Multiple sequence alignment - TraesCS3D01G294500

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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 TraesCS3D01G294500 chr3D 100.000 2627 0 0 1 2627 405843481 405846107 0.000000e+00 4852
1 TraesCS3D01G294500 chr3D 97.552 2165 27 6 1 2139 502027923 502025759 0.000000e+00 3681
2 TraesCS3D01G294500 chr3D 98.717 1949 20 1 1 1949 367348009 367349952 0.000000e+00 3456
3 TraesCS3D01G294500 chr3D 97.273 1797 28 4 414 2193 94447180 94448972 0.000000e+00 3027
4 TraesCS3D01G294500 chr3D 95.918 784 9 5 1171 1949 210993195 210993960 0.000000e+00 1249
5 TraesCS3D01G294500 chr3D 87.262 526 47 18 1984 2501 502020761 502020248 1.360000e-162 582
6 TraesCS3D01G294500 chr3D 93.333 300 20 0 2146 2445 287304161 287304460 6.670000e-121 444
7 TraesCS3D01G294500 chr2D 96.091 2558 48 6 1 2509 601044638 601042084 0.000000e+00 4122
8 TraesCS3D01G294500 chr2D 96.619 2159 62 8 1 2153 537201180 537203333 0.000000e+00 3572
9 TraesCS3D01G294500 chr2D 98.820 1949 23 0 1 1949 158254585 158256533 0.000000e+00 3472
10 TraesCS3D01G294500 chr4D 96.855 2162 51 10 1 2161 480148422 480146277 0.000000e+00 3600
11 TraesCS3D01G294500 chr4D 96.533 2163 56 12 1 2162 41949485 41947341 0.000000e+00 3561
12 TraesCS3D01G294500 chr4D 93.241 503 17 6 2023 2509 480145264 480144763 0.000000e+00 725
13 TraesCS3D01G294500 chr4D 93.533 433 25 3 2078 2509 508996464 508996034 2.200000e-180 641
14 TraesCS3D01G294500 chr4D 91.315 426 23 3 2097 2509 61992349 61992773 1.060000e-158 569
15 TraesCS3D01G294500 chr4D 90.281 391 24 3 2133 2509 508997553 508997163 1.400000e-137 499
16 TraesCS3D01G294500 chr4D 99.184 245 1 1 2266 2509 61993807 61994051 8.630000e-120 440
17 TraesCS3D01G294500 chr4D 100.000 121 0 0 2507 2627 61992888 61993008 9.460000e-55 224
18 TraesCS3D01G294500 chr4D 100.000 121 0 0 2507 2627 61994166 61994286 9.460000e-55 224
19 TraesCS3D01G294500 chr4D 100.000 121 0 0 2507 2627 480144648 480144528 9.460000e-55 224
20 TraesCS3D01G294500 chr4D 100.000 121 0 0 2507 2627 508995919 508995799 9.460000e-55 224
21 TraesCS3D01G294500 chr4D 100.000 121 0 0 2507 2627 508997048 508996928 9.460000e-55 224
22 TraesCS3D01G294500 chr6D 96.534 2135 55 3 1 2118 18600961 18603093 0.000000e+00 3515
23 TraesCS3D01G294500 chr6D 95.765 425 6 1 2097 2509 18603582 18604006 0.000000e+00 675
24 TraesCS3D01G294500 chr6D 100.000 121 0 0 2507 2627 18604121 18604241 9.460000e-55 224
25 TraesCS3D01G294500 chr6D 100.000 121 0 0 2507 2627 400560931 400561051 9.460000e-55 224
26 TraesCS3D01G294500 chr5D 98.871 1949 22 0 1 1949 156737576 156739524 0.000000e+00 3478
27 TraesCS3D01G294500 chr5D 92.995 414 26 3 2098 2509 156741010 156741422 3.740000e-168 601
28 TraesCS3D01G294500 chr5D 100.000 121 0 0 2507 2627 156741537 156741657 9.460000e-55 224
29 TraesCS3D01G294500 chr7D 97.442 1955 26 6 1 1949 116696448 116698384 0.000000e+00 3312
30 TraesCS3D01G294500 chr7D 97.807 1505 15 2 698 2185 105213525 105215028 0.000000e+00 2580
31 TraesCS3D01G294500 chr7D 86.921 367 35 9 1878 2239 53446223 53446581 1.460000e-107 399
32 TraesCS3D01G294500 chr1D 96.692 393 12 1 2118 2509 318140072 318140464 0.000000e+00 652
33 TraesCS3D01G294500 chr1D 90.281 391 24 3 2133 2509 485466053 485465663 1.400000e-137 499
34 TraesCS3D01G294500 chr1D 100.000 121 0 0 2507 2627 485465548 485465428 9.460000e-55 224
35 TraesCS3D01G294500 chr4B 84.554 505 57 10 1951 2451 574709088 574709575 5.090000e-132 481
36 TraesCS3D01G294500 chr2A 87.893 413 44 4 1878 2285 445749709 445749298 5.090000e-132 481
37 TraesCS3D01G294500 chr2A 88.049 410 43 4 1878 2282 628681017 628681425 5.090000e-132 481
38 TraesCS3D01G294500 chr7B 85.411 377 48 5 1878 2250 197006351 197006724 4.100000e-103 385
39 TraesCS3D01G294500 chr1B 84.103 390 56 5 1878 2267 676753002 676752619 3.190000e-99 372


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 TraesCS3D01G294500 chr3D 405843481 405846107 2626 False 4852.000000 4852 100.000000 1 2627 1 chr3D.!!$F5 2626
1 TraesCS3D01G294500 chr3D 502025759 502027923 2164 True 3681.000000 3681 97.552000 1 2139 1 chr3D.!!$R2 2138
2 TraesCS3D01G294500 chr3D 367348009 367349952 1943 False 3456.000000 3456 98.717000 1 1949 1 chr3D.!!$F4 1948
3 TraesCS3D01G294500 chr3D 94447180 94448972 1792 False 3027.000000 3027 97.273000 414 2193 1 chr3D.!!$F1 1779
4 TraesCS3D01G294500 chr3D 210993195 210993960 765 False 1249.000000 1249 95.918000 1171 1949 1 chr3D.!!$F2 778
5 TraesCS3D01G294500 chr3D 502020248 502020761 513 True 582.000000 582 87.262000 1984 2501 1 chr3D.!!$R1 517
6 TraesCS3D01G294500 chr2D 601042084 601044638 2554 True 4122.000000 4122 96.091000 1 2509 1 chr2D.!!$R1 2508
7 TraesCS3D01G294500 chr2D 537201180 537203333 2153 False 3572.000000 3572 96.619000 1 2153 1 chr2D.!!$F2 2152
8 TraesCS3D01G294500 chr2D 158254585 158256533 1948 False 3472.000000 3472 98.820000 1 1949 1 chr2D.!!$F1 1948
9 TraesCS3D01G294500 chr4D 41947341 41949485 2144 True 3561.000000 3561 96.533000 1 2162 1 chr4D.!!$R1 2161
10 TraesCS3D01G294500 chr4D 480144528 480148422 3894 True 1516.333333 3600 96.698667 1 2627 3 chr4D.!!$R2 2626
11 TraesCS3D01G294500 chr4D 508995799 508997553 1754 True 397.000000 641 95.953500 2078 2627 4 chr4D.!!$R3 549
12 TraesCS3D01G294500 chr4D 61992349 61994286 1937 False 364.250000 569 97.624750 2097 2627 4 chr4D.!!$F1 530
13 TraesCS3D01G294500 chr6D 18600961 18604241 3280 False 1471.333333 3515 97.433000 1 2627 3 chr6D.!!$F2 2626
14 TraesCS3D01G294500 chr5D 156737576 156741657 4081 False 1434.333333 3478 97.288667 1 2627 3 chr5D.!!$F1 2626
15 TraesCS3D01G294500 chr7D 116696448 116698384 1936 False 3312.000000 3312 97.442000 1 1949 1 chr7D.!!$F3 1948
16 TraesCS3D01G294500 chr7D 105213525 105215028 1503 False 2580.000000 2580 97.807000 698 2185 1 chr7D.!!$F2 1487
17 TraesCS3D01G294500 chr1D 485465428 485466053 625 True 361.500000 499 95.140500 2133 2627 2 chr1D.!!$R1 494

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
40 41 1.212195 GAGCAAGGGTTAGGGTTAGGG 59.788 57.143 0.00 0.0 0.00 3.53 F
852 856 2.925563 GCTGTGCAAATCCAGTTAATGC 59.074 45.455 4.22 0.0 37.52 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1498 1502 2.362077 GGTTTTCCTTGAGCTTCAGCAA 59.638 45.455 0.75 0.0 39.31 3.91 R
2268 7684 2.430694 AGAAGCACTTTGGGTTTTGGTC 59.569 45.455 0.00 0.0 0.00 4.02 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
40 41 1.212195 GAGCAAGGGTTAGGGTTAGGG 59.788 57.143 0.00 0.0 0.00 3.53
79 80 6.263617 GGATTTTTGTGTGTAGGTGGTCTTTA 59.736 38.462 0.00 0.0 0.00 1.85
219 220 4.456280 AGATCTGATAGTGTTGTGCGAA 57.544 40.909 0.00 0.0 0.00 4.70
852 856 2.925563 GCTGTGCAAATCCAGTTAATGC 59.074 45.455 4.22 0.0 37.52 3.56
953 957 5.123979 CCTTCTAATTTTTCCAGGAAGGTCG 59.876 44.000 1.07 0.0 42.56 4.79
1362 1366 5.592282 TCAAGCAACTGTCATCCAAAACTTA 59.408 36.000 0.00 0.0 0.00 2.24
1498 1502 1.074405 TGAAGCTCCAGGTTGCTGATT 59.926 47.619 9.83 0.0 39.71 2.57
2055 3669 4.284746 AGCCTAGATGATAGGTTTAGGTGC 59.715 45.833 3.05 0.0 37.06 5.01
2268 7684 1.957186 TTTTCGTTGACCCCGAGCG 60.957 57.895 0.00 0.0 35.49 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 3.081087 TCCTAACCCTAACCCTAACCCTT 59.919 47.826 0.00 0.0 0.00 3.95
40 41 6.995686 ACACAAAAATCCCCAAATTTCCTAAC 59.004 34.615 0.00 0.0 0.00 2.34
79 80 9.927668 AATCAAATCAAACGAAATCCTAACAAT 57.072 25.926 0.00 0.0 0.00 2.71
852 856 3.009723 CAGTACCTAATGTTGGCACTGG 58.990 50.000 5.49 0.0 42.39 4.00
953 957 3.492482 CCACTGAACAAACCCACAATTCC 60.492 47.826 0.00 0.0 0.00 3.01
1293 1297 7.068716 AGGAGTTCATACTTTTGTTGAAGCTTT 59.931 33.333 0.00 0.0 33.84 3.51
1362 1366 9.799106 TCCTTCTCTTTCATATTCTTCAACTTT 57.201 29.630 0.00 0.0 0.00 2.66
1498 1502 2.362077 GGTTTTCCTTGAGCTTCAGCAA 59.638 45.455 0.75 0.0 39.31 3.91
2055 3669 2.434359 GCTCGGGGTGGACGAAAG 60.434 66.667 0.00 0.0 40.16 2.62
2268 7684 2.430694 AGAAGCACTTTGGGTTTTGGTC 59.569 45.455 0.00 0.0 0.00 4.02


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

AutoCloner maintained by Alex Coulton.