Multiple sequence alignment - TraesCS7A01G019600

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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 TraesCS7A01G019600 chr7A 100.000 1374 0 0 966 2339 8053864 8055237 0.000000e+00 2538
1 TraesCS7A01G019600 chr7A 98.668 1351 16 2 990 2339 8174528 8175877 0.000000e+00 2394
2 TraesCS7A01G019600 chr7A 96.765 711 15 4 991 1700 8217117 8217820 0.000000e+00 1179
3 TraesCS7A01G019600 chr7A 100.000 568 0 0 1 568 8052899 8053466 0.000000e+00 1050
4 TraesCS7A01G019600 chr7A 98.594 569 7 1 1 568 8173588 8174156 0.000000e+00 1005
5 TraesCS7A01G019600 chr7A 96.226 583 20 2 1697 2277 8217783 8218365 0.000000e+00 953
6 TraesCS7A01G019600 chr7A 95.775 568 23 1 1 568 8216114 8216680 0.000000e+00 915
7 TraesCS7A01G019600 chr7A 93.793 580 23 4 1 568 7963856 7964434 0.000000e+00 859
8 TraesCS7A01G019600 chr7A 95.690 232 9 1 338 568 8103255 8103486 2.840000e-99 372
9 TraesCS7A01G019600 chr7A 87.050 278 28 5 1 277 156128166 156128436 8.120000e-80 307
10 TraesCS7A01G019600 chr3D 96.546 579 19 1 1700 2277 327463333 327462755 0.000000e+00 957
11 TraesCS7A01G019600 chr3D 94.982 279 11 3 1425 1701 327463575 327463298 3.570000e-118 435
12 TraesCS7A01G019600 chr3D 96.970 66 2 0 2274 2339 250065818 250065753 6.830000e-21 111
13 TraesCS7A01G019600 chr6D 96.028 579 22 1 1700 2277 71360276 71359698 0.000000e+00 941
14 TraesCS7A01G019600 chr6D 95.455 396 18 0 969 1364 338920639 338921034 1.180000e-177 632
15 TraesCS7A01G019600 chr6D 95.255 274 10 3 1429 1701 328837298 328837569 4.620000e-117 431
16 TraesCS7A01G019600 chr6D 95.149 268 11 2 1435 1701 71360507 71360241 2.780000e-114 422
17 TraesCS7A01G019600 chr7D 95.855 579 20 2 1700 2277 32385851 32385276 0.000000e+00 933
18 TraesCS7A01G019600 chr7D 89.775 577 56 3 1700 2274 602782945 602783520 0.000000e+00 736
19 TraesCS7A01G019600 chr7D 95.472 265 10 2 1438 1701 32386079 32385816 2.780000e-114 422
20 TraesCS7A01G019600 chr7D 94.403 268 13 2 1435 1701 530557115 530556849 6.020000e-111 411
21 TraesCS7A01G019600 chr7D 85.197 304 29 9 267 562 7216208 7216503 4.890000e-77 298
22 TraesCS7A01G019600 chr7D 90.698 215 14 4 353 562 7197996 7198209 4.920000e-72 281
23 TraesCS7A01G019600 chrUn 95.682 579 21 2 1700 2277 185729031 185728456 0.000000e+00 928
24 TraesCS7A01G019600 chrUn 95.472 265 10 2 1438 1701 185729259 185728996 2.780000e-114 422
25 TraesCS7A01G019600 chrUn 96.923 65 2 0 2275 2339 20512419 20512483 2.460000e-20 110
26 TraesCS7A01G019600 chr3A 87.952 581 64 5 1701 2277 621921441 621920863 0.000000e+00 680
27 TraesCS7A01G019600 chr3A 87.780 581 63 5 1701 2277 590371091 590370515 0.000000e+00 673
28 TraesCS7A01G019600 chr3A 96.970 66 2 0 2274 2339 353466222 353466157 6.830000e-21 111
29 TraesCS7A01G019600 chr2B 95.707 396 17 0 969 1364 793363933 793364328 2.530000e-179 638
30 TraesCS7A01G019600 chr4A 95.707 396 16 1 969 1363 683420706 683421101 9.120000e-179 636
31 TraesCS7A01G019600 chr4A 88.849 278 27 3 271 544 732904118 732903841 2.880000e-89 339
32 TraesCS7A01G019600 chr4A 87.143 280 31 4 267 541 732486810 732487089 1.750000e-81 313
33 TraesCS7A01G019600 chr4A 100.000 61 0 0 2279 2339 44581381 44581441 1.900000e-21 113
34 TraesCS7A01G019600 chr2D 95.443 395 18 0 969 1363 308681767 308681373 4.240000e-177 630
35 TraesCS7A01G019600 chr2D 95.190 395 19 0 969 1363 308678336 308677942 1.970000e-175 625
36 TraesCS7A01G019600 chr2D 90.146 274 25 2 3 275 4377929 4378201 2.860000e-94 355
37 TraesCS7A01G019600 chr2D 89.781 274 26 2 3 275 4321206 4321478 1.330000e-92 350
38 TraesCS7A01G019600 chr2D 89.531 277 21 7 3 279 630677422 630677154 6.190000e-91 344
39 TraesCS7A01G019600 chr3B 94.962 397 20 0 969 1365 161677877 161677481 7.100000e-175 623
40 TraesCS7A01G019600 chr3B 94.118 408 21 2 966 1372 772413867 772413462 3.300000e-173 617
41 TraesCS7A01G019600 chr5D 90.476 273 19 4 1 273 543510982 543510717 1.030000e-93 353
42 TraesCS7A01G019600 chr7B 89.734 263 22 5 15 274 426536641 426536381 4.820000e-87 331
43 TraesCS7A01G019600 chr7B 100.000 61 0 0 2279 2339 137021045 137020985 1.900000e-21 113
44 TraesCS7A01G019600 chr1D 95.652 184 5 3 1428 1609 417587853 417587671 2.270000e-75 292
45 TraesCS7A01G019600 chr1A 100.000 61 0 0 2279 2339 34188645 34188705 1.900000e-21 113
46 TraesCS7A01G019600 chr1A 97.015 67 2 0 2273 2339 129083881 129083947 1.900000e-21 113
47 TraesCS7A01G019600 chr5B 96.923 65 2 0 2275 2339 197417473 197417409 2.460000e-20 110


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 TraesCS7A01G019600 chr7A 8052899 8055237 2338 False 1794.000000 2538 100.000000 1 2339 2 chr7A.!!$F4 2338
1 TraesCS7A01G019600 chr7A 8173588 8175877 2289 False 1699.500000 2394 98.631000 1 2339 2 chr7A.!!$F5 2338
2 TraesCS7A01G019600 chr7A 8216114 8218365 2251 False 1015.666667 1179 96.255333 1 2277 3 chr7A.!!$F6 2276
3 TraesCS7A01G019600 chr7A 7963856 7964434 578 False 859.000000 859 93.793000 1 568 1 chr7A.!!$F1 567
4 TraesCS7A01G019600 chr3D 327462755 327463575 820 True 696.000000 957 95.764000 1425 2277 2 chr3D.!!$R2 852
5 TraesCS7A01G019600 chr6D 71359698 71360507 809 True 681.500000 941 95.588500 1435 2277 2 chr6D.!!$R1 842
6 TraesCS7A01G019600 chr7D 602782945 602783520 575 False 736.000000 736 89.775000 1700 2274 1 chr7D.!!$F3 574
7 TraesCS7A01G019600 chr7D 32385276 32386079 803 True 677.500000 933 95.663500 1438 2277 2 chr7D.!!$R2 839
8 TraesCS7A01G019600 chrUn 185728456 185729259 803 True 675.000000 928 95.577000 1438 2277 2 chrUn.!!$R1 839
9 TraesCS7A01G019600 chr3A 621920863 621921441 578 True 680.000000 680 87.952000 1701 2277 1 chr3A.!!$R3 576
10 TraesCS7A01G019600 chr3A 590370515 590371091 576 True 673.000000 673 87.780000 1701 2277 1 chr3A.!!$R2 576
11 TraesCS7A01G019600 chr2D 308677942 308681767 3825 True 627.500000 630 95.316500 969 1363 2 chr2D.!!$R2 394

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
299 311 1.669115 CAGTCTGACGGTTGGCCTG 60.669 63.158 3.32 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1599 3521 1.804748 GGCCGATGAGAAACGAAAACT 59.195 47.619 0.0 0.0 0.0 2.66 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
289 301 4.633126 TGCTCTAATCATTTGCAGTCTGAC 59.367 41.667 3.32 0.00 0.00 3.51
299 311 1.669115 CAGTCTGACGGTTGGCCTG 60.669 63.158 3.32 0.00 0.00 4.85
451 463 4.132336 TCTGCTAATCATCTGCATTCCAC 58.868 43.478 0.00 0.00 36.07 4.02
1026 1305 4.376311 GCTGAAGCTTTGGCGTTAAAATTG 60.376 41.667 0.00 0.00 44.37 2.32
1405 2182 1.000019 ACAGTAGTCTGGCCGGCTA 60.000 57.895 28.56 21.41 45.14 3.93
1486 2548 3.883489 GCAGGAGGGTACAATTTCATACC 59.117 47.826 0.00 2.80 40.25 2.73
1599 3521 0.602638 GGCACACATCGGTCACTTCA 60.603 55.000 0.00 0.00 0.00 3.02
1882 3892 4.391830 TCACTCGCATATGGTTTTTCTGTC 59.608 41.667 4.56 0.00 0.00 3.51
2098 4341 6.964370 TGACTGAAACAAGTGTCGTTTAAATG 59.036 34.615 0.63 0.63 36.72 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
164 165 2.759795 GTTCCCAGCTGAAGCCCT 59.240 61.111 17.39 0.0 43.38 5.19
289 301 3.901797 GACCAGTCCAGGCCAACCG 62.902 68.421 5.01 0.0 42.76 4.44
299 311 3.547746 TGTGTTAAACCAAGACCAGTCC 58.452 45.455 0.00 0.0 29.30 3.85
451 463 5.349817 AGTGCAGACTATTGTTCTTGATTCG 59.650 40.000 0.00 0.0 0.00 3.34
965 978 3.545703 CACCAGTCAATCTTACCATCCC 58.454 50.000 0.00 0.0 0.00 3.85
966 979 2.945668 GCACCAGTCAATCTTACCATCC 59.054 50.000 0.00 0.0 0.00 3.51
967 980 2.609459 CGCACCAGTCAATCTTACCATC 59.391 50.000 0.00 0.0 0.00 3.51
1486 2548 7.935338 ACTTGAGTCAATATGCAAGTTTTTG 57.065 32.000 5.91 0.0 46.15 2.44
1599 3521 1.804748 GGCCGATGAGAAACGAAAACT 59.195 47.619 0.00 0.0 0.00 2.66
1882 3892 3.184379 CCTGATTATCAACCATACGCACG 59.816 47.826 0.00 0.0 0.00 5.34


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

AutoCloner maintained by Alex Coulton.