Multiple sequence alignment - TraesCS5A01G503000

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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 TraesCS5A01G503000 chr5A 100.000 3074 0 0 1 3074 667850156 667847083 0.000000e+00 5677
1 TraesCS5A01G503000 chr1A 97.302 3076 80 3 1 3074 94730655 94733729 0.000000e+00 5217
2 TraesCS5A01G503000 chr1A 97.684 2979 64 2 1 2974 94590942 94587964 0.000000e+00 5114
3 TraesCS5A01G503000 chr2D 96.868 2522 75 4 255 2774 306160382 306157863 0.000000e+00 4217
4 TraesCS5A01G503000 chr2D 96.871 2269 68 3 509 2774 17997189 17994921 0.000000e+00 3794
5 TraesCS5A01G503000 chrUn 98.062 2270 40 3 509 2774 209404251 209406520 0.000000e+00 3945
6 TraesCS5A01G503000 chrUn 98.018 2270 41 3 509 2774 267894057 267891788 0.000000e+00 3940
7 TraesCS5A01G503000 chrUn 98.137 322 6 0 2753 3074 480524612 480524291 2.070000e-156 562
8 TraesCS5A01G503000 chrUn 97.516 322 8 0 2753 3074 86469974 86469653 4.480000e-153 551
9 TraesCS5A01G503000 chrUn 99.234 261 2 0 3 263 171012260 171012520 3.590000e-129 472
10 TraesCS5A01G503000 chrUn 98.859 263 3 0 1 263 393029623 393029885 1.290000e-128 470
11 TraesCS5A01G503000 chr7D 97.885 2270 44 3 509 2774 579003644 579001375 0.000000e+00 3923
12 TraesCS5A01G503000 chr6B 98.016 2218 40 3 561 2774 596595677 596593460 0.000000e+00 3849
13 TraesCS5A01G503000 chr6B 98.859 263 3 0 1 263 596597886 596597624 1.290000e-128 470
14 TraesCS5A01G503000 chr6D 97.003 2269 62 6 509 2774 283200296 283198031 0.000000e+00 3808
15 TraesCS5A01G503000 chr7A 96.522 460 16 0 1 460 211334589 211334130 0.000000e+00 761
16 TraesCS5A01G503000 chr7A 98.137 322 6 0 2753 3074 60251116 60251437 2.070000e-156 562
17 TraesCS5A01G503000 chr7A 99.240 263 2 0 1 263 638503692 638503430 2.770000e-130 475
18 TraesCS5A01G503000 chr7A 98.859 263 3 0 1 263 211266797 211266535 1.290000e-128 470
19 TraesCS5A01G503000 chr1B 92.857 476 30 2 255 730 311127091 311126620 0.000000e+00 688
20 TraesCS5A01G503000 chr1B 97.826 322 7 0 2753 3074 672582332 672582011 9.630000e-155 556
21 TraesCS5A01G503000 chr2B 96.591 352 12 0 255 606 357565001 357565352 4.420000e-163 584
22 TraesCS5A01G503000 chr2B 95.455 352 16 0 255 606 357448433 357448082 2.070000e-156 562
23 TraesCS5A01G503000 chr6A 98.447 322 5 0 2753 3074 64689515 64689194 4.450000e-158 568
24 TraesCS5A01G503000 chr5D 95.739 352 13 1 255 606 80056946 80057295 1.600000e-157 566
25 TraesCS5A01G503000 chr7B 95.455 352 16 0 255 606 139573388 139573739 2.070000e-156 562
26 TraesCS5A01G503000 chr3B 98.137 322 6 0 2753 3074 669819661 669819340 2.070000e-156 562
27 TraesCS5A01G503000 chr3B 98.137 322 6 0 2753 3074 669844898 669844577 2.070000e-156 562
28 TraesCS5A01G503000 chr4A 99.240 263 2 0 1 263 79640802 79640540 2.770000e-130 475


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 TraesCS5A01G503000 chr5A 667847083 667850156 3073 True 5677.0 5677 100.0000 1 3074 1 chr5A.!!$R1 3073
1 TraesCS5A01G503000 chr1A 94730655 94733729 3074 False 5217.0 5217 97.3020 1 3074 1 chr1A.!!$F1 3073
2 TraesCS5A01G503000 chr1A 94587964 94590942 2978 True 5114.0 5114 97.6840 1 2974 1 chr1A.!!$R1 2973
3 TraesCS5A01G503000 chr2D 306157863 306160382 2519 True 4217.0 4217 96.8680 255 2774 1 chr2D.!!$R2 2519
4 TraesCS5A01G503000 chr2D 17994921 17997189 2268 True 3794.0 3794 96.8710 509 2774 1 chr2D.!!$R1 2265
5 TraesCS5A01G503000 chrUn 209404251 209406520 2269 False 3945.0 3945 98.0620 509 2774 1 chrUn.!!$F2 2265
6 TraesCS5A01G503000 chrUn 267891788 267894057 2269 True 3940.0 3940 98.0180 509 2774 1 chrUn.!!$R2 2265
7 TraesCS5A01G503000 chr7D 579001375 579003644 2269 True 3923.0 3923 97.8850 509 2774 1 chr7D.!!$R1 2265
8 TraesCS5A01G503000 chr6B 596593460 596597886 4426 True 2159.5 3849 98.4375 1 2774 2 chr6B.!!$R1 2773
9 TraesCS5A01G503000 chr6D 283198031 283200296 2265 True 3808.0 3808 97.0030 509 2774 1 chr6D.!!$R1 2265

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
450 1011 0.180171 CTTCCCCGCCACATCACATA 59.820 55.0 0.00 0.0 0.00 2.29 F
1443 3093 0.244450 TAAATGACGCGAGAACCCGT 59.756 50.0 15.93 0.0 40.85 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1724 3374 0.389025 TCTGTTGTGCTCAGCGAAGA 59.611 50.000 0.0 0.0 33.48 2.87 R
2987 4642 1.987855 TCCCTGCGGTAAGTGGGAG 60.988 63.158 0.0 0.0 43.20 4.30 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
450 1011 0.180171 CTTCCCCGCCACATCACATA 59.820 55.000 0.00 0.00 0.00 2.29
507 1069 0.396435 ACATTCTCCCACGTGCTTCA 59.604 50.000 10.91 0.00 0.00 3.02
576 2226 4.574013 GCAATTCCTCAATCGATCAGAAGT 59.426 41.667 0.00 0.00 0.00 3.01
642 2292 7.274468 GTGCAATGAATATCGTAGATAGAGTGG 59.726 40.741 0.00 0.00 45.12 4.00
686 2336 5.399596 GCTTTCCTTTCAAAGTGAAACGATC 59.600 40.000 8.79 0.00 45.86 3.69
735 2385 7.781324 ATTGGATTTCATTTCACCACTACTT 57.219 32.000 0.00 0.00 0.00 2.24
759 2409 3.059868 CGTAACGCACAGAAAACACTGAT 60.060 43.478 0.00 0.00 40.63 2.90
794 2444 0.958822 CAACCACTGCCACTTTACCC 59.041 55.000 0.00 0.00 0.00 3.69
800 2450 0.392998 CTGCCACTTTACCCGAGCAT 60.393 55.000 0.00 0.00 0.00 3.79
1004 2654 4.097589 TGATTCAACGAAATATGCCATGCA 59.902 37.500 0.00 0.00 44.86 3.96
1028 2678 7.114247 GCAAGCATTAAGATTTAAAACGTGTCA 59.886 33.333 0.00 0.00 0.00 3.58
1098 2748 3.053455 CCGTATTCTCCGAAGATTGAGC 58.947 50.000 0.00 0.00 0.00 4.26
1184 2834 7.542534 AATCACAAACTACACGAAAGTTGTA 57.457 32.000 0.00 0.00 46.40 2.41
1424 3074 9.326413 CCACGGTGATCTAATATCTTTTAAAGT 57.674 33.333 10.28 0.00 0.00 2.66
1443 3093 0.244450 TAAATGACGCGAGAACCCGT 59.756 50.000 15.93 0.00 40.85 5.28
1507 3157 7.603404 CAGTTGGAAAAATCATAGGCAAATTCA 59.397 33.333 0.00 0.00 0.00 2.57
1588 3238 7.013750 GGAGAAGAACAAAAGAAGAATGGTTCT 59.986 37.037 0.00 0.00 44.77 3.01
1939 3589 7.690952 AGGATCGAACTACCTACTCATTATC 57.309 40.000 0.00 0.00 31.78 1.75
1966 3616 7.495934 CGGAGGTGAATCATAGAACACTAAAAT 59.504 37.037 0.00 0.00 34.28 1.82
2030 3680 7.278646 TCACGACATAAGATTGAAAGATCCAAG 59.721 37.037 0.00 0.00 0.00 3.61
2075 3725 4.379603 CGGACGTGGCCAAAACATATAAAA 60.380 41.667 7.24 0.00 0.00 1.52
2372 4023 5.390040 CGTCATAGAGCAGTCGACTATAAGG 60.390 48.000 19.57 6.62 0.00 2.69
2468 4119 4.019771 ACGGGCAACAATTGGGAATAAAAT 60.020 37.500 10.83 0.00 39.74 1.82
2760 4415 2.025699 CCCCTTTATTTCCCTCGGAACA 60.026 50.000 0.00 0.00 41.87 3.18
2879 4534 2.237143 CCCTGTGCCTAGTGATTTCTCA 59.763 50.000 0.00 0.00 0.00 3.27
2987 4642 1.349627 CATCGGCTGTCACATTCGC 59.650 57.895 0.00 0.00 0.00 4.70
3018 4673 2.213499 CGCAGGGATGGATCAAGTAAC 58.787 52.381 0.00 0.00 0.00 2.50
3038 4693 5.774498 AACTGGTGATTCTTTTCAAGGTC 57.226 39.130 0.00 0.00 0.00 3.85
3045 4700 5.182760 GTGATTCTTTTCAAGGTCAGATGCT 59.817 40.000 0.00 0.00 0.00 3.79
3067 4722 8.738645 TGCTTTTTGGGCTTATTTTCTAAAAA 57.261 26.923 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
450 1011 3.612479 CGGATTAGCAAAAGCAAGCAAGT 60.612 43.478 0.00 0.00 0.00 3.16
538 1112 4.885907 AGGAATTGCTGATAATGACACCAG 59.114 41.667 0.00 0.00 0.00 4.00
576 2226 3.914435 GAGGGGCAGGTTATATTCCCTTA 59.086 47.826 0.00 0.00 44.11 2.69
642 2292 7.274686 GGAAAGCTAGCTATATGAGATCGAAAC 59.725 40.741 19.70 0.00 0.00 2.78
735 2385 2.931325 AGTGTTTTCTGTGCGTTACGAA 59.069 40.909 9.62 0.00 0.00 3.85
759 2409 0.306533 GTTGAAAGCGAGCGGAAACA 59.693 50.000 0.00 0.00 0.00 2.83
794 2444 1.417592 GACTGCGTCACAATGCTCG 59.582 57.895 4.20 0.00 38.30 5.03
800 2450 0.874175 CTTGACCGACTGCGTCACAA 60.874 55.000 8.91 9.55 35.23 3.33
1004 2654 9.341899 GATGACACGTTTTAAATCTTAATGCTT 57.658 29.630 0.00 0.00 0.00 3.91
1028 2678 4.469945 TCCGAACATTTCCTGGAAGTAGAT 59.530 41.667 9.42 0.00 0.00 1.98
1098 2748 7.928307 TCTTTTAATGGATCTCCTCTTGTTG 57.072 36.000 0.00 0.00 36.82 3.33
1424 3074 3.038946 CGGGTTCTCGCGTCATTTA 57.961 52.632 5.77 0.00 43.36 1.40
1443 3093 8.940397 AGAAAGATCTCCTTATTTCAAAACCA 57.060 30.769 0.00 0.00 34.77 3.67
1507 3157 4.908601 TTCCAACTGATATGGCCGATAT 57.091 40.909 0.00 2.68 37.88 1.63
1576 3226 4.997395 TGTGAGTAAGCAGAACCATTCTTC 59.003 41.667 0.00 0.00 38.11 2.87
1588 3238 2.300152 CCCTCTGAGTTGTGAGTAAGCA 59.700 50.000 3.66 0.00 0.00 3.91
1724 3374 0.389025 TCTGTTGTGCTCAGCGAAGA 59.611 50.000 0.00 0.00 33.48 2.87
1868 3518 1.048601 GGATCCGGAGCAATAGGTCA 58.951 55.000 23.22 0.00 43.97 4.02
1939 3589 3.133003 AGTGTTCTATGATTCACCTCCGG 59.867 47.826 0.00 0.00 0.00 5.14
1966 3616 6.199376 TGTTAGGTCCATAAGATACCACAGA 58.801 40.000 0.00 0.00 35.64 3.41
2075 3725 0.824759 AGCGACTAGGCCGATCTTTT 59.175 50.000 10.39 0.00 0.00 2.27
2162 3813 7.575499 TCTCTATCCACAGAGATACCTATCA 57.425 40.000 0.00 0.00 44.82 2.15
2372 4023 3.894427 TCTCTCAGGCCATCAGTCTTATC 59.106 47.826 5.01 0.00 0.00 1.75
2468 4119 9.295825 ACATTTTAAACTCATGTTCATGGTCTA 57.704 29.630 12.02 0.00 34.96 2.59
2760 4415 3.559384 GGAATCTCGTCTTGTTCCCCTTT 60.559 47.826 0.00 0.00 35.24 3.11
2879 4534 3.784511 AGAATGGGATGAATCGAGCAT 57.215 42.857 3.47 3.47 0.00 3.79
2987 4642 1.987855 TCCCTGCGGTAAGTGGGAG 60.988 63.158 0.00 0.00 43.20 4.30
3038 4693 6.168389 AGAAAATAAGCCCAAAAAGCATCTG 58.832 36.000 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.