Multiple sequence alignment - TraesCS3B01G428600

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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 TraesCS3B01G428600 chr3B 100.000 4415 0 0 1 4415 667633469 667637883 0 8154
1 TraesCS3B01G428600 chr1B 97.310 4424 108 7 1 4415 567735307 567730886 0 7500
2 TraesCS3B01G428600 chr1B 97.242 4424 107 11 1 4415 676864121 676859704 0 7480
3 TraesCS3B01G428600 chr1B 96.641 4257 132 7 1 4248 7902533 7898279 0 7059
4 TraesCS3B01G428600 chr4A 97.265 4424 110 7 1 4415 673171002 673166581 0 7489
5 TraesCS3B01G428600 chr2B 96.925 4423 123 8 1 4415 785300485 785296068 0 7402
6 TraesCS3B01G428600 chr2B 96.302 4408 126 11 1 4404 662568345 662572719 0 7203
7 TraesCS3B01G428600 chr5B 96.632 4424 126 9 1 4415 18261242 18256833 0 7323
8 TraesCS3B01G428600 chr5B 96.585 2196 59 5 2212 4404 568809872 568812054 0 3626
9 TraesCS3B01G428600 chr7B 96.313 4421 133 7 1 4415 629987879 629992275 0 7234
10 TraesCS3B01G428600 chr6B 97.063 4256 113 8 1 4248 572516010 572511759 0 7156


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 TraesCS3B01G428600 chr3B 667633469 667637883 4414 False 8154 8154 100.000 1 4415 1 chr3B.!!$F1 4414
1 TraesCS3B01G428600 chr1B 567730886 567735307 4421 True 7500 7500 97.310 1 4415 1 chr1B.!!$R2 4414
2 TraesCS3B01G428600 chr1B 676859704 676864121 4417 True 7480 7480 97.242 1 4415 1 chr1B.!!$R3 4414
3 TraesCS3B01G428600 chr1B 7898279 7902533 4254 True 7059 7059 96.641 1 4248 1 chr1B.!!$R1 4247
4 TraesCS3B01G428600 chr4A 673166581 673171002 4421 True 7489 7489 97.265 1 4415 1 chr4A.!!$R1 4414
5 TraesCS3B01G428600 chr2B 785296068 785300485 4417 True 7402 7402 96.925 1 4415 1 chr2B.!!$R1 4414
6 TraesCS3B01G428600 chr2B 662568345 662572719 4374 False 7203 7203 96.302 1 4404 1 chr2B.!!$F1 4403
7 TraesCS3B01G428600 chr5B 18256833 18261242 4409 True 7323 7323 96.632 1 4415 1 chr5B.!!$R1 4414
8 TraesCS3B01G428600 chr5B 568809872 568812054 2182 False 3626 3626 96.585 2212 4404 1 chr5B.!!$F1 2192
9 TraesCS3B01G428600 chr7B 629987879 629992275 4396 False 7234 7234 96.313 1 4415 1 chr7B.!!$F1 4414
10 TraesCS3B01G428600 chr6B 572511759 572516010 4251 True 7156 7156 97.063 1 4248 1 chr6B.!!$R1 4247

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
286 287 3.314331 CTCGTGTGGGCAGAGGGT 61.314 66.667 0.00 0.0 0.00 4.34 F
1777 1786 1.348064 ACGTCAAGGAGTTGGGATGA 58.652 50.000 0.00 0.0 34.09 2.92 F
2437 2448 1.514678 GAAGCATGCACACCGAACCA 61.515 55.000 21.98 0.0 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1964 1973 2.224523 ACAGTTGATGACGAACATGGGT 60.225 45.455 0.0 0.0 39.56 4.51 R
2926 2937 0.759436 ACTCCTCCTTGACGGTGTGT 60.759 55.000 0.0 0.0 0.00 3.72 R
3469 3482 0.897621 ACGGGACTAAAACCCTACCG 59.102 55.000 0.0 0.0 44.72 4.02 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
286 287 3.314331 CTCGTGTGGGCAGAGGGT 61.314 66.667 0.00 0.00 0.00 4.34
863 865 6.012113 TGATGATGATTTTGTGAGAAGGGTT 58.988 36.000 0.00 0.00 0.00 4.11
887 889 4.553330 ACTGGTTCTTATGGGTACAGTG 57.447 45.455 0.00 0.00 36.46 3.66
965 967 4.933330 ACGTGAACGCTATCAAGTCATAT 58.067 39.130 2.11 0.00 44.43 1.78
1154 1158 7.062956 CGACTAGTTGTGTTTACTATCATGCAA 59.937 37.037 0.00 0.00 0.00 4.08
1410 1419 1.705256 TTGCGTTAGCCAAGAGTACG 58.295 50.000 0.00 0.00 44.33 3.67
1456 1465 4.227864 GGACTGTCCCAGATGAAGAAAT 57.772 45.455 16.14 0.00 35.18 2.17
1777 1786 1.348064 ACGTCAAGGAGTTGGGATGA 58.652 50.000 0.00 0.00 34.09 2.92
1871 1880 8.044060 ACATCTTTCACGTGTTTCAATGATAT 57.956 30.769 16.51 2.35 0.00 1.63
2152 2161 4.702131 GCAGTCAGGACAATGAAGGTAAAT 59.298 41.667 1.84 0.00 0.00 1.40
2158 2167 6.211184 TCAGGACAATGAAGGTAAATGCAAAT 59.789 34.615 0.00 0.00 0.00 2.32
2345 2356 5.351948 TCGTCACCATATTCAATTCTGGA 57.648 39.130 5.83 0.00 32.92 3.86
2437 2448 1.514678 GAAGCATGCACACCGAACCA 61.515 55.000 21.98 0.00 0.00 3.67
2451 2462 1.540146 CGAACCATGGTCGATATGCCA 60.540 52.381 20.07 1.40 39.33 4.92
2520 2531 6.553100 TCCTCAAGTTTAAATGGTTGAATGGT 59.447 34.615 10.19 0.00 0.00 3.55
3343 3355 4.769688 AGATCGCTGGACACATGAATTTA 58.230 39.130 0.00 0.00 0.00 1.40
3469 3482 5.775701 TGGAGAAGGAGTAGGTATTAGCATC 59.224 44.000 0.00 0.00 0.00 3.91
3502 3515 1.066358 GTCCCGTAGAAGGTTTCCCTG 60.066 57.143 0.00 0.00 41.56 4.45
3563 3576 3.309954 GCACTGGGATAGATTTCGACAAC 59.690 47.826 0.00 0.00 0.00 3.32
3567 3580 6.149474 CACTGGGATAGATTTCGACAACTTTT 59.851 38.462 0.00 0.00 0.00 2.27
3701 3714 5.245531 TGTTTGGTTCATGACTTAGCTAGG 58.754 41.667 0.48 0.48 0.00 3.02
3741 3754 4.680708 CGTGCCACATCTTTCTAGGTACAT 60.681 45.833 0.00 0.00 35.10 2.29
3856 3910 4.984161 CCACACTTTGCTGTAGAAATTTGG 59.016 41.667 0.00 0.00 0.00 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
687 689 0.322816 TCACCCTCGTTACGTAGCCT 60.323 55.000 4.24 0.00 0.00 4.58
863 865 5.046878 CACTGTACCCATAAGAACCAGTACA 60.047 44.000 0.00 0.00 38.12 2.90
887 889 1.904287 TGGTGGATTGTGGTGCTAAC 58.096 50.000 0.00 0.00 0.00 2.34
1154 1158 9.740710 GGCTCAACTTTTTCCCAGTATATATAT 57.259 33.333 0.00 0.00 0.00 0.86
1456 1465 4.577283 CACCTTTCCGTTTAGGTTTCTTCA 59.423 41.667 0.00 0.00 42.01 3.02
1642 1651 8.991243 AAATGAAACACGATCATCATTTGAAT 57.009 26.923 16.86 1.54 45.68 2.57
1651 1660 6.272318 ACAAACACAAATGAAACACGATCAT 58.728 32.000 0.00 0.00 39.15 2.45
1777 1786 3.788227 TGACTTGTACTGGCCATTCTT 57.212 42.857 5.51 0.00 0.00 2.52
1926 1935 6.923508 CGTGTATAATGAAAGGATCAGTAGCA 59.076 38.462 0.00 0.00 41.47 3.49
1964 1973 2.224523 ACAGTTGATGACGAACATGGGT 60.225 45.455 0.00 0.00 39.56 4.51
2152 2161 3.906014 TTTCGACGGATTTCATTTGCA 57.094 38.095 0.00 0.00 0.00 4.08
2158 2167 6.729391 TTGACAATATTTCGACGGATTTCA 57.271 33.333 0.00 0.00 0.00 2.69
2345 2356 7.893124 TCCGGAGTCATATTAAGAGTACTTT 57.107 36.000 0.00 0.00 37.53 2.66
2520 2531 6.952773 AAAACCAAACTCATACTTACAGCA 57.047 33.333 0.00 0.00 0.00 4.41
2926 2937 0.759436 ACTCCTCCTTGACGGTGTGT 60.759 55.000 0.00 0.00 0.00 3.72
3020 3031 6.545508 TCTGAATGCGAGTGTGAAAATTATG 58.454 36.000 0.00 0.00 0.00 1.90
3022 3033 6.552859 TTCTGAATGCGAGTGTGAAAATTA 57.447 33.333 0.00 0.00 0.00 1.40
3072 3083 7.701924 CAGCTCTCTGAAACAAATTAACAAACA 59.298 33.333 0.00 0.00 42.95 2.83
3343 3355 5.809001 TGACTCATTAATCTCTTGCTGGTT 58.191 37.500 0.00 0.00 0.00 3.67
3469 3482 0.897621 ACGGGACTAAAACCCTACCG 59.102 55.000 0.00 0.00 44.72 4.02
3502 3515 3.485216 CGATCAAAGTATCCAACAACGGC 60.485 47.826 0.00 0.00 0.00 5.68
3563 3576 9.498433 CGAAAGCAATAAATAAAACGTGAAAAG 57.502 29.630 0.00 0.00 0.00 2.27
3567 3580 7.541743 CACGAAAGCAATAAATAAAACGTGA 57.458 32.000 0.00 0.00 46.10 4.35
3634 3647 4.623932 AACTGATGCACTTTAGGACAGA 57.376 40.909 0.00 0.00 0.00 3.41
3648 3661 1.376543 ATCGCAGAGGCAAACTGATG 58.623 50.000 9.76 2.93 43.63 3.07
3701 3714 2.331451 GTCACACCTTTGGCGTGC 59.669 61.111 0.33 0.00 34.45 5.34
3717 3730 1.623811 ACCTAGAAAGATGTGGCACGT 59.376 47.619 13.11 13.11 0.00 4.49
3856 3910 5.914898 ACATTTAGGGGCAAATTCTACAC 57.085 39.130 0.00 0.00 0.00 2.90
4199 4254 1.774254 ACAGATCGCCATATTCCCCAA 59.226 47.619 0.00 0.00 0.00 4.12
4200 4255 1.347707 GACAGATCGCCATATTCCCCA 59.652 52.381 0.00 0.00 0.00 4.96
4323 4379 2.733227 CGAAGACGCGGGTATGTTAACT 60.733 50.000 12.47 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.