Multiple sequence alignment - TraesCS4D01G146400

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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 TraesCS4D01G146400 chr4D 100.000 2356 0 0 1 2356 135006221 135003866 0 4351
1 TraesCS4D01G146400 chr4D 97.457 2359 56 4 1 2356 483696359 483698716 0 4021
2 TraesCS4D01G146400 chr4D 96.058 2359 88 5 1 2356 241143245 241140889 0 3836
3 TraesCS4D01G146400 chr5D 95.589 2358 101 3 1 2356 79865255 79867611 0 3775
4 TraesCS4D01G146400 chr5D 93.896 2359 136 7 3 2356 197839898 197837543 0 3552
5 TraesCS4D01G146400 chr7D 97.772 1885 39 3 1 1882 579015578 579017462 0 3245
6 TraesCS4D01G146400 chr6B 95.530 2036 74 8 1 2026 53079007 53081035 0 3240
7 TraesCS4D01G146400 chrUn 97.666 1885 38 4 1 1882 237257830 237255949 0 3232
8 TraesCS4D01G146400 chr7A 97.418 1898 47 2 1 1896 563531481 563529584 0 3232
9 TraesCS4D01G146400 chr7A 98.193 498 9 0 1859 2356 4954288 4954785 0 870
10 TraesCS4D01G146400 chr3A 97.367 1899 47 3 1 1896 191855549 191857447 0 3227
11 TraesCS4D01G146400 chr1D 97.352 793 20 1 1565 2356 185763599 185764391 0 1347
12 TraesCS4D01G146400 chr5B 95.369 799 36 1 1559 2356 87747596 87748394 0 1269
13 TraesCS4D01G146400 chr3B 98.394 498 8 0 1859 2356 92194034 92194531 0 876
14 TraesCS4D01G146400 chr6A 98.193 498 9 0 1859 2356 289123072 289123569 0 870


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 TraesCS4D01G146400 chr4D 135003866 135006221 2355 True 4351 4351 100.000 1 2356 1 chr4D.!!$R1 2355
1 TraesCS4D01G146400 chr4D 483696359 483698716 2357 False 4021 4021 97.457 1 2356 1 chr4D.!!$F1 2355
2 TraesCS4D01G146400 chr4D 241140889 241143245 2356 True 3836 3836 96.058 1 2356 1 chr4D.!!$R2 2355
3 TraesCS4D01G146400 chr5D 79865255 79867611 2356 False 3775 3775 95.589 1 2356 1 chr5D.!!$F1 2355
4 TraesCS4D01G146400 chr5D 197837543 197839898 2355 True 3552 3552 93.896 3 2356 1 chr5D.!!$R1 2353
5 TraesCS4D01G146400 chr7D 579015578 579017462 1884 False 3245 3245 97.772 1 1882 1 chr7D.!!$F1 1881
6 TraesCS4D01G146400 chr6B 53079007 53081035 2028 False 3240 3240 95.530 1 2026 1 chr6B.!!$F1 2025
7 TraesCS4D01G146400 chrUn 237255949 237257830 1881 True 3232 3232 97.666 1 1882 1 chrUn.!!$R1 1881
8 TraesCS4D01G146400 chr7A 563529584 563531481 1897 True 3232 3232 97.418 1 1896 1 chr7A.!!$R1 1895
9 TraesCS4D01G146400 chr3A 191855549 191857447 1898 False 3227 3227 97.367 1 1896 1 chr3A.!!$F1 1895
10 TraesCS4D01G146400 chr1D 185763599 185764391 792 False 1347 1347 97.352 1565 2356 1 chr1D.!!$F1 791
11 TraesCS4D01G146400 chr5B 87747596 87748394 798 False 1269 1269 95.369 1559 2356 1 chr5B.!!$F1 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
697 708 0.767375 TTGAGCAAGCTCCTCCACTT 59.233 50.0 18.54 0.0 42.09 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2287 2307 1.423921 GGAAGGTCAGAGGTGGGAAAA 59.576 52.381 0.0 0.0 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
141 142 3.650950 GGCAGGTGAGGAAGGGCA 61.651 66.667 0.00 0.00 0.00 5.36
174 175 2.251818 CCCTGTCTTCTCTCTTGGTCA 58.748 52.381 0.00 0.00 0.00 4.02
179 180 4.480115 TGTCTTCTCTCTTGGTCAGGTTA 58.520 43.478 0.00 0.00 0.00 2.85
186 187 2.569404 CTCTTGGTCAGGTTAGAGGCTT 59.431 50.000 0.00 0.00 32.41 4.35
318 321 4.211125 TGGATAGAGTCTTTCTCGCTCAT 58.789 43.478 10.01 0.00 46.86 2.90
487 490 2.092375 GGGTTCGAATCCCATTTCCTCT 60.092 50.000 17.16 0.00 44.05 3.69
504 507 1.546476 CTCTGGCACGGAAGTAGAACT 59.454 52.381 0.00 0.00 46.55 3.01
514 517 2.202756 GTAGAACTGGCGGGCGAG 60.203 66.667 0.00 0.88 0.00 5.03
554 565 1.137675 CTCAGATTGATGGAGTCCGCA 59.862 52.381 4.30 2.29 0.00 5.69
672 683 3.618855 TAGTCCCTGGCCGGCTCTT 62.619 63.158 28.56 7.82 0.00 2.85
697 708 0.767375 TTGAGCAAGCTCCTCCACTT 59.233 50.000 18.54 0.00 42.09 3.16
874 885 6.597832 TTTTTCTTGTTTCAGTGGGAAGAA 57.402 33.333 0.00 0.00 36.72 2.52
882 893 0.771127 CAGTGGGAAGAACAAGGGGA 59.229 55.000 0.00 0.00 0.00 4.81
1054 1068 3.129638 AGTGATCAGTCCGCTAGTTTCTC 59.870 47.826 0.00 0.00 0.00 2.87
1280 1294 8.910944 CAAGATTGATCTATTTGGATCTTGGTT 58.089 33.333 13.36 0.00 43.07 3.67
1446 1461 5.849510 TCGTCATGGTAGAGAAGAAAAACA 58.150 37.500 0.00 0.00 0.00 2.83
1598 1614 6.638168 ATCGACATGATATATTTGCTCACG 57.362 37.500 0.00 0.00 34.83 4.35
1674 1693 1.731720 AGAGTGAAAGATTCGCCAGC 58.268 50.000 0.35 0.00 40.99 4.85
1763 1782 9.282569 GAAGATCTAAATATGGTGCAGAAAGAT 57.717 33.333 0.00 0.00 0.00 2.40
1831 1851 0.396974 TGGGGGCAATATGGAAGCAC 60.397 55.000 0.00 0.00 0.00 4.40
1868 1888 7.270047 TCCCTTATTACGTTACCATTTCTCTG 58.730 38.462 0.00 0.00 0.00 3.35
2248 2268 2.415625 CCTCTTCCCTTCAACTCGTACG 60.416 54.545 9.53 9.53 0.00 3.67
2287 2307 7.340487 CCAGTAAGCATTTCCTCTATTTCCTTT 59.660 37.037 0.00 0.00 0.00 3.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
174 175 6.213600 TGAATGAGAAACTAAGCCTCTAACCT 59.786 38.462 0.00 0.00 0.00 3.50
179 180 5.486526 CACTGAATGAGAAACTAAGCCTCT 58.513 41.667 0.00 0.00 0.00 3.69
186 187 4.593206 ACCTCACCACTGAATGAGAAACTA 59.407 41.667 10.40 0.00 44.32 2.24
243 244 1.555967 CCCATCCAAACCAAATCCGT 58.444 50.000 0.00 0.00 0.00 4.69
318 321 0.986992 GCGCGCGTACTCTTCTTTAA 59.013 50.000 32.35 0.00 0.00 1.52
375 378 3.684908 TGTTGATCGGAATTGGATGTGT 58.315 40.909 0.00 0.00 0.00 3.72
487 490 0.320374 CCAGTTCTACTTCCGTGCCA 59.680 55.000 0.00 0.00 0.00 4.92
504 507 3.454573 ACGTAATCTCGCCCGCCA 61.455 61.111 0.00 0.00 0.00 5.69
514 517 5.710984 TGAGGTTCTTTCTCTCACGTAATC 58.289 41.667 0.00 0.00 33.21 1.75
554 565 1.479709 AGCAGCTATTCTGTCCGACT 58.520 50.000 0.00 0.00 44.66 4.18
654 665 3.618855 AAGAGCCGGCCAGGGACTA 62.619 63.158 26.15 0.00 41.48 2.59
672 683 0.767375 AGGAGCTTGCTCAAGAACCA 59.233 50.000 21.97 0.00 40.79 3.67
697 708 5.003096 TCATCTATGAGCATCCTACCTGA 57.997 43.478 0.00 0.00 32.11 3.86
882 893 4.020839 CACTGAAGGATTTCAAGGGCAATT 60.021 41.667 0.00 0.00 42.48 2.32
964 978 1.377333 TTCTCTCGCTCTCCTCGCA 60.377 57.895 0.00 0.00 0.00 5.10
1054 1068 1.276421 AGGAACACCGAGTGGAATCAG 59.724 52.381 8.57 0.00 37.94 2.90
1280 1294 8.319881 TCAAAATCAATAAAAAGGCCATCATGA 58.680 29.630 5.01 0.00 0.00 3.07
1446 1461 4.112341 GAGTACGGTCCGTGCGCT 62.112 66.667 27.20 20.13 46.19 5.92
1598 1614 2.396590 TTATGACCTTCGCCTGGAAC 57.603 50.000 0.00 0.00 0.00 3.62
1674 1693 4.368315 TCGAATACGATGGGATTTCACAG 58.632 43.478 0.00 0.00 43.81 3.66
1701 1720 2.169144 GGAATTCCCAGCAAATCCTTGG 59.831 50.000 14.03 0.00 31.90 3.61
1763 1782 7.255242 GGCATCTTCCATTCATTTCGATTTAGA 60.255 37.037 0.00 0.00 0.00 2.10
1831 1851 4.262506 CGTAATAAGGGAAAGGGAGCTAGG 60.263 50.000 0.00 0.00 0.00 3.02
1887 1907 5.554070 GGTAAGTTAAGTAAGTCAAGCCCA 58.446 41.667 0.00 0.00 0.00 5.36
2248 2268 3.206964 GCTTACTGGGACATAGCCTTTC 58.793 50.000 0.00 0.00 38.20 2.62
2287 2307 1.423921 GGAAGGTCAGAGGTGGGAAAA 59.576 52.381 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.