Multiple sequence alignment - TraesCS2B01G143000

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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 TraesCS2B01G143000 chr2B 100.000 2468 0 0 1 2468 109886716 109889183 0.000000e+00 4558
1 TraesCS2B01G143000 chr2B 97.488 2030 51 0 439 2468 614643420 614645449 0.000000e+00 3467
2 TraesCS2B01G143000 chr2B 96.712 365 9 2 1 364 614642685 614643047 2.710000e-169 604
3 TraesCS2B01G143000 chr5B 96.747 2490 48 6 1 2468 525550057 525547579 0.000000e+00 4119
4 TraesCS2B01G143000 chr1B 96.079 2474 87 8 1 2468 126921399 126923868 0.000000e+00 4023
5 TraesCS2B01G143000 chr1D 93.651 1638 89 12 1 1626 288858309 288859943 0.000000e+00 2435
6 TraesCS2B01G143000 chr1D 97.476 832 21 0 1637 2468 288860317 288861148 0.000000e+00 1421
7 TraesCS2B01G143000 chr2A 94.162 1576 78 11 1 1567 354528925 354530495 0.000000e+00 2388
8 TraesCS2B01G143000 chr2A 94.106 1578 81 9 1 1570 494101295 494099722 0.000000e+00 2388
9 TraesCS2B01G143000 chr2A 96.514 832 23 1 1637 2468 354530501 354531326 0.000000e+00 1371
10 TraesCS2B01G143000 chr2A 96.596 235 7 1 1637 1871 494099719 494099486 2.980000e-104 388
11 TraesCS2B01G143000 chr7A 93.599 1578 82 15 1 1567 320507535 320509104 0.000000e+00 2337
12 TraesCS2B01G143000 chr7A 96.635 832 28 0 1637 2468 320509110 320509941 0.000000e+00 1382
13 TraesCS2B01G143000 chr7D 91.946 1639 111 15 1 1629 61524214 61522587 0.000000e+00 2276
14 TraesCS2B01G143000 chr7D 97.476 832 21 0 1637 2468 61522216 61521385 0.000000e+00 1421
15 TraesCS2B01G143000 chr1A 91.849 1644 111 14 2 1626 408631022 408632661 0.000000e+00 2272
16 TraesCS2B01G143000 chr4D 96.995 832 25 0 1637 2468 382847075 382846244 0.000000e+00 1399
17 TraesCS2B01G143000 chr4D 94.150 359 17 3 1 357 382849350 382848994 6.000000e-151 544
18 TraesCS2B01G143000 chr6D 93.883 703 33 3 1775 2468 93876313 93877014 0.000000e+00 1051
19 TraesCS2B01G143000 chr3A 91.885 382 25 5 1 378 34899594 34899215 1.680000e-146 529


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 TraesCS2B01G143000 chr2B 109886716 109889183 2467 False 4558.0 4558 100.0000 1 2468 1 chr2B.!!$F1 2467
1 TraesCS2B01G143000 chr2B 614642685 614645449 2764 False 2035.5 3467 97.1000 1 2468 2 chr2B.!!$F2 2467
2 TraesCS2B01G143000 chr5B 525547579 525550057 2478 True 4119.0 4119 96.7470 1 2468 1 chr5B.!!$R1 2467
3 TraesCS2B01G143000 chr1B 126921399 126923868 2469 False 4023.0 4023 96.0790 1 2468 1 chr1B.!!$F1 2467
4 TraesCS2B01G143000 chr1D 288858309 288861148 2839 False 1928.0 2435 95.5635 1 2468 2 chr1D.!!$F1 2467
5 TraesCS2B01G143000 chr2A 354528925 354531326 2401 False 1879.5 2388 95.3380 1 2468 2 chr2A.!!$F1 2467
6 TraesCS2B01G143000 chr2A 494099486 494101295 1809 True 1388.0 2388 95.3510 1 1871 2 chr2A.!!$R1 1870
7 TraesCS2B01G143000 chr7A 320507535 320509941 2406 False 1859.5 2337 95.1170 1 2468 2 chr7A.!!$F1 2467
8 TraesCS2B01G143000 chr7D 61521385 61524214 2829 True 1848.5 2276 94.7110 1 2468 2 chr7D.!!$R1 2467
9 TraesCS2B01G143000 chr1A 408631022 408632661 1639 False 2272.0 2272 91.8490 2 1626 1 chr1A.!!$F1 1624
10 TraesCS2B01G143000 chr4D 382846244 382849350 3106 True 971.5 1399 95.5725 1 2468 2 chr4D.!!$R1 2467
11 TraesCS2B01G143000 chr6D 93876313 93877014 701 False 1051.0 1051 93.8830 1775 2468 1 chr6D.!!$F1 693

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
369 395 1.007118 AGTCATTTTCCATCCACCCCC 59.993 52.381 0.0 0.0 0.0 5.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1577 2771 5.344128 TCGTTAACTATCGCTGAAGAACAAC 59.656 40.0 3.71 0.0 0.0 3.32 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
275 299 2.415608 GGACCTCTCACGCGGATCA 61.416 63.158 12.47 0.0 0.00 2.92
300 324 2.486663 ATACGCCGTCCGATGCTCA 61.487 57.895 0.00 0.0 41.02 4.26
367 393 3.555966 CCTAGTCATTTTCCATCCACCC 58.444 50.000 0.00 0.0 0.00 4.61
368 394 2.532250 AGTCATTTTCCATCCACCCC 57.468 50.000 0.00 0.0 0.00 4.95
369 395 1.007118 AGTCATTTTCCATCCACCCCC 59.993 52.381 0.00 0.0 0.00 5.40
401 705 1.552792 CCTCCTTTCTTTCCTCGCTCT 59.447 52.381 0.00 0.0 0.00 4.09
593 926 3.168528 GCCCGAATCCCTAGCCCA 61.169 66.667 0.00 0.0 0.00 5.36
618 951 1.669999 GCTAGGGTTTCGGTCGCCTA 61.670 60.000 0.00 0.0 0.00 3.93
636 969 1.096967 TACAACTCGATCCCGCGCTA 61.097 55.000 5.56 0.0 35.37 4.26
746 1080 4.687215 ATGCGCACCGACAGCAGT 62.687 61.111 14.90 0.0 44.55 4.40
805 1139 1.627297 GGTCTCCCGCTCCCAAATCT 61.627 60.000 0.00 0.0 0.00 2.40
1019 1357 1.639635 ATGCTGGAAGGGAAGGCGAT 61.640 55.000 0.00 0.0 0.00 4.58
1149 1489 5.470098 GCACATCAAGAAGGTGAGAAACTTA 59.530 40.000 8.76 0.0 34.52 2.24
1150 1490 6.348050 GCACATCAAGAAGGTGAGAAACTTAG 60.348 42.308 8.76 0.0 34.52 2.18
1162 1502 2.238898 AGAAACTTAGCAATACCGCCCT 59.761 45.455 0.00 0.0 0.00 5.19
1577 2771 2.995258 GGTGGCATTTTACATGCTGTTG 59.005 45.455 3.29 0.0 44.02 3.33
1620 2814 3.945285 ACGATCTAAATGGTTCGGCATTT 59.055 39.130 0.00 0.0 35.98 2.32
1742 2942 7.544622 AGTTATGTGATTCGTTCTGTAGCTTA 58.455 34.615 0.00 0.0 0.00 3.09
2389 3595 8.239998 GCTCTGCTTGATAATTCTTTTACTGTT 58.760 33.333 0.00 0.0 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
93 95 5.087397 CCAAAACGTGAACAAGTTTTCGTA 58.913 37.500 21.44 0.00 45.17 3.43
94 96 3.915569 CCAAAACGTGAACAAGTTTTCGT 59.084 39.130 21.44 9.32 45.17 3.85
95 97 3.915569 ACCAAAACGTGAACAAGTTTTCG 59.084 39.130 21.44 18.77 45.17 3.46
275 299 1.664649 CGGACGGCGTATGATGCAT 60.665 57.895 14.74 0.00 0.00 3.96
375 401 1.378646 GAAAGAAAGGAGGCGGGGG 60.379 63.158 0.00 0.00 0.00 5.40
401 705 3.506455 CGACAGAGAAGACTAGGGTTTCA 59.494 47.826 0.00 0.00 0.00 2.69
593 926 1.205460 ACCGAAACCCTAGCCACCAT 61.205 55.000 0.00 0.00 0.00 3.55
618 951 2.412323 TAGCGCGGGATCGAGTTGT 61.412 57.895 8.83 0.00 38.44 3.32
735 1068 0.613292 AGGAGATCACTGCTGTCGGT 60.613 55.000 0.00 0.00 42.97 4.69
739 1072 1.484038 GGAGAGGAGATCACTGCTGT 58.516 55.000 0.00 0.00 44.53 4.40
746 1080 2.595655 TCGCCGGAGAGGAGATCA 59.404 61.111 5.05 0.00 44.12 2.92
794 1128 2.103263 AGACCGTGATAGATTTGGGAGC 59.897 50.000 0.00 0.00 0.00 4.70
1086 1425 3.680338 GAGGACGTCGAAGCGGTCC 62.680 68.421 9.92 14.85 35.98 4.46
1149 1489 1.212935 AGATTTGAGGGCGGTATTGCT 59.787 47.619 0.00 0.00 34.52 3.91
1150 1490 1.680338 AGATTTGAGGGCGGTATTGC 58.320 50.000 0.00 0.00 0.00 3.56
1162 1502 7.056006 TGCAAATTCAGAGGCTATAGATTTGA 58.944 34.615 22.75 8.81 0.00 2.69
1577 2771 5.344128 TCGTTAACTATCGCTGAAGAACAAC 59.656 40.000 3.71 0.00 0.00 3.32
1716 2916 6.398918 AGCTACAGAACGAATCACATAACTT 58.601 36.000 0.00 0.00 0.00 2.66
1742 2942 6.056884 TCTGTTATTTCCAAGTACCAAACGT 58.943 36.000 0.00 0.00 0.00 3.99
2079 3279 8.947115 ACATTAGTAAAAACAAGTCTATCAGGC 58.053 33.333 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.