Multiple sequence alignment - TraesCS4B01G146400

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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 TraesCS4B01G146400 chr4B 100.000 2303 0 0 1 2303 209117175 209114873 0.000000e+00 4253
1 TraesCS4B01G146400 chr4B 97.509 2248 44 1 68 2303 495577652 495579899 0.000000e+00 3831
2 TraesCS4B01G146400 chr2B 97.999 2249 32 2 68 2303 449208733 449210981 0.000000e+00 3892
3 TraesCS4B01G146400 chr2B 97.865 2248 36 1 68 2303 234530565 234532812 0.000000e+00 3875
4 TraesCS4B01G146400 chr3A 97.865 2248 36 1 68 2303 495091945 495094192 0.000000e+00 3875
5 TraesCS4B01G146400 chr3A 98.571 70 1 0 1 70 495091811 495091880 8.640000e-25 124
6 TraesCS4B01G146400 chr7A 97.575 2268 39 5 51 2303 60220151 60222417 0.000000e+00 3869
7 TraesCS4B01G146400 chr3B 97.777 2249 37 2 68 2303 6000171 6002419 0.000000e+00 3864
8 TraesCS4B01G146400 chr3B 98.751 881 11 0 1423 2303 101914993 101915873 0.000000e+00 1567
9 TraesCS4B01G146400 chr1B 97.374 2247 47 1 68 2302 619184736 619186982 0.000000e+00 3812
10 TraesCS4B01G146400 chr2D 95.687 2249 89 5 61 2303 377991109 377988863 0.000000e+00 3609
11 TraesCS4B01G146400 chr2D 98.571 70 1 0 1 70 18022931 18022862 8.640000e-25 124
12 TraesCS4B01G146400 chrUn 97.433 1714 31 2 68 1768 231559555 231561268 0.000000e+00 2909
13 TraesCS4B01G146400 chrUn 97.791 1313 17 1 1003 2303 403938465 403937153 0.000000e+00 2254
14 TraesCS4B01G146400 chrUn 98.571 70 1 0 1 70 231559421 231559490 8.640000e-25 124
15 TraesCS4B01G146400 chrUn 98.571 70 1 0 1 70 273328706 273328637 8.640000e-25 124
16 TraesCS4B01G146400 chr7D 97.371 1141 29 1 1163 2303 307137134 307138273 0.000000e+00 1940
17 TraesCS4B01G146400 chr7D 98.571 70 1 0 1 70 6942803 6942734 8.640000e-25 124
18 TraesCS4B01G146400 chr7D 98.571 70 1 0 1 70 307131317 307131386 8.640000e-25 124
19 TraesCS4B01G146400 chr6D 98.571 70 1 0 1 70 458917617 458917686 8.640000e-25 124
20 TraesCS4B01G146400 chr6B 98.571 70 1 0 1 70 311356762 311356693 8.640000e-25 124
21 TraesCS4B01G146400 chr3D 98.571 70 1 0 1 70 48694895 48694826 8.640000e-25 124


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 TraesCS4B01G146400 chr4B 209114873 209117175 2302 True 4253.0 4253 100.000 1 2303 1 chr4B.!!$R1 2302
1 TraesCS4B01G146400 chr4B 495577652 495579899 2247 False 3831.0 3831 97.509 68 2303 1 chr4B.!!$F1 2235
2 TraesCS4B01G146400 chr2B 449208733 449210981 2248 False 3892.0 3892 97.999 68 2303 1 chr2B.!!$F2 2235
3 TraesCS4B01G146400 chr2B 234530565 234532812 2247 False 3875.0 3875 97.865 68 2303 1 chr2B.!!$F1 2235
4 TraesCS4B01G146400 chr3A 495091811 495094192 2381 False 1999.5 3875 98.218 1 2303 2 chr3A.!!$F1 2302
5 TraesCS4B01G146400 chr7A 60220151 60222417 2266 False 3869.0 3869 97.575 51 2303 1 chr7A.!!$F1 2252
6 TraesCS4B01G146400 chr3B 6000171 6002419 2248 False 3864.0 3864 97.777 68 2303 1 chr3B.!!$F1 2235
7 TraesCS4B01G146400 chr3B 101914993 101915873 880 False 1567.0 1567 98.751 1423 2303 1 chr3B.!!$F2 880
8 TraesCS4B01G146400 chr1B 619184736 619186982 2246 False 3812.0 3812 97.374 68 2302 1 chr1B.!!$F1 2234
9 TraesCS4B01G146400 chr2D 377988863 377991109 2246 True 3609.0 3609 95.687 61 2303 1 chr2D.!!$R2 2242
10 TraesCS4B01G146400 chrUn 403937153 403938465 1312 True 2254.0 2254 97.791 1003 2303 1 chrUn.!!$R2 1300
11 TraesCS4B01G146400 chrUn 231559421 231561268 1847 False 1516.5 2909 98.002 1 1768 2 chrUn.!!$F1 1767
12 TraesCS4B01G146400 chr7D 307137134 307138273 1139 False 1940.0 1940 97.371 1163 2303 1 chr7D.!!$F2 1140


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
289 357 1.000866 GCCCTTCAATGCCTCCCTT 59.999 57.895 0.0 0.0 0.0 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2071 2159 1.549203 ATTCTGGTGTGGATGGCAAC 58.451 50.0 0.0 0.0 0.0 4.17 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
129 197 7.815068 GTCTAAGCGACATATGGATCAATAAGT 59.185 37.037 7.80 0.00 42.37 2.24
289 357 1.000866 GCCCTTCAATGCCTCCCTT 59.999 57.895 0.00 0.00 0.00 3.95
311 379 2.623889 CGGATCCACTAACTCGGAAGAT 59.376 50.000 13.41 0.00 40.84 2.40
592 661 1.813192 GAGAGGAGCTCCGTGAAGG 59.187 63.158 26.95 0.00 42.08 3.46
857 930 6.976925 GCAAGAGAAAGATGGAATTTGGTATG 59.023 38.462 0.00 0.00 0.00 2.39
862 935 7.589993 AGAAAGATGGAATTTGGTATGAGGAT 58.410 34.615 0.00 0.00 0.00 3.24
968 1044 6.536941 GGACTTCTTTCTAAGCCTCACATAAG 59.463 42.308 0.00 0.00 0.00 1.73
1001 1077 5.009631 TCTGACATTCCATGTTTCCGAAAT 58.990 37.500 0.00 0.00 45.03 2.17
1122 1198 7.554211 TGCCAATTGAATCAATGTTATTAGCA 58.446 30.769 9.47 8.10 34.04 3.49
1330 1406 9.751542 CATAACTACAGGAGAGTTACCAAATAG 57.248 37.037 0.00 0.00 41.07 1.73
1339 1415 9.322769 AGGAGAGTTACCAAATAGAAAGTTCTA 57.677 33.333 3.33 3.33 43.35 2.10
1486 1574 5.104941 TCGATTCAATAGAAGCCCAAAGAGA 60.105 40.000 0.00 0.00 36.84 3.10
1742 1830 0.670162 CTAGCGCCCATTCCCATTTG 59.330 55.000 2.29 0.00 0.00 2.32
1937 2025 6.210584 TGGAATTGTTTGATCTTAAAGGGGAC 59.789 38.462 0.00 0.00 0.00 4.46
1959 2047 9.569122 GGGACCTTCTATAATTTAGCACATAAA 57.431 33.333 0.00 0.00 37.75 1.40
2071 2159 5.200483 TGAAACCAAGAAATATAGGCCTGG 58.800 41.667 17.99 8.06 0.00 4.45
2104 2192 7.400339 TCCACACCAGAATAGATAGAGTTTTCT 59.600 37.037 0.00 0.00 37.46 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 1.737793 GAGCAATCAACGAATTCCGGT 59.262 47.619 0.00 0.00 43.93 5.28
289 357 2.022195 CTTCCGAGTTAGTGGATCCGA 58.978 52.381 7.39 0.00 33.42 4.55
311 379 5.182001 GTCAGCCAGAAAAGCTTTGAATAGA 59.818 40.000 13.54 2.95 38.95 1.98
489 558 8.980481 TTTTGTAGAGAACTTTCCTCTCAAAT 57.020 30.769 1.07 0.00 41.58 2.32
657 726 2.037772 GTCTGTTCAGGAGCTCCTTCAA 59.962 50.000 33.33 24.03 46.09 2.69
857 930 1.737793 ACGCGTTTGATTTCCATCCTC 59.262 47.619 5.58 0.00 0.00 3.71
862 935 2.853731 AACAACGCGTTTGATTTCCA 57.146 40.000 24.21 0.00 38.73 3.53
1239 1315 5.404946 CCTCGGACTCGAAAAGTAATAACA 58.595 41.667 0.00 0.00 45.47 2.41
1330 1406 9.145865 AGAGAACGAAATGAGAATAGAACTTTC 57.854 33.333 0.00 0.00 0.00 2.62
1358 1434 6.877236 TGACTCAGGCAAAAAGAAAAGAAAT 58.123 32.000 0.00 0.00 0.00 2.17
1742 1830 1.700955 TAGTAGATCTGTTCCGCCCC 58.299 55.000 5.18 0.00 0.00 5.80
1937 2025 9.574516 ACCCTTTATGTGCTAAATTATAGAAGG 57.425 33.333 0.00 0.00 0.00 3.46
1959 2047 4.077108 GGACGAAACCAAGAAATAACCCT 58.923 43.478 0.00 0.00 0.00 4.34
2071 2159 1.549203 ATTCTGGTGTGGATGGCAAC 58.451 50.000 0.00 0.00 0.00 4.17
2104 2192 2.303022 CCTCCACTAGCAGGTTTCTTCA 59.697 50.000 2.09 0.00 0.00 3.02



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

AutoCloner maintained by Alex Coulton.