Multiple sequence alignment - TraesCS1D01G164400

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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 TraesCS1D01G164400 chr1D 100.000 2303 0 0 1 2303 235548247 235545945 0.000000e+00 4253
1 TraesCS1D01G164400 chr1B 94.937 2311 84 11 1 2298 253826132 253823842 0.000000e+00 3589
2 TraesCS1D01G164400 chr1B 96.769 681 18 3 1 679 578102933 578103611 0.000000e+00 1133
3 TraesCS1D01G164400 chr5D 95.996 1873 63 7 428 2296 462907619 462909483 0.000000e+00 3033
4 TraesCS1D01G164400 chr5D 98.095 420 6 2 1 420 462906871 462907288 0.000000e+00 730
5 TraesCS1D01G164400 chr7A 94.216 1850 90 10 458 2297 439030854 439032696 0.000000e+00 2808
6 TraesCS1D01G164400 chr2B 94.472 1628 81 6 673 2297 13184003 13185624 0.000000e+00 2499
7 TraesCS1D01G164400 chr3D 95.527 1498 51 8 450 1938 143483574 143482084 0.000000e+00 2381
8 TraesCS1D01G164400 chr7D 96.301 1433 41 5 867 2297 635929324 635927902 0.000000e+00 2342
9 TraesCS1D01G164400 chr7D 97.947 682 10 3 4 682 635930006 635929326 0.000000e+00 1179
10 TraesCS1D01G164400 chr2A 95.894 1437 58 1 861 2297 441110111 441111546 0.000000e+00 2326
11 TraesCS1D01G164400 chr2A 96.916 681 18 2 1 679 441109433 441110112 0.000000e+00 1138
12 TraesCS1D01G164400 chr5B 95.338 1437 61 4 861 2297 89745418 89746848 0.000000e+00 2278
13 TraesCS1D01G164400 chr5B 96.957 493 13 2 1 493 89742448 89742938 0.000000e+00 826
14 TraesCS1D01G164400 chr4A 95.178 1431 62 3 867 2296 281593799 281592375 0.000000e+00 2254
15 TraesCS1D01G164400 chr7B 94.356 1010 37 9 1297 2297 634824607 634825605 0.000000e+00 1531
16 TraesCS1D01G164400 chr7B 94.964 278 11 2 450 724 634824331 634824608 1.260000e-117 433
17 TraesCS1D01G164400 chr6D 94.023 937 43 5 1243 2179 298130733 298129810 0.000000e+00 1408
18 TraesCS1D01G164400 chr6D 95.625 800 33 1 450 1247 298140118 298139319 0.000000e+00 1282
19 TraesCS1D01G164400 chr6B 95.395 152 7 0 1 152 1494942 1494791 2.290000e-60 243


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 TraesCS1D01G164400 chr1D 235545945 235548247 2302 True 4253.0 4253 100.0000 1 2303 1 chr1D.!!$R1 2302
1 TraesCS1D01G164400 chr1B 253823842 253826132 2290 True 3589.0 3589 94.9370 1 2298 1 chr1B.!!$R1 2297
2 TraesCS1D01G164400 chr1B 578102933 578103611 678 False 1133.0 1133 96.7690 1 679 1 chr1B.!!$F1 678
3 TraesCS1D01G164400 chr5D 462906871 462909483 2612 False 1881.5 3033 97.0455 1 2296 2 chr5D.!!$F1 2295
4 TraesCS1D01G164400 chr7A 439030854 439032696 1842 False 2808.0 2808 94.2160 458 2297 1 chr7A.!!$F1 1839
5 TraesCS1D01G164400 chr2B 13184003 13185624 1621 False 2499.0 2499 94.4720 673 2297 1 chr2B.!!$F1 1624
6 TraesCS1D01G164400 chr3D 143482084 143483574 1490 True 2381.0 2381 95.5270 450 1938 1 chr3D.!!$R1 1488
7 TraesCS1D01G164400 chr7D 635927902 635930006 2104 True 1760.5 2342 97.1240 4 2297 2 chr7D.!!$R1 2293
8 TraesCS1D01G164400 chr2A 441109433 441111546 2113 False 1732.0 2326 96.4050 1 2297 2 chr2A.!!$F1 2296
9 TraesCS1D01G164400 chr5B 89742448 89746848 4400 False 1552.0 2278 96.1475 1 2297 2 chr5B.!!$F1 2296
10 TraesCS1D01G164400 chr4A 281592375 281593799 1424 True 2254.0 2254 95.1780 867 2296 1 chr4A.!!$R1 1429
11 TraesCS1D01G164400 chr7B 634824331 634825605 1274 False 982.0 1531 94.6600 450 2297 2 chr7B.!!$F1 1847
12 TraesCS1D01G164400 chr6D 298129810 298130733 923 True 1408.0 1408 94.0230 1243 2179 1 chr6D.!!$R1 936
13 TraesCS1D01G164400 chr6D 298139319 298140118 799 True 1282.0 1282 95.6250 450 1247 1 chr6D.!!$R2 797

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
179 180 0.969894 AGTGGTGCTCTGTACTGACC 59.030 55.0 0.00 0.65 0.0 4.02 F
865 3487 1.087501 GGAACTCGAGGCAAATGTCC 58.912 55.0 18.41 7.55 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1161 3788 2.292267 CGTCCAGGGAATTCAAGATGG 58.708 52.381 7.93 9.11 0.0 3.51 R
2212 4875 1.534595 GCTACTACTACGGCGCTACAT 59.465 52.381 6.90 0.00 0.0 2.29 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
179 180 0.969894 AGTGGTGCTCTGTACTGACC 59.030 55.000 0.00 0.65 0.00 4.02
583 3203 6.976349 CCATGTTAATCAGAATGTGGTGAATG 59.024 38.462 0.00 0.00 37.40 2.67
698 3320 2.040939 TGTCGTGGAACTTTGACCCTA 58.959 47.619 0.00 0.00 31.75 3.53
814 3436 2.531771 TCTTGGTGTATTCGAGGGTGA 58.468 47.619 0.00 0.00 0.00 4.02
833 3455 8.613922 AGGGTGATTTTTGAAATCCTATTGAT 57.386 30.769 10.04 0.00 34.22 2.57
858 3480 2.631160 TTTTCAAGGAACTCGAGGCA 57.369 45.000 18.41 0.00 38.49 4.75
865 3487 1.087501 GGAACTCGAGGCAAATGTCC 58.912 55.000 18.41 7.55 0.00 4.02
1073 3700 4.042062 AGAACTTCCACATTCACTCATGGA 59.958 41.667 0.00 0.00 39.50 3.41
1391 4021 9.553064 GTCTGATCTCTACCAATATGAATTTGT 57.447 33.333 0.00 0.00 0.00 2.83
1643 4280 3.793797 AACAAGTTTTCACTTTCCCGG 57.206 42.857 0.00 0.00 40.66 5.73
1713 4361 2.042464 TGCTCTTCAACCACTCAGAGT 58.958 47.619 0.00 0.00 36.02 3.24
1723 4371 1.157585 CACTCAGAGTCGGACTTCGA 58.842 55.000 12.67 10.64 46.77 3.71
1844 4492 2.047655 GATTCGTGTCCACCGGCA 60.048 61.111 0.00 0.00 0.00 5.69
1979 4627 9.396022 GTTAAATGGAATCTTGAGATGGTTCTA 57.604 33.333 0.00 0.00 34.49 2.10
2003 4652 0.107945 TTGGTTTGGTTTGCACTGGC 60.108 50.000 0.00 0.00 41.68 4.85
2008 4657 1.448922 TTGGTTTGCACTGGCCGTAC 61.449 55.000 0.00 0.00 40.13 3.67
2147 4808 1.105167 TAGTAGTAGCGCGGGTGCAT 61.105 55.000 8.83 0.00 42.97 3.96
2212 4875 5.728351 ACGCGCTATTGCTAAAAATTAGA 57.272 34.783 5.73 0.00 36.97 2.10
2226 4889 4.317671 AAATTAGATGTAGCGCCGTAGT 57.682 40.909 2.29 0.00 0.00 2.73
2298 4964 6.752168 TGGTAGTGTTTTTCCTAGTAGTGTC 58.248 40.000 0.00 0.00 0.00 3.67
2299 4965 6.552350 TGGTAGTGTTTTTCCTAGTAGTGTCT 59.448 38.462 0.00 0.00 0.00 3.41
2300 4966 6.867293 GGTAGTGTTTTTCCTAGTAGTGTCTG 59.133 42.308 0.00 0.00 0.00 3.51
2301 4967 5.855045 AGTGTTTTTCCTAGTAGTGTCTGG 58.145 41.667 0.00 0.00 0.00 3.86
2302 4968 4.995487 GTGTTTTTCCTAGTAGTGTCTGGG 59.005 45.833 0.00 0.00 37.41 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
425 426 3.825014 TGGCGGATCTAGGATTACACTAC 59.175 47.826 0.00 0.00 0.00 2.73
658 3280 8.746751 CACGACATATAGAACATCTACAAAGTG 58.253 37.037 0.00 0.00 30.79 3.16
833 3455 6.882140 TGCCTCGAGTTCCTTGAAAAATATTA 59.118 34.615 12.31 0.00 0.00 0.98
858 3480 2.554370 TCTTCGAAACCGGGACATTT 57.446 45.000 6.32 0.00 0.00 2.32
865 3487 1.508632 TTCTGCTTCTTCGAAACCGG 58.491 50.000 0.00 0.00 0.00 5.28
958 3583 4.573201 GGCAACATTGGATCCAAATGAATG 59.427 41.667 30.28 23.99 39.55 2.67
1095 3722 6.037940 CCAGATGTCTGAAACCAATGATACAG 59.962 42.308 11.47 0.00 46.59 2.74
1161 3788 2.292267 CGTCCAGGGAATTCAAGATGG 58.708 52.381 7.93 9.11 0.00 3.51
1376 4006 5.245751 TGCCAACAGACAAATTCATATTGGT 59.754 36.000 0.00 0.00 38.09 3.67
1391 4021 4.314740 GGTAACAACAAATGCCAACAGA 57.685 40.909 0.00 0.00 0.00 3.41
1417 4048 6.515272 TTCTAAATGGCTGAAAAGTGATCC 57.485 37.500 0.00 0.00 0.00 3.36
1539 4170 4.510038 AAGCTCAATGTCAAACATCACC 57.490 40.909 0.00 0.00 37.97 4.02
1643 4280 4.783621 TCACCTCTGCGCCCATGC 62.784 66.667 4.18 0.00 0.00 4.06
1790 4438 4.477975 GCGTCGAGGTCCTCCACG 62.478 72.222 28.52 28.52 45.11 4.94
1844 4492 4.873010 TCTACAAGGCTAGGAGTTCAGAT 58.127 43.478 0.00 0.00 0.00 2.90
1979 4627 2.765699 AGTGCAAACCAAACCAACTCAT 59.234 40.909 0.00 0.00 0.00 2.90
2003 4652 5.769484 AGTACTCATGAATGGTAGTACGG 57.231 43.478 12.42 0.00 45.70 4.02
2147 4808 5.739161 GCTAAAAAGTTAGTAGTAGCGCGTA 59.261 40.000 8.43 0.00 39.23 4.42
2212 4875 1.534595 GCTACTACTACGGCGCTACAT 59.465 52.381 6.90 0.00 0.00 2.29
2226 4889 1.759299 ATGGGTTCCCGCGCTACTA 60.759 57.895 5.56 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.