Multiple sequence alignment - TraesCS1D01G367500

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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 TraesCS1D01G367500 chr1D 100.000 2608 0 0 1 2608 447349226 447346619 0 4817
1 TraesCS1D01G367500 chr7D 98.198 2608 45 2 1 2608 52435755 52433150 0 4554
2 TraesCS1D01G367500 chr7D 97.971 2612 45 7 1 2608 622016204 622013597 0 4523
3 TraesCS1D01G367500 chr5D 98.234 2605 44 2 1 2605 346023485 346026087 0 4554
4 TraesCS1D01G367500 chr3D 98.234 2605 43 3 1 2605 84530779 84533380 0 4553
5 TraesCS1D01G367500 chr3D 98.119 2605 46 3 1 2605 54664376 54661775 0 4536
6 TraesCS1D01G367500 chr3D 98.045 2609 48 3 1 2608 546357508 546354902 0 4532
7 TraesCS1D01G367500 chr2D 98.119 2605 46 2 1 2605 559267719 559270320 0 4536
8 TraesCS1D01G367500 chr6D 98.042 2605 50 1 1 2605 395490743 395493346 0 4527
9 TraesCS1D01G367500 chrUn 97.968 2608 49 4 1 2608 27645313 27642710 0 4519


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 TraesCS1D01G367500 chr1D 447346619 447349226 2607 True 4817 4817 100.000 1 2608 1 chr1D.!!$R1 2607
1 TraesCS1D01G367500 chr7D 52433150 52435755 2605 True 4554 4554 98.198 1 2608 1 chr7D.!!$R1 2607
2 TraesCS1D01G367500 chr7D 622013597 622016204 2607 True 4523 4523 97.971 1 2608 1 chr7D.!!$R2 2607
3 TraesCS1D01G367500 chr5D 346023485 346026087 2602 False 4554 4554 98.234 1 2605 1 chr5D.!!$F1 2604
4 TraesCS1D01G367500 chr3D 84530779 84533380 2601 False 4553 4553 98.234 1 2605 1 chr3D.!!$F1 2604
5 TraesCS1D01G367500 chr3D 54661775 54664376 2601 True 4536 4536 98.119 1 2605 1 chr3D.!!$R1 2604
6 TraesCS1D01G367500 chr3D 546354902 546357508 2606 True 4532 4532 98.045 1 2608 1 chr3D.!!$R2 2607
7 TraesCS1D01G367500 chr2D 559267719 559270320 2601 False 4536 4536 98.119 1 2605 1 chr2D.!!$F1 2604
8 TraesCS1D01G367500 chr6D 395490743 395493346 2603 False 4527 4527 98.042 1 2605 1 chr6D.!!$F1 2604
9 TraesCS1D01G367500 chrUn 27642710 27645313 2603 True 4519 4519 97.968 1 2608 1 chrUn.!!$R1 2607

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
354 355 1.22738 GATGGCAGGCTTCGTCGAT 60.227 57.895 0.0 0.0 0.0 3.59 F
1376 1381 0.82999 TCGGATATGGACAGCAAGCA 59.170 50.000 0.0 0.0 0.0 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1444 1449 0.318275 GAGATCGCACGGGCTTCTAG 60.318 60.0 8.62 0.00 38.10 2.43 R
2218 2226 1.100463 TTCTTGCAGCTTCCACGCAA 61.100 50.0 8.01 8.01 43.02 4.85 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
172 173 3.420893 TCTCGCATTTCACAAATTCCCT 58.579 40.909 0.00 0.00 0.00 4.20
215 216 3.119990 CCGATATGGTTGTCAAACGCTTT 60.120 43.478 0.00 0.00 37.15 3.51
353 354 2.184322 GATGGCAGGCTTCGTCGA 59.816 61.111 0.00 0.00 0.00 4.20
354 355 1.227380 GATGGCAGGCTTCGTCGAT 60.227 57.895 0.00 0.00 0.00 3.59
406 407 4.066139 GGGAGGCAATGGTGGGCT 62.066 66.667 0.00 0.00 44.69 5.19
408 409 2.036256 GAGGCAATGGTGGGCTGT 59.964 61.111 0.00 0.00 41.74 4.40
513 514 4.319911 CCCAAAAGATCGTGCTCGTTAAAA 60.320 41.667 8.17 0.00 38.33 1.52
731 735 1.604378 CACGGCTCCTCCCATCTTT 59.396 57.895 0.00 0.00 0.00 2.52
1074 1078 2.026301 CGCCGGGAGATCGACTTC 59.974 66.667 2.18 0.00 0.00 3.01
1212 1216 6.073765 TGCGTCTTGAGATTGAAGAAAAGTAC 60.074 38.462 0.00 0.00 31.27 2.73
1350 1355 2.212812 TGGATGCCTATGTGTTGCAA 57.787 45.000 0.00 0.00 38.69 4.08
1376 1381 0.829990 TCGGATATGGACAGCAAGCA 59.170 50.000 0.00 0.00 0.00 3.91
1444 1449 2.639065 TCCGTTTGGAAGGACATATGC 58.361 47.619 1.58 0.00 42.85 3.14
1504 1510 5.592587 TGTCTTCAATTTTTCTCCCCCTA 57.407 39.130 0.00 0.00 0.00 3.53
1646 1654 1.517257 CGCCATCCACTCGAGACAC 60.517 63.158 21.68 0.01 0.00 3.67
2102 2110 3.006940 GCATACTTTGATGAACACCCGA 58.993 45.455 0.00 0.00 0.00 5.14
2104 2112 1.508632 ACTTTGATGAACACCCGACG 58.491 50.000 0.00 0.00 0.00 5.12
2201 2209 3.679389 CAAACTGGGAGCAGAACTGTAT 58.321 45.455 3.77 0.00 0.00 2.29
2211 2219 7.038587 TGGGAGCAGAACTGTATTACTTCTTAA 60.039 37.037 3.77 0.00 0.00 1.85
2215 2223 6.810182 GCAGAACTGTATTACTTCTTAACCGA 59.190 38.462 3.77 0.00 0.00 4.69
2218 2226 8.583296 AGAACTGTATTACTTCTTAACCGAGTT 58.417 33.333 0.00 0.00 0.00 3.01
2233 2241 1.785041 GAGTTTGCGTGGAAGCTGCA 61.785 55.000 1.02 0.00 38.13 4.41
2238 2246 1.100463 TGCGTGGAAGCTGCAAGAAA 61.100 50.000 1.02 0.00 35.33 2.52
2526 2536 5.676331 GCGGAGAAAGAACAAGAACAACTTT 60.676 40.000 0.00 0.00 36.61 2.66
2605 2615 1.819632 GCCCGACGCAATCTCCAAT 60.820 57.895 0.00 0.00 37.47 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
172 173 3.309121 GGAGAAGAATGGAAACCATGGGA 60.309 47.826 18.09 0.00 44.40 4.37
273 274 2.037620 GCCTCTCCGTCATCATGGCT 62.038 60.000 0.00 0.00 36.32 4.75
353 354 6.155049 CCCACCAAATTGTTATTCTTCTCCAT 59.845 38.462 0.00 0.00 0.00 3.41
354 355 5.480073 CCCACCAAATTGTTATTCTTCTCCA 59.520 40.000 0.00 0.00 0.00 3.86
1074 1078 0.454957 CGCGATCCTTTTGCACCTTG 60.455 55.000 0.00 0.00 33.97 3.61
1212 1216 1.374758 GTCCTCACAGTCCCGCTTG 60.375 63.158 0.00 0.00 0.00 4.01
1350 1355 0.821517 TGTCCATATCCGAACGTGCT 59.178 50.000 0.00 0.00 0.00 4.40
1444 1449 0.318275 GAGATCGCACGGGCTTCTAG 60.318 60.000 8.62 0.00 38.10 2.43
1504 1510 4.585955 ACAATCGGTGCGAGATACTTAT 57.414 40.909 0.00 0.00 39.91 1.73
1646 1654 0.456221 AACGGGTGACTCTATCGCAG 59.544 55.000 0.00 0.00 39.82 5.18
2119 2127 1.104577 GGTCACTTTGGCGGGTTCAA 61.105 55.000 0.00 0.00 0.00 2.69
2201 2209 4.209703 CACGCAAACTCGGTTAAGAAGTAA 59.790 41.667 0.00 0.00 0.00 2.24
2211 2219 2.251642 GCTTCCACGCAAACTCGGT 61.252 57.895 0.00 0.00 0.00 4.69
2215 2223 1.383456 TTGCAGCTTCCACGCAAACT 61.383 50.000 5.98 0.00 42.34 2.66
2218 2226 1.100463 TTCTTGCAGCTTCCACGCAA 61.100 50.000 8.01 8.01 43.02 4.85
2233 2241 6.266103 TCCTGCAATCAAGAACATTCTTTCTT 59.734 34.615 4.08 0.00 44.70 2.52
2238 2246 3.760684 GGTCCTGCAATCAAGAACATTCT 59.239 43.478 0.00 0.00 39.74 2.40


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

AutoCloner maintained by Alex Coulton.