 1.269448 GGTTGACGTGCAATTGACCAT 59.731 47.619 10.34 0.00 39.03 3.55
153 157 2.239402 TGACCATACATGTGTCATGCCT 59.761 45.455 9.11 0.00 34.97 4.75
244 285 7.148656 GCAATGATTGTAGTTAAATGCCGTTTT 60.149 33.333 7.05 0.00 0.00 2.43
266 307 5.777850 TCGATCCGAGGTATAATTGAACA 57.222 39.130 0.00 0.00 0.00 3.18
322 363 9.665264 ATGTTTCAAACGAGATCTTAAACTTTC 57.335 29.630 0.00 0.00 0.00 2.62
392 434 7.542477 CGGACTAAATAATCAGCATATCTTCGT 59.458 37.037 0.00 0.00 0.00 3.85
393 435 8.651588 GGACTAAATAATCAGCATATCTTCGTG 58.348 37.037 0.00 0.00 0.00 4.35
434 476 6.227298 TGTACTTTGCATTTTCCAAGGAAA 57.773 33.333 10.12 10.12 41.69 3.13
519 566 2.654749 AAATCTGCATGACGACGAGA 57.345 45.000 0.00 0.00 0.00 4.04
551 621 4.824289 CGCTGGTCTAAACCTTAAACCTA 58.176 43.478 0.00 0.00 46.60 3.08
611 688 1.950909 TCTTACCAGCAAAACAACCCG 59.049 47.619 0.00 0.00 0.00 5.28
1245 1336 2.735237 CGGCCTCCCTTATCCGTC 59.265 66.667 0.00 0.00 37.33 4.79
1791 1882 0.031994 CGTTTCCCCTTTGGCTTGTG 59.968 55.000 0.00 0.00 0.00 3.33
1792 1883 1.408969 GTTTCCCCTTTGGCTTGTGA 58.591 50.000 0.00 0.00 0.00 3.58
1793 1884 1.970640 GTTTCCCCTTTGGCTTGTGAT 59.029 47.619 0.00 0.00 0.00 3.06
1794 1885 1.923356 TTCCCCTTTGGCTTGTGATC 58.077 50.000 0.00 0.00 0.00 2.92
2380 2491 3.339141 TGTTACACACACTTGCAGTCAA 58.661 40.909 0.00 0.00 0.00 3.18
2767 2878 4.592778 ACATTGGGTAGTCAAATTTGGCTT 59.407 37.500 28.83 13.98 40.96 4.35
3088 3199 5.004726 GCTTCAAAATGTATTCATTGACGCC 59.995 40.000 0.00 0.00 42.60 5.68
3803 3941 6.292811 GCCATTATATGAAACAAAATTGCGGG 60.293 38.462 0.00 0.00 0.00 6.13
3973 4330 6.864685 CCAGAAACTACATTGTTCAGTACGTA 59.135 38.462 0.00 0.00 0.00 3.57
4017 4374 1.955778 CTTGGCAATTATCGCATCCCA 59.044 47.619 0.00 0.00 0.00 4.37
4085 4442 1.301423 TGTGGTTGAAACGTGCCTAC 58.699 50.000 0.00 0.00 0.00 3.18
4228 4585 1.523938 GGTAATCTGCCTCGGCCAC 60.524 63.158 2.24 0.00 41.09 5.01
4285 4642 8.982723 AGAAACAGATATGCTAAGAGTTCCTTA 58.017 33.333 0.00 0.00 36.34 2.69
4391 4748 5.296780 TCTGAAGATGTTCAACACACTTTCC 59.703 40.000 6.75 3.46 42.27 3.13
4419 4776 6.969473 GCTTGGCTACAGATATTGAAAAGAAC 59.031 38.462 0.00 0.00 0.00 3.01
4456 4813 7.845066 CCTAATAGGTAACAGACACTTTTCC 57.155 40.000 0.00 0.00 41.41 3.13
4481 4838 7.013655 CCCTATATGTTGCTATATTGATTGGCC 59.986 40.741 0.00 0.00 0.00 5.36
4569 4926 0.679002 CTGGCTGGGGATGTTGTCAG 60.679 60.000 0.00 0.00 0.00 3.51
4709 5066 6.190954 ACACCTTTTAGTTTGTGTGAACTC 57.809 37.500 0.00 0.00 40.24 3.01
4716 5073 8.973835 TTTTAGTTTGTGTGAACTCGAATTTT 57.026 26.923 0.00 0.00 40.24 1.82
4980 5352 9.995003 TGCAAATACATCTTCCTTGTTTTTATT 57.005 25.926 0.00 0.00 30.47 1.40
5023 5395 4.966965 AACACTGACTACATAGGAGTCG 57.033 45.455 5.03 3.08 45.29 4.18
5098 5470 9.010029 ACGGTGTTCATATTTCAACTTTTCTAT 57.990 29.630 0.00 0.00 0.00 1.98
5261 5666 2.715046 TCTTGTTGGGATGATGCTGAC 58.285 47.619 0.00 0.00 0.00 3.51
5290 5695 0.958091 CAATTGCTTGGTTGGACCGA 59.042 50.000 0.00 0.00 42.58 4.69
5311 5716 6.817140 ACCGATTTCTAGTGAGTGGAAAATAC 59.183 38.462 2.91 0.00 38.94 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 65 5.720371 TGTGGCATATTTAACTGTTGCTT 57.280 34.783 2.69 0.00 33.86 3.91
81 84 4.215399 AGGACGGTAAATGTCACAAATGTG 59.785 41.667 7.22 7.22 46.91 3.21
83 86 4.379394 CCAGGACGGTAAATGTCACAAATG 60.379 45.833 0.00 0.00 38.10 2.32
138 142 3.769300 ACAGACTAGGCATGACACATGTA 59.231 43.478 0.00 0.00 0.00 2.29
153 157 1.218047 GCCATGGCACGACAGACTA 59.782 57.895 32.08 0.00 41.49 2.59
173 214 6.942976 ACTCGTTCACATTTTCTAAGGGATA 58.057 36.000 0.00 0.00 0.00 2.59
244 285 5.777850 TGTTCAATTATACCTCGGATCGA 57.222 39.130 0.00 0.00 0.00 3.59
266 307 7.843490 TTTAACTGTATCTCTGCGCTAAATT 57.157 32.000 9.73 0.00 0.00 1.82
322 363 6.607689 TGGTATATTTCTTCACGCAAAGTTG 58.392 36.000 0.00 0.00 0.00 3.16
434 476 6.108015 CACATATGCAATGCTAACCCTTTTT 58.892 36.000 6.82 0.00 0.00 1.94
511 558 1.389106 GCGCTGTTTAATTCTCGTCGT 59.611 47.619 0.00 0.00 0.00 4.34
519 566 4.082949 GGTTTAGACCAGCGCTGTTTAATT 60.083 41.667 33.75 16.05 45.77 1.40
658 735 0.674895 CGAAGCCTGTTCTTGAGGGG 60.675 60.000 0.00 0.00 0.00 4.79
1034 1125 4.851214 GGCGCCTCTCCTCCTCCT 62.851 72.222 22.15 0.00 0.00 3.69
1245 1336 1.444553 GAGCGACAGAACCCTCGTG 60.445 63.158 0.00 0.00 32.30 4.35
1462 1553 2.434331 CCCAGGAAACGCCCTTGA 59.566 61.111 0.00 0.00 37.37 3.02
1791 1882 1.339151 ACCGGCAAGACCAGAAAGATC 60.339 52.381 0.00 0.00 39.03 2.75
1792 1883 0.693049 ACCGGCAAGACCAGAAAGAT 59.307 50.000 0.00 0.00 39.03 2.40
1793 1884 0.472471 AACCGGCAAGACCAGAAAGA 59.528 50.000 0.00 0.00 39.03 2.52
1794 1885 0.875059 GAACCGGCAAGACCAGAAAG 59.125 55.000 0.00 0.00 39.03 2.62
2420 2531 6.322712 ACTGTTTATTGAAGTTGGTAGCCAAA 59.677 34.615 1.79 0.00 45.73 3.28
2421 2532 5.830991 ACTGTTTATTGAAGTTGGTAGCCAA 59.169 36.000 0.00 0.00 41.69 4.52
2707 2818 1.417517 TCTGTGATGTTGTGGTCTGCT 59.582 47.619 0.00 0.00 0.00 4.24
2767 2878 2.449464 CTTCTCATGGCCATGGTCAAA 58.551 47.619 38.81 26.19 39.24 2.69
3803 3941 8.428852 AGACAACAAAATTTATATAATGCCCCC 58.571 33.333 0.00 0.00 0.00 5.40
3973 4330 3.951680 ACGATGGGTTTCTTTGTTTCAGT 59.048 39.130 0.00 0.00 0.00 3.41
4017 4374 7.179338 AGAGTGTCACATAATTAGACCTGAAGT 59.821 37.037 5.62 0.00 0.00 3.01
4085 4442 8.877779 AGATCGATCTCTGTCATTAAAAACTTG 58.122 33.333 22.32 0.00 29.30 3.16
4285 4642 1.694696 GAAGAGGAACCTGGACACAGT 59.305 52.381 0.00 0.00 43.36 3.55
4391 4748 3.982475 TCAATATCTGTAGCCAAGCTCG 58.018 45.455 0.00 0.00 40.44 5.03
4456 4813 7.013655 GGGCCAATCAATATAGCAACATATAGG 59.986 40.741 4.39 0.00 0.00 2.57
4481 4838 3.266510 TGGCTGCTGAATAAGTACAGG 57.733 47.619 0.00 0.00 35.05 4.00
4569 4926 2.512515 GACGCCCACCAGATGAGC 60.513 66.667 0.00 0.00 0.00 4.26
4653 5010 5.179533 GGGGTATTTGTCTCAAGAGAGTTC 58.820 45.833 0.00 0.00 42.66 3.01
4709 5066 4.867608 ACAACAAACCACAAGGAAAATTCG 59.132 37.500 0.00 0.00 38.69 3.34
4716 5073 0.820871 GGCACAACAAACCACAAGGA 59.179 50.000 0.00 0.00 38.69 3.36
5023 5395 1.526917 CCCCGATCTTGATGCCACC 60.527 63.158 0.00 0.00 0.00 4.61
5261 5666 1.201647 CCAAGCAATTGGAGCTGTGAG 59.798 52.381 7.72 0.00 44.82 3.51
5290 5695 8.529476 ACGTAGTATTTTCCACTCACTAGAAAT 58.471 33.333 0.00 0.00 41.94 2.17
5311 5716 0.713883 CGCAAACTGCAGGTACGTAG 59.286 55.000 19.93 1.16 45.36 3.51


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

AutoCloner maintained by Alex Coulton.