Multiple sequence alignment - TraesCS4D01G138900

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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 TraesCS4D01G138900 chr4D 100.000 3394 0 0 1 3394 123469975 123466582 0 6268
1 TraesCS4D01G138900 chr4D 98.528 3396 47 3 1 3394 123638850 123642244 0 5991
2 TraesCS4D01G138900 chrUn 98.792 3395 40 1 1 3394 182449186 182445792 0 6041
3 TraesCS4D01G138900 chrUn 97.427 855 10 2 1 843 281719519 281720373 0 1447
4 TraesCS4D01G138900 chr7A 98.326 3405 44 3 1 3392 60349359 60345955 0 5960
5 TraesCS4D01G138900 chr7A 97.300 3408 54 5 1 3394 60174223 60177606 0 5749
6 TraesCS4D01G138900 chr7A 97.907 1242 13 3 1 1230 60158361 60157121 0 2137
7 TraesCS4D01G138900 chr5A 98.238 3406 48 2 1 3394 16538881 16535476 0 5947
8 TraesCS4D01G138900 chr7B 98.121 3406 52 2 1 3394 716910724 716907319 0 5925
9 TraesCS4D01G138900 chr7B 98.121 3406 51 3 1 3394 742954439 742957843 0 5923
10 TraesCS4D01G138900 chr7B 98.033 3406 54 3 1 3394 716778907 716775503 0 5906
11 TraesCS4D01G138900 chr2B 97.975 3407 55 4 1 3394 391172743 391169338 0 5897
12 TraesCS4D01G138900 chr7D 98.822 3055 32 1 340 3394 382102547 382099497 0 5439


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 TraesCS4D01G138900 chr4D 123466582 123469975 3393 True 6268 6268 100.000 1 3394 1 chr4D.!!$R1 3393
1 TraesCS4D01G138900 chr4D 123638850 123642244 3394 False 5991 5991 98.528 1 3394 1 chr4D.!!$F1 3393
2 TraesCS4D01G138900 chrUn 182445792 182449186 3394 True 6041 6041 98.792 1 3394 1 chrUn.!!$R1 3393
3 TraesCS4D01G138900 chrUn 281719519 281720373 854 False 1447 1447 97.427 1 843 1 chrUn.!!$F1 842
4 TraesCS4D01G138900 chr7A 60345955 60349359 3404 True 5960 5960 98.326 1 3392 1 chr7A.!!$R2 3391
5 TraesCS4D01G138900 chr7A 60174223 60177606 3383 False 5749 5749 97.300 1 3394 1 chr7A.!!$F1 3393
6 TraesCS4D01G138900 chr7A 60157121 60158361 1240 True 2137 2137 97.907 1 1230 1 chr7A.!!$R1 1229
7 TraesCS4D01G138900 chr5A 16535476 16538881 3405 True 5947 5947 98.238 1 3394 1 chr5A.!!$R1 3393
8 TraesCS4D01G138900 chr7B 716907319 716910724 3405 True 5925 5925 98.121 1 3394 1 chr7B.!!$R2 3393
9 TraesCS4D01G138900 chr7B 742954439 742957843 3404 False 5923 5923 98.121 1 3394 1 chr7B.!!$F1 3393
10 TraesCS4D01G138900 chr7B 716775503 716778907 3404 True 5906 5906 98.033 1 3394 1 chr7B.!!$R1 3393
11 TraesCS4D01G138900 chr2B 391169338 391172743 3405 True 5897 5897 97.975 1 3394 1 chr2B.!!$R1 3393
12 TraesCS4D01G138900 chr7D 382099497 382102547 3050 True 5439 5439 98.822 340 3394 1 chr7D.!!$R1 3054

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
94 96 1.353022 ACCTCCTTTGCGGAATACCAA 59.647 47.619 0.00 0.0 42.53 3.67 F
230 232 3.578282 CTGCCAAAACTTTCCTTGGGTAT 59.422 43.478 3.21 0.0 42.08 2.73 F
2115 2134 0.306533 GCAACGGAAAGAAGCGAACA 59.693 50.000 0.00 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1013 1032 1.188219 AGCAGAAGAGCGTTCTCCCA 61.188 55.000 0.98 0.00 40.22 4.37 R
2144 2163 2.034558 CCGATTTTTGGACACTTGCTGT 59.965 45.455 0.00 0.00 34.96 4.40 R
3034 3053 2.750888 GGTTGCATCGAAGGCGGAC 61.751 63.158 7.77 8.47 38.28 4.79 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
94 96 1.353022 ACCTCCTTTGCGGAATACCAA 59.647 47.619 0.00 0.0 42.53 3.67
230 232 3.578282 CTGCCAAAACTTTCCTTGGGTAT 59.422 43.478 3.21 0.0 42.08 2.73
517 519 4.158025 CAGAAGCCTCGTCTCCTTTAACTA 59.842 45.833 0.00 0.0 0.00 2.24
1013 1032 2.017623 GCTCAGCATGTCTGGAAGCAT 61.018 52.381 17.79 0.0 40.46 3.79
1334 1353 5.416271 AAGAAAGAATAGGGTTGTCGCTA 57.584 39.130 0.00 0.0 41.92 4.26
1395 1414 8.910944 TGTAGTATTTCCGCTCTTTCTATAAGT 58.089 33.333 0.00 0.0 0.00 2.24
1576 1595 1.325476 CGCTTTCTAGGTACCCCCGT 61.325 60.000 8.74 0.0 38.74 5.28
1577 1596 0.907486 GCTTTCTAGGTACCCCCGTT 59.093 55.000 8.74 0.0 38.74 4.44
1789 1808 3.411446 CATTGTCTACAACCCTGAAGCA 58.589 45.455 0.00 0.0 38.86 3.91
1861 1880 3.071167 GGGCTTGGTCTCGAAAGGTATAT 59.929 47.826 0.00 0.0 0.00 0.86
2100 2119 2.525055 TGAAACAAGCGTTGAAGCAAC 58.475 42.857 0.00 0.0 40.54 4.17
2115 2134 0.306533 GCAACGGAAAGAAGCGAACA 59.693 50.000 0.00 0.0 0.00 3.18
2341 2360 6.833933 AGCCGACAAGGGATTTTCTTAATAAT 59.166 34.615 0.00 0.0 41.48 1.28
2466 2485 3.259064 GTTAGCTGTTCACGGATTAGCA 58.741 45.455 0.00 0.0 36.87 3.49
2783 2802 8.206867 AGACTGCAAAAGATAGATACAATGCTA 58.793 33.333 0.00 0.0 33.87 3.49
3034 3053 2.288395 GCGGCCCTCATTATGGAATTTG 60.288 50.000 0.00 0.0 0.00 2.32
3224 3243 1.271102 GCAATGTTTAGTGCGGGGAAA 59.729 47.619 0.00 0.0 38.20 3.13
3294 3313 2.294074 CAAAAAGGGACTCGTTCACCA 58.706 47.619 0.00 0.0 38.49 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 8.992835 TTCTTCATGGATATGTTGATCTATCG 57.007 34.615 0.00 0.00 35.73 2.92
94 96 6.426328 GTGATCCGCTAATTCATCTCTTGATT 59.574 38.462 0.00 0.00 33.34 2.57
230 232 3.890756 ACCTGCTTTGAACATGACATTCA 59.109 39.130 0.00 0.00 34.27 2.57
315 317 6.384015 TCAGGCTCATAAAGAGGATGAAACTA 59.616 38.462 0.00 0.00 44.86 2.24
732 745 3.300388 AGAGGCTGTGATCGATAAAGGA 58.700 45.455 0.00 0.00 0.00 3.36
1013 1032 1.188219 AGCAGAAGAGCGTTCTCCCA 61.188 55.000 0.98 0.00 40.22 4.37
1334 1353 5.234329 CGACATCTAATCCAAACAGCGTATT 59.766 40.000 0.00 0.00 0.00 1.89
1395 1414 5.009710 ACCGATTATGCGACATCTCTCTTAA 59.990 40.000 0.00 0.00 0.00 1.85
1576 1595 5.651530 CTCAAAGGCGATGACTAGTAGAAA 58.348 41.667 3.59 0.00 0.00 2.52
1577 1596 4.440250 GCTCAAAGGCGATGACTAGTAGAA 60.440 45.833 3.59 0.00 0.00 2.10
1772 1791 3.477530 AGTTTGCTTCAGGGTTGTAGAC 58.522 45.455 0.00 0.00 0.00 2.59
1861 1880 4.534500 TCTTTCCAAGCTTCTGGTGGTATA 59.466 41.667 0.00 0.00 37.74 1.47
2100 2119 3.664537 GCTTAACTGTTCGCTTCTTTCCG 60.665 47.826 0.00 0.00 0.00 4.30
2144 2163 2.034558 CCGATTTTTGGACACTTGCTGT 59.965 45.455 0.00 0.00 34.96 4.40
2341 2360 1.000731 CCAAAGAATCAAAGCGCCCAA 59.999 47.619 2.29 0.00 0.00 4.12
2466 2485 6.946340 TCATATGTGTTGTCATTCCAGTACT 58.054 36.000 1.90 0.00 0.00 2.73
2783 2802 1.863325 TTGCATGCATGGTGGGTAAT 58.137 45.000 27.34 0.00 0.00 1.89
3034 3053 2.750888 GGTTGCATCGAAGGCGGAC 61.751 63.158 7.77 8.47 38.28 4.79
3224 3243 7.831691 AGCATCTGAGTACAATAGTGTAGAT 57.168 36.000 2.71 1.97 40.94 1.98
3294 3313 4.813161 GCATAGCTGTATTGGATGCGATAT 59.187 41.667 0.00 0.00 34.16 1.63


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

AutoCloner maintained by Alex Coulton.