Multiple sequence alignment - TraesCS1D01G138900

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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 TraesCS1D01G138900 chr1D 100.000 2574 0 0 1 2574 190762425 190764998 0.000000e+00 4754.0
1 TraesCS1D01G138900 chr1B 96.785 2582 44 11 1 2574 264341030 264343580 0.000000e+00 4272.0
2 TraesCS1D01G138900 chr1A 91.565 1316 59 16 252 1567 168553184 168554447 0.000000e+00 1768.0
3 TraesCS1D01G138900 chr1A 95.030 825 31 3 1595 2414 168554507 168555326 0.000000e+00 1288.0
4 TraesCS1D01G138900 chr1A 89.474 152 15 1 1 151 168547454 168547605 9.400000e-45 191.0
5 TraesCS1D01G138900 chr1A 94.915 59 3 0 2414 2472 168567459 168567517 2.730000e-15 93.5
6 TraesCS1D01G138900 chr7B 93.333 45 2 1 170 214 285360215 285360258 5.940000e-07 65.8
7 TraesCS1D01G138900 chr7A 95.122 41 2 0 174 214 367010832 367010872 5.940000e-07 65.8
8 TraesCS1D01G138900 chr7D 90.698 43 3 1 177 219 303313591 303313550 3.580000e-04 56.5
9 TraesCS1D01G138900 chrUn 100.000 28 0 0 187 214 284606602 284606575 5.000000e-03 52.8


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 TraesCS1D01G138900 chr1D 190762425 190764998 2573 False 4754 4754 100.0000 1 2574 1 chr1D.!!$F1 2573
1 TraesCS1D01G138900 chr1B 264341030 264343580 2550 False 4272 4272 96.7850 1 2574 1 chr1B.!!$F1 2573
2 TraesCS1D01G138900 chr1A 168553184 168555326 2142 False 1528 1768 93.2975 252 2414 2 chr1A.!!$F3 2162


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
946 950 0.300491 CACGCACACACACACAGTAC 59.7 55.0 0.0 0.0 0.0 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2534 2588 0.108089 ATGTACGCCGGTGCATAACA 60.108 50.0 16.69 14.61 45.92 2.41 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
97 98 5.200454 CAGTATGCATTATTGTTGTCTCGC 58.800 41.667 3.54 0.00 0.00 5.03
128 132 6.348458 CCTTGATGTTGTGTCGTTGATGTAAT 60.348 38.462 0.00 0.00 0.00 1.89
339 343 4.070552 GACCGCTCACCTTCGCCT 62.071 66.667 0.00 0.00 0.00 5.52
552 556 1.799157 AACCCATGCAGGCCCTAACA 61.799 55.000 0.00 0.00 35.39 2.41
558 562 1.036707 TGCAGGCCCTAACAAAACAC 58.963 50.000 0.00 0.00 0.00 3.32
722 726 1.425267 CCGCAATTCCGCATGTACGA 61.425 55.000 0.00 0.00 34.06 3.43
723 727 0.371989 CGCAATTCCGCATGTACGAA 59.628 50.000 0.00 0.00 34.06 3.85
724 728 1.592110 CGCAATTCCGCATGTACGAAG 60.592 52.381 0.00 0.00 34.06 3.79
943 947 1.365368 TTCCACGCACACACACACAG 61.365 55.000 0.00 0.00 0.00 3.66
945 949 0.808060 CCACGCACACACACACAGTA 60.808 55.000 0.00 0.00 0.00 2.74
946 950 0.300491 CACGCACACACACACAGTAC 59.700 55.000 0.00 0.00 0.00 2.73
1053 1057 7.912056 ACATTTATATGTAATCTGCATCGCT 57.088 32.000 0.00 0.00 43.12 4.93
1395 1399 4.145807 TCTGGTTCTCTTCTCTCTTCGTT 58.854 43.478 0.00 0.00 0.00 3.85
1580 1584 3.878778 ACAGTTCAATATGGAGGCTCAC 58.121 45.455 17.69 6.44 0.00 3.51
1880 1934 2.436646 AAGACCCGCATCTTGCCG 60.437 61.111 0.00 0.00 41.12 5.69
2184 2238 5.105310 TCACTCTATTTGTAAGAGACAGGGC 60.105 44.000 7.09 0.00 42.63 5.19
2185 2239 4.777896 ACTCTATTTGTAAGAGACAGGGCA 59.222 41.667 7.09 0.00 42.63 5.36
2214 2268 5.982890 ACATAACAACATCAAGGGGAAAG 57.017 39.130 0.00 0.00 0.00 2.62
2219 2273 5.948742 ACAACATCAAGGGGAAAGAAAAA 57.051 34.783 0.00 0.00 0.00 1.94
2235 2289 2.197792 AAAACGGTTCGGTTCAAAGC 57.802 45.000 0.00 0.00 34.97 3.51
2273 2327 1.553248 ACGTTCGGGAGGATGAATGAA 59.447 47.619 1.55 0.00 35.56 2.57
2336 2390 1.132643 ACGCGCACCAACTTTAACAAA 59.867 42.857 5.73 0.00 0.00 2.83
2445 2499 6.522946 AGGAGTTAACTCTAAACCAGAACAC 58.477 40.000 29.66 12.16 42.48 3.32
2495 2549 3.356529 AATTCAAAGTCAGGAGGCGAT 57.643 42.857 0.00 0.00 0.00 4.58
2499 2553 2.166459 TCAAAGTCAGGAGGCGATAGTG 59.834 50.000 0.00 0.00 39.35 2.74
2515 2569 6.309251 GGCGATAGTGCTACATTTAAGAGATC 59.691 42.308 0.00 0.00 39.35 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
85 86 0.107654 GGCCTAGGCGAGACAACAAT 60.108 55.000 27.24 0.00 43.06 2.71
97 98 2.359900 GACACAACATCAAGGCCTAGG 58.640 52.381 5.16 3.67 0.00 3.02
722 726 7.048512 GCAAGGTTTCATGAGGTATACTACTT 58.951 38.462 2.25 0.00 0.00 2.24
723 727 6.583562 GCAAGGTTTCATGAGGTATACTACT 58.416 40.000 2.25 0.00 0.00 2.57
724 728 5.462398 CGCAAGGTTTCATGAGGTATACTAC 59.538 44.000 2.25 0.00 0.00 2.73
943 947 2.427232 TAAGGCGAGTGTGTGTGTAC 57.573 50.000 0.00 0.00 0.00 2.90
945 949 3.887621 ATATAAGGCGAGTGTGTGTGT 57.112 42.857 0.00 0.00 0.00 3.72
946 950 6.089551 GCTTATATATAAGGCGAGTGTGTGTG 59.910 42.308 26.50 4.94 40.01 3.82
1580 1584 6.642950 TGACATAATTTAACTTTTTGGTGCCG 59.357 34.615 0.00 0.00 0.00 5.69
2120 2174 1.789576 ATTGCCGGGACCTTGACCTT 61.790 55.000 2.18 0.00 0.00 3.50
2184 2238 5.794945 CCTTGATGTTGTTATGTTAGCGTTG 59.205 40.000 0.00 0.00 0.00 4.10
2185 2239 5.106317 CCCTTGATGTTGTTATGTTAGCGTT 60.106 40.000 0.00 0.00 0.00 4.84
2214 2268 2.532723 GCTTTGAACCGAACCGTTTTTC 59.467 45.455 0.00 0.00 0.00 2.29
2219 2273 1.782028 GCAGCTTTGAACCGAACCGT 61.782 55.000 0.00 0.00 0.00 4.83
2273 2327 1.004044 CAGTTCCAAGATCCCTGTGCT 59.996 52.381 0.00 0.00 0.00 4.40
2417 2471 7.133133 TCTGGTTTAGAGTTAACTCCTTTGT 57.867 36.000 28.05 14.34 43.88 2.83
2418 2472 7.497909 TGTTCTGGTTTAGAGTTAACTCCTTTG 59.502 37.037 28.05 14.07 43.88 2.77
2419 2473 7.498239 GTGTTCTGGTTTAGAGTTAACTCCTTT 59.502 37.037 28.05 15.01 43.88 3.11
2420 2474 6.990939 GTGTTCTGGTTTAGAGTTAACTCCTT 59.009 38.462 28.05 15.68 43.88 3.36
2445 2499 8.803201 ATTACATGTCTATGAATACTGTGTCG 57.197 34.615 0.00 0.00 37.73 4.35
2483 2537 1.001158 GTAGCACTATCGCCTCCTGAC 60.001 57.143 0.00 0.00 0.00 3.51
2534 2588 0.108089 ATGTACGCCGGTGCATAACA 60.108 50.000 16.69 14.61 45.92 2.41



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

AutoCloner maintained by Alex Coulton.