Multiple sequence alignment - TraesCS6B01G314100

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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 TraesCS6B01G314100 chr6B 100.000 2516 0 0 1 2516 561743466 561740951 0.000000e+00 4647
1 TraesCS6B01G314100 chr2B 96.440 1264 41 4 1252 2513 575352345 575353606 0.000000e+00 2082
2 TraesCS6B01G314100 chr2B 94.737 1273 56 9 1252 2516 405162907 405164176 0.000000e+00 1969
3 TraesCS6B01G314100 chr2B 94.580 1273 60 7 1252 2516 279188239 279186968 0.000000e+00 1960
4 TraesCS6B01G314100 chr2B 92.370 1232 87 4 1 1230 575351202 575352428 0.000000e+00 1748
5 TraesCS6B01G314100 chr2B 87.405 1310 110 33 1230 2516 550078110 550076833 0.000000e+00 1454
6 TraesCS6B01G314100 chr2B 82.900 1000 113 32 1542 2516 272993547 272992581 0.000000e+00 846
7 TraesCS6B01G314100 chr2B 89.474 95 9 1 2422 2516 465448976 465448883 4.400000e-23 119
8 TraesCS6B01G314100 chr1B 95.212 1274 50 8 1252 2516 475664293 475665564 0.000000e+00 2004
9 TraesCS6B01G314100 chr1B 90.130 1307 105 14 1230 2516 367659489 367660791 0.000000e+00 1677
10 TraesCS6B01G314100 chr1B 90.407 1230 118 0 1 1230 534467630 534468859 0.000000e+00 1618
11 TraesCS6B01G314100 chr7B 95.779 1232 48 4 1 1230 182946643 182945414 0.000000e+00 1984
12 TraesCS6B01G314100 chr7B 93.014 1231 85 1 1 1230 240199730 240200960 0.000000e+00 1796
13 TraesCS6B01G314100 chr7B 90.692 1300 103 13 1230 2516 550726069 550724775 0.000000e+00 1714
14 TraesCS6B01G314100 chr3B 94.554 1267 45 12 1252 2516 289836350 289837594 0.000000e+00 1936
15 TraesCS6B01G314100 chr3B 94.153 1180 69 0 1 1180 81050299 81051478 0.000000e+00 1797
16 TraesCS6B01G314100 chr3B 90.407 1230 117 1 1 1230 289835205 289836433 0.000000e+00 1616
17 TraesCS6B01G314100 chr3B 97.701 87 2 0 1144 1230 128994523 128994437 1.560000e-32 150
18 TraesCS6B01G314100 chr4B 94.634 1230 66 0 1 1230 486848100 486846871 0.000000e+00 1906
19 TraesCS6B01G314100 chr4B 93.008 1230 84 2 1 1230 353677742 353678969 0.000000e+00 1794
20 TraesCS6B01G314100 chr4B 92.199 1269 75 10 1252 2516 207926711 207925463 0.000000e+00 1773
21 TraesCS6B01G314100 chr4B 90.488 1230 117 0 1 1230 207927857 207926628 0.000000e+00 1624
22 TraesCS6B01G314100 chrUn 91.570 1293 83 15 1230 2516 387047980 387049252 0.000000e+00 1760


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 TraesCS6B01G314100 chr6B 561740951 561743466 2515 True 4647.0 4647 100.0000 1 2516 1 chr6B.!!$R1 2515
1 TraesCS6B01G314100 chr2B 405162907 405164176 1269 False 1969.0 1969 94.7370 1252 2516 1 chr2B.!!$F1 1264
2 TraesCS6B01G314100 chr2B 279186968 279188239 1271 True 1960.0 1960 94.5800 1252 2516 1 chr2B.!!$R2 1264
3 TraesCS6B01G314100 chr2B 575351202 575353606 2404 False 1915.0 2082 94.4050 1 2513 2 chr2B.!!$F2 2512
4 TraesCS6B01G314100 chr2B 550076833 550078110 1277 True 1454.0 1454 87.4050 1230 2516 1 chr2B.!!$R4 1286
5 TraesCS6B01G314100 chr2B 272992581 272993547 966 True 846.0 846 82.9000 1542 2516 1 chr2B.!!$R1 974
6 TraesCS6B01G314100 chr1B 475664293 475665564 1271 False 2004.0 2004 95.2120 1252 2516 1 chr1B.!!$F2 1264
7 TraesCS6B01G314100 chr1B 367659489 367660791 1302 False 1677.0 1677 90.1300 1230 2516 1 chr1B.!!$F1 1286
8 TraesCS6B01G314100 chr1B 534467630 534468859 1229 False 1618.0 1618 90.4070 1 1230 1 chr1B.!!$F3 1229
9 TraesCS6B01G314100 chr7B 182945414 182946643 1229 True 1984.0 1984 95.7790 1 1230 1 chr7B.!!$R1 1229
10 TraesCS6B01G314100 chr7B 240199730 240200960 1230 False 1796.0 1796 93.0140 1 1230 1 chr7B.!!$F1 1229
11 TraesCS6B01G314100 chr7B 550724775 550726069 1294 True 1714.0 1714 90.6920 1230 2516 1 chr7B.!!$R2 1286
12 TraesCS6B01G314100 chr3B 81050299 81051478 1179 False 1797.0 1797 94.1530 1 1180 1 chr3B.!!$F1 1179
13 TraesCS6B01G314100 chr3B 289835205 289837594 2389 False 1776.0 1936 92.4805 1 2516 2 chr3B.!!$F2 2515
14 TraesCS6B01G314100 chr4B 486846871 486848100 1229 True 1906.0 1906 94.6340 1 1230 1 chr4B.!!$R1 1229
15 TraesCS6B01G314100 chr4B 353677742 353678969 1227 False 1794.0 1794 93.0080 1 1230 1 chr4B.!!$F1 1229
16 TraesCS6B01G314100 chr4B 207925463 207927857 2394 True 1698.5 1773 91.3435 1 2516 2 chr4B.!!$R2 2515
17 TraesCS6B01G314100 chrUn 387047980 387049252 1272 False 1760.0 1760 91.5700 1230 2516 1 chrUn.!!$F1 1286

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
215 217 0.820871 GGCTACTCTCACACTCCAGG 59.179 60.0 0.0 0.0 0.0 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1997 2017 1.051812 ATGCTACCGATCCAGGGAAG 58.948 55.0 0.0 0.0 35.02 3.46 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
176 178 2.323999 TGTGGATTTCAGGGCCATTT 57.676 45.000 6.18 0.00 33.66 2.32
215 217 0.820871 GGCTACTCTCACACTCCAGG 59.179 60.000 0.00 0.00 0.00 4.45
379 381 5.305644 GGATTTAGGTATGAAGAGGAGAGCA 59.694 44.000 0.00 0.00 0.00 4.26
412 414 5.757808 GCACCACAACAATTTTATTCACCTT 59.242 36.000 0.00 0.00 0.00 3.50
450 452 2.308570 ACACCAGGAGATGTTGCCAATA 59.691 45.455 0.00 0.00 0.00 1.90
664 666 7.093992 AGAAGTAAGGAAGATTGAGAAGAACG 58.906 38.462 0.00 0.00 0.00 3.95
889 891 8.588290 AGTTGAAGACTCATCATCTACTACTT 57.412 34.615 0.00 0.00 37.03 2.24
966 968 5.491070 TGGCCTATTATCATACATGAGCAC 58.509 41.667 3.32 0.00 40.64 4.40
1327 1329 4.539726 TGCTGATTTCTGCCATCCTAAAT 58.460 39.130 6.93 0.00 39.65 1.40
1341 1343 7.611467 TGCCATCCTAAATATGTGCTTTATAGG 59.389 37.037 0.00 0.00 0.00 2.57
1416 1421 7.042992 CGTATCACTTGTAGTTCTTTGTGTGAA 60.043 37.037 0.00 0.00 36.88 3.18
1434 1439 6.267471 TGTGTGAATCCTATTTCAGGCTTTTT 59.733 34.615 0.00 0.00 45.10 1.94
1997 2017 5.738909 ACCACTATGGATTAGCATGCTATC 58.261 41.667 27.35 22.99 40.96 2.08
2256 2284 2.024846 TGTTCCTTTGGGGAGACAAACA 60.025 45.455 0.00 0.00 46.01 2.83
2478 2529 6.702972 TTTGGCACATTCATCATTTAAACG 57.297 33.333 0.00 0.00 39.30 3.60
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
194 196 2.106566 CTGGAGTGTGAGAGTAGCCAT 58.893 52.381 0.00 0.00 0.00 4.40
215 217 2.053627 CGAAGCTCATGCCAAAACAAC 58.946 47.619 0.00 0.00 40.80 3.32
379 381 4.935352 ATTGTTGTGGTGCATAGTTGTT 57.065 36.364 0.00 0.00 0.00 2.83
412 414 5.833667 CCTGGTGTTGAGGTATATGAGTAGA 59.166 44.000 0.00 0.00 0.00 2.59
531 533 3.508012 ACTCGAGACTAAGCAATGTGAGT 59.492 43.478 21.68 0.00 0.00 3.41
664 666 3.855689 AATAGTGTTGCCAGCATTGAC 57.144 42.857 0.00 0.00 0.00 3.18
889 891 4.039730 AGCAGCTTCTTGTACTTCTTCAGA 59.960 41.667 0.00 0.00 0.00 3.27
966 968 2.465860 TGGGTAAACCTGACACATCG 57.534 50.000 0.00 0.00 41.11 3.84
1144 1146 5.921962 TTAAGCTCAAGACTAGCATGAGA 57.078 39.130 18.91 1.68 43.28 3.27
1434 1439 5.047306 AGCATGTAGTAAACAGTGCAGTAGA 60.047 40.000 0.00 0.00 42.70 2.59
1997 2017 1.051812 ATGCTACCGATCCAGGGAAG 58.948 55.000 0.00 0.00 35.02 3.46
2114 2137 3.614092 CAGGGAACATGACATGCTACTT 58.386 45.455 15.49 2.04 0.00 2.24
2195 2222 5.450818 ACATGGTATACACCTGGTTTGAT 57.549 39.130 5.01 0.00 45.98 2.57
2391 2430 7.862274 TGATCAGATCACTTATTACCAGGAT 57.138 36.000 9.21 0.00 33.59 3.24


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

AutoCloner maintained by Alex Coulton.