Multiple sequence alignment - TraesCS6B01G226100

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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 TraesCS6B01G226100 chr6B 100.000 2549 0 0 1 2549 347769228 347766680 0.000000e+00 4708
1 TraesCS6B01G226100 chr6B 91.045 603 52 2 1 601 354210428 354211030 0.000000e+00 813
2 TraesCS6B01G226100 chr6B 90.333 600 57 1 1 599 501930785 501930186 0.000000e+00 785
3 TraesCS6B01G226100 chr6B 89.604 606 61 2 1 604 414822800 414822195 0.000000e+00 769
4 TraesCS6B01G226100 chr2B 96.302 2001 26 12 596 2549 781094235 781096234 0.000000e+00 3241
5 TraesCS6B01G226100 chr2B 95.414 2006 38 9 594 2549 776449267 776447266 0.000000e+00 3145
6 TraesCS6B01G226100 chr2B 91.987 599 47 1 2 599 567631720 567632318 0.000000e+00 839
7 TraesCS6B01G226100 chr3A 95.918 2009 32 16 591 2549 77771301 77773309 0.000000e+00 3210
8 TraesCS6B01G226100 chr6A 95.752 2001 33 7 598 2549 616131292 616133289 0.000000e+00 3177
9 TraesCS6B01G226100 chr4B 95.566 2007 37 10 592 2549 368430377 368428374 0.000000e+00 3166
10 TraesCS6B01G226100 chr4B 92.027 602 47 1 1 601 358503258 358503859 0.000000e+00 845
11 TraesCS6B01G226100 chr4B 89.000 600 65 1 1 599 135390819 135390220 0.000000e+00 741
12 TraesCS6B01G226100 chr4B 88.274 614 68 4 1 610 411194295 411193682 0.000000e+00 732
13 TraesCS6B01G226100 chr4B 87.772 597 70 2 1 596 491384381 491384975 0.000000e+00 695
14 TraesCS6B01G226100 chr4B 87.437 597 74 1 4 599 107620812 107620216 0.000000e+00 686
15 TraesCS6B01G226100 chr4B 87.437 597 74 1 1 596 206947078 206947674 0.000000e+00 686
16 TraesCS6B01G226100 chr7B 95.566 2007 34 8 592 2549 202776906 202778906 0.000000e+00 3162
17 TraesCS6B01G226100 chr7B 90.579 605 56 1 1 604 289602694 289602090 0.000000e+00 800
18 TraesCS6B01G226100 chr7B 89.884 603 57 4 1 601 536352527 536353127 0.000000e+00 773
19 TraesCS6B01G226100 chr2A 95.563 2006 34 10 595 2549 682509141 682507140 0.000000e+00 3160
20 TraesCS6B01G226100 chr2A 95.417 1942 61 8 601 2519 744582028 744583964 0.000000e+00 3068
21 TraesCS6B01G226100 chr2A 94.567 1988 66 15 598 2549 677958473 677956492 0.000000e+00 3035
22 TraesCS6B01G226100 chr2A 93.634 1948 94 14 595 2519 677413614 677411674 0.000000e+00 2883
23 TraesCS6B01G226100 chr5B 96.283 1937 50 5 602 2517 3450172 3448237 0.000000e+00 3158
24 TraesCS6B01G226100 chr5B 90.588 595 55 1 1 594 89998092 89998686 0.000000e+00 787
25 TraesCS6B01G226100 chr5B 90.033 602 59 1 1 601 656338540 656339141 0.000000e+00 778
26 TraesCS6B01G226100 chr5B 89.867 602 56 3 2 601 241956149 241956747 0.000000e+00 769
27 TraesCS6B01G226100 chr5B 89.167 600 62 3 1 599 285465644 285465047 0.000000e+00 745
28 TraesCS6B01G226100 chr1A 95.448 1999 37 10 601 2549 72554875 72556869 0.000000e+00 3138
29 TraesCS6B01G226100 chr7A 95.356 1938 65 9 602 2519 36946200 36948132 0.000000e+00 3057
30 TraesCS6B01G226100 chr5A 94.585 1939 76 13 601 2519 689446508 689444579 0.000000e+00 2972
31 TraesCS6B01G226100 chr7D 93.943 1948 80 14 598 2519 63995386 63997321 0.000000e+00 2909
32 TraesCS6B01G226100 chrUn 97.497 1638 22 2 930 2549 284635198 284636834 0.000000e+00 2780
33 TraesCS6B01G226100 chrUn 89.966 588 57 2 2 587 346375137 346375724 0.000000e+00 758
34 TraesCS6B01G226100 chrUn 86.964 606 77 2 1 604 66232440 66231835 0.000000e+00 680
35 TraesCS6B01G226100 chrUn 82.239 518 78 13 88 598 181645192 181644682 3.890000e-118 435
36 TraesCS6B01G226100 chrUn 81.853 518 80 13 88 598 144699919 144699409 8.430000e-115 424
37 TraesCS6B01G226100 chrUn 82.919 322 51 4 287 606 480049143 480048824 1.150000e-73 287
38 TraesCS6B01G226100 chrUn 80.132 302 57 3 301 601 266710317 266710616 3.300000e-54 222
39 TraesCS6B01G226100 chrUn 80.132 302 57 3 301 601 266719163 266719462 3.300000e-54 222
40 TraesCS6B01G226100 chrUn 80.268 299 56 3 304 601 279843081 279842785 3.300000e-54 222
41 TraesCS6B01G226100 chr1D 92.687 1723 76 11 596 2273 25464313 25466030 0.000000e+00 2438
42 TraesCS6B01G226100 chr1D 82.724 602 101 2 1 601 208978733 208979332 1.340000e-147 532
43 TraesCS6B01G226100 chr1D 81.818 583 99 5 1 579 455146606 455146027 1.370000e-132 483
44 TraesCS6B01G226100 chr1D 81.324 589 107 3 1 587 62049032 62049619 2.290000e-130 475
45 TraesCS6B01G226100 chr1D 80.672 595 112 3 1 593 365500324 365500917 2.310000e-125 459
46 TraesCS6B01G226100 chr1D 80.333 600 115 3 1 598 75139257 75138659 3.870000e-123 451
47 TraesCS6B01G226100 chr4D 92.981 1382 70 15 597 1958 496435131 496433757 0.000000e+00 1989
48 TraesCS6B01G226100 chr4D 90.000 600 59 1 1 599 332747586 332746987 0.000000e+00 774
49 TraesCS6B01G226100 chr4D 85.479 606 80 8 1 601 332664727 332665329 2.150000e-175 625
50 TraesCS6B01G226100 chr4D 81.803 599 103 5 1 596 235573400 235572805 4.900000e-137 497
51 TraesCS6B01G226100 chr3B 91.269 607 48 5 1 604 579982439 579981835 0.000000e+00 822
52 TraesCS6B01G226100 chr3B 90.816 588 52 2 1 587 644736305 644735719 0.000000e+00 785
53 TraesCS6B01G226100 chr1B 89.867 602 59 2 1 601 270537718 270538318 0.000000e+00 773
54 TraesCS6B01G226100 chr1B 89.037 602 63 3 1 601 515060525 515061124 0.000000e+00 743
55 TraesCS6B01G226100 chr2D 87.086 604 74 4 1 601 573338541 573339143 0.000000e+00 680
56 TraesCS6B01G226100 chr3D 86.545 602 79 2 1 601 614751545 614752145 0.000000e+00 662
57 TraesCS6B01G226100 chr5D 86.469 606 77 4 1 604 247951353 247950751 0.000000e+00 660
58 TraesCS6B01G226100 chr5D 85.997 607 75 9 1 601 454968318 454967716 2.140000e-180 641
59 TraesCS6B01G226100 chr5D 85.406 603 86 2 1 601 455039607 455039005 2.150000e-175 625
60 TraesCS6B01G226100 chr5D 85.314 606 81 7 1 601 455111535 455110933 1.000000e-173 619
61 TraesCS6B01G226100 chr6D 83.779 598 95 2 1 596 295554891 295555488 1.320000e-157 566
62 TraesCS6B01G226100 chr6D 82.633 547 91 4 53 596 409598023 409597478 4.930000e-132 481
63 TraesCS6B01G226100 chr6D 80.134 599 114 4 3 596 88170858 88170260 2.330000e-120 442
64 TraesCS6B01G226100 chr6D 80.235 597 110 7 1 594 259550401 259549810 2.330000e-120 442
65 TraesCS6B01G226100 chr6D 79.636 604 114 9 1 599 368951825 368951226 2.340000e-115 425
66 TraesCS6B01G226100 chr6D 78.930 598 118 8 3 596 437211539 437212132 1.420000e-107 399


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 TraesCS6B01G226100 chr6B 347766680 347769228 2548 True 4708 4708 100.000 1 2549 1 chr6B.!!$R1 2548
1 TraesCS6B01G226100 chr6B 354210428 354211030 602 False 813 813 91.045 1 601 1 chr6B.!!$F1 600
2 TraesCS6B01G226100 chr6B 501930186 501930785 599 True 785 785 90.333 1 599 1 chr6B.!!$R3 598
3 TraesCS6B01G226100 chr6B 414822195 414822800 605 True 769 769 89.604 1 604 1 chr6B.!!$R2 603
4 TraesCS6B01G226100 chr2B 781094235 781096234 1999 False 3241 3241 96.302 596 2549 1 chr2B.!!$F2 1953
5 TraesCS6B01G226100 chr2B 776447266 776449267 2001 True 3145 3145 95.414 594 2549 1 chr2B.!!$R1 1955
6 TraesCS6B01G226100 chr2B 567631720 567632318 598 False 839 839 91.987 2 599 1 chr2B.!!$F1 597
7 TraesCS6B01G226100 chr3A 77771301 77773309 2008 False 3210 3210 95.918 591 2549 1 chr3A.!!$F1 1958
8 TraesCS6B01G226100 chr6A 616131292 616133289 1997 False 3177 3177 95.752 598 2549 1 chr6A.!!$F1 1951
9 TraesCS6B01G226100 chr4B 368428374 368430377 2003 True 3166 3166 95.566 592 2549 1 chr4B.!!$R3 1957
10 TraesCS6B01G226100 chr4B 358503258 358503859 601 False 845 845 92.027 1 601 1 chr4B.!!$F2 600
11 TraesCS6B01G226100 chr4B 135390220 135390819 599 True 741 741 89.000 1 599 1 chr4B.!!$R2 598
12 TraesCS6B01G226100 chr4B 411193682 411194295 613 True 732 732 88.274 1 610 1 chr4B.!!$R4 609
13 TraesCS6B01G226100 chr4B 491384381 491384975 594 False 695 695 87.772 1 596 1 chr4B.!!$F3 595
14 TraesCS6B01G226100 chr4B 107620216 107620812 596 True 686 686 87.437 4 599 1 chr4B.!!$R1 595
15 TraesCS6B01G226100 chr4B 206947078 206947674 596 False 686 686 87.437 1 596 1 chr4B.!!$F1 595
16 TraesCS6B01G226100 chr7B 202776906 202778906 2000 False 3162 3162 95.566 592 2549 1 chr7B.!!$F1 1957
17 TraesCS6B01G226100 chr7B 289602090 289602694 604 True 800 800 90.579 1 604 1 chr7B.!!$R1 603
18 TraesCS6B01G226100 chr7B 536352527 536353127 600 False 773 773 89.884 1 601 1 chr7B.!!$F2 600
19 TraesCS6B01G226100 chr2A 682507140 682509141 2001 True 3160 3160 95.563 595 2549 1 chr2A.!!$R3 1954
20 TraesCS6B01G226100 chr2A 744582028 744583964 1936 False 3068 3068 95.417 601 2519 1 chr2A.!!$F1 1918
21 TraesCS6B01G226100 chr2A 677956492 677958473 1981 True 3035 3035 94.567 598 2549 1 chr2A.!!$R2 1951
22 TraesCS6B01G226100 chr2A 677411674 677413614 1940 True 2883 2883 93.634 595 2519 1 chr2A.!!$R1 1924
23 TraesCS6B01G226100 chr5B 3448237 3450172 1935 True 3158 3158 96.283 602 2517 1 chr5B.!!$R1 1915
24 TraesCS6B01G226100 chr5B 89998092 89998686 594 False 787 787 90.588 1 594 1 chr5B.!!$F1 593
25 TraesCS6B01G226100 chr5B 656338540 656339141 601 False 778 778 90.033 1 601 1 chr5B.!!$F3 600
26 TraesCS6B01G226100 chr5B 241956149 241956747 598 False 769 769 89.867 2 601 1 chr5B.!!$F2 599
27 TraesCS6B01G226100 chr5B 285465047 285465644 597 True 745 745 89.167 1 599 1 chr5B.!!$R2 598
28 TraesCS6B01G226100 chr1A 72554875 72556869 1994 False 3138 3138 95.448 601 2549 1 chr1A.!!$F1 1948
29 TraesCS6B01G226100 chr7A 36946200 36948132 1932 False 3057 3057 95.356 602 2519 1 chr7A.!!$F1 1917
30 TraesCS6B01G226100 chr5A 689444579 689446508 1929 True 2972 2972 94.585 601 2519 1 chr5A.!!$R1 1918
31 TraesCS6B01G226100 chr7D 63995386 63997321 1935 False 2909 2909 93.943 598 2519 1 chr7D.!!$F1 1921
32 TraesCS6B01G226100 chrUn 284635198 284636834 1636 False 2780 2780 97.497 930 2549 1 chrUn.!!$F3 1619
33 TraesCS6B01G226100 chrUn 346375137 346375724 587 False 758 758 89.966 2 587 1 chrUn.!!$F4 585
34 TraesCS6B01G226100 chrUn 66231835 66232440 605 True 680 680 86.964 1 604 1 chrUn.!!$R1 603
35 TraesCS6B01G226100 chrUn 181644682 181645192 510 True 435 435 82.239 88 598 1 chrUn.!!$R3 510
36 TraesCS6B01G226100 chrUn 144699409 144699919 510 True 424 424 81.853 88 598 1 chrUn.!!$R2 510
37 TraesCS6B01G226100 chr1D 25464313 25466030 1717 False 2438 2438 92.687 596 2273 1 chr1D.!!$F1 1677
38 TraesCS6B01G226100 chr1D 208978733 208979332 599 False 532 532 82.724 1 601 1 chr1D.!!$F3 600
39 TraesCS6B01G226100 chr1D 455146027 455146606 579 True 483 483 81.818 1 579 1 chr1D.!!$R2 578
40 TraesCS6B01G226100 chr1D 62049032 62049619 587 False 475 475 81.324 1 587 1 chr1D.!!$F2 586
41 TraesCS6B01G226100 chr1D 365500324 365500917 593 False 459 459 80.672 1 593 1 chr1D.!!$F4 592
42 TraesCS6B01G226100 chr1D 75138659 75139257 598 True 451 451 80.333 1 598 1 chr1D.!!$R1 597
43 TraesCS6B01G226100 chr4D 496433757 496435131 1374 True 1989 1989 92.981 597 1958 1 chr4D.!!$R3 1361
44 TraesCS6B01G226100 chr4D 332746987 332747586 599 True 774 774 90.000 1 599 1 chr4D.!!$R2 598
45 TraesCS6B01G226100 chr4D 332664727 332665329 602 False 625 625 85.479 1 601 1 chr4D.!!$F1 600
46 TraesCS6B01G226100 chr4D 235572805 235573400 595 True 497 497 81.803 1 596 1 chr4D.!!$R1 595
47 TraesCS6B01G226100 chr3B 579981835 579982439 604 True 822 822 91.269 1 604 1 chr3B.!!$R1 603
48 TraesCS6B01G226100 chr3B 644735719 644736305 586 True 785 785 90.816 1 587 1 chr3B.!!$R2 586
49 TraesCS6B01G226100 chr1B 270537718 270538318 600 False 773 773 89.867 1 601 1 chr1B.!!$F1 600
50 TraesCS6B01G226100 chr1B 515060525 515061124 599 False 743 743 89.037 1 601 1 chr1B.!!$F2 600
51 TraesCS6B01G226100 chr2D 573338541 573339143 602 False 680 680 87.086 1 601 1 chr2D.!!$F1 600
52 TraesCS6B01G226100 chr3D 614751545 614752145 600 False 662 662 86.545 1 601 1 chr3D.!!$F1 600
53 TraesCS6B01G226100 chr5D 247950751 247951353 602 True 660 660 86.469 1 604 1 chr5D.!!$R1 603
54 TraesCS6B01G226100 chr5D 454967716 454968318 602 True 641 641 85.997 1 601 1 chr5D.!!$R2 600
55 TraesCS6B01G226100 chr5D 455039005 455039607 602 True 625 625 85.406 1 601 1 chr5D.!!$R3 600
56 TraesCS6B01G226100 chr5D 455110933 455111535 602 True 619 619 85.314 1 601 1 chr5D.!!$R4 600
57 TraesCS6B01G226100 chr6D 295554891 295555488 597 False 566 566 83.779 1 596 1 chr6D.!!$F1 595
58 TraesCS6B01G226100 chr6D 409597478 409598023 545 True 481 481 82.633 53 596 1 chr6D.!!$R4 543
59 TraesCS6B01G226100 chr6D 88170260 88170858 598 True 442 442 80.134 3 596 1 chr6D.!!$R1 593
60 TraesCS6B01G226100 chr6D 259549810 259550401 591 True 442 442 80.235 1 594 1 chr6D.!!$R2 593
61 TraesCS6B01G226100 chr6D 368951226 368951825 599 True 425 425 79.636 1 599 1 chr6D.!!$R3 598
62 TraesCS6B01G226100 chr6D 437211539 437212132 593 False 399 399 78.930 3 596 1 chr6D.!!$F2 593

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
230 246 1.348064 TCCTTTCCTCTTCGAAGGCA 58.652 50.000 24.37 5.86 39.78 4.75 F
1019 1065 1.280133 CATGTCTTCCTCAAGCTCCCA 59.720 52.381 0.00 0.00 0.00 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1143 1189 1.672030 CCCATTCTCGCTGCACACA 60.672 57.895 0.0 0.0 0.00 3.72 R
2015 2107 1.732917 CTCTACCAGAGCTGAGGCG 59.267 63.158 0.0 0.0 44.37 5.52 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
206 222 3.886505 TGATAAAGGCTCGGTTGTGTTTT 59.113 39.130 0.00 0.00 0.00 2.43
212 228 4.866921 AGGCTCGGTTGTGTTTTTATTTC 58.133 39.130 0.00 0.00 0.00 2.17
230 246 1.348064 TCCTTTCCTCTTCGAAGGCA 58.652 50.000 24.37 5.86 39.78 4.75
244 260 4.175337 GGCATGCCCAGCGTAGGA 62.175 66.667 27.24 0.00 0.00 2.94
252 268 2.490148 CCAGCGTAGGAGCCGATCA 61.490 63.158 0.00 0.00 38.01 2.92
317 334 3.525537 CATTTGGAGCACGAGATAGTGT 58.474 45.455 0.00 0.00 43.61 3.55
400 417 3.787001 CAGGGAGAAGGCCGGGAC 61.787 72.222 2.18 0.00 0.00 4.46
515 532 4.048470 GGGGTCAAGGGCCTGGTC 62.048 72.222 6.92 0.25 0.00 4.02
749 766 3.790691 TCAACCTTTTGACTCGGCA 57.209 47.368 0.00 0.00 36.79 5.69
841 858 1.654220 GCAAAGAGCCGTTGAGCAA 59.346 52.632 5.35 0.00 37.23 3.91
915 932 2.126307 CAGAGAGCACGACGGTGG 60.126 66.667 0.00 0.00 44.54 4.61
1019 1065 1.280133 CATGTCTTCCTCAAGCTCCCA 59.720 52.381 0.00 0.00 0.00 4.37
1143 1189 3.181478 GGAACCAGAATCGTCCGTTCTAT 60.181 47.826 0.00 0.00 35.40 1.98
1198 1244 1.300481 TGCACCATTTTTGTCGTCGA 58.700 45.000 0.00 0.00 0.00 4.20
1363 1409 3.680786 CCACACCACGAGCTCCGA 61.681 66.667 8.47 0.00 41.76 4.55
2015 2107 6.790285 AGACCAAAATGTCATGAAAAATGC 57.210 33.333 0.00 0.00 37.73 3.56
2042 2134 1.798079 GCTCTGGTAGAGGTTTACGCG 60.798 57.143 3.53 3.53 42.54 6.01
2263 2357 9.352191 GGAAAGAAGGTATACATAGTGAGACTA 57.648 37.037 5.01 0.00 34.82 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
206 222 4.941873 GCCTTCGAAGAGGAAAGGAAATAA 59.058 41.667 26.61 0.00 38.43 1.40
212 228 2.012673 CATGCCTTCGAAGAGGAAAGG 58.987 52.381 26.61 9.78 38.43 3.11
230 246 3.866582 GGCTCCTACGCTGGGCAT 61.867 66.667 8.92 0.00 0.00 4.40
244 260 1.893786 GACTCACAGGTGATCGGCT 59.106 57.895 2.09 0.00 39.13 5.52
297 313 3.525537 CACACTATCTCGTGCTCCAAAT 58.474 45.455 0.00 0.00 38.45 2.32
317 334 1.133181 TCATTCTGCCTCACCCACCA 61.133 55.000 0.00 0.00 0.00 4.17
400 417 2.821366 GGCCATCACCGCTGACTG 60.821 66.667 0.00 0.00 0.00 3.51
515 532 2.047844 CACAGCCAGAGGACCACG 60.048 66.667 0.00 0.00 0.00 4.94
749 766 1.489560 GCCTGGTCCCACCTGTAAGT 61.490 60.000 0.00 0.00 39.58 2.24
915 932 3.119709 CTCTCTCTCTCGCCGTGGC 62.120 68.421 0.00 0.00 37.85 5.01
1143 1189 1.672030 CCCATTCTCGCTGCACACA 60.672 57.895 0.00 0.00 0.00 3.72
1198 1244 3.499338 TCAACCCATTGCTCAAACATCT 58.501 40.909 0.00 0.00 35.63 2.90
1363 1409 3.539604 CTTCGCCATCCATCTCTTCTTT 58.460 45.455 0.00 0.00 0.00 2.52
2015 2107 1.732917 CTCTACCAGAGCTGAGGCG 59.267 63.158 0.00 0.00 44.37 5.52
2042 2134 7.671495 AAATGTTCATTTATTTTGGCACCTC 57.329 32.000 8.73 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.