Multiple sequence alignment - TraesCS5D01G220100

Loading Multiple Alignment...

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 TraesCS5D01G220100 chr5D 100.000 2411 0 0 1 2411 329123999 329126409 0.000000e+00 4453.0
1 TraesCS5D01G220100 chr5D 98.047 768 10 3 1645 2409 299972244 299973009 0.000000e+00 1330.0
2 TraesCS5D01G220100 chr5D 97.914 767 12 3 1645 2409 6253012 6253776 0.000000e+00 1325.0
3 TraesCS5D01G220100 chr5D 97.526 768 14 2 1645 2409 503339704 503338939 0.000000e+00 1308.0
4 TraesCS5D01G220100 chrUn 97.568 1645 24 6 1 1629 93415914 93417558 0.000000e+00 2802.0
5 TraesCS5D01G220100 chrUn 97.266 768 16 3 1645 2409 261568429 261569194 0.000000e+00 1297.0
6 TraesCS5D01G220100 chr3A 97.670 1631 34 3 1 1629 672913918 672915546 0.000000e+00 2798.0
7 TraesCS5D01G220100 chr3A 97.789 769 11 3 1645 2409 105556693 105557459 0.000000e+00 1321.0
8 TraesCS5D01G220100 chr3B 97.612 1633 30 7 4 1629 201523095 201521465 0.000000e+00 2791.0
9 TraesCS5D01G220100 chr3B 97.789 769 11 3 1645 2409 101925140 101924374 0.000000e+00 1321.0
10 TraesCS5D01G220100 chr3B 95.868 121 5 0 4 124 460132543 460132663 1.890000e-46 196.0
11 TraesCS5D01G220100 chr3B 97.619 42 0 1 439 479 710390276 710390317 1.200000e-08 71.3
12 TraesCS5D01G220100 chr2D 97.439 1640 31 5 1 1629 272797803 272799442 0.000000e+00 2785.0
13 TraesCS5D01G220100 chr6A 97.236 1628 35 6 4 1629 271185858 271184239 0.000000e+00 2748.0
14 TraesCS5D01G220100 chr7B 96.337 1638 43 8 4 1629 559141406 559139774 0.000000e+00 2676.0
15 TraesCS5D01G220100 chr7B 98.177 768 9 3 1645 2409 662754771 662755536 0.000000e+00 1336.0
16 TraesCS5D01G220100 chr2B 95.895 1632 56 7 4 1629 369624131 369622505 0.000000e+00 2632.0
17 TraesCS5D01G220100 chr1A 95.890 1630 56 7 1 1629 168442209 168443828 0.000000e+00 2628.0
18 TraesCS5D01G220100 chr4D 95.554 1642 49 10 4 1629 19924883 19923250 0.000000e+00 2606.0
19 TraesCS5D01G220100 chr5B 97.919 769 10 3 1645 2409 57514861 57515627 0.000000e+00 1327.0
20 TraesCS5D01G220100 chr1B 97.917 768 11 3 1645 2409 633717235 633716470 0.000000e+00 1325.0
21 TraesCS5D01G220100 chr2A 95.614 228 10 0 4 231 588085767 588085540 1.360000e-97 366.0
22 TraesCS5D01G220100 chr7A 93.627 204 12 1 77 280 571441567 571441769 1.080000e-78 303.0
23 TraesCS5D01G220100 chr7A 98.571 70 0 1 351 420 712250106 712250174 3.260000e-24 122.0


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 TraesCS5D01G220100 chr5D 329123999 329126409 2410 False 4453 4453 100.000 1 2411 1 chr5D.!!$F3 2410
1 TraesCS5D01G220100 chr5D 299972244 299973009 765 False 1330 1330 98.047 1645 2409 1 chr5D.!!$F2 764
2 TraesCS5D01G220100 chr5D 6253012 6253776 764 False 1325 1325 97.914 1645 2409 1 chr5D.!!$F1 764
3 TraesCS5D01G220100 chr5D 503338939 503339704 765 True 1308 1308 97.526 1645 2409 1 chr5D.!!$R1 764
4 TraesCS5D01G220100 chrUn 93415914 93417558 1644 False 2802 2802 97.568 1 1629 1 chrUn.!!$F1 1628
5 TraesCS5D01G220100 chrUn 261568429 261569194 765 False 1297 1297 97.266 1645 2409 1 chrUn.!!$F2 764
6 TraesCS5D01G220100 chr3A 672913918 672915546 1628 False 2798 2798 97.670 1 1629 1 chr3A.!!$F2 1628
7 TraesCS5D01G220100 chr3A 105556693 105557459 766 False 1321 1321 97.789 1645 2409 1 chr3A.!!$F1 764
8 TraesCS5D01G220100 chr3B 201521465 201523095 1630 True 2791 2791 97.612 4 1629 1 chr3B.!!$R2 1625
9 TraesCS5D01G220100 chr3B 101924374 101925140 766 True 1321 1321 97.789 1645 2409 1 chr3B.!!$R1 764
10 TraesCS5D01G220100 chr2D 272797803 272799442 1639 False 2785 2785 97.439 1 1629 1 chr2D.!!$F1 1628
11 TraesCS5D01G220100 chr6A 271184239 271185858 1619 True 2748 2748 97.236 4 1629 1 chr6A.!!$R1 1625
12 TraesCS5D01G220100 chr7B 559139774 559141406 1632 True 2676 2676 96.337 4 1629 1 chr7B.!!$R1 1625
13 TraesCS5D01G220100 chr7B 662754771 662755536 765 False 1336 1336 98.177 1645 2409 1 chr7B.!!$F1 764
14 TraesCS5D01G220100 chr2B 369622505 369624131 1626 True 2632 2632 95.895 4 1629 1 chr2B.!!$R1 1625
15 TraesCS5D01G220100 chr1A 168442209 168443828 1619 False 2628 2628 95.890 1 1629 1 chr1A.!!$F1 1628
16 TraesCS5D01G220100 chr4D 19923250 19924883 1633 True 2606 2606 95.554 4 1629 1 chr4D.!!$R1 1625
17 TraesCS5D01G220100 chr5B 57514861 57515627 766 False 1327 1327 97.919 1645 2409 1 chr5B.!!$F1 764
18 TraesCS5D01G220100 chr1B 633716470 633717235 765 True 1325 1325 97.917 1645 2409 1 chr1B.!!$R1 764

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
110 119 0.463204 CCTGGATCACAGCGAGACAT 59.537 55.0 0.0 0.0 46.14 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1698 1741 4.875544 TCAACAAAGGAAGTCTTTCACG 57.124 40.909 0.0 0.0 43.32 4.35 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
92 101 1.896660 TCAAGCACTTGAACCCGCC 60.897 57.895 10.58 0.00 45.56 6.13
101 110 1.773856 TTGAACCCGCCTGGATCACA 61.774 55.000 0.00 0.00 44.82 3.58
110 119 0.463204 CCTGGATCACAGCGAGACAT 59.537 55.000 0.00 0.00 46.14 3.06
128 137 3.983741 ACATATAGAAGCAGGACGAAGC 58.016 45.455 0.00 0.00 0.00 3.86
148 157 2.286125 GCGCAATAACACGATATGCACA 60.286 45.455 0.30 0.00 0.00 4.57
541 561 5.140454 TGTAGCAGATAATAGTGGAGCTCA 58.860 41.667 17.19 0.00 32.49 4.26
684 704 7.169308 CCGAAGTAATTCGAGCTGTAATTGTAT 59.831 37.037 25.41 0.62 46.52 2.29
693 713 6.475402 TCGAGCTGTAATTGTATGTACATGTG 59.525 38.462 18.81 0.00 35.89 3.21
696 716 8.560355 AGCTGTAATTGTATGTACATGTGAAA 57.440 30.769 18.81 7.56 35.89 2.69
826 846 6.260936 GCCGAGGAATTGAGAGAATTGAATTA 59.739 38.462 0.00 0.00 0.00 1.40
1419 1445 4.467082 TGTTATATATGGTAATCGCCCCGT 59.533 41.667 0.00 0.00 0.00 5.28
1629 1672 6.069963 ACACCATCATCCTAGGCTATATTTCC 60.070 42.308 2.96 0.00 0.00 3.13
1630 1673 6.032039 ACCATCATCCTAGGCTATATTTCCA 58.968 40.000 2.96 0.00 0.00 3.53
1631 1674 6.505344 ACCATCATCCTAGGCTATATTTCCAA 59.495 38.462 2.96 0.00 0.00 3.53
1632 1675 7.052873 CCATCATCCTAGGCTATATTTCCAAG 58.947 42.308 2.96 0.00 0.00 3.61
1633 1676 6.054860 TCATCCTAGGCTATATTTCCAAGC 57.945 41.667 2.96 0.00 35.47 4.01
1641 1684 5.126396 GCTATATTTCCAAGCCATGAACC 57.874 43.478 0.00 0.00 0.00 3.62
1642 1685 4.584325 GCTATATTTCCAAGCCATGAACCA 59.416 41.667 0.00 0.00 0.00 3.67
1643 1686 5.244626 GCTATATTTCCAAGCCATGAACCAT 59.755 40.000 0.00 0.00 0.00 3.55
1698 1741 3.725490 AGTCTTACGTCTTGTTTGACCC 58.275 45.455 0.00 0.00 34.30 4.46
1786 1829 4.834496 TCCACTTTCCTAAACTAAGGACGA 59.166 41.667 0.00 0.00 45.49 4.20
2089 2139 7.466590 GCTTCCATAAAAGCTAGACTAAGCAAG 60.467 40.741 0.00 0.00 46.51 4.01
2228 2278 2.229543 CCAGCAGCAATAACAGAAGCAA 59.770 45.455 0.00 0.00 0.00 3.91
2409 2459 7.156000 TGTGAATTGTCCGAACTACATAGAAA 58.844 34.615 0.00 0.00 0.00 2.52
2410 2460 7.330946 TGTGAATTGTCCGAACTACATAGAAAG 59.669 37.037 0.00 0.00 0.00 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 8.239998 CCTTTCATTCTTCCTCTATGTTGTTTC 58.760 37.037 0.00 0.00 0.00 2.78
92 101 3.657015 ATATGTCTCGCTGTGATCCAG 57.343 47.619 6.79 6.79 44.53 3.86
101 110 3.254657 GTCCTGCTTCTATATGTCTCGCT 59.745 47.826 0.00 0.00 0.00 4.93
110 119 1.269102 GCGCTTCGTCCTGCTTCTATA 60.269 52.381 0.00 0.00 0.00 1.31
128 137 3.584095 TGTGCATATCGTGTTATTGCG 57.416 42.857 0.00 0.00 0.00 4.85
148 157 3.976015 ACCCATATTTTTCCACCACGAT 58.024 40.909 0.00 0.00 0.00 3.73
684 704 5.685068 CGCATTTGAACTTTTCACATGTACA 59.315 36.000 13.74 0.00 45.21 2.90
693 713 3.664025 CCGTCTTCGCATTTGAACTTTTC 59.336 43.478 0.00 0.00 35.54 2.29
696 716 2.218603 ACCGTCTTCGCATTTGAACTT 58.781 42.857 0.00 0.00 35.54 2.66
1419 1445 7.309177 GCGAGATAGAATTTGAGCACTATAGA 58.691 38.462 6.78 0.00 0.00 1.98
1629 1672 7.514784 TGAATCTATTATGGTTCATGGCTTG 57.485 36.000 0.00 0.00 0.00 4.01
1630 1673 8.716674 ATTGAATCTATTATGGTTCATGGCTT 57.283 30.769 0.00 0.00 31.39 4.35
1631 1674 8.168725 AGATTGAATCTATTATGGTTCATGGCT 58.831 33.333 5.78 0.00 38.00 4.75
1632 1675 8.345724 AGATTGAATCTATTATGGTTCATGGC 57.654 34.615 5.78 0.00 38.00 4.40
1698 1741 4.875544 TCAACAAAGGAAGTCTTTCACG 57.124 40.909 0.00 0.00 43.32 4.35
1786 1829 8.713036 AGAAGATATGCTCACCTTCTTATTTCT 58.287 33.333 0.00 0.00 41.61 2.52
2089 2139 7.201504 GCAGAAGGTAAAATACGAGGTACTTTC 60.202 40.741 0.00 0.00 41.55 2.62
2228 2278 4.400251 CACCATGAATCCACTAATTGCTGT 59.600 41.667 0.00 0.00 0.00 4.40
2273 2323 9.753674 TGATTGTATCCTTAACCATTTCTTTCT 57.246 29.630 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.