Multiple sequence alignment - TraesCS4D01G261200

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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 TraesCS4D01G261200 chr4D 100.000 2828 0 0 1 2828 431723231 431720404 0.000000e+00 5223.0
1 TraesCS4D01G261200 chr4D 96.550 2116 70 2 715 2828 431555187 431553073 0.000000e+00 3500.0
2 TraesCS4D01G261200 chr4D 96.645 2116 54 7 715 2826 431674314 431672212 0.000000e+00 3498.0
3 TraesCS4D01G261200 chr4D 95.827 2133 62 5 715 2828 431620952 431618828 0.000000e+00 3421.0
4 TraesCS4D01G261200 chr4D 97.902 715 15 0 1 715 431730561 431729847 0.000000e+00 1238.0
5 TraesCS4D01G261200 chr4D 92.414 290 18 3 1932 2218 262025454 262025742 7.290000e-111 411.0
6 TraesCS4D01G261200 chr4D 92.657 286 18 2 1937 2219 314234542 314234827 2.620000e-110 409.0
7 TraesCS4D01G261200 chr4D 95.238 42 1 1 2593 2633 431553343 431553302 6.540000e-07 65.8
8 TraesCS4D01G261200 chr4D 95.238 42 1 1 2558 2599 431720639 431720599 6.540000e-07 65.8
9 TraesCS4D01G261200 chr4D 95.238 42 1 1 2593 2633 431720674 431720633 6.540000e-07 65.8
10 TraesCS4D01G261200 chr4D 93.023 43 2 1 2558 2600 431553308 431553267 8.460000e-06 62.1
11 TraesCS4D01G261200 chrUn 89.563 1121 99 12 716 1833 256114573 256115678 0.000000e+00 1406.0
12 TraesCS4D01G261200 chrUn 89.563 1121 99 12 716 1833 390478394 390479499 0.000000e+00 1406.0
13 TraesCS4D01G261200 chr5B 89.563 1121 99 12 716 1833 660880433 660879328 0.000000e+00 1406.0
14 TraesCS4D01G261200 chr5B 89.295 1121 102 10 716 1833 660926382 660925277 0.000000e+00 1389.0
15 TraesCS4D01G261200 chr4A 91.149 949 76 8 901 1847 32714959 32714017 0.000000e+00 1280.0
16 TraesCS4D01G261200 chr4A 84.015 782 103 11 901 1675 592927462 592926696 0.000000e+00 732.0
17 TraesCS4D01G261200 chr4A 92.690 342 22 3 2290 2631 32707486 32707148 9.100000e-135 490.0
18 TraesCS4D01G261200 chr4A 90.452 199 18 1 2558 2756 32707186 32706989 7.770000e-66 261.0
19 TraesCS4D01G261200 chr4A 91.053 190 13 4 715 903 32715175 32714989 1.300000e-63 254.0
20 TraesCS4D01G261200 chr4A 79.798 99 15 5 2613 2710 611412266 611412172 1.820000e-07 67.6
21 TraesCS4D01G261200 chr3D 98.042 715 14 0 1 715 442058637 442059351 0.000000e+00 1243.0
22 TraesCS4D01G261200 chr3D 98.039 714 14 0 1 714 442075336 442076049 0.000000e+00 1242.0
23 TraesCS4D01G261200 chr3D 97.762 715 16 0 1 715 118040216 118040930 0.000000e+00 1232.0
24 TraesCS4D01G261200 chr2D 97.902 715 15 0 1 715 80275483 80274769 0.000000e+00 1238.0
25 TraesCS4D01G261200 chr6D 97.899 714 15 0 1 714 251650413 251649700 0.000000e+00 1236.0
26 TraesCS4D01G261200 chr6D 97.759 714 16 0 1 714 234915043 234915756 0.000000e+00 1230.0
27 TraesCS4D01G261200 chr1D 97.639 720 17 0 1 720 295358478 295357759 0.000000e+00 1236.0
28 TraesCS4D01G261200 chr7D 96.257 748 23 5 1 744 362701411 362702157 0.000000e+00 1221.0
29 TraesCS4D01G261200 chr4B 80.313 1021 160 25 779 1771 21158449 21157442 0.000000e+00 734.0
30 TraesCS4D01G261200 chr2B 86.816 402 46 4 2292 2689 778780908 778781306 2.590000e-120 442.0
31 TraesCS4D01G261200 chr2B 91.447 304 21 4 1937 2235 480355599 480355296 2.030000e-111 412.0
32 TraesCS4D01G261200 chr2B 91.391 302 21 3 1935 2232 535614394 535614094 2.620000e-110 409.0
33 TraesCS4D01G261200 chr7B 92.683 287 17 3 1937 2219 527368321 527368607 7.290000e-111 411.0
34 TraesCS4D01G261200 chr7B 90.759 303 22 4 1933 2229 642087896 642087594 1.580000e-107 399.0
35 TraesCS4D01G261200 chr7A 86.420 81 11 0 2677 2757 125484306 125484386 3.880000e-14 89.8


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 TraesCS4D01G261200 chr4D 431720404 431723231 2827 True 1784.866667 5223 96.825333 1 2828 3 chr4D.!!$R5 2827
1 TraesCS4D01G261200 chr4D 431672212 431674314 2102 True 3498.000000 3498 96.645000 715 2826 1 chr4D.!!$R2 2111
2 TraesCS4D01G261200 chr4D 431618828 431620952 2124 True 3421.000000 3421 95.827000 715 2828 1 chr4D.!!$R1 2113
3 TraesCS4D01G261200 chr4D 431729847 431730561 714 True 1238.000000 1238 97.902000 1 715 1 chr4D.!!$R3 714
4 TraesCS4D01G261200 chr4D 431553073 431555187 2114 True 1209.300000 3500 94.937000 715 2828 3 chr4D.!!$R4 2113
5 TraesCS4D01G261200 chrUn 256114573 256115678 1105 False 1406.000000 1406 89.563000 716 1833 1 chrUn.!!$F1 1117
6 TraesCS4D01G261200 chrUn 390478394 390479499 1105 False 1406.000000 1406 89.563000 716 1833 1 chrUn.!!$F2 1117
7 TraesCS4D01G261200 chr5B 660879328 660880433 1105 True 1406.000000 1406 89.563000 716 1833 1 chr5B.!!$R1 1117
8 TraesCS4D01G261200 chr5B 660925277 660926382 1105 True 1389.000000 1389 89.295000 716 1833 1 chr5B.!!$R2 1117
9 TraesCS4D01G261200 chr4A 32714017 32715175 1158 True 767.000000 1280 91.101000 715 1847 2 chr4A.!!$R4 1132
10 TraesCS4D01G261200 chr4A 592926696 592927462 766 True 732.000000 732 84.015000 901 1675 1 chr4A.!!$R1 774
11 TraesCS4D01G261200 chr3D 442058637 442059351 714 False 1243.000000 1243 98.042000 1 715 1 chr3D.!!$F2 714
12 TraesCS4D01G261200 chr3D 442075336 442076049 713 False 1242.000000 1242 98.039000 1 714 1 chr3D.!!$F3 713
13 TraesCS4D01G261200 chr3D 118040216 118040930 714 False 1232.000000 1232 97.762000 1 715 1 chr3D.!!$F1 714
14 TraesCS4D01G261200 chr2D 80274769 80275483 714 True 1238.000000 1238 97.902000 1 715 1 chr2D.!!$R1 714
15 TraesCS4D01G261200 chr6D 251649700 251650413 713 True 1236.000000 1236 97.899000 1 714 1 chr6D.!!$R1 713
16 TraesCS4D01G261200 chr6D 234915043 234915756 713 False 1230.000000 1230 97.759000 1 714 1 chr6D.!!$F1 713
17 TraesCS4D01G261200 chr1D 295357759 295358478 719 True 1236.000000 1236 97.639000 1 720 1 chr1D.!!$R1 719
18 TraesCS4D01G261200 chr7D 362701411 362702157 746 False 1221.000000 1221 96.257000 1 744 1 chr7D.!!$F1 743
19 TraesCS4D01G261200 chr4B 21157442 21158449 1007 True 734.000000 734 80.313000 779 1771 1 chr4B.!!$R1 992

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
449 450 0.10852 GTGCTACAACCCGGATTCGA 60.109 55.0 0.73 0.0 39.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1861 1925 0.179189 GCCGGATGAAAAACTGCGAG 60.179 55.0 5.05 0.0 0.0 5.03 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
25 26 4.655963 ACTTGTATGCTCTGAATGTTGGT 58.344 39.130 0.00 0.00 0.00 3.67
35 36 4.971939 TCTGAATGTTGGTTCATGAGACA 58.028 39.130 0.00 0.83 37.47 3.41
354 355 0.178973 TCCTGTGTCTGTCCCTTCGA 60.179 55.000 0.00 0.00 0.00 3.71
449 450 0.108520 GTGCTACAACCCGGATTCGA 60.109 55.000 0.73 0.00 39.00 3.71
498 499 0.907704 TTCACGTATGCCTGTCCCCT 60.908 55.000 0.00 0.00 0.00 4.79
537 538 2.230508 GGGTTCACGACTAGTCATGTCA 59.769 50.000 22.37 6.59 34.37 3.58
834 835 6.896860 TCTAATTGATTGGTTTGTGGGATGAT 59.103 34.615 0.00 0.00 0.00 2.45
979 1023 2.034053 CGTACTGTGCAAACCAACCAAT 59.966 45.455 0.00 0.00 0.00 3.16
1122 1166 0.325203 AACAACCCAAGGCCACAACT 60.325 50.000 5.01 0.00 0.00 3.16
1326 1370 2.659610 GTCTTCGCTCAGGTGGCT 59.340 61.111 0.00 0.00 0.00 4.75
1642 1686 0.971386 GGACTACAAGTTCGTCCCCA 59.029 55.000 9.09 0.00 41.00 4.96
1680 1724 2.682952 AGAAGATGTACGCCGTATCG 57.317 50.000 0.00 0.00 0.00 2.92
1694 1738 2.290464 CGTATCGGTTCCTGAGAGTCT 58.710 52.381 0.00 0.00 0.00 3.24
1975 2039 7.038302 AGGTGAATAAGTCATCTTAGGTTGTGA 60.038 37.037 0.00 0.00 46.15 3.58
1976 2040 7.278868 GGTGAATAAGTCATCTTAGGTTGTGAG 59.721 40.741 0.00 0.00 39.17 3.51
2337 2403 3.892162 CCCCCGTCCCCAACACAA 61.892 66.667 0.00 0.00 0.00 3.33
2451 2517 4.641645 TTGCCGTCAGCCCTGGTG 62.642 66.667 0.00 0.00 42.71 4.17
2487 2553 1.203441 TCCCCTCTTCAGCATGCAGT 61.203 55.000 21.98 0.00 34.76 4.40
2633 2699 1.423921 GGTTCCTGTTTCCTTCCCTGA 59.576 52.381 0.00 0.00 0.00 3.86
2760 2826 1.902508 TGCAAACAAACACCTCCCAAA 59.097 42.857 0.00 0.00 0.00 3.28
2775 2841 1.209504 CCCAAAAGTCTATCGGCTCCA 59.790 52.381 0.00 0.00 0.00 3.86
2816 2882 2.440539 ATGAAACGCTCGTTGACTCT 57.559 45.000 8.50 0.00 38.47 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 8.353684 CCGAGGAGCGAGATATTACAAATATAT 58.646 37.037 0.00 0.00 44.57 0.86
143 144 5.574055 CACACATACCAAGCATTTCAATCAC 59.426 40.000 0.00 0.00 0.00 3.06
354 355 1.369692 TCACCGCGTGACATTTCCT 59.630 52.632 4.92 0.00 37.67 3.36
438 439 2.125673 CAGCGTTCGAATCCGGGT 60.126 61.111 0.00 0.00 36.24 5.28
449 450 2.029288 CATGTCGGTCAGCAGCGTT 61.029 57.895 0.00 0.00 44.16 4.84
498 499 4.173290 ACCCAAAGTGGCACTAACTTAA 57.827 40.909 22.37 0.00 36.87 1.85
537 538 0.325296 TATGACAGAGAACCCGGGCT 60.325 55.000 24.08 8.98 0.00 5.19
588 589 1.357334 GACCGTTTGCGCCTTTTGA 59.643 52.632 4.18 0.00 36.67 2.69
860 861 4.911522 TCCTCCTCTCAACTCCCTTTTTAA 59.088 41.667 0.00 0.00 0.00 1.52
872 873 5.965033 AATTAGCAATCTCCTCCTCTCAA 57.035 39.130 0.00 0.00 0.00 3.02
873 874 5.397221 CCAAATTAGCAATCTCCTCCTCTCA 60.397 44.000 0.00 0.00 0.00 3.27
979 1023 2.574450 TGTTGATGCTCTTGTCTTGCA 58.426 42.857 0.00 0.00 41.13 4.08
1546 1590 0.391597 GTGGACTTGTCCTTGGTCGA 59.608 55.000 19.11 0.00 0.00 4.20
1642 1686 1.532604 TTGACGGCAGACTCGATGGT 61.533 55.000 0.00 0.00 0.00 3.55
1680 1724 1.099689 CCTCGAGACTCTCAGGAACC 58.900 60.000 15.71 0.00 33.66 3.62
1694 1738 2.451490 AGATGAAGCTCTTGTCCTCGA 58.549 47.619 0.00 0.00 0.00 4.04
1784 1837 4.316823 AGGCGGGAGTGGGAGTGA 62.317 66.667 0.00 0.00 0.00 3.41
1861 1925 0.179189 GCCGGATGAAAAACTGCGAG 60.179 55.000 5.05 0.00 0.00 5.03
1975 2039 1.415672 TTTCCTCCTTGGTCACGGCT 61.416 55.000 0.00 0.00 37.07 5.52
1976 2040 0.536460 TTTTCCTCCTTGGTCACGGC 60.536 55.000 0.00 0.00 37.07 5.68
2337 2403 0.603065 GTGGGCGGCAAGAGATTTTT 59.397 50.000 12.47 0.00 0.00 1.94
2451 2517 3.978571 GAAGCTCGGGACCTTGGCC 62.979 68.421 0.00 0.00 0.00 5.36
2760 2826 3.997672 GCATGGAGCCGATAGACTT 57.002 52.632 0.00 0.00 37.23 3.01


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

AutoCloner maintained by Alex Coulton.