Multiple sequence alignment - TraesCS3D01G311000

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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 TraesCS3D01G311000 chr3D 100.000 4610 0 0 1495 6104 425158895 425154286 0.000000e+00 8514.0
1 TraesCS3D01G311000 chr3D 100.000 1125 0 0 1 1125 425160389 425159265 0.000000e+00 2078.0
2 TraesCS3D01G311000 chr3A 97.324 4447 76 22 1495 5912 562908524 562912956 0.000000e+00 7513.0
3 TraesCS3D01G311000 chr3A 94.599 685 36 1 1 684 399115541 399116225 0.000000e+00 1059.0
4 TraesCS3D01G311000 chr3A 85.457 777 48 21 5376 6102 563387264 563388025 0.000000e+00 749.0
5 TraesCS3D01G311000 chr3A 95.067 223 8 3 802 1022 562907891 562908112 1.260000e-91 348.0
6 TraesCS3D01G311000 chr3B 98.374 2890 40 4 1568 4456 555273668 555270785 0.000000e+00 5070.0
7 TraesCS3D01G311000 chr3B 95.087 1201 52 5 3567 4765 270858608 270859803 0.000000e+00 1884.0
8 TraesCS3D01G311000 chr3B 95.226 1194 42 7 4409 5601 555204368 555203189 0.000000e+00 1875.0
9 TraesCS3D01G311000 chr3B 98.158 923 11 3 4705 5627 555270786 555269870 0.000000e+00 1605.0
10 TraesCS3D01G311000 chr3B 91.058 794 57 7 4759 5551 270870041 270870821 0.000000e+00 1061.0
11 TraesCS3D01G311000 chr3B 90.949 685 61 1 1 684 764486908 764487592 0.000000e+00 920.0
12 TraesCS3D01G311000 chr3B 95.751 353 11 4 684 1035 555274306 555273957 3.190000e-157 566.0
13 TraesCS3D01G311000 chr3B 86.598 485 37 10 5644 6104 555269788 555269308 1.520000e-140 510.0
14 TraesCS3D01G311000 chr3B 94.634 205 9 2 3175 3377 270858408 270858612 3.550000e-82 316.0
15 TraesCS3D01G311000 chr3B 96.552 116 4 0 4303 4418 555226542 555226427 6.240000e-45 193.0
16 TraesCS3D01G311000 chr3B 88.034 117 11 3 5867 5981 808758145 808758030 1.070000e-27 135.0
17 TraesCS3D01G311000 chr3B 100.000 28 0 0 5617 5644 555269841 555269814 1.100000e-02 52.8
18 TraesCS3D01G311000 chr7D 95.777 1184 44 4 3732 4913 277556626 277557805 0.000000e+00 1905.0
19 TraesCS3D01G311000 chr7D 92.230 592 30 7 4962 5551 277557800 277558377 0.000000e+00 824.0
20 TraesCS3D01G311000 chr7D 96.954 197 4 2 3175 3370 277556435 277556630 4.560000e-86 329.0
21 TraesCS3D01G311000 chr4D 96.188 682 26 0 1 682 472156524 472155843 0.000000e+00 1116.0
22 TraesCS3D01G311000 chr2D 95.461 683 30 1 1 683 342078718 342078037 0.000000e+00 1088.0
23 TraesCS3D01G311000 chr2D 91.534 378 26 4 5175 5551 70028631 70029003 3.260000e-142 516.0
24 TraesCS3D01G311000 chr2D 86.857 175 17 6 5676 5848 590938004 590937834 2.250000e-44 191.0
25 TraesCS3D01G311000 chr2D 93.636 110 5 1 3175 3284 70028502 70028609 4.900000e-36 163.0
26 TraesCS3D01G311000 chr2D 94.681 94 5 0 5883 5976 151333921 151333828 4.930000e-31 147.0
27 TraesCS3D01G311000 chr2D 92.929 99 7 0 5883 5981 445616982 445616884 1.770000e-30 145.0
28 TraesCS3D01G311000 chr6B 90.365 685 65 1 1 684 319515178 319514494 0.000000e+00 898.0
29 TraesCS3D01G311000 chr6B 94.681 94 5 0 5883 5976 664692385 664692478 4.930000e-31 147.0
30 TraesCS3D01G311000 chr4B 90.190 683 64 3 1 682 285626197 285626877 0.000000e+00 887.0
31 TraesCS3D01G311000 chr4B 89.503 181 16 2 5678 5855 27243824 27243644 6.160000e-55 226.0
32 TraesCS3D01G311000 chr4B 87.719 171 15 5 5676 5840 147699473 147699303 1.740000e-45 195.0
33 TraesCS3D01G311000 chr4B 94.000 100 5 1 5880 5978 179836905 179837004 3.810000e-32 150.0
34 TraesCS3D01G311000 chr7B 89.971 688 62 6 1 684 176244839 176244155 0.000000e+00 881.0
35 TraesCS3D01G311000 chr7B 93.939 99 6 0 5883 5981 627306442 627306344 3.810000e-32 150.0
36 TraesCS3D01G311000 chr2A 93.782 579 36 0 105 683 438735857 438735279 0.000000e+00 870.0
37 TraesCS3D01G311000 chr1B 86.745 679 85 5 1 677 550941044 550941719 0.000000e+00 750.0
38 TraesCS3D01G311000 chr2B 91.601 381 25 5 5175 5551 773921019 773921396 2.520000e-143 520.0
39 TraesCS3D01G311000 chr2B 95.455 110 5 0 3175 3284 773920888 773920997 6.290000e-40 176.0
40 TraesCS3D01G311000 chr7A 86.932 176 18 4 5678 5852 725442920 725443091 6.240000e-45 193.0
41 TraesCS3D01G311000 chr7A 86.034 179 21 3 5677 5852 639578808 639578985 8.080000e-44 189.0
42 TraesCS3D01G311000 chr6A 84.530 181 22 6 5678 5852 598634026 598634206 2.260000e-39 174.0
43 TraesCS3D01G311000 chr1D 88.496 113 10 3 5867 5977 342577681 342577792 3.840000e-27 134.0
44 TraesCS3D01G311000 chr1A 76.757 185 32 8 3091 3272 447744159 447743983 6.510000e-15 93.5


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 TraesCS3D01G311000 chr3D 425154286 425160389 6103 True 5296.000000 8514 100.0000 1 6104 2 chr3D.!!$R1 6103
1 TraesCS3D01G311000 chr3A 562907891 562912956 5065 False 3930.500000 7513 96.1955 802 5912 2 chr3A.!!$F3 5110
2 TraesCS3D01G311000 chr3A 399115541 399116225 684 False 1059.000000 1059 94.5990 1 684 1 chr3A.!!$F1 683
3 TraesCS3D01G311000 chr3A 563387264 563388025 761 False 749.000000 749 85.4570 5376 6102 1 chr3A.!!$F2 726
4 TraesCS3D01G311000 chr3B 555203189 555204368 1179 True 1875.000000 1875 95.2260 4409 5601 1 chr3B.!!$R1 1192
5 TraesCS3D01G311000 chr3B 555269308 555274306 4998 True 1560.760000 5070 95.7762 684 6104 5 chr3B.!!$R4 5420
6 TraesCS3D01G311000 chr3B 270858408 270859803 1395 False 1100.000000 1884 94.8605 3175 4765 2 chr3B.!!$F3 1590
7 TraesCS3D01G311000 chr3B 270870041 270870821 780 False 1061.000000 1061 91.0580 4759 5551 1 chr3B.!!$F1 792
8 TraesCS3D01G311000 chr3B 764486908 764487592 684 False 920.000000 920 90.9490 1 684 1 chr3B.!!$F2 683
9 TraesCS3D01G311000 chr7D 277556435 277558377 1942 False 1019.333333 1905 94.9870 3175 5551 3 chr7D.!!$F1 2376
10 TraesCS3D01G311000 chr4D 472155843 472156524 681 True 1116.000000 1116 96.1880 1 682 1 chr4D.!!$R1 681
11 TraesCS3D01G311000 chr2D 342078037 342078718 681 True 1088.000000 1088 95.4610 1 683 1 chr2D.!!$R2 682
12 TraesCS3D01G311000 chr2D 70028502 70029003 501 False 339.500000 516 92.5850 3175 5551 2 chr2D.!!$F1 2376
13 TraesCS3D01G311000 chr6B 319514494 319515178 684 True 898.000000 898 90.3650 1 684 1 chr6B.!!$R1 683
14 TraesCS3D01G311000 chr4B 285626197 285626877 680 False 887.000000 887 90.1900 1 682 1 chr4B.!!$F2 681
15 TraesCS3D01G311000 chr7B 176244155 176244839 684 True 881.000000 881 89.9710 1 684 1 chr7B.!!$R1 683
16 TraesCS3D01G311000 chr2A 438735279 438735857 578 True 870.000000 870 93.7820 105 683 1 chr2A.!!$R1 578
17 TraesCS3D01G311000 chr1B 550941044 550941719 675 False 750.000000 750 86.7450 1 677 1 chr1B.!!$F1 676
18 TraesCS3D01G311000 chr2B 773920888 773921396 508 False 348.000000 520 93.5280 3175 5551 2 chr2B.!!$F1 2376

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
268 272 0.250513 CTAGGCAGGTGTGGTTCCTC 59.749 60.000 0.00 0.00 32.37 3.71 F
1634 1955 0.399833 GATCCCTCCTCCTGCCATTC 59.600 60.000 0.00 0.00 0.00 2.67 F
1855 2176 2.925706 TGACACGCCCCTGCCTTA 60.926 61.111 0.00 0.00 0.00 2.69 F
2746 3067 1.425066 ACCATGTCCCTTGTGTCATGT 59.575 47.619 0.00 0.00 36.81 3.21 F
3863 4186 3.695437 CTGTGACAATGCGGTTACAGCA 61.695 50.000 13.01 13.01 44.76 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1922 2243 0.792640 CGGACAAGCACAAGCAGTAG 59.207 55.000 0.00 0.00 45.49 2.57 R
2746 3067 2.092429 GCCCATAAACACCAGGAGATGA 60.092 50.000 0.00 0.00 0.00 2.92 R
3863 4186 3.475566 CCAGTGTGGTCGATATCCAAT 57.524 47.619 0.00 0.00 36.68 3.16 R
3905 4228 4.843147 TCAAATTATTTGATACCTGCGCG 58.157 39.130 15.46 0.00 44.21 6.86 R
5575 5907 0.736053 ACGTGCCAATTTGTGAACGT 59.264 45.000 14.52 14.52 42.15 3.99 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
268 272 0.250513 CTAGGCAGGTGTGGTTCCTC 59.749 60.000 0.00 0.00 32.37 3.71
282 286 1.892819 TTCCTCTGCTTCGCCAGGAG 61.893 60.000 0.00 0.00 42.42 3.69
373 377 0.671472 CAGTGCAGAAGACCATGCGA 60.671 55.000 0.00 0.00 45.54 5.10
821 827 3.386237 GGACAGGAGCACGAGCCT 61.386 66.667 0.00 0.00 43.56 4.58
1015 1023 2.125106 AAATGGCGGGCGACTCTC 60.125 61.111 0.00 0.00 0.00 3.20
1634 1955 0.399833 GATCCCTCCTCCTGCCATTC 59.600 60.000 0.00 0.00 0.00 2.67
1734 2055 4.430765 CGGCAAGGGCTACGTCGT 62.431 66.667 2.21 2.21 40.87 4.34
1854 2175 4.335647 CTGACACGCCCCTGCCTT 62.336 66.667 0.00 0.00 0.00 4.35
1855 2176 2.925706 TGACACGCCCCTGCCTTA 60.926 61.111 0.00 0.00 0.00 2.69
1875 2196 5.287992 CCTTATTAGACGAAACGAGACCAAC 59.712 44.000 0.00 0.00 0.00 3.77
1893 2214 3.490526 CCAACATGTTGCTAAGTTTGTGC 59.509 43.478 29.42 0.00 39.16 4.57
1894 2215 2.998772 ACATGTTGCTAAGTTTGTGCG 58.001 42.857 0.00 0.00 0.00 5.34
1916 2237 5.137403 CGCGGTGCTGTAATTAATGTAATC 58.863 41.667 0.00 0.00 0.00 1.75
1922 2243 8.062448 GGTGCTGTAATTAATGTAATCTCGAAC 58.938 37.037 0.00 0.00 0.00 3.95
1931 2252 6.893958 AATGTAATCTCGAACTACTGCTTG 57.106 37.500 0.00 0.00 0.00 4.01
2389 2710 7.547019 TGTCTTCTGTGTCAATGATGAAGTATC 59.453 37.037 13.42 0.00 37.30 2.24
2673 2994 6.493189 TTTGGTTTCAAGGGCTAAGAAAAT 57.507 33.333 0.00 0.00 33.54 1.82
2746 3067 1.425066 ACCATGTCCCTTGTGTCATGT 59.575 47.619 0.00 0.00 36.81 3.21
3151 3472 4.583489 TCCTGTCTATTCCCGTATCTTGAC 59.417 45.833 0.00 0.00 0.00 3.18
3863 4186 3.695437 CTGTGACAATGCGGTTACAGCA 61.695 50.000 13.01 13.01 44.76 4.41
4224 4547 3.127721 GCTTCCACTTTTATCTCACCAGC 59.872 47.826 0.00 0.00 0.00 4.85
4823 5147 6.650807 TGTAGCTGACTTGTATTTTCTTCTGG 59.349 38.462 0.00 0.00 0.00 3.86
5649 6047 3.586470 TTCACTTTTTGGGTCTGCCTA 57.414 42.857 0.00 0.00 34.45 3.93
5654 6052 4.752879 TTGGGTCTGCCTACGCGC 62.753 66.667 5.73 0.00 38.08 6.86
5669 6067 2.520904 GCGCGATGGAGCAGACTTC 61.521 63.158 12.10 0.00 38.98 3.01
5812 6216 6.631971 TGCATGTAAATTCACTTGACTGAA 57.368 33.333 0.00 0.00 34.65 3.02
5815 6219 6.917477 GCATGTAAATTCACTTGACTGAAACA 59.083 34.615 0.00 0.00 33.85 2.83
5827 6231 7.592533 CACTTGACTGAAACATGGTTAAATCTG 59.407 37.037 0.00 0.00 0.00 2.90
5852 6256 0.115349 ACTGAGACCTAGCCACACCT 59.885 55.000 0.00 0.00 0.00 4.00
5856 6260 2.441750 TGAGACCTAGCCACACCTTTTT 59.558 45.455 0.00 0.00 0.00 1.94
5860 6264 5.990668 AGACCTAGCCACACCTTTTTATAG 58.009 41.667 0.00 0.00 0.00 1.31
5925 6329 2.418368 CACCTGCCTTTGTGCCTATA 57.582 50.000 0.00 0.00 0.00 1.31
5978 6382 2.121506 AGGGACCCAAAGGCAGGA 60.122 61.111 14.60 0.00 36.11 3.86
6004 6428 1.202855 GCACCTGCATGGGTATGATCT 60.203 52.381 0.00 0.00 41.11 2.75
6014 6438 4.526438 TGGGTATGATCTCTGTCTCTGA 57.474 45.455 0.00 0.00 0.00 3.27
6042 6466 8.520351 ACACTAGCCCATGTAACTTTTAATTTC 58.480 33.333 0.00 0.00 0.00 2.17
6045 6469 7.539034 AGCCCATGTAACTTTTAATTTCACT 57.461 32.000 0.00 0.00 0.00 3.41
6061 6485 4.963318 TTCACTGTTGGAACTCAGATCT 57.037 40.909 0.00 0.00 35.73 2.75
6081 6505 6.489361 AGATCTGTTTTCATCATTAGCCCATC 59.511 38.462 0.00 0.00 0.00 3.51
6097 6521 8.974060 TTAGCCCATCTAACTTTTAATTCGAT 57.026 30.769 0.00 0.00 32.57 3.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
282 286 0.468771 CAGGGCAAGATCAATCCCCC 60.469 60.000 11.24 5.88 39.59 5.40
373 377 6.647895 GCATCACAAATGAATCAAAGTCCTTT 59.352 34.615 0.00 0.00 38.69 3.11
592 597 0.597637 AAGCGACGTCCACTTCACAG 60.598 55.000 10.58 0.00 0.00 3.66
776 782 5.181245 CCTGGTCTTCAACATTAACATTCGT 59.819 40.000 0.00 0.00 0.00 3.85
821 827 4.308458 CCGGCGTTGGGAGTGTCA 62.308 66.667 6.01 0.00 0.00 3.58
996 1004 2.125106 GAGTCGCCCGCCATTTCT 60.125 61.111 0.00 0.00 0.00 2.52
1506 1827 1.690985 GGGAGGTTGAGGAGGAGGG 60.691 68.421 0.00 0.00 0.00 4.30
1643 1964 1.135315 CCCAGCGCATGAAAACGAG 59.865 57.895 11.47 0.00 0.00 4.18
1734 2055 1.341778 GGAGGAGGAAGTTCCGGTAGA 60.342 57.143 16.31 0.00 42.75 2.59
1850 2171 3.795639 GGTCTCGTTTCGTCTAATAAGGC 59.204 47.826 0.00 0.00 0.00 4.35
1853 2174 5.771469 TGTTGGTCTCGTTTCGTCTAATAA 58.229 37.500 0.00 0.00 0.00 1.40
1854 2175 5.375417 TGTTGGTCTCGTTTCGTCTAATA 57.625 39.130 0.00 0.00 0.00 0.98
1855 2176 4.247267 TGTTGGTCTCGTTTCGTCTAAT 57.753 40.909 0.00 0.00 0.00 1.73
1875 2196 1.715519 GCGCACAAACTTAGCAACATG 59.284 47.619 0.30 0.00 0.00 3.21
1893 2214 4.523853 TTACATTAATTACAGCACCGCG 57.476 40.909 0.00 0.00 0.00 6.46
1894 2215 6.300354 AGATTACATTAATTACAGCACCGC 57.700 37.500 0.00 0.00 0.00 5.68
1916 2237 2.071688 AGCACAAGCAGTAGTTCGAG 57.928 50.000 0.00 0.00 45.49 4.04
1922 2243 0.792640 CGGACAAGCACAAGCAGTAG 59.207 55.000 0.00 0.00 45.49 2.57
1931 2252 1.797025 AGAAACTAGCGGACAAGCAC 58.203 50.000 0.00 0.00 40.15 4.40
2673 2994 4.251103 TGCTACTAGGTGGAGATCTCAA 57.749 45.455 23.85 10.78 0.00 3.02
2746 3067 2.092429 GCCCATAAACACCAGGAGATGA 60.092 50.000 0.00 0.00 0.00 2.92
3863 4186 3.475566 CCAGTGTGGTCGATATCCAAT 57.524 47.619 0.00 0.00 36.68 3.16
3905 4228 4.843147 TCAAATTATTTGATACCTGCGCG 58.157 39.130 15.46 0.00 44.21 6.86
4224 4547 5.412640 TGCTGAAATGCCAATAACAGAATG 58.587 37.500 0.00 0.00 46.00 2.67
4823 5147 2.939103 CCACTGCCAGTAACTTCATAGC 59.061 50.000 0.00 0.00 0.00 2.97
4916 5240 7.338800 AGATGCAAAAAGTATAGGGACAATG 57.661 36.000 0.00 0.00 0.00 2.82
4918 5242 8.871629 TTAAGATGCAAAAAGTATAGGGACAA 57.128 30.769 0.00 0.00 0.00 3.18
5575 5907 0.736053 ACGTGCCAATTTGTGAACGT 59.264 45.000 14.52 14.52 42.15 3.99
5654 6052 2.886862 ATGAGAAGTCTGCTCCATCG 57.113 50.000 5.31 0.00 0.00 3.84
5669 6067 8.087982 TGAGACTTAGCAAAACTGTTTATGAG 57.912 34.615 6.16 5.06 0.00 2.90
5715 6114 8.894731 TCTTATGGATATAGCATCGACTAAGAC 58.105 37.037 0.00 0.00 0.00 3.01
5780 6184 7.375106 AGTGAATTTACATGCAAGAGAGAAG 57.625 36.000 2.93 0.00 0.00 2.85
5796 6200 6.469782 ACCATGTTTCAGTCAAGTGAATTT 57.530 33.333 1.30 0.00 36.34 1.82
5798 6202 7.581213 TTAACCATGTTTCAGTCAAGTGAAT 57.419 32.000 1.30 0.00 36.34 2.57
5799 6203 7.397892 TTTAACCATGTTTCAGTCAAGTGAA 57.602 32.000 0.00 0.00 34.56 3.18
5812 6216 5.639506 CAGTCGACTCAGATTTAACCATGTT 59.360 40.000 16.96 0.00 0.00 2.71
5815 6219 5.419155 TCTCAGTCGACTCAGATTTAACCAT 59.581 40.000 15.85 0.00 0.00 3.55
5827 6231 1.018910 GGCTAGGTCTCAGTCGACTC 58.981 60.000 16.96 4.03 34.38 3.36
5852 6256 5.873164 GGTGCTCTCGTTCCTTCTATAAAAA 59.127 40.000 0.00 0.00 0.00 1.94
5856 6260 3.632604 CAGGTGCTCTCGTTCCTTCTATA 59.367 47.826 0.00 0.00 0.00 1.31
5860 6264 1.016653 GCAGGTGCTCTCGTTCCTTC 61.017 60.000 0.00 0.00 38.21 3.46
5925 6329 0.398381 ACTTGTTGGGCCCACATGTT 60.398 50.000 28.70 6.21 0.00 2.71
5949 6353 2.436646 GTCCCTGACATGTGGGCG 60.437 66.667 15.11 6.51 43.04 6.13
6004 6428 3.053619 TGGGCTAGTGTATCAGAGACAGA 60.054 47.826 0.00 0.00 0.00 3.41
6014 6438 9.695155 AATTAAAAGTTACATGGGCTAGTGTAT 57.305 29.630 0.00 0.00 31.48 2.29
6042 6466 4.000331 ACAGATCTGAGTTCCAACAGTG 58.000 45.455 29.27 0.00 35.84 3.66
6045 6469 5.436175 TGAAAACAGATCTGAGTTCCAACA 58.564 37.500 29.27 15.34 0.00 3.33
6061 6485 7.118723 AGTTAGATGGGCTAATGATGAAAACA 58.881 34.615 0.00 0.00 40.94 2.83


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

AutoCloner maintained by Alex Coulton.