Multiple sequence alignment - TraesCS2D01G530500

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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 TraesCS2D01G530500 chr2D 100.000 2303 0 0 1 2303 616988191 616990493 0.000000e+00 4253.0
1 TraesCS2D01G530500 chr2D 99.016 1930 17 1 1 1928 536084126 536082197 0.000000e+00 3458.0
2 TraesCS2D01G530500 chr2D 98.395 1931 27 3 1 1928 8945881 8947810 0.000000e+00 3391.0
3 TraesCS2D01G530500 chr2D 97.989 895 18 0 1034 1928 577708574 577707680 0.000000e+00 1554.0
4 TraesCS2D01G530500 chr2D 98.820 339 4 0 1965 2303 536082116 536081778 2.530000e-169 604.0
5 TraesCS2D01G530500 chr2D 98.230 339 6 0 1965 2303 8947891 8948229 5.480000e-166 593.0
6 TraesCS2D01G530500 chr2D 92.798 361 4 1 1965 2303 577707599 577707239 9.500000e-139 503.0
7 TraesCS2D01G530500 chr2D 100.000 50 0 0 1920 1969 8947888 8947937 2.440000e-15 93.5
8 TraesCS2D01G530500 chr2D 100.000 50 0 0 1920 1969 536082119 536082070 2.440000e-15 93.5
9 TraesCS2D01G530500 chr2D 100.000 50 0 0 1920 1969 577707602 577707553 2.440000e-15 93.5
10 TraesCS2D01G530500 chr5D 97.554 2330 27 14 1 2303 357884349 357886675 0.000000e+00 3960.0
11 TraesCS2D01G530500 chr5D 95.497 1288 40 6 1 1270 385494708 385493421 0.000000e+00 2041.0
12 TraesCS2D01G530500 chr5D 86.486 518 57 6 1356 1869 385493140 385492632 7.190000e-155 556.0
13 TraesCS2D01G530500 chr5D 97.619 42 1 0 1928 1969 357886342 357886383 3.170000e-09 73.1
14 TraesCS2D01G530500 chr3D 98.785 1564 16 1 1 1561 420457956 420459519 0.000000e+00 2780.0
15 TraesCS2D01G530500 chr3D 99.115 339 3 0 1965 2303 420459892 420460230 5.440000e-171 610.0
16 TraesCS2D01G530500 chr3D 100.000 50 0 0 1920 1969 420459889 420459938 2.440000e-15 93.5
17 TraesCS2D01G530500 chr7B 95.764 1322 31 7 1 1306 659927198 659925886 0.000000e+00 2108.0
18 TraesCS2D01G530500 chr7B 88.956 661 56 3 1284 1928 659925849 659925190 0.000000e+00 800.0
19 TraesCS2D01G530500 chr7B 97.640 339 8 0 1965 2303 659925109 659924771 1.190000e-162 582.0
20 TraesCS2D01G530500 chr7B 100.000 50 0 0 1920 1969 659925112 659925063 2.440000e-15 93.5
21 TraesCS2D01G530500 chr7A 95.540 1323 39 13 1 1306 483750176 483748857 0.000000e+00 2098.0
22 TraesCS2D01G530500 chr7A 88.365 679 59 13 1268 1928 483748837 483748161 0.000000e+00 798.0
23 TraesCS2D01G530500 chr7A 96.460 339 10 2 1965 2301 483748080 483747742 2.000000e-155 558.0
24 TraesCS2D01G530500 chr7A 100.000 50 0 0 1920 1969 483748083 483748034 2.440000e-15 93.5
25 TraesCS2D01G530500 chr2B 90.269 1634 110 21 1 1597 679648706 679647085 0.000000e+00 2091.0
26 TraesCS2D01G530500 chr2B 89.738 458 46 1 1384 1840 679647268 679646811 3.300000e-163 584.0
27 TraesCS2D01G530500 chr6B 92.158 1339 72 18 1 1311 671654048 671652715 0.000000e+00 1860.0
28 TraesCS2D01G530500 chr6B 88.115 589 64 4 1335 1923 671649546 671648964 0.000000e+00 695.0
29 TraesCS2D01G530500 chr6B 93.878 196 11 1 2109 2303 671648781 671648586 6.220000e-76 294.0
30 TraesCS2D01G530500 chr6B 91.262 103 9 0 1965 2067 671648890 671648788 8.580000e-30 141.0
31 TraesCS2D01G530500 chr6B 92.000 50 4 0 1920 1969 671648893 671648844 1.140000e-08 71.3
32 TraesCS2D01G530500 chr7D 89.610 1232 125 3 4 1233 633359743 633358513 0.000000e+00 1563.0


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 TraesCS2D01G530500 chr2D 616988191 616990493 2302 False 4253.000000 4253 100.000000 1 2303 1 chr2D.!!$F1 2302
1 TraesCS2D01G530500 chr2D 536081778 536084126 2348 True 1385.166667 3458 99.278667 1 2303 3 chr2D.!!$R1 2302
2 TraesCS2D01G530500 chr2D 8945881 8948229 2348 False 1359.166667 3391 98.875000 1 2303 3 chr2D.!!$F2 2302
3 TraesCS2D01G530500 chr2D 577707239 577708574 1335 True 716.833333 1554 96.929000 1034 2303 3 chr2D.!!$R2 1269
4 TraesCS2D01G530500 chr5D 357884349 357886675 2326 False 2016.550000 3960 97.586500 1 2303 2 chr5D.!!$F1 2302
5 TraesCS2D01G530500 chr5D 385492632 385494708 2076 True 1298.500000 2041 90.991500 1 1869 2 chr5D.!!$R1 1868
6 TraesCS2D01G530500 chr3D 420457956 420460230 2274 False 1161.166667 2780 99.300000 1 2303 3 chr3D.!!$F1 2302
7 TraesCS2D01G530500 chr7B 659924771 659927198 2427 True 895.875000 2108 95.590000 1 2303 4 chr7B.!!$R1 2302
8 TraesCS2D01G530500 chr7A 483747742 483750176 2434 True 886.875000 2098 95.091250 1 2301 4 chr7A.!!$R1 2300
9 TraesCS2D01G530500 chr2B 679646811 679648706 1895 True 1337.500000 2091 90.003500 1 1840 2 chr2B.!!$R1 1839
10 TraesCS2D01G530500 chr6B 671648586 671654048 5462 True 612.260000 1860 91.482600 1 2303 5 chr6B.!!$R1 2302
11 TraesCS2D01G530500 chr7D 633358513 633359743 1230 True 1563.000000 1563 89.610000 4 1233 1 chr7D.!!$R1 1229

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
157 158 1.225373 ATGTATCCAGTGGCATGGGT 58.775 50.0 3.51 10.36 41.01 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1987 5544 0.315886 CTGGCAGTCAATTGCAAGCA 59.684 50.0 6.28 0.0 45.86 3.91 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
32 33 3.005791 GCTTTAATGCACTGAAGTTGGGT 59.994 43.478 8.38 0.00 0.00 4.51
157 158 1.225373 ATGTATCCAGTGGCATGGGT 58.775 50.000 3.51 10.36 41.01 4.51
1592 5062 0.621571 ACTGCCCCAGGAAGAGCATA 60.622 55.000 0.00 0.00 35.51 3.14
1910 5381 8.464770 TGTTTGCTACAATTTTCTTATGATGC 57.535 30.769 0.00 0.00 32.64 3.91
1961 5518 2.514205 ACTTGGTTGCAATTGACTGC 57.486 45.000 10.34 0.00 42.95 4.40
1962 5519 1.069049 ACTTGGTTGCAATTGACTGCC 59.931 47.619 10.34 5.78 41.90 4.85
1963 5520 1.068895 CTTGGTTGCAATTGACTGCCA 59.931 47.619 10.34 8.36 41.90 4.92
1964 5521 0.675083 TGGTTGCAATTGACTGCCAG 59.325 50.000 10.34 0.00 41.90 4.85
1965 5522 0.961019 GGTTGCAATTGACTGCCAGA 59.039 50.000 10.34 0.00 41.90 3.86
1966 5523 1.547372 GGTTGCAATTGACTGCCAGAT 59.453 47.619 10.34 0.00 41.90 2.90
1967 5524 2.416431 GGTTGCAATTGACTGCCAGATC 60.416 50.000 10.34 0.00 41.90 2.75
1968 5525 2.203470 TGCAATTGACTGCCAGATCA 57.797 45.000 10.34 0.00 41.90 2.92
1969 5526 2.089201 TGCAATTGACTGCCAGATCAG 58.911 47.619 10.34 0.00 41.90 2.90
1970 5527 2.290450 TGCAATTGACTGCCAGATCAGA 60.290 45.455 10.34 0.00 41.90 3.27
1971 5528 2.355132 GCAATTGACTGCCAGATCAGAG 59.645 50.000 10.34 0.00 37.51 3.35
1972 5529 3.870274 CAATTGACTGCCAGATCAGAGA 58.130 45.455 0.00 0.00 37.51 3.10
1973 5530 4.259356 CAATTGACTGCCAGATCAGAGAA 58.741 43.478 0.00 0.00 37.51 2.87
1974 5531 3.606595 TTGACTGCCAGATCAGAGAAG 57.393 47.619 0.00 0.00 37.51 2.85
1975 5532 2.533916 TGACTGCCAGATCAGAGAAGT 58.466 47.619 0.00 0.00 37.51 3.01
1976 5533 3.701664 TGACTGCCAGATCAGAGAAGTA 58.298 45.455 0.00 0.00 37.51 2.24
1977 5534 4.089361 TGACTGCCAGATCAGAGAAGTAA 58.911 43.478 0.00 0.00 37.51 2.24
1978 5535 4.713814 TGACTGCCAGATCAGAGAAGTAAT 59.286 41.667 0.00 0.00 37.51 1.89
1979 5536 5.893824 TGACTGCCAGATCAGAGAAGTAATA 59.106 40.000 0.00 0.00 37.51 0.98
1980 5537 6.552725 TGACTGCCAGATCAGAGAAGTAATAT 59.447 38.462 0.00 0.00 37.51 1.28
1981 5538 7.725844 TGACTGCCAGATCAGAGAAGTAATATA 59.274 37.037 0.00 0.00 37.51 0.86
1982 5539 8.663209 ACTGCCAGATCAGAGAAGTAATATAT 57.337 34.615 0.00 0.00 37.51 0.86
1983 5540 9.760926 ACTGCCAGATCAGAGAAGTAATATATA 57.239 33.333 0.00 0.00 37.51 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 0.112218 TCCTGCAGCCAGCCTTAAAA 59.888 50.000 8.66 0.00 44.83 1.52
157 158 7.311092 TCATTAGTTTCCCTCTCAACAACTA 57.689 36.000 0.00 0.00 0.00 2.24
1592 5062 2.391678 CTCTTGGGGGCTTAAATGCAT 58.608 47.619 0.00 0.00 34.04 3.96
1910 5381 6.010294 ACTTCTCTGATCATTTGCAAACAG 57.990 37.500 15.41 16.51 0.00 3.16
1976 5533 9.740239 CAGTCAATTGCAAGCAAGTTATATATT 57.260 29.630 13.35 0.00 39.47 1.28
1977 5534 7.864379 GCAGTCAATTGCAAGCAAGTTATATAT 59.136 33.333 13.35 0.00 43.53 0.86
1978 5535 7.195646 GCAGTCAATTGCAAGCAAGTTATATA 58.804 34.615 13.35 0.00 43.53 0.86
1979 5536 6.038356 GCAGTCAATTGCAAGCAAGTTATAT 58.962 36.000 13.35 0.00 43.53 0.86
1980 5537 5.401550 GCAGTCAATTGCAAGCAAGTTATA 58.598 37.500 13.35 0.00 43.53 0.98
1981 5538 4.240096 GCAGTCAATTGCAAGCAAGTTAT 58.760 39.130 13.35 0.00 43.53 1.89
1982 5539 3.552684 GGCAGTCAATTGCAAGCAAGTTA 60.553 43.478 13.35 0.00 45.86 2.24
1983 5540 2.476821 GCAGTCAATTGCAAGCAAGTT 58.523 42.857 13.35 5.37 43.53 2.66
1984 5541 1.269936 GGCAGTCAATTGCAAGCAAGT 60.270 47.619 13.35 7.80 45.86 3.16
1985 5542 1.269883 TGGCAGTCAATTGCAAGCAAG 60.270 47.619 13.35 0.90 45.86 4.01
1986 5543 0.751452 TGGCAGTCAATTGCAAGCAA 59.249 45.000 10.19 10.19 45.86 3.91
1987 5544 0.315886 CTGGCAGTCAATTGCAAGCA 59.684 50.000 6.28 0.00 45.86 3.91
1988 5545 0.599558 TCTGGCAGTCAATTGCAAGC 59.400 50.000 15.27 0.89 43.47 4.01
1989 5546 2.490509 TGATCTGGCAGTCAATTGCAAG 59.509 45.455 15.27 0.00 44.84 4.01
1990 5547 2.229543 GTGATCTGGCAGTCAATTGCAA 59.770 45.455 15.27 0.00 45.86 4.08
1991 5548 1.814394 GTGATCTGGCAGTCAATTGCA 59.186 47.619 15.27 1.00 45.86 4.08
1992 5549 1.814394 TGTGATCTGGCAGTCAATTGC 59.186 47.619 15.27 6.47 43.34 3.56
1993 5550 4.508461 TTTGTGATCTGGCAGTCAATTG 57.492 40.909 15.27 0.00 0.00 2.32
1994 5551 5.733620 AATTTGTGATCTGGCAGTCAATT 57.266 34.783 15.27 10.81 0.00 2.32
1995 5552 5.244402 TGAAATTTGTGATCTGGCAGTCAAT 59.756 36.000 15.27 0.00 0.00 2.57
1996 5553 4.583907 TGAAATTTGTGATCTGGCAGTCAA 59.416 37.500 15.27 12.49 0.00 3.18
1997 5554 4.143543 TGAAATTTGTGATCTGGCAGTCA 58.856 39.130 15.27 14.16 0.00 3.41
1998 5555 4.771590 TGAAATTTGTGATCTGGCAGTC 57.228 40.909 15.27 11.73 0.00 3.51
1999 5556 5.337009 GGAATGAAATTTGTGATCTGGCAGT 60.337 40.000 15.27 1.47 36.07 4.40
2000 5557 5.107133 GGAATGAAATTTGTGATCTGGCAG 58.893 41.667 8.58 8.58 36.07 4.85
2106 5685 7.654568 CAATGTATGGATCTTGTATGCAATGT 58.345 34.615 0.00 0.00 33.65 2.71


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

AutoCloner maintained by Alex Coulton.