Multiple sequence alignment - TraesCS3A01G041100

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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 TraesCS3A01G041100 chr3A 100.000 2399 0 0 1 2399 21413704 21416102 0 4431
1 TraesCS3A01G041100 chr3A 96.758 2406 70 6 1 2399 523400220 523397816 0 4004
2 TraesCS3A01G041100 chr3A 96.467 2406 76 7 1 2399 530749562 530747159 0 3964
3 TraesCS3A01G041100 chr7A 96.800 2406 69 6 1 2399 363385313 363387717 0 4010
4 TraesCS3A01G041100 chr7A 96.633 2406 73 6 1 2399 373512493 373510089 0 3988
5 TraesCS3A01G041100 chr2A 96.266 2410 77 8 2 2399 195019472 195021880 0 3940
6 TraesCS3A01G041100 chr2A 96.215 2404 81 9 2 2399 183082815 183085214 0 3927
7 TraesCS3A01G041100 chr4A 96.224 2410 78 8 1 2399 414241043 414238636 0 3934
8 TraesCS3A01G041100 chr1A 96.101 2411 81 9 1 2399 206162865 206165274 0 3919
9 TraesCS3A01G041100 chr5A 96.058 2410 81 11 1 2397 395978610 395981018 0 3912


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 TraesCS3A01G041100 chr3A 21413704 21416102 2398 False 4431 4431 100.000 1 2399 1 chr3A.!!$F1 2398
1 TraesCS3A01G041100 chr3A 523397816 523400220 2404 True 4004 4004 96.758 1 2399 1 chr3A.!!$R1 2398
2 TraesCS3A01G041100 chr3A 530747159 530749562 2403 True 3964 3964 96.467 1 2399 1 chr3A.!!$R2 2398
3 TraesCS3A01G041100 chr7A 363385313 363387717 2404 False 4010 4010 96.800 1 2399 1 chr7A.!!$F1 2398
4 TraesCS3A01G041100 chr7A 373510089 373512493 2404 True 3988 3988 96.633 1 2399 1 chr7A.!!$R1 2398
5 TraesCS3A01G041100 chr2A 195019472 195021880 2408 False 3940 3940 96.266 2 2399 1 chr2A.!!$F2 2397
6 TraesCS3A01G041100 chr2A 183082815 183085214 2399 False 3927 3927 96.215 2 2399 1 chr2A.!!$F1 2397
7 TraesCS3A01G041100 chr4A 414238636 414241043 2407 True 3934 3934 96.224 1 2399 1 chr4A.!!$R1 2398
8 TraesCS3A01G041100 chr1A 206162865 206165274 2409 False 3919 3919 96.101 1 2399 1 chr1A.!!$F1 2398
9 TraesCS3A01G041100 chr5A 395978610 395981018 2408 False 3912 3912 96.058 1 2397 1 chr5A.!!$F1 2396

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
935 944 0.734889 CATGGGACGCATTGGAGAAC 59.265 55.0 1.56 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2358 2379 0.905357 ATTGTGCGAGCTACCTCCTT 59.095 50.0 0.0 0.0 34.49 3.36 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
34 35 7.715657 TGGGTTATGTTTAATGATGATGCTTC 58.284 34.615 0.00 0.00 0.00 3.86
44 45 8.709272 TTAATGATGATGCTTCATTGGGATTA 57.291 30.769 15.56 12.23 42.73 1.75
76 77 7.581213 TGTCAACCATTCTCAATGTTTAACT 57.419 32.000 0.00 0.00 37.18 2.24
152 155 6.470557 TTACGCAAAACTGTAACCATAGAC 57.529 37.500 0.00 0.00 0.00 2.59
204 208 8.147058 AGTATAGCTGTTCATTCCATTACTCTG 58.853 37.037 0.00 0.00 0.00 3.35
382 389 6.927381 GCCTTCCGCTGTTATAGTTATTAGAA 59.073 38.462 0.00 0.00 0.00 2.10
385 393 7.046292 TCCGCTGTTATAGTTATTAGAAGCA 57.954 36.000 0.00 0.00 0.00 3.91
445 453 5.779922 ACACTCGATGTAATAAGTGTGTGT 58.220 37.500 6.23 0.00 45.94 3.72
701 710 4.081142 TCACACAACCGGATGAAGATACAT 60.081 41.667 19.77 0.00 0.00 2.29
801 810 3.510360 ACTTTACCTGAAGAAGAGCGCTA 59.490 43.478 11.50 0.00 0.00 4.26
865 874 3.055094 TCACTGAGCCCATAGAGTTTTCC 60.055 47.826 0.00 0.00 0.00 3.13
935 944 0.734889 CATGGGACGCATTGGAGAAC 59.265 55.000 1.56 0.00 0.00 3.01
1045 1055 5.889853 AGATCAATTGCAGCTTTTATCCAGA 59.110 36.000 0.00 0.00 0.00 3.86
1168 1178 6.096423 ACTCAAGGCTACACGTGAAGATTATA 59.904 38.462 25.01 0.61 0.00 0.98
1178 1188 8.480643 ACACGTGAAGATTATAAAGAGGAAAG 57.519 34.615 25.01 0.00 0.00 2.62
1192 1202 5.825593 AGAGGAAAGTGAAGTATTGGTGA 57.174 39.130 0.00 0.00 0.00 4.02
1194 1204 6.601332 AGAGGAAAGTGAAGTATTGGTGAAA 58.399 36.000 0.00 0.00 0.00 2.69
1242 1252 5.661503 TTGGAATATTTATGAGAGGCCCA 57.338 39.130 0.00 0.00 0.00 5.36
1528 1541 3.540314 TTTTGCTTTTGCCTCATGTGT 57.460 38.095 0.00 0.00 46.87 3.72
1672 1687 3.011818 CCAGCAGCAGAACACATTGATA 58.988 45.455 0.00 0.00 0.00 2.15
1852 1873 0.767375 AGTTGACCACAGCAGGATGT 59.233 50.000 0.00 0.00 39.31 3.06
1970 1991 2.054021 TCACATGGGACCAGTTTCAGA 58.946 47.619 0.00 0.00 0.00 3.27
2000 2021 2.094675 GTACTGCCCATGTTTCAGCAT 58.905 47.619 6.15 0.00 34.16 3.79
2308 2329 2.574006 ACAATTCAGGAGCTCAGCAA 57.426 45.000 17.19 4.46 0.00 3.91
2358 2379 3.953612 GGACATTTTCAGCATACCCATGA 59.046 43.478 0.00 0.00 33.67 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 5.840243 TGACAGCATTCTTAATCCCAATG 57.160 39.130 0.00 0.00 0.00 2.82
105 106 7.790782 AAGCCAATTTTCCCTACTTCAAATA 57.209 32.000 0.00 0.00 0.00 1.40
106 107 6.686484 AAGCCAATTTTCCCTACTTCAAAT 57.314 33.333 0.00 0.00 0.00 2.32
152 155 2.159057 GCATATTTGGCTGGTGGAAAGG 60.159 50.000 0.00 0.00 0.00 3.11
204 208 2.432444 TGCTGGCAAGGTAACACATAC 58.568 47.619 0.00 0.00 41.41 2.39
445 453 6.525629 GGAGGATTTATAGCAGAGTAGCAAA 58.474 40.000 0.00 0.00 36.85 3.68
701 710 2.484770 CCTTCAAGTGACGTCCAAAGGA 60.485 50.000 14.12 1.47 34.97 3.36
801 810 5.709164 CCTGGAACTTGAACTTGAATCATCT 59.291 40.000 0.00 0.00 0.00 2.90
865 874 2.624838 ACTCCAAGTTGGTGCATCAAAG 59.375 45.455 21.35 10.37 39.03 2.77
935 944 2.223923 CCTTGAGATCCTTGCGGTAGAG 60.224 54.545 0.00 0.00 0.00 2.43
1059 1069 2.422479 CTGGTTCTCCTGTCGTCGAATA 59.578 50.000 0.00 0.00 34.23 1.75
1168 1178 6.601332 TCACCAATACTTCACTTTCCTCTTT 58.399 36.000 0.00 0.00 0.00 2.52
1178 1188 9.113876 CGTTATTCTTTTTCACCAATACTTCAC 57.886 33.333 0.00 0.00 0.00 3.18
1192 1202 7.979444 TCTTGATCAGGTCGTTATTCTTTTT 57.021 32.000 4.57 0.00 0.00 1.94
1194 1204 7.386851 TCTTCTTGATCAGGTCGTTATTCTTT 58.613 34.615 4.57 0.00 0.00 2.52
1201 1211 4.020218 TCCAATCTTCTTGATCAGGTCGTT 60.020 41.667 4.57 0.00 33.57 3.85
1234 1244 2.203877 TACGGGTGTTGGGCCTCT 60.204 61.111 4.53 0.00 0.00 3.69
1242 1252 2.165167 TCGTCTTCATCTACGGGTGTT 58.835 47.619 0.00 0.00 39.52 3.32
1578 1591 4.998051 AGGCATCTGAGGGTTTAGAAAAA 58.002 39.130 0.00 0.00 0.00 1.94
1672 1687 3.834813 TCTGATTCTGGACTAGCAACTGT 59.165 43.478 0.00 0.00 0.00 3.55
1852 1873 1.847328 TCACCTTCTCCGCATCTGTA 58.153 50.000 0.00 0.00 0.00 2.74
1970 1991 1.002502 GGGCAGTACGGAAAGCCTT 60.003 57.895 11.08 0.00 46.23 4.35
2000 2021 2.747467 GCTTCTTCATGGCCATAGCTCA 60.747 50.000 24.25 7.80 39.73 4.26
2308 2329 2.372837 TCTAGGGGTAAAACGTGGCTTT 59.627 45.455 0.00 0.00 0.00 3.51
2358 2379 0.905357 ATTGTGCGAGCTACCTCCTT 59.095 50.000 0.00 0.00 34.49 3.36


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

AutoCloner maintained by Alex Coulton.