Multiple sequence alignment - TraesCS7D01G082300

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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 TraesCS7D01G082300 chr7D 100.000 2582 0 0 1 2582 49234166 49231585 0.000000e+00 4769.0
1 TraesCS7D01G082300 chr7D 97.684 2202 19 10 399 2582 12125520 12127707 0.000000e+00 3755.0
2 TraesCS7D01G082300 chr7D 90.511 685 58 5 1899 2582 592359717 592359039 0.000000e+00 898.0
3 TraesCS7D01G082300 chr7D 82.830 961 156 9 749 1706 12188780 12187826 0.000000e+00 852.0
4 TraesCS7D01G082300 chr7D 85.756 688 80 16 1898 2575 59610692 59611371 0.000000e+00 712.0
5 TraesCS7D01G082300 chr7D 98.753 401 2 2 1 401 12125078 12125475 0.000000e+00 710.0
6 TraesCS7D01G082300 chr7D 94.321 405 18 3 1 401 540405211 540405614 1.310000e-172 616.0
7 TraesCS7D01G082300 chr7D 92.768 401 21 3 1 401 633451024 633451416 8.010000e-160 573.0
8 TraesCS7D01G082300 chr7D 82.160 213 14 6 446 634 12082217 12082429 7.390000e-36 161.0
9 TraesCS7D01G082300 chr7D 81.776 214 14 6 446 634 49267242 49267029 3.440000e-34 156.0
10 TraesCS7D01G082300 chr7D 95.833 96 4 0 539 634 540400915 540401010 3.440000e-34 156.0
11 TraesCS7D01G082300 chr7D 94.872 78 4 0 428 505 540405726 540405803 3.490000e-24 122.0
12 TraesCS7D01G082300 chr7D 96.667 60 2 0 446 505 540400779 540400838 1.630000e-17 100.0
13 TraesCS7D01G082300 chr7D 100.000 35 0 0 399 433 540405659 540405693 5.960000e-07 65.8
14 TraesCS7D01G082300 chr1A 89.796 686 62 4 1898 2582 103789222 103789900 0.000000e+00 872.0
15 TraesCS7D01G082300 chr7A 80.696 1150 191 20 749 1895 11844486 11845607 0.000000e+00 865.0
16 TraesCS7D01G082300 chr7A 80.589 1154 189 22 749 1895 11944078 11945203 0.000000e+00 857.0
17 TraesCS7D01G082300 chr7A 82.124 951 159 11 749 1695 11582385 11581442 0.000000e+00 804.0
18 TraesCS7D01G082300 chr7A 77.811 676 107 23 1133 1785 11106209 11106864 6.740000e-101 377.0
19 TraesCS7D01G082300 chr7A 84.188 234 35 1 1327 1560 11869517 11869286 2.590000e-55 226.0
20 TraesCS7D01G082300 chr7A 86.449 214 14 9 437 635 115789913 115790126 1.200000e-53 220.0
21 TraesCS7D01G082300 chr7A 86.275 204 13 9 446 634 115832504 115832301 9.360000e-50 207.0
22 TraesCS7D01G082300 chr7A 86.486 111 8 6 529 636 3779079 3779185 5.840000e-22 115.0
23 TraesCS7D01G082300 chr7A 100.000 35 0 0 399 433 115827677 115827643 5.960000e-07 65.8
24 TraesCS7D01G082300 chr5A 86.792 689 80 10 1898 2582 137658535 137657854 0.000000e+00 758.0
25 TraesCS7D01G082300 chr2D 86.455 694 76 14 1898 2580 330625899 330625213 0.000000e+00 745.0
26 TraesCS7D01G082300 chr2D 85.942 690 80 13 1899 2580 326123810 326123130 0.000000e+00 721.0
27 TraesCS7D01G082300 chr3D 85.859 693 84 9 1893 2578 357367865 357367180 0.000000e+00 725.0
28 TraesCS7D01G082300 chr1D 85.673 691 78 14 1899 2580 234258262 234257584 0.000000e+00 708.0
29 TraesCS7D01G082300 chr7B 94.892 372 18 1 1 372 670817711 670818081 4.790000e-162 580.0
30 TraesCS7D01G082300 chr7B 93.017 401 19 2 1 401 671214910 671215301 6.200000e-161 577.0
31 TraesCS7D01G082300 chr7B 92.099 405 27 2 1 401 552797838 552798241 1.340000e-157 566.0
32 TraesCS7D01G082300 chr7B 96.809 94 3 0 539 632 670818338 670818431 9.560000e-35 158.0
33 TraesCS7D01G082300 chr7B 95.699 93 4 0 543 635 671029146 671029238 1.600000e-32 150.0
34 TraesCS7D01G082300 chr7B 93.548 93 6 0 543 635 670964729 670964821 3.460000e-29 139.0
35 TraesCS7D01G082300 chrUn 93.017 401 19 2 1 401 147265024 147265415 6.200000e-161 577.0
36 TraesCS7D01G082300 chrUn 93.017 401 19 2 1 401 353776284 353775893 6.200000e-161 577.0
37 TraesCS7D01G082300 chrUn 92.519 401 21 2 1 401 147194737 147195128 1.340000e-157 566.0
38 TraesCS7D01G082300 chrUn 81.391 575 69 22 1327 1894 284350330 284349787 3.950000e-118 435.0
39 TraesCS7D01G082300 chrUn 81.391 575 69 22 1327 1894 311024731 311024188 3.950000e-118 435.0
40 TraesCS7D01G082300 chrUn 89.600 125 9 1 515 635 147118458 147118582 3.440000e-34 156.0
41 TraesCS7D01G082300 chrUn 96.774 93 3 0 543 635 147195363 147195455 3.440000e-34 156.0
42 TraesCS7D01G082300 chr1B 86.392 316 29 11 122 435 430085633 430085936 1.480000e-87 333.0
43 TraesCS7D01G082300 chr1B 85.057 87 9 3 539 622 87807187 87807272 4.580000e-13 86.1
44 TraesCS7D01G082300 chr5D 84.270 178 13 10 469 632 559937934 559938110 2.660000e-35 159.0
45 TraesCS7D01G082300 chr5D 97.297 37 1 0 399 435 559952205 559952241 2.140000e-06 63.9
46 TraesCS7D01G082300 chr5B 93.023 43 1 2 428 469 81360107 81360148 7.710000e-06 62.1


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 TraesCS7D01G082300 chr7D 49231585 49234166 2581 True 4769.000000 4769 100.000000 1 2582 1 chr7D.!!$R2 2581
1 TraesCS7D01G082300 chr7D 12125078 12127707 2629 False 2232.500000 3755 98.218500 1 2582 2 chr7D.!!$F4 2581
2 TraesCS7D01G082300 chr7D 592359039 592359717 678 True 898.000000 898 90.511000 1899 2582 1 chr7D.!!$R4 683
3 TraesCS7D01G082300 chr7D 12187826 12188780 954 True 852.000000 852 82.830000 749 1706 1 chr7D.!!$R1 957
4 TraesCS7D01G082300 chr7D 59610692 59611371 679 False 712.000000 712 85.756000 1898 2575 1 chr7D.!!$F2 677
5 TraesCS7D01G082300 chr7D 540405211 540405803 592 False 267.933333 616 96.397667 1 505 3 chr7D.!!$F6 504
6 TraesCS7D01G082300 chr1A 103789222 103789900 678 False 872.000000 872 89.796000 1898 2582 1 chr1A.!!$F1 684
7 TraesCS7D01G082300 chr7A 11844486 11845607 1121 False 865.000000 865 80.696000 749 1895 1 chr7A.!!$F3 1146
8 TraesCS7D01G082300 chr7A 11944078 11945203 1125 False 857.000000 857 80.589000 749 1895 1 chr7A.!!$F4 1146
9 TraesCS7D01G082300 chr7A 11581442 11582385 943 True 804.000000 804 82.124000 749 1695 1 chr7A.!!$R1 946
10 TraesCS7D01G082300 chr7A 11106209 11106864 655 False 377.000000 377 77.811000 1133 1785 1 chr7A.!!$F2 652
11 TraesCS7D01G082300 chr5A 137657854 137658535 681 True 758.000000 758 86.792000 1898 2582 1 chr5A.!!$R1 684
12 TraesCS7D01G082300 chr2D 330625213 330625899 686 True 745.000000 745 86.455000 1898 2580 1 chr2D.!!$R2 682
13 TraesCS7D01G082300 chr2D 326123130 326123810 680 True 721.000000 721 85.942000 1899 2580 1 chr2D.!!$R1 681
14 TraesCS7D01G082300 chr3D 357367180 357367865 685 True 725.000000 725 85.859000 1893 2578 1 chr3D.!!$R1 685
15 TraesCS7D01G082300 chr1D 234257584 234258262 678 True 708.000000 708 85.673000 1899 2580 1 chr1D.!!$R1 681
16 TraesCS7D01G082300 chr7B 670817711 670818431 720 False 369.000000 580 95.850500 1 632 2 chr7B.!!$F5 631
17 TraesCS7D01G082300 chrUn 284349787 284350330 543 True 435.000000 435 81.391000 1327 1894 1 chrUn.!!$R1 567
18 TraesCS7D01G082300 chrUn 311024188 311024731 543 True 435.000000 435 81.391000 1327 1894 1 chrUn.!!$R2 567
19 TraesCS7D01G082300 chrUn 147194737 147195455 718 False 361.000000 566 94.646500 1 635 2 chrUn.!!$F3 634

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
138 139 0.250252 TTGTGTCATGGAGCGCAAGA 60.25 50.0 11.47 0.0 43.02 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1980 2144 0.981183 TAGCGCCTCTTTTTCTCCCA 59.019 50.0 2.29 0.0 0.0 4.37 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
138 139 0.250252 TTGTGTCATGGAGCGCAAGA 60.250 50.000 11.47 0.00 43.02 3.02
371 372 8.320396 TGATTTTCATTTTGTCAGAGAGAGAG 57.680 34.615 0.00 0.00 0.00 3.20
372 373 8.152898 TGATTTTCATTTTGTCAGAGAGAGAGA 58.847 33.333 0.00 0.00 0.00 3.10
505 597 7.040494 GGAGAGGATGTTTAACTTGTACCTAC 58.960 42.308 0.00 0.00 0.00 3.18
507 599 7.384477 AGAGGATGTTTAACTTGTACCTACAC 58.616 38.462 0.00 0.00 35.64 2.90
508 600 6.470278 AGGATGTTTAACTTGTACCTACACC 58.530 40.000 0.00 0.00 35.64 4.16
509 601 5.349543 GGATGTTTAACTTGTACCTACACCG 59.650 44.000 0.00 0.00 35.64 4.94
510 602 5.528043 TGTTTAACTTGTACCTACACCGA 57.472 39.130 0.00 0.00 35.64 4.69
511 603 6.100404 TGTTTAACTTGTACCTACACCGAT 57.900 37.500 0.00 0.00 35.64 4.18
512 604 6.158598 TGTTTAACTTGTACCTACACCGATC 58.841 40.000 0.00 0.00 35.64 3.69
513 605 3.498927 AACTTGTACCTACACCGATCG 57.501 47.619 8.51 8.51 35.64 3.69
528 634 4.023622 CACCGATCGATCTCTCTGTAATGT 60.024 45.833 22.43 0.00 0.00 2.71
1953 2117 2.869636 GCAGCAGAGCAGTACAGAAACT 60.870 50.000 0.00 0.00 0.00 2.66
1970 2134 4.093556 AGAAACTTGCGCTACTGCTAATTC 59.906 41.667 9.73 1.34 36.97 2.17
2300 2465 5.507315 CCGAAGCATATACCACATTTTTCCC 60.507 44.000 0.00 0.00 0.00 3.97
2381 2557 3.766591 CTCCTCTCTCCTTCACTTTGCTA 59.233 47.826 0.00 0.00 0.00 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
138 139 3.817647 CCTTGAGACAGTAGCTTGCTTTT 59.182 43.478 0.00 0.00 0.00 2.27
250 251 3.429141 CTTGCAGCCTGTGGAGCG 61.429 66.667 0.00 0.00 34.64 5.03
371 372 2.943033 AGCTTTCGAGCTACTCTCTCTC 59.057 50.000 0.00 0.00 44.28 3.20
372 373 2.682856 CAGCTTTCGAGCTACTCTCTCT 59.317 50.000 0.00 0.00 44.30 3.10
505 597 4.023622 ACATTACAGAGAGATCGATCGGTG 60.024 45.833 19.33 16.23 0.00 4.94
507 599 4.378978 GGACATTACAGAGAGATCGATCGG 60.379 50.000 19.33 10.37 0.00 4.18
508 600 4.378978 GGGACATTACAGAGAGATCGATCG 60.379 50.000 19.33 9.36 0.00 3.69
509 601 4.082463 GGGGACATTACAGAGAGATCGATC 60.082 50.000 17.91 17.91 0.00 3.69
510 602 3.829601 GGGGACATTACAGAGAGATCGAT 59.170 47.826 0.00 0.00 0.00 3.59
511 603 3.117474 AGGGGACATTACAGAGAGATCGA 60.117 47.826 0.00 0.00 0.00 3.59
512 604 3.226777 AGGGGACATTACAGAGAGATCG 58.773 50.000 0.00 0.00 0.00 3.69
513 605 5.363939 CAAAGGGGACATTACAGAGAGATC 58.636 45.833 0.00 0.00 0.00 2.75
528 634 1.007238 AGAGAGATCGACCAAAGGGGA 59.993 52.381 0.00 0.00 41.15 4.81
1194 1318 2.029020 TCGATTGTCTGACTTGAGGGTG 60.029 50.000 9.51 0.00 0.00 4.61
1300 1425 6.648192 TGGTGTTTTCCAACATTTTCTTGAT 58.352 32.000 0.00 0.00 44.85 2.57
1970 2134 2.743636 TTTTCTCCCACGCTACTGAG 57.256 50.000 0.00 0.00 0.00 3.35
1980 2144 0.981183 TAGCGCCTCTTTTTCTCCCA 59.019 50.000 2.29 0.00 0.00 4.37
2300 2465 4.179599 GGAGAGGGGGAGGGGGAG 62.180 77.778 0.00 0.00 0.00 4.30
2381 2557 2.643304 GGGGGAAAAGTAGTGAGGAAGT 59.357 50.000 0.00 0.00 0.00 3.01
2493 2670 1.435563 TCAACTAGTGGAGGGGGAAGA 59.564 52.381 0.00 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.