Multiple sequence alignment - TraesCS1D01G170700

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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 TraesCS1D01G170700 chr1D 100.000 2144 0 0 1 2144 244423814 244421671 0.000000e+00 3960
1 TraesCS1D01G170700 chr1D 97.158 2146 53 6 1 2144 244408277 244406138 0.000000e+00 3618
2 TraesCS1D01G170700 chr1D 96.970 2145 59 5 1 2144 244401826 244399687 0.000000e+00 3596
3 TraesCS1D01G170700 chr1D 94.196 2171 95 11 1 2144 254489361 254487195 0.000000e+00 3282
4 TraesCS1D01G170700 chr2D 95.060 2166 80 10 1 2144 628285329 628283169 0.000000e+00 3382
5 TraesCS1D01G170700 chr2D 94.023 1623 66 13 1 1601 334225585 334223972 0.000000e+00 2431
6 TraesCS1D01G170700 chr3D 94.101 2170 97 12 1 2144 21897220 21895056 0.000000e+00 3269
7 TraesCS1D01G170700 chr3B 93.850 2179 93 16 1 2144 201506239 201504067 0.000000e+00 3243
8 TraesCS1D01G170700 chr3B 94.355 124 6 1 51 174 21016929 21017051 2.810000e-44 189
9 TraesCS1D01G170700 chr6D 94.881 2051 83 9 1 2036 431399690 431397647 0.000000e+00 3186
10 TraesCS1D01G170700 chr2A 93.300 2179 106 15 1 2144 276441413 276443586 0.000000e+00 3179
11 TraesCS1D01G170700 chr5A 93.213 2166 107 16 1 2144 684325248 684323101 0.000000e+00 3149
12 TraesCS1D01G170700 chr1A 94.588 1940 78 10 227 2144 554465601 554467535 0.000000e+00 2976
13 TraesCS1D01G170700 chr5D 93.516 694 26 5 1466 2144 6209465 6210154 0.000000e+00 1014
14 TraesCS1D01G170700 chrUn 91.647 419 18 4 1741 2144 390489169 390489585 3.990000e-157 564
15 TraesCS1D01G170700 chr6A 91.990 412 17 4 1747 2144 592890529 592890938 3.990000e-157 564
16 TraesCS1D01G170700 chr1B 89.811 265 14 2 1893 2144 633726824 633726560 5.710000e-86 327
17 TraesCS1D01G170700 chr4B 88.341 223 12 3 1935 2144 288361966 288361745 2.730000e-64 255
18 TraesCS1D01G170700 chr2B 98.020 101 2 0 29 129 655916504 655916404 2.190000e-40 176
19 TraesCS1D01G170700 chr2B 86.713 143 6 5 94 223 482854069 482853927 1.710000e-31 147


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 TraesCS1D01G170700 chr1D 244421671 244423814 2143 True 3960 3960 100.000 1 2144 1 chr1D.!!$R3 2143
1 TraesCS1D01G170700 chr1D 244406138 244408277 2139 True 3618 3618 97.158 1 2144 1 chr1D.!!$R2 2143
2 TraesCS1D01G170700 chr1D 244399687 244401826 2139 True 3596 3596 96.970 1 2144 1 chr1D.!!$R1 2143
3 TraesCS1D01G170700 chr1D 254487195 254489361 2166 True 3282 3282 94.196 1 2144 1 chr1D.!!$R4 2143
4 TraesCS1D01G170700 chr2D 628283169 628285329 2160 True 3382 3382 95.060 1 2144 1 chr2D.!!$R2 2143
5 TraesCS1D01G170700 chr2D 334223972 334225585 1613 True 2431 2431 94.023 1 1601 1 chr2D.!!$R1 1600
6 TraesCS1D01G170700 chr3D 21895056 21897220 2164 True 3269 3269 94.101 1 2144 1 chr3D.!!$R1 2143
7 TraesCS1D01G170700 chr3B 201504067 201506239 2172 True 3243 3243 93.850 1 2144 1 chr3B.!!$R1 2143
8 TraesCS1D01G170700 chr6D 431397647 431399690 2043 True 3186 3186 94.881 1 2036 1 chr6D.!!$R1 2035
9 TraesCS1D01G170700 chr2A 276441413 276443586 2173 False 3179 3179 93.300 1 2144 1 chr2A.!!$F1 2143
10 TraesCS1D01G170700 chr5A 684323101 684325248 2147 True 3149 3149 93.213 1 2144 1 chr5A.!!$R1 2143
11 TraesCS1D01G170700 chr1A 554465601 554467535 1934 False 2976 2976 94.588 227 2144 1 chr1A.!!$F1 1917
12 TraesCS1D01G170700 chr5D 6209465 6210154 689 False 1014 1014 93.516 1466 2144 1 chr5D.!!$F1 678

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
708 725 1.202734 TCGCGGACTAGCTGTACCTAT 60.203 52.381 6.13 0.0 34.4 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1939 1984 0.107848 AGGTCCCGGCATTTCTTACG 60.108 55.0 0.0 0.0 0.0 3.18 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
208 223 3.809279 CCAGGCAAAACCAGATTTTTGTC 59.191 43.478 5.05 5.05 46.81 3.18
261 277 7.465513 CGCTATACTCAAAATACACCTTTGGTC 60.466 40.741 0.00 0.00 35.03 4.02
279 295 6.477053 TTGGTCCAAAATTGACAATCTCAA 57.523 33.333 0.40 0.00 43.28 3.02
511 528 4.463539 TCAGTACGGGTTTAGCTTATGACA 59.536 41.667 0.00 0.00 0.00 3.58
566 583 2.159382 GGAAAGCCGACAAGGAATTCA 58.841 47.619 7.93 0.00 45.00 2.57
657 674 4.948847 TCAATGACCATAGATCGAACCTG 58.051 43.478 0.00 0.00 0.00 4.00
662 679 2.695666 ACCATAGATCGAACCTGTCCTG 59.304 50.000 0.00 0.00 0.00 3.86
690 707 1.595109 TGCGATGGCTGGCTATTCG 60.595 57.895 14.04 14.04 40.82 3.34
708 725 1.202734 TCGCGGACTAGCTGTACCTAT 60.203 52.381 6.13 0.00 34.40 2.57
811 829 4.054671 TCAAACCCGAATGAACAAAATGC 58.945 39.130 0.00 0.00 0.00 3.56
1165 1184 4.585162 AGTAATCGGAGGGACTAGATTGTG 59.415 45.833 0.00 0.00 42.75 3.33
1224 1243 4.322349 CCCCTTTATCTGATTAGAGCGGAG 60.322 50.000 0.00 0.00 36.14 4.63
1329 1348 8.049655 TCACTCGAGGATCTAATATCTCATTG 57.950 38.462 18.41 0.00 0.00 2.82
1432 1464 6.731292 AGCCTAAAAGAAAACCTTCAATGT 57.269 33.333 0.00 0.00 33.02 2.71
1435 1467 8.141909 AGCCTAAAAGAAAACCTTCAATGTAAC 58.858 33.333 0.00 0.00 33.02 2.50
1443 1475 9.185680 AGAAAACCTTCAATGTAACAGTTTACT 57.814 29.630 0.00 0.00 35.39 2.24
1547 1584 1.133915 TGTCCCCCGCCATATTTTCTC 60.134 52.381 0.00 0.00 0.00 2.87
1654 1695 9.765795 ATAGTAATCTTTGACGAATTAGGAAGG 57.234 33.333 0.00 0.00 0.00 3.46
1791 1832 2.489938 ATTGTTCTCGCCTTTGCCTA 57.510 45.000 0.00 0.00 0.00 3.93
1939 1984 8.593492 AATCAAAGCTTTTTACCAACTTGATC 57.407 30.769 9.53 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
208 223 9.440761 AATTAGTATAGCTATCCTTCCTATGGG 57.559 37.037 10.16 0.00 0.00 4.00
261 277 7.874016 TCATCCTTTTGAGATTGTCAATTTTGG 59.126 33.333 0.00 0.00 44.89 3.28
511 528 1.075374 TGGCCTAGGACTTGCAAACAT 59.925 47.619 17.75 0.00 0.00 2.71
566 583 6.652062 AGAATCAAAACGGTCGGTTATTAACT 59.348 34.615 6.52 0.00 38.08 2.24
614 631 3.580895 GAGGGCCTCCTAAAAGGATCTAG 59.419 52.174 23.49 0.00 44.81 2.43
657 674 3.364964 CCATCGCACTGTAAAAACAGGAC 60.365 47.826 10.08 1.19 41.76 3.85
662 679 2.584791 CAGCCATCGCACTGTAAAAAC 58.415 47.619 0.00 0.00 37.52 2.43
690 707 3.410508 ACTATAGGTACAGCTAGTCCGC 58.589 50.000 4.43 0.00 0.00 5.54
708 725 9.973661 TTGATATTGATCCCAAGAAAAAGACTA 57.026 29.630 0.00 0.00 35.48 2.59
811 829 8.353684 AGTATAGACTGGTACGATTCAATTCAG 58.646 37.037 0.00 0.00 33.41 3.02
925 944 8.794335 GGATGGTATCCTTCCAATTTAGATAC 57.206 38.462 13.53 0.00 44.38 2.24
1067 1086 2.691526 CCAATCACAGCAATACCAGCAT 59.308 45.455 0.00 0.00 0.00 3.79
1068 1087 2.093890 CCAATCACAGCAATACCAGCA 58.906 47.619 0.00 0.00 0.00 4.41
1224 1243 1.399440 GTAAAAATTCCGCGGGTCCTC 59.601 52.381 27.83 5.05 0.00 3.71
1282 1301 6.636044 GTGATCTCTTTTTCTTGTTGCTTCAG 59.364 38.462 0.00 0.00 0.00 3.02
1325 1344 3.951979 GGATACTTCCTTCGTGCAATG 57.048 47.619 0.00 0.00 39.14 2.82
1403 1422 6.264518 TGAAGGTTTTCTTTTAGGCTAGTTGG 59.735 38.462 0.00 0.00 35.50 3.77
1547 1584 1.003233 GTAGTGGACAAACAGAGGGGG 59.997 57.143 0.00 0.00 0.00 5.40
1767 1808 3.673338 GGCAAAGGCGAGAACAATAAAAC 59.327 43.478 0.00 0.00 42.47 2.43
1791 1832 4.021916 CCCATGCAAAAGAAGAGAATCCT 58.978 43.478 0.00 0.00 33.66 3.24
1918 1963 6.144078 ACGATCAAGTTGGTAAAAAGCTTT 57.856 33.333 5.69 5.69 0.00 3.51
1939 1984 0.107848 AGGTCCCGGCATTTCTTACG 60.108 55.000 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.