Multiple sequence alignment - TraesCS5A01G339900

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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 TraesCS5A01G339900 chr5A 100.000 2460 0 0 1 2460 546846144 546848603 0.000000e+00 4543
1 TraesCS5A01G339900 chr5A 95.864 2466 91 8 1 2460 640388905 640386445 0.000000e+00 3978
2 TraesCS5A01G339900 chr5A 97.344 1958 44 6 1 1953 697625529 697627483 0.000000e+00 3321
3 TraesCS5A01G339900 chr5A 96.142 1918 65 5 547 2460 593748119 593750031 0.000000e+00 3123
4 TraesCS5A01G339900 chr5A 97.674 129 2 1 4 131 697642073 697641945 1.150000e-53 220
5 TraesCS5A01G339900 chr4D 96.061 2488 64 10 1 2460 392724690 392722209 0.000000e+00 4021
6 TraesCS5A01G339900 chr7D 95.981 2488 59 10 1 2460 538836207 538838681 0.000000e+00 4002
7 TraesCS5A01G339900 chr7D 94.496 2489 65 14 1 2460 426837080 426834635 0.000000e+00 3771
8 TraesCS5A01G339900 chr5D 95.740 2488 62 10 1 2460 422770524 422772995 0.000000e+00 3967
9 TraesCS5A01G339900 chr3D 95.540 2489 59 15 1 2460 52842598 52845063 0.000000e+00 3934
10 TraesCS5A01G339900 chr3D 97.503 961 24 0 1500 2460 534218086 534217126 0.000000e+00 1642
11 TraesCS5A01G339900 chr1A 97.957 1958 35 3 1 1953 13813778 13811821 0.000000e+00 3389
12 TraesCS5A01G339900 chr1A 97.704 1960 37 5 1 1953 34337602 34339560 0.000000e+00 3363
13 TraesCS5A01G339900 chr1A 97.446 1958 45 3 1 1953 566074718 566072761 0.000000e+00 3334
14 TraesCS5A01G339900 chr4A 97.753 1958 36 4 1 1953 628882146 628884100 0.000000e+00 3365
15 TraesCS5A01G339900 chr7A 97.651 1958 37 5 1 1953 576403988 576405941 0.000000e+00 3352
16 TraesCS5A01G339900 chr2A 97.344 1958 47 3 1 1953 752883016 752881059 0.000000e+00 3323
17 TraesCS5A01G339900 chr2A 77.204 465 83 19 136 589 773340754 773340302 1.460000e-62 250


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 TraesCS5A01G339900 chr5A 546846144 546848603 2459 False 4543 4543 100.000 1 2460 1 chr5A.!!$F1 2459
1 TraesCS5A01G339900 chr5A 640386445 640388905 2460 True 3978 3978 95.864 1 2460 1 chr5A.!!$R1 2459
2 TraesCS5A01G339900 chr5A 697625529 697627483 1954 False 3321 3321 97.344 1 1953 1 chr5A.!!$F3 1952
3 TraesCS5A01G339900 chr5A 593748119 593750031 1912 False 3123 3123 96.142 547 2460 1 chr5A.!!$F2 1913
4 TraesCS5A01G339900 chr4D 392722209 392724690 2481 True 4021 4021 96.061 1 2460 1 chr4D.!!$R1 2459
5 TraesCS5A01G339900 chr7D 538836207 538838681 2474 False 4002 4002 95.981 1 2460 1 chr7D.!!$F1 2459
6 TraesCS5A01G339900 chr7D 426834635 426837080 2445 True 3771 3771 94.496 1 2460 1 chr7D.!!$R1 2459
7 TraesCS5A01G339900 chr5D 422770524 422772995 2471 False 3967 3967 95.740 1 2460 1 chr5D.!!$F1 2459
8 TraesCS5A01G339900 chr3D 52842598 52845063 2465 False 3934 3934 95.540 1 2460 1 chr3D.!!$F1 2459
9 TraesCS5A01G339900 chr3D 534217126 534218086 960 True 1642 1642 97.503 1500 2460 1 chr3D.!!$R1 960
10 TraesCS5A01G339900 chr1A 13811821 13813778 1957 True 3389 3389 97.957 1 1953 1 chr1A.!!$R1 1952
11 TraesCS5A01G339900 chr1A 34337602 34339560 1958 False 3363 3363 97.704 1 1953 1 chr1A.!!$F1 1952
12 TraesCS5A01G339900 chr1A 566072761 566074718 1957 True 3334 3334 97.446 1 1953 1 chr1A.!!$R2 1952
13 TraesCS5A01G339900 chr4A 628882146 628884100 1954 False 3365 3365 97.753 1 1953 1 chr4A.!!$F1 1952
14 TraesCS5A01G339900 chr7A 576403988 576405941 1953 False 3352 3352 97.651 1 1953 1 chr7A.!!$F1 1952
15 TraesCS5A01G339900 chr2A 752881059 752883016 1957 True 3323 3323 97.344 1 1953 1 chr2A.!!$R1 1952

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
155 159 4.068599 CACTCACTCTCACTCACTCACTA 58.931 47.826 0.0 0.0 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2136 2211 0.109086 CAGAGGTGCACGAAGACGAT 60.109 55.0 11.45 0.0 42.66 3.73 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
155 159 4.068599 CACTCACTCTCACTCACTCACTA 58.931 47.826 0.00 0.0 0.00 2.74
591 596 6.747414 TTGGATGTGCTACTATGGTAAGAT 57.253 37.500 0.00 0.0 0.00 2.40
742 748 9.136323 TCATGTGTTAGCTAAATCTCTGATAGA 57.864 33.333 7.99 0.0 39.02 1.98
794 800 8.161699 TGGTCTAACTGAATTTCTTTGTTACC 57.838 34.615 0.00 6.7 0.00 2.85
1094 1126 4.408270 AGTCAGCTTGTGGATGATGTATCT 59.592 41.667 0.00 0.0 42.56 1.98
1403 1447 1.260544 GGTGCAAGGAAAAGCTGGAT 58.739 50.000 0.00 0.0 0.00 3.41
1437 1481 4.990526 AGTTGTCATGGAGGAGTGATTTT 58.009 39.130 0.00 0.0 0.00 1.82
1687 1756 9.833917 GTTAAGAACCTTATTATCTAAGCCTGT 57.166 33.333 0.00 0.0 0.00 4.00
1702 1774 4.826274 AGCCTGTTGCAGTTTCTATCTA 57.174 40.909 0.00 0.0 44.83 1.98
2071 2143 3.017442 TCCTCTTCGTCTTCATCGATGT 58.983 45.455 24.09 0.0 37.18 3.06
2126 2198 0.457853 GTTGGCTGTGCGACGATCTA 60.458 55.000 0.00 0.0 0.00 1.98
2156 2231 1.007271 CGTCTTCGTGCACCTCTGT 60.007 57.895 12.15 0.0 0.00 3.41
2159 2234 0.464036 TCTTCGTGCACCTCTGTTGT 59.536 50.000 12.15 0.0 0.00 3.32
2317 2392 1.227764 CCATAGCGCTGCTCCATGT 60.228 57.895 22.90 0.0 40.44 3.21
2338 2413 1.066573 GCTGCTTCTCCTTGCTAGTCA 60.067 52.381 0.00 0.0 0.00 3.41
2408 2483 0.824109 TACCTCATGGCGACCTTCAG 59.176 55.000 0.00 0.0 36.63 3.02
2438 2513 2.357034 GAGTTCTTGGTCGCCGCA 60.357 61.111 0.00 0.0 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
155 159 0.555769 AGAGAGAGCTCGGGGAGATT 59.444 55.000 8.37 0.0 45.98 2.40
591 596 8.908903 ACATGAAAACCACTAACAATTAGTTGA 58.091 29.630 4.81 0.0 43.70 3.18
794 800 6.260377 ACATATCAATGTTTGTCTGAATGCG 58.740 36.000 0.00 0.0 44.07 4.73
1008 1040 4.734266 TCAGCCTCTATCTCATGAGCTTA 58.266 43.478 18.36 10.8 0.00 3.09
1094 1126 5.949354 CCCATCCTGGTAATCAAACAACTTA 59.051 40.000 0.00 0.0 35.17 2.24
1403 1447 6.881065 CCTCCATGACAACTTCTTTGATCTTA 59.119 38.462 0.00 0.0 38.73 2.10
1437 1481 8.908903 CATATTTACTTACCAACCATGCCTAAA 58.091 33.333 0.00 0.0 0.00 1.85
1644 1713 6.247229 TCTTAACTTAGCATCAGGGCATTA 57.753 37.500 0.00 0.0 35.83 1.90
1957 2029 6.572509 GCAGGACAGACAACTAAGTGAATCTA 60.573 42.308 0.00 0.0 0.00 1.98
2071 2143 1.123077 CGTCCTCCTCCCATCATCAA 58.877 55.000 0.00 0.0 0.00 2.57
2108 2180 0.459899 ATAGATCGTCGCACAGCCAA 59.540 50.000 0.00 0.0 0.00 4.52
2126 2198 2.031807 CACGAAGACGATGACGACCTAT 59.968 50.000 0.00 0.0 42.66 2.57
2136 2211 0.109086 CAGAGGTGCACGAAGACGAT 60.109 55.000 11.45 0.0 42.66 3.73
2156 2231 5.199024 AGCTACATCAAATGCAAACACAA 57.801 34.783 0.00 0.0 0.00 3.33
2159 2234 4.983538 CACAAGCTACATCAAATGCAAACA 59.016 37.500 0.00 0.0 0.00 2.83
2317 2392 0.979665 ACTAGCAAGGAGAAGCAGCA 59.020 50.000 0.00 0.0 0.00 4.41
2338 2413 2.903135 CAGAGGAAGTGAGGAAGAAGGT 59.097 50.000 0.00 0.0 0.00 3.50
2408 2483 3.119424 CCAAGAACTCTTCCTCGACTACC 60.119 52.174 0.00 0.0 33.11 3.18


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

AutoCloner maintained by Alex Coulton.