Multiple sequence alignment - TraesCS2A01G242100

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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 TraesCS2A01G242100 chr2A 100.000 2162 0 0 1 2162 335838117 335840278 0 3993
1 TraesCS2A01G242100 chr5D 97.780 2162 47 1 1 2162 503217707 503219867 0 3725
2 TraesCS2A01G242100 chr5D 97.456 2162 54 1 1 2162 503278737 503276577 0 3687
3 TraesCS2A01G242100 chr5D 97.364 2162 56 1 1 2162 6188429 6190589 0 3675
4 TraesCS2A01G242100 chr3B 97.734 2162 48 1 1 2162 201526513 201528673 0 3720
5 TraesCS2A01G242100 chr1A 97.734 2162 48 1 1 2162 554511737 554513897 0 3720
6 TraesCS2A01G242100 chr3D 97.456 2162 51 3 1 2162 589280053 589277896 0 3685
7 TraesCS2A01G242100 chrUn 97.271 2162 57 2 1 2162 216519113 216516954 0 3664
8 TraesCS2A01G242100 chr3A 97.225 2162 58 2 1 2162 672910518 672908359 0 3659


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 TraesCS2A01G242100 chr2A 335838117 335840278 2161 False 3993 3993 100.000 1 2162 1 chr2A.!!$F1 2161
1 TraesCS2A01G242100 chr5D 503217707 503219867 2160 False 3725 3725 97.780 1 2162 1 chr5D.!!$F2 2161
2 TraesCS2A01G242100 chr5D 503276577 503278737 2160 True 3687 3687 97.456 1 2162 1 chr5D.!!$R1 2161
3 TraesCS2A01G242100 chr5D 6188429 6190589 2160 False 3675 3675 97.364 1 2162 1 chr5D.!!$F1 2161
4 TraesCS2A01G242100 chr3B 201526513 201528673 2160 False 3720 3720 97.734 1 2162 1 chr3B.!!$F1 2161
5 TraesCS2A01G242100 chr1A 554511737 554513897 2160 False 3720 3720 97.734 1 2162 1 chr1A.!!$F1 2161
6 TraesCS2A01G242100 chr3D 589277896 589280053 2157 True 3685 3685 97.456 1 2162 1 chr3D.!!$R1 2161
7 TraesCS2A01G242100 chrUn 216516954 216519113 2159 True 3664 3664 97.271 1 2162 1 chrUn.!!$R1 2161
8 TraesCS2A01G242100 chr3A 672908359 672910518 2159 True 3659 3659 97.225 1 2162 1 chr3A.!!$R1 2161

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
413 414 0.746659 GGAGCCATCCCAATTTTCCG 59.253 55.0 0.0 0.0 40.03 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1944 1946 1.702957 TCCCGGTTGTTCAATCCTTCT 59.297 47.619 0.0 0.0 0.0 2.85 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
174 175 7.971168 AGCATACGACTTTCTAGATGTATATGC 59.029 37.037 25.18 25.18 38.81 3.14
188 189 6.887002 AGATGTATATGCCGATCTCTAGACAA 59.113 38.462 0.00 0.00 0.00 3.18
265 266 2.951642 GGAATCCAAATCTGCCGAATCA 59.048 45.455 0.00 0.00 0.00 2.57
299 300 6.916909 TGATCTTCTACATCCTAGGTCTCTT 58.083 40.000 9.08 0.00 0.00 2.85
300 301 7.358263 TGATCTTCTACATCCTAGGTCTCTTT 58.642 38.462 9.08 0.00 0.00 2.52
342 343 7.876936 ATGTTCTTCATGTAGCATTCAGATT 57.123 32.000 0.00 0.00 35.19 2.40
398 399 5.867716 CACATATTATGGGTAACGTAGGAGC 59.132 44.000 8.48 0.00 37.60 4.70
413 414 0.746659 GGAGCCATCCCAATTTTCCG 59.253 55.000 0.00 0.00 40.03 4.30
498 499 1.730851 AACCCGTCCTCCTCTCTTTT 58.269 50.000 0.00 0.00 0.00 2.27
541 542 2.458951 TGTGCGTGCTTCAAACAATTC 58.541 42.857 0.00 0.00 0.00 2.17
554 555 7.587037 TTCAAACAATTCTGTCTTCTCCATT 57.413 32.000 0.00 0.00 33.45 3.16
555 556 8.690203 TTCAAACAATTCTGTCTTCTCCATTA 57.310 30.769 0.00 0.00 33.45 1.90
909 910 5.182570 TCGATTAGGGTCGTATTCTATGGTG 59.817 44.000 0.00 0.00 42.07 4.17
912 913 3.912248 AGGGTCGTATTCTATGGTGACT 58.088 45.455 0.00 0.00 0.00 3.41
1006 1007 5.222079 TCTATGCCTTGCGGTAATGATTA 57.778 39.130 0.00 0.00 0.00 1.75
1009 1010 4.409718 TGCCTTGCGGTAATGATTACTA 57.590 40.909 14.34 0.38 36.39 1.82
1092 1093 0.601558 TCACTTGCCTGTCTACGGTC 59.398 55.000 0.00 0.00 0.00 4.79
1347 1348 6.272822 ACCCAATGCTTTATTTCTGTCTTC 57.727 37.500 0.00 0.00 0.00 2.87
1944 1946 8.871629 TTTAGCAAAGAATGACCTTGGTTATA 57.128 30.769 0.00 0.00 0.00 0.98
1945 1947 8.506168 TTAGCAAAGAATGACCTTGGTTATAG 57.494 34.615 0.00 0.00 0.00 1.31
2003 2005 5.897377 ACCTAGTTGGCATTGATAACAAC 57.103 39.130 0.00 0.00 42.51 3.32
2070 2072 9.561069 AAAGACGTATATTCCTTGCTCATTATT 57.439 29.630 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
156 157 7.613801 AGAGATCGGCATATACATCTAGAAAGT 59.386 37.037 0.00 1.14 0.00 2.66
174 175 5.720371 AGATCCATTTGTCTAGAGATCGG 57.280 43.478 10.21 3.55 36.19 4.18
265 266 8.489676 AGGATGTAGAAGATCATAACATGAGT 57.510 34.615 0.00 0.00 43.53 3.41
342 343 7.477494 TCGACGTAATTTCATAGAGTCATTCA 58.523 34.615 0.00 0.00 0.00 2.57
398 399 1.437160 CGGCGGAAAATTGGGATGG 59.563 57.895 0.00 0.00 0.00 3.51
405 406 2.361992 GACCCCCGGCGGAAAATT 60.362 61.111 30.79 6.33 0.00 1.82
413 414 0.547553 TGGTAATTAAGACCCCCGGC 59.452 55.000 0.00 0.00 35.99 6.13
498 499 1.673009 CGGAAGCGCCCCTTGTTTA 60.673 57.895 2.29 0.00 32.78 2.01
541 542 9.253832 AGAGATATGGTATAATGGAGAAGACAG 57.746 37.037 0.00 0.00 0.00 3.51
745 746 3.421844 GAAATGCCCTACCTTTGAGTGT 58.578 45.455 0.00 0.00 0.00 3.55
1006 1007 6.070653 TGTGGTAAAGGTCGTAATTCCATAGT 60.071 38.462 0.00 0.00 0.00 2.12
1009 1010 5.168647 TGTGGTAAAGGTCGTAATTCCAT 57.831 39.130 0.00 0.00 0.00 3.41
1283 1284 2.187958 AGGTGGTAGCTGTGAATAGCA 58.812 47.619 0.00 0.00 46.07 3.49
1429 1431 6.265422 GGGAAAGTCGATTTATGGATGGAATT 59.735 38.462 0.00 0.00 0.00 2.17
1532 1534 9.382275 CATCCATCATCCATACATAACGAATTA 57.618 33.333 0.00 0.00 0.00 1.40
1761 1763 8.791327 AAAATTTGCCATCTCGGAATATTTTT 57.209 26.923 0.00 0.00 36.56 1.94
1784 1786 5.642063 GGTGTTTTCATAGTCATCTCCGAAA 59.358 40.000 0.00 0.00 0.00 3.46
1944 1946 1.702957 TCCCGGTTGTTCAATCCTTCT 59.297 47.619 0.00 0.00 0.00 2.85
1945 1947 2.194201 TCCCGGTTGTTCAATCCTTC 57.806 50.000 0.00 0.00 0.00 3.46
2070 2072 7.027874 AGGTTTGGGAATAAGTGATTGTCTA 57.972 36.000 0.00 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.