Multiple sequence alignment - TraesCS3A01G451600

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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 TraesCS3A01G451600 chr3A 100.000 2653 0 0 1 2653 689607891 689610543 0.000000e+00 4900.0
1 TraesCS3A01G451600 chr3A 98.642 2651 36 0 3 2653 689578115 689580765 0.000000e+00 4697.0
2 TraesCS3A01G451600 chr3A 98.213 1399 22 2 315 1710 689523296 689524694 0.000000e+00 2442.0
3 TraesCS3A01G451600 chr3A 88.069 1274 125 17 411 1665 689659666 689660931 0.000000e+00 1485.0
4 TraesCS3A01G451600 chr3A 88.110 1270 125 16 414 1665 689662507 689663768 0.000000e+00 1485.0
5 TraesCS3A01G451600 chr3A 86.998 1269 134 17 414 1665 689666322 689667576 0.000000e+00 1415.0
6 TraesCS3A01G451600 chr3A 85.697 818 100 8 860 1665 686281128 686280316 0.000000e+00 846.0
7 TraesCS3A01G451600 chr3A 86.198 797 90 9 700 1476 689867182 689867978 0.000000e+00 845.0
8 TraesCS3A01G451600 chr3A 85.696 797 94 9 700 1476 689846868 689847664 0.000000e+00 822.0
9 TraesCS3A01G451600 chr3A 88.268 537 53 5 414 943 689866848 689867381 3.730000e-178 634.0
10 TraesCS3A01G451600 chr3A 89.184 490 48 4 315 801 686281530 686281043 8.120000e-170 606.0
11 TraesCS3A01G451600 chr3A 97.885 331 7 0 2323 2653 689524697 689525027 8.240000e-160 573.0
12 TraesCS3A01G451600 chr3A 97.143 315 8 1 1 314 689657663 689657977 5.030000e-147 531.0
13 TraesCS3A01G451600 chr3A 96.825 315 9 1 1 314 689651627 689651941 2.340000e-145 525.0
14 TraesCS3A01G451600 chr3A 94.921 315 15 1 1 314 689781488 689781802 2.370000e-135 492.0
15 TraesCS3A01G451600 chr3A 85.808 458 56 5 1993 2442 686278647 686278191 6.640000e-131 477.0
16 TraesCS3A01G451600 chr3A 78.528 163 19 10 2507 2653 47273907 47274069 2.810000e-15 93.5
17 TraesCS3A01G451600 chr3D 91.125 1262 92 10 414 1662 553357146 553358400 0.000000e+00 1692.0
18 TraesCS3A01G451600 chr3D 85.970 948 100 12 750 1665 553405894 553406840 0.000000e+00 983.0
19 TraesCS3A01G451600 chr3D 93.926 461 24 2 1981 2437 553362093 553362553 0.000000e+00 693.0
20 TraesCS3A01G451600 chr3D 91.039 491 37 6 315 801 548999983 548999496 0.000000e+00 656.0
21 TraesCS3A01G451600 chr3D 85.855 509 63 8 1939 2442 548987847 548987343 1.400000e-147 532.0
22 TraesCS3A01G451600 chr3D 95.238 315 14 1 1 314 553355552 553355866 5.100000e-137 497.0
23 TraesCS3A01G451600 chr3D 95.045 222 10 1 2433 2653 553372169 553372390 5.440000e-92 348.0
24 TraesCS3A01G451600 chr3D 84.718 301 35 6 1369 1665 548999104 548998811 9.290000e-75 291.0
25 TraesCS3A01G451600 chr3D 92.308 156 9 3 1662 1816 548998602 548998449 4.450000e-53 219.0
26 TraesCS3A01G451600 chr3D 90.076 131 4 2 1736 1865 553359000 553359122 7.600000e-36 161.0
27 TraesCS3A01G451600 chr3D 90.435 115 8 2 1867 1979 553359179 553359292 5.920000e-32 148.0
28 TraesCS3A01G451600 chr3B 87.263 581 67 5 1868 2442 728293607 728293028 0.000000e+00 656.0
29 TraesCS3A01G451600 chr3B 85.135 296 34 5 1369 1661 728294962 728294674 7.180000e-76 294.0
30 TraesCS3A01G451600 chr1A 85.494 324 38 7 1 315 245123364 245123687 1.970000e-86 329.0
31 TraesCS3A01G451600 chr1A 85.580 319 37 8 1 314 253048388 253048074 2.550000e-85 326.0
32 TraesCS3A01G451600 chr1A 78.528 163 19 10 2507 2653 14802912 14803074 2.810000e-15 93.5
33 TraesCS3A01G451600 chr1D 85.358 321 40 6 1 314 453184030 453184350 2.550000e-85 326.0
34 TraesCS3A01G451600 chr7D 84.830 323 40 6 2 315 368815061 368815383 1.530000e-82 316.0
35 TraesCS3A01G451600 chr2B 81.595 163 14 10 2507 2653 757859051 757859213 1.290000e-23 121.0
36 TraesCS3A01G451600 chr2A 80.368 163 16 10 2507 2653 16896446 16896608 2.790000e-20 110.0
37 TraesCS3A01G451600 chr2A 80.368 163 16 5 2507 2653 81691066 81690904 2.790000e-20 110.0
38 TraesCS3A01G451600 chr4B 74.403 293 44 17 2383 2653 223394347 223394630 2.170000e-16 97.1


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 TraesCS3A01G451600 chr3A 689607891 689610543 2652 False 4900.000000 4900 100.000000 1 2653 1 chr3A.!!$F3 2652
1 TraesCS3A01G451600 chr3A 689578115 689580765 2650 False 4697.000000 4697 98.642000 3 2653 1 chr3A.!!$F2 2650
2 TraesCS3A01G451600 chr3A 689523296 689525027 1731 False 1507.500000 2442 98.049000 315 2653 2 chr3A.!!$F7 2338
3 TraesCS3A01G451600 chr3A 689657663 689667576 9913 False 1229.000000 1485 90.080000 1 1665 4 chr3A.!!$F8 1664
4 TraesCS3A01G451600 chr3A 689846868 689847664 796 False 822.000000 822 85.696000 700 1476 1 chr3A.!!$F6 776
5 TraesCS3A01G451600 chr3A 689866848 689867978 1130 False 739.500000 845 87.233000 414 1476 2 chr3A.!!$F9 1062
6 TraesCS3A01G451600 chr3A 686278191 686281530 3339 True 643.000000 846 86.896333 315 2442 3 chr3A.!!$R1 2127
7 TraesCS3A01G451600 chr3D 553405894 553406840 946 False 983.000000 983 85.970000 750 1665 1 chr3D.!!$F2 915
8 TraesCS3A01G451600 chr3D 553355552 553362553 7001 False 638.200000 1692 92.160000 1 2437 5 chr3D.!!$F3 2436
9 TraesCS3A01G451600 chr3D 548987343 548987847 504 True 532.000000 532 85.855000 1939 2442 1 chr3D.!!$R1 503
10 TraesCS3A01G451600 chr3D 548998449 548999983 1534 True 388.666667 656 89.355000 315 1816 3 chr3D.!!$R2 1501
11 TraesCS3A01G451600 chr3B 728293028 728294962 1934 True 475.000000 656 86.199000 1369 2442 2 chr3B.!!$R1 1073

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
147 148 3.696051 GGCTGCAAAGGAACATAAGATCA 59.304 43.478 0.5 0.0 0.0 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2016 11664 2.035832 GTGGTTGTGGGGAACATCTTTG 59.964 50.0 0.0 0.0 38.99 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
55 56 7.122650 TCTGCATACATGTATCTCATATTCGGA 59.877 37.037 15.60 6.64 34.67 4.55
147 148 3.696051 GGCTGCAAAGGAACATAAGATCA 59.304 43.478 0.50 0.00 0.00 2.92
1049 5731 1.973281 CTTGGCCATGGCGTTCAGT 60.973 57.895 29.90 0.00 43.06 3.41
1374 6061 2.288213 TGAGCTCAACGAAGACAACGAT 60.288 45.455 15.67 0.00 34.70 3.73
1543 6263 2.544903 CCATATGTACGTGATGTGCCGA 60.545 50.000 0.00 0.00 31.26 5.54
2016 11664 2.417515 GCAGAGTAGGGTGTCTTGTAGC 60.418 54.545 0.00 0.00 0.00 3.58
2017 11665 2.826128 CAGAGTAGGGTGTCTTGTAGCA 59.174 50.000 0.00 0.00 0.00 3.49
2262 11923 1.378531 CATTAGCTTGTTGCCCGCTA 58.621 50.000 0.00 0.00 44.23 4.26
2350 12074 0.557729 ATTGGGGATCGATTTGGCCT 59.442 50.000 3.32 0.00 0.00 5.19
2569 12330 1.794151 CGGCATGTGTGTTGCTTCCA 61.794 55.000 0.00 0.00 40.03 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 5.279708 GCATGTGTAGTATGGAGATAAGGCT 60.280 44.000 0.00 0.0 0.00 4.58
147 148 4.097286 AGTTTGTTAATGTCCGTTTGCAGT 59.903 37.500 0.00 0.0 0.00 4.40
1374 6061 4.142773 GGTCGTTTGTGAAAGAAGTTGTCA 60.143 41.667 0.00 0.0 0.00 3.58
1563 6283 3.252974 GCTGCCACTAGCTTCTTCTTA 57.747 47.619 0.00 0.0 44.23 2.10
2016 11664 2.035832 GTGGTTGTGGGGAACATCTTTG 59.964 50.000 0.00 0.0 38.99 2.77
2017 11665 2.091333 AGTGGTTGTGGGGAACATCTTT 60.091 45.455 0.00 0.0 38.99 2.52
2262 11923 2.111384 ACCATAATCTCGTCCAGCAGT 58.889 47.619 0.00 0.0 0.00 4.40
2350 12074 0.758734 ATTCCATCAAGCCGGATCGA 59.241 50.000 5.05 0.0 0.00 3.59
2569 12330 1.681166 GGCAACAGAGCATCATCCAGT 60.681 52.381 0.00 0.0 37.82 4.00


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

AutoCloner maintained by Alex Coulton.