Multiple sequence alignment - TraesCS3B01G275300

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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 TraesCS3B01G275300 chr3B 100.000 2595 0 0 1 2595 445129722 445127128 0 4793
1 TraesCS3B01G275300 chr3B 95.457 2069 70 2 549 2595 52685185 52687251 0 3278
2 TraesCS3B01G275300 chr6B 96.485 2617 66 4 1 2594 646659099 646656486 0 4300
3 TraesCS3B01G275300 chr5B 96.144 2619 70 6 1 2595 649475265 649477876 0 4248
4 TraesCS3B01G275300 chr5B 95.954 2620 77 12 1 2595 686097300 686099915 0 4224
5 TraesCS3B01G275300 chr5B 97.301 2186 55 3 411 2595 27520569 27518387 0 3707
6 TraesCS3B01G275300 chr2B 95.953 2619 76 10 1 2594 709465054 709462441 0 4222
7 TraesCS3B01G275300 chr7B 96.935 2186 61 4 411 2595 694212608 694214788 0 3661
8 TraesCS3B01G275300 chr7B 96.845 2187 63 5 411 2595 607604824 607607006 0 3651
9 TraesCS3B01G275300 chr4A 95.605 2207 69 9 412 2595 650641287 650643488 0 3513


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 TraesCS3B01G275300 chr3B 445127128 445129722 2594 True 4793 4793 100.000 1 2595 1 chr3B.!!$R1 2594
1 TraesCS3B01G275300 chr3B 52685185 52687251 2066 False 3278 3278 95.457 549 2595 1 chr3B.!!$F1 2046
2 TraesCS3B01G275300 chr6B 646656486 646659099 2613 True 4300 4300 96.485 1 2594 1 chr6B.!!$R1 2593
3 TraesCS3B01G275300 chr5B 649475265 649477876 2611 False 4248 4248 96.144 1 2595 1 chr5B.!!$F1 2594
4 TraesCS3B01G275300 chr5B 686097300 686099915 2615 False 4224 4224 95.954 1 2595 1 chr5B.!!$F2 2594
5 TraesCS3B01G275300 chr5B 27518387 27520569 2182 True 3707 3707 97.301 411 2595 1 chr5B.!!$R1 2184
6 TraesCS3B01G275300 chr2B 709462441 709465054 2613 True 4222 4222 95.953 1 2594 1 chr2B.!!$R1 2593
7 TraesCS3B01G275300 chr7B 694212608 694214788 2180 False 3661 3661 96.935 411 2595 1 chr7B.!!$F2 2184
8 TraesCS3B01G275300 chr7B 607604824 607607006 2182 False 3651 3651 96.845 411 2595 1 chr7B.!!$F1 2184
9 TraesCS3B01G275300 chr4A 650641287 650643488 2201 False 3513 3513 95.605 412 2595 1 chr4A.!!$F1 2183

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
272 273 0.90891 ATCGGCAGTGAACCATACCA 59.091 50.0 0.0 0.0 0.0 3.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2206 2260 1.302033 CTTCTGGCAGCTTCCACGT 60.302 57.895 10.34 0.0 31.74 4.49 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
79 80 7.489239 TCCCAATTCCGAGGAAATAAAAATT 57.511 32.000 8.79 0.00 37.69 1.82
168 169 2.686558 TGCTCTCGCATTTCACAAAC 57.313 45.000 0.00 0.00 42.25 2.93
272 273 0.908910 ATCGGCAGTGAACCATACCA 59.091 50.000 0.00 0.00 0.00 3.25
327 328 2.360844 GACATCTCTCGTCTCTCACCA 58.639 52.381 0.00 0.00 0.00 4.17
510 513 0.996462 CCAAAAGATCGCGCTCGTTA 59.004 50.000 11.32 0.00 36.96 3.18
591 595 8.065627 TCACGGATATATACCTTCCCATTCTAT 58.934 37.037 0.00 0.00 0.00 1.98
658 662 2.357517 CATAGCCATCGCCGGGAC 60.358 66.667 2.18 0.00 34.57 4.46
842 891 7.399191 TGAGTAGTTCTGGTGTAATTGGAGTAT 59.601 37.037 0.00 0.00 0.00 2.12
888 937 8.827177 TTTGACTGATAGTTTGTAGTAGTTGG 57.173 34.615 0.00 0.00 0.00 3.77
991 1040 7.611770 TCATACTATGGGTATATGTGTTGCTC 58.388 38.462 0.00 0.00 38.92 4.26
1225 1274 4.504858 AGAAAAGTATAAGCGGGACTGTG 58.495 43.478 0.00 0.00 0.00 3.66
1284 1335 2.859526 TGCATCAAACGTTGCAGAAA 57.140 40.000 8.51 0.00 43.54 2.52
1285 1336 3.156511 TGCATCAAACGTTGCAGAAAA 57.843 38.095 8.51 0.00 43.54 2.29
1302 1353 4.038402 CAGAAAAACCAGAAGCTTGTGGAT 59.962 41.667 40.58 30.23 43.86 3.41
1453 1504 5.902681 TGGAAGGACATATGTTAGAAGACG 58.097 41.667 10.30 0.00 0.00 4.18
2184 2238 1.419762 TGCAAACTGGGAGCAGAACTA 59.580 47.619 0.00 0.00 33.75 2.24
2206 2260 5.653255 ATACTACTTCTTACCCGGGTCTA 57.347 43.478 34.27 19.14 0.00 2.59
2262 2316 4.943705 GCAGGACCAGATGATGTAGAAAAA 59.056 41.667 0.00 0.00 0.00 1.94
2356 2410 3.643159 TCCCGAGTATGACATTGATCG 57.357 47.619 0.00 1.67 0.00 3.69
2495 2549 1.410517 CTTGCTAGAGAGATGGCGGAA 59.589 52.381 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 80 7.328404 TGCTATGAATTCTGACCCCATATTA 57.672 36.000 7.05 0.00 0.00 0.98
83 84 4.524802 TTGCTATGAATTCTGACCCCAT 57.475 40.909 7.05 0.00 0.00 4.00
168 169 2.440247 GGAAACCATGGGCGGGAG 60.440 66.667 18.09 0.00 0.00 4.30
272 273 2.021068 CTCTCCGTCATCATGGCCGT 62.021 60.000 0.00 0.00 0.00 5.68
591 595 5.198965 GGTTAGGATAGGGTAGATATGCGA 58.801 45.833 0.00 0.00 0.00 5.10
802 851 6.428159 CAGAACTACTCAACTATGGCAAAAGT 59.572 38.462 0.00 0.00 0.00 2.66
842 891 6.151480 TCAAAAAGCTCTTGCATGACATCATA 59.849 34.615 0.00 0.00 42.74 2.15
991 1040 2.315176 CTCTGAGACCATGGTCCCTAG 58.685 57.143 36.09 29.35 45.59 3.02
1062 1111 1.344438 TGCACCTTCAAGTCGATCTGT 59.656 47.619 0.00 0.00 0.00 3.41
1063 1112 2.084610 TGCACCTTCAAGTCGATCTG 57.915 50.000 0.00 0.00 0.00 2.90
1249 1300 3.193267 TGATGCATTTCCTTGTAGCCAAC 59.807 43.478 0.00 0.00 0.00 3.77
1284 1335 4.373156 ACTATCCACAAGCTTCTGGTTT 57.627 40.909 18.92 11.21 0.00 3.27
1285 1336 5.700402 ATACTATCCACAAGCTTCTGGTT 57.300 39.130 18.92 13.82 0.00 3.67
1302 1353 7.215085 TGACTCGCTCTGTCTGTATAATACTA 58.785 38.462 0.00 0.00 35.63 1.82
1453 1504 4.451150 TGGCCGTGAGATCGCACC 62.451 66.667 21.83 10.35 35.37 5.01
2184 2238 4.533001 AGACCCGGGTAAGAAGTAGTAT 57.467 45.455 30.38 0.00 0.00 2.12
2206 2260 1.302033 CTTCTGGCAGCTTCCACGT 60.302 57.895 10.34 0.00 31.74 4.49
2262 2316 5.046878 TGCCATTCAGATCAGAAAGCATTTT 60.047 36.000 18.80 0.00 39.27 1.82
2263 2317 4.464951 TGCCATTCAGATCAGAAAGCATTT 59.535 37.500 18.80 0.00 43.98 2.32


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

AutoCloner maintained by Alex Coulton.