Multiple sequence alignment - TraesCS2D01G047000

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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 TraesCS2D01G047000 chr2D 100.000 2246 0 0 1 2246 17238191 17235946 0.000000e+00 4148
1 TraesCS2D01G047000 chr2D 86.425 663 59 13 928 1578 17182299 17181656 0.000000e+00 697
2 TraesCS2D01G047000 chr2D 86.233 661 64 15 928 1578 17326632 17325989 0.000000e+00 691
3 TraesCS2D01G047000 chr2D 91.094 393 32 3 535 926 17327054 17326664 1.530000e-146 529
4 TraesCS2D01G047000 chr2D 90.840 393 33 3 535 926 17182721 17182331 7.110000e-145 523
5 TraesCS2D01G047000 chr2D 86.620 284 34 4 14 294 17183052 17182770 6.020000e-81 311
6 TraesCS2D01G047000 chr2D 86.620 284 35 3 14 295 17327384 17327102 6.020000e-81 311
7 TraesCS2D01G047000 chr2B 91.641 2285 135 36 1 2246 29871429 29873696 0.000000e+00 3110
8 TraesCS2D01G047000 chr2B 85.396 1212 123 26 464 1644 29055311 29054123 0.000000e+00 1208
9 TraesCS2D01G047000 chr2B 86.416 1119 100 21 464 1540 29980320 29981428 0.000000e+00 1177
10 TraesCS2D01G047000 chr2B 86.207 696 63 21 487 1151 28995786 28995093 0.000000e+00 723
11 TraesCS2D01G047000 chr2B 86.004 493 46 14 1153 1641 28993416 28992943 7.160000e-140 507
12 TraesCS2D01G047000 chr2B 86.786 280 34 3 14 291 28996075 28995797 2.170000e-80 309
13 TraesCS2D01G047000 chr2A 92.136 1793 101 20 251 2007 18675381 18673593 0.000000e+00 2494
14 TraesCS2D01G047000 chr2A 85.689 1146 91 31 464 1567 18646890 18645776 0.000000e+00 1140
15 TraesCS2D01G047000 chr2A 90.086 464 44 1 464 927 18614222 18613761 3.190000e-168 601
16 TraesCS2D01G047000 chr2A 91.774 389 32 0 928 1316 18613730 18613342 1.960000e-150 542
17 TraesCS2D01G047000 chr2A 91.639 299 18 6 1 295 18676061 18675766 7.470000e-110 407
18 TraesCS2D01G047000 chr2A 83.281 317 33 13 1314 1626 18613219 18612919 7.900000e-70 274
19 TraesCS2D01G047000 chr2A 89.506 162 17 0 295 456 680277628 680277467 2.920000e-49 206
20 TraesCS2D01G047000 chr2A 86.624 157 20 1 299 455 11897878 11897723 2.970000e-39 172
21 TraesCS2D01G047000 chr2A 86.420 162 17 4 296 455 267885449 267885291 2.970000e-39 172
22 TraesCS2D01G047000 chr3D 89.506 162 13 4 296 456 374360465 374360307 3.780000e-48 202
23 TraesCS2D01G047000 chr3D 88.485 165 18 1 294 457 597295668 597295504 4.890000e-47 198
24 TraesCS2D01G047000 chr3B 87.898 157 18 1 299 455 177086365 177086520 1.370000e-42 183
25 TraesCS2D01G047000 chr1D 86.335 161 20 2 295 455 231021204 231021046 8.250000e-40 174


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 TraesCS2D01G047000 chr2D 17235946 17238191 2245 True 4148.000000 4148 100.000000 1 2246 1 chr2D.!!$R1 2245
1 TraesCS2D01G047000 chr2D 17181656 17183052 1396 True 510.333333 697 87.961667 14 1578 3 chr2D.!!$R2 1564
2 TraesCS2D01G047000 chr2D 17325989 17327384 1395 True 510.333333 691 87.982333 14 1578 3 chr2D.!!$R3 1564
3 TraesCS2D01G047000 chr2B 29871429 29873696 2267 False 3110.000000 3110 91.641000 1 2246 1 chr2B.!!$F1 2245
4 TraesCS2D01G047000 chr2B 29054123 29055311 1188 True 1208.000000 1208 85.396000 464 1644 1 chr2B.!!$R1 1180
5 TraesCS2D01G047000 chr2B 29980320 29981428 1108 False 1177.000000 1177 86.416000 464 1540 1 chr2B.!!$F2 1076
6 TraesCS2D01G047000 chr2B 28992943 28996075 3132 True 513.000000 723 86.332333 14 1641 3 chr2B.!!$R2 1627
7 TraesCS2D01G047000 chr2A 18673593 18676061 2468 True 1450.500000 2494 91.887500 1 2007 2 chr2A.!!$R6 2006
8 TraesCS2D01G047000 chr2A 18645776 18646890 1114 True 1140.000000 1140 85.689000 464 1567 1 chr2A.!!$R2 1103
9 TraesCS2D01G047000 chr2A 18612919 18614222 1303 True 472.333333 601 88.380333 464 1626 3 chr2A.!!$R5 1162


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
334 344 1.49091 CCTCTTACCCCCTCCATTCAC 59.509 57.143 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1987 4471 0.621571 CCTCCTCCACCTCCCATTCA 60.622 60.0 0.0 0.0 0.0 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
26 27 4.502087 GAGCAAGCAAATTTTGGTTCCTCT 60.502 41.667 26.49 20.34 46.89 3.69
39 40 2.417719 GTTCCTCTCTGCGACAACATT 58.582 47.619 0.00 0.00 0.00 2.71
40 41 2.084610 TCCTCTCTGCGACAACATTG 57.915 50.000 0.00 0.00 0.00 2.82
85 86 7.493320 TGCCGAAATAGAACGATTAACAATACT 59.507 33.333 0.00 0.00 0.00 2.12
118 125 7.864307 GCAAGGAGCATAATATGATGAAAAC 57.136 36.000 4.02 0.00 44.79 2.43
334 344 1.490910 CCTCTTACCCCCTCCATTCAC 59.509 57.143 0.00 0.00 0.00 3.18
344 354 1.579698 CTCCATTCACATGAGAGGCG 58.420 55.000 0.00 0.00 31.07 5.52
363 373 4.710375 AGGCGAGAAGGTAAGAGTTAATCA 59.290 41.667 0.00 0.00 0.00 2.57
387 397 8.289618 TCAAACTCACTACTTAATGCAATCAAC 58.710 33.333 0.00 0.00 0.00 3.18
401 411 6.915544 TGCAATCAACAGTTCAGATCTATC 57.084 37.500 0.00 0.00 0.00 2.08
434 444 4.815533 TCTCTCATGTGAAAAGAGGAGG 57.184 45.455 8.14 0.00 37.67 4.30
438 448 6.270000 TCTCTCATGTGAAAAGAGGAGGTAAA 59.730 38.462 8.14 0.00 37.67 2.01
615 626 6.558771 TTCACAATGTTTAGAGACACATGG 57.441 37.500 0.00 0.00 33.76 3.66
677 688 3.443681 CAGGTACATCAAATTCACCCACC 59.556 47.826 0.00 0.00 0.00 4.61
687 698 2.818751 TTCACCCACCTTCAGTTGTT 57.181 45.000 0.00 0.00 0.00 2.83
805 1422 5.762825 AGTGCATCACCATATCACATTTC 57.237 39.130 0.00 0.00 34.49 2.17
855 1474 2.485814 CCTTTAGCTCCACTTCAGCAAC 59.514 50.000 0.00 0.00 39.56 4.17
996 1648 1.526225 GGGCCCGCAAGAAGTATCC 60.526 63.158 5.69 0.00 43.02 2.59
1022 1674 4.630894 TGAAAGTCATTGTGTTGGTGAC 57.369 40.909 0.00 0.00 41.88 3.67
1098 1750 2.835764 AGGGAATGCAATGCAAGTGAAT 59.164 40.909 13.45 0.00 43.62 2.57
1182 3512 0.976641 ATCATGTGTGTCCACGAGGT 59.023 50.000 0.00 0.00 44.92 3.85
1490 3967 9.260002 GAACAATAAATTGAACCACAACATTCT 57.740 29.630 9.60 0.00 41.52 2.40
1615 4092 7.446013 TCAAGTACTTTGGTATTTGGTAAGTGG 59.554 37.037 5.07 0.00 42.26 4.00
1651 4130 6.130298 TCTTGTTTTATGTCAATATGCCCG 57.870 37.500 0.00 0.00 0.00 6.13
1689 4168 3.013921 TGTATTCGCCTTTGTTGGGATC 58.986 45.455 0.00 0.00 0.00 3.36
1705 4184 4.836825 TGGGATCTTTCTCATTCTCACAC 58.163 43.478 0.00 0.00 0.00 3.82
1780 4259 1.663388 CACCTACAACTGCGCACGA 60.663 57.895 5.66 0.00 0.00 4.35
1818 4298 4.484537 AATGGTCATCAGAGAAGGACAG 57.515 45.455 0.00 0.00 32.00 3.51
1833 4313 5.905913 AGAAGGACAGCAGTTTATATACCCT 59.094 40.000 0.00 0.00 0.00 4.34
1901 4382 4.069304 GACGCATGGTTAATTAGGCCATA 58.931 43.478 17.75 0.00 40.68 2.74
1908 4389 7.281100 GCATGGTTAATTAGGCCATAGATCTAC 59.719 40.741 17.75 0.00 40.68 2.59
1987 4471 1.541620 GAAGGAGGGTGGGGAAGGT 60.542 63.158 0.00 0.00 0.00 3.50
1999 4483 0.034089 GGGAAGGTGAATGGGAGGTG 60.034 60.000 0.00 0.00 0.00 4.00
2061 4545 0.255604 TGGGTAGGGTGCATGACATG 59.744 55.000 11.27 11.27 0.00 3.21
2084 4568 6.517605 TGTAATTAAGGGCTTGTTTGGTTTC 58.482 36.000 0.00 0.00 0.00 2.78
2100 4584 4.681744 TGGTTTCAGTTGCATCTTTTGTC 58.318 39.130 0.00 0.00 0.00 3.18
2140 4624 0.941542 GTTTCAGTTGCCACGCTGTA 59.058 50.000 0.00 0.00 34.57 2.74
2205 4689 4.416738 GGCTGGACTCCTGGCACC 62.417 72.222 20.00 3.18 44.90 5.01
2210 4694 2.743928 GACTCCTGGCACCGCAAG 60.744 66.667 0.00 0.00 0.00 4.01
2239 4723 0.168128 CCAGGCGACCGAATTCAAAC 59.832 55.000 6.22 0.00 0.00 2.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 4.975502 GTGAAATTTCAATGTTGTCGCAGA 59.024 37.500 22.07 0.00 39.21 4.26
118 125 1.408340 TCAGCACCACCACAACATTTG 59.592 47.619 0.00 0.00 0.00 2.32
299 309 5.656859 GGGTAAGAGGGAGCATGTTAAAATT 59.343 40.000 0.00 0.00 0.00 1.82
334 344 2.690497 TCTTACCTTCTCGCCTCTCATG 59.310 50.000 0.00 0.00 0.00 3.07
363 373 8.165239 TGTTGATTGCATTAAGTAGTGAGTTT 57.835 30.769 0.00 0.00 0.00 2.66
409 419 6.985645 CCTCCTCTTTTCACATGAGAGATAAG 59.014 42.308 9.38 9.48 39.36 1.73
414 424 4.550076 ACCTCCTCTTTTCACATGAGAG 57.450 45.455 0.00 0.00 37.30 3.20
458 468 8.879427 AGTGCCTTATTAAACCATTAAGAAGT 57.121 30.769 12.17 0.00 43.74 3.01
459 469 9.178758 AGAGTGCCTTATTAAACCATTAAGAAG 57.821 33.333 8.13 8.13 44.36 2.85
460 470 9.528489 AAGAGTGCCTTATTAAACCATTAAGAA 57.472 29.630 0.00 0.00 34.62 2.52
505 516 5.048504 TGAATGCTTCTACTTTTTCAGCTGG 60.049 40.000 15.13 0.00 0.00 4.85
762 1379 9.197306 TGCACTACTTATAGGAGATAAAAGTGA 57.803 33.333 16.28 6.04 33.69 3.41
805 1422 3.685139 TCACCTTCTCTTGGTAGCAAG 57.315 47.619 25.37 25.37 35.80 4.01
888 1507 8.915871 AAGTAATACAACATCAAATGCACATC 57.084 30.769 0.00 0.00 0.00 3.06
1022 1674 4.659111 TTGATAAGAAGCATTGCCATGG 57.341 40.909 7.63 7.63 0.00 3.66
1098 1750 1.264020 GAAGTCAGTTTGCGCATGTCA 59.736 47.619 12.75 0.00 0.00 3.58
1674 4153 2.162408 GAGAAAGATCCCAACAAAGGCG 59.838 50.000 0.00 0.00 0.00 5.52
1677 4156 6.432162 TGAGAATGAGAAAGATCCCAACAAAG 59.568 38.462 0.00 0.00 0.00 2.77
1689 4168 5.178252 ACATGTTCGTGTGAGAATGAGAAAG 59.822 40.000 0.00 0.00 32.25 2.62
1818 4298 5.543020 AGGTGGTCTAGGGTATATAAACTGC 59.457 44.000 0.00 0.00 0.00 4.40
1833 4313 1.855295 TAACGCCATGAGGTGGTCTA 58.145 50.000 0.00 0.00 43.38 2.59
1848 4329 7.136772 TCAGTCTATTATTCGACCACATAACG 58.863 38.462 0.00 0.00 0.00 3.18
1849 4330 8.867112 TTCAGTCTATTATTCGACCACATAAC 57.133 34.615 0.00 0.00 0.00 1.89
1901 4382 1.410517 CACCCTCACATGCGTAGATCT 59.589 52.381 0.00 0.00 0.00 2.75
1908 4389 1.884464 CCGATCACCCTCACATGCG 60.884 63.158 0.00 0.00 0.00 4.73
1987 4471 0.621571 CCTCCTCCACCTCCCATTCA 60.622 60.000 0.00 0.00 0.00 2.57
1999 4483 3.049344 ACCCTATTGATGTTCCTCCTCC 58.951 50.000 0.00 0.00 0.00 4.30
2061 4545 6.517605 TGAAACCAAACAAGCCCTTAATTAC 58.482 36.000 0.00 0.00 0.00 1.89
2084 4568 3.755378 AGGCTAGACAAAAGATGCAACTG 59.245 43.478 0.00 0.00 0.00 3.16
2100 4584 2.035632 CTAGGGACAACTCCAGGCTAG 58.964 57.143 0.00 0.00 38.52 3.42
2167 4651 7.502226 CCAGCCAGGATAATTACAATACAAAGA 59.498 37.037 0.00 0.00 41.22 2.52
2205 4689 1.227380 CTGGGCTAGGCTACTTGCG 60.227 63.158 16.80 0.00 44.78 4.85



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

AutoCloner maintained by Alex Coulton.