Multiple sequence alignment - TraesCS2D01G022500

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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 TraesCS2D01G022500 chr2D 100.000 2960 0 0 1 2960 10293003 10295962 0.000000e+00 5467.0
1 TraesCS2D01G022500 chr2D 99.056 2967 21 1 1 2960 10512522 10509556 0.000000e+00 5317.0
2 TraesCS2D01G022500 chr2D 98.955 2967 24 1 1 2960 10495471 10492505 0.000000e+00 5301.0
3 TraesCS2D01G022500 chr2D 94.605 2317 113 3 367 2675 10801043 10798731 0.000000e+00 3576.0
4 TraesCS2D01G022500 chr2D 92.901 324 23 0 1 324 10801361 10801038 3.450000e-129 472.0
5 TraesCS2D01G022500 chr2D 96.154 286 10 1 2675 2960 10224179 10224463 1.610000e-127 466.0
6 TraesCS2D01G022500 chr2D 87.105 380 44 4 1 376 37012936 37013314 2.730000e-115 425.0
7 TraesCS2D01G022500 chr2A 91.890 2503 174 8 182 2675 11310595 11308113 0.000000e+00 3470.0
8 TraesCS2D01G022500 chr2A 89.706 68 6 1 2768 2834 296955916 296955983 5.260000e-13 86.1
9 TraesCS2D01G022500 chr2B 93.687 2075 115 4 602 2675 15883327 15881268 0.000000e+00 3092.0
10 TraesCS2D01G022500 chr2B 93.446 2075 119 9 602 2675 15962722 15960664 0.000000e+00 3062.0
11 TraesCS2D01G022500 chr2B 93.308 2077 119 12 602 2675 15790571 15788512 0.000000e+00 3048.0
12 TraesCS2D01G022500 chr2B 93.304 2076 120 11 602 2675 15727504 15725446 0.000000e+00 3046.0
13 TraesCS2D01G022500 chr2B 93.821 1926 109 8 754 2675 15818710 15816791 0.000000e+00 2889.0
14 TraesCS2D01G022500 chr2B 93.769 1926 110 8 754 2675 15917681 15915762 0.000000e+00 2883.0
15 TraesCS2D01G022500 chr2B 93.718 1926 111 8 754 2675 15695404 15693485 0.000000e+00 2878.0
16 TraesCS2D01G022500 chr2B 90.998 822 63 2 602 1423 15983581 15982771 0.000000e+00 1098.0
17 TraesCS2D01G022500 chrUn 93.590 2075 116 5 602 2675 339546441 339548499 0.000000e+00 3079.0
18 TraesCS2D01G022500 chrUn 93.446 2075 119 5 602 2675 339561602 339559544 0.000000e+00 3062.0
19 TraesCS2D01G022500 chrUn 93.713 2052 113 4 602 2652 349087491 349085455 0.000000e+00 3061.0
20 TraesCS2D01G022500 chrUn 93.665 2052 114 4 602 2652 349092566 349094602 0.000000e+00 3055.0
21 TraesCS2D01G022500 chrUn 87.660 235 16 4 602 835 328699764 328699986 8.140000e-66 261.0
22 TraesCS2D01G022500 chrUn 87.395 238 17 4 602 838 433700886 433700661 8.140000e-66 261.0
23 TraesCS2D01G022500 chr7D 84.307 599 74 10 1 592 169836888 169836303 4.280000e-158 568.0
24 TraesCS2D01G022500 chr7D 82.305 616 71 19 1 594 249618919 249619518 1.580000e-137 499.0
25 TraesCS2D01G022500 chr7A 83.961 611 64 14 1 594 172463742 172463149 3.330000e-154 555.0
26 TraesCS2D01G022500 chr7A 89.189 74 5 3 2763 2834 208230384 208230456 4.060000e-14 89.8
27 TraesCS2D01G022500 chr1D 82.832 565 64 24 1 535 346392134 346391573 2.670000e-130 475.0
28 TraesCS2D01G022500 chr1D 80.508 236 30 11 367 592 462299547 462299318 1.820000e-37 167.0
29 TraesCS2D01G022500 chr3B 89.136 359 34 4 1 358 783421064 783421418 2.710000e-120 442.0
30 TraesCS2D01G022500 chr3B 93.529 170 11 0 383 552 257778798 257778629 1.360000e-63 254.0
31 TraesCS2D01G022500 chr3B 88.732 71 7 1 2766 2835 325067881 325067811 5.260000e-13 86.1
32 TraesCS2D01G022500 chr6D 87.701 374 42 3 1 372 62130848 62131219 1.630000e-117 433.0
33 TraesCS2D01G022500 chr6D 87.467 375 44 3 1 372 472758507 472758133 2.110000e-116 429.0
34 TraesCS2D01G022500 chr6D 90.625 64 5 1 2776 2838 289067104 289067041 1.890000e-12 84.2
35 TraesCS2D01G022500 chr1A 87.259 259 24 4 342 593 538778183 538778439 1.340000e-73 287.0
36 TraesCS2D01G022500 chr3D 84.825 257 30 4 345 594 498726636 498726382 1.760000e-62 250.0
37 TraesCS2D01G022500 chr5B 84.651 215 28 4 384 594 10172189 10172402 2.990000e-50 209.0
38 TraesCS2D01G022500 chr4D 87.500 80 7 2 2758 2834 392250265 392250344 4.060000e-14 89.8
39 TraesCS2D01G022500 chr5D 88.571 70 4 3 2766 2834 34237686 34237620 6.800000e-12 82.4


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 TraesCS2D01G022500 chr2D 10293003 10295962 2959 False 5467 5467 100.000 1 2960 1 chr2D.!!$F2 2959
1 TraesCS2D01G022500 chr2D 10509556 10512522 2966 True 5317 5317 99.056 1 2960 1 chr2D.!!$R2 2959
2 TraesCS2D01G022500 chr2D 10492505 10495471 2966 True 5301 5301 98.955 1 2960 1 chr2D.!!$R1 2959
3 TraesCS2D01G022500 chr2D 10798731 10801361 2630 True 2024 3576 93.753 1 2675 2 chr2D.!!$R3 2674
4 TraesCS2D01G022500 chr2A 11308113 11310595 2482 True 3470 3470 91.890 182 2675 1 chr2A.!!$R1 2493
5 TraesCS2D01G022500 chr2B 15881268 15883327 2059 True 3092 3092 93.687 602 2675 1 chr2B.!!$R5 2073
6 TraesCS2D01G022500 chr2B 15960664 15962722 2058 True 3062 3062 93.446 602 2675 1 chr2B.!!$R7 2073
7 TraesCS2D01G022500 chr2B 15788512 15790571 2059 True 3048 3048 93.308 602 2675 1 chr2B.!!$R3 2073
8 TraesCS2D01G022500 chr2B 15725446 15727504 2058 True 3046 3046 93.304 602 2675 1 chr2B.!!$R2 2073
9 TraesCS2D01G022500 chr2B 15816791 15818710 1919 True 2889 2889 93.821 754 2675 1 chr2B.!!$R4 1921
10 TraesCS2D01G022500 chr2B 15915762 15917681 1919 True 2883 2883 93.769 754 2675 1 chr2B.!!$R6 1921
11 TraesCS2D01G022500 chr2B 15693485 15695404 1919 True 2878 2878 93.718 754 2675 1 chr2B.!!$R1 1921
12 TraesCS2D01G022500 chr2B 15982771 15983581 810 True 1098 1098 90.998 602 1423 1 chr2B.!!$R8 821
13 TraesCS2D01G022500 chrUn 339546441 339548499 2058 False 3079 3079 93.590 602 2675 1 chrUn.!!$F2 2073
14 TraesCS2D01G022500 chrUn 339559544 339561602 2058 True 3062 3062 93.446 602 2675 1 chrUn.!!$R1 2073
15 TraesCS2D01G022500 chrUn 349085455 349087491 2036 True 3061 3061 93.713 602 2652 1 chrUn.!!$R2 2050
16 TraesCS2D01G022500 chrUn 349092566 349094602 2036 False 3055 3055 93.665 602 2652 1 chrUn.!!$F3 2050
17 TraesCS2D01G022500 chr7D 169836303 169836888 585 True 568 568 84.307 1 592 1 chr7D.!!$R1 591
18 TraesCS2D01G022500 chr7D 249618919 249619518 599 False 499 499 82.305 1 594 1 chr7D.!!$F1 593
19 TraesCS2D01G022500 chr7A 172463149 172463742 593 True 555 555 83.961 1 594 1 chr7A.!!$R1 593
20 TraesCS2D01G022500 chr1D 346391573 346392134 561 True 475 475 82.832 1 535 1 chr1D.!!$R1 534

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
130 132 1.971357 CACCGGCAACTATATCTCCCT 59.029 52.381 0.0 0.0 0.0 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2616 2855 7.406031 TCTTGGAGATTGATACTCTTAACGT 57.594 36.0 0.0 0.0 35.1 3.99 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 3.126703 TTTCCCCCGAAGCAGCACA 62.127 57.895 0.00 0.00 0.00 4.57
130 132 1.971357 CACCGGCAACTATATCTCCCT 59.029 52.381 0.00 0.00 0.00 4.20
394 435 2.845550 CGGCACAGATCGGATCGGA 61.846 63.158 22.17 5.34 0.00 4.55
2301 2540 0.466124 GAGGCCTTCCGCTTACATCT 59.534 55.000 6.77 0.00 37.74 2.90
2616 2855 0.472471 ACTTGGACAAAGCTTCCCGA 59.528 50.000 0.00 0.83 39.76 5.14
2854 3094 4.351874 TTCAGACCTACCCTGTTTTCTG 57.648 45.455 0.00 0.00 33.57 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 4.056050 GTGTAACTGTTGTCGATCCACTT 58.944 43.478 2.69 0.00 0.00 3.16
130 132 1.558294 TCTAGTCCTGGCTACGAGTCA 59.442 52.381 0.00 0.00 0.00 3.41
394 435 0.316772 CGATTCGTATGGAGACGCGT 60.317 55.000 13.85 13.85 42.62 6.01
2616 2855 7.406031 TCTTGGAGATTGATACTCTTAACGT 57.594 36.000 0.00 0.00 35.10 3.99


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

AutoCloner maintained by Alex Coulton.