Multiple sequence alignment - TraesCS2D01G265800

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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 TraesCS2D01G265800 chr2D 100.000 3278 0 0 1 3278 324592240 324595517 0.000000e+00 6054
1 TraesCS2D01G265800 chr2B 96.596 3320 62 15 1 3278 393462191 393465501 0.000000e+00 5457
2 TraesCS2D01G265800 chr2B 85.248 1288 183 6 996 2278 472898489 472899774 0.000000e+00 1319
3 TraesCS2D01G265800 chr2A 97.121 2431 52 6 1 2417 394023803 394021377 0.000000e+00 4085
4 TraesCS2D01G265800 chr2A 84.950 1289 185 8 996 2278 536623645 536624930 0.000000e+00 1297
5 TraesCS2D01G265800 chr2A 94.987 778 15 8 2524 3278 394021163 394020387 0.000000e+00 1199
6 TraesCS2D01G265800 chr2A 98.413 63 1 0 2410 2472 394021356 394021294 9.610000e-21 111


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 TraesCS2D01G265800 chr2D 324592240 324595517 3277 False 6054.000000 6054 100.000000 1 3278 1 chr2D.!!$F1 3277
1 TraesCS2D01G265800 chr2B 393462191 393465501 3310 False 5457.000000 5457 96.596000 1 3278 1 chr2B.!!$F1 3277
2 TraesCS2D01G265800 chr2B 472898489 472899774 1285 False 1319.000000 1319 85.248000 996 2278 1 chr2B.!!$F2 1282
3 TraesCS2D01G265800 chr2A 394020387 394023803 3416 True 1798.333333 4085 96.840333 1 3278 3 chr2A.!!$R1 3277
4 TraesCS2D01G265800 chr2A 536623645 536624930 1285 False 1297.000000 1297 84.950000 996 2278 1 chr2A.!!$F1 1282

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
279 287 1.304879 GGCTTGGGGTACAATGGCA 60.305 57.895 0.0 0.0 38.65 4.92 F
411 423 1.378514 CATGCCCGCTACCAAGGTT 60.379 57.895 0.0 0.0 0.00 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1362 1379 1.275573 AGGAAGGTACGTTTCTCTGCC 59.724 52.381 3.16 0.0 0.0 4.85 R
2407 2436 3.261580 CTGTATTTCCATCACGCAGACA 58.738 45.455 0.00 0.0 0.0 3.41 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
65 66 5.179533 GGGATTCTCAGTTCTAGGTTGTTC 58.820 45.833 0.00 0.00 0.00 3.18
71 72 6.253758 TCTCAGTTCTAGGTTGTTCCATCTA 58.746 40.000 0.00 0.00 39.02 1.98
72 73 6.724441 TCTCAGTTCTAGGTTGTTCCATCTAA 59.276 38.462 0.00 0.00 39.02 2.10
137 138 4.388499 CCCGTGGAACCTCACCGG 62.388 72.222 0.00 0.00 34.36 5.28
164 165 6.938507 TGAGAAAAGGGGAATCATCAATTTG 58.061 36.000 0.00 0.00 0.00 2.32
279 287 1.304879 GGCTTGGGGTACAATGGCA 60.305 57.895 0.00 0.00 38.65 4.92
411 423 1.378514 CATGCCCGCTACCAAGGTT 60.379 57.895 0.00 0.00 0.00 3.50
486 498 1.762957 TGCATAGGAGCTGACTTACCC 59.237 52.381 0.00 0.00 34.99 3.69
645 657 3.374764 TGGCTGAGCTCCTCTTAATACA 58.625 45.455 12.15 0.00 0.00 2.29
958 972 5.684030 GCCTTCTTGGTCGACCTGATTTATA 60.684 44.000 33.39 15.26 38.35 0.98
1008 1022 1.676014 GGTGTACTGACCATGTCTGCC 60.676 57.143 0.00 0.00 35.41 4.85
1362 1379 0.253044 AGATGGTGGAATGGACACGG 59.747 55.000 0.00 0.00 39.69 4.94
1459 1476 4.249661 CACTGAAGCTCTTACCCTTCTTC 58.750 47.826 0.00 0.00 38.55 2.87
2365 2394 3.829026 TGCCTGTGTGTTGCCATTATTTA 59.171 39.130 0.00 0.00 0.00 1.40
2368 2397 5.291614 GCCTGTGTGTTGCCATTATTTATTG 59.708 40.000 0.00 0.00 0.00 1.90
2482 2544 6.449635 TCTAGTGCAATGTTCTGTTGTTTT 57.550 33.333 0.00 0.00 0.00 2.43
2483 2545 6.862209 TCTAGTGCAATGTTCTGTTGTTTTT 58.138 32.000 0.00 0.00 0.00 1.94
2484 2546 5.783100 AGTGCAATGTTCTGTTGTTTTTG 57.217 34.783 0.00 0.00 0.00 2.44
2485 2547 4.630940 AGTGCAATGTTCTGTTGTTTTTGG 59.369 37.500 0.00 0.00 0.00 3.28
2486 2548 3.373439 TGCAATGTTCTGTTGTTTTTGGC 59.627 39.130 0.00 0.00 0.00 4.52
2492 2554 5.995055 TGTTCTGTTGTTTTTGGCTTTTTG 58.005 33.333 0.00 0.00 0.00 2.44
2556 2695 4.334759 CACTGCAGTAATGCAAGATTAGCT 59.665 41.667 21.20 0.00 44.88 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 72 7.472543 GTCAGCTAACGAACAAATCCATATTT 58.527 34.615 0.00 0.00 35.65 1.40
72 73 6.238103 CGTCAGCTAACGAACAAATCCATATT 60.238 38.462 2.25 0.00 45.37 1.28
107 108 2.011222 TCCACGGGTATTTTGCGAATC 58.989 47.619 0.00 0.00 0.00 2.52
137 138 6.780457 TTGATGATTCCCCTTTTCTCAATC 57.220 37.500 0.00 0.00 0.00 2.67
164 165 3.673338 GGAAAGCAACAAGGCGTTAAATC 59.327 43.478 0.00 0.00 35.63 2.17
486 498 6.625873 AAAGAACAGCTTAAGGTTTCAGAG 57.374 37.500 21.05 8.38 35.24 3.35
645 657 8.733092 TTATACTGAATCATCTGGAGAGGAAT 57.267 34.615 0.00 0.00 38.42 3.01
768 780 2.178912 TTTACTGAGGCCCAAAGTCG 57.821 50.000 0.00 0.00 0.00 4.18
958 972 9.645128 TCACAACAGGATATGGATTATTCAAAT 57.355 29.630 0.00 0.00 0.00 2.32
1008 1022 4.378149 GCAGGAAGATACGATGATTGCATG 60.378 45.833 0.00 0.00 34.11 4.06
1362 1379 1.275573 AGGAAGGTACGTTTCTCTGCC 59.724 52.381 3.16 0.00 0.00 4.85
1459 1476 4.383552 CCTCACTTCCTTGATAAGACCAGG 60.384 50.000 0.00 0.00 0.00 4.45
2365 2394 4.952460 ACAGAAGACAATTTGCAAGCAAT 58.048 34.783 8.46 0.00 35.70 3.56
2368 2397 4.383948 GCTAACAGAAGACAATTTGCAAGC 59.616 41.667 0.00 0.00 0.00 4.01
2407 2436 3.261580 CTGTATTTCCATCACGCAGACA 58.738 45.455 0.00 0.00 0.00 3.41
2408 2437 3.262420 ACTGTATTTCCATCACGCAGAC 58.738 45.455 0.00 0.00 0.00 3.51
2482 2544 2.036475 ACACACACACACAAAAAGCCAA 59.964 40.909 0.00 0.00 0.00 4.52
2483 2545 1.615883 ACACACACACACAAAAAGCCA 59.384 42.857 0.00 0.00 0.00 4.75
2484 2546 1.991965 CACACACACACACAAAAAGCC 59.008 47.619 0.00 0.00 0.00 4.35
2485 2547 2.408032 CACACACACACACACAAAAAGC 59.592 45.455 0.00 0.00 0.00 3.51
2486 2548 3.424861 CACACACACACACACACAAAAAG 59.575 43.478 0.00 0.00 0.00 2.27
2492 2554 0.958382 ACCCACACACACACACACAC 60.958 55.000 0.00 0.00 0.00 3.82
2556 2695 2.093235 CCCCTTTCACCAAACAAGCAAA 60.093 45.455 0.00 0.00 0.00 3.68
2934 3098 1.301479 GAACTTGAAGGACGCCGGT 60.301 57.895 1.90 0.00 0.00 5.28


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

AutoCloner maintained by Alex Coulton.