Multiple sequence alignment - TraesCS5B01G453400

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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 TraesCS5B01G453400 chr5B 100.000 2501 0 0 1 2501 626141555 626139055 0.000000e+00 4619
1 TraesCS5B01G453400 chr5B 92.142 2507 175 17 1 2501 626085855 626083365 0.000000e+00 3518
2 TraesCS5B01G453400 chr5B 92.112 2472 176 13 36 2501 631355096 631352638 0.000000e+00 3467
3 TraesCS5B01G453400 chr5B 88.743 2434 246 18 82 2501 626107817 626105398 0.000000e+00 2952
4 TraesCS5B01G453400 chr5B 91.241 1998 169 6 1 1996 631379602 631377609 0.000000e+00 2715
5 TraesCS5B01G453400 chr5B 89.526 506 44 7 1996 2497 631368714 631368214 1.260000e-177 632
6 TraesCS5B01G453400 chr5D 96.527 2505 80 6 1 2501 502538024 502535523 0.000000e+00 4137
7 TraesCS5B01G453400 chr5D 96.883 1957 52 6 548 2501 502365265 502363315 0.000000e+00 3267
8 TraesCS5B01G453400 chr5A 86.924 2516 267 40 3 2501 631085825 631083355 0.000000e+00 2767
9 TraesCS5B01G453400 chr5A 89.021 1093 82 22 1416 2501 631111365 631110304 0.000000e+00 1319
10 TraesCS5B01G453400 chr5A 85.696 762 101 8 3 757 631112123 631111363 0.000000e+00 797
11 TraesCS5B01G453400 chr5A 79.103 914 150 28 3 901 631254731 631253844 2.140000e-165 592
12 TraesCS5B01G453400 chr5A 83.333 222 30 5 746 960 631260377 631260156 5.460000e-47 198


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 TraesCS5B01G453400 chr5B 626139055 626141555 2500 True 4619 4619 100.0000 1 2501 1 chr5B.!!$R3 2500
1 TraesCS5B01G453400 chr5B 626083365 626085855 2490 True 3518 3518 92.1420 1 2501 1 chr5B.!!$R1 2500
2 TraesCS5B01G453400 chr5B 631352638 631355096 2458 True 3467 3467 92.1120 36 2501 1 chr5B.!!$R4 2465
3 TraesCS5B01G453400 chr5B 626105398 626107817 2419 True 2952 2952 88.7430 82 2501 1 chr5B.!!$R2 2419
4 TraesCS5B01G453400 chr5B 631377609 631379602 1993 True 2715 2715 91.2410 1 1996 1 chr5B.!!$R6 1995
5 TraesCS5B01G453400 chr5B 631368214 631368714 500 True 632 632 89.5260 1996 2497 1 chr5B.!!$R5 501
6 TraesCS5B01G453400 chr5D 502535523 502538024 2501 True 4137 4137 96.5270 1 2501 1 chr5D.!!$R2 2500
7 TraesCS5B01G453400 chr5D 502363315 502365265 1950 True 3267 3267 96.8830 548 2501 1 chr5D.!!$R1 1953
8 TraesCS5B01G453400 chr5A 631083355 631085825 2470 True 2767 2767 86.9240 3 2501 1 chr5A.!!$R1 2498
9 TraesCS5B01G453400 chr5A 631110304 631112123 1819 True 1058 1319 87.3585 3 2501 2 chr5A.!!$R4 2498
10 TraesCS5B01G453400 chr5A 631253844 631254731 887 True 592 592 79.1030 3 901 1 chr5A.!!$R2 898

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
994 1021 0.60813 CCAACCTCCGTCACAGATCA 59.392 55.0 0.0 0.0 0.0 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2171 2212 0.388907 CGATTGCTTGCCCACCAAAG 60.389 55.0 0.0 0.0 31.94 2.77 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
24 25 4.517075 TCTCAACGCCAAAATCATGTACAA 59.483 37.500 0.00 0.00 0.00 2.41
50 52 2.330231 AACATGCCACGATTGAAACG 57.670 45.000 0.00 0.00 0.00 3.60
126 133 3.838244 TCCATCCTTTTCTACATCCGG 57.162 47.619 0.00 0.00 0.00 5.14
129 136 3.278574 CATCCTTTTCTACATCCGGCAA 58.721 45.455 0.00 0.00 0.00 4.52
226 233 2.038426 TGGGAAGTGAAAAGCTCGATGA 59.962 45.455 0.00 0.00 0.00 2.92
242 250 2.678336 CGATGAAAAGAGGTTAGTGGCC 59.322 50.000 0.00 0.00 0.00 5.36
259 267 1.404583 GGCCGTCGTACAGGTACAAAT 60.405 52.381 9.97 0.00 35.87 2.32
266 274 3.998341 TCGTACAGGTACAAATTGGAAGC 59.002 43.478 9.97 0.00 35.87 3.86
279 287 6.017687 ACAAATTGGAAGCAGAATTTTCTTGC 60.018 34.615 0.00 6.62 34.74 4.01
292 300 1.369839 TTCTTGCCGTGCGTGAACAA 61.370 50.000 0.00 0.00 0.00 2.83
301 309 1.210155 GCGTGAACAACTCCATGCC 59.790 57.895 0.00 0.00 38.88 4.40
440 451 5.337250 CGGGGATATGATCGAATTGGTTCTA 60.337 44.000 0.00 0.00 32.00 2.10
672 692 2.184322 CGGCAGCGTACCTGTGAT 59.816 61.111 11.47 0.00 43.71 3.06
987 1014 2.606519 CCCCTCCAACCTCCGTCA 60.607 66.667 0.00 0.00 0.00 4.35
994 1021 0.608130 CCAACCTCCGTCACAGATCA 59.392 55.000 0.00 0.00 0.00 2.92
1150 1177 0.260230 TTGGGTGTTTGAAGAGGCCA 59.740 50.000 5.01 0.00 0.00 5.36
1480 1512 2.751436 GGATCCAGGCGCTTGCAA 60.751 61.111 15.01 4.55 41.71 4.08
1522 1554 2.045536 CTTCCTGGCAGGCAGTCC 60.046 66.667 29.02 0.00 34.61 3.85
1565 1597 2.988570 AGTCGACGACTCCTACAATCT 58.011 47.619 24.44 0.00 38.71 2.40
1593 1625 8.801715 TTGTTGCTTCATTTTCAAGTAAGATC 57.198 30.769 0.00 0.00 0.00 2.75
1714 1752 4.024387 CGAAAAGTCTTCGGTGGATTTTCA 60.024 41.667 12.89 0.00 36.78 2.69
2171 2212 2.433146 GGTCCGCCCCCTAAGAGAC 61.433 68.421 0.00 0.00 0.00 3.36
2195 2236 0.527565 GTGGGCAAGCAATCGATGTT 59.472 50.000 0.00 0.00 0.00 2.71
2424 2473 7.910441 CCAATTTTTCATGGCTAGATTTGTT 57.090 32.000 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 4.022416 GGCATGTTTTGGTCTTGTACATGA 60.022 41.667 15.42 7.33 45.46 3.07
21 22 1.066908 CGTGGCATGTTTTGGTCTTGT 59.933 47.619 0.00 0.00 0.00 3.16
24 25 1.909700 ATCGTGGCATGTTTTGGTCT 58.090 45.000 6.60 0.00 0.00 3.85
50 52 4.236147 TGCAATGTGTTGTGTGATATTGC 58.764 39.130 11.55 11.55 46.26 3.56
126 133 3.595709 TGCTAATATAAACCGCGTTGC 57.404 42.857 4.92 0.00 0.00 4.17
129 136 3.735591 ACCATGCTAATATAAACCGCGT 58.264 40.909 4.92 0.00 0.00 6.01
142 149 1.845791 ACCATCACCATGACCATGCTA 59.154 47.619 4.53 0.00 37.49 3.49
203 210 2.925724 TCGAGCTTTTCACTTCCCAAA 58.074 42.857 0.00 0.00 0.00 3.28
209 216 5.049129 CCTCTTTTCATCGAGCTTTTCACTT 60.049 40.000 0.00 0.00 0.00 3.16
226 233 1.607251 CGACGGCCACTAACCTCTTTT 60.607 52.381 2.24 0.00 0.00 2.27
242 250 3.577667 TCCAATTTGTACCTGTACGACG 58.422 45.455 0.00 0.00 38.85 5.12
259 267 3.552684 CGGCAAGAAAATTCTGCTTCCAA 60.553 43.478 13.42 0.00 37.65 3.53
266 274 1.330306 CGCACGGCAAGAAAATTCTG 58.670 50.000 0.00 0.00 37.65 3.02
279 287 1.227999 ATGGAGTTGTTCACGCACGG 61.228 55.000 0.00 0.00 0.00 4.94
301 309 4.906792 GCGCTGAGCCCTAGCCAG 62.907 72.222 0.00 0.00 41.25 4.85
334 342 2.307098 CTCCAGACATTTTCCCAGTCCT 59.693 50.000 0.00 0.00 32.82 3.85
383 392 1.320344 TGCATACGTCCCTTCGCTCT 61.320 55.000 0.00 0.00 0.00 4.09
389 398 0.392998 CCTTGCTGCATACGTCCCTT 60.393 55.000 1.84 0.00 0.00 3.95
440 451 2.617021 CCTTATTAACCCCGTGCACACT 60.617 50.000 18.64 0.00 0.00 3.55
491 503 3.650139 ACTAACAGTCACCTTACAAGCG 58.350 45.455 0.00 0.00 0.00 4.68
672 692 2.288763 TGACGCTGCATCAGTTTCAGTA 60.289 45.455 0.00 0.00 33.43 2.74
987 1014 1.208052 CCTTCCATCACCGTGATCTGT 59.792 52.381 11.24 0.00 34.28 3.41
994 1021 1.789576 AAAGGCCCTTCCATCACCGT 61.790 55.000 0.00 0.00 37.29 4.83
1043 1070 3.437795 CCTCGTCGGTACCTGCGT 61.438 66.667 19.56 0.00 0.00 5.24
1052 1079 2.278857 CCATCTTCGCCTCGTCGG 60.279 66.667 0.00 0.00 0.00 4.79
1150 1177 2.777692 TCCAACTTTGTTCCTCCTCTGT 59.222 45.455 0.00 0.00 0.00 3.41
1372 1404 2.342650 GCACCACCCGCACATCATT 61.343 57.895 0.00 0.00 0.00 2.57
1401 1433 2.405805 TGAAATCACCCGCGCCATG 61.406 57.895 0.00 0.00 0.00 3.66
1402 1434 2.045438 TGAAATCACCCGCGCCAT 60.045 55.556 0.00 0.00 0.00 4.40
1421 1453 4.459089 GGGAGTGACGAGGCAGCC 62.459 72.222 1.84 1.84 0.00 4.85
1565 1597 9.429359 TCTTACTTGAAAATGAAGCAACAAAAA 57.571 25.926 0.00 0.00 0.00 1.94
1593 1625 9.081997 GGATGTAAATATTTCTAGAGATCAGCG 57.918 37.037 3.39 0.00 0.00 5.18
1714 1752 6.420638 TCAATGACATGATCAACTTCCATCT 58.579 36.000 0.00 0.00 41.93 2.90
1837 1875 7.975616 AGATTTCCACCAATAACATCGAAATTG 59.024 33.333 0.00 0.00 30.73 2.32
2171 2212 0.388907 CGATTGCTTGCCCACCAAAG 60.389 55.000 0.00 0.00 31.94 2.77
2195 2236 3.592059 CGTAGCAGTAAAGCCTTACCAA 58.408 45.455 1.48 0.00 38.59 3.67
2423 2472 6.945435 TCTTATTGTCATCTGCCTACCAAAAA 59.055 34.615 0.00 0.00 0.00 1.94
2424 2473 6.480763 TCTTATTGTCATCTGCCTACCAAAA 58.519 36.000 0.00 0.00 0.00 2.44


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

AutoCloner maintained by Alex Coulton.