Multiple sequence alignment - TraesCS5B01G150800

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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 TraesCS5B01G150800 chr5B 100.000 2699 0 0 1 2699 278469339 278466641 0.000000e+00 4985.0
1 TraesCS5B01G150800 chr5B 94.118 51 1 2 1 50 475592353 475592402 2.880000e-10 76.8
2 TraesCS5B01G150800 chr5B 93.478 46 1 2 1 46 684749857 684749900 1.730000e-07 67.6
3 TraesCS5B01G150800 chr5D 96.289 2668 75 11 36 2687 245200192 245197533 0.000000e+00 4357.0
4 TraesCS5B01G150800 chr5A 94.253 2697 98 27 36 2692 329242048 329239369 0.000000e+00 4069.0
5 TraesCS5B01G150800 chr7B 100.000 40 0 0 1 40 610373567 610373606 1.040000e-09 75.0
6 TraesCS5B01G150800 chr7D 97.674 43 0 1 1 43 617806847 617806806 3.730000e-09 73.1
7 TraesCS5B01G150800 chr6D 97.674 43 0 1 1 43 36066957 36066998 3.730000e-09 73.1
8 TraesCS5B01G150800 chr4A 97.674 43 0 1 1 42 667225247 667225289 3.730000e-09 73.1
9 TraesCS5B01G150800 chr3A 97.619 42 1 0 1 42 550458813 550458854 3.730000e-09 73.1
10 TraesCS5B01G150800 chr2A 95.652 46 0 2 1 45 19244257 19244213 3.730000e-09 73.1
11 TraesCS5B01G150800 chr3B 95.556 45 1 1 1 44 826069455 826069411 1.340000e-08 71.3
12 TraesCS5B01G150800 chr1A 100.000 29 0 0 2452 2480 464115008 464114980 1.000000e-03 54.7


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 TraesCS5B01G150800 chr5B 278466641 278469339 2698 True 4985 4985 100.000 1 2699 1 chr5B.!!$R1 2698
1 TraesCS5B01G150800 chr5D 245197533 245200192 2659 True 4357 4357 96.289 36 2687 1 chr5D.!!$R1 2651
2 TraesCS5B01G150800 chr5A 329239369 329242048 2679 True 4069 4069 94.253 36 2692 1 chr5A.!!$R1 2656

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
102 103 1.232119 TGTCCGCATGATGATGATGC 58.768 50.000 6.8 6.8 42.41 3.91 F
940 972 1.747355 GTGTGCATGGAATTAGCAGCT 59.253 47.619 0.0 0.0 39.21 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1088 1120 1.903860 TCCTCTTTGCTACGGGCTTAA 59.096 47.619 4.43 0.0 42.39 1.85 R
2521 2569 1.335182 AGATAGCACTGGATGACGTCG 59.665 52.381 11.62 0.0 0.00 5.12 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
24 25 7.524294 GTGCTGAAATTTTTCTGAAACTGAA 57.476 32.000 12.42 0.00 38.07 3.02
25 26 7.962917 GTGCTGAAATTTTTCTGAAACTGAAA 58.037 30.769 12.42 0.00 38.07 2.69
26 27 8.606602 GTGCTGAAATTTTTCTGAAACTGAAAT 58.393 29.630 12.42 0.00 38.07 2.17
27 28 9.165035 TGCTGAAATTTTTCTGAAACTGAAATT 57.835 25.926 12.42 3.83 38.07 1.82
28 29 9.429600 GCTGAAATTTTTCTGAAACTGAAATTG 57.570 29.630 12.42 0.00 38.07 2.32
35 36 8.839310 TTTTCTGAAACTGAAATTGAAAACCA 57.161 26.923 1.58 0.00 32.91 3.67
36 37 9.447157 TTTTCTGAAACTGAAATTGAAAACCAT 57.553 25.926 1.58 0.00 32.91 3.55
37 38 8.422973 TTCTGAAACTGAAATTGAAAACCATG 57.577 30.769 0.00 0.00 0.00 3.66
38 39 7.555087 TCTGAAACTGAAATTGAAAACCATGT 58.445 30.769 0.00 0.00 0.00 3.21
39 40 7.492020 TCTGAAACTGAAATTGAAAACCATGTG 59.508 33.333 0.00 0.00 0.00 3.21
102 103 1.232119 TGTCCGCATGATGATGATGC 58.768 50.000 6.80 6.80 42.41 3.91
231 236 9.944663 TGTTGTTTTCTCACTGTATTTGATTAC 57.055 29.630 0.00 0.00 0.00 1.89
280 285 7.833786 AGCATTGAAGATTGAATTGAAGCTAA 58.166 30.769 0.00 0.00 0.00 3.09
312 318 8.543774 AGTACATCACCAATTTGTAGAGAAGAT 58.456 33.333 0.00 0.00 0.00 2.40
467 481 3.476552 CTCATTTATGCGGGGAAGCTAA 58.523 45.455 0.00 0.00 38.13 3.09
613 635 8.420222 AGTGTCAAATATTGATCCAGACTCTAG 58.580 37.037 0.00 0.00 42.47 2.43
728 760 9.241317 CTAATAATCAACCTTTGCTGCTAAATG 57.759 33.333 0.00 0.00 0.00 2.32
742 774 4.243007 GCTAAATGCAGACAAACAAGGT 57.757 40.909 0.00 0.00 42.31 3.50
792 824 2.898729 CCAGTAGGTACATGGCTCTG 57.101 55.000 0.00 0.00 0.00 3.35
895 927 9.816354 AAACTAGTTTATCATGCTTGTTTGTTT 57.184 25.926 19.26 0.00 37.03 2.83
916 948 6.814146 TGTTTGTTTGTTTGTCCTGATTAACC 59.186 34.615 0.00 0.00 0.00 2.85
940 972 1.747355 GTGTGCATGGAATTAGCAGCT 59.253 47.619 0.00 0.00 39.21 4.24
952 984 1.781786 TAGCAGCTAACCTCCCTCAG 58.218 55.000 0.00 0.00 0.00 3.35
975 1007 3.231818 GACACCTAGCTTAGCCTCCATA 58.768 50.000 0.00 0.00 0.00 2.74
1088 1120 9.401058 CTCTATCTTCTCTTCTCTTCTCTTCTT 57.599 37.037 0.00 0.00 0.00 2.52
1663 1704 5.884232 CCCTATGGACATGATCATTATGTGG 59.116 44.000 5.16 0.28 38.78 4.17
1664 1705 6.479006 CCTATGGACATGATCATTATGTGGT 58.521 40.000 5.16 0.00 38.78 4.16
1777 1818 5.299028 AGTTGATTGCTTGTGACACATGTTA 59.701 36.000 19.33 10.37 0.00 2.41
1794 1835 7.123997 ACACATGTTATTTTGGATAATGCCTCA 59.876 33.333 0.00 0.00 0.00 3.86
1895 1943 6.014584 AGACAAAAACTGGTTGAGGTTTTCTT 60.015 34.615 0.00 0.00 46.83 2.52
1919 1967 8.514330 TTAACCACAAAGTTCAGTTAGTTCAT 57.486 30.769 0.00 0.00 0.00 2.57
1962 2010 1.073897 AGGAGTGCCTTTGTGCTCC 59.926 57.895 0.00 0.00 43.90 4.70
2078 2126 0.460109 TCACGACATGAAGCATCCCG 60.460 55.000 0.00 0.00 33.02 5.14
2212 2260 7.323420 TCACTAACATTTGACCTGTCAGATAG 58.677 38.462 0.00 2.98 41.13 2.08
2265 2313 1.335142 CGGATCTTACGTAGCTCCTGC 60.335 57.143 14.47 0.00 37.08 4.85
2311 2359 9.582648 ACCAATACAGACAAAACCTAATTAAGT 57.417 29.630 0.00 0.00 0.00 2.24
2512 2560 2.444624 CCGCGGACACTTGACATCG 61.445 63.158 24.07 0.00 0.00 3.84
2541 2589 1.335182 CGACGTCATCCAGTGCTATCT 59.665 52.381 17.16 0.00 0.00 1.98
2547 2595 4.701765 GTCATCCAGTGCTATCTGTCAAT 58.298 43.478 0.00 0.00 34.02 2.57
2676 2724 6.449698 AGCACTGGATGTTCAATAAGTTTTG 58.550 36.000 0.00 0.00 0.00 2.44
2692 2740 4.798882 AGTTTTGTACCTCCATCAAACCA 58.201 39.130 0.00 0.00 32.08 3.67
2693 2741 4.827284 AGTTTTGTACCTCCATCAAACCAG 59.173 41.667 0.00 0.00 32.08 4.00
2694 2742 4.447138 TTTGTACCTCCATCAAACCAGT 57.553 40.909 0.00 0.00 0.00 4.00
2695 2743 5.570205 TTTGTACCTCCATCAAACCAGTA 57.430 39.130 0.00 0.00 0.00 2.74
2696 2744 4.819105 TGTACCTCCATCAAACCAGTAG 57.181 45.455 0.00 0.00 0.00 2.57
2697 2745 4.164981 TGTACCTCCATCAAACCAGTAGT 58.835 43.478 0.00 0.00 0.00 2.73
2698 2746 5.335261 TGTACCTCCATCAAACCAGTAGTA 58.665 41.667 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.524294 TTCAGTTTCAGAAAAATTTCAGCAC 57.476 32.000 8.47 1.84 39.61 4.40
9 10 9.277783 TGGTTTTCAATTTCAGTTTCAGAAAAA 57.722 25.926 0.00 0.00 38.36 1.94
10 11 8.839310 TGGTTTTCAATTTCAGTTTCAGAAAA 57.161 26.923 0.00 0.00 38.36 2.29
11 12 8.881743 CATGGTTTTCAATTTCAGTTTCAGAAA 58.118 29.630 0.00 0.00 39.11 2.52
12 13 8.040132 ACATGGTTTTCAATTTCAGTTTCAGAA 58.960 29.630 0.00 0.00 0.00 3.02
13 14 7.492020 CACATGGTTTTCAATTTCAGTTTCAGA 59.508 33.333 0.00 0.00 0.00 3.27
14 15 7.278424 ACACATGGTTTTCAATTTCAGTTTCAG 59.722 33.333 0.00 0.00 0.00 3.02
15 16 7.102346 ACACATGGTTTTCAATTTCAGTTTCA 58.898 30.769 0.00 0.00 0.00 2.69
16 17 7.538303 ACACATGGTTTTCAATTTCAGTTTC 57.462 32.000 0.00 0.00 0.00 2.78
17 18 7.224557 GCTACACATGGTTTTCAATTTCAGTTT 59.775 33.333 0.00 0.00 0.00 2.66
18 19 6.701400 GCTACACATGGTTTTCAATTTCAGTT 59.299 34.615 0.00 0.00 0.00 3.16
19 20 6.183360 TGCTACACATGGTTTTCAATTTCAGT 60.183 34.615 0.00 0.00 0.00 3.41
20 21 6.215121 TGCTACACATGGTTTTCAATTTCAG 58.785 36.000 0.00 0.00 0.00 3.02
21 22 6.154203 TGCTACACATGGTTTTCAATTTCA 57.846 33.333 0.00 0.00 0.00 2.69
22 23 6.215845 ACTGCTACACATGGTTTTCAATTTC 58.784 36.000 0.00 0.00 0.00 2.17
23 24 6.160576 ACTGCTACACATGGTTTTCAATTT 57.839 33.333 0.00 0.00 0.00 1.82
24 25 5.789643 ACTGCTACACATGGTTTTCAATT 57.210 34.783 0.00 0.00 0.00 2.32
25 26 5.183140 GGTACTGCTACACATGGTTTTCAAT 59.817 40.000 0.00 0.00 0.00 2.57
26 27 4.517453 GGTACTGCTACACATGGTTTTCAA 59.483 41.667 0.00 0.00 0.00 2.69
27 28 4.069304 GGTACTGCTACACATGGTTTTCA 58.931 43.478 0.00 0.00 0.00 2.69
28 29 3.124636 CGGTACTGCTACACATGGTTTTC 59.875 47.826 0.00 0.00 0.00 2.29
29 30 3.071479 CGGTACTGCTACACATGGTTTT 58.929 45.455 0.00 0.00 0.00 2.43
30 31 2.038033 ACGGTACTGCTACACATGGTTT 59.962 45.455 0.23 0.00 0.00 3.27
31 32 1.621814 ACGGTACTGCTACACATGGTT 59.378 47.619 0.23 0.00 0.00 3.67
32 33 1.263356 ACGGTACTGCTACACATGGT 58.737 50.000 0.23 0.00 0.00 3.55
33 34 2.094182 AGAACGGTACTGCTACACATGG 60.094 50.000 0.23 0.00 0.00 3.66
34 35 3.232213 AGAACGGTACTGCTACACATG 57.768 47.619 0.23 0.00 0.00 3.21
35 36 4.015084 ACTAGAACGGTACTGCTACACAT 58.985 43.478 0.23 0.00 0.00 3.21
36 37 3.189910 CACTAGAACGGTACTGCTACACA 59.810 47.826 0.23 0.00 0.00 3.72
37 38 3.756069 CACTAGAACGGTACTGCTACAC 58.244 50.000 0.23 0.00 0.00 2.90
38 39 2.163010 GCACTAGAACGGTACTGCTACA 59.837 50.000 0.23 0.00 0.00 2.74
39 40 2.163010 TGCACTAGAACGGTACTGCTAC 59.837 50.000 0.23 0.00 0.00 3.58
231 236 8.071368 GCTAATCAACTACAGTACTAGCACTAG 58.929 40.741 0.00 3.10 39.04 2.57
280 285 9.251440 TCTACAAATTGGTGATGTACTACTACT 57.749 33.333 0.00 0.00 0.00 2.57
312 318 3.390135 GACGTGAGGATGTCTGTTTCAA 58.610 45.455 0.00 0.00 35.50 2.69
698 724 6.094603 AGCAGCAAAGGTTGATTATTAGTCTG 59.905 38.462 0.00 0.00 0.00 3.51
728 760 2.226674 GCCTTCTACCTTGTTTGTCTGC 59.773 50.000 0.00 0.00 0.00 4.26
742 774 3.805807 GCAGTGTGTGTAAAGGCCTTCTA 60.806 47.826 20.79 10.67 0.00 2.10
892 924 6.814146 TGGTTAATCAGGACAAACAAACAAAC 59.186 34.615 0.00 0.00 0.00 2.93
893 925 6.936279 TGGTTAATCAGGACAAACAAACAAA 58.064 32.000 0.00 0.00 0.00 2.83
894 926 6.531503 TGGTTAATCAGGACAAACAAACAA 57.468 33.333 0.00 0.00 0.00 2.83
895 927 6.142818 CTGGTTAATCAGGACAAACAAACA 57.857 37.500 7.93 0.00 0.00 2.83
916 948 1.406539 GCTAATTCCATGCACACCCTG 59.593 52.381 0.00 0.00 0.00 4.45
940 972 1.149288 AGGTGTCACTGAGGGAGGTTA 59.851 52.381 2.35 0.00 0.00 2.85
952 984 1.137282 GGAGGCTAAGCTAGGTGTCAC 59.863 57.143 0.00 0.00 0.00 3.67
975 1007 1.305623 CAGCCAGCCAGGAAGGAAT 59.694 57.895 1.81 0.00 41.22 3.01
1088 1120 1.903860 TCCTCTTTGCTACGGGCTTAA 59.096 47.619 4.43 0.00 42.39 1.85
1794 1835 2.669569 GGGTGTGTGTGCGATGCT 60.670 61.111 0.00 0.00 0.00 3.79
1895 1943 7.468084 GCATGAACTAACTGAACTTTGTGGTTA 60.468 37.037 0.00 0.00 0.00 2.85
1919 1967 4.558226 ACATGTCTTGTGGAGATAAGCA 57.442 40.909 0.00 0.00 37.11 3.91
1962 2010 5.531634 ACAAACAACAATATCTGCAACTGG 58.468 37.500 0.00 0.00 0.00 4.00
2078 2126 9.047371 GGAAGCATTAATTAGTTCTTCTACCTC 57.953 37.037 16.01 1.21 32.77 3.85
2212 2260 9.712305 ATCATAAGGTCTGTATATAACAAGCAC 57.288 33.333 0.00 0.00 37.74 4.40
2521 2569 1.335182 AGATAGCACTGGATGACGTCG 59.665 52.381 11.62 0.00 0.00 5.12
2676 2724 4.820894 ACTACTGGTTTGATGGAGGTAC 57.179 45.455 0.00 0.00 0.00 3.34


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

AutoCloner maintained by Alex Coulton.