Multiple sequence alignment - TraesCS5B01G261700

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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 TraesCS5B01G261700 chr5B 100.000 2538 0 0 1 2538 446269078 446266541 0.000000e+00 4687
1 TraesCS5B01G261700 chr5B 98.523 1964 25 2 577 2538 447277621 447279582 0.000000e+00 3463
2 TraesCS5B01G261700 chr5B 96.296 378 10 4 202 577 447272092 447272467 3.590000e-173 617
3 TraesCS5B01G261700 chr5B 96.804 219 6 1 1 219 447270337 447270554 5.160000e-97 364
4 TraesCS5B01G261700 chr4A 89.167 240 24 2 84 322 527515383 527515621 5.310000e-77 298
5 TraesCS5B01G261700 chr4A 87.083 240 30 1 84 322 89431041 89430802 1.160000e-68 270
6 TraesCS5B01G261700 chr4D 87.179 234 30 0 89 322 500720383 500720150 1.500000e-67 267
7 TraesCS5B01G261700 chr7D 85.827 254 31 4 81 331 58790400 58790149 5.380000e-67 265
8 TraesCS5B01G261700 chr1A 85.774 239 33 1 85 322 22999045 22999283 4.190000e-63 252
9 TraesCS5B01G261700 chr1B 84.362 243 34 4 83 322 357188149 357188390 4.220000e-58 235
10 TraesCS5B01G261700 chr1B 83.794 253 33 7 76 323 94200879 94200630 1.520000e-57 233


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 TraesCS5B01G261700 chr5B 446266541 446269078 2537 True 4687.0 4687 100.000 1 2538 1 chr5B.!!$R1 2537
1 TraesCS5B01G261700 chr5B 447277621 447279582 1961 False 3463.0 3463 98.523 577 2538 1 chr5B.!!$F1 1961
2 TraesCS5B01G261700 chr5B 447270337 447272467 2130 False 490.5 617 96.550 1 577 2 chr5B.!!$F2 576

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
489 2046 0.838122 AGCAGTAGCCCAACACTCCT 60.838 55.000 0.0 0.0 43.56 3.69 F
895 2453 2.476051 CTGACGGTGCATGTTCGC 59.524 61.111 0.0 0.0 0.00 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1366 2924 0.401738 TCAGAGGCCTCACTTTTGGG 59.598 55.0 33.9 12.41 0.0 4.12 R
1933 3493 0.755686 AGGGCATCTCGGTTCTGATC 59.244 55.0 0.0 0.00 0.0 2.92 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
93 94 8.730948 ACATAATTAGTAGTAGTACTCCCTCCA 58.269 37.037 13.60 0.00 40.23 3.86
115 116 1.790755 TCACAATGTAGTGCGTCCAC 58.209 50.000 0.00 0.00 42.39 4.02
126 127 3.822192 CGTCCACGCATCCCGAGA 61.822 66.667 0.00 0.00 41.02 4.04
238 1794 1.570813 GCATAATTTTTGCTCCCGCC 58.429 50.000 4.78 0.00 37.14 6.13
265 1821 7.012044 GCAGTTGGTCTCGTTGGTTAAATATAT 59.988 37.037 0.00 0.00 0.00 0.86
305 1861 1.623081 AAACGCGGACGCACTACATG 61.623 55.000 17.35 0.00 45.53 3.21
371 1927 1.133945 TCCACACACAGCCTAGCAAAA 60.134 47.619 0.00 0.00 0.00 2.44
489 2046 0.838122 AGCAGTAGCCCAACACTCCT 60.838 55.000 0.00 0.00 43.56 3.69
748 2306 8.900781 TCTAGTATAAAGGTGATCAGTGTGTAC 58.099 37.037 0.00 0.00 0.00 2.90
780 2338 8.147058 AGCAGACCTGAAGTAATGATGTTATAG 58.853 37.037 0.47 0.00 0.00 1.31
895 2453 2.476051 CTGACGGTGCATGTTCGC 59.524 61.111 0.00 0.00 0.00 4.70
916 2474 3.810386 GCTTTCCTTTCTTCTCTTCGTGT 59.190 43.478 0.00 0.00 0.00 4.49
1366 2924 0.324285 CCCATCATCCTAGCAGAGCC 59.676 60.000 0.00 0.00 0.00 4.70
1475 3033 8.943909 TTTGTCACCGTAATTTTTGGTAAATT 57.056 26.923 0.00 0.00 33.82 1.82
1502 3060 3.947834 GTGCTTGCATCTACTTTGGGTAT 59.052 43.478 0.00 0.00 0.00 2.73
1504 3062 3.565902 GCTTGCATCTACTTTGGGTATCC 59.434 47.826 0.00 0.00 0.00 2.59
1845 3405 5.415389 ACCTGCATTTGGAAAATTATTTGGC 59.585 36.000 0.00 0.00 0.00 4.52
1933 3493 5.235305 AGTGCAGTAAACACTTGTTTCTG 57.765 39.130 10.58 16.24 46.01 3.02
2157 3717 4.225984 TGCGTCAAACAAAGTGAATATGC 58.774 39.130 0.00 0.00 0.00 3.14
2268 3828 3.425659 TGTGTGGCTGGCACAAATTATA 58.574 40.909 34.26 15.91 42.96 0.98
2277 3837 5.005971 GCTGGCACAAATTATAACATTGCTG 59.994 40.000 11.04 9.87 38.70 4.41
2327 3887 6.575244 TCAGGGGAATAAAAGCAAGAGATA 57.425 37.500 0.00 0.00 0.00 1.98
2473 4033 5.539048 ACACAACGTTCTAGAAAGCATACT 58.461 37.500 17.03 0.00 0.00 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
93 94 3.188460 GTGGACGCACTACATTGTGAAAT 59.812 43.478 0.00 0.00 40.12 2.17
115 116 2.797156 CAAACTTAGATCTCGGGATGCG 59.203 50.000 0.20 0.00 31.46 4.73
126 127 7.933033 TGGTTAAACTTACGGTCAAACTTAGAT 59.067 33.333 0.00 0.00 0.00 1.98
204 205 9.086336 CAAAAATTATGCCACTGAATTCGTATT 57.914 29.630 0.04 0.00 0.00 1.89
238 1794 1.157870 AACCAACGAGACCAACTGCG 61.158 55.000 0.00 0.00 0.00 5.18
265 1821 7.621426 GCGTTTTTCGAGATCTAACTTTGATCA 60.621 37.037 13.53 0.00 42.86 2.92
283 1839 0.449993 GTAGTGCGTCCGCGTTTTTC 60.450 55.000 4.92 0.00 45.51 2.29
305 1861 0.253327 GACACTCCCTCCATTCCACC 59.747 60.000 0.00 0.00 0.00 4.61
371 1927 0.466555 TTTGCAGGCTGTTACGGGTT 60.467 50.000 17.16 0.00 0.00 4.11
433 1990 8.180706 TCATGTGAGATCCATTTTCTTTTCAA 57.819 30.769 0.00 0.00 0.00 2.69
748 2306 0.946221 ACTTCAGGTCTGCTTTCGCG 60.946 55.000 0.00 0.00 39.65 5.87
895 2453 6.647067 ACATACACGAAGAGAAGAAAGGAAAG 59.353 38.462 0.00 0.00 0.00 2.62
916 2474 5.647658 CCTTTGTGGCTTGTCAAGATACATA 59.352 40.000 16.99 12.72 0.00 2.29
1158 2716 3.490759 CGTCGTGTGGATGCAGGC 61.491 66.667 0.00 0.00 0.00 4.85
1366 2924 0.401738 TCAGAGGCCTCACTTTTGGG 59.598 55.000 33.90 12.41 0.00 4.12
1475 3033 0.613260 AGTAGATGCAAGCACGGGAA 59.387 50.000 0.00 0.00 0.00 3.97
1504 3062 1.989966 ATACACGGAGACAGGCGACG 61.990 60.000 0.00 0.00 0.00 5.12
1845 3405 4.222124 ACAACTCTAATAAGCTGTGGGG 57.778 45.455 0.00 0.00 0.00 4.96
1881 3441 1.342074 TCAGTAAGCAGTGCCTCACT 58.658 50.000 12.58 9.71 46.51 3.41
1933 3493 0.755686 AGGGCATCTCGGTTCTGATC 59.244 55.000 0.00 0.00 0.00 2.92
2305 3865 5.532779 GGTATCTCTTGCTTTTATTCCCCTG 59.467 44.000 0.00 0.00 0.00 4.45
2327 3887 8.970859 TGAATTTTTGGACATTGTTTATTGGT 57.029 26.923 0.00 0.00 0.00 3.67
2370 3930 6.974677 AAAAATATTAATGCACGCTCATCG 57.025 33.333 0.00 0.00 45.38 3.84


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

AutoCloner maintained by Alex Coulton.