Multiple sequence alignment - TraesCS2B01G552000

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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 TraesCS2B01G552000 chr2B 100.000 2276 0 0 1 2276 747922157 747919882 0 4204
1 TraesCS2B01G552000 chr7B 94.954 2279 109 5 1 2276 35584175 35581900 0 3567
2 TraesCS2B01G552000 chr7B 94.262 2283 116 9 1 2276 115033329 115031055 0 3476
3 TraesCS2B01G552000 chr1B 94.776 2278 111 8 1 2276 518058718 518056447 0 3541
4 TraesCS2B01G552000 chr6B 94.522 2282 112 8 1 2276 568678612 568676338 0 3509
5 TraesCS2B01G552000 chr6B 94.221 2284 118 11 1 2276 593121553 593123830 0 3474
6 TraesCS2B01G552000 chr5B 94.476 2281 113 12 1 2276 122800522 122802794 0 3502
7 TraesCS2B01G552000 chr3B 94.205 2278 123 6 1 2276 532591012 532588742 0 3467
8 TraesCS2B01G552000 chr3B 94.079 2280 126 5 1 2276 441031157 441028883 0 3454
9 TraesCS2B01G552000 chr3B 94.364 1455 78 4 1 1454 39156631 39155180 0 2230
10 TraesCS2B01G552000 chr3B 93.643 1164 61 9 1121 2276 240081289 240082447 0 1727


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 TraesCS2B01G552000 chr2B 747919882 747922157 2275 True 4204 4204 100.000 1 2276 1 chr2B.!!$R1 2275
1 TraesCS2B01G552000 chr7B 35581900 35584175 2275 True 3567 3567 94.954 1 2276 1 chr7B.!!$R1 2275
2 TraesCS2B01G552000 chr7B 115031055 115033329 2274 True 3476 3476 94.262 1 2276 1 chr7B.!!$R2 2275
3 TraesCS2B01G552000 chr1B 518056447 518058718 2271 True 3541 3541 94.776 1 2276 1 chr1B.!!$R1 2275
4 TraesCS2B01G552000 chr6B 568676338 568678612 2274 True 3509 3509 94.522 1 2276 1 chr6B.!!$R1 2275
5 TraesCS2B01G552000 chr6B 593121553 593123830 2277 False 3474 3474 94.221 1 2276 1 chr6B.!!$F1 2275
6 TraesCS2B01G552000 chr5B 122800522 122802794 2272 False 3502 3502 94.476 1 2276 1 chr5B.!!$F1 2275
7 TraesCS2B01G552000 chr3B 532588742 532591012 2270 True 3467 3467 94.205 1 2276 1 chr3B.!!$R3 2275
8 TraesCS2B01G552000 chr3B 441028883 441031157 2274 True 3454 3454 94.079 1 2276 1 chr3B.!!$R2 2275
9 TraesCS2B01G552000 chr3B 39155180 39156631 1451 True 2230 2230 94.364 1 1454 1 chr3B.!!$R1 1453
10 TraesCS2B01G552000 chr3B 240081289 240082447 1158 False 1727 1727 93.643 1121 2276 1 chr3B.!!$F1 1155

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
493 496 1.039068 CTCTCCATCTGCGACTCCAT 58.961 55.0 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1899 1918 0.104725 ATGAGGCCTAGGAAGGGGAG 60.105 60.0 14.75 0.0 43.87 4.3 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
324 327 1.218875 TGTACGCACGGCTTTGTCAG 61.219 55.000 0.00 0.00 0.00 3.51
340 343 6.617105 GCTTTGTCAGCTTAATCAACAAATGC 60.617 38.462 9.18 10.38 46.27 3.56
382 385 1.529226 TGTTAATCCAACAGCCGTGG 58.471 50.000 0.00 0.00 42.29 4.94
399 402 2.561419 CGTGGTCCTTCTTCAACCTCTA 59.439 50.000 0.00 0.00 34.05 2.43
400 403 3.006537 CGTGGTCCTTCTTCAACCTCTAA 59.993 47.826 0.00 0.00 34.05 2.10
409 412 6.365970 TTCTTCAACCTCTAATCTTGCTCT 57.634 37.500 0.00 0.00 0.00 4.09
493 496 1.039068 CTCTCCATCTGCGACTCCAT 58.961 55.000 0.00 0.00 0.00 3.41
531 534 3.277133 CGGGTCGTTCCGGTCTTA 58.723 61.111 0.00 0.00 45.78 2.10
605 608 2.484742 TGACTGTACGTGAGAGGCTA 57.515 50.000 0.00 0.00 0.00 3.93
685 688 1.269621 CGTGGTCAAGGAACGACTTCT 60.270 52.381 0.00 0.00 39.64 2.85
826 829 5.011586 TCAAGATTTCATGTGATGGAGCAA 58.988 37.500 0.00 0.00 0.00 3.91
834 837 5.438833 TCATGTGATGGAGCAATCAATGTA 58.561 37.500 0.00 0.00 38.28 2.29
996 1001 1.269723 CTTCGAGGCCTATCGCATGTA 59.730 52.381 4.42 0.00 42.43 2.29
1073 1078 0.320073 CGTTCGGTTGTGGCTCCTAA 60.320 55.000 0.00 0.00 0.00 2.69
1141 1146 9.513906 TTGAGATTCAACATGTATTAAGGTCAA 57.486 29.630 0.00 1.21 30.26 3.18
1324 1331 6.368779 AAGTAAGTGCCTCCTTATTACACA 57.631 37.500 0.00 0.00 33.69 3.72
1581 1599 3.587506 ACTTGTGGGCCTACTAAGTTGAT 59.412 43.478 21.02 4.11 0.00 2.57
1636 1654 3.701542 TGAACGATTCTAGCTCCAGTGAT 59.298 43.478 0.00 0.00 0.00 3.06
1655 1673 3.320826 TGATCGTACGATGTCCATCCAAT 59.679 43.478 33.86 7.43 34.60 3.16
1697 1715 0.324285 CTGGTCTTCTTGCTCCAGCT 59.676 55.000 0.00 0.00 40.43 4.24
1732 1750 1.676678 GGTCGTGCCTCATGCTCCTA 61.677 60.000 0.00 0.00 42.00 2.94
1986 2005 4.515404 GGAACGACTTCCATCGGG 57.485 61.111 0.08 0.00 46.56 5.14
1996 2015 1.683917 CTTCCATCGGGAGAGTACTGG 59.316 57.143 0.00 0.00 46.01 4.00
2110 2133 5.473931 CAAATCTTTCAAGACGAGGAGAGA 58.526 41.667 0.00 0.00 37.98 3.10
2151 2174 5.461327 AGAAAATGGCCCATCAGTAATGAT 58.539 37.500 0.00 0.00 37.59 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
304 307 0.601576 TGACAAAGCCGTGCGTACAT 60.602 50.000 4.09 0.00 0.00 2.29
324 327 6.802950 GCTAGAAGCATTTGTTGATTAAGC 57.197 37.500 0.00 0.00 41.89 3.09
340 343 3.386078 TCCAATAGTCCAGCTGCTAGAAG 59.614 47.826 8.66 0.00 0.00 2.85
382 385 5.352846 GCAAGATTAGAGGTTGAAGAAGGAC 59.647 44.000 0.00 0.00 0.00 3.85
399 402 1.625818 ACGGGAGACAAGAGCAAGATT 59.374 47.619 0.00 0.00 0.00 2.40
400 403 1.066573 CACGGGAGACAAGAGCAAGAT 60.067 52.381 0.00 0.00 0.00 2.40
446 449 0.544697 AACTTCACTGGTTCGGGTGT 59.455 50.000 0.00 0.00 35.26 4.16
493 496 2.938798 ATGGGGAAGACGGGGCAA 60.939 61.111 0.00 0.00 0.00 4.52
525 528 1.071567 GTGTCGAGCGCACTAAGACC 61.072 60.000 11.47 2.43 34.49 3.85
546 549 0.655733 GTTGACCACGTTGACCACAG 59.344 55.000 0.00 0.00 0.00 3.66
605 608 2.829384 ATGGTGCGTCCCCACTGTT 61.829 57.895 0.00 0.00 34.07 3.16
685 688 6.936335 TCTCCACGTACAATATACTTCCGATA 59.064 38.462 0.00 0.00 0.00 2.92
826 829 3.181471 CCTCGACCTTCTGCTACATTGAT 60.181 47.826 0.00 0.00 0.00 2.57
834 837 1.077625 ACCTCCTCGACCTTCTGCT 59.922 57.895 0.00 0.00 0.00 4.24
1073 1078 7.302184 ACTAAGCTCTCCTATTTCATCTAGGT 58.698 38.462 0.00 0.00 37.58 3.08
1141 1146 4.521256 ACATAAATGTGCCGGTAAGTTTGT 59.479 37.500 1.90 0.00 40.03 2.83
1324 1331 7.890127 TGTCAGTTGGAGGAATCATTATTTTCT 59.110 33.333 0.00 0.00 0.00 2.52
1581 1599 4.617200 CAAAGCCCTTTGTCCCCA 57.383 55.556 11.60 0.00 43.52 4.96
1588 1606 4.532834 TGACTAAGTTGACAAAGCCCTTT 58.467 39.130 0.00 0.00 0.00 3.11
1636 1654 3.092334 CATTGGATGGACATCGTACGA 57.908 47.619 21.93 21.93 38.69 3.43
1655 1673 0.394938 TTGAAGAAGCACTACGGCCA 59.605 50.000 2.24 0.00 0.00 5.36
1899 1918 0.104725 ATGAGGCCTAGGAAGGGGAG 60.105 60.000 14.75 0.00 43.87 4.30
1986 2005 2.011222 CTCTCCACGTCCAGTACTCTC 58.989 57.143 0.00 0.00 0.00 3.20
1996 2015 0.458716 GCTGTTAGCCTCTCCACGTC 60.459 60.000 0.00 0.00 34.48 4.34
2052 2074 3.131396 CTGACAAAGCGACTTACTTGGT 58.869 45.455 0.00 0.00 33.90 3.67
2151 2174 9.262358 GTGTTTTAAAAATGTACAGCCCATTTA 57.738 29.630 1.31 0.21 40.62 1.40


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

AutoCloner maintained by Alex Coulton.