Multiple sequence alignment - TraesCS1A01G153600

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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 TraesCS1A01G153600 chr1A 100.000 5105 0 0 1 5105 267182043 267176939 0.000000e+00 9428
1 TraesCS1A01G153600 chr1A 94.658 599 27 4 1 597 176414137 176414732 0.000000e+00 924
2 TraesCS1A01G153600 chr1A 95.783 166 7 0 4403 4568 267157929 267157764 8.430000e-68 268
3 TraesCS1A01G153600 chr1A 85.088 114 12 5 4426 4536 207982206 207982317 1.500000e-20 111
4 TraesCS1A01G153600 chr1B 92.992 3168 139 43 853 3991 305153384 305156497 0.000000e+00 4543
5 TraesCS1A01G153600 chr1B 96.560 407 12 1 3987 4391 305156525 305156931 0.000000e+00 673
6 TraesCS1A01G153600 chr1B 81.584 543 52 22 4569 5105 107521361 107521861 6.150000e-109 405
7 TraesCS1A01G153600 chr1D 92.318 2213 115 32 1589 3784 211695911 211693737 0.000000e+00 3094
8 TraesCS1A01G153600 chr1D 95.652 713 19 7 853 1561 211696612 211695908 0.000000e+00 1134
9 TraesCS1A01G153600 chr1D 97.356 416 9 1 3990 4403 211693404 211692989 0.000000e+00 706
10 TraesCS1A01G153600 chr1D 96.154 208 6 2 3785 3991 211693641 211693435 6.330000e-89 339
11 TraesCS1A01G153600 chr1D 79.599 549 52 26 4569 5105 348121558 348121058 6.330000e-89 339
12 TraesCS1A01G153600 chr1D 77.637 237 44 8 4569 4801 67977395 67977164 8.920000e-28 135
13 TraesCS1A01G153600 chr1D 82.069 145 21 5 4568 4711 460987474 460987614 8.980000e-23 119
14 TraesCS1A01G153600 chr6D 94.269 855 43 4 1 850 74270859 74270006 0.000000e+00 1303
15 TraesCS1A01G153600 chr6D 94.360 851 43 3 1 847 74273966 74274815 0.000000e+00 1301
16 TraesCS1A01G153600 chr6D 94.517 839 37 8 1 834 256249603 256250437 0.000000e+00 1286
17 TraesCS1A01G153600 chr6D 94.224 831 42 5 1 829 73838262 73839088 0.000000e+00 1264
18 TraesCS1A01G153600 chr3A 93.445 839 48 6 1 836 296903923 296904757 0.000000e+00 1238
19 TraesCS1A01G153600 chr3A 88.983 118 9 2 3536 3653 100052648 100052535 5.330000e-30 143
20 TraesCS1A01G153600 chr3B 93.818 825 43 5 1 822 473402915 473403734 0.000000e+00 1234
21 TraesCS1A01G153600 chr3B 91.481 540 36 4 4569 5105 650054121 650053589 0.000000e+00 734
22 TraesCS1A01G153600 chr3B 86.525 141 16 3 4569 4709 650049086 650049223 8.850000e-33 152
23 TraesCS1A01G153600 chr2A 93.486 829 47 6 1 827 192065835 192065012 0.000000e+00 1225
24 TraesCS1A01G153600 chr2A 85.821 134 11 7 3537 3665 4211718 4211848 8.920000e-28 135
25 TraesCS1A01G153600 chr6B 93.037 833 48 9 1 831 199013365 199012541 0.000000e+00 1208
26 TraesCS1A01G153600 chr6B 91.358 486 35 5 4568 5048 487800461 487799978 0.000000e+00 658
27 TraesCS1A01G153600 chr6B 79.636 550 70 20 4568 5105 399043775 399044294 1.750000e-94 357
28 TraesCS1A01G153600 chr6B 94.030 134 6 2 4425 4557 384186798 384186930 8.670000e-48 202
29 TraesCS1A01G153600 chr6B 92.537 134 8 2 4425 4557 384183298 384183430 1.880000e-44 191
30 TraesCS1A01G153600 chr7B 92.473 837 45 9 1 829 355692552 355691726 0.000000e+00 1181
31 TraesCS1A01G153600 chr7B 80.839 548 57 32 4565 5105 29630483 29630989 2.230000e-103 387
32 TraesCS1A01G153600 chr7B 81.364 440 59 13 4569 4989 149679812 149679377 2.280000e-88 337
33 TraesCS1A01G153600 chr7B 84.173 139 16 6 3538 3676 566581177 566581045 4.150000e-26 130
34 TraesCS1A01G153600 chr7B 82.963 135 12 7 4426 4556 688133695 688133822 1.500000e-20 111
35 TraesCS1A01G153600 chr7D 82.092 564 62 18 4571 5105 260724622 260724069 3.630000e-121 446
36 TraesCS1A01G153600 chr7D 91.139 158 12 2 4403 4560 499837603 499837758 4.000000e-51 213
37 TraesCS1A01G153600 chr7D 90.000 100 9 1 4461 4560 499841322 499841420 1.490000e-25 128
38 TraesCS1A01G153600 chr2D 91.941 273 19 1 4569 4838 645281586 645281314 3.730000e-101 379
39 TraesCS1A01G153600 chr2D 97.596 208 4 1 4898 5105 645281318 645281112 6.290000e-94 355
40 TraesCS1A01G153600 chr2D 80.000 145 21 8 4569 4711 567620918 567621056 3.250000e-17 100
41 TraesCS1A01G153600 chr7A 86.636 217 14 7 4898 5105 95120042 95120252 5.140000e-55 226
42 TraesCS1A01G153600 chr2B 88.321 137 14 2 4403 4539 441489925 441489791 4.090000e-36 163
43 TraesCS1A01G153600 chr2B 88.136 118 12 1 3540 3655 385195544 385195427 6.890000e-29 139
44 TraesCS1A01G153600 chr5B 90.435 115 6 3 3540 3653 472118158 472118268 4.120000e-31 147
45 TraesCS1A01G153600 chr5B 84.173 139 16 6 3538 3676 86581338 86581206 4.150000e-26 130
46 TraesCS1A01G153600 chr4B 87.302 126 12 4 3540 3665 659672199 659672320 1.920000e-29 141
47 TraesCS1A01G153600 chr4A 85.088 114 12 5 4426 4536 589898046 589898157 1.500000e-20 111


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 TraesCS1A01G153600 chr1A 267176939 267182043 5104 True 9428.00 9428 100.000 1 5105 1 chr1A.!!$R2 5104
1 TraesCS1A01G153600 chr1A 176414137 176414732 595 False 924.00 924 94.658 1 597 1 chr1A.!!$F1 596
2 TraesCS1A01G153600 chr1B 305153384 305156931 3547 False 2608.00 4543 94.776 853 4391 2 chr1B.!!$F2 3538
3 TraesCS1A01G153600 chr1B 107521361 107521861 500 False 405.00 405 81.584 4569 5105 1 chr1B.!!$F1 536
4 TraesCS1A01G153600 chr1D 211692989 211696612 3623 True 1318.25 3094 95.370 853 4403 4 chr1D.!!$R3 3550
5 TraesCS1A01G153600 chr1D 348121058 348121558 500 True 339.00 339 79.599 4569 5105 1 chr1D.!!$R2 536
6 TraesCS1A01G153600 chr6D 74270006 74270859 853 True 1303.00 1303 94.269 1 850 1 chr6D.!!$R1 849
7 TraesCS1A01G153600 chr6D 74273966 74274815 849 False 1301.00 1301 94.360 1 847 1 chr6D.!!$F2 846
8 TraesCS1A01G153600 chr6D 256249603 256250437 834 False 1286.00 1286 94.517 1 834 1 chr6D.!!$F3 833
9 TraesCS1A01G153600 chr6D 73838262 73839088 826 False 1264.00 1264 94.224 1 829 1 chr6D.!!$F1 828
10 TraesCS1A01G153600 chr3A 296903923 296904757 834 False 1238.00 1238 93.445 1 836 1 chr3A.!!$F1 835
11 TraesCS1A01G153600 chr3B 473402915 473403734 819 False 1234.00 1234 93.818 1 822 1 chr3B.!!$F1 821
12 TraesCS1A01G153600 chr3B 650053589 650054121 532 True 734.00 734 91.481 4569 5105 1 chr3B.!!$R1 536
13 TraesCS1A01G153600 chr2A 192065012 192065835 823 True 1225.00 1225 93.486 1 827 1 chr2A.!!$R1 826
14 TraesCS1A01G153600 chr6B 199012541 199013365 824 True 1208.00 1208 93.037 1 831 1 chr6B.!!$R1 830
15 TraesCS1A01G153600 chr6B 399043775 399044294 519 False 357.00 357 79.636 4568 5105 1 chr6B.!!$F1 537
16 TraesCS1A01G153600 chr7B 355691726 355692552 826 True 1181.00 1181 92.473 1 829 1 chr7B.!!$R2 828
17 TraesCS1A01G153600 chr7B 29630483 29630989 506 False 387.00 387 80.839 4565 5105 1 chr7B.!!$F1 540
18 TraesCS1A01G153600 chr7D 260724069 260724622 553 True 446.00 446 82.092 4571 5105 1 chr7D.!!$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
818 832 0.878416 TGCTATTTGACACAACGGGC 59.122 50.0 0.00 0.0 0.0 6.13 F
1924 1955 0.182775 ACTTTGCAGGTTCGGAGGTT 59.817 50.0 0.00 0.0 0.0 3.50 F
2758 2800 0.591170 TAACTTCTGTGCGCCTTTGC 59.409 50.0 4.18 0.0 0.0 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2552 2591 0.107456 CCTGCATCGCCTAAGGACAT 59.893 55.0 0.0 0.0 30.92 3.06 R
3398 3442 0.034089 ATTCTTCCTTTGGGAGCCGG 60.034 55.0 0.0 0.0 43.29 6.13 R
4555 4732 0.175073 CCCGTCCGAAAAGAGGGTAG 59.825 60.0 0.0 0.0 39.65 3.18 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)



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AutoCloner maintained by Alex Coulton.