Multiple sequence alignment - TraesCS3A01G227200

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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 TraesCS3A01G227200 chr3A 100.000 3351 0 0 1 3351 424726680 424730030 0.000000e+00 6189
1 TraesCS3A01G227200 chr6B 99.332 2695 16 1 657 3351 232742712 232745404 0.000000e+00 4876
2 TraesCS3A01G227200 chr6B 89.716 282 26 3 483 761 653303169 653303450 1.140000e-94 357
3 TraesCS3A01G227200 chr2B 95.575 2147 74 4 1210 3351 57499404 57501534 0.000000e+00 3419
4 TraesCS3A01G227200 chr2B 92.251 1213 64 13 1 1213 57498187 57499369 0.000000e+00 1692
5 TraesCS3A01G227200 chr2B 92.168 1213 65 13 1 1213 57496267 57497449 0.000000e+00 1687
6 TraesCS3A01G227200 chr2B 96.788 467 13 1 1210 1674 57497484 57497950 0.000000e+00 778
7 TraesCS3A01G227200 chr2B 100.000 57 0 0 1 57 218064633 218064577 4.570000e-19 106
8 TraesCS3A01G227200 chr7B 95.527 2146 76 4 1210 3351 707913644 707911515 0.000000e+00 3413
9 TraesCS3A01G227200 chr7B 92.498 1213 61 13 1 1213 707914861 707913679 0.000000e+00 1709
10 TraesCS3A01G227200 chr7B 87.029 239 29 2 512 748 465550512 465550750 5.510000e-68 268
11 TraesCS3A01G227200 chr4D 96.439 1067 36 2 2287 3351 499725341 499726407 0.000000e+00 1759
12 TraesCS3A01G227200 chr4D 95.787 1068 39 5 2287 3351 508479233 508480297 0.000000e+00 1718
13 TraesCS3A01G227200 chr4D 95.614 456 17 2 1841 2293 499724654 499725109 0.000000e+00 728
14 TraesCS3A01G227200 chr4D 95.165 455 19 2 1841 2293 508478543 508478996 0.000000e+00 715
15 TraesCS3A01G227200 chr2D 95.122 1066 51 1 2287 3351 331545541 331544476 0.000000e+00 1679
16 TraesCS3A01G227200 chr2D 94.714 454 21 2 1841 2291 331546225 331545772 0.000000e+00 702
17 TraesCS3A01G227200 chr5A 94.668 1069 50 7 2287 3351 692551613 692552678 0.000000e+00 1652
18 TraesCS3A01G227200 chr5A 94.387 1069 53 7 2287 3351 692545044 692546109 0.000000e+00 1635
19 TraesCS3A01G227200 chr5A 94.079 456 24 2 1841 2293 692550929 692551384 0.000000e+00 689
20 TraesCS3A01G227200 chr5A 96.552 261 9 0 1582 1842 245499368 245499108 1.850000e-117 433
21 TraesCS3A01G227200 chr5A 96.124 258 10 0 1582 1839 329389164 329389421 4.000000e-114 422
22 TraesCS3A01G227200 chr3B 94.574 1069 51 7 2287 3351 793121970 793123035 0.000000e+00 1646
23 TraesCS3A01G227200 chr3B 87.348 656 56 7 1 656 480336428 480335800 0.000000e+00 726
24 TraesCS3A01G227200 chr3B 94.298 456 23 2 1841 2293 793121286 793121741 0.000000e+00 695
25 TraesCS3A01G227200 chr3B 93.111 450 30 1 764 1213 480335510 480335062 0.000000e+00 658
26 TraesCS3A01G227200 chr3B 91.484 364 31 0 1 364 699799882 699799519 4.990000e-138 501
27 TraesCS3A01G227200 chr5B 94.305 755 42 1 1 755 508618307 508619060 0.000000e+00 1155
28 TraesCS3A01G227200 chr5B 93.681 364 23 0 1 364 321527836 321527473 2.270000e-151 545
29 TraesCS3A01G227200 chr5B 95.019 261 13 0 1582 1842 166649366 166649106 8.650000e-111 411
30 TraesCS3A01G227200 chr5B 89.606 279 26 1 766 1044 508619257 508619532 5.320000e-93 351
31 TraesCS3A01G227200 chr5B 97.000 100 3 0 1210 1309 508619700 508619799 5.750000e-38 169
32 TraesCS3A01G227200 chr5D 94.683 489 26 0 267 755 108540821 108540333 0.000000e+00 760
33 TraesCS3A01G227200 chr5D 93.827 486 28 2 267 752 542112517 542113000 0.000000e+00 730
34 TraesCS3A01G227200 chr5D 95.333 450 17 3 764 1213 108540142 108539697 0.000000e+00 712
35 TraesCS3A01G227200 chr5D 94.222 450 26 0 764 1213 542113194 542113643 0.000000e+00 688
36 TraesCS3A01G227200 chr5D 96.691 272 8 1 1317 1588 108538715 108538445 5.100000e-123 451
37 TraesCS3A01G227200 chr5D 94.891 274 14 0 1315 1588 542114549 542114822 2.390000e-116 429
38 TraesCS3A01G227200 chr5D 97.000 100 3 0 1210 1309 108539662 108539563 5.750000e-38 169
39 TraesCS3A01G227200 chr5D 97.000 100 3 0 1210 1309 542113678 542113777 5.750000e-38 169
40 TraesCS3A01G227200 chr6D 94.518 456 22 2 1841 2293 337762390 337762845 0.000000e+00 701
41 TraesCS3A01G227200 chr4B 89.890 455 36 1 765 1209 91125699 91125245 8.060000e-161 577
42 TraesCS3A01G227200 chr7D 89.111 450 35 6 207 656 529720028 529720463 6.320000e-152 547
43 TraesCS3A01G227200 chr7D 94.030 201 12 0 1 201 529719410 529719610 4.200000e-79 305
44 TraesCS3A01G227200 chr4A 97.318 261 7 0 1582 1842 140709029 140708769 8.530000e-121 444
45 TraesCS3A01G227200 chr4A 94.485 272 15 0 1317 1588 95157981 95158252 1.440000e-113 420
46 TraesCS3A01G227200 chr2A 97.287 258 7 0 1582 1839 178159406 178159663 3.970000e-119 438
47 TraesCS3A01G227200 chr2A 91.176 204 18 0 458 661 662939553 662939350 9.160000e-71 278
48 TraesCS3A01G227200 chr1A 96.124 258 10 0 1582 1839 75390206 75390463 4.000000e-114 422
49 TraesCS3A01G227200 chrUn 94.485 272 15 0 1317 1588 391236954 391236683 1.440000e-113 420
50 TraesCS3A01G227200 chr7A 94.485 272 15 0 1317 1588 238535943 238535672 1.440000e-113 420
51 TraesCS3A01G227200 chr7A 94.677 263 11 3 997 1256 238537250 238536988 4.030000e-109 405
52 TraesCS3A01G227200 chr6A 95.312 256 9 3 1004 1256 393233565 393233820 1.450000e-108 403
53 TraesCS3A01G227200 chr1B 91.388 209 12 5 1 203 645944779 645944571 7.080000e-72 281


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 TraesCS3A01G227200 chr3A 424726680 424730030 3350 False 6189.000000 6189 100.00000 1 3351 1 chr3A.!!$F1 3350
1 TraesCS3A01G227200 chr6B 232742712 232745404 2692 False 4876.000000 4876 99.33200 657 3351 1 chr6B.!!$F1 2694
2 TraesCS3A01G227200 chr2B 57496267 57501534 5267 False 1894.000000 3419 94.19550 1 3351 4 chr2B.!!$F1 3350
3 TraesCS3A01G227200 chr7B 707911515 707914861 3346 True 2561.000000 3413 94.01250 1 3351 2 chr7B.!!$R1 3350
4 TraesCS3A01G227200 chr4D 499724654 499726407 1753 False 1243.500000 1759 96.02650 1841 3351 2 chr4D.!!$F1 1510
5 TraesCS3A01G227200 chr4D 508478543 508480297 1754 False 1216.500000 1718 95.47600 1841 3351 2 chr4D.!!$F2 1510
6 TraesCS3A01G227200 chr2D 331544476 331546225 1749 True 1190.500000 1679 94.91800 1841 3351 2 chr2D.!!$R1 1510
7 TraesCS3A01G227200 chr5A 692545044 692546109 1065 False 1635.000000 1635 94.38700 2287 3351 1 chr5A.!!$F2 1064
8 TraesCS3A01G227200 chr5A 692550929 692552678 1749 False 1170.500000 1652 94.37350 1841 3351 2 chr5A.!!$F3 1510
9 TraesCS3A01G227200 chr3B 793121286 793123035 1749 False 1170.500000 1646 94.43600 1841 3351 2 chr3B.!!$F1 1510
10 TraesCS3A01G227200 chr3B 480335062 480336428 1366 True 692.000000 726 90.22950 1 1213 2 chr3B.!!$R2 1212
11 TraesCS3A01G227200 chr5B 508618307 508619799 1492 False 558.333333 1155 93.63700 1 1309 3 chr5B.!!$F1 1308
12 TraesCS3A01G227200 chr5D 108538445 108540821 2376 True 523.000000 760 95.92675 267 1588 4 chr5D.!!$R1 1321
13 TraesCS3A01G227200 chr5D 542112517 542114822 2305 False 504.000000 730 94.98500 267 1588 4 chr5D.!!$F1 1321
14 TraesCS3A01G227200 chr7D 529719410 529720463 1053 False 426.000000 547 91.57050 1 656 2 chr7D.!!$F1 655
15 TraesCS3A01G227200 chr7A 238535672 238537250 1578 True 412.500000 420 94.58100 997 1588 2 chr7A.!!$R1 591

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
530 2889 0.249868 CCGTGTCCTGCTCAAACTCA 60.250 55.000 0.0 0.0 0.00 3.41 F
629 3048 1.679032 GCCAGAATCGTAAACCAGGCT 60.679 52.381 0.0 0.0 37.89 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1739 5392 1.606889 AAGGTCCGAGAGCCGAACT 60.607 57.895 0.0 0.0 41.76 3.01 R
2472 6377 5.738619 TCTGAAATCTGCCACTGTAACTA 57.261 39.130 0.0 0.0 0.00 2.24 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
72 73 3.699894 AGGTGCTGCAGAGACGGG 61.700 66.667 20.43 0.0 0.00 5.28
117 118 2.205462 CGGGGGAGGATGGAGGAT 59.795 66.667 0.00 0.0 0.00 3.24
260 261 2.284258 ACCCTTCAGCTCGCCTCT 60.284 61.111 0.00 0.0 0.00 3.69
264 265 3.306595 CTTCAGCTCGCCTCTGCCA 62.307 63.158 0.00 0.0 0.00 4.92
520 2879 1.903877 AATCCTGCTCCCGTGTCCTG 61.904 60.000 0.00 0.0 0.00 3.86
530 2889 0.249868 CCGTGTCCTGCTCAAACTCA 60.250 55.000 0.00 0.0 0.00 3.41
563 2922 3.066203 TCCTTCTCAAACAAAGAAACCGC 59.934 43.478 0.00 0.0 32.60 5.68
620 3039 3.410631 TTGTTCTTGGCCAGAATCGTA 57.589 42.857 17.14 0.0 43.72 3.43
629 3048 1.679032 GCCAGAATCGTAAACCAGGCT 60.679 52.381 0.00 0.0 37.89 4.58
1198 3807 2.224769 CCTTCCCTCAAGCCTTTGTGTA 60.225 50.000 0.00 0.0 35.73 2.90
1739 5392 1.463214 TCAGGTGGAGGCCAAGGAA 60.463 57.895 5.01 0.0 34.18 3.36
2472 6377 5.461032 TTTCGGTGGCAAGATTTTTGTAT 57.539 34.783 0.00 0.0 0.00 2.29
2763 6670 1.148310 CCGTTTGCTCACGAGAACAT 58.852 50.000 9.49 0.0 43.15 2.71
2821 6728 5.122519 TCTTTGAATTTGCCACTTTTTCCC 58.877 37.500 0.00 0.0 0.00 3.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
243 244 2.284258 AGAGGCGAGCTGAAGGGT 60.284 61.111 0.00 0.00 0.00 4.34
314 2647 3.382832 AGAGGCGGTCTCCCAACG 61.383 66.667 5.89 0.00 43.44 4.10
315 2648 2.266055 CAGAGGCGGTCTCCCAAC 59.734 66.667 5.89 0.00 43.44 3.77
316 2649 3.706373 GCAGAGGCGGTCTCCCAA 61.706 66.667 5.89 0.00 43.44 4.12
319 2652 4.154347 CAGGCAGAGGCGGTCTCC 62.154 72.222 5.89 0.00 43.44 3.71
320 2653 4.828925 GCAGGCAGAGGCGGTCTC 62.829 72.222 0.18 0.18 42.47 3.36
520 2879 0.674895 ACGGGAGCATGAGTTTGAGC 60.675 55.000 0.00 0.00 0.00 4.26
530 2889 0.904865 TGAGAAGGACACGGGAGCAT 60.905 55.000 0.00 0.00 0.00 3.79
629 3048 3.300934 CTGCTCACTGGTGGCGCTA 62.301 63.158 7.64 0.00 32.09 4.26
1739 5392 1.606889 AAGGTCCGAGAGCCGAACT 60.607 57.895 0.00 0.00 41.76 3.01
2472 6377 5.738619 TCTGAAATCTGCCACTGTAACTA 57.261 39.130 0.00 0.00 0.00 2.24
2821 6728 4.327357 GGACAGATTATATCCGTGAATGCG 59.673 45.833 0.00 0.00 0.00 4.73


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

AutoCloner maintained by Alex Coulton.