Multiple sequence alignment - TraesCS4D01G161400

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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 TraesCS4D01G161400 chr4D 100.000 2356 0 0 1 2356 241143244 241140889 0 4351
1 TraesCS4D01G161400 chr4D 96.607 2358 77 3 1 2356 483696360 483698716 0 3908
2 TraesCS4D01G161400 chr4D 96.056 2358 88 5 1 2356 135006220 135003866 0 3834
3 TraesCS4D01G161400 chr5D 94.741 2358 120 4 1 2356 79865256 79867611 0 3664
4 TraesCS4D01G161400 chr5D 93.184 2362 148 11 2 2356 197839898 197837543 0 3458
5 TraesCS4D01G161400 chr7D 97.081 1884 53 2 1 1882 579015579 579017462 0 3173
6 TraesCS4D01G161400 chr7A 96.839 1898 57 3 1 1896 563531480 563529584 0 3169
7 TraesCS4D01G161400 chr7A 96.988 498 15 0 1859 2356 4954288 4954785 0 837
8 TraesCS4D01G161400 chr3A 96.733 1898 60 2 1 1896 191855550 191857447 0 3160
9 TraesCS4D01G161400 chr6B 94.745 2036 89 6 1 2026 53079008 53081035 0 3151
10 TraesCS4D01G161400 chr1A 96.630 1899 61 3 1 1896 278506347 278508245 0 3149
11 TraesCS4D01G161400 chr1D 97.100 793 23 0 1564 2356 185763599 185764391 0 1338
12 TraesCS4D01G161400 chr5B 95.369 799 37 0 1558 2356 87747596 87748394 0 1271
13 TraesCS4D01G161400 chr3B 97.189 498 14 0 1859 2356 92194034 92194531 0 843
14 TraesCS4D01G161400 chr6A 96.988 498 15 0 1859 2356 289123072 289123569 0 837


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 TraesCS4D01G161400 chr4D 241140889 241143244 2355 True 4351 4351 100.000 1 2356 1 chr4D.!!$R2 2355
1 TraesCS4D01G161400 chr4D 483696360 483698716 2356 False 3908 3908 96.607 1 2356 1 chr4D.!!$F1 2355
2 TraesCS4D01G161400 chr4D 135003866 135006220 2354 True 3834 3834 96.056 1 2356 1 chr4D.!!$R1 2355
3 TraesCS4D01G161400 chr5D 79865256 79867611 2355 False 3664 3664 94.741 1 2356 1 chr5D.!!$F1 2355
4 TraesCS4D01G161400 chr5D 197837543 197839898 2355 True 3458 3458 93.184 2 2356 1 chr5D.!!$R1 2354
5 TraesCS4D01G161400 chr7D 579015579 579017462 1883 False 3173 3173 97.081 1 1882 1 chr7D.!!$F1 1881
6 TraesCS4D01G161400 chr7A 563529584 563531480 1896 True 3169 3169 96.839 1 1896 1 chr7A.!!$R1 1895
7 TraesCS4D01G161400 chr3A 191855550 191857447 1897 False 3160 3160 96.733 1 1896 1 chr3A.!!$F1 1895
8 TraesCS4D01G161400 chr6B 53079008 53081035 2027 False 3151 3151 94.745 1 2026 1 chr6B.!!$F1 2025
9 TraesCS4D01G161400 chr1A 278506347 278508245 1898 False 3149 3149 96.630 1 1896 1 chr1A.!!$F1 1895
10 TraesCS4D01G161400 chr1D 185763599 185764391 792 False 1338 1338 97.100 1564 2356 1 chr1D.!!$F1 792
11 TraesCS4D01G161400 chr5B 87747596 87748394 798 False 1271 1271 95.369 1558 2356 1 chr5B.!!$F1 798

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 0.251033 TTCTCTCTTGGTCGGGTCGA 60.251 55.0 0.0 0.0 0.0 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2121 2139 0.249398 AAGGTTGCTAGGTACCGCTG 59.751 55.0 6.18 1.79 39.46 5.18 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
99 100 5.179533 GGCTTTTTCCTTTCTCGACTAGAT 58.820 41.667 0.00 0.00 33.05 1.98
142 143 3.322466 CAGGTGAGGAAGGGCGGT 61.322 66.667 0.00 0.00 0.00 5.68
179 180 0.251033 TTCTCTCTTGGTCGGGTCGA 60.251 55.000 0.00 0.00 0.00 4.20
256 257 0.388520 GAGTGGCGGATTTGGTTTGC 60.389 55.000 0.00 0.00 0.00 3.68
313 316 5.690865 AGATCTGGATAGAGTCTTTCTCGT 58.309 41.667 10.01 0.00 46.86 4.18
334 337 4.225208 GTTCAGTAAAGAAGAGTACGCGT 58.775 43.478 19.17 19.17 0.00 6.01
359 362 1.739067 GGCTTACGCAGTGGATCTTT 58.261 50.000 0.00 0.00 45.73 2.52
471 474 6.484288 ACAAGAAGATTGTATCATGGGTTCA 58.516 36.000 0.00 0.00 0.00 3.18
476 479 6.624352 AGATTGTATCATGGGTTCAAATCG 57.376 37.500 0.00 0.00 0.00 3.34
573 584 2.414824 CCGTCGGATAGAATAGCTGCTC 60.415 54.545 4.91 0.00 32.26 4.26
624 635 1.480789 TCTTGGTGGCGTCTATAGCA 58.519 50.000 0.00 0.00 36.08 3.49
709 720 1.153086 CCACTGCAGGTAGGATGCC 60.153 63.158 19.93 0.00 43.18 4.40
897 908 2.594342 GGCATTGCCCCTGAAATGA 58.406 52.632 17.28 0.00 44.06 2.57
1006 1019 0.605319 GTGGGCTTTGGTGATGTCGA 60.605 55.000 0.00 0.00 0.00 4.20
1092 1106 4.335400 TCCTTTTCCATTTGCTTCCAAC 57.665 40.909 0.00 0.00 0.00 3.77
1264 1279 6.630413 GCAGTACCTCCTAACAAGATTGATCA 60.630 42.308 0.00 0.00 0.00 2.92
1296 1311 3.784178 TGGTCCATGATGGCCTTTTTAA 58.216 40.909 20.41 2.63 37.47 1.52
1332 1348 7.658982 CGATTGGATCTCTCTATGAATGGAAAA 59.341 37.037 0.00 0.00 0.00 2.29
1343 1359 2.247358 GAATGGAAAAGGGGTGCTTCA 58.753 47.619 0.00 0.00 0.00 3.02
1436 1453 4.060900 CAATTGATCCGTCATGGTAGAGG 58.939 47.826 0.00 0.00 39.52 3.69
1452 1470 1.503818 GAGGAGAAAAACGGCGCACA 61.504 55.000 10.83 0.00 0.00 4.57
1489 1507 1.210478 CGGATCAATGTCCCCAGAAGT 59.790 52.381 0.00 0.00 34.67 3.01
1668 1686 5.420421 CAGAGGAGGTAGAGTGAAAGATTCA 59.580 44.000 0.00 0.00 37.33 2.57
1870 1888 7.270047 CCTTATTACGTTACCATTTCTCTCCA 58.730 38.462 0.00 0.00 0.00 3.86
1971 1989 3.313526 CGCCTGATGAGATAGGGTTTTTG 59.686 47.826 0.00 0.00 34.58 2.44
2152 2170 2.165998 AGCAACCTTCATTCCTGCTTC 58.834 47.619 0.00 0.00 40.36 3.86
2155 2173 3.683802 CAACCTTCATTCCTGCTTCTCT 58.316 45.455 0.00 0.00 0.00 3.10
2306 2324 1.850345 TGTTTCCCACCTCTGACCTTT 59.150 47.619 0.00 0.00 0.00 3.11
2340 2358 5.084519 TGACCAGTCCACTAATAAGTCAGT 58.915 41.667 0.00 0.00 31.97 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 87 8.698973 AATATCTCCTTCATCTAGTCGAGAAA 57.301 34.615 0.00 0.00 37.85 2.52
99 100 7.229308 CCTGAATGGAATGAATATCTCCTTCA 58.771 38.462 0.00 0.00 38.35 3.02
179 180 5.006386 CCACTGAATGAGAAACTTAGCCTT 58.994 41.667 0.00 0.00 0.00 4.35
256 257 1.450312 GTCCAAGCGAGACCCCATG 60.450 63.158 0.00 0.00 0.00 3.66
313 316 4.224433 CACGCGTACTCTTCTTTACTGAA 58.776 43.478 13.44 0.00 0.00 3.02
373 376 2.684881 GTTGATCGGAATTGGATGTGCT 59.315 45.455 0.00 0.00 0.00 4.40
560 571 4.824537 CCTAGTCACTGAGCAGCTATTCTA 59.175 45.833 0.00 0.00 0.00 2.10
573 584 1.435515 GCTCCGCTCCTAGTCACTG 59.564 63.158 0.00 0.00 0.00 3.66
593 604 1.133792 CCACCAAGAACAAGACAGGGT 60.134 52.381 0.00 0.00 0.00 4.34
598 609 0.586802 GACGCCACCAAGAACAAGAC 59.413 55.000 0.00 0.00 0.00 3.01
624 635 1.690352 TCGTTCGGGAAGGTCTTCTTT 59.310 47.619 10.13 0.00 39.45 2.52
709 720 9.323985 CCTAAAGTCTCTTTTCTTCATCTATGG 57.676 37.037 0.15 0.00 0.00 2.74
896 907 3.861840 TGTGGATTCGAACCTCTGAATC 58.138 45.455 0.00 6.43 46.18 2.52
897 908 3.981071 TGTGGATTCGAACCTCTGAAT 57.019 42.857 0.00 0.00 37.52 2.57
903 914 2.419297 GCTCAGATGTGGATTCGAACCT 60.419 50.000 0.00 0.00 0.00 3.50
1092 1106 5.643777 ACATTTTTCTGGATAGGTCGAACTG 59.356 40.000 14.77 0.00 0.00 3.16
1192 1207 9.686683 CTTCCGGATCAGGGATAATAAATAAAT 57.313 33.333 4.15 0.00 32.58 1.40
1296 1311 6.590068 AGAGAGATCCAATCGTCAAAATCAT 58.410 36.000 0.00 0.00 0.00 2.45
1332 1348 2.370445 CCCGATCTGAAGCACCCCT 61.370 63.158 0.00 0.00 0.00 4.79
1343 1359 3.581332 TCAAAAGTGGTTACTCCCGATCT 59.419 43.478 0.00 0.00 35.69 2.75
1422 1439 3.887621 TTTTCTCCTCTACCATGACGG 57.112 47.619 0.00 0.00 42.50 4.79
1436 1453 0.384353 GTCTGTGCGCCGTTTTTCTC 60.384 55.000 4.18 0.00 0.00 2.87
1452 1470 1.025812 CCGAAGCTCGAGTATGGTCT 58.974 55.000 15.13 0.00 43.74 3.85
1489 1507 1.191535 ACACGCAGGCATACTCCTTA 58.808 50.000 0.00 0.00 33.25 2.69
1668 1686 1.340017 CGATGGGATTTCACACCTGGT 60.340 52.381 0.00 0.00 28.47 4.00
1896 1914 6.523840 TCGGGAAAGCAGTAAGTTAAGTAAA 58.476 36.000 0.00 0.00 0.00 2.01
1979 1997 1.680522 CCATACCGACAGCAGCTCCT 61.681 60.000 0.00 0.00 0.00 3.69
2121 2139 0.249398 AAGGTTGCTAGGTACCGCTG 59.751 55.000 6.18 1.79 39.46 5.18
2152 2170 5.423015 TCAAGTAGCAAAGGCAAGATAGAG 58.577 41.667 0.00 0.00 44.61 2.43
2155 2173 5.187772 TCTCTCAAGTAGCAAAGGCAAGATA 59.812 40.000 0.00 0.00 44.61 1.98
2306 2324 1.409064 GGACTGGTCATGTCATAGCGA 59.591 52.381 3.10 0.00 36.26 4.93


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

AutoCloner maintained by Alex Coulton.