Multiple sequence alignment - TraesCS3B01G409900

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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 TraesCS3B01G409900 chr3B 100.000 3735 0 0 1 3735 646717702 646713968 0.000000e+00 6898
1 TraesCS3B01G409900 chr3B 80.483 538 78 21 63 583 15074123 15073596 1.630000e-103 387
2 TraesCS3B01G409900 chr3B 85.065 308 31 11 1874 2176 60257578 60257281 2.180000e-77 300
3 TraesCS3B01G409900 chr3B 92.248 129 10 0 3607 3735 285200627 285200755 2.290000e-42 183
4 TraesCS3B01G409900 chr1A 97.653 3110 36 9 630 3735 111990318 111987242 0.000000e+00 5304
5 TraesCS3B01G409900 chr1A 88.509 818 56 14 2800 3583 510300027 510299214 0.000000e+00 955
6 TraesCS3B01G409900 chr1A 88.161 473 45 7 2331 2799 518954326 518953861 1.520000e-153 553
7 TraesCS3B01G409900 chr1A 91.270 126 11 0 3607 3732 214730328 214730203 4.960000e-39 172
8 TraesCS3B01G409900 chr2B 97.473 2414 44 3 1333 3733 138123055 138120646 0.000000e+00 4104
9 TraesCS3B01G409900 chr2B 94.093 711 34 5 632 1338 138123824 138123118 0.000000e+00 1074
10 TraesCS3B01G409900 chr2B 89.750 839 47 18 2800 3606 697436865 697436034 0.000000e+00 1037
11 TraesCS3B01G409900 chr7B 97.807 1961 38 2 1333 3293 73925808 73923853 0.000000e+00 3378
12 TraesCS3B01G409900 chr7B 94.126 715 35 5 628 1338 73926582 73925871 0.000000e+00 1081
13 TraesCS3B01G409900 chr7B 98.201 389 6 1 3348 3735 73923857 73923469 0.000000e+00 678
14 TraesCS3B01G409900 chr3A 97.809 1506 30 1 1333 2838 565330391 565331893 0.000000e+00 2595
15 TraesCS3B01G409900 chr3A 94.159 719 35 5 624 1338 565329613 565330328 0.000000e+00 1088
16 TraesCS3B01G409900 chr3A 98.482 461 6 1 2833 3293 565340941 565341400 0.000000e+00 811
17 TraesCS3B01G409900 chr3A 89.189 629 34 17 1 605 626673816 626673198 0.000000e+00 754
18 TraesCS3B01G409900 chr3A 98.201 389 6 1 3348 3735 565341396 565341784 0.000000e+00 678
19 TraesCS3B01G409900 chr3A 83.333 492 67 13 13 497 111084553 111084070 1.230000e-119 440
20 TraesCS3B01G409900 chr3A 92.737 179 5 5 646 820 565343539 565343713 6.190000e-63 252
21 TraesCS3B01G409900 chr1B 89.988 839 49 17 2800 3606 130938746 130937911 0.000000e+00 1051
22 TraesCS3B01G409900 chr1B 89.725 837 54 14 2800 3606 223853333 223852499 0.000000e+00 1040
23 TraesCS3B01G409900 chr1B 88.917 785 49 17 2800 3554 575124533 575125309 0.000000e+00 933
24 TraesCS3B01G409900 chr1B 89.641 473 40 5 2331 2799 572288837 572288370 8.930000e-166 593
25 TraesCS3B01G409900 chr1B 95.385 130 5 1 3607 3735 575126002 575126131 4.890000e-49 206
26 TraesCS3B01G409900 chr3D 88.509 818 54 18 2800 3583 301346351 301345540 0.000000e+00 953
27 TraesCS3B01G409900 chr3D 89.522 544 40 6 1638 2176 112301237 112300706 0.000000e+00 673
28 TraesCS3B01G409900 chr3D 90.114 263 20 3 1333 1593 112301492 112301234 1.660000e-88 337
29 TraesCS3B01G409900 chr6D 87.897 818 59 15 2800 3583 436500462 436499651 0.000000e+00 926
30 TraesCS3B01G409900 chr2A 98.742 477 6 0 2575 3051 191918741 191918265 0.000000e+00 848
31 TraesCS3B01G409900 chr2A 87.890 545 48 7 1638 2176 5960129 5959597 3.170000e-175 625
32 TraesCS3B01G409900 chr2A 88.410 371 34 6 801 1168 662740790 662740426 4.430000e-119 438
33 TraesCS3B01G409900 chr2A 79.545 528 83 22 92 605 91142380 91142896 1.650000e-93 353
34 TraesCS3B01G409900 chr2A 89.734 263 20 4 1333 1593 5960383 5960126 2.780000e-86 329
35 TraesCS3B01G409900 chr2A 93.458 107 6 1 3630 3735 734550693 734550799 1.390000e-34 158
36 TraesCS3B01G409900 chr2D 92.362 563 36 5 2238 2799 633593201 633593757 0.000000e+00 795
37 TraesCS3B01G409900 chr2D 89.461 408 42 1 930 1336 73913582 73913175 7.150000e-142 514
38 TraesCS3B01G409900 chr2D 89.461 408 42 1 930 1336 74119827 74120234 7.150000e-142 514
39 TraesCS3B01G409900 chr2D 78.275 626 88 37 1 605 601986544 601987142 3.550000e-95 359
40 TraesCS3B01G409900 chr5A 90.409 563 45 7 2238 2799 565941080 565940526 0.000000e+00 732
41 TraesCS3B01G409900 chr5A 81.150 626 81 26 1 605 597422616 597423225 5.650000e-128 468
42 TraesCS3B01G409900 chr5A 92.097 329 24 2 1391 1718 566039731 566039404 2.630000e-126 462
43 TraesCS3B01G409900 chr6B 89.319 543 43 4 1638 2176 668008202 668007671 0.000000e+00 667
44 TraesCS3B01G409900 chr6B 80.671 626 85 26 1 604 667226118 667225507 1.580000e-123 453
45 TraesCS3B01G409900 chr6B 88.736 364 35 4 803 1165 95585461 95585819 1.230000e-119 440
46 TraesCS3B01G409900 chr6B 90.494 263 18 4 1333 1593 668008456 668008199 1.280000e-89 340
47 TraesCS3B01G409900 chr6A 87.085 542 55 6 1638 2176 587376512 587375983 1.920000e-167 599
48 TraesCS3B01G409900 chr6A 90.000 260 20 3 1336 1593 587376764 587376509 7.730000e-87 331
49 TraesCS3B01G409900 chr1D 89.641 473 38 7 2331 2799 423036034 423035569 3.210000e-165 592
50 TraesCS3B01G409900 chr1D 85.655 481 32 15 3105 3554 51927137 51927611 4.370000e-129 472
51 TraesCS3B01G409900 chr1D 79.190 543 85 23 81 604 25699662 25699129 5.940000e-93 351
52 TraesCS3B01G409900 chrUn 88.767 365 40 1 801 1165 30200595 30200958 2.650000e-121 446
53 TraesCS3B01G409900 chr5D 80.038 531 79 23 1 519 309672367 309672882 5.890000e-98 368
54 TraesCS3B01G409900 chr4D 84.084 333 32 5 3288 3600 12700126 12699795 6.060000e-78 302
55 TraesCS3B01G409900 chr4B 83.784 333 33 5 3288 3600 23404435 23404104 2.820000e-76 296
56 TraesCS3B01G409900 chr4A 82.493 337 29 10 3293 3606 589603213 589602884 6.150000e-68 268
57 TraesCS3B01G409900 chr4A 93.458 107 6 1 3630 3735 599902995 599902889 1.390000e-34 158


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 TraesCS3B01G409900 chr3B 646713968 646717702 3734 True 6898.000000 6898 100.000000 1 3735 1 chr3B.!!$R3 3734
1 TraesCS3B01G409900 chr3B 15073596 15074123 527 True 387.000000 387 80.483000 63 583 1 chr3B.!!$R1 520
2 TraesCS3B01G409900 chr1A 111987242 111990318 3076 True 5304.000000 5304 97.653000 630 3735 1 chr1A.!!$R1 3105
3 TraesCS3B01G409900 chr1A 510299214 510300027 813 True 955.000000 955 88.509000 2800 3583 1 chr1A.!!$R3 783
4 TraesCS3B01G409900 chr2B 138120646 138123824 3178 True 2589.000000 4104 95.783000 632 3733 2 chr2B.!!$R2 3101
5 TraesCS3B01G409900 chr2B 697436034 697436865 831 True 1037.000000 1037 89.750000 2800 3606 1 chr2B.!!$R1 806
6 TraesCS3B01G409900 chr7B 73923469 73926582 3113 True 1712.333333 3378 96.711333 628 3735 3 chr7B.!!$R1 3107
7 TraesCS3B01G409900 chr3A 565329613 565331893 2280 False 1841.500000 2595 95.984000 624 2838 2 chr3A.!!$F1 2214
8 TraesCS3B01G409900 chr3A 626673198 626673816 618 True 754.000000 754 89.189000 1 605 1 chr3A.!!$R2 604
9 TraesCS3B01G409900 chr3A 565340941 565343713 2772 False 580.333333 811 96.473333 646 3735 3 chr3A.!!$F2 3089
10 TraesCS3B01G409900 chr1B 130937911 130938746 835 True 1051.000000 1051 89.988000 2800 3606 1 chr1B.!!$R1 806
11 TraesCS3B01G409900 chr1B 223852499 223853333 834 True 1040.000000 1040 89.725000 2800 3606 1 chr1B.!!$R2 806
12 TraesCS3B01G409900 chr1B 575124533 575126131 1598 False 569.500000 933 92.151000 2800 3735 2 chr1B.!!$F1 935
13 TraesCS3B01G409900 chr3D 301345540 301346351 811 True 953.000000 953 88.509000 2800 3583 1 chr3D.!!$R1 783
14 TraesCS3B01G409900 chr3D 112300706 112301492 786 True 505.000000 673 89.818000 1333 2176 2 chr3D.!!$R2 843
15 TraesCS3B01G409900 chr6D 436499651 436500462 811 True 926.000000 926 87.897000 2800 3583 1 chr6D.!!$R1 783
16 TraesCS3B01G409900 chr2A 5959597 5960383 786 True 477.000000 625 88.812000 1333 2176 2 chr2A.!!$R3 843
17 TraesCS3B01G409900 chr2A 91142380 91142896 516 False 353.000000 353 79.545000 92 605 1 chr2A.!!$F1 513
18 TraesCS3B01G409900 chr2D 633593201 633593757 556 False 795.000000 795 92.362000 2238 2799 1 chr2D.!!$F3 561
19 TraesCS3B01G409900 chr2D 601986544 601987142 598 False 359.000000 359 78.275000 1 605 1 chr2D.!!$F2 604
20 TraesCS3B01G409900 chr5A 565940526 565941080 554 True 732.000000 732 90.409000 2238 2799 1 chr5A.!!$R1 561
21 TraesCS3B01G409900 chr5A 597422616 597423225 609 False 468.000000 468 81.150000 1 605 1 chr5A.!!$F1 604
22 TraesCS3B01G409900 chr6B 668007671 668008456 785 True 503.500000 667 89.906500 1333 2176 2 chr6B.!!$R2 843
23 TraesCS3B01G409900 chr6B 667225507 667226118 611 True 453.000000 453 80.671000 1 604 1 chr6B.!!$R1 603
24 TraesCS3B01G409900 chr6A 587375983 587376764 781 True 465.000000 599 88.542500 1336 2176 2 chr6A.!!$R1 840
25 TraesCS3B01G409900 chr1D 25699129 25699662 533 True 351.000000 351 79.190000 81 604 1 chr1D.!!$R1 523
26 TraesCS3B01G409900 chr5D 309672367 309672882 515 False 368.000000 368 80.038000 1 519 1 chr5D.!!$F1 518

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
677 707 0.311165 CCGATCGCTTCTGGTCGTAT 59.689 55.0 10.32 0.0 32.55 3.06 F
945 978 0.689412 CCACTCTCCCTTCTCCTCCC 60.689 65.0 0.00 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2251 2487 4.154918 AGAAGAAAACCGCTCATAGCTTTG 59.845 41.667 0.0 0.0 39.6 2.77 R
2876 3155 5.012251 TGTTTGGTGTGCTACTGGAATACTA 59.988 40.000 0.0 0.0 0.0 1.82 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
79 97 4.738252 GTGTTTCATTCTTGTTCGTTTCCC 59.262 41.667 0.00 0.00 0.00 3.97
177 198 9.952341 GTTTGTTTTTGTTTCACTCTACATTTC 57.048 29.630 0.00 0.00 0.00 2.17
420 450 9.824534 GTTGTTGAACATTTTTCAAATTCTTGT 57.175 25.926 0.00 0.00 39.76 3.16
463 493 9.702726 ATTCGTTCAACATTTTTCATATACTCG 57.297 29.630 0.00 0.00 0.00 4.18
464 494 8.246908 TCGTTCAACATTTTTCATATACTCGT 57.753 30.769 0.00 0.00 0.00 4.18
465 495 8.377681 TCGTTCAACATTTTTCATATACTCGTC 58.622 33.333 0.00 0.00 0.00 4.20
466 496 7.634817 CGTTCAACATTTTTCATATACTCGTCC 59.365 37.037 0.00 0.00 0.00 4.79
467 497 8.447833 GTTCAACATTTTTCATATACTCGTCCA 58.552 33.333 0.00 0.00 0.00 4.02
468 498 8.554835 TCAACATTTTTCATATACTCGTCCAA 57.445 30.769 0.00 0.00 0.00 3.53
469 499 8.447833 TCAACATTTTTCATATACTCGTCCAAC 58.552 33.333 0.00 0.00 0.00 3.77
470 500 7.915293 ACATTTTTCATATACTCGTCCAACA 57.085 32.000 0.00 0.00 0.00 3.33
471 501 8.506168 ACATTTTTCATATACTCGTCCAACAT 57.494 30.769 0.00 0.00 0.00 2.71
472 502 8.956426 ACATTTTTCATATACTCGTCCAACATT 58.044 29.630 0.00 0.00 0.00 2.71
473 503 9.787532 CATTTTTCATATACTCGTCCAACATTT 57.212 29.630 0.00 0.00 0.00 2.32
677 707 0.311165 CCGATCGCTTCTGGTCGTAT 59.689 55.000 10.32 0.00 32.55 3.06
945 978 0.689412 CCACTCTCCCTTCTCCTCCC 60.689 65.000 0.00 0.00 0.00 4.30
947 980 1.097722 ACTCTCCCTTCTCCTCCCTT 58.902 55.000 0.00 0.00 0.00 3.95
1057 1090 4.337177 TCCACGCCAAATCCGCCA 62.337 61.111 0.00 0.00 0.00 5.69
1410 1512 4.976731 GTGGTATGATGCGACTACAACTAG 59.023 45.833 0.00 0.00 0.00 2.57
1505 1607 6.509418 TTATAATGCACAACTCAAAGGACC 57.491 37.500 0.00 0.00 0.00 4.46
2196 2432 1.191489 TCATCCGTGTTCTGCTCCCA 61.191 55.000 0.00 0.00 0.00 4.37
2251 2487 6.348868 GCATCTACTTTGCCATTATAGGAAGC 60.349 42.308 0.00 0.00 33.95 3.86
2407 2685 6.447162 TCTACGTCAATCTAGCATGGTTATG 58.553 40.000 1.12 0.00 37.36 1.90
2876 3155 2.489329 CGATGATTTCCTGGCAGTTTGT 59.511 45.455 14.43 0.00 0.00 2.83
3016 3295 7.748031 TGTGTAAATTTTGACATGTGTTCAC 57.252 32.000 1.15 0.71 0.00 3.18
3041 3320 2.696187 TCCGTTATGCAGTAGCCATACA 59.304 45.455 0.00 0.00 41.13 2.29
3699 4658 8.687242 GCTATCTAATATATAGTGTGTGCTCCA 58.313 37.037 0.00 0.00 30.91 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 57 7.080099 CGAACAAGAATGAAACACATCTGATT 58.920 34.615 0.00 0.00 38.38 2.57
394 424 9.824534 ACAAGAATTTGAAAAATGTTCAACAAC 57.175 25.926 0.00 0.00 38.05 3.32
437 467 9.702726 CGAGTATATGAAAAATGTTGAACGAAT 57.297 29.630 0.00 0.00 0.00 3.34
438 468 8.714179 ACGAGTATATGAAAAATGTTGAACGAA 58.286 29.630 0.00 0.00 0.00 3.85
439 469 8.246908 ACGAGTATATGAAAAATGTTGAACGA 57.753 30.769 0.00 0.00 0.00 3.85
440 470 7.634817 GGACGAGTATATGAAAAATGTTGAACG 59.365 37.037 0.00 0.00 0.00 3.95
441 471 8.447833 TGGACGAGTATATGAAAAATGTTGAAC 58.552 33.333 0.00 0.00 0.00 3.18
442 472 8.554835 TGGACGAGTATATGAAAAATGTTGAA 57.445 30.769 0.00 0.00 0.00 2.69
443 473 8.447833 GTTGGACGAGTATATGAAAAATGTTGA 58.552 33.333 0.00 0.00 0.00 3.18
444 474 8.233868 TGTTGGACGAGTATATGAAAAATGTTG 58.766 33.333 0.00 0.00 0.00 3.33
445 475 8.330466 TGTTGGACGAGTATATGAAAAATGTT 57.670 30.769 0.00 0.00 0.00 2.71
446 476 7.915293 TGTTGGACGAGTATATGAAAAATGT 57.085 32.000 0.00 0.00 0.00 2.71
447 477 9.787532 AAATGTTGGACGAGTATATGAAAAATG 57.212 29.630 0.00 0.00 0.00 2.32
600 630 9.255304 GATATAACCAAAAACACTCAGCAAAAA 57.745 29.630 0.00 0.00 0.00 1.94
601 631 8.637986 AGATATAACCAAAAACACTCAGCAAAA 58.362 29.630 0.00 0.00 0.00 2.44
602 632 8.177119 AGATATAACCAAAAACACTCAGCAAA 57.823 30.769 0.00 0.00 0.00 3.68
603 633 7.759489 AGATATAACCAAAAACACTCAGCAA 57.241 32.000 0.00 0.00 0.00 3.91
604 634 7.759489 AAGATATAACCAAAAACACTCAGCA 57.241 32.000 0.00 0.00 0.00 4.41
643 673 8.737175 AGAAGCGATCGGTGATTTATTAGTATA 58.263 33.333 22.01 0.00 0.00 1.47
644 674 7.542477 CAGAAGCGATCGGTGATTTATTAGTAT 59.458 37.037 22.01 0.00 0.00 2.12
677 707 0.251354 TTGCAAAAAGGGCAGCAACA 59.749 45.000 0.00 0.00 43.05 3.33
701 731 6.183360 GCGGGTTAATTTCTAATAAACGGACA 60.183 38.462 0.00 0.00 0.00 4.02
702 732 6.183360 TGCGGGTTAATTTCTAATAAACGGAC 60.183 38.462 0.00 0.00 0.00 4.79
705 738 6.778108 ACTGCGGGTTAATTTCTAATAAACG 58.222 36.000 0.00 0.00 0.00 3.60
712 745 2.841881 AGGGACTGCGGGTTAATTTCTA 59.158 45.455 0.00 0.00 37.18 2.10
778 811 2.188817 GTGGTCTGGTGGATTAGAGGT 58.811 52.381 0.00 0.00 0.00 3.85
928 961 1.097722 AAGGGAGGAGAAGGGAGAGT 58.902 55.000 0.00 0.00 0.00 3.24
945 978 3.699038 AGGTGAGAGGAGATCGAGAAAAG 59.301 47.826 0.00 0.00 0.00 2.27
947 980 3.053991 AGAGGTGAGAGGAGATCGAGAAA 60.054 47.826 0.00 0.00 0.00 2.52
1125 1158 3.953775 CAGGTTGAGCGGGGTGGT 61.954 66.667 0.00 0.00 0.00 4.16
1505 1607 4.868067 ACCTTATCTTACCAATAGCGTCG 58.132 43.478 0.00 0.00 0.00 5.12
1684 1788 8.187913 TCATGTTTGAATTTTATGTCCAAGGA 57.812 30.769 0.00 0.00 0.00 3.36
2196 2432 4.476752 ACACACACAACCGGCGGT 62.477 61.111 28.83 28.83 37.65 5.68
2251 2487 4.154918 AGAAGAAAACCGCTCATAGCTTTG 59.845 41.667 0.00 0.00 39.60 2.77
2407 2685 7.097047 CGTAATGAAGTCAACATTCAACAACAC 60.097 37.037 0.00 0.00 39.92 3.32
2876 3155 5.012251 TGTTTGGTGTGCTACTGGAATACTA 59.988 40.000 0.00 0.00 0.00 1.82
3016 3295 2.159099 TGGCTACTGCATAACGGAAGAG 60.159 50.000 0.00 0.00 41.91 2.85


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

AutoCloner maintained by Alex Coulton.