Multiple sequence alignment - TraesCS1A01G238400

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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 TraesCS1A01G238400 chr1A 100.000 2434 0 0 1 2434 424800652 424803085 0.000000e+00 4495
1 TraesCS1A01G238400 chr5A 98.509 2415 33 3 1 2414 365326310 365328722 0.000000e+00 4257
2 TraesCS1A01G238400 chr7D 96.330 2452 43 10 1 2414 473873254 473870812 0.000000e+00 3986
3 TraesCS1A01G238400 chr7D 87.979 965 71 7 1 930 61279328 61278374 0.000000e+00 1098
4 TraesCS1A01G238400 chr4B 96.375 1407 48 2 1010 2414 316989448 316990853 0.000000e+00 2313
5 TraesCS1A01G238400 chr4B 96.370 1405 50 1 1010 2414 146016884 146015481 0.000000e+00 2311
6 TraesCS1A01G238400 chr4B 83.186 339 33 8 596 930 10720712 10720394 3.060000e-74 289
7 TraesCS1A01G238400 chr3A 83.285 1370 147 38 1062 2414 302494803 302493499 0.000000e+00 1186
8 TraesCS1A01G238400 chr7B 84.009 1282 147 32 1166 2414 146357428 146356172 0.000000e+00 1179
9 TraesCS1A01G238400 chr4A 88.599 921 61 6 46 930 191356115 191357027 0.000000e+00 1079
10 TraesCS1A01G238400 chr4A 82.967 364 37 17 594 935 360504383 360504743 3.040000e-79 305
11 TraesCS1A01G238400 chr6A 84.492 1122 125 24 1166 2259 230684191 230683091 0.000000e+00 1062
12 TraesCS1A01G238400 chr3B 87.073 967 78 17 1 930 139391327 139392283 0.000000e+00 1050
13 TraesCS1A01G238400 chr3B 85.521 960 103 20 1062 2000 158633531 158634475 0.000000e+00 970
14 TraesCS1A01G238400 chr3B 84.514 762 85 14 1062 1807 678845618 678844874 0.000000e+00 723
15 TraesCS1A01G238400 chr3B 83.844 359 36 4 594 930 279964297 279964655 3.020000e-84 322
16 TraesCS1A01G238400 chr3B 83.008 359 34 5 594 930 726148310 726148663 1.410000e-77 300
17 TraesCS1A01G238400 chr7A 88.274 759 63 8 1673 2408 678119717 678120472 0.000000e+00 885
18 TraesCS1A01G238400 chr7A 89.137 313 25 5 924 1231 678119294 678119602 4.910000e-102 381
19 TraesCS1A01G238400 chr6D 86.239 654 67 11 1071 1716 172389054 172389692 0.000000e+00 688
20 TraesCS1A01G238400 chr5B 84.615 637 61 22 1805 2414 247445903 247445277 1.250000e-167 599
21 TraesCS1A01G238400 chr5B 84.590 597 69 10 1217 1808 247450243 247449665 2.720000e-159 571
22 TraesCS1A01G238400 chr5B 85.906 149 10 5 1072 1212 247343118 247342973 5.420000e-32 148
23 TraesCS1A01G238400 chr6B 88.915 433 30 13 516 930 417852378 417851946 3.590000e-143 518
24 TraesCS1A01G238400 chr6B 85.622 466 40 4 3 450 417852831 417852375 4.740000e-127 464
25 TraesCS1A01G238400 chr6B 83.565 359 36 16 594 930 436206010 436205653 5.050000e-82 315
26 TraesCS1A01G238400 chr1D 87.907 215 21 3 721 930 195771203 195771417 5.200000e-62 248


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 TraesCS1A01G238400 chr1A 424800652 424803085 2433 False 4495 4495 100.0000 1 2434 1 chr1A.!!$F1 2433
1 TraesCS1A01G238400 chr5A 365326310 365328722 2412 False 4257 4257 98.5090 1 2414 1 chr5A.!!$F1 2413
2 TraesCS1A01G238400 chr7D 473870812 473873254 2442 True 3986 3986 96.3300 1 2414 1 chr7D.!!$R2 2413
3 TraesCS1A01G238400 chr7D 61278374 61279328 954 True 1098 1098 87.9790 1 930 1 chr7D.!!$R1 929
4 TraesCS1A01G238400 chr4B 316989448 316990853 1405 False 2313 2313 96.3750 1010 2414 1 chr4B.!!$F1 1404
5 TraesCS1A01G238400 chr4B 146015481 146016884 1403 True 2311 2311 96.3700 1010 2414 1 chr4B.!!$R2 1404
6 TraesCS1A01G238400 chr3A 302493499 302494803 1304 True 1186 1186 83.2850 1062 2414 1 chr3A.!!$R1 1352
7 TraesCS1A01G238400 chr7B 146356172 146357428 1256 True 1179 1179 84.0090 1166 2414 1 chr7B.!!$R1 1248
8 TraesCS1A01G238400 chr4A 191356115 191357027 912 False 1079 1079 88.5990 46 930 1 chr4A.!!$F1 884
9 TraesCS1A01G238400 chr6A 230683091 230684191 1100 True 1062 1062 84.4920 1166 2259 1 chr6A.!!$R1 1093
10 TraesCS1A01G238400 chr3B 139391327 139392283 956 False 1050 1050 87.0730 1 930 1 chr3B.!!$F1 929
11 TraesCS1A01G238400 chr3B 158633531 158634475 944 False 970 970 85.5210 1062 2000 1 chr3B.!!$F2 938
12 TraesCS1A01G238400 chr3B 678844874 678845618 744 True 723 723 84.5140 1062 1807 1 chr3B.!!$R1 745
13 TraesCS1A01G238400 chr7A 678119294 678120472 1178 False 633 885 88.7055 924 2408 2 chr7A.!!$F1 1484
14 TraesCS1A01G238400 chr6D 172389054 172389692 638 False 688 688 86.2390 1071 1716 1 chr6D.!!$F1 645
15 TraesCS1A01G238400 chr5B 247445277 247450243 4966 True 585 599 84.6025 1217 2414 2 chr5B.!!$R2 1197
16 TraesCS1A01G238400 chr6B 417851946 417852831 885 True 491 518 87.2685 3 930 2 chr6B.!!$R2 927

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
436 456 1.210478 ACTTATGAGGCGCAAGGTGAT 59.79 47.619 10.83 0.0 38.28 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1954 5835 3.642848 ACTGAATGTCCCAGCAAAACAAT 59.357 39.13 0.0 0.0 35.14 2.71 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
55 56 2.261729 TGTGCATCACCCTGGTAAGTA 58.738 47.619 0.00 0.00 32.73 2.24
436 456 1.210478 ACTTATGAGGCGCAAGGTGAT 59.790 47.619 10.83 0.00 38.28 3.06
1259 1331 1.625818 GGGAGAAGAAGCAACCAGAGA 59.374 52.381 0.00 0.00 0.00 3.10
1552 1627 3.315191 GTGTTTTCTGCAAGCCTCTAACA 59.685 43.478 0.00 0.00 0.00 2.41
1580 1655 9.658799 GCTGTTTGGTCATATATATGTAGACAT 57.341 33.333 19.78 0.08 40.22 3.06
1716 1828 6.038161 CACGGCAAGAGTGAATATCCAATTAA 59.962 38.462 0.00 0.00 41.83 1.40
1717 1829 6.601613 ACGGCAAGAGTGAATATCCAATTAAA 59.398 34.615 0.00 0.00 0.00 1.52
1848 5728 6.576778 TTCCCTTCTCTTTATTCCCCTTAG 57.423 41.667 0.00 0.00 0.00 2.18
1954 5835 7.332557 TCTTCAAACTCTTGTGGTACAGTTTA 58.667 34.615 6.47 0.00 41.80 2.01
2056 5942 4.715896 CACATTGAGGACAAAACATCTCG 58.284 43.478 0.00 0.00 39.54 4.04
2129 6020 6.458232 AAGAAGTATGCGAGTCAAGTATCT 57.542 37.500 0.00 0.00 0.00 1.98
2418 6333 3.076092 AGCTTCACTGAGGCAGGG 58.924 61.111 14.98 0.00 37.11 4.45
2419 6334 2.045536 GCTTCACTGAGGCAGGGG 60.046 66.667 8.22 0.00 35.28 4.79
2420 6335 2.045536 CTTCACTGAGGCAGGGGC 60.046 66.667 0.00 0.00 35.28 5.80
2421 6336 3.965539 CTTCACTGAGGCAGGGGCG 62.966 68.421 0.00 0.00 42.47 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
436 456 2.743636 CCTGTTACAGGCGAAGAAGA 57.256 50.000 19.16 0.00 45.13 2.87
709 729 3.983741 ACTCCTTTCTTCTCTGTCGTTG 58.016 45.455 0.00 0.00 0.00 4.10
713 733 6.334102 TCAACTACTCCTTTCTTCTCTGTC 57.666 41.667 0.00 0.00 0.00 3.51
889 928 4.082679 CGCAGGACTGTAGAGTAAAAGACT 60.083 45.833 0.00 0.00 42.90 3.24
1552 1627 9.658799 GTCTACATATATATGACCAAACAGCAT 57.341 33.333 26.05 4.85 37.15 3.79
1716 1828 8.908786 TTTATCTGTCTGACTTCATGAACTTT 57.091 30.769 3.38 0.00 0.00 2.66
1717 1829 8.908786 TTTTATCTGTCTGACTTCATGAACTT 57.091 30.769 3.38 0.00 0.00 2.66
1848 5728 6.553852 TGATCTAGGGGTAGGATAAACAGAAC 59.446 42.308 0.00 0.00 0.00 3.01
1954 5835 3.642848 ACTGAATGTCCCAGCAAAACAAT 59.357 39.130 0.00 0.00 35.14 2.71
2056 5942 5.689383 TCTGCAGTAGATGGAAAACAAAC 57.311 39.130 14.67 0.00 0.00 2.93
2061 5950 4.640771 AGGTTCTGCAGTAGATGGAAAA 57.359 40.909 14.67 0.00 34.80 2.29
2062 5951 4.777896 AGTAGGTTCTGCAGTAGATGGAAA 59.222 41.667 14.67 0.00 34.80 3.13
2129 6020 5.769162 TGATTTTCATCAGTTGGTCATCACA 59.231 36.000 0.00 0.00 34.22 3.58


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

AutoCloner maintained by Alex Coulton.