Multiple sequence alignment - TraesCS2B01G399800

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 TraesCS2B01G399800 chr2B 100.000 2606 0 0 1 2606 568274037 568276642 0.000000e+00 4813
1 TraesCS2B01G399800 chr2D 97.714 2625 30 11 1 2606 483257438 483254825 0.000000e+00 4488
2 TraesCS2B01G399800 chr2A 94.657 2040 66 15 1 2023 626590799 626588786 0.000000e+00 3123
3 TraesCS2B01G399800 chr2A 96.975 595 12 1 2010 2604 626588745 626588157 0.000000e+00 994
4 TraesCS2B01G399800 chr6B 88.742 453 48 2 1097 1549 460928684 460929133 3.790000e-153 551
5 TraesCS2B01G399800 chr6B 86.618 411 53 2 1107 1516 687525408 687524999 1.100000e-123 453
6 TraesCS2B01G399800 chr6D 88.667 450 48 3 1100 1549 296348060 296347614 1.760000e-151 545
7 TraesCS2B01G399800 chr6A 88.667 450 48 3 1100 1549 422328681 422328235 1.760000e-151 545
8 TraesCS2B01G399800 chr6A 86.618 411 53 2 1107 1516 598619731 598619322 1.100000e-123 453
9 TraesCS2B01G399800 chr1D 85.948 427 55 4 1095 1517 214068359 214067934 3.950000e-123 451
10 TraesCS2B01G399800 chr1A 85.748 428 54 6 1095 1517 271620276 271619851 1.840000e-121 446


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 TraesCS2B01G399800 chr2B 568274037 568276642 2605 False 4813.0 4813 100.000 1 2606 1 chr2B.!!$F1 2605
1 TraesCS2B01G399800 chr2D 483254825 483257438 2613 True 4488.0 4488 97.714 1 2606 1 chr2D.!!$R1 2605
2 TraesCS2B01G399800 chr2A 626588157 626590799 2642 True 2058.5 3123 95.816 1 2604 2 chr2A.!!$R1 2603

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
621 630 0.606401 ATCAGCTTCCAACACCACCG 60.606 55.0 0.0 0.0 0.0 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1655 1678 0.679505 CCGGCCAAATAGGAGATCGA 59.32 55.0 2.24 0.0 41.22 3.59 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
184 187 2.159184 GCAGTACTAGCAGTGCATCTCA 60.159 50.000 19.20 0.0 43.14 3.27
483 486 1.500474 TCCAGATCGCTCTCCCAAAT 58.500 50.000 0.00 0.0 0.00 2.32
494 501 4.095036 CGCTCTCCCAAATTAACCTTTCTC 59.905 45.833 0.00 0.0 0.00 2.87
496 503 5.712446 GCTCTCCCAAATTAACCTTTCTCTT 59.288 40.000 0.00 0.0 0.00 2.85
531 538 7.099764 TGTGTCCTCTGATGTTTTCTATCTTC 58.900 38.462 0.00 0.0 0.00 2.87
533 540 5.233263 GTCCTCTGATGTTTTCTATCTTCGC 59.767 44.000 0.00 0.0 0.00 4.70
609 618 0.883833 CGCCAAACCAAGATCAGCTT 59.116 50.000 0.00 0.0 37.29 3.74
621 630 0.606401 ATCAGCTTCCAACACCACCG 60.606 55.000 0.00 0.0 0.00 4.94
780 793 4.424626 CAAACAGATCGCTAGCTCAAGTA 58.575 43.478 13.93 0.0 0.00 2.24
850 871 5.966742 AGGAACAGTGCTATTTCTTTTCC 57.033 39.130 0.00 0.0 39.44 3.13
1299 1322 3.330720 CCCTTCTTCGGCCACCCT 61.331 66.667 2.24 0.0 0.00 4.34
1563 1586 1.973281 CAGCTTCCACGGCAACCAT 60.973 57.895 0.00 0.0 0.00 3.55
1615 1638 1.416813 CGGTTGCTGAGCTGATCGAC 61.417 60.000 5.83 0.0 0.00 4.20
1655 1678 2.833582 AGCCGGTGGTCGATCGAT 60.834 61.111 22.50 0.0 42.43 3.59
1841 1864 5.671493 GACCTAGTTGGCTTTGATTAGCTA 58.329 41.667 0.00 0.0 40.99 3.32
1967 1990 1.958579 CATGCAGGGAGAGAGAGAGAG 59.041 57.143 0.00 0.0 0.00 3.20
1969 1992 1.212688 TGCAGGGAGAGAGAGAGAGAG 59.787 57.143 0.00 0.0 0.00 3.20
1970 1993 1.490490 GCAGGGAGAGAGAGAGAGAGA 59.510 57.143 0.00 0.0 0.00 3.10
1971 1994 2.107204 GCAGGGAGAGAGAGAGAGAGAT 59.893 54.545 0.00 0.0 0.00 2.75
1972 1995 3.327757 GCAGGGAGAGAGAGAGAGAGATA 59.672 52.174 0.00 0.0 0.00 1.98
1973 1996 4.804261 GCAGGGAGAGAGAGAGAGAGATAC 60.804 54.167 0.00 0.0 0.00 2.24
2097 2174 5.734503 GCATCATGTGTCAACTCGATCTAGA 60.735 44.000 0.47 0.0 0.00 2.43
2434 2511 7.907841 TTCCTGGTACTTGAAGCATAGTATA 57.092 36.000 0.00 0.0 0.00 1.47
2435 2512 8.492415 TTCCTGGTACTTGAAGCATAGTATAT 57.508 34.615 0.00 0.0 0.00 0.86
2436 2513 9.596308 TTCCTGGTACTTGAAGCATAGTATATA 57.404 33.333 0.00 0.0 0.00 0.86
2437 2514 9.769677 TCCTGGTACTTGAAGCATAGTATATAT 57.230 33.333 0.00 0.0 0.00 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.393539 GTCATTTGATGTCACCGGTCG 59.606 52.381 2.59 0.00 0.00 4.79
494 501 7.173907 ACATCAGAGGACACATACAAGAAAAAG 59.826 37.037 0.00 0.00 0.00 2.27
496 503 6.533730 ACATCAGAGGACACATACAAGAAAA 58.466 36.000 0.00 0.00 0.00 2.29
531 538 3.184683 GGCTTGAGAGTCTGCGCG 61.185 66.667 0.00 0.00 0.00 6.86
533 540 1.294659 GGTTGGCTTGAGAGTCTGCG 61.295 60.000 0.00 0.00 0.00 5.18
609 618 3.650023 ACCTTCGGTGGTGTTGGA 58.350 55.556 0.00 0.00 39.17 3.53
621 630 7.173218 GGAAAGGAAATTTTTGGAATCACCTTC 59.827 37.037 0.00 0.00 39.86 3.46
637 646 6.144845 TGGAGATCTTTCAGGAAAGGAAAT 57.855 37.500 18.74 7.75 45.80 2.17
780 793 8.733458 GGTCAATGATTACATGTGTGCATATAT 58.267 33.333 9.11 0.00 36.79 0.86
1655 1678 0.679505 CCGGCCAAATAGGAGATCGA 59.320 55.000 2.24 0.00 41.22 3.59
1841 1864 7.395489 TGATAAACTCGACTAGAACTTAACCCT 59.605 37.037 0.00 0.00 0.00 4.34
1967 1990 8.461222 CAAGAGAGATCTCCATACATGTATCTC 58.539 40.741 19.30 19.68 43.88 2.75
1969 1992 7.035004 GCAAGAGAGATCTCCATACATGTATC 58.965 42.308 19.30 5.69 43.88 2.24
1970 1993 6.725369 AGCAAGAGAGATCTCCATACATGTAT 59.275 38.462 19.30 12.75 43.88 2.29
1971 1994 6.073981 AGCAAGAGAGATCTCCATACATGTA 58.926 40.000 19.30 8.27 43.88 2.29
1972 1995 4.900652 AGCAAGAGAGATCTCCATACATGT 59.099 41.667 19.30 2.69 43.88 3.21
1973 1996 5.471556 AGCAAGAGAGATCTCCATACATG 57.528 43.478 19.30 11.94 43.88 3.21
2097 2174 6.701400 AGCAAAACAAGAAACAATAAGCGATT 59.299 30.769 0.00 0.00 0.00 3.34
2434 2511 7.173032 CCCCTATCACATGCATGCATATATAT 58.827 38.462 31.73 22.52 34.91 0.86
2435 2512 6.466182 CCCCCTATCACATGCATGCATATATA 60.466 42.308 31.73 24.22 34.91 0.86
2436 2513 5.382616 CCCCTATCACATGCATGCATATAT 58.617 41.667 31.73 24.38 34.91 0.86
2437 2514 4.385532 CCCCCTATCACATGCATGCATATA 60.386 45.833 31.73 23.13 34.91 0.86
2438 2515 3.626475 CCCCCTATCACATGCATGCATAT 60.626 47.826 31.73 23.25 34.91 1.78
2439 2516 2.291089 CCCCCTATCACATGCATGCATA 60.291 50.000 31.73 18.03 34.91 3.14


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

AutoCloner maintained by Alex Coulton.