Multiple sequence alignment - TraesCS2D01G503200

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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 TraesCS2D01G503200 chr2D 100.000 5396 0 0 1 5396 597938532 597943927 0.000000e+00 9928.0
1 TraesCS2D01G503200 chr2D 98.769 3818 39 5 1584 5396 641960814 641964628 0.000000e+00 6783.0
2 TraesCS2D01G503200 chr2D 99.302 1577 7 1 1 1573 641959793 641961369 0.000000e+00 2848.0
3 TraesCS2D01G503200 chr2D 99.640 556 2 0 1584 2139 597939549 597940104 0.000000e+00 1016.0
4 TraesCS2D01G503200 chr2D 99.640 556 2 0 1018 1573 597940115 597940670 0.000000e+00 1016.0
5 TraesCS2D01G503200 chr2D 86.709 158 21 0 997 1154 513093661 513093818 5.550000e-40 176.0
6 TraesCS2D01G503200 chrUn 100.000 394 0 0 3530 3923 479437173 479436780 0.000000e+00 728.0
7 TraesCS2D01G503200 chr6D 80.448 491 68 21 984 1454 6982156 6982638 3.090000e-92 350.0
8 TraesCS2D01G503200 chr6D 80.645 434 57 20 1606 2020 6982213 6982638 1.460000e-80 311.0
9 TraesCS2D01G503200 chr1A 81.074 391 50 15 965 1349 61575806 61576178 1.900000e-74 291.0
10 TraesCS2D01G503200 chr1A 78.673 422 61 20 888 1302 61713563 61713962 2.490000e-63 254.0
11 TraesCS2D01G503200 chr1A 95.000 40 2 0 1617 1656 99148804 99148843 4.510000e-06 63.9
12 TraesCS2D01G503200 chr1D 78.657 417 59 21 944 1349 63543526 63543923 3.230000e-62 250.0
13 TraesCS2D01G503200 chr1D 95.000 40 2 0 1617 1656 80633516 80633555 4.510000e-06 63.9
14 TraesCS2D01G503200 chr1B 85.185 243 27 7 944 1178 101591860 101591619 1.940000e-59 241.0
15 TraesCS2D01G503200 chr1B 86.512 215 26 2 967 1178 101519209 101519423 3.250000e-57 233.0
16 TraesCS2D01G503200 chr1B 92.500 40 3 0 1617 1656 133429825 133429864 2.100000e-04 58.4
17 TraesCS2D01G503200 chr5D 83.544 158 21 5 1000 1153 371872971 371872815 5.630000e-30 143.0


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 TraesCS2D01G503200 chr2D 597938532 597943927 5395 False 9928.0 9928 100.0000 1 5396 1 chr2D.!!$F2 5395
1 TraesCS2D01G503200 chr2D 641959793 641964628 4835 False 4815.5 6783 99.0355 1 5396 2 chr2D.!!$F4 5395
2 TraesCS2D01G503200 chr2D 597939549 597940670 1121 False 1016.0 1016 99.6400 1018 2139 2 chr2D.!!$F3 1121

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
594 599 1.606885 AATGCAAGGCGTTGGATGGG 61.607 55.000 23.97 0.0 43.42 4.00 F
640 645 3.453717 CTCCAGATCATCCTTGTCCTGAA 59.546 47.826 0.00 0.0 0.00 3.02 F
2139 2144 7.945664 ACTTGTTAATTTTGGGGTATCAGTACA 59.054 33.333 0.00 0.0 32.25 2.90 F
3528 3538 1.530323 AAACCGGACCAATGCAGTAC 58.470 50.000 9.46 0.0 0.00 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2139 2144 6.348498 TGTTGATTCGGATCATGAACAGTAT 58.652 36.000 7.35 0.0 41.71 2.12 R
2155 2160 7.349412 AGATGGTACCTACTACTGTTGATTC 57.651 40.000 14.36 0.0 0.00 2.52 R
3923 3933 1.466866 CGCGTGACTCTGGAAATACGA 60.467 52.381 0.00 0.0 33.78 3.43 R
5003 5013 1.378514 AAGCCCAATAGCACACGGG 60.379 57.895 0.00 0.0 42.03 5.28 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
45 50 2.852495 GAAATCGCCGGAGTCAGCCA 62.852 60.000 5.05 0.00 0.00 4.75
135 140 3.436704 CACCTGAACAGTGTTAATCGCAT 59.563 43.478 8.88 0.00 0.00 4.73
154 159 7.984422 TCGCATAACTGAATATTCATTCCAT 57.016 32.000 18.26 7.60 39.97 3.41
594 599 1.606885 AATGCAAGGCGTTGGATGGG 61.607 55.000 23.97 0.00 43.42 4.00
640 645 3.453717 CTCCAGATCATCCTTGTCCTGAA 59.546 47.826 0.00 0.00 0.00 3.02
2139 2144 7.945664 ACTTGTTAATTTTGGGGTATCAGTACA 59.054 33.333 0.00 0.00 32.25 2.90
2170 2175 6.739112 TCATGATCCGAATCAACAGTAGTAG 58.261 40.000 0.00 0.00 44.85 2.57
2223 2228 2.049156 CTGACGGCTCGAGTTGCA 60.049 61.111 15.13 6.75 0.00 4.08
2744 2753 3.775316 CCCTCTACACCAAGTTCCATAGT 59.225 47.826 0.00 0.00 0.00 2.12
2752 2761 1.662629 CAAGTTCCATAGTGCTCGCTG 59.337 52.381 0.00 0.00 0.00 5.18
2933 2943 2.722094 GTGGGCCATCAACACAGATAA 58.278 47.619 10.70 0.00 35.30 1.75
2935 2945 3.701040 GTGGGCCATCAACACAGATAAAT 59.299 43.478 10.70 0.00 35.30 1.40
2936 2946 4.160252 GTGGGCCATCAACACAGATAAATT 59.840 41.667 10.70 0.00 35.30 1.82
3071 3081 9.829507 TCAAATGATGATGTTGTTTTAAAAGGT 57.170 25.926 0.00 0.00 31.50 3.50
3528 3538 1.530323 AAACCGGACCAATGCAGTAC 58.470 50.000 9.46 0.00 0.00 2.73
4182 4192 2.094854 GCTGAAAAAGGTGCTGGAGATG 60.095 50.000 0.00 0.00 0.00 2.90
4311 4321 4.145807 CAGTCCTATTCGACTCATACCCT 58.854 47.826 0.00 0.00 41.23 4.34
4800 4810 1.698874 AGGATCAACCCCTTTCCCAT 58.301 50.000 0.00 0.00 40.05 4.00
5003 5013 0.967380 CATTGGGTCCTCCTGTTGGC 60.967 60.000 0.00 0.00 36.20 4.52
5081 5091 2.154389 GCGTACAACGTTTACTCCACTG 59.846 50.000 0.00 0.00 44.73 3.66
5152 5162 4.447138 TCGCTATTTTTACCCATCCCAT 57.553 40.909 0.00 0.00 0.00 4.00
5160 5170 0.923729 TACCCATCCCATGCCAACCT 60.924 55.000 0.00 0.00 0.00 3.50
5339 5349 9.345517 CATTTTCTTGGTGATTTATGTGTACAG 57.654 33.333 0.00 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 50 1.625315 TCAGCATTGAGTAGTGCAGGT 59.375 47.619 0.00 0.00 43.63 4.00
118 123 6.403333 TCAGTTATGCGATTAACACTGTTC 57.597 37.500 0.00 0.00 35.05 3.18
154 159 5.471116 GCATATGCATAGAAGTTCCACATCA 59.529 40.000 22.84 0.00 41.59 3.07
594 599 6.836953 GGAGAATTTAGAGTTCTGCTTTCAC 58.163 40.000 0.93 0.00 39.87 3.18
640 645 9.855021 CTACCGTGAATTATCCTTTTTCATTTT 57.145 29.630 0.00 0.00 32.48 1.82
2139 2144 6.348498 TGTTGATTCGGATCATGAACAGTAT 58.652 36.000 7.35 0.00 41.71 2.12
2155 2160 7.349412 AGATGGTACCTACTACTGTTGATTC 57.651 40.000 14.36 0.00 0.00 2.52
2223 2228 7.876068 TCTTAACTATGTTCACCGAACTTGATT 59.124 33.333 8.23 4.34 42.39 2.57
2319 2324 8.023128 ACACGTAACGTCTAAAGCTCTAAATAA 58.977 33.333 0.00 0.00 38.32 1.40
2519 2524 8.261908 GTGTATTAATATGAACACGACGTAACC 58.738 37.037 0.00 0.00 33.60 2.85
2752 2761 1.847818 GTTTCCAAAAACCTCGGTGC 58.152 50.000 0.00 0.00 39.10 5.01
2974 2984 9.798885 CTTTTCAAACAGTTTATCGAGAACTAG 57.201 33.333 14.41 11.81 35.68 2.57
3071 3081 8.988064 TGCACTTTTGTAAAAATACTTGAACA 57.012 26.923 0.00 0.00 0.00 3.18
3457 3467 4.734398 TTGCTTCTCTTTTGCCTTTTGA 57.266 36.364 0.00 0.00 0.00 2.69
3528 3538 7.198306 AGTACACTAGTTTTCCCGATTTTTG 57.802 36.000 0.00 0.00 0.00 2.44
3923 3933 1.466866 CGCGTGACTCTGGAAATACGA 60.467 52.381 0.00 0.00 33.78 3.43
4009 4019 4.462483 GTCCACCATTATGGCTTCTTTCAA 59.538 41.667 11.72 0.00 42.67 2.69
4022 4032 3.310193 TCGGTCCATATGTCCACCATTA 58.690 45.455 13.44 0.13 34.86 1.90
4158 4168 2.363359 CTCCAGCACCTTTTTCAGCTTT 59.637 45.455 0.00 0.00 34.61 3.51
4182 4192 2.380084 TGGACAAATGCTCCTCGTAC 57.620 50.000 0.00 0.00 0.00 3.67
4660 4670 5.636123 TGGAAGTAAGTGGCAAAAGGAATA 58.364 37.500 0.00 0.00 0.00 1.75
4742 4752 5.163034 TGGTTTTTCCTTCTTGGGATGTAGA 60.163 40.000 0.00 0.00 35.07 2.59
5003 5013 1.378514 AAGCCCAATAGCACACGGG 60.379 57.895 0.00 0.00 42.03 5.28
5106 5116 2.355756 GGCACACAATTCATCGCATAGT 59.644 45.455 0.00 0.00 0.00 2.12
5152 5162 2.345991 GTACTCGGCAGGTTGGCA 59.654 61.111 3.51 0.00 43.94 4.92
5185 5195 4.235079 TGGATGGGTAATGTTCCTCTTG 57.765 45.455 0.00 0.00 0.00 3.02
5295 5305 2.273538 TGTAAAAAGGGCGGTTGCTA 57.726 45.000 0.00 0.00 42.25 3.49
5339 5349 6.465084 ACAAAAGAGGTAGTAGAACACATCC 58.535 40.000 0.00 0.00 0.00 3.51
5353 5363 6.127196 TGCAAAACAAGGATTACAAAAGAGGT 60.127 34.615 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.