Multiple sequence alignment - TraesCS3A01G188200

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 TraesCS3A01G188200 chr3A 100.000 2159 0 0 1 2159 227638789 227636631 0 3988
1 TraesCS3A01G188200 chr7A 97.817 1145 17 1 3 1147 4953895 4952759 0 1969
2 TraesCS3A01G188200 chr7A 97.366 1139 20 1 3 1141 120911777 120912905 0 1929
3 TraesCS3A01G188200 chr7A 97.366 1139 20 1 3 1141 671946621 671947749 0 1929
4 TraesCS3A01G188200 chr7A 98.242 1024 18 0 1136 2159 671947791 671948814 0 1792
5 TraesCS3A01G188200 chr7A 98.145 1024 19 0 1136 2159 4952723 4951700 0 1786
6 TraesCS3A01G188200 chr5A 97.629 1139 17 1 3 1141 600285676 600286804 0 1945
7 TraesCS3A01G188200 chr5A 97.278 1139 21 4 3 1141 16608876 16610004 0 1923
8 TraesCS3A01G188200 chr5A 97.031 1145 23 2 3 1147 300062909 300061776 0 1916
9 TraesCS3A01G188200 chr5A 98.535 1024 15 0 1136 2159 300061740 300060717 0 1808
10 TraesCS3A01G188200 chr5A 98.438 1024 16 0 1136 2159 16610046 16611069 0 1803
11 TraesCS3A01G188200 chr5A 98.145 1024 19 0 1136 2159 600286846 600287869 0 1786
12 TraesCS3A01G188200 chr6A 97.293 1145 21 1 3 1147 289157052 289155918 0 1934
13 TraesCS3A01G188200 chr6A 96.856 1145 26 1 3 1147 289122679 289121545 0 1906
14 TraesCS3A01G188200 chr6A 98.145 1024 19 0 1136 2159 289121509 289120486 0 1786
15 TraesCS3A01G188200 chr6A 97.949 1024 21 0 1136 2159 289155882 289154859 0 1775
16 TraesCS3A01G188200 chr7B 97.205 1145 22 1 3 1147 743080234 743079100 0 1929
17 TraesCS3A01G188200 chr7B 98.242 1024 18 0 1136 2159 743079064 743078041 0 1792
18 TraesCS3A01G188200 chr6B 97.191 1139 22 1 3 1141 394436892 394438020 0 1917
19 TraesCS3A01G188200 chr4D 96.943 1145 24 2 3 1147 123406919 123405786 0 1910
20 TraesCS3A01G188200 chr5B 97.015 1139 24 1 3 1141 713031872 713033000 0 1906
21 TraesCS3A01G188200 chr3B 98.242 1024 18 0 1136 2159 92192471 92191448 0 1792


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 TraesCS3A01G188200 chr3A 227636631 227638789 2158 True 3988.0 3988 100.0000 1 2159 1 chr3A.!!$R1 2158
1 TraesCS3A01G188200 chr7A 120911777 120912905 1128 False 1929.0 1929 97.3660 3 1141 1 chr7A.!!$F1 1138
2 TraesCS3A01G188200 chr7A 4951700 4953895 2195 True 1877.5 1969 97.9810 3 2159 2 chr7A.!!$R1 2156
3 TraesCS3A01G188200 chr7A 671946621 671948814 2193 False 1860.5 1929 97.8040 3 2159 2 chr7A.!!$F2 2156
4 TraesCS3A01G188200 chr5A 600285676 600287869 2193 False 1865.5 1945 97.8870 3 2159 2 chr5A.!!$F2 2156
5 TraesCS3A01G188200 chr5A 16608876 16611069 2193 False 1863.0 1923 97.8580 3 2159 2 chr5A.!!$F1 2156
6 TraesCS3A01G188200 chr5A 300060717 300062909 2192 True 1862.0 1916 97.7830 3 2159 2 chr5A.!!$R1 2156
7 TraesCS3A01G188200 chr6A 289154859 289157052 2193 True 1854.5 1934 97.6210 3 2159 2 chr6A.!!$R2 2156
8 TraesCS3A01G188200 chr6A 289120486 289122679 2193 True 1846.0 1906 97.5005 3 2159 2 chr6A.!!$R1 2156
9 TraesCS3A01G188200 chr7B 743078041 743080234 2193 True 1860.5 1929 97.7235 3 2159 2 chr7B.!!$R1 2156
10 TraesCS3A01G188200 chr6B 394436892 394438020 1128 False 1917.0 1917 97.1910 3 1141 1 chr6B.!!$F1 1138
11 TraesCS3A01G188200 chr4D 123405786 123406919 1133 True 1910.0 1910 96.9430 3 1147 1 chr4D.!!$R1 1144
12 TraesCS3A01G188200 chr5B 713031872 713033000 1128 False 1906.0 1906 97.0150 3 1141 1 chr5B.!!$F1 1138
13 TraesCS3A01G188200 chr3B 92191448 92192471 1023 True 1792.0 1792 98.2420 1136 2159 1 chr3B.!!$R1 1023

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
319 320 1.070786 CAACACCACGTAGGGCAGT 59.929 57.895 8.57 0.0 43.89 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1277 1373 2.443394 TTGCTCGATGGCTAGGGGG 61.443 63.158 0.0 0.0 0.0 5.4 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
110 111 8.902540 ATCAAACTAGTTATGTTGACAGACAA 57.097 30.769 8.92 0.0 36.02 3.18
319 320 1.070786 CAACACCACGTAGGGCAGT 59.929 57.895 8.57 0.0 43.89 4.40
557 558 5.185454 TGCTACTTTCAGAGAGAGAGAGAG 58.815 45.833 0.00 0.0 32.94 3.20
558 559 5.045942 TGCTACTTTCAGAGAGAGAGAGAGA 60.046 44.000 0.00 0.0 32.94 3.10
559 560 5.525378 GCTACTTTCAGAGAGAGAGAGAGAG 59.475 48.000 0.00 0.0 32.94 3.20
560 561 5.762179 ACTTTCAGAGAGAGAGAGAGAGA 57.238 43.478 0.00 0.0 32.94 3.10
561 562 5.738909 ACTTTCAGAGAGAGAGAGAGAGAG 58.261 45.833 0.00 0.0 32.94 3.20
562 563 5.485353 ACTTTCAGAGAGAGAGAGAGAGAGA 59.515 44.000 0.00 0.0 32.94 3.10
563 564 5.604758 TTCAGAGAGAGAGAGAGAGAGAG 57.395 47.826 0.00 0.0 0.00 3.20
564 565 4.871822 TCAGAGAGAGAGAGAGAGAGAGA 58.128 47.826 0.00 0.0 0.00 3.10
576 577 5.364446 AGAGAGAGAGAGAATAGGTCGTACA 59.636 44.000 0.00 0.0 0.00 2.90
624 625 4.196971 GTCCCATTGCGGAGTAGTTAAAT 58.803 43.478 0.00 0.0 36.56 1.40
690 691 5.785243 AGCTTACTAGAACTTCAACCTCAC 58.215 41.667 0.00 0.0 0.00 3.51
746 747 8.287904 TGAACCTATTCTATGGATAAATGGGT 57.712 34.615 0.00 0.0 43.56 4.51
771 772 1.902508 TCTGTCTCCTAAGGGCAACTG 59.097 52.381 0.00 0.0 0.00 3.16
805 806 2.039216 TCTTTCAAGAATGCGGGTACCA 59.961 45.455 15.35 0.0 39.83 3.25
884 886 4.319984 GGAAAAACGTCGGCTAAAGAACAT 60.320 41.667 0.00 0.0 0.00 2.71
927 929 2.093128 GCCCCGAAAGAAAGTGGATCTA 60.093 50.000 0.00 0.0 0.00 1.98
1131 1133 4.759693 AGCAATCAAACGGACATTTCTACA 59.240 37.500 0.00 0.0 0.00 2.74
1390 1486 4.792068 TGGTGGATCTTGTCTGTTCTTTT 58.208 39.130 0.00 0.0 0.00 2.27
1465 1561 5.451937 CGTATCTTTAGACCATTCAGAGCCA 60.452 44.000 0.00 0.0 0.00 4.75
1557 1653 5.289675 CGTGTTATTGGCTAGAGAAAGACAG 59.710 44.000 0.00 0.0 35.44 3.51
1573 1669 6.321690 AGAAAGACAGCCGATTGTACTACTAT 59.678 38.462 0.00 0.0 0.00 2.12
1592 1688 6.083487 ACTATAGTGTTGAGTACCCCAGTA 57.917 41.667 4.10 0.0 0.00 2.74
1642 1738 3.455910 CTCAGGAGTGGTGGAATGGATTA 59.544 47.826 0.00 0.0 0.00 1.75
1929 2025 2.271777 TGGATTCTTTCCCCGGTAGTT 58.728 47.619 0.00 0.0 44.77 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.220206 CCAGTCGATGAGCCTGCTT 59.780 57.895 0.00 0.0 0.00 3.91
1 2 1.986757 ACCAGTCGATGAGCCTGCT 60.987 57.895 0.00 0.0 0.00 4.24
110 111 6.238897 CGAACATCTGCTTCTATAGGAGTTCT 60.239 42.308 9.87 0.0 42.52 3.01
235 236 8.832735 TCCAAAGGATTTAGGTATTTGACTAGT 58.167 33.333 0.00 0.0 35.03 2.57
319 320 2.209064 GAGGCTAGTTCGCGTGGACA 62.209 60.000 10.62 0.0 0.00 4.02
473 474 5.470437 CCTAGTTCGAAAGCTTTTCCTTCTT 59.530 40.000 14.05 0.0 0.00 2.52
557 558 6.267070 CCTTTTGTACGACCTATTCTCTCTC 58.733 44.000 0.00 0.0 0.00 3.20
558 559 5.127356 CCCTTTTGTACGACCTATTCTCTCT 59.873 44.000 0.00 0.0 0.00 3.10
559 560 5.349809 CCCTTTTGTACGACCTATTCTCTC 58.650 45.833 0.00 0.0 0.00 3.20
560 561 4.161754 CCCCTTTTGTACGACCTATTCTCT 59.838 45.833 0.00 0.0 0.00 3.10
561 562 4.161001 TCCCCTTTTGTACGACCTATTCTC 59.839 45.833 0.00 0.0 0.00 2.87
562 563 4.081254 GTCCCCTTTTGTACGACCTATTCT 60.081 45.833 0.00 0.0 0.00 2.40
563 564 4.186926 GTCCCCTTTTGTACGACCTATTC 58.813 47.826 0.00 0.0 0.00 1.75
564 565 3.054875 GGTCCCCTTTTGTACGACCTATT 60.055 47.826 6.60 0.0 39.94 1.73
576 577 0.482887 CTCAAGGTGGGTCCCCTTTT 59.517 55.000 5.13 0.0 40.35 2.27
690 691 4.897224 AGACGCATTGATGTTAATGAACG 58.103 39.130 0.00 0.0 39.79 3.95
746 747 2.023404 TGCCCTTAGGAGACAGATGGTA 60.023 50.000 0.00 0.0 33.47 3.25
771 772 6.405278 TTCTTGAAAGAAAAAGGGATGGAC 57.595 37.500 3.00 0.0 41.75 4.02
805 806 7.420800 GCATATTTCACTTGCTTTGCTACTAT 58.579 34.615 0.00 0.0 33.61 2.12
884 886 8.107095 GGGGCCATCAATACAATAGAATAGTTA 58.893 37.037 4.39 0.0 0.00 2.24
1131 1133 4.163427 TCCTGGATTGAGAGAGTTCACTT 58.837 43.478 0.00 0.0 0.00 3.16
1277 1373 2.443394 TTGCTCGATGGCTAGGGGG 61.443 63.158 0.00 0.0 0.00 5.40
1390 1486 5.870433 TCACTCGTTTGTAGAAACACTTTCA 59.130 36.000 15.04 0.0 41.48 2.69
1465 1561 7.906327 ACTAAATCCCAACACTTAATGCAAAT 58.094 30.769 0.00 0.0 0.00 2.32
1557 1653 6.732154 TCAACACTATAGTAGTACAATCGGC 58.268 40.000 4.74 0.0 37.23 5.54
1573 1669 3.094572 GCTACTGGGGTACTCAACACTA 58.905 50.000 0.00 0.0 0.00 2.74


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

AutoCloner maintained by Alex Coulton.