Multiple sequence alignment - TraesCS3D01G409400

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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 TraesCS3D01G409400 chr3D 100.000 2606 0 0 1 2606 523335226 523337831 0.000000e+00 4813
1 TraesCS3D01G409400 chr3D 83.904 1839 251 24 38 1855 523408563 523410377 0.000000e+00 1714
2 TraesCS3D01G409400 chr3D 80.854 1990 297 52 1 1950 523555980 523557925 0.000000e+00 1487
3 TraesCS3D01G409400 chr3D 86.275 663 84 7 953 1611 523562704 523563363 0.000000e+00 713
4 TraesCS3D01G409400 chr3D 84.834 211 16 8 1838 2048 523416204 523416398 5.690000e-47 198
5 TraesCS3D01G409400 chr3B 96.366 2064 41 13 1 2055 642214899 642212861 0.000000e+00 3365
6 TraesCS3D01G409400 chr3B 81.011 2096 320 51 1 2055 689006795 689004737 0.000000e+00 1594
7 TraesCS3D01G409400 chr3B 82.455 1613 270 11 1 1611 690447557 690449158 0.000000e+00 1399
8 TraesCS3D01G409400 chr3B 82.222 1620 270 15 1 1610 689351440 689349829 0.000000e+00 1380
9 TraesCS3D01G409400 chr3B 81.864 1588 264 19 1 1579 690431143 690432715 0.000000e+00 1315
10 TraesCS3D01G409400 chr3B 80.643 1617 295 12 1 1610 690460532 690462137 0.000000e+00 1236
11 TraesCS3D01G409400 chr3B 85.605 1042 71 26 1613 2597 690432717 690433736 0.000000e+00 1020
12 TraesCS3D01G409400 chr3B 89.399 566 38 9 2053 2606 642211436 642210881 0.000000e+00 693
13 TraesCS3D01G409400 chr3A 84.114 2518 326 42 1 2473 658304213 658306701 0.000000e+00 2366
14 TraesCS3D01G409400 chr3A 81.919 2074 314 38 1 2048 658289702 658291740 0.000000e+00 1696
15 TraesCS3D01G409400 chr3A 79.470 1661 296 33 1 1636 36070674 36069034 0.000000e+00 1136
16 TraesCS3D01G409400 chr3A 85.656 488 24 7 1925 2368 658247898 658248383 3.040000e-129 472
17 TraesCS3D01G409400 chr3A 94.958 119 6 0 2488 2606 658306937 658307055 1.230000e-43 187
18 TraesCS3D01G409400 chr3A 93.617 94 6 0 2385 2478 658251943 658252036 9.720000e-30 141
19 TraesCS3D01G409400 chr3A 89.109 101 10 1 2493 2593 658252080 658252179 9.790000e-25 124
20 TraesCS3D01G409400 chrUn 81.531 2090 305 36 1 2044 342677932 342679986 0.000000e+00 1646
21 TraesCS3D01G409400 chrUn 83.019 1272 154 24 807 2044 405666925 405668168 0.000000e+00 1096
22 TraesCS3D01G409400 chrUn 85.835 593 30 10 1925 2473 353196828 353197410 4.830000e-162 580
23 TraesCS3D01G409400 chrUn 88.050 318 19 6 1626 1927 353196076 353196390 2.470000e-95 359
24 TraesCS3D01G409400 chrUn 95.175 228 10 1 1701 1927 471389946 471389719 2.470000e-95 359


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 TraesCS3D01G409400 chr3D 523335226 523337831 2605 False 4813.000000 4813 100.000000 1 2606 1 chr3D.!!$F1 2605
1 TraesCS3D01G409400 chr3D 523408563 523410377 1814 False 1714.000000 1714 83.904000 38 1855 1 chr3D.!!$F2 1817
2 TraesCS3D01G409400 chr3D 523555980 523557925 1945 False 1487.000000 1487 80.854000 1 1950 1 chr3D.!!$F4 1949
3 TraesCS3D01G409400 chr3D 523562704 523563363 659 False 713.000000 713 86.275000 953 1611 1 chr3D.!!$F5 658
4 TraesCS3D01G409400 chr3B 642210881 642214899 4018 True 2029.000000 3365 92.882500 1 2606 2 chr3B.!!$R3 2605
5 TraesCS3D01G409400 chr3B 689004737 689006795 2058 True 1594.000000 1594 81.011000 1 2055 1 chr3B.!!$R1 2054
6 TraesCS3D01G409400 chr3B 690447557 690449158 1601 False 1399.000000 1399 82.455000 1 1611 1 chr3B.!!$F1 1610
7 TraesCS3D01G409400 chr3B 689349829 689351440 1611 True 1380.000000 1380 82.222000 1 1610 1 chr3B.!!$R2 1609
8 TraesCS3D01G409400 chr3B 690460532 690462137 1605 False 1236.000000 1236 80.643000 1 1610 1 chr3B.!!$F2 1609
9 TraesCS3D01G409400 chr3B 690431143 690433736 2593 False 1167.500000 1315 83.734500 1 2597 2 chr3B.!!$F3 2596
10 TraesCS3D01G409400 chr3A 658289702 658291740 2038 False 1696.000000 1696 81.919000 1 2048 1 chr3A.!!$F1 2047
11 TraesCS3D01G409400 chr3A 658304213 658307055 2842 False 1276.500000 2366 89.536000 1 2606 2 chr3A.!!$F3 2605
12 TraesCS3D01G409400 chr3A 36069034 36070674 1640 True 1136.000000 1136 79.470000 1 1636 1 chr3A.!!$R1 1635
13 TraesCS3D01G409400 chr3A 658247898 658252179 4281 False 245.666667 472 89.460667 1925 2593 3 chr3A.!!$F2 668
14 TraesCS3D01G409400 chrUn 342677932 342679986 2054 False 1646.000000 1646 81.531000 1 2044 1 chrUn.!!$F1 2043
15 TraesCS3D01G409400 chrUn 405666925 405668168 1243 False 1096.000000 1096 83.019000 807 2044 1 chrUn.!!$F2 1237
16 TraesCS3D01G409400 chrUn 353196076 353197410 1334 False 469.500000 580 86.942500 1626 2473 2 chrUn.!!$F3 847

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
135 136 1.139498 TTGGAGGCCACATCTTCCCA 61.139 55.0 5.01 0.0 30.78 4.37 F
1398 1417 2.159226 ACCTACGCAAATCGAAGAGAGG 60.159 50.0 0.00 0.0 43.63 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1454 1476 0.881796 GTACAGCCAGAACCCAAAGC 59.118 55.0 0.0 0.0 0.00 3.51 R
2485 8042 0.603065 GGAACCTTCCGCAGCAATTT 59.397 50.0 0.0 0.0 37.65 1.82 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
135 136 1.139498 TTGGAGGCCACATCTTCCCA 61.139 55.000 5.01 0.00 30.78 4.37
574 587 3.673599 GCAACTCCTTCAGTGGCC 58.326 61.111 0.00 0.00 45.61 5.36
760 773 3.971245 AGAGCTTACCTGGACTCAAAG 57.029 47.619 0.00 0.00 0.00 2.77
1398 1417 2.159226 ACCTACGCAAATCGAAGAGAGG 60.159 50.000 0.00 0.00 43.63 3.69
1454 1476 1.108727 TTTGTGGCTGCTGGGTTCAG 61.109 55.000 0.00 0.00 43.64 3.02
1622 1646 2.438868 TGATGAAGAGTGTCACGTGG 57.561 50.000 17.00 0.00 0.00 4.94
1623 1647 1.686587 TGATGAAGAGTGTCACGTGGT 59.313 47.619 17.00 0.00 0.00 4.16
1722 1781 8.362304 CGGTTTGTTGTAATTTGATGTTATTCG 58.638 33.333 0.00 0.00 0.00 3.34
1906 2001 4.630940 CACTTCTTGTGCAACCATTTTGTT 59.369 37.500 0.00 0.00 40.06 2.83
2113 4087 2.271800 GTAGAAGCACCGGTGAAGATG 58.728 52.381 38.30 11.31 0.00 2.90
2295 4292 4.837860 ACTCTGTCAGAATCTGTTTCCTCT 59.162 41.667 10.36 0.00 34.67 3.69
2360 4361 2.288186 CAGTGATCTGCTGTGATGATGC 59.712 50.000 8.93 0.00 34.79 3.91
2362 4363 2.681344 GTGATCTGCTGTGATGATGCAA 59.319 45.455 0.00 0.00 36.22 4.08
2363 4364 3.128068 GTGATCTGCTGTGATGATGCAAA 59.872 43.478 0.00 0.00 36.22 3.68
2364 4365 3.759618 TGATCTGCTGTGATGATGCAAAA 59.240 39.130 0.00 0.00 36.22 2.44
2365 4366 3.842732 TCTGCTGTGATGATGCAAAAG 57.157 42.857 0.00 0.00 36.22 2.27
2366 4367 2.094906 TCTGCTGTGATGATGCAAAAGC 60.095 45.455 0.00 0.00 36.22 3.51
2367 4368 1.614413 TGCTGTGATGATGCAAAAGCA 59.386 42.857 0.00 0.00 37.39 3.91
2368 4369 2.232696 TGCTGTGATGATGCAAAAGCAT 59.767 40.909 2.13 2.13 37.70 3.79
2369 4370 3.259064 GCTGTGATGATGCAAAAGCATT 58.741 40.909 4.29 0.00 34.22 3.56
2457 8009 4.627467 AGAGAGCACGTATGTTGAATTGTC 59.373 41.667 0.00 0.00 0.00 3.18
2478 8035 5.163499 TGTCCGCCTTTGTTTTCTGTTATTT 60.163 36.000 0.00 0.00 0.00 1.40
2479 8036 6.039493 TGTCCGCCTTTGTTTTCTGTTATTTA 59.961 34.615 0.00 0.00 0.00 1.40
2480 8037 6.919115 GTCCGCCTTTGTTTTCTGTTATTTAA 59.081 34.615 0.00 0.00 0.00 1.52
2482 8039 7.980099 TCCGCCTTTGTTTTCTGTTATTTAAAA 59.020 29.630 0.00 0.00 0.00 1.52
2483 8040 8.604890 CCGCCTTTGTTTTCTGTTATTTAAAAA 58.395 29.630 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
135 136 2.433970 GAGACTGCTATTCCCAAGCTCT 59.566 50.000 0.00 0.00 40.73 4.09
574 587 1.550524 TGTCCTCGAGAATGGAACCAG 59.449 52.381 15.71 0.00 33.72 4.00
760 773 5.198274 GTGTTTGATGACAGACGAAGAAAC 58.802 41.667 0.00 0.00 34.45 2.78
1398 1417 2.692557 TGTCTCTCTATCTTCAGCCTGC 59.307 50.000 0.00 0.00 0.00 4.85
1454 1476 0.881796 GTACAGCCAGAACCCAAAGC 59.118 55.000 0.00 0.00 0.00 3.51
1622 1646 4.032900 CGATACACCATTACTTCAGCACAC 59.967 45.833 0.00 0.00 0.00 3.82
1623 1647 4.180817 CGATACACCATTACTTCAGCACA 58.819 43.478 0.00 0.00 0.00 4.57
1722 1781 1.477105 GTTTCAGCGCCACAAAACTC 58.523 50.000 2.29 0.00 0.00 3.01
1758 1845 3.606687 AGCCTTAGGTACCAAACAATCG 58.393 45.455 15.94 0.00 0.00 3.34
2295 4292 9.636789 ATGGATGATATTCATTCAGAAACAGAA 57.363 29.630 4.87 0.00 44.90 3.02
2360 4361 3.187022 GCCTGGTTGCTTTAATGCTTTTG 59.813 43.478 13.80 2.23 0.00 2.44
2362 4363 2.368221 TGCCTGGTTGCTTTAATGCTTT 59.632 40.909 13.80 0.00 0.00 3.51
2363 4364 1.969923 TGCCTGGTTGCTTTAATGCTT 59.030 42.857 13.80 0.00 0.00 3.91
2364 4365 1.273327 GTGCCTGGTTGCTTTAATGCT 59.727 47.619 13.80 0.00 0.00 3.79
2365 4366 1.000731 TGTGCCTGGTTGCTTTAATGC 59.999 47.619 6.39 6.39 0.00 3.56
2366 4367 3.598019 ATGTGCCTGGTTGCTTTAATG 57.402 42.857 0.00 0.00 0.00 1.90
2367 4368 4.622260 AAATGTGCCTGGTTGCTTTAAT 57.378 36.364 0.00 0.00 0.00 1.40
2368 4369 5.011533 ACATAAATGTGCCTGGTTGCTTTAA 59.988 36.000 0.00 0.00 40.03 1.52
2369 4370 4.526262 ACATAAATGTGCCTGGTTGCTTTA 59.474 37.500 0.00 0.00 40.03 1.85
2427 7979 6.631016 TCAACATACGTGCTCTCTATTTTCT 58.369 36.000 0.00 0.00 0.00 2.52
2428 7980 6.887376 TCAACATACGTGCTCTCTATTTTC 57.113 37.500 0.00 0.00 0.00 2.29
2457 8009 7.701809 TTTAAATAACAGAAAACAAAGGCGG 57.298 32.000 0.00 0.00 0.00 6.13
2483 8040 2.547855 GGAACCTTCCGCAGCAATTTTT 60.548 45.455 0.00 0.00 37.65 1.94
2485 8042 0.603065 GGAACCTTCCGCAGCAATTT 59.397 50.000 0.00 0.00 37.65 1.82
2486 8043 2.267045 GGAACCTTCCGCAGCAATT 58.733 52.632 0.00 0.00 37.65 2.32
2511 8289 6.710597 TCAAATACCGCTGTAGAAGTCTAT 57.289 37.500 0.00 0.00 0.00 1.98


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

AutoCloner maintained by Alex Coulton.