Multiple sequence alignment - TraesCS5D01G236500

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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 TraesCS5D01G236500 chr5D 100.000 2900 0 0 1 2900 344886362 344883463 0.000000e+00 5356
1 TraesCS5D01G236500 chr5B 94.162 2895 111 33 39 2900 406875141 406878010 0.000000e+00 4357
2 TraesCS5D01G236500 chr5A 93.958 2913 104 31 26 2900 447303778 447306656 0.000000e+00 4338
3 TraesCS5D01G236500 chr7B 96.907 97 3 0 1300 1396 79051426 79051522 2.310000e-36 163
4 TraesCS5D01G236500 chr7A 96.907 97 3 0 1300 1396 122207649 122207745 2.310000e-36 163
5 TraesCS5D01G236500 chr7D 95.876 97 4 0 1300 1396 117792114 117792210 1.080000e-34 158


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 TraesCS5D01G236500 chr5D 344883463 344886362 2899 True 5356 5356 100.000 1 2900 1 chr5D.!!$R1 2899
1 TraesCS5D01G236500 chr5B 406875141 406878010 2869 False 4357 4357 94.162 39 2900 1 chr5B.!!$F1 2861
2 TraesCS5D01G236500 chr5A 447303778 447306656 2878 False 4338 4338 93.958 26 2900 1 chr5A.!!$F1 2874

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
532 539 0.110192 CCGCTTCTTTTTCTGGCGTC 60.11 55.0 0.0 0.0 43.57 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2440 2517 2.419198 CTAGGCCGGTGCTAGCAG 59.581 66.667 20.03 7.99 37.74 4.24 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
31 32 6.043127 ACAAGTTCCAATTATTTTTGGGAGCT 59.957 34.615 3.56 0.00 45.21 4.09
183 185 8.982723 AGACACATATAGGTGACAAGTTTCTAT 58.017 33.333 23.38 0.00 41.32 1.98
238 245 9.921637 GATGGTTTCATGTTAGTATTTTCCAAA 57.078 29.630 0.00 0.00 32.98 3.28
253 260 4.412060 TTCCAAATTTAGGTGATGGGGT 57.588 40.909 0.00 0.00 0.00 4.95
299 306 8.729529 ATTCTCGACAATAATATGTACACTCG 57.270 34.615 0.00 0.00 32.57 4.18
309 316 3.881780 ATGTACACTCGCTCGATAGTC 57.118 47.619 0.00 0.00 37.40 2.59
371 378 2.680841 TGGTTGAACCAGTCGAAAAGTG 59.319 45.455 14.05 0.00 44.79 3.16
441 448 1.337071 GATAAGGTCAGATCACGCGGA 59.663 52.381 12.47 5.24 0.00 5.54
445 452 3.068064 TCAGATCACGCGGAGGCA 61.068 61.111 12.47 0.00 39.92 4.75
461 468 4.142315 CGGAGGCATGAGACAAATTCAAAT 60.142 41.667 0.00 0.00 0.00 2.32
530 537 1.210155 CCCGCTTCTTTTTCTGGCG 59.790 57.895 0.00 0.00 44.48 5.69
531 538 1.515521 CCCGCTTCTTTTTCTGGCGT 61.516 55.000 0.00 0.00 43.57 5.68
532 539 0.110192 CCGCTTCTTTTTCTGGCGTC 60.110 55.000 0.00 0.00 43.57 5.19
533 540 0.586319 CGCTTCTTTTTCTGGCGTCA 59.414 50.000 0.00 0.00 40.78 4.35
534 541 1.197721 CGCTTCTTTTTCTGGCGTCAT 59.802 47.619 0.00 0.00 40.78 3.06
535 542 2.589014 GCTTCTTTTTCTGGCGTCATG 58.411 47.619 0.00 0.00 0.00 3.07
536 543 2.226437 GCTTCTTTTTCTGGCGTCATGA 59.774 45.455 0.00 0.00 0.00 3.07
537 544 3.119708 GCTTCTTTTTCTGGCGTCATGAT 60.120 43.478 0.00 0.00 0.00 2.45
538 545 4.409570 CTTCTTTTTCTGGCGTCATGATG 58.590 43.478 10.76 10.76 0.00 3.07
539 546 2.162208 TCTTTTTCTGGCGTCATGATGC 59.838 45.455 28.35 28.35 42.40 3.91
626 644 9.887406 AAAACGACAACAAATATTTATTCGAGT 57.113 25.926 18.91 4.39 0.00 4.18
704 722 5.385198 AGTACATTTCCAATGTGACCAACT 58.615 37.500 11.59 4.71 33.76 3.16
857 875 5.566826 CGTCGATCCCAACATATTACCATCT 60.567 44.000 0.00 0.00 0.00 2.90
868 886 5.983720 ACATATTACCATCTCGCAACAGTAC 59.016 40.000 0.00 0.00 0.00 2.73
937 955 3.996124 CCCTCCATCCCTAGCGCG 61.996 72.222 0.00 0.00 0.00 6.86
1945 1987 2.981859 ATTAGCGGGTTCGTGAAGAT 57.018 45.000 0.00 0.00 38.89 2.40
1948 1990 2.981859 AGCGGGTTCGTGAAGATTAT 57.018 45.000 0.00 0.00 38.89 1.28
1951 1993 2.540101 GCGGGTTCGTGAAGATTATGAG 59.460 50.000 0.00 0.00 38.89 2.90
2055 2101 5.106357 GGGTGTCAATTTTTGCAGTGTTTTT 60.106 36.000 0.00 0.00 0.00 1.94
2056 2102 6.020984 GGTGTCAATTTTTGCAGTGTTTTTC 58.979 36.000 0.00 0.00 0.00 2.29
2060 2106 6.960992 GTCAATTTTTGCAGTGTTTTTCTTCC 59.039 34.615 0.00 0.00 0.00 3.46
2061 2107 6.878389 TCAATTTTTGCAGTGTTTTTCTTCCT 59.122 30.769 0.00 0.00 0.00 3.36
2063 2109 4.385358 TTTGCAGTGTTTTTCTTCCTCC 57.615 40.909 0.00 0.00 0.00 4.30
2064 2110 3.297134 TGCAGTGTTTTTCTTCCTCCT 57.703 42.857 0.00 0.00 0.00 3.69
2145 2195 4.536295 ACGGAGGGGAAATAAATGGAAT 57.464 40.909 0.00 0.00 0.00 3.01
2162 2212 2.505407 GGAATGAAAGGGAAAATGGGGG 59.495 50.000 0.00 0.00 0.00 5.40
2188 2244 8.514594 GGTGTTGTCATTTTCATATTCTTGAGA 58.485 33.333 0.00 0.00 0.00 3.27
2189 2245 9.552114 GTGTTGTCATTTTCATATTCTTGAGAG 57.448 33.333 0.00 0.00 0.00 3.20
2381 2437 3.347958 TCAGTTTTTGCCACTTTAGCG 57.652 42.857 0.00 0.00 0.00 4.26
2527 2604 1.065491 AGCCTAACGAATGTCCATGCA 60.065 47.619 0.00 0.00 0.00 3.96
2572 2649 1.717194 CCTGCAAATTGACCATGCAC 58.283 50.000 0.00 0.00 44.52 4.57
2610 2687 3.425359 CGAATTGATTGTCTCCACAGTGC 60.425 47.826 0.00 0.00 32.71 4.40
2829 2910 0.432361 CATCGTCTATGCGTGCATCG 59.568 55.000 11.16 9.17 43.12 3.84
2831 2912 2.302952 CGTCTATGCGTGCATCGGG 61.303 63.158 11.16 3.62 40.26 5.14
2842 2923 0.683828 TGCATCGGGGCATGAATGTT 60.684 50.000 0.00 0.00 39.25 2.71
2843 2924 0.249155 GCATCGGGGCATGAATGTTG 60.249 55.000 0.00 0.00 0.00 3.33
2894 2975 7.627298 TCCTTAACCTACTCGCTATGATATC 57.373 40.000 0.00 0.00 0.00 1.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
134 136 6.376864 TCTCACACTTCTCATTCAAAAACCAA 59.623 34.615 0.00 0.00 0.00 3.67
211 215 8.877864 TGGAAAATACTAACATGAAACCATCT 57.122 30.769 0.00 0.00 0.00 2.90
234 238 2.765699 CCACCCCATCACCTAAATTTGG 59.234 50.000 0.00 0.00 0.00 3.28
238 245 1.569072 GTCCCACCCCATCACCTAAAT 59.431 52.381 0.00 0.00 0.00 1.40
313 320 6.879993 TCTTAGGACAAGTGTGTGTTTTAACA 59.120 34.615 0.00 0.00 38.41 2.41
371 378 1.257750 GCACCCCCATTTTCTGGTCC 61.258 60.000 0.00 0.00 44.30 4.46
375 382 1.856629 AGATGCACCCCCATTTTCTG 58.143 50.000 0.00 0.00 0.00 3.02
441 448 9.558396 TTTAAAATTTGAATTTGTCTCATGCCT 57.442 25.926 2.71 0.00 38.53 4.75
461 468 8.688747 AAGGCACAAATCATCCAAATTTAAAA 57.311 26.923 0.00 0.00 0.00 1.52
510 517 1.530323 GCCAGAAAAAGAAGCGGGTA 58.470 50.000 0.00 0.00 0.00 3.69
530 537 8.488651 TCTGAATATGATACATGCATCATGAC 57.511 34.615 25.52 17.61 43.81 3.06
531 538 9.681062 AATCTGAATATGATACATGCATCATGA 57.319 29.630 25.52 16.37 43.81 3.07
532 539 9.722056 CAATCTGAATATGATACATGCATCATG 57.278 33.333 25.52 12.41 43.77 3.07
533 540 8.903820 CCAATCTGAATATGATACATGCATCAT 58.096 33.333 22.09 22.09 45.45 2.45
534 541 7.886446 ACCAATCTGAATATGATACATGCATCA 59.114 33.333 11.03 11.03 39.20 3.07
535 542 8.277490 ACCAATCTGAATATGATACATGCATC 57.723 34.615 0.00 0.00 0.00 3.91
536 543 8.645814 AACCAATCTGAATATGATACATGCAT 57.354 30.769 0.00 0.00 0.00 3.96
537 544 8.467963 AAACCAATCTGAATATGATACATGCA 57.532 30.769 0.00 0.00 0.00 3.96
538 545 9.754382 AAAAACCAATCTGAATATGATACATGC 57.246 29.630 0.00 0.00 0.00 4.06
704 722 8.027771 ACGAAACTGTTTAATGGTTTTTGTGTA 58.972 29.630 5.64 0.00 34.00 2.90
714 732 5.457473 GGTTGACAACGAAACTGTTTAATGG 59.543 40.000 12.07 0.00 0.00 3.16
823 841 2.269529 GGATCGACGGAGCTAGGGG 61.270 68.421 0.00 0.00 0.00 4.79
834 852 5.794894 AGATGGTAATATGTTGGGATCGAC 58.205 41.667 0.00 0.00 0.00 4.20
857 875 1.000506 GGTCTTCCTGTACTGTTGCGA 59.999 52.381 0.00 0.00 0.00 5.10
868 886 4.512484 GGATTCTTCTCTTGGTCTTCCTG 58.488 47.826 0.00 0.00 34.23 3.86
997 1015 2.507452 CTCGCTCATGGCCATGGA 59.493 61.111 38.81 28.12 39.24 3.41
1973 2017 4.436242 AACGAATTCACGAGCTAGAGAA 57.564 40.909 8.94 8.94 37.03 2.87
1974 2018 4.436242 AAACGAATTCACGAGCTAGAGA 57.564 40.909 6.22 0.00 37.03 3.10
2055 2101 5.627182 ATGAGTACGTACTAGGAGGAAGA 57.373 43.478 27.44 4.64 36.50 2.87
2056 2102 5.050227 CGAATGAGTACGTACTAGGAGGAAG 60.050 48.000 27.44 10.91 36.50 3.46
2060 2106 4.210955 GGACGAATGAGTACGTACTAGGAG 59.789 50.000 27.44 18.79 42.74 3.69
2061 2107 4.122776 GGACGAATGAGTACGTACTAGGA 58.877 47.826 27.44 14.95 42.74 2.94
2162 2212 8.514594 TCTCAAGAATATGAAAATGACAACACC 58.485 33.333 0.00 0.00 0.00 4.16
2188 2244 6.714278 AGATTAAAAATGGCTGGAAAATGCT 58.286 32.000 0.00 0.00 0.00 3.79
2189 2245 6.990341 AGATTAAAAATGGCTGGAAAATGC 57.010 33.333 0.00 0.00 0.00 3.56
2381 2437 7.573968 AAGCAAATGATAAGGATAACTGTCC 57.426 36.000 0.00 0.00 38.62 4.02
2439 2516 3.798954 CTAGGCCGGTGCTAGCAGC 62.799 68.421 32.12 32.12 42.82 5.25
2440 2517 2.419198 CTAGGCCGGTGCTAGCAG 59.581 66.667 20.03 7.99 37.74 4.24
2441 2518 3.849951 GCTAGGCCGGTGCTAGCA 61.850 66.667 14.93 14.93 40.69 3.49
2442 2519 4.951963 CGCTAGGCCGGTGCTAGC 62.952 72.222 8.10 8.10 39.13 3.42
2443 2520 4.286320 CCGCTAGGCCGGTGCTAG 62.286 72.222 1.90 4.19 43.24 3.42
2527 2604 5.564550 AGAATCATTCAAGTGGTAAGCAGT 58.435 37.500 0.00 0.00 0.00 4.40
2572 2649 0.742990 TTCGGTAGCTGGGAAATGCG 60.743 55.000 0.00 0.00 0.00 4.73
2829 2910 0.538118 ACATGCAACATTCATGCCCC 59.462 50.000 0.00 0.00 43.71 5.80
2831 2912 1.003851 GCACATGCAACATTCATGCC 58.996 50.000 0.00 0.00 43.71 4.40
2843 2924 1.660560 GGACTGGTGGATGCACATGC 61.661 60.000 19.67 5.53 42.50 4.06


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

AutoCloner maintained by Alex Coulton.