Multiple sequence alignment - TraesCS1A01G047900

Loading Multiple Alignment...

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 TraesCS1A01G047900 chr1A 100.000 2876 0 0 1 2876 29790452 29793327 0.000000e+00 5312
1 TraesCS1A01G047900 chr5A 97.881 2879 58 2 1 2876 671174607 671171729 0.000000e+00 4975
2 TraesCS1A01G047900 chr5A 97.472 2611 63 3 268 2876 132296901 132294292 0.000000e+00 4453
3 TraesCS1A01G047900 chr5A 97.318 2610 64 4 269 2876 6674433 6671828 0.000000e+00 4427
4 TraesCS1A01G047900 chr5A 97.203 2610 70 3 269 2876 547391261 547388653 0.000000e+00 4412
5 TraesCS1A01G047900 chr6A 97.625 2610 57 4 269 2876 463536537 463533931 0.000000e+00 4471
6 TraesCS1A01G047900 chr7A 97.586 2610 60 3 269 2876 5440228 5437620 0.000000e+00 4468
7 TraesCS1A01G047900 chr7A 97.471 2610 63 3 269 2876 696841535 696844143 0.000000e+00 4451
8 TraesCS1A01G047900 chr4A 97.548 2610 58 6 271 2876 625823807 625826414 0.000000e+00 4460
9 TraesCS1A01G047900 chr4A 97.344 2598 67 2 281 2876 603111929 603109332 0.000000e+00 4414
10 TraesCS1A01G047900 chr4A 96.296 351 5 2 1 343 278350229 278350579 1.160000e-158 569


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 TraesCS1A01G047900 chr1A 29790452 29793327 2875 False 5312 5312 100.000 1 2876 1 chr1A.!!$F1 2875
1 TraesCS1A01G047900 chr5A 671171729 671174607 2878 True 4975 4975 97.881 1 2876 1 chr5A.!!$R4 2875
2 TraesCS1A01G047900 chr5A 132294292 132296901 2609 True 4453 4453 97.472 268 2876 1 chr5A.!!$R2 2608
3 TraesCS1A01G047900 chr5A 6671828 6674433 2605 True 4427 4427 97.318 269 2876 1 chr5A.!!$R1 2607
4 TraesCS1A01G047900 chr5A 547388653 547391261 2608 True 4412 4412 97.203 269 2876 1 chr5A.!!$R3 2607
5 TraesCS1A01G047900 chr6A 463533931 463536537 2606 True 4471 4471 97.625 269 2876 1 chr6A.!!$R1 2607
6 TraesCS1A01G047900 chr7A 5437620 5440228 2608 True 4468 4468 97.586 269 2876 1 chr7A.!!$R1 2607
7 TraesCS1A01G047900 chr7A 696841535 696844143 2608 False 4451 4451 97.471 269 2876 1 chr7A.!!$F1 2607
8 TraesCS1A01G047900 chr4A 625823807 625826414 2607 False 4460 4460 97.548 271 2876 1 chr4A.!!$F2 2605
9 TraesCS1A01G047900 chr4A 603109332 603111929 2597 True 4414 4414 97.344 281 2876 1 chr4A.!!$R1 2595

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
982 985 0.248621 GCGTGCTCAGTTGTTTGCTT 60.249 50.0 0.0 0.0 0.0 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2668 2677 1.465387 GAGAGATACGCATCCGACGAT 59.535 52.381 0.0 0.0 38.29 3.73 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
38 39 4.530857 CCCGCCCGTGATCCAGTC 62.531 72.222 0.00 0.00 0.00 3.51
44 45 3.822192 CGTGATCCAGTCGCCCGA 61.822 66.667 0.00 0.00 33.71 5.14
178 179 1.000827 CCCGATTGAGACTCCTGATCG 60.001 57.143 18.53 18.53 36.04 3.69
518 521 1.065126 GGCTAAGGTTGCTGATGAGGT 60.065 52.381 0.00 0.00 0.00 3.85
521 524 2.664402 AAGGTTGCTGATGAGGTTGT 57.336 45.000 0.00 0.00 0.00 3.32
601 604 2.484770 GGTGCTCTGTCTGTTTACACCA 60.485 50.000 0.00 0.00 44.32 4.17
718 721 0.813184 GATGTGGACCCGTCTTCGTA 59.187 55.000 0.00 0.00 35.01 3.43
763 766 4.809193 TGCCTTATACCTCTCTGTGATCT 58.191 43.478 0.00 0.00 0.00 2.75
982 985 0.248621 GCGTGCTCAGTTGTTTGCTT 60.249 50.000 0.00 0.00 0.00 3.91
1187 1190 4.715523 CCCCCGTCCACATTGCGT 62.716 66.667 0.00 0.00 0.00 5.24
1304 1307 1.447489 CCTCGACAGCTTCAGCCAG 60.447 63.158 0.00 0.00 43.38 4.85
1345 1348 3.577649 TTCTGAGACTTAAGCGTCTGG 57.422 47.619 1.29 0.00 43.91 3.86
1418 1421 1.376424 CCCGCACTGAGCAATCACT 60.376 57.895 0.00 0.00 46.13 3.41
1705 1708 4.340097 TCCTTGACGTTGACTCTTGTTCTA 59.660 41.667 0.00 0.00 0.00 2.10
1764 1767 2.586079 CGCCGCCGTGATTCTCAT 60.586 61.111 0.00 0.00 0.00 2.90
1991 1995 3.192001 GTCATCTTGGCAAGCAGATTCAA 59.808 43.478 22.31 2.82 0.00 2.69
2021 2025 4.521130 TTCACATAGTGAGTCAGTGTCC 57.479 45.455 10.90 0.00 43.69 4.02
2077 2081 3.961414 TCCGGCCCCTTTCGCTTT 61.961 61.111 0.00 0.00 0.00 3.51
2218 2222 5.540337 TGGTTCATACTCAGTTCTCTTCACT 59.460 40.000 0.00 0.00 0.00 3.41
2595 2602 1.433053 CGAACGCACCAAACTGACCA 61.433 55.000 0.00 0.00 0.00 4.02
2668 2677 4.771114 ATCGTTGTTGGGATCCTATTGA 57.229 40.909 12.58 1.58 0.00 2.57
2728 2737 0.702902 TCTCGTCCCTTCTACCCACT 59.297 55.000 0.00 0.00 0.00 4.00
2838 2847 3.244249 CCGTTCCACTTTCTCTCCTTCTT 60.244 47.826 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 3.550431 CTGGATCGTGGGCGGGAT 61.550 66.667 0.00 0.00 38.89 3.85
55 56 4.554036 GGACCGGGCAGCTGGATC 62.554 72.222 17.12 0.00 0.00 3.36
150 151 1.612146 TCTCAATCGGGACCTGGCA 60.612 57.895 0.00 0.00 0.00 4.92
178 179 0.251341 AGGAATCAGTGGTGGCCAAC 60.251 55.000 15.99 15.99 34.18 3.77
518 521 5.418676 TCTCATCATAAGCACGATCAACAA 58.581 37.500 0.00 0.00 0.00 2.83
521 524 4.502087 CCCTCTCATCATAAGCACGATCAA 60.502 45.833 0.00 0.00 0.00 2.57
601 604 2.950309 GAGCATCATCATCAAGCCACTT 59.050 45.455 0.00 0.00 33.17 3.16
763 766 0.978907 TGAAGAGCATGCTCCTGACA 59.021 50.000 37.79 28.38 43.70 3.58
982 985 2.419990 CCATGAGAGAAATACGGCCACA 60.420 50.000 2.24 0.00 0.00 4.17
1187 1190 6.124340 AGATGACCATCATTGTTGCAATAGA 58.876 36.000 0.59 0.00 37.20 1.98
1255 1258 0.465705 GTCCCGGAAGATGATGAGCA 59.534 55.000 0.73 0.00 0.00 4.26
1257 1260 2.544694 CGAAGTCCCGGAAGATGATGAG 60.545 54.545 0.73 0.00 0.00 2.90
1304 1307 1.818642 ATCCTGCTCAGTCAAAGCAC 58.181 50.000 0.00 0.00 44.51 4.40
1345 1348 1.627550 GAAGAACCTGAAGCCGCGAC 61.628 60.000 8.23 0.00 0.00 5.19
1418 1421 4.270834 GGATGTACCTGACTGTGTAGAGA 58.729 47.826 0.00 0.00 35.41 3.10
1705 1708 2.970639 CGTGTGACGGTCCTGGAT 59.029 61.111 5.55 0.00 38.08 3.41
1764 1767 1.073763 CAGTCCAACTCCCAATGACCA 59.926 52.381 0.00 0.00 0.00 4.02
1769 1772 0.779997 AAGCCAGTCCAACTCCCAAT 59.220 50.000 0.00 0.00 0.00 3.16
1991 1995 8.928448 ACTGACTCACTATGTGAATATGGTAAT 58.072 33.333 2.00 0.00 42.26 1.89
2021 2025 3.062234 GGACTAAATCGAAAGGACGCTTG 59.938 47.826 0.00 0.00 0.00 4.01
2218 2222 2.609916 TCAGCACGAAAAACACGAATGA 59.390 40.909 0.00 0.00 34.70 2.57
2430 2437 6.326161 TGATAAGATAGGTGGATGTGGAGAT 58.674 40.000 0.00 0.00 0.00 2.75
2536 2543 1.816224 AGCAAACACAACCAAACGAGT 59.184 42.857 0.00 0.00 0.00 4.18
2668 2677 1.465387 GAGAGATACGCATCCGACGAT 59.535 52.381 0.00 0.00 38.29 3.73
2728 2737 3.326588 TGAAAAAGTCGAGGAAGATGGGA 59.673 43.478 0.00 0.00 0.00 4.37
2838 2847 3.691118 GGCTGCAAATCAACTAGATGTGA 59.309 43.478 0.50 0.00 43.53 3.58


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

AutoCloner maintained by Alex Coulton.