Multiple sequence alignment - TraesCS3B01G481900

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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 TraesCS3B01G481900 chr3B 100.000 3268 0 0 1 3268 729226728 729229995 0 6035
1 TraesCS3B01G481900 chr2B 95.247 3219 151 2 1 3217 791334689 791331471 0 5096
2 TraesCS3B01G481900 chr2B 94.094 3268 190 3 3 3268 637162649 637165915 0 4963
3 TraesCS3B01G481900 chr2B 95.090 2892 139 3 378 3268 177237104 177239993 0 4551
4 TraesCS3B01G481900 chr2B 93.322 584 37 2 4 586 111719648 111720230 0 861
5 TraesCS3B01G481900 chr2B 92.491 586 41 2 4 586 700192444 700191859 0 835
6 TraesCS3B01G481900 chr4A 94.803 3271 163 5 1 3268 655846296 655849562 0 5092
7 TraesCS3B01G481900 chr4A 94.650 3271 168 5 1 3268 655893447 655896713 0 5064
8 TraesCS3B01G481900 chr4A 95.642 2891 126 0 378 3268 656355766 656358656 0 4641
9 TraesCS3B01G481900 chr4A 95.227 2891 138 0 378 3268 656148468 656151358 0 4575
10 TraesCS3B01G481900 chr6B 94.371 3269 179 5 1 3266 216894759 216898025 0 5012
11 TraesCS3B01G481900 chr6B 93.559 590 34 2 1 586 639182008 639182597 0 876
12 TraesCS3B01G481900 chr4B 93.307 3272 211 7 1 3268 637699209 637695942 0 4822


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 TraesCS3B01G481900 chr3B 729226728 729229995 3267 False 6035 6035 100.000 1 3268 1 chr3B.!!$F1 3267
1 TraesCS3B01G481900 chr2B 791331471 791334689 3218 True 5096 5096 95.247 1 3217 1 chr2B.!!$R2 3216
2 TraesCS3B01G481900 chr2B 637162649 637165915 3266 False 4963 4963 94.094 3 3268 1 chr2B.!!$F3 3265
3 TraesCS3B01G481900 chr2B 177237104 177239993 2889 False 4551 4551 95.090 378 3268 1 chr2B.!!$F2 2890
4 TraesCS3B01G481900 chr2B 111719648 111720230 582 False 861 861 93.322 4 586 1 chr2B.!!$F1 582
5 TraesCS3B01G481900 chr2B 700191859 700192444 585 True 835 835 92.491 4 586 1 chr2B.!!$R1 582
6 TraesCS3B01G481900 chr4A 655846296 655849562 3266 False 5092 5092 94.803 1 3268 1 chr4A.!!$F1 3267
7 TraesCS3B01G481900 chr4A 655893447 655896713 3266 False 5064 5064 94.650 1 3268 1 chr4A.!!$F2 3267
8 TraesCS3B01G481900 chr4A 656355766 656358656 2890 False 4641 4641 95.642 378 3268 1 chr4A.!!$F4 2890
9 TraesCS3B01G481900 chr4A 656148468 656151358 2890 False 4575 4575 95.227 378 3268 1 chr4A.!!$F3 2890
10 TraesCS3B01G481900 chr6B 216894759 216898025 3266 False 5012 5012 94.371 1 3266 1 chr6B.!!$F1 3265
11 TraesCS3B01G481900 chr6B 639182008 639182597 589 False 876 876 93.559 1 586 1 chr6B.!!$F2 585
12 TraesCS3B01G481900 chr4B 637695942 637699209 3267 True 4822 4822 93.307 1 3268 1 chr4B.!!$R1 3267

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
880 885 0.036294 CCTCCTCGACCCAAACCTTC 60.036 60.0 0.0 0.0 0.0 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2665 2675 0.880278 CACCTGCACTAACACACGCT 60.88 55.0 0.0 0.0 0.0 5.07 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
103 105 1.377202 GAGGCACGGCATTGAAGGA 60.377 57.895 0.00 0.00 0.00 3.36
137 139 0.252057 TGCAGGTACAGGAGGCACTA 60.252 55.000 0.00 0.00 41.55 2.74
367 372 1.429930 TGGAACACCAGGCTCTACAA 58.570 50.000 0.00 0.00 0.00 2.41
459 464 4.633126 GCATGCATCTGAAGACTTACTCAA 59.367 41.667 14.21 0.00 0.00 3.02
490 495 6.756221 ACGGTTGTGAAGTCTTTAGAGTTAT 58.244 36.000 0.00 0.00 37.79 1.89
557 562 2.761208 GTGGTAGTAGAGGCATCAGTGT 59.239 50.000 0.00 0.00 0.00 3.55
821 826 0.110688 CAACCACGAACGCATGTCTG 60.111 55.000 0.00 0.00 0.00 3.51
880 885 0.036294 CCTCCTCGACCCAAACCTTC 60.036 60.000 0.00 0.00 0.00 3.46
881 886 0.685097 CTCCTCGACCCAAACCTTCA 59.315 55.000 0.00 0.00 0.00 3.02
936 941 5.004448 TCAATTACGGAAACACTATTGCCA 58.996 37.500 0.00 0.00 0.00 4.92
1004 1010 1.522569 GCTGGAGGAGCGTAATGGT 59.477 57.895 0.00 0.00 38.15 3.55
1066 1072 1.367471 CAGAGCACCGAGGTTGACA 59.633 57.895 0.00 0.00 0.00 3.58
1143 1149 0.398696 TCCACGGCAAGGAAAAGCTA 59.601 50.000 0.00 0.00 30.71 3.32
1256 1262 4.377021 GGCATTGATGTCGAGTATACCAA 58.623 43.478 0.00 0.00 0.00 3.67
1390 1396 4.327680 ACCTCTCCATGTTTCTGTTTAGC 58.672 43.478 0.00 0.00 0.00 3.09
1467 1474 9.482627 CAGTGAAGTTTCTGAAGTAGATAAAGT 57.517 33.333 3.82 0.00 34.80 2.66
1498 1505 6.774656 AGATTTTGAACTTGACTCACCAGATT 59.225 34.615 0.00 0.00 0.00 2.40
1745 1753 4.702831 TGTGTTTGTGAACTCTGCATAGA 58.297 39.130 6.05 0.00 36.70 1.98
1931 1940 4.890158 TGAAGGTGACAAAGAGATGCTA 57.110 40.909 0.00 0.00 0.00 3.49
1959 1968 0.407918 TGGTTTGGAGATCAACCCCC 59.592 55.000 9.53 6.42 37.15 5.40
1964 1973 0.404040 TGGAGATCAACCCCCACAAC 59.596 55.000 0.00 0.00 0.00 3.32
1971 1980 2.058705 TCAACCCCCACAACTACATCA 58.941 47.619 0.00 0.00 0.00 3.07
2232 2242 1.074405 TGGAGAGTGCAAAAGAGGCAT 59.926 47.619 0.00 0.00 44.11 4.40
2233 2243 1.471684 GGAGAGTGCAAAAGAGGCATG 59.528 52.381 0.00 0.00 44.11 4.06
2247 2257 5.378230 AGAGGCATGGAAGAATTATGACA 57.622 39.130 0.00 0.00 32.21 3.58
2665 2675 0.831711 TGCAGTCTGTAGAGCCACCA 60.832 55.000 0.93 0.00 0.00 4.17
2731 2741 3.233507 ACAGAAATGAAGGCACCACAAT 58.766 40.909 0.00 0.00 0.00 2.71
2771 2781 3.598273 ACGGAGTAGCAGAGGTGAT 57.402 52.632 0.00 0.00 41.94 3.06
3107 3118 3.508845 AAGTGTGGTACCAGAAGCATT 57.491 42.857 16.93 3.44 0.00 3.56
3128 3139 2.756760 TCTTCCGAATACGCAGTTAGGT 59.243 45.455 0.00 0.00 37.78 3.08
3155 3166 6.641314 GTCACGATTGTCAAGTCTCTAGAAAA 59.359 38.462 0.00 0.00 0.00 2.29
3211 3222 4.570874 GGGCTTCGAGGGGCATCC 62.571 72.222 13.95 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 52 2.108157 TGCCTCGCGTGACACTTT 59.892 55.556 10.21 0.00 0.00 2.66
103 105 2.045926 GCATCCGTGCCTCCTGTT 60.046 61.111 0.00 0.00 45.76 3.16
137 139 5.481122 GGTCTCCTCTTAGGTTCAGTACTTT 59.519 44.000 0.00 0.00 36.53 2.66
367 372 5.290493 TCTATAATTCCAATGTCGGTGCT 57.710 39.130 0.00 0.00 0.00 4.40
510 515 0.729478 CGACGCATCACTCTCACGTT 60.729 55.000 0.00 0.00 37.05 3.99
557 562 7.129457 ACCAATGCTCTCTGATTACTATTCA 57.871 36.000 0.00 0.00 0.00 2.57
694 699 7.772332 ACAAATGTTTTTGCGTAAACCATTA 57.228 28.000 17.47 0.00 45.01 1.90
821 826 1.090052 GTCGTGGTAATGAGGGCAGC 61.090 60.000 0.00 0.00 0.00 5.25
880 885 0.871163 CGCAGTTGCCCTTTTGTGTG 60.871 55.000 0.00 0.00 37.91 3.82
881 886 1.437160 CGCAGTTGCCCTTTTGTGT 59.563 52.632 0.00 0.00 37.91 3.72
936 941 4.093011 AGAGTTGCTAGTTGAGATGGAGT 58.907 43.478 0.00 0.00 0.00 3.85
1004 1010 2.111999 CTTGGCAGACGGTTCCTCCA 62.112 60.000 0.00 0.00 35.57 3.86
1143 1149 0.536724 TGCTGGTGCATACGACATCT 59.463 50.000 0.00 0.00 45.31 2.90
1256 1262 0.605589 CTGCAGAGGTTCGTCTTCCT 59.394 55.000 8.42 0.00 36.70 3.36
1297 1303 1.444553 GACAGAGTTCCTCCACGCG 60.445 63.158 3.53 3.53 0.00 6.01
1467 1474 9.436957 GGTGAGTCAAGTTCAAAATCTATTCTA 57.563 33.333 0.00 0.00 0.00 2.10
1565 1572 2.722094 ACAGAAAGTGCACAGGAACAA 58.278 42.857 21.04 0.00 0.00 2.83
1571 1578 4.122776 ACACTAGAACAGAAAGTGCACAG 58.877 43.478 21.04 5.77 43.53 3.66
1572 1579 4.137116 ACACTAGAACAGAAAGTGCACA 57.863 40.909 21.04 0.00 43.53 4.57
1618 1625 8.562892 ACACATCAATTCAAGAAACTGAACTAG 58.437 33.333 0.00 0.00 38.12 2.57
1797 1805 5.624159 TGGATCCATCAAGTATCCATCAAC 58.376 41.667 11.44 0.00 43.27 3.18
1931 1940 3.071023 TGATCTCCAAACCAGAACTTCGT 59.929 43.478 0.00 0.00 0.00 3.85
1959 1968 4.378770 GCACTGGATGTTGATGTAGTTGTG 60.379 45.833 0.00 0.00 0.00 3.33
1964 1973 5.337554 CATTTGCACTGGATGTTGATGTAG 58.662 41.667 0.00 0.00 0.00 2.74
1971 1980 3.087031 CTCTCCATTTGCACTGGATGTT 58.913 45.455 15.72 0.00 41.83 2.71
2162 2171 1.404391 CAAGACTCGTAGGTGGCGTAT 59.596 52.381 0.00 0.00 0.00 3.06
2232 2242 9.832445 GTAGTAAGGATTGTCATAATTCTTCCA 57.168 33.333 0.00 0.00 28.92 3.53
2233 2243 8.979574 CGTAGTAAGGATTGTCATAATTCTTCC 58.020 37.037 0.00 0.00 28.92 3.46
2247 2257 5.688807 TCACTAGTAGGCGTAGTAAGGATT 58.311 41.667 1.45 0.00 0.00 3.01
2665 2675 0.880278 CACCTGCACTAACACACGCT 60.880 55.000 0.00 0.00 0.00 5.07
2731 2741 0.977627 ACGTGCCTCTGGATGGATGA 60.978 55.000 0.00 0.00 0.00 2.92
2771 2781 5.452255 ACCCTGTAACTATGTATTCGGAGA 58.548 41.667 0.00 0.00 0.00 3.71
3107 3118 2.756760 ACCTAACTGCGTATTCGGAAGA 59.243 45.455 0.00 0.00 36.90 2.87
3128 3139 6.171213 TCTAGAGACTTGACAATCGTGACTA 58.829 40.000 0.00 0.00 0.00 2.59
3155 3166 1.361668 GATGCCAGAACACGCGTGAT 61.362 55.000 42.94 33.53 0.00 3.06
3211 3222 1.153168 CATAGGGTTGAGGGCCACG 60.153 63.158 6.18 0.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.