Multiple sequence alignment - TraesCS1A01G093600

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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 TraesCS1A01G093600 chr1A 100.000 2257 0 0 1 2257 86621533 86623789 0 4169
1 TraesCS1A01G093600 chr1A 76.789 2236 470 41 27 2241 554994641 554992434 0 1208
2 TraesCS1A01G093600 chr7B 94.115 2260 122 10 1 2257 641484698 641486949 0 3426
3 TraesCS1A01G093600 chr2B 91.199 2261 184 12 1 2257 756588181 756590430 0 3059
4 TraesCS1A01G093600 chr6A 91.195 2260 184 12 1 2257 133775364 133777611 0 3057
5 TraesCS1A01G093600 chr7A 86.428 2262 281 20 3 2257 19150221 19147979 0 2453
6 TraesCS1A01G093600 chr5B 80.352 2046 369 25 225 2257 523639028 523637003 0 1520
7 TraesCS1A01G093600 chr1D 77.241 2276 474 36 3 2257 443789363 443787111 0 1293
8 TraesCS1A01G093600 chr1D 77.056 2249 462 42 33 2257 427866830 427864612 0 1245
9 TraesCS1A01G093600 chr3D 77.392 2247 459 40 33 2257 508093261 508091042 0 1290
10 TraesCS1A01G093600 chr3A 74.508 2032 464 45 236 2241 625212202 625214205 0 833


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 TraesCS1A01G093600 chr1A 86621533 86623789 2256 False 4169 4169 100.000 1 2257 1 chr1A.!!$F1 2256
1 TraesCS1A01G093600 chr1A 554992434 554994641 2207 True 1208 1208 76.789 27 2241 1 chr1A.!!$R1 2214
2 TraesCS1A01G093600 chr7B 641484698 641486949 2251 False 3426 3426 94.115 1 2257 1 chr7B.!!$F1 2256
3 TraesCS1A01G093600 chr2B 756588181 756590430 2249 False 3059 3059 91.199 1 2257 1 chr2B.!!$F1 2256
4 TraesCS1A01G093600 chr6A 133775364 133777611 2247 False 3057 3057 91.195 1 2257 1 chr6A.!!$F1 2256
5 TraesCS1A01G093600 chr7A 19147979 19150221 2242 True 2453 2453 86.428 3 2257 1 chr7A.!!$R1 2254
6 TraesCS1A01G093600 chr5B 523637003 523639028 2025 True 1520 1520 80.352 225 2257 1 chr5B.!!$R1 2032
7 TraesCS1A01G093600 chr1D 443787111 443789363 2252 True 1293 1293 77.241 3 2257 1 chr1D.!!$R2 2254
8 TraesCS1A01G093600 chr1D 427864612 427866830 2218 True 1245 1245 77.056 33 2257 1 chr1D.!!$R1 2224
9 TraesCS1A01G093600 chr3D 508091042 508093261 2219 True 1290 1290 77.392 33 2257 1 chr3D.!!$R1 2224
10 TraesCS1A01G093600 chr3A 625212202 625214205 2003 False 833 833 74.508 236 2241 1 chr3A.!!$F1 2005

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
495 497 0.388659 ACGCAGGCAAATGCAGAAAA 59.611 45.0 7.8 0.0 46.87 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1539 1551 1.339097 GACCACGTATAGCATCCCCT 58.661 55.0 0.0 0.0 0.0 4.79 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
120 121 5.279556 CCATGACTAGAGAGCATGATGATGT 60.280 44.000 15.78 0.00 38.46 3.06
270 271 4.650131 GGATTATTACTCCTATCCCTCCCG 59.350 50.000 0.00 0.00 32.20 5.14
362 364 0.547712 GGCCCTCCCTGCCTCATATA 60.548 60.000 0.00 0.00 45.70 0.86
365 367 2.559931 GCCCTCCCTGCCTCATATAGTA 60.560 54.545 0.00 0.00 0.00 1.82
429 431 5.189736 AGCACCTATACTGTTGAATCTCCAA 59.810 40.000 0.00 0.00 0.00 3.53
430 432 6.058183 GCACCTATACTGTTGAATCTCCAAT 58.942 40.000 0.00 0.00 0.00 3.16
495 497 0.388659 ACGCAGGCAAATGCAGAAAA 59.611 45.000 7.80 0.00 46.87 2.29
582 587 8.541899 ACCCAACTCTAAAAACCAATTTTCTA 57.458 30.769 0.00 0.00 41.42 2.10
614 619 9.511144 TCTGATAATGCCATTATATTACGTACG 57.489 33.333 15.01 15.01 35.68 3.67
615 620 9.297586 CTGATAATGCCATTATATTACGTACGT 57.702 33.333 25.98 25.98 35.68 3.57
839 844 7.603784 ACCATTTATCCTTGTTCAATCAAAAGC 59.396 33.333 0.00 0.00 0.00 3.51
942 949 5.952347 GTCAAAAGAAAATGGGAGAGGGTAT 59.048 40.000 0.00 0.00 0.00 2.73
945 952 3.747852 AGAAAATGGGAGAGGGTATGGA 58.252 45.455 0.00 0.00 0.00 3.41
960 967 2.123018 ATGGATGCTATGGACCCTGA 57.877 50.000 0.00 0.00 0.00 3.86
1227 1236 6.897413 AGGTATTCTTTGTGGCCTCAATAAAT 59.103 34.615 20.29 21.15 0.00 1.40
1539 1551 9.693739 TTGGTTTAAGAGAAATTCATATGGCTA 57.306 29.630 2.13 0.00 0.00 3.93
1626 1639 1.133167 TGTCTCCTGAGTGGGAAGACA 60.133 52.381 0.00 0.00 39.15 3.41
1670 1685 7.176515 TGAGCAAGCTGGTTAAAGAATTATCAA 59.823 33.333 0.00 0.00 0.00 2.57
1805 1821 2.760092 GCTGATATTTGGTCAAGGCCAA 59.240 45.455 5.01 1.23 45.83 4.52
1882 1898 2.552093 TTTTCAAAGGTTGGGGGTCA 57.448 45.000 0.00 0.00 0.00 4.02
2138 2157 1.444836 TGGGCGTCATAGGAAAAACG 58.555 50.000 0.00 0.00 38.13 3.60
2207 2226 3.354948 ACTTGCTATCTCATGCCACAA 57.645 42.857 0.00 0.00 0.00 3.33
2238 2257 2.283173 CCTTTTTGGGCCGGCTCT 60.283 61.111 29.93 0.00 0.00 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
270 271 7.559486 TCATCATGATAGAGGTATAATGGTGC 58.441 38.462 8.15 0.0 38.09 5.01
429 431 3.392616 GTGTCATGGATAGGAGACCCAAT 59.607 47.826 0.00 0.0 33.15 3.16
430 432 2.771943 GTGTCATGGATAGGAGACCCAA 59.228 50.000 0.00 0.0 33.15 4.12
474 476 1.171549 TTCTGCATTTGCCTGCGTGA 61.172 50.000 0.00 0.0 45.30 4.35
495 497 0.252284 ACTTCCTCCACTCGTCCCAT 60.252 55.000 0.00 0.0 0.00 4.00
612 617 1.221840 CCCCATAAGAGCAGCACGT 59.778 57.895 0.00 0.0 0.00 4.49
613 618 1.524621 CCCCCATAAGAGCAGCACG 60.525 63.158 0.00 0.0 0.00 5.34
614 619 0.034089 AACCCCCATAAGAGCAGCAC 60.034 55.000 0.00 0.0 0.00 4.40
615 620 1.590591 TAACCCCCATAAGAGCAGCA 58.409 50.000 0.00 0.0 0.00 4.41
839 844 6.310224 TCTGCGTTTTTCTTTCTTTTTCCTTG 59.690 34.615 0.00 0.0 0.00 3.61
891 898 8.016301 TCTTGTCATATGTCTAGCAGATCTTT 57.984 34.615 1.90 0.0 0.00 2.52
942 949 1.131638 GTCAGGGTCCATAGCATCCA 58.868 55.000 0.00 0.0 0.00 3.41
945 952 1.765314 GTCTGTCAGGGTCCATAGCAT 59.235 52.381 0.00 0.0 0.00 3.79
1227 1236 9.607988 TTTAGAGCCGAGAACATCAAATTTATA 57.392 29.630 0.00 0.0 0.00 0.98
1479 1491 9.374838 GATAACCGAGTTAAATACCTCTGAAAA 57.625 33.333 1.45 0.0 31.56 2.29
1539 1551 1.339097 GACCACGTATAGCATCCCCT 58.661 55.000 0.00 0.0 0.00 4.79
1626 1639 3.545703 CTCACGAAGCAAGGGGAAATAT 58.454 45.455 0.00 0.0 0.00 1.28
1670 1685 4.172807 TCCAATAGTAGAGGGTTGTGGTT 58.827 43.478 0.00 0.0 0.00 3.67
1760 1776 4.944317 CACTAAGGGAGGAAACTTTGGATC 59.056 45.833 0.00 0.0 44.43 3.36
1766 1782 2.040412 CAGCCACTAAGGGAGGAAACTT 59.960 50.000 0.00 0.0 38.51 2.66
1773 1789 4.141390 ACCAAATATCAGCCACTAAGGGAG 60.141 45.833 0.00 0.0 38.09 4.30
2138 2157 2.614057 CGTACTCAAGGGATTTCATGGC 59.386 50.000 0.00 0.0 0.00 4.40
2207 2226 9.168451 CGGCCCAAAAAGGTTTTTATAATATTT 57.832 29.630 0.00 0.0 38.23 1.40


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

AutoCloner maintained by Alex Coulton.