Multiple sequence alignment - TraesCS5B01G375200

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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 TraesCS5B01G375200 chr5B 100.000 3278 0 0 1 3278 552748267 552751544 0.000000e+00 6054
1 TraesCS5B01G375200 chr5D 96.797 3247 67 12 39 3276 452483787 452487005 0.000000e+00 5385
2 TraesCS5B01G375200 chr5A 93.993 2930 94 34 1 2887 571325525 571328415 0.000000e+00 4361
3 TraesCS5B01G375200 chr5A 95.695 302 13 0 2880 3181 571328716 571329017 1.370000e-133 486


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 TraesCS5B01G375200 chr5B 552748267 552751544 3277 False 6054.0 6054 100.000 1 3278 1 chr5B.!!$F1 3277
1 TraesCS5B01G375200 chr5D 452483787 452487005 3218 False 5385.0 5385 96.797 39 3276 1 chr5D.!!$F1 3237
2 TraesCS5B01G375200 chr5A 571325525 571329017 3492 False 2423.5 4361 94.844 1 3181 2 chr5A.!!$F1 3180

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
33 34 0.253394 AAAAGGGAGAGGGAGAGGGG 60.253 60.0 0.0 0.0 0.0 4.79 F
282 304 0.327964 CTCCTCCCCATCTTCCCCTT 60.328 60.0 0.0 0.0 0.0 3.95 F
1353 1398 1.048601 ATGCCGATCCATACTCCGTT 58.951 50.0 0.0 0.0 0.0 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1799 1844 0.313672 CTCCTCTGGATAGCACGAGC 59.686 60.000 0.00 0.0 42.56 5.03 R
2052 2097 1.337387 GCCTAGTCACGTAGGATGACC 59.663 57.143 6.28 0.0 46.38 4.02 R
2750 2795 0.108329 CCGACCAGCACCGTCTATTT 60.108 55.000 0.00 0.0 0.00 1.40 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
25 26 6.968263 AAGAAAAGAAGAAAAAGGGAGAGG 57.032 37.500 0.00 0.00 0.00 3.69
31 32 2.556766 AGAAAAAGGGAGAGGGAGAGG 58.443 52.381 0.00 0.00 0.00 3.69
33 34 0.253394 AAAAGGGAGAGGGAGAGGGG 60.253 60.000 0.00 0.00 0.00 4.79
280 296 1.004891 ACTCCTCCCCATCTTCCCC 59.995 63.158 0.00 0.00 0.00 4.81
282 304 0.327964 CTCCTCCCCATCTTCCCCTT 60.328 60.000 0.00 0.00 0.00 3.95
468 503 4.773117 GCAGTCGGTCGGTCGGTC 62.773 72.222 0.00 0.00 0.00 4.79
469 504 4.456253 CAGTCGGTCGGTCGGTCG 62.456 72.222 0.00 0.00 0.00 4.79
625 667 3.752167 GGGAGGGAGGGAGACGGA 61.752 72.222 0.00 0.00 0.00 4.69
922 967 8.329203 TCTTTAAAAATCTGCTCTTTCTCTCC 57.671 34.615 0.00 0.00 0.00 3.71
1284 1329 1.517257 CATCGTCTTCTCGCCGCTT 60.517 57.895 0.00 0.00 0.00 4.68
1344 1389 1.070601 CTGTATGTCCATGCCGATCCA 59.929 52.381 0.00 0.00 0.00 3.41
1353 1398 1.048601 ATGCCGATCCATACTCCGTT 58.951 50.000 0.00 0.00 0.00 4.44
1365 1410 1.324005 ACTCCGTTCTAGAGCTGCCC 61.324 60.000 4.99 0.00 34.56 5.36
1653 1698 1.590792 GTACTATGCCCGCGGTGAC 60.591 63.158 26.12 13.87 0.00 3.67
1755 1800 1.302511 GGTTGTGAGGGACATGCGT 60.303 57.895 0.00 0.00 33.40 5.24
1799 1844 1.291184 TGTCTGGTCGAGCGCAATTG 61.291 55.000 11.47 0.00 0.00 2.32
1905 1950 3.070018 GGTGAACTGGACAGATCAAGTG 58.930 50.000 12.90 0.00 38.25 3.16
1929 1974 1.296056 GCCACCCACACACGTATCAC 61.296 60.000 0.00 0.00 0.00 3.06
2052 2097 0.103026 TGATGGAGATTGCGGACTCG 59.897 55.000 0.00 0.00 39.81 4.18
2123 2168 6.721668 TCGGATAAACTGAGATGATGAGGTAT 59.278 38.462 0.00 0.00 0.00 2.73
2295 2340 3.408288 AAAGTTGCACGCTTCGTTAAA 57.592 38.095 3.52 0.00 38.32 1.52
2303 2348 4.562000 TGCACGCTTCGTTAAATCGTTATA 59.438 37.500 0.00 0.00 38.32 0.98
2488 2533 7.984617 TGTATATGTACATTGCTACAGAAAGCA 59.015 33.333 14.77 0.00 41.88 3.91
2519 2564 5.298026 TCTCTCTGGATTATTGTCAGACTCG 59.702 44.000 1.31 0.00 34.33 4.18
2612 2657 3.140325 TCTGGGGTTCTGTTAGCAAAG 57.860 47.619 0.00 0.00 0.00 2.77
2750 2795 7.670979 TCTTCCATGATTGAAAGATTTTCTGGA 59.329 33.333 0.00 5.75 0.00 3.86
2939 3292 8.005466 CAGCTTTTGTAGTTTTTATTGCATGTG 58.995 33.333 0.00 0.00 0.00 3.21
2969 3322 3.006003 TGTCACGCCTGTTGTGAATACTA 59.994 43.478 0.00 0.00 46.99 1.82
3213 3566 6.925610 TCTTCCTTTCCATATTGTGAATCG 57.074 37.500 0.00 0.00 0.00 3.34
3237 3590 2.426738 TGGACAAGCTTTGTTTGGTGAG 59.573 45.455 0.00 0.00 45.52 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 3.843619 CTCTCCCTCTCCCTTTTTCTTCT 59.156 47.826 0.00 0.00 0.00 2.85
35 36 4.893601 GCGCGTCTAGAAGCCCCC 62.894 72.222 22.52 9.40 32.09 5.40
37 38 4.493747 ACGCGCGTCTAGAAGCCC 62.494 66.667 32.73 14.21 32.09 5.19
288 310 1.404851 GCCGAGAAGAAGGAAGAGGTG 60.405 57.143 0.00 0.00 0.00 4.00
289 311 0.899019 GCCGAGAAGAAGGAAGAGGT 59.101 55.000 0.00 0.00 0.00 3.85
293 315 0.898320 TGAGGCCGAGAAGAAGGAAG 59.102 55.000 0.00 0.00 0.00 3.46
294 316 0.608640 GTGAGGCCGAGAAGAAGGAA 59.391 55.000 0.00 0.00 0.00 3.36
295 317 0.541998 TGTGAGGCCGAGAAGAAGGA 60.542 55.000 0.00 0.00 0.00 3.36
296 318 0.321671 TTGTGAGGCCGAGAAGAAGG 59.678 55.000 0.00 0.00 0.00 3.46
473 508 3.056328 GCCAGGAACGGAGCAACC 61.056 66.667 0.00 0.00 0.00 3.77
600 642 4.179599 CCTCCCTCCCTCCCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
601 643 4.179599 CCCTCCCTCCCTCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
602 644 3.036959 TCCCTCCCTCCCTCCCTC 61.037 72.222 0.00 0.00 0.00 4.30
603 645 3.039526 CTCCCTCCCTCCCTCCCT 61.040 72.222 0.00 0.00 0.00 4.20
604 646 3.036959 TCTCCCTCCCTCCCTCCC 61.037 72.222 0.00 0.00 0.00 4.30
605 647 2.284151 GTCTCCCTCCCTCCCTCC 59.716 72.222 0.00 0.00 0.00 4.30
606 648 2.123640 CGTCTCCCTCCCTCCCTC 60.124 72.222 0.00 0.00 0.00 4.30
607 649 3.756783 CCGTCTCCCTCCCTCCCT 61.757 72.222 0.00 0.00 0.00 4.20
971 1016 3.483869 GCAGGAGGGCGGGAGAAT 61.484 66.667 0.00 0.00 0.00 2.40
1057 1102 1.321074 AAGACGACCGGGATGGAGAC 61.321 60.000 6.32 0.00 42.00 3.36
1284 1329 2.026262 GCCATGGAAGTACTTCTCCCAA 60.026 50.000 29.66 14.23 39.45 4.12
1344 1389 1.957877 GGCAGCTCTAGAACGGAGTAT 59.042 52.381 0.00 0.00 45.00 2.12
1353 1398 2.359169 CGTTGGGGGCAGCTCTAGA 61.359 63.158 0.00 0.00 0.00 2.43
1755 1800 5.063880 GGCAACTTAAACTTCTTCCAGAGA 58.936 41.667 0.00 0.00 0.00 3.10
1799 1844 0.313672 CTCCTCTGGATAGCACGAGC 59.686 60.000 0.00 0.00 42.56 5.03
1905 1950 4.660938 GTGTGTGGGTGGCCCTCC 62.661 72.222 0.00 2.28 45.70 4.30
1947 1992 2.419851 CCTCAGCTCCCTGATCAAGTTC 60.420 54.545 0.00 0.00 46.44 3.01
2052 2097 1.337387 GCCTAGTCACGTAGGATGACC 59.663 57.143 6.28 0.00 46.38 4.02
2123 2168 2.752322 GCAGCAAGTGCGCATTTCCA 62.752 55.000 15.91 0.00 43.99 3.53
2341 2386 5.234466 ACTGTCCTACAAGAAGCTGAAAT 57.766 39.130 0.00 0.00 0.00 2.17
2343 2388 5.077564 TCTACTGTCCTACAAGAAGCTGAA 58.922 41.667 0.00 0.00 0.00 3.02
2488 2533 8.311395 TGACAATAATCCAGAGAGACAGTAAT 57.689 34.615 0.00 0.00 0.00 1.89
2519 2564 6.385033 AGCAAATCAAATTACTTCAGTGCTC 58.615 36.000 0.00 0.00 33.54 4.26
2612 2657 4.743057 AGGAGCATTGCCCTAAAATTTC 57.257 40.909 14.69 0.00 29.87 2.17
2750 2795 0.108329 CCGACCAGCACCGTCTATTT 60.108 55.000 0.00 0.00 0.00 1.40
2939 3292 5.751509 TCACAACAGGCGTGACATATTATAC 59.248 40.000 14.38 0.00 38.45 1.47
2969 3322 7.606073 GCTATGAACAAAACAACCCCAAAATAT 59.394 33.333 0.00 0.00 0.00 1.28
3054 3407 6.437162 TCCTAAAGCAAAAGTCAAATATGCCT 59.563 34.615 0.00 0.00 37.73 4.75
3213 3566 2.427095 ACCAAACAAAGCTTGTCCAGTC 59.573 45.455 0.00 0.00 44.59 3.51
3237 3590 4.645809 CCTTGGTAGGGCAGAAGC 57.354 61.111 0.00 0.00 37.94 3.86


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

AutoCloner maintained by Alex Coulton.