Multiple sequence alignment - TraesCS5D01G345400

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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 TraesCS5D01G345400 chr5D 100.000 2414 0 0 1 2414 432405247 432402834 0.000000e+00 4458
1 TraesCS5D01G345400 chr5D 97.642 2417 53 4 1 2414 6187188 6189603 0.000000e+00 4145
2 TraesCS5D01G345400 chr5D 97.559 2417 54 5 1 2414 503279977 503277563 0.000000e+00 4132
3 TraesCS5D01G345400 chr5D 97.871 2114 40 5 304 2414 503216770 503218881 0.000000e+00 3650
4 TraesCS5D01G345400 chr3D 97.643 2418 48 8 1 2414 589281293 589278881 0.000000e+00 4141
5 TraesCS5D01G345400 chr1D 97.189 2419 61 7 1 2414 254399862 254397446 0.000000e+00 4084
6 TraesCS5D01G345400 chr5A 96.445 2419 79 7 1 2414 607272647 607275063 0.000000e+00 3984
7 TraesCS5D01G345400 chr2A 96.030 2418 70 9 1 2414 335836896 335839291 0.000000e+00 3910
8 TraesCS5D01G345400 chr4B 95.248 2420 94 10 1 2414 308694730 308697134 0.000000e+00 3812
9 TraesCS5D01G345400 chr4A 95.138 2427 101 13 1 2414 309513371 309515793 0.000000e+00 3812
10 TraesCS5D01G345400 chr6D 98.013 2114 38 4 304 2414 168253477 168255589 0.000000e+00 3668
11 TraesCS5D01G345400 chrUn 97.871 2114 40 5 304 2414 93411079 93408968 0.000000e+00 3650
12 TraesCS5D01G345400 chrUn 97.834 554 10 2 1 553 239346016 239345464 0.000000e+00 955
13 TraesCS5D01G345400 chr7D 94.558 147 7 1 224 370 204018550 204018405 2.410000e-55 226


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 TraesCS5D01G345400 chr5D 432402834 432405247 2413 True 4458 4458 100.000 1 2414 1 chr5D.!!$R1 2413
1 TraesCS5D01G345400 chr5D 6187188 6189603 2415 False 4145 4145 97.642 1 2414 1 chr5D.!!$F1 2413
2 TraesCS5D01G345400 chr5D 503277563 503279977 2414 True 4132 4132 97.559 1 2414 1 chr5D.!!$R2 2413
3 TraesCS5D01G345400 chr5D 503216770 503218881 2111 False 3650 3650 97.871 304 2414 1 chr5D.!!$F2 2110
4 TraesCS5D01G345400 chr3D 589278881 589281293 2412 True 4141 4141 97.643 1 2414 1 chr3D.!!$R1 2413
5 TraesCS5D01G345400 chr1D 254397446 254399862 2416 True 4084 4084 97.189 1 2414 1 chr1D.!!$R1 2413
6 TraesCS5D01G345400 chr5A 607272647 607275063 2416 False 3984 3984 96.445 1 2414 1 chr5A.!!$F1 2413
7 TraesCS5D01G345400 chr2A 335836896 335839291 2395 False 3910 3910 96.030 1 2414 1 chr2A.!!$F1 2413
8 TraesCS5D01G345400 chr4B 308694730 308697134 2404 False 3812 3812 95.248 1 2414 1 chr4B.!!$F1 2413
9 TraesCS5D01G345400 chr4A 309513371 309515793 2422 False 3812 3812 95.138 1 2414 1 chr4A.!!$F1 2413
10 TraesCS5D01G345400 chr6D 168253477 168255589 2112 False 3668 3668 98.013 304 2414 1 chr6D.!!$F1 2110
11 TraesCS5D01G345400 chrUn 93408968 93411079 2111 True 3650 3650 97.871 304 2414 1 chrUn.!!$R1 2110
12 TraesCS5D01G345400 chrUn 239345464 239346016 552 True 955 955 97.834 1 553 1 chrUn.!!$R2 552

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
961 1002 2.897969 TCCTAGTTCTTCTTCCAAGCGT 59.102 45.455 0.0 0.0 0.0 5.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2118 2166 1.949465 ACGACCCTAATCGAAATGCC 58.051 50.0 1.63 0.0 45.13 4.4 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
79 86 7.905604 TTCAACCAATCTGTAGTTGATAGTG 57.094 36.000 5.72 0.00 46.64 2.74
177 184 3.445008 TGCTCACAACTTCCCTCTAGAT 58.555 45.455 0.00 0.00 0.00 1.98
301 309 9.998106 GTTCTAGCAAGATATTGGGTATTTCTA 57.002 33.333 1.67 0.00 0.00 2.10
676 712 7.303634 TCCGTTTTAAAGAGTGCATTCTATC 57.696 36.000 12.63 0.00 0.00 2.08
698 734 6.729391 TCTCCAATATCTCGATCGAAGTAG 57.271 41.667 19.92 7.52 0.00 2.57
961 1002 2.897969 TCCTAGTTCTTCTTCCAAGCGT 59.102 45.455 0.00 0.00 0.00 5.07
1232 1275 5.336372 CCGATTTACCCTCTTTTGCAATGAA 60.336 40.000 0.00 0.00 0.00 2.57
1236 1279 8.922931 ATTTACCCTCTTTTGCAATGAATTTT 57.077 26.923 0.00 0.00 0.00 1.82
1414 1460 7.759886 GCATACGGCTTTCTAGATGTATATGAA 59.240 37.037 0.00 0.00 40.25 2.57
1415 1461 9.639601 CATACGGCTTTCTAGATGTATATGAAA 57.360 33.333 0.00 0.00 0.00 2.69
1467 1513 9.445878 GAATCATATGATGAAGTACCACATGAT 57.554 33.333 18.85 6.98 43.50 2.45
1504 1550 2.294512 GGAATCCAAATCTGCCGAATCC 59.705 50.000 0.00 0.00 0.00 3.01
1559 1605 2.545113 GCGTTCCGTCATCTGGCTTATA 60.545 50.000 0.00 0.00 0.00 0.98
1576 1622 8.696043 TGGCTTATATTCTTCATGTAGCATTT 57.304 30.769 0.00 0.00 0.00 2.32
1585 1631 5.810587 TCTTCATGTAGCATTTAGACCGAAC 59.189 40.000 0.00 0.00 0.00 3.95
1775 1821 1.001378 GGTTCTGTGCGTGCTTCAAAT 60.001 47.619 0.00 0.00 0.00 2.32
1776 1822 2.543653 GGTTCTGTGCGTGCTTCAAATT 60.544 45.455 0.00 0.00 0.00 1.82
1777 1823 3.115554 GTTCTGTGCGTGCTTCAAATTT 58.884 40.909 0.00 0.00 0.00 1.82
1889 1935 5.799213 CAGTTTTCTGTTGAGGTCTATCCT 58.201 41.667 0.00 0.00 44.95 3.24
1928 1974 4.876125 TGGATCAGTGATCGATTTCTAGC 58.124 43.478 23.56 9.49 39.72 3.42
1944 1990 3.829948 TCTAGCTTTCGTCGTAAACCTG 58.170 45.455 0.00 0.00 0.00 4.00
2118 2166 6.931281 CCCCATAGTGTATGAGACAAATGTAG 59.069 42.308 3.97 0.00 40.66 2.74
2159 2207 8.502387 GTCGTATTCTATGGTTACGATTCTACT 58.498 37.037 15.61 0.00 46.31 2.57
2376 2424 6.977213 AGGTGTTTTGTATAAATGTTTCGCT 58.023 32.000 0.00 0.00 0.00 4.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 86 5.050567 CCCAAGTATTAATAACGCGACCTTC 60.051 44.000 15.93 0.00 0.00 3.46
177 184 3.550820 TGGAACTTCAACAGCAGCTAAA 58.449 40.909 0.00 0.00 0.00 1.85
655 690 8.268850 TGGAGATAGAATGCACTCTTTAAAAC 57.731 34.615 1.62 0.00 0.00 2.43
676 712 5.163703 CCCTACTTCGATCGAGATATTGGAG 60.164 48.000 18.54 12.31 0.00 3.86
961 1002 2.210644 CAACCCCTTGGGGTTATCCTA 58.789 52.381 34.97 0.00 42.24 2.94
1042 1085 5.851418 AGTAAGAGGGGTAGTTATGAACCT 58.149 41.667 0.00 0.00 35.97 3.50
1232 1275 2.288395 GCAGCAGGTGTTGTAGCAAAAT 60.288 45.455 0.66 0.00 0.00 1.82
1236 1279 0.603707 GAGCAGCAGGTGTTGTAGCA 60.604 55.000 0.66 0.00 33.14 3.49
1281 1324 5.149273 GCCATGCATAACATAGAAATCACG 58.851 41.667 0.00 0.00 36.64 4.35
1504 1550 7.905265 AGGATGTAGAAGATCATAACATGAGG 58.095 38.462 0.00 0.00 43.53 3.86
1559 1605 6.582636 TCGGTCTAAATGCTACATGAAGAAT 58.417 36.000 0.00 0.00 0.00 2.40
1576 1622 6.446781 AATTTCATAGAGTCGTTCGGTCTA 57.553 37.500 7.34 7.34 0.00 2.59
1580 1626 5.032863 ACGTAATTTCATAGAGTCGTTCGG 58.967 41.667 0.00 0.00 0.00 4.30
1626 1672 5.532664 AAATAGGGATGTCTCCTACGTTC 57.467 43.478 0.00 0.00 41.74 3.95
1889 1935 6.440647 ACTGATCCAATTTGACTACCTCTACA 59.559 38.462 0.00 0.00 0.00 2.74
1928 1974 4.322101 CCAATCAGGTTTACGACGAAAG 57.678 45.455 0.00 0.00 0.00 2.62
2118 2166 1.949465 ACGACCCTAATCGAAATGCC 58.051 50.000 1.63 0.00 45.13 4.40
2159 2207 7.485810 TCGACGGAATCAAAAAGACATATCTA 58.514 34.615 0.00 0.00 33.57 1.98


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

AutoCloner maintained by Alex Coulton.