Multiple sequence alignment - TraesCS3B01G077400

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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 TraesCS3B01G077400 chr3B 100.000 4111 0 0 1 4111 47684635 47680525 0.000000e+00 7592.0
1 TraesCS3B01G077400 chr3B 99.253 3481 14 5 633 4111 48027016 48023546 0.000000e+00 6274.0
2 TraesCS3B01G077400 chr3B 95.246 2524 66 19 876 3369 49116451 49118950 0.000000e+00 3947.0
3 TraesCS3B01G077400 chr3B 97.126 661 9 2 3451 4111 49118949 49119599 0.000000e+00 1107.0
4 TraesCS3B01G077400 chr3B 98.703 617 8 0 1 617 48027617 48027001 0.000000e+00 1096.0
5 TraesCS3B01G077400 chr3B 90.054 372 23 5 876 1241 47830488 47830125 1.730000e-128 470.0
6 TraesCS3B01G077400 chr3B 90.054 372 22 6 876 1241 47701308 47700946 6.220000e-128 468.0
7 TraesCS3B01G077400 chr3B 89.516 372 25 5 876 1241 48101153 48100790 3.740000e-125 459.0
8 TraesCS3B01G077400 chr3B 89.516 372 24 9 876 1241 47764029 47763667 1.350000e-124 457.0
9 TraesCS3B01G077400 chr3B 89.247 372 26 8 876 1241 48039172 48038809 1.740000e-123 453.0
10 TraesCS3B01G077400 chr3B 88.978 372 27 5 876 1241 47769168 47768805 8.110000e-122 448.0
11 TraesCS3B01G077400 chr3B 93.333 90 6 0 3363 3452 745923138 745923049 2.580000e-27 134.0
12 TraesCS3B01G077400 chr3B 91.398 93 7 1 3361 3452 766392168 766392260 4.310000e-25 126.0
13 TraesCS3B01G077400 chr3B 100.000 28 0 0 585 612 49116251 49116224 7.000000e-03 52.8
14 TraesCS3B01G077400 chr3D 97.009 2775 40 9 633 3369 28732815 28735584 0.000000e+00 4625.0
15 TraesCS3B01G077400 chr3D 98.206 1951 28 2 1422 3369 28744932 28746878 0.000000e+00 3402.0
16 TraesCS3B01G077400 chr3D 96.272 617 23 0 1 617 28732214 28732830 0.000000e+00 1013.0
17 TraesCS3B01G077400 chr3D 96.272 617 23 0 1 617 28743207 28743823 0.000000e+00 1013.0
18 TraesCS3B01G077400 chr3D 94.061 623 22 4 3451 4073 28746877 28747484 0.000000e+00 931.0
19 TraesCS3B01G077400 chr3D 95.798 238 9 1 3451 3688 28735583 28735819 2.320000e-102 383.0
20 TraesCS3B01G077400 chr3D 91.919 99 2 3 633 726 28743808 28743905 2.580000e-27 134.0
21 TraesCS3B01G077400 chr3D 100.000 31 0 0 4080 4110 28747478 28747508 1.600000e-04 58.4
22 TraesCS3B01G077400 chr3D 100.000 29 0 0 4083 4111 28735820 28735848 2.000000e-03 54.7
23 TraesCS3B01G077400 chr3A 94.087 1945 67 7 1435 3369 38290753 38288847 0.000000e+00 2911.0
24 TraesCS3B01G077400 chr3A 95.506 267 8 1 3451 3713 38288848 38288582 1.370000e-114 424.0
25 TraesCS3B01G077400 chr3A 87.455 279 27 7 279 554 38293035 38292762 8.580000e-82 315.0
26 TraesCS3B01G077400 chr3A 94.495 109 5 1 1206 1314 38292242 38292135 2.540000e-37 167.0
27 TraesCS3B01G077400 chr3A 89.796 98 10 0 661 758 38292688 38292591 4.310000e-25 126.0
28 TraesCS3B01G077400 chr6B 95.049 1737 60 4 1633 3369 131222536 131220826 0.000000e+00 2708.0
29 TraesCS3B01G077400 chr6B 96.168 809 24 3 772 1576 131223338 131222533 0.000000e+00 1315.0
30 TraesCS3B01G077400 chr6B 94.856 661 17 5 3451 4111 131220827 131220184 0.000000e+00 1016.0
31 TraesCS3B01G077400 chr6B 87.558 217 20 2 305 521 131287880 131287671 1.140000e-60 244.0
32 TraesCS3B01G077400 chr2D 84.901 2073 211 38 1207 3250 648385899 648387898 0.000000e+00 2001.0
33 TraesCS3B01G077400 chrUn 84.453 1280 149 25 1207 2465 30962032 30960782 0.000000e+00 1216.0
34 TraesCS3B01G077400 chrUn 100.000 398 0 0 3056 3453 479036147 479036544 0.000000e+00 736.0
35 TraesCS3B01G077400 chr5B 94.318 88 4 1 3368 3454 648279310 648279397 2.580000e-27 134.0
36 TraesCS3B01G077400 chr5B 92.308 91 5 2 3364 3453 648279398 648279309 1.200000e-25 128.0
37 TraesCS3B01G077400 chr1B 90.385 104 6 4 3362 3461 624302612 624302715 2.580000e-27 134.0
38 TraesCS3B01G077400 chr1B 92.222 90 6 1 3364 3452 624302708 624302619 4.310000e-25 126.0
39 TraesCS3B01G077400 chr6D 94.253 87 4 1 3367 3452 63329720 63329806 9.270000e-27 132.0
40 TraesCS3B01G077400 chr2A 91.304 46 4 0 2788 2833 138526707 138526662 3.430000e-06 63.9


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 TraesCS3B01G077400 chr3B 47680525 47684635 4110 True 7592.000000 7592 100.000000 1 4111 1 chr3B.!!$R1 4110
1 TraesCS3B01G077400 chr3B 48023546 48027617 4071 True 3685.000000 6274 98.978000 1 4111 2 chr3B.!!$R10 4110
2 TraesCS3B01G077400 chr3B 49116451 49119599 3148 False 2527.000000 3947 96.186000 876 4111 2 chr3B.!!$F2 3235
3 TraesCS3B01G077400 chr3D 28732214 28735848 3634 False 1518.925000 4625 97.269750 1 4111 4 chr3D.!!$F1 4110
4 TraesCS3B01G077400 chr3D 28743207 28747508 4301 False 1107.680000 3402 96.091600 1 4110 5 chr3D.!!$F2 4109
5 TraesCS3B01G077400 chr3A 38288582 38293035 4453 True 788.600000 2911 92.267800 279 3713 5 chr3A.!!$R1 3434
6 TraesCS3B01G077400 chr6B 131220184 131223338 3154 True 1679.666667 2708 95.357667 772 4111 3 chr6B.!!$R2 3339
7 TraesCS3B01G077400 chr2D 648385899 648387898 1999 False 2001.000000 2001 84.901000 1207 3250 1 chr2D.!!$F1 2043
8 TraesCS3B01G077400 chrUn 30960782 30962032 1250 True 1216.000000 1216 84.453000 1207 2465 1 chrUn.!!$R1 1258

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
602 604 0.109086 AAGTGACGCGAGGATGACAG 60.109 55.0 15.93 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3728 5470 7.122138 AGTAATGTGACTGATCTCATGTCAT 57.878 36.0 12.41 0.07 41.78 3.06 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
156 157 1.809619 GCTGCAATGTAGCGGTCGA 60.810 57.895 7.70 0.00 42.87 4.20
375 377 1.067516 GACTGCATGTTGTTGCCTTGT 59.932 47.619 0.00 0.00 42.06 3.16
441 443 1.308047 AGAAGAACAACATGCGTGCA 58.692 45.000 5.64 0.00 0.00 4.57
477 479 1.408822 GCTGGGAGGAACAAATCGGAT 60.409 52.381 0.00 0.00 0.00 4.18
542 544 2.171870 GGACCTGGATAAATCCCGAACA 59.828 50.000 0.00 0.00 46.59 3.18
601 603 0.388520 CAAGTGACGCGAGGATGACA 60.389 55.000 15.93 0.00 0.00 3.58
602 604 0.109086 AAGTGACGCGAGGATGACAG 60.109 55.000 15.93 0.00 0.00 3.51
604 606 1.977009 TGACGCGAGGATGACAGGT 60.977 57.895 15.93 0.00 0.00 4.00
605 607 1.215647 GACGCGAGGATGACAGGTT 59.784 57.895 15.93 0.00 0.00 3.50
606 608 0.389948 GACGCGAGGATGACAGGTTT 60.390 55.000 15.93 0.00 0.00 3.27
608 610 1.135083 ACGCGAGGATGACAGGTTTAG 60.135 52.381 15.93 0.00 0.00 1.85
611 613 2.673368 GCGAGGATGACAGGTTTAGTTG 59.327 50.000 0.00 0.00 0.00 3.16
612 614 3.262420 CGAGGATGACAGGTTTAGTTGG 58.738 50.000 0.00 0.00 0.00 3.77
613 615 3.010420 GAGGATGACAGGTTTAGTTGGC 58.990 50.000 0.00 0.00 0.00 4.52
614 616 2.644798 AGGATGACAGGTTTAGTTGGCT 59.355 45.455 0.00 0.00 0.00 4.75
615 617 2.749621 GGATGACAGGTTTAGTTGGCTG 59.250 50.000 0.00 0.00 0.00 4.85
616 618 3.559171 GGATGACAGGTTTAGTTGGCTGA 60.559 47.826 0.00 0.00 0.00 4.26
617 619 3.788227 TGACAGGTTTAGTTGGCTGAT 57.212 42.857 0.00 0.00 0.00 2.90
618 620 3.674997 TGACAGGTTTAGTTGGCTGATC 58.325 45.455 0.00 0.00 0.00 2.92
619 621 3.010420 GACAGGTTTAGTTGGCTGATCC 58.990 50.000 0.00 0.00 0.00 3.36
620 622 2.290960 ACAGGTTTAGTTGGCTGATCCC 60.291 50.000 0.00 0.00 0.00 3.85
621 623 1.065418 AGGTTTAGTTGGCTGATCCCG 60.065 52.381 0.00 0.00 0.00 5.14
622 624 0.733150 GTTTAGTTGGCTGATCCCGC 59.267 55.000 0.00 0.00 0.00 6.13
623 625 0.326595 TTTAGTTGGCTGATCCCGCA 59.673 50.000 6.45 0.00 0.00 5.69
624 626 0.326595 TTAGTTGGCTGATCCCGCAA 59.673 50.000 6.45 0.00 0.00 4.85
625 627 0.326595 TAGTTGGCTGATCCCGCAAA 59.673 50.000 6.45 0.00 0.00 3.68
626 628 0.539438 AGTTGGCTGATCCCGCAAAA 60.539 50.000 6.45 0.00 0.00 2.44
627 629 0.316841 GTTGGCTGATCCCGCAAAAA 59.683 50.000 6.45 0.00 0.00 1.94
769 776 7.394816 AGTACTAATAACAAGCTTGTGTGGAT 58.605 34.615 31.73 18.31 41.31 3.41
800 832 3.865745 CGGTGCTTCTCGATCTATTTGTT 59.134 43.478 0.00 0.00 0.00 2.83
3852 5594 3.194005 TCTCCACAGGTTTTCAGACAC 57.806 47.619 0.00 0.00 0.00 3.67
3879 5621 4.998051 TCCTTCCTTTGGCTATGTTCTTT 58.002 39.130 0.00 0.00 0.00 2.52
3880 5622 5.393866 TCCTTCCTTTGGCTATGTTCTTTT 58.606 37.500 0.00 0.00 0.00 2.27
3881 5623 5.838521 TCCTTCCTTTGGCTATGTTCTTTTT 59.161 36.000 0.00 0.00 0.00 1.94
3882 5624 6.015434 TCCTTCCTTTGGCTATGTTCTTTTTC 60.015 38.462 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
156 157 2.493278 GGTAAGCACTCCATTGCAACAT 59.507 45.455 0.00 0.00 45.62 2.71
375 377 7.033791 CCTGCTTTGATCTCGTTTAGTAGTAA 58.966 38.462 0.00 0.00 0.00 2.24
477 479 2.487762 GTCAACCGATTGATTTCAGCCA 59.512 45.455 0.00 0.00 46.43 4.75
542 544 4.599041 TCTTCCATGGTCAAATTCCGAAT 58.401 39.130 12.58 0.00 0.00 3.34
601 603 1.065418 CGGGATCAGCCAACTAAACCT 60.065 52.381 0.00 0.00 38.95 3.50
602 604 1.379527 CGGGATCAGCCAACTAAACC 58.620 55.000 0.00 0.00 38.95 3.27
604 606 0.326595 TGCGGGATCAGCCAACTAAA 59.673 50.000 9.48 0.00 38.95 1.85
605 607 0.326595 TTGCGGGATCAGCCAACTAA 59.673 50.000 9.48 0.00 38.95 2.24
606 608 0.326595 TTTGCGGGATCAGCCAACTA 59.673 50.000 9.48 0.00 38.95 2.24
608 610 0.316841 TTTTTGCGGGATCAGCCAAC 59.683 50.000 9.48 0.00 38.95 3.77
628 630 5.932619 AGTTCAGCCAACTAAACCTTTTT 57.067 34.783 0.00 0.00 44.13 1.94
629 631 5.660460 CAAGTTCAGCCAACTAAACCTTTT 58.340 37.500 0.00 0.00 45.32 2.27
630 632 4.441495 GCAAGTTCAGCCAACTAAACCTTT 60.441 41.667 0.00 0.00 45.32 3.11
631 633 3.068165 GCAAGTTCAGCCAACTAAACCTT 59.932 43.478 0.00 0.00 45.32 3.50
3728 5470 7.122138 AGTAATGTGACTGATCTCATGTCAT 57.878 36.000 12.41 0.07 41.78 3.06
3852 5594 2.899303 TAGCCAAAGGAAGGAAAGGG 57.101 50.000 0.00 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.