Multiple sequence alignment - TraesCS2A01G049000

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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 TraesCS2A01G049000 chr2A 100.000 2374 0 0 1 2374 19028920 19026547 0.000000e+00 4385.0
1 TraesCS2A01G049000 chr2D 98.354 2066 27 5 1 2063 17606701 17604640 0.000000e+00 3620.0
2 TraesCS2A01G049000 chr2D 98.110 2064 33 5 1 2063 17632453 17630395 0.000000e+00 3591.0
3 TraesCS2A01G049000 chr2D 96.000 325 11 1 2052 2374 17602764 17602440 5.810000e-146 527.0
4 TraesCS2A01G049000 chr2D 96.000 325 11 1 2052 2374 17625975 17625651 5.810000e-146 527.0
5 TraesCS2A01G049000 chr2D 88.119 404 41 6 1974 2374 587358852 587359251 7.680000e-130 473.0
6 TraesCS2A01G049000 chr2B 93.105 1871 96 15 531 2374 29555805 29557669 0.000000e+00 2710.0
7 TraesCS2A01G049000 chr2B 98.815 422 4 1 1 422 29555365 29555785 0.000000e+00 750.0
8 TraesCS2A01G049000 chr2B 80.122 327 23 26 53 371 29319609 29319901 3.090000e-49 206.0
9 TraesCS2A01G049000 chr2B 80.122 327 23 24 53 371 29350728 29351020 3.090000e-49 206.0
10 TraesCS2A01G049000 chr2B 79.817 327 24 26 53 371 29264372 29264664 1.440000e-47 200.0
11 TraesCS2A01G049000 chr6B 88.264 409 40 6 1969 2374 30300212 30300615 1.280000e-132 483.0
12 TraesCS2A01G049000 chr6B 87.901 405 41 7 1974 2374 132127796 132128196 9.930000e-129 470.0
13 TraesCS2A01G049000 chr5A 88.060 402 43 5 1974 2374 640131375 640131772 2.760000e-129 472.0
14 TraesCS2A01G049000 chr1D 88.000 400 41 5 1976 2374 449128147 449127754 1.290000e-127 466.0
15 TraesCS2A01G049000 chr7A 86.449 428 47 10 1952 2374 708020642 708021063 2.150000e-125 459.0
16 TraesCS2A01G049000 chr6D 77.982 218 32 11 1604 1808 139368473 139368259 3.200000e-24 122.0
17 TraesCS2A01G049000 chr3D 83.562 73 8 3 1649 1721 523333326 523333394 5.480000e-07 65.8
18 TraesCS2A01G049000 chr3B 86.207 58 8 0 1653 1710 642216802 642216745 1.970000e-06 63.9


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 TraesCS2A01G049000 chr2A 19026547 19028920 2373 True 4385.0 4385 100.000 1 2374 1 chr2A.!!$R1 2373
1 TraesCS2A01G049000 chr2D 17630395 17632453 2058 True 3591.0 3591 98.110 1 2063 1 chr2D.!!$R2 2062
2 TraesCS2A01G049000 chr2D 17602440 17606701 4261 True 2073.5 3620 97.177 1 2374 2 chr2D.!!$R3 2373
3 TraesCS2A01G049000 chr2B 29555365 29557669 2304 False 1730.0 2710 95.960 1 2374 2 chr2B.!!$F4 2373

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
744 747 0.80338 TGAGATGCTCATGTCGTGCG 60.803 55.0 0.0 0.0 35.39 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1886 1916 1.541588 GGCTTGACTGGTTGGACATTC 59.458 52.381 0.0 0.0 0.0 2.67 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
547 550 4.692041 TGACCATGGCCCTCCCCA 62.692 66.667 13.04 0.00 39.65 4.96
744 747 0.803380 TGAGATGCTCATGTCGTGCG 60.803 55.000 0.00 0.00 35.39 5.34
905 908 2.251040 CGCGCGTATATAAGCATGTCT 58.749 47.619 24.19 0.00 0.00 3.41
940 943 7.496529 TCCTAACTTGTCATTCAGAGTTTTG 57.503 36.000 0.00 0.00 33.27 2.44
947 950 4.583907 TGTCATTCAGAGTTTTGCAATCCA 59.416 37.500 0.00 0.00 0.00 3.41
1223 1226 3.196207 TTCAGAGGTGGTGCCAGCC 62.196 63.158 15.83 8.82 44.62 4.85
1497 1500 1.206132 TCACCGCGATGTTATCCTTGT 59.794 47.619 8.23 0.00 0.00 3.16
1552 1555 2.368548 AGAAAAGAAAATGTGTGGCCCC 59.631 45.455 0.00 0.00 0.00 5.80
1886 1916 1.648504 GGAACCAGATTTCGGGTACG 58.351 55.000 2.74 0.00 43.61 3.67
1961 1991 4.020573 TGGACAGGTCTACGAATGAAACAT 60.021 41.667 0.00 0.00 0.00 2.71
2014 2044 1.352622 TGGAGGTGTGTTGGAAGCCT 61.353 55.000 0.00 0.00 0.00 4.58
2100 4016 0.991920 CTTCCTAGTGAAGGGGGCAA 59.008 55.000 11.22 0.00 45.66 4.52
2129 4045 1.616628 CCTAGCCACTCCACCCCTT 60.617 63.158 0.00 0.00 0.00 3.95
2290 4208 1.002792 GAGGTTCAAACGTGCTTGGAC 60.003 52.381 3.20 3.20 34.50 4.02
2296 4214 0.823356 AAACGTGCTTGGACTGGCAT 60.823 50.000 0.00 0.00 40.66 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
547 550 1.398692 AATTTGTGGTTGGTCGTGCT 58.601 45.000 0.00 0.00 0.00 4.40
905 908 4.081697 TGACAAGTTAGGATCGATGCTTGA 60.082 41.667 25.06 11.33 37.39 3.02
940 943 9.503427 GTAAAATGTACACTTATCTTGGATTGC 57.497 33.333 0.00 0.00 0.00 3.56
947 950 6.315393 CGCCCTGTAAAATGTACACTTATCTT 59.685 38.462 0.00 0.00 0.00 2.40
1223 1226 1.080230 CTCACACTCTCGTGCCTGG 60.080 63.158 0.00 0.00 45.10 4.45
1497 1500 7.038659 ACAAAACATTTTCCTTCATTCGAACA 58.961 30.769 0.00 0.00 0.00 3.18
1552 1555 3.055602 TGTGATCCCATGAACACTCTCAG 60.056 47.826 0.00 0.00 42.84 3.35
1886 1916 1.541588 GGCTTGACTGGTTGGACATTC 59.458 52.381 0.00 0.00 0.00 2.67
1961 1991 6.539173 ACTTAACCCAACACTATTCACATCA 58.461 36.000 0.00 0.00 0.00 3.07
2014 2044 6.070481 TGTGTTAGACTTATGGGCTGATGTTA 60.070 38.462 0.00 0.00 33.70 2.41
2100 4016 3.244946 GGAGTGGCTAGGGTTTTCTTCTT 60.245 47.826 0.00 0.00 0.00 2.52
2129 4045 2.769652 GAATGGCTGCCACCACCAGA 62.770 60.000 25.99 0.00 44.17 3.86
2290 4208 2.232941 AGCTCACCAATTTTGATGCCAG 59.767 45.455 0.00 0.00 0.00 4.85
2296 4214 6.916360 AAGGAATAAGCTCACCAATTTTGA 57.084 33.333 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.