Multiple sequence alignment - TraesCS4B01G059300

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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 TraesCS4B01G059300 chr4B 100.000 2876 0 0 1 2876 50442297 50445172 0.000000e+00 5312.0
1 TraesCS4B01G059300 chr4B 96.550 2116 36 14 1 2093 50401352 50399251 0.000000e+00 3469.0
2 TraesCS4B01G059300 chr3B 93.711 1272 22 11 849 2077 144069648 144070904 0.000000e+00 1853.0
3 TraesCS4B01G059300 chr3B 93.569 1275 26 11 849 2080 144058329 144057068 0.000000e+00 1849.0
4 TraesCS4B01G059300 chr3B 91.611 751 26 10 1 741 144059040 144058317 0.000000e+00 1003.0
5 TraesCS4B01G059300 chr3B 87.387 222 13 11 1887 2093 144074552 144074773 1.030000e-59 241.0
6 TraesCS4B01G059300 chr3B 87.907 215 6 6 537 741 144069456 144069660 4.790000e-58 235.0
7 TraesCS4B01G059300 chr3A 93.060 1268 41 14 849 2093 547254582 547255825 0.000000e+00 1810.0
8 TraesCS4B01G059300 chr3A 92.151 1274 51 24 849 2093 547235118 547233865 0.000000e+00 1753.0
9 TraesCS4B01G059300 chr3A 89.072 787 77 5 2089 2874 358338865 358338087 0.000000e+00 968.0
10 TraesCS4B01G059300 chr3A 93.750 528 23 6 1 521 547252909 547253433 0.000000e+00 784.0
11 TraesCS4B01G059300 chr3A 89.573 211 9 6 537 741 547235309 547235106 3.680000e-64 255.0
12 TraesCS4B01G059300 chr3D 91.883 1269 42 19 849 2077 92750788 92749541 0.000000e+00 1716.0
13 TraesCS4B01G059300 chr3D 91.898 1259 46 18 858 2076 92783210 92784452 0.000000e+00 1709.0
14 TraesCS4B01G059300 chr3D 88.584 657 22 17 97 741 92751392 92750777 0.000000e+00 749.0
15 TraesCS4B01G059300 chr3D 97.561 123 3 0 3 125 92751528 92751406 8.070000e-51 211.0
16 TraesCS4B01G059300 chr3D 89.933 149 7 2 544 692 92781794 92781934 4.890000e-43 185.0
17 TraesCS4B01G059300 chr2D 94.981 797 31 5 2080 2874 608403125 608402336 0.000000e+00 1242.0
18 TraesCS4B01G059300 chr4A 92.579 795 46 5 2088 2874 74596031 74595242 0.000000e+00 1129.0
19 TraesCS4B01G059300 chr4A 82.281 491 56 18 59 523 368110410 368110895 2.080000e-106 396.0
20 TraesCS4B01G059300 chr2A 89.691 485 30 6 2391 2874 766420920 766420455 4.100000e-168 601.0
21 TraesCS4B01G059300 chr2A 91.558 308 23 1 2089 2396 766437511 766437207 3.430000e-114 422.0
22 TraesCS4B01G059300 chr6A 83.181 547 61 18 3 523 359067805 359068346 3.350000e-129 472.0
23 TraesCS4B01G059300 chr1A 85.021 474 50 16 2220 2680 567502884 567502419 2.020000e-126 462.0
24 TraesCS4B01G059300 chr5D 80.338 473 82 7 1383 1854 480154987 480154525 5.900000e-92 348.0
25 TraesCS4B01G059300 chr5D 88.095 168 17 1 989 1153 480155401 480155234 2.260000e-46 196.0
26 TraesCS4B01G059300 chr5A 80.462 476 76 10 1383 1854 598637742 598637280 5.900000e-92 348.0
27 TraesCS4B01G059300 chr5B 86.395 147 15 1 1007 1153 588156780 588156639 3.840000e-34 156.0
28 TraesCS4B01G059300 chr6B 94.444 36 2 0 750 785 257975138 257975103 4.000000e-04 56.5
29 TraesCS4B01G059300 chr6B 94.444 36 2 0 750 785 333175847 333175882 4.000000e-04 56.5
30 TraesCS4B01G059300 chr1B 94.444 36 2 0 750 785 28052416 28052381 4.000000e-04 56.5


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 TraesCS4B01G059300 chr4B 50442297 50445172 2875 False 5312.000000 5312 100.000000 1 2876 1 chr4B.!!$F1 2875
1 TraesCS4B01G059300 chr4B 50399251 50401352 2101 True 3469.000000 3469 96.550000 1 2093 1 chr4B.!!$R1 2092
2 TraesCS4B01G059300 chr3B 144057068 144059040 1972 True 1426.000000 1849 92.590000 1 2080 2 chr3B.!!$R1 2079
3 TraesCS4B01G059300 chr3B 144069456 144074773 5317 False 776.333333 1853 89.668333 537 2093 3 chr3B.!!$F1 1556
4 TraesCS4B01G059300 chr3A 547252909 547255825 2916 False 1297.000000 1810 93.405000 1 2093 2 chr3A.!!$F1 2092
5 TraesCS4B01G059300 chr3A 547233865 547235309 1444 True 1004.000000 1753 90.862000 537 2093 2 chr3A.!!$R2 1556
6 TraesCS4B01G059300 chr3A 358338087 358338865 778 True 968.000000 968 89.072000 2089 2874 1 chr3A.!!$R1 785
7 TraesCS4B01G059300 chr3D 92781794 92784452 2658 False 947.000000 1709 90.915500 544 2076 2 chr3D.!!$F1 1532
8 TraesCS4B01G059300 chr3D 92749541 92751528 1987 True 892.000000 1716 92.676000 3 2077 3 chr3D.!!$R1 2074
9 TraesCS4B01G059300 chr2D 608402336 608403125 789 True 1242.000000 1242 94.981000 2080 2874 1 chr2D.!!$R1 794
10 TraesCS4B01G059300 chr4A 74595242 74596031 789 True 1129.000000 1129 92.579000 2088 2874 1 chr4A.!!$R1 786
11 TraesCS4B01G059300 chr6A 359067805 359068346 541 False 472.000000 472 83.181000 3 523 1 chr6A.!!$F1 520
12 TraesCS4B01G059300 chr5D 480154525 480155401 876 True 272.000000 348 84.216500 989 1854 2 chr5D.!!$R1 865

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
525 720 0.965866 TGCTCGTGATCTCTCCCGTT 60.966 55.0 0.0 0.0 0.0 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2200 8430 0.798776 CATGCCGAACGAGCTTCTTT 59.201 50.0 0.0 0.0 0.0 2.52 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
435 494 8.960591 CCACAATTTCTAGAACAAGGAATATGT 58.039 33.333 4.18 0.88 0.00 2.29
495 569 7.068716 GTGCTTATCCCTAAAAATCTGGAACAT 59.931 37.037 0.00 0.00 38.20 2.71
525 720 0.965866 TGCTCGTGATCTCTCCCGTT 60.966 55.000 0.00 0.00 0.00 4.44
621 1313 3.083122 AGAGCTCATTTGGCAGTCATT 57.917 42.857 17.77 0.00 0.00 2.57
901 3141 2.032681 GCCTCCTCCCACACACAC 59.967 66.667 0.00 0.00 0.00 3.82
902 3142 2.818169 GCCTCCTCCCACACACACA 61.818 63.158 0.00 0.00 0.00 3.72
1415 3763 1.067060 CATCGCGAAGTACATCCTCCA 59.933 52.381 15.24 0.00 0.00 3.86
1719 4072 0.249120 TCGCCGATCTGAACCACATT 59.751 50.000 0.00 0.00 0.00 2.71
1885 4238 4.804139 GTGCGCAGTACTAGATGTTTATGT 59.196 41.667 12.22 0.00 40.86 2.29
1982 8199 2.885266 GTGATCATCTGCCCGTCTACTA 59.115 50.000 0.00 0.00 0.00 1.82
2102 8332 9.783256 AGTAAATAAACAACGGAATCAATAAGC 57.217 29.630 0.00 0.00 0.00 3.09
2103 8333 9.783256 GTAAATAAACAACGGAATCAATAAGCT 57.217 29.630 0.00 0.00 0.00 3.74
2114 8344 4.650754 ATCAATAAGCTCCGAACGTACT 57.349 40.909 0.00 0.00 0.00 2.73
2121 8351 3.981211 AGCTCCGAACGTACTGTTTTTA 58.019 40.909 0.00 0.00 42.09 1.52
2150 8380 0.810016 GTCCGAACGCCTTCTCTACT 59.190 55.000 0.00 0.00 0.00 2.57
2197 8427 0.724453 CACCAAAAATCGCCACGTCG 60.724 55.000 0.00 0.00 0.00 5.12
2280 8510 6.264518 GTCTCTATCCTTTTCTCCTCCTACAG 59.735 46.154 0.00 0.00 0.00 2.74
2291 8521 3.442076 TCCTCCTACAGTCCTTTCTTCC 58.558 50.000 0.00 0.00 0.00 3.46
2310 8540 1.380785 CCCTGATGCCTGCAACCAT 60.381 57.895 0.00 0.00 0.00 3.55
2440 8671 3.760035 GACGCCTTCCTCTCGCCA 61.760 66.667 0.00 0.00 0.00 5.69
2441 8672 3.077556 ACGCCTTCCTCTCGCCAT 61.078 61.111 0.00 0.00 0.00 4.40
2550 8781 3.135348 CCTTCTTCCTCATCTACATGCCA 59.865 47.826 0.00 0.00 0.00 4.92
2602 8833 3.842923 CGGCGCCAGACTCTCCAT 61.843 66.667 28.98 0.00 0.00 3.41
2734 8972 2.485426 CGGTCACGTTCCTAGTCTACAA 59.515 50.000 5.23 0.00 34.81 2.41
2737 8975 4.082354 GGTCACGTTCCTAGTCTACAACAT 60.082 45.833 0.00 0.00 0.00 2.71
2874 9112 3.516300 TGAGCAATGCTTCATTCCCAATT 59.484 39.130 9.91 0.00 39.88 2.32
2875 9113 4.020039 TGAGCAATGCTTCATTCCCAATTT 60.020 37.500 9.91 0.00 39.88 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
112 113 3.461085 AGATGACTTCATATGGCAACCCT 59.539 43.478 2.13 0.0 36.57 4.34
250 301 0.602638 GTCCAGCATCAACCACGACA 60.603 55.000 0.00 0.0 0.00 4.35
495 569 4.380531 AGATCACGAGCACTTTGAAAAGA 58.619 39.130 9.71 0.0 39.31 2.52
525 720 6.269077 TCGCATACTCCCTCTTAAATTATCCA 59.731 38.462 0.00 0.0 0.00 3.41
901 3141 0.300491 GTAGCGTGTGTGTGTGTGTG 59.700 55.000 0.00 0.0 0.00 3.82
902 3142 0.108567 TGTAGCGTGTGTGTGTGTGT 60.109 50.000 0.00 0.0 0.00 3.72
1719 4072 5.338381 GGTCATGAAGTAGAAGGTGAATGGA 60.338 44.000 0.00 0.0 0.00 3.41
1982 8199 4.890088 TGAAACTGAAAGCGTATACTGGT 58.110 39.130 0.56 0.0 37.60 4.00
2102 8332 6.701432 ATCTTAAAAACAGTACGTTCGGAG 57.299 37.500 0.00 0.0 36.59 4.63
2103 8333 6.925165 AGAATCTTAAAAACAGTACGTTCGGA 59.075 34.615 0.00 0.0 36.59 4.55
2114 8344 6.073980 CGTTCGGACTGAGAATCTTAAAAACA 60.074 38.462 0.00 0.0 34.92 2.83
2121 8351 1.404315 GGCGTTCGGACTGAGAATCTT 60.404 52.381 0.00 0.0 34.92 2.40
2150 8380 3.978217 GGATTCGTGCGAAAAATCAAACA 59.022 39.130 11.09 0.0 37.69 2.83
2197 8427 1.497722 CCGAACGAGCTTCTTTGCC 59.502 57.895 0.00 0.0 0.00 4.52
2200 8430 0.798776 CATGCCGAACGAGCTTCTTT 59.201 50.000 0.00 0.0 0.00 2.52
2280 8510 1.683319 GCATCAGGGGGAAGAAAGGAC 60.683 57.143 0.00 0.0 0.00 3.85
2291 8521 2.757099 GGTTGCAGGCATCAGGGG 60.757 66.667 0.00 0.0 0.00 4.79
2310 8540 4.155733 CGCCACCTCGTATGGGCA 62.156 66.667 0.00 0.0 46.75 5.36
2357 8587 2.270205 CAGGCATCAGGGACGCTT 59.730 61.111 0.00 0.0 0.00 4.68
2358 8588 4.479993 GCAGGCATCAGGGACGCT 62.480 66.667 0.00 0.0 0.00 5.07
2734 8972 1.001974 TGCTCGTCTTGCTGGTAATGT 59.998 47.619 0.00 0.0 0.00 2.71
2737 8975 1.795768 CTTGCTCGTCTTGCTGGTAA 58.204 50.000 0.00 0.0 0.00 2.85
2773 9011 1.827789 GGAACAAGCTGTGGGCACA 60.828 57.895 0.00 0.0 44.79 4.57
2806 9044 2.264794 GCGGAAGTCACGGGTCAT 59.735 61.111 0.00 0.0 0.00 3.06


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

AutoCloner maintained by Alex Coulton.