Multiple sequence alignment - TraesCS2D01G240600

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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 TraesCS2D01G240600 chr2D 100.000 2677 0 0 1 2677 259237996 259240672 0 4944
1 TraesCS2D01G240600 chr4D 96.678 2047 67 1 1 2047 201258654 201256609 0 3402
2 TraesCS2D01G240600 chr4D 98.101 632 11 1 2046 2677 201256548 201255918 0 1099
3 TraesCS2D01G240600 chr2A 95.224 2052 87 11 1 2047 116987684 116989729 0 3236
4 TraesCS2D01G240600 chr2A 94.988 2055 90 11 1 2047 160664746 160666795 0 3212
5 TraesCS2D01G240600 chr2A 94.461 2058 100 11 1 2047 109285535 109287589 0 3157
6 TraesCS2D01G240600 chr2A 96.682 633 20 1 2046 2677 116989790 116990422 0 1051
7 TraesCS2D01G240600 chr2A 96.682 633 19 2 2046 2677 160666856 160667487 0 1051
8 TraesCS2D01G240600 chr7A 95.034 2054 93 7 1 2047 458652747 458654798 0 3219
9 TraesCS2D01G240600 chr7A 96.840 633 19 1 2046 2677 458654859 458655491 0 1057
10 TraesCS2D01G240600 chrUn 94.973 2049 96 7 1 2045 47164580 47162535 0 3206
11 TraesCS2D01G240600 chr5A 94.881 2051 95 8 1 2045 154808600 154810646 0 3197
12 TraesCS2D01G240600 chr5A 96.682 633 20 1 2046 2677 154810709 154811341 0 1051
13 TraesCS2D01G240600 chr6A 94.645 2054 96 11 1 2046 490168073 490170120 0 3171
14 TraesCS2D01G240600 chr6A 94.637 2051 99 7 1 2047 337975534 337977577 0 3168
15 TraesCS2D01G240600 chr6A 97.003 634 17 2 2045 2677 337977637 337978269 0 1064
16 TraesCS2D01G240600 chr7D 97.785 632 13 1 2046 2677 291615808 291615178 0 1088
17 TraesCS2D01G240600 chr3D 96.677 632 21 0 2046 2677 421483632 421483001 0 1051
18 TraesCS2D01G240600 chr1D 96.677 632 21 0 2046 2677 88005350 88005981 0 1051


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 TraesCS2D01G240600 chr2D 259237996 259240672 2676 False 4944.0 4944 100.0000 1 2677 1 chr2D.!!$F1 2676
1 TraesCS2D01G240600 chr4D 201255918 201258654 2736 True 2250.5 3402 97.3895 1 2677 2 chr4D.!!$R1 2676
2 TraesCS2D01G240600 chr2A 109285535 109287589 2054 False 3157.0 3157 94.4610 1 2047 1 chr2A.!!$F1 2046
3 TraesCS2D01G240600 chr2A 116987684 116990422 2738 False 2143.5 3236 95.9530 1 2677 2 chr2A.!!$F2 2676
4 TraesCS2D01G240600 chr2A 160664746 160667487 2741 False 2131.5 3212 95.8350 1 2677 2 chr2A.!!$F3 2676
5 TraesCS2D01G240600 chr7A 458652747 458655491 2744 False 2138.0 3219 95.9370 1 2677 2 chr7A.!!$F1 2676
6 TraesCS2D01G240600 chrUn 47162535 47164580 2045 True 3206.0 3206 94.9730 1 2045 1 chrUn.!!$R1 2044
7 TraesCS2D01G240600 chr5A 154808600 154811341 2741 False 2124.0 3197 95.7815 1 2677 2 chr5A.!!$F1 2676
8 TraesCS2D01G240600 chr6A 490168073 490170120 2047 False 3171.0 3171 94.6450 1 2046 1 chr6A.!!$F1 2045
9 TraesCS2D01G240600 chr6A 337975534 337978269 2735 False 2116.0 3168 95.8200 1 2677 2 chr6A.!!$F2 2676
10 TraesCS2D01G240600 chr7D 291615178 291615808 630 True 1088.0 1088 97.7850 2046 2677 1 chr7D.!!$R1 631
11 TraesCS2D01G240600 chr3D 421483001 421483632 631 True 1051.0 1051 96.6770 2046 2677 1 chr3D.!!$R1 631
12 TraesCS2D01G240600 chr1D 88005350 88005981 631 False 1051.0 1051 96.6770 2046 2677 1 chr1D.!!$F1 631

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
434 439 0.258774 TGCCTTATCTTGCTTCCCCC 59.741 55.0 0.00 0.0 0.00 5.40 F
1098 1108 0.179111 ACCGATGTAGCGTGGACATG 60.179 55.0 4.09 0.0 37.65 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1663 1678 2.610479 GCCAAAGGCTAAAACTCCTTGC 60.610 50.00 0.00 0.0 46.69 4.01 R
2143 2225 5.854010 AATCTGGCTAGAGATCACGTAAA 57.146 39.13 5.82 0.0 36.14 2.01 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
316 318 3.377485 TGAGAAGTATGCGGAGTGAGTAC 59.623 47.826 0.00 0.00 0.00 2.73
321 323 1.853963 ATGCGGAGTGAGTACCTCTT 58.146 50.000 0.00 0.00 0.00 2.85
322 324 0.888619 TGCGGAGTGAGTACCTCTTG 59.111 55.000 0.00 0.00 0.00 3.02
387 391 9.823647 CTAGATAAATGTGACCTGAACTGTTAT 57.176 33.333 0.00 0.00 0.00 1.89
434 439 0.258774 TGCCTTATCTTGCTTCCCCC 59.741 55.000 0.00 0.00 0.00 5.40
484 489 7.330454 CAGGAATACATTCTCAATGATACCTCG 59.670 40.741 3.24 0.00 41.46 4.63
488 493 0.673985 TCTCAATGATACCTCGGCCG 59.326 55.000 22.12 22.12 0.00 6.13
589 594 8.493607 TGTAATGGACTTCCTCATTGATGATTA 58.506 33.333 0.00 0.00 36.02 1.75
590 595 9.342308 GTAATGGACTTCCTCATTGATGATTAA 57.658 33.333 0.00 0.00 36.02 1.40
593 598 8.827832 TGGACTTCCTCATTGATGATTAAAAT 57.172 30.769 0.00 0.00 36.02 1.82
681 686 5.041287 TCACGGTAATCAATCAGATCGTTC 58.959 41.667 0.00 0.00 33.89 3.95
750 758 3.960102 ACTTTGCTTGTTGATCCTTTCCA 59.040 39.130 0.00 0.00 0.00 3.53
769 777 7.883311 CCTTTCCACCTGTCTATTTCTTTTCTA 59.117 37.037 0.00 0.00 0.00 2.10
832 842 8.921670 GGTGATGAAAATAAAGCGTTTAATGTT 58.078 29.630 0.00 0.00 0.00 2.71
904 914 1.069765 CACTGCCGACCTTGTGAGT 59.930 57.895 0.00 0.00 32.72 3.41
1098 1108 0.179111 ACCGATGTAGCGTGGACATG 60.179 55.000 4.09 0.00 37.65 3.21
1128 1138 5.974108 TCTTTACCTTATCCGAAGAACCAG 58.026 41.667 0.00 0.00 0.00 4.00
1129 1139 5.482878 TCTTTACCTTATCCGAAGAACCAGT 59.517 40.000 0.00 0.00 0.00 4.00
1663 1678 1.649664 CTTCTGGTGATGGAGCTTCG 58.350 55.000 0.00 0.00 0.00 3.79
1783 1799 6.952773 TGTAGGCTTTGATTGTAGTGTTTT 57.047 33.333 0.00 0.00 0.00 2.43
2020 2039 8.877195 TCTGTACCCTCTTTTCTTGTACTTATT 58.123 33.333 0.00 0.00 34.37 1.40
2059 2140 3.134623 ACTGAATTGTGAGTGGAGTGACA 59.865 43.478 0.00 0.00 0.00 3.58
2143 2225 9.634163 GGATTGAAATTATTTACGACCAAGTTT 57.366 29.630 0.00 0.00 0.00 2.66
2171 2253 6.703607 ACGTGATCTCTAGCCAGATTTTATTG 59.296 38.462 0.00 0.00 32.94 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
316 318 4.884247 AGAAGAGGAAACGTAACAAGAGG 58.116 43.478 0.00 0.00 0.00 3.69
321 323 5.677567 AGGAAAAGAAGAGGAAACGTAACA 58.322 37.500 0.00 0.00 0.00 2.41
322 324 5.990386 AGAGGAAAAGAAGAGGAAACGTAAC 59.010 40.000 0.00 0.00 0.00 2.50
393 397 6.253746 GCATTCATAGCAGTTCAAGTTGTAG 58.746 40.000 2.11 0.00 0.00 2.74
434 439 2.108700 CACGGACAAGAACAAAAAGCG 58.891 47.619 0.00 0.00 0.00 4.68
484 489 0.669625 GGTTACGCTATCATCCGGCC 60.670 60.000 0.00 0.00 0.00 6.13
488 493 2.821991 AGCTGGTTACGCTATCATCC 57.178 50.000 0.00 0.00 35.63 3.51
602 607 7.022979 CAGACGCAAAATCAACATTTCTATCA 58.977 34.615 0.00 0.00 30.37 2.15
681 686 4.511826 AGGCAGTCTTGTTTAAGAGAAACG 59.488 41.667 0.00 0.00 43.29 3.60
750 758 6.628644 AGCCTAGAAAAGAAATAGACAGGT 57.371 37.500 0.00 0.00 0.00 4.00
769 777 0.179076 GCACAACCTGCAAAAAGCCT 60.179 50.000 0.00 0.00 46.29 4.58
795 805 9.763465 CTTTATTTTCATCACCGTAAAACGTAT 57.237 29.630 0.00 0.00 40.58 3.06
832 842 1.180907 AATCTCTCGCTGCACTCTCA 58.819 50.000 0.00 0.00 0.00 3.27
1092 1102 3.944087 AGGTAAAGAGTCAAGCATGTCC 58.056 45.455 0.00 0.00 0.00 4.02
1098 1108 5.007385 TCGGATAAGGTAAAGAGTCAAGC 57.993 43.478 0.00 0.00 0.00 4.01
1129 1139 5.560722 TGATAGGTGTTCTTTGAAGGACA 57.439 39.130 0.69 0.69 42.14 4.02
1208 1218 2.325583 AGCAGAAACAAAGACGTGGA 57.674 45.000 0.00 0.00 0.00 4.02
1663 1678 2.610479 GCCAAAGGCTAAAACTCCTTGC 60.610 50.000 0.00 0.00 46.69 4.01
1783 1799 9.681692 CACAACTATCAAAAATCAAAGACATCA 57.318 29.630 0.00 0.00 0.00 3.07
1818 1834 6.723298 TTCCCAATGAAACATACACAAGTT 57.277 33.333 0.00 0.00 0.00 2.66
2143 2225 5.854010 AATCTGGCTAGAGATCACGTAAA 57.146 39.130 5.82 0.00 36.14 2.01


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

AutoCloner maintained by Alex Coulton.