Multiple sequence alignment - TraesCS2D01G250100

Loading Multiple Alignment...

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 TraesCS2D01G250100 chr2D 100.000 4081 0 0 1 4081 297601681 297597601 0.000000e+00 7537.0
1 TraesCS2D01G250100 chr2B 98.483 3691 43 6 399 4078 364134007 364137695 0.000000e+00 6493.0
2 TraesCS2D01G250100 chr2B 96.526 403 12 2 1 401 364120099 364120501 0.000000e+00 665.0
3 TraesCS2D01G250100 chr2B 83.363 559 65 11 866 1412 757706845 757707387 3.670000e-135 492.0
4 TraesCS2D01G250100 chr2A 96.199 3341 54 17 277 3596 371047640 371044352 0.000000e+00 5398.0
5 TraesCS2D01G250100 chr2A 91.624 394 23 3 3696 4081 370967876 370967485 1.670000e-148 536.0
6 TraesCS2D01G250100 chr2A 94.265 279 14 2 1 277 371048230 371047952 3.770000e-115 425.0
7 TraesCS2D01G250100 chr2A 100.000 77 0 0 3550 3626 371044351 371044275 4.250000e-30 143.0
8 TraesCS2D01G250100 chr2A 85.981 107 14 1 3604 3709 382275145 382275039 3.330000e-21 113.0
9 TraesCS2D01G250100 chr2A 85.981 107 14 1 3604 3709 382311051 382311157 3.330000e-21 113.0
10 TraesCS2D01G250100 chr2A 85.981 107 14 1 3604 3709 382311581 382311687 3.330000e-21 113.0
11 TraesCS2D01G250100 chr5D 85.714 1043 102 28 827 1854 410193731 410194741 0.000000e+00 1057.0
12 TraesCS2D01G250100 chr5D 81.651 109 18 2 3602 3708 526611702 526611810 5.620000e-14 89.8
13 TraesCS2D01G250100 chr3D 85.523 1043 103 27 827 1854 69648249 69649258 0.000000e+00 1046.0
14 TraesCS2D01G250100 chr4D 85.227 1056 105 28 827 1863 51308981 51310004 0.000000e+00 1038.0
15 TraesCS2D01G250100 chr6B 83.302 1054 125 34 837 1869 100636301 100637324 0.000000e+00 924.0
16 TraesCS2D01G250100 chr6B 89.437 142 12 2 1346 1484 144959106 144959247 4.190000e-40 176.0
17 TraesCS2D01G250100 chr4B 85.383 561 52 12 866 1412 623068927 623068383 4.610000e-154 555.0
18 TraesCS2D01G250100 chr1D 85.027 561 51 13 866 1412 60431220 60431761 1.290000e-149 540.0
19 TraesCS2D01G250100 chr5B 84.492 561 57 12 866 1412 536513085 536513629 1.000000e-145 527.0
20 TraesCS2D01G250100 chr6D 90.141 142 11 2 1346 1484 69940493 69940634 9.010000e-42 182.0
21 TraesCS2D01G250100 chr3A 96.053 76 3 0 1695 1770 146768485 146768410 1.540000e-24 124.0
22 TraesCS2D01G250100 chr3A 83.486 109 13 4 3604 3708 625816949 625816842 3.360000e-16 97.1
23 TraesCS2D01G250100 chr7D 86.916 107 12 2 3602 3706 104583046 104583152 7.170000e-23 119.0
24 TraesCS2D01G250100 chr6A 89.286 84 7 2 3630 3711 507114145 507114062 2.010000e-18 104.0
25 TraesCS2D01G250100 chr3B 83.333 108 14 4 3604 3709 406873338 406873443 3.360000e-16 97.1


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 TraesCS2D01G250100 chr2D 297597601 297601681 4080 True 7537.000000 7537 100.000000 1 4081 1 chr2D.!!$R1 4080
1 TraesCS2D01G250100 chr2B 364134007 364137695 3688 False 6493.000000 6493 98.483000 399 4078 1 chr2B.!!$F2 3679
2 TraesCS2D01G250100 chr2B 757706845 757707387 542 False 492.000000 492 83.363000 866 1412 1 chr2B.!!$F3 546
3 TraesCS2D01G250100 chr2A 371044275 371048230 3955 True 1988.666667 5398 96.821333 1 3626 3 chr2A.!!$R3 3625
4 TraesCS2D01G250100 chr5D 410193731 410194741 1010 False 1057.000000 1057 85.714000 827 1854 1 chr5D.!!$F1 1027
5 TraesCS2D01G250100 chr3D 69648249 69649258 1009 False 1046.000000 1046 85.523000 827 1854 1 chr3D.!!$F1 1027
6 TraesCS2D01G250100 chr4D 51308981 51310004 1023 False 1038.000000 1038 85.227000 827 1863 1 chr4D.!!$F1 1036
7 TraesCS2D01G250100 chr6B 100636301 100637324 1023 False 924.000000 924 83.302000 837 1869 1 chr6B.!!$F1 1032
8 TraesCS2D01G250100 chr4B 623068383 623068927 544 True 555.000000 555 85.383000 866 1412 1 chr4B.!!$R1 546
9 TraesCS2D01G250100 chr1D 60431220 60431761 541 False 540.000000 540 85.027000 866 1412 1 chr1D.!!$F1 546
10 TraesCS2D01G250100 chr5B 536513085 536513629 544 False 527.000000 527 84.492000 866 1412 1 chr5B.!!$F1 546

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
218 219 0.171455 GAGTGTGGCTGACTACTCCG 59.829 60.000 7.09 0.0 34.84 4.63 F
584 905 2.013807 CACGCGGAGAGAGAGAGAG 58.986 63.158 12.47 0.0 0.00 3.20 F
1792 2151 2.047061 TGTTGTAGGTGCCAGAGAAGT 58.953 47.619 0.00 0.0 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1233 1574 2.151202 GCTTGCAGCTTGTAACCTGTA 58.849 47.619 0.00 0.00 38.45 2.74 R
2428 2791 1.619654 TTGATCCAACAGGGCAGTTG 58.380 50.000 13.22 13.22 46.44 3.16 R
3450 3814 3.091545 GGAATCCAAGACTGCCAAATCA 58.908 45.455 0.00 0.00 0.00 2.57 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
32 33 1.810151 TGTTTTGCTCGTCCATAAGGC 59.190 47.619 0.00 0.00 33.74 4.35
50 51 3.575297 CGAGAATTGCAAGCGACTG 57.425 52.632 4.94 0.00 0.00 3.51
54 55 0.242017 GAATTGCAAGCGACTGCCTT 59.758 50.000 4.94 0.00 44.31 4.35
70 71 2.311542 TGCCTTTGGGTCATCAATACCT 59.688 45.455 0.00 0.00 37.18 3.08
86 87 2.935481 ACCTTCCGTGATAGTTCGAC 57.065 50.000 0.00 0.00 0.00 4.20
108 109 4.035324 ACGTGTCACTATAGGAAGATGACG 59.965 45.833 12.98 14.83 42.09 4.35
132 133 0.700564 AGATTTTGGCAGGAGCAGGA 59.299 50.000 0.00 0.00 44.61 3.86
193 194 5.289917 TCGCATATGTTAACAACTGTTGG 57.710 39.130 23.15 6.91 38.90 3.77
218 219 0.171455 GAGTGTGGCTGACTACTCCG 59.829 60.000 7.09 0.00 34.84 4.63
223 224 2.299521 GTGGCTGACTACTCCGTCTAT 58.700 52.381 0.00 0.00 35.00 1.98
230 231 5.300411 TGACTACTCCGTCTATGGACATA 57.700 43.478 10.08 0.00 42.21 2.29
269 270 7.016858 TCCTTAAATAAAGTGGGTACTGTGTCT 59.983 37.037 0.00 0.00 37.19 3.41
270 271 8.316214 CCTTAAATAAAGTGGGTACTGTGTCTA 58.684 37.037 0.00 0.00 37.19 2.59
271 272 9.715121 CTTAAATAAAGTGGGTACTGTGTCTAA 57.285 33.333 0.00 0.00 37.19 2.10
299 614 9.775854 AAAATTCCAGATATCTGTATGTCTCTG 57.224 33.333 27.03 11.56 42.27 3.35
300 615 5.973899 TCCAGATATCTGTATGTCTCTGC 57.026 43.478 27.03 0.00 42.27 4.26
362 683 3.350833 ACATCCTTGCAGAGTGAAATCC 58.649 45.455 0.00 0.00 0.00 3.01
363 684 3.245016 ACATCCTTGCAGAGTGAAATCCA 60.245 43.478 0.00 0.00 0.00 3.41
364 685 3.507162 TCCTTGCAGAGTGAAATCCAA 57.493 42.857 0.00 0.00 0.00 3.53
365 686 3.415212 TCCTTGCAGAGTGAAATCCAAG 58.585 45.455 0.00 0.00 0.00 3.61
366 687 3.072915 TCCTTGCAGAGTGAAATCCAAGA 59.927 43.478 0.00 0.00 33.40 3.02
367 688 3.439476 CCTTGCAGAGTGAAATCCAAGAG 59.561 47.826 0.00 0.00 33.40 2.85
368 689 2.430465 TGCAGAGTGAAATCCAAGAGC 58.570 47.619 0.00 0.00 0.00 4.09
369 690 2.039480 TGCAGAGTGAAATCCAAGAGCT 59.961 45.455 0.00 0.00 0.00 4.09
370 691 3.261643 TGCAGAGTGAAATCCAAGAGCTA 59.738 43.478 0.00 0.00 0.00 3.32
371 692 4.256920 GCAGAGTGAAATCCAAGAGCTAA 58.743 43.478 0.00 0.00 0.00 3.09
372 693 4.697352 GCAGAGTGAAATCCAAGAGCTAAA 59.303 41.667 0.00 0.00 0.00 1.85
373 694 5.182001 GCAGAGTGAAATCCAAGAGCTAAAA 59.818 40.000 0.00 0.00 0.00 1.52
374 695 6.294176 GCAGAGTGAAATCCAAGAGCTAAAAA 60.294 38.462 0.00 0.00 0.00 1.94
422 743 2.088950 ACATTAGCACCACACCGTAC 57.911 50.000 0.00 0.00 0.00 3.67
583 904 2.109739 GCACGCGGAGAGAGAGAGA 61.110 63.158 12.47 0.00 0.00 3.10
584 905 2.013807 CACGCGGAGAGAGAGAGAG 58.986 63.158 12.47 0.00 0.00 3.20
1233 1574 5.976458 TCTGGTTTCTTGTTTTGAATTGCT 58.024 33.333 0.00 0.00 0.00 3.91
1463 1805 9.261180 TGATTCGAGAGTCACATTATATTTTCC 57.739 33.333 0.00 0.00 0.00 3.13
1792 2151 2.047061 TGTTGTAGGTGCCAGAGAAGT 58.953 47.619 0.00 0.00 0.00 3.01
2308 2671 3.087031 TGAAACTACCTCTAGTGACCCG 58.913 50.000 0.00 0.00 33.14 5.28
2428 2791 9.712305 ATACTAGTGCACAATAATACTTCATCC 57.288 33.333 21.04 0.00 0.00 3.51
3205 3569 4.768968 ACCAAAGATGCAGCTGTAAAGAAT 59.231 37.500 16.64 0.00 0.00 2.40
3253 3617 1.297304 GTGCAACGTCAACCACACG 60.297 57.895 0.00 0.00 43.13 4.49
3318 3682 1.542915 CCAGTTGTTTCATCAGGCCAG 59.457 52.381 5.01 0.00 0.00 4.85
3638 4049 5.936956 TGTGCCATTGATATTTTGGGTTTTC 59.063 36.000 0.00 0.00 0.00 2.29
3676 4087 9.462606 CTTCCTCTGGTTTAAAATATAAGGTGT 57.537 33.333 0.00 0.00 0.00 4.16
3741 4153 6.821388 TCTTCTTAGGCTCAATAATCTGGAC 58.179 40.000 0.00 0.00 0.00 4.02
3748 4160 5.426833 AGGCTCAATAATCTGGACACTAAGT 59.573 40.000 0.00 0.00 0.00 2.24
3826 4238 6.975197 GCTTTCTTAGCCATGAATTTAGAACC 59.025 38.462 0.00 0.00 44.48 3.62
3899 4311 1.271163 ACGGCCATATTATCAACCCGG 60.271 52.381 2.24 0.00 38.59 5.73
3994 4406 6.819397 ACATTCTTTTAGGTTAGGAGCAAC 57.181 37.500 0.00 0.00 0.00 4.17
4044 4458 4.360951 AAACAAGTATTTCTCCCGGACA 57.639 40.909 0.73 0.00 0.00 4.02
4045 4459 3.329929 ACAAGTATTTCTCCCGGACAC 57.670 47.619 0.73 0.00 0.00 3.67
4047 4461 3.263425 ACAAGTATTTCTCCCGGACACAT 59.737 43.478 0.73 0.00 0.00 3.21
4048 4462 3.821421 AGTATTTCTCCCGGACACATC 57.179 47.619 0.73 0.00 0.00 3.06
4078 4499 2.165030 CGTCGGCCTTCCTTCTACTTAA 59.835 50.000 0.00 0.00 0.00 1.85
4079 4500 3.181478 CGTCGGCCTTCCTTCTACTTAAT 60.181 47.826 0.00 0.00 0.00 1.40
4080 4501 4.120589 GTCGGCCTTCCTTCTACTTAATG 58.879 47.826 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 0.519999 GCAGTCGCTTGCAATTCTCG 60.520 55.000 0.00 1.86 43.53 4.04
50 51 3.018423 AGGTATTGATGACCCAAAGGC 57.982 47.619 0.00 0.00 37.73 4.35
54 55 2.574369 ACGGAAGGTATTGATGACCCAA 59.426 45.455 0.00 0.00 37.73 4.12
70 71 1.536766 ACACGTCGAACTATCACGGAA 59.463 47.619 0.00 0.00 35.68 4.30
86 87 4.272748 TCGTCATCTTCCTATAGTGACACG 59.727 45.833 16.36 13.41 39.20 4.49
108 109 1.747924 GCTCCTGCCAAAATCTCCTTC 59.252 52.381 0.00 0.00 0.00 3.46
338 659 4.572985 TTTCACTCTGCAAGGATGTTTG 57.427 40.909 0.00 0.00 0.00 2.93
374 695 2.087646 GGCTCCAGCTCTTCGATTTTT 58.912 47.619 0.00 0.00 41.70 1.94
375 696 1.003580 TGGCTCCAGCTCTTCGATTTT 59.996 47.619 0.00 0.00 41.70 1.82
376 697 0.615331 TGGCTCCAGCTCTTCGATTT 59.385 50.000 0.00 0.00 41.70 2.17
377 698 0.615331 TTGGCTCCAGCTCTTCGATT 59.385 50.000 0.00 0.00 41.70 3.34
378 699 0.615331 TTTGGCTCCAGCTCTTCGAT 59.385 50.000 0.00 0.00 41.70 3.59
379 700 0.615331 ATTTGGCTCCAGCTCTTCGA 59.385 50.000 0.00 0.00 41.70 3.71
380 701 2.315925 TATTTGGCTCCAGCTCTTCG 57.684 50.000 0.00 0.00 41.70 3.79
422 743 4.366684 GAGCAGGGTTGGTGGGGG 62.367 72.222 0.00 0.00 34.61 5.40
583 904 1.623811 TGGCCGCTTTAACTCTCTTCT 59.376 47.619 0.00 0.00 0.00 2.85
584 905 2.094762 TGGCCGCTTTAACTCTCTTC 57.905 50.000 0.00 0.00 0.00 2.87
1233 1574 2.151202 GCTTGCAGCTTGTAACCTGTA 58.849 47.619 0.00 0.00 38.45 2.74
1463 1805 7.221452 GCATCCAAAATATAAACTGCAACTCTG 59.779 37.037 0.00 0.00 0.00 3.35
1761 2120 5.356751 TGGCACCTACAACATCAATTACATC 59.643 40.000 0.00 0.00 0.00 3.06
1989 2352 2.480073 CGAGCATTGGATGGCGAAAAAT 60.480 45.455 0.00 0.00 34.54 1.82
2308 2671 6.566197 ACTTGTGGTGAATCTGAAGAAATC 57.434 37.500 0.00 0.00 0.00 2.17
2428 2791 1.619654 TTGATCCAACAGGGCAGTTG 58.380 50.000 13.22 13.22 46.44 3.16
2534 2897 7.822822 AGGTCATTATGTAGTGAGTGTTAAACC 59.177 37.037 0.00 0.00 0.00 3.27
3205 3569 5.951148 TGGCTCATATCATTCTTGAAACCAA 59.049 36.000 0.00 0.00 34.96 3.67
3253 3617 3.121445 CGAAGAAACGAACAAGAGCTACC 59.879 47.826 0.00 0.00 35.09 3.18
3450 3814 3.091545 GGAATCCAAGACTGCCAAATCA 58.908 45.455 0.00 0.00 0.00 2.57
3748 4160 6.169800 TCCGATTCAGATTAATTGACACACA 58.830 36.000 0.00 0.00 0.00 3.72
3826 4238 6.896021 AAATCATGAGCCTCCATATTTGAG 57.104 37.500 0.09 0.00 0.00 3.02
3899 4311 4.489679 ACTTGGACAAAGAAAAGATCGC 57.510 40.909 0.00 0.00 39.38 4.58
4041 4455 0.521735 GACGGCCAAAAGGATGTGTC 59.478 55.000 2.24 0.00 0.00 3.67
4042 4456 1.234615 CGACGGCCAAAAGGATGTGT 61.235 55.000 2.24 0.00 0.00 3.72
4044 4458 1.674322 CCGACGGCCAAAAGGATGT 60.674 57.895 2.24 0.00 0.00 3.06
4045 4459 3.051392 GCCGACGGCCAAAAGGATG 62.051 63.158 28.74 0.00 44.06 3.51


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

AutoCloner maintained by Alex Coulton.