Multiple sequence alignment - TraesCS3A01G478200

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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 TraesCS3A01G478200 chr3A 100.000 2363 0 0 1 2363 710297948 710295586 0.000000e+00 4364
1 TraesCS3A01G478200 chr3A 95.421 677 31 0 1687 2363 574086599 574085923 0.000000e+00 1079
2 TraesCS3A01G478200 chr3A 95.273 677 32 0 1687 2363 659586968 659587644 0.000000e+00 1074
3 TraesCS3A01G478200 chr3A 95.126 677 33 0 1687 2363 422763160 422762484 0.000000e+00 1068
4 TraesCS3A01G478200 chr2D 91.467 1711 91 27 1 1693 352901964 352900291 0.000000e+00 2300
5 TraesCS3A01G478200 chr2D 90.287 1709 102 23 1 1693 141823580 141821920 0.000000e+00 2178
6 TraesCS3A01G478200 chr2D 86.082 388 45 5 555 934 181591167 181591553 2.190000e-110 409
7 TraesCS3A01G478200 chr2D 83.712 264 40 3 219 481 181590871 181591132 1.810000e-61 246
8 TraesCS3A01G478200 chr7A 89.063 1719 125 32 1 1693 94881709 94880028 0.000000e+00 2074
9 TraesCS3A01G478200 chr7A 95.407 675 30 1 1689 2363 126004836 126005509 0.000000e+00 1074
10 TraesCS3A01G478200 chr7A 95.273 677 32 0 1687 2363 629221784 629221108 0.000000e+00 1074
11 TraesCS3A01G478200 chr7A 95.126 677 33 0 1687 2363 229053949 229054625 0.000000e+00 1068
12 TraesCS3A01G478200 chr7A 85.309 388 48 5 555 934 616795267 616795653 2.200000e-105 392
13 TraesCS3A01G478200 chr7A 84.470 264 38 3 219 481 616794971 616795232 8.380000e-65 257
14 TraesCS3A01G478200 chr3D 90.077 1552 124 18 154 1693 447469641 447471174 0.000000e+00 1986
15 TraesCS3A01G478200 chr6A 87.674 1720 134 46 1 1693 564643663 564645331 0.000000e+00 1930
16 TraesCS3A01G478200 chr6A 95.126 677 33 0 1687 2363 574752619 574751943 0.000000e+00 1068
17 TraesCS3A01G478200 chr6A 81.416 339 52 10 146 479 261509643 261509975 1.390000e-67 267
18 TraesCS3A01G478200 chr6A 81.194 335 54 8 151 481 261512866 261512537 6.480000e-66 261
19 TraesCS3A01G478200 chr2B 84.857 1684 184 39 35 1693 116764995 116763358 0.000000e+00 1631
20 TraesCS3A01G478200 chr4D 91.570 1032 72 10 663 1687 474384729 474385752 0.000000e+00 1410
21 TraesCS3A01G478200 chr4D 85.102 443 47 12 42 470 474382675 474383112 3.610000e-118 435
22 TraesCS3A01G478200 chr4A 84.406 1321 150 30 121 1416 649502179 649503468 0.000000e+00 1247
23 TraesCS3A01G478200 chr4A 95.516 669 30 0 1693 2361 208983215 208982547 0.000000e+00 1070
24 TraesCS3A01G478200 chr4A 95.126 677 33 0 1687 2363 177162315 177162991 0.000000e+00 1068
25 TraesCS3A01G478200 chr5D 92.092 784 55 6 912 1694 44458375 44457598 0.000000e+00 1098
26 TraesCS3A01G478200 chr7B 86.340 388 44 5 555 934 475725271 475725657 4.700000e-112 414
27 TraesCS3A01G478200 chr7B 85.572 402 48 7 555 947 665650878 665651278 1.690000e-111 412
28 TraesCS3A01G478200 chr7B 83.712 264 40 3 219 481 475724975 475725236 1.810000e-61 246
29 TraesCS3A01G478200 chrUn 84.091 264 39 3 219 481 134401469 134401730 3.900000e-63 252
30 TraesCS3A01G478200 chr1B 82.197 264 44 3 219 481 426490703 426490442 8.500000e-55 224


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 TraesCS3A01G478200 chr3A 710295586 710297948 2362 True 4364.0 4364 100.0000 1 2363 1 chr3A.!!$R3 2362
1 TraesCS3A01G478200 chr3A 574085923 574086599 676 True 1079.0 1079 95.4210 1687 2363 1 chr3A.!!$R2 676
2 TraesCS3A01G478200 chr3A 659586968 659587644 676 False 1074.0 1074 95.2730 1687 2363 1 chr3A.!!$F1 676
3 TraesCS3A01G478200 chr3A 422762484 422763160 676 True 1068.0 1068 95.1260 1687 2363 1 chr3A.!!$R1 676
4 TraesCS3A01G478200 chr2D 352900291 352901964 1673 True 2300.0 2300 91.4670 1 1693 1 chr2D.!!$R2 1692
5 TraesCS3A01G478200 chr2D 141821920 141823580 1660 True 2178.0 2178 90.2870 1 1693 1 chr2D.!!$R1 1692
6 TraesCS3A01G478200 chr2D 181590871 181591553 682 False 327.5 409 84.8970 219 934 2 chr2D.!!$F1 715
7 TraesCS3A01G478200 chr7A 94880028 94881709 1681 True 2074.0 2074 89.0630 1 1693 1 chr7A.!!$R1 1692
8 TraesCS3A01G478200 chr7A 126004836 126005509 673 False 1074.0 1074 95.4070 1689 2363 1 chr7A.!!$F1 674
9 TraesCS3A01G478200 chr7A 629221108 629221784 676 True 1074.0 1074 95.2730 1687 2363 1 chr7A.!!$R2 676
10 TraesCS3A01G478200 chr7A 229053949 229054625 676 False 1068.0 1068 95.1260 1687 2363 1 chr7A.!!$F2 676
11 TraesCS3A01G478200 chr7A 616794971 616795653 682 False 324.5 392 84.8895 219 934 2 chr7A.!!$F3 715
12 TraesCS3A01G478200 chr3D 447469641 447471174 1533 False 1986.0 1986 90.0770 154 1693 1 chr3D.!!$F1 1539
13 TraesCS3A01G478200 chr6A 564643663 564645331 1668 False 1930.0 1930 87.6740 1 1693 1 chr6A.!!$F2 1692
14 TraesCS3A01G478200 chr6A 574751943 574752619 676 True 1068.0 1068 95.1260 1687 2363 1 chr6A.!!$R2 676
15 TraesCS3A01G478200 chr2B 116763358 116764995 1637 True 1631.0 1631 84.8570 35 1693 1 chr2B.!!$R1 1658
16 TraesCS3A01G478200 chr4D 474382675 474385752 3077 False 922.5 1410 88.3360 42 1687 2 chr4D.!!$F1 1645
17 TraesCS3A01G478200 chr4A 649502179 649503468 1289 False 1247.0 1247 84.4060 121 1416 1 chr4A.!!$F2 1295
18 TraesCS3A01G478200 chr4A 208982547 208983215 668 True 1070.0 1070 95.5160 1693 2361 1 chr4A.!!$R1 668
19 TraesCS3A01G478200 chr4A 177162315 177162991 676 False 1068.0 1068 95.1260 1687 2363 1 chr4A.!!$F1 676
20 TraesCS3A01G478200 chr5D 44457598 44458375 777 True 1098.0 1098 92.0920 912 1694 1 chr5D.!!$R1 782
21 TraesCS3A01G478200 chr7B 475724975 475725657 682 False 330.0 414 85.0260 219 934 2 chr7B.!!$F2 715

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
612 665 0.881118 AGCACACCCTTTATTGCGTG 59.119 50.0 0.0 0.0 40.04 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1452 3104 1.731709 CACGCAGTAGCAAACAGCATA 59.268 47.619 7.25 0.0 44.24 3.14 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
44 45 8.574251 TGTTGTTGCATCCTTAGTAATGTATT 57.426 30.769 0.00 0.00 0.00 1.89
110 115 5.261209 TGGATTTTGTGTCTGAGTTTTGG 57.739 39.130 0.00 0.00 0.00 3.28
119 131 6.237901 TGTGTCTGAGTTTTGGCAGTATATT 58.762 36.000 0.00 0.00 33.90 1.28
203 223 4.816385 CGATCCTGGTATGTTAACAGCAAT 59.184 41.667 14.65 0.00 42.17 3.56
253 284 7.810766 TTTTTGTTTTGTTTTTGCACACAAA 57.189 24.000 12.04 12.04 43.97 2.83
299 337 4.394439 TTGGTTTACTTGCCAGGTTTTC 57.606 40.909 0.00 0.00 36.00 2.29
307 345 4.666512 ACTTGCCAGGTTTTCTATGTGAT 58.333 39.130 0.00 0.00 0.00 3.06
311 349 4.832266 TGCCAGGTTTTCTATGTGATTTGT 59.168 37.500 0.00 0.00 0.00 2.83
385 426 9.649167 TTCTTTTAGTGTAGTAGGAACTAATGC 57.351 33.333 0.00 0.00 45.48 3.56
451 492 3.667497 ATCGTGATGCTAATCCATCGT 57.333 42.857 0.00 0.00 43.52 3.73
481 522 6.358974 TTGAAGATCATCAAGAGGTGTGTA 57.641 37.500 9.24 0.00 34.50 2.90
483 524 6.768483 TGAAGATCATCAAGAGGTGTGTAAA 58.232 36.000 0.00 0.00 0.00 2.01
484 525 6.650807 TGAAGATCATCAAGAGGTGTGTAAAC 59.349 38.462 0.00 0.00 0.00 2.01
485 526 6.114187 AGATCATCAAGAGGTGTGTAAACA 57.886 37.500 0.00 0.00 0.00 2.83
486 527 6.533730 AGATCATCAAGAGGTGTGTAAACAA 58.466 36.000 0.00 0.00 0.00 2.83
487 528 7.170965 AGATCATCAAGAGGTGTGTAAACAAT 58.829 34.615 0.00 0.00 0.00 2.71
488 529 7.667219 AGATCATCAAGAGGTGTGTAAACAATT 59.333 33.333 0.00 0.00 0.00 2.32
489 530 7.581213 TCATCAAGAGGTGTGTAAACAATTT 57.419 32.000 0.00 0.00 0.00 1.82
490 531 7.648142 TCATCAAGAGGTGTGTAAACAATTTC 58.352 34.615 0.00 0.00 0.00 2.17
491 532 7.502226 TCATCAAGAGGTGTGTAAACAATTTCT 59.498 33.333 0.00 0.00 0.00 2.52
492 533 7.259290 TCAAGAGGTGTGTAAACAATTTCTC 57.741 36.000 0.00 0.00 0.00 2.87
493 534 6.826231 TCAAGAGGTGTGTAAACAATTTCTCA 59.174 34.615 0.00 0.00 0.00 3.27
494 535 7.338196 TCAAGAGGTGTGTAAACAATTTCTCAA 59.662 33.333 0.00 0.00 0.00 3.02
495 536 7.823745 AGAGGTGTGTAAACAATTTCTCAAT 57.176 32.000 0.00 0.00 0.00 2.57
496 537 8.237811 AGAGGTGTGTAAACAATTTCTCAATT 57.762 30.769 0.00 0.00 32.36 2.32
585 638 4.219507 TGTTTGTGTCTTCTTTTTGCAGGA 59.780 37.500 0.00 0.00 0.00 3.86
612 665 0.881118 AGCACACCCTTTATTGCGTG 59.119 50.000 0.00 0.00 40.04 5.34
623 676 2.202703 TATTGCGTGTCAGCGTCGGA 62.203 55.000 0.00 0.00 40.67 4.55
687 2314 3.826524 TCAACAGCAATCCCAGTGTTTA 58.173 40.909 0.00 0.00 30.69 2.01
788 2415 1.065053 ACCAGGTAACACACAGTTGCA 60.065 47.619 0.00 0.00 43.66 4.08
934 2585 8.233190 CCTTCAAGCTGAATAAACTTCTTGTAG 58.767 37.037 0.00 0.00 35.59 2.74
935 2586 8.902540 TTCAAGCTGAATAAACTTCTTGTAGA 57.097 30.769 0.00 0.00 30.26 2.59
1045 2696 5.245977 TGGATAATGAAGCACTATGATCCGA 59.754 40.000 0.00 0.00 35.40 4.55
1063 2714 4.058124 TCCGAAGAAGTCACAGATTGTTG 58.942 43.478 0.00 0.00 0.00 3.33
1109 2760 3.742433 AGATGCAGCTAGTGTCCATAC 57.258 47.619 0.55 0.00 0.00 2.39
1149 2800 0.044855 AGGGGAGGAAGGTGTGCTAT 59.955 55.000 0.00 0.00 0.00 2.97
1243 2894 4.094739 TCACTGCATGGTGTAAAATGATCG 59.905 41.667 6.04 0.00 38.28 3.69
1252 2903 6.176896 TGGTGTAAAATGATCGAAGGAATGA 58.823 36.000 0.00 0.00 0.00 2.57
1277 2928 1.144503 AGCCCATGATGATGACTTCCC 59.855 52.381 0.00 0.00 0.00 3.97
1379 3031 4.694509 GCTCTGATGGATGTCAATGGTATC 59.305 45.833 0.00 0.00 0.00 2.24
1452 3104 2.869503 ATCGTCCCGCGGCAAGAAAT 62.870 55.000 22.85 6.42 41.72 2.17
1568 3239 4.476862 GGCAACGGAATTTCTTCTTCTTC 58.523 43.478 0.00 0.00 0.00 2.87
1913 3588 4.163649 TCAGCATGATCATCAAGACTTCCT 59.836 41.667 4.86 0.00 42.56 3.36
1933 3608 3.073946 CCTCCAAGTCTTCCCAAAGGTTA 59.926 47.826 0.00 0.00 33.03 2.85
1966 3641 9.791838 GCACAAACACTAATTAAAAGCATAAAC 57.208 29.630 0.00 0.00 0.00 2.01
1986 3661 2.026822 ACCCACATCTAAACAGAGGCTG 60.027 50.000 0.00 0.00 37.52 4.85
2105 3780 5.468540 AGGCATGATGATTTCAATGATGG 57.531 39.130 0.00 0.00 38.03 3.51
2301 3976 6.478344 GCACATAGAGAGGAAACTTGATACTG 59.522 42.308 0.00 0.00 44.43 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 3.529533 CTTCCAATGCACACCAAACAAA 58.470 40.909 0.00 0.00 0.00 2.83
110 115 8.213518 TCCAGATGACTTTTTGAATATACTGC 57.786 34.615 0.00 0.00 0.00 4.40
119 131 7.111247 ACAACAAATCCAGATGACTTTTTGA 57.889 32.000 0.00 0.00 0.00 2.69
203 223 6.061441 CAGCAATCATATAAGGGGTGTGTTA 58.939 40.000 0.00 0.00 0.00 2.41
247 276 4.101430 AGGCAAATCACCTTCAATTTGTGT 59.899 37.500 8.96 0.00 42.29 3.72
253 284 2.893424 ACCAGGCAAATCACCTTCAAT 58.107 42.857 0.00 0.00 34.42 2.57
299 337 8.720562 TCACACAAATACTGACAAATCACATAG 58.279 33.333 0.00 0.00 0.00 2.23
307 345 7.899178 ATATCGTCACACAAATACTGACAAA 57.101 32.000 0.00 0.00 35.06 2.83
311 349 7.543756 TCTGAATATCGTCACACAAATACTGA 58.456 34.615 0.00 0.00 0.00 3.41
385 426 1.608801 GCCCTTTTTGCTTGGTCCATG 60.609 52.381 0.00 0.00 0.00 3.66
451 492 5.065602 CCTCTTGATGATCTTCAATCGCAAA 59.934 40.000 20.67 1.60 35.20 3.68
563 615 4.562789 GTCCTGCAAAAAGAAGACACAAAC 59.437 41.667 0.00 0.00 0.00 2.93
585 638 0.846693 AAAGGGTGTGCTTCTCTGGT 59.153 50.000 0.00 0.00 0.00 4.00
612 665 1.341606 CTTTCTTCTCCGACGCTGAC 58.658 55.000 0.00 0.00 0.00 3.51
623 676 2.437651 GGGCAGCTATCTCCTTTCTTCT 59.562 50.000 0.00 0.00 0.00 2.85
687 2314 1.064505 CATTTTCGTCGCCATCTGCAT 59.935 47.619 0.00 0.00 41.33 3.96
736 2363 4.623595 GTCTTTTGACGTTTTGCTTTTGGA 59.376 37.500 0.00 0.00 39.89 3.53
788 2415 4.432712 GGCAAGTGTTGATCAAAAGTTGT 58.567 39.130 32.47 9.28 39.82 3.32
934 2585 4.519906 TGATAACCCCCTTTTGGAGATC 57.480 45.455 0.00 0.00 44.07 2.75
935 2586 5.043432 TCAATGATAACCCCCTTTTGGAGAT 60.043 40.000 0.00 0.00 44.07 2.75
1045 2696 5.680619 TGGTACAACAATCTGTGACTTCTT 58.319 37.500 0.00 0.00 31.92 2.52
1063 2714 2.172930 GGATCTTCCCCCTTTCTGGTAC 59.827 54.545 0.00 0.00 0.00 3.34
1109 2760 0.321653 GTTAGGCAGCCCCCATATCG 60.322 60.000 8.22 0.00 0.00 2.92
1149 2800 2.027285 TGTGATTTCAGGCCGAATCTCA 60.027 45.455 21.89 21.13 32.32 3.27
1243 2894 2.442236 TGGGCTCCATTCATTCCTTC 57.558 50.000 0.00 0.00 0.00 3.46
1252 2903 2.445905 AGTCATCATCATGGGCTCCATT 59.554 45.455 4.15 0.00 42.23 3.16
1359 3011 4.976864 TGGATACCATTGACATCCATCAG 58.023 43.478 12.55 0.00 42.55 2.90
1452 3104 1.731709 CACGCAGTAGCAAACAGCATA 59.268 47.619 7.25 0.00 44.24 3.14
1890 3565 4.163649 AGGAAGTCTTGATGATCATGCTGA 59.836 41.667 14.30 5.04 0.00 4.26
1913 3588 5.550403 AGTATAACCTTTGGGAAGACTTGGA 59.450 40.000 0.00 0.00 34.71 3.53
1933 3608 9.691362 CTTTTAATTAGTGTTTGTGCCAAGTAT 57.309 29.630 0.00 0.00 0.00 2.12
1966 3641 2.636830 CAGCCTCTGTTTAGATGTGGG 58.363 52.381 0.00 0.00 31.21 4.61
2105 3780 8.514594 TGTTTCAATTCTCATCCTTTATGTGAC 58.485 33.333 0.00 0.00 37.72 3.67
2301 3976 7.809806 GGAATATATGCTTGTAGGAATTGCAAC 59.190 37.037 0.00 0.00 37.20 4.17


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

AutoCloner maintained by Alex Coulton.