Multiple sequence alignment - TraesCS6B01G005900

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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 TraesCS6B01G005900 chr6B 100.000 2339 0 0 1 2339 4276106 4278444 0.000000e+00 4320.0
1 TraesCS6B01G005900 chr7B 97.300 1926 39 2 3 1916 689857014 689855090 0.000000e+00 3256.0
2 TraesCS6B01G005900 chr7B 97.930 483 9 1 1858 2339 689855062 689854580 0.000000e+00 835.0
3 TraesCS6B01G005900 chr2B 97.519 1330 31 2 1 1329 769993674 769995002 0.000000e+00 2272.0
4 TraesCS6B01G005900 chr2B 88.654 1278 143 2 2 1278 679648703 679647427 0.000000e+00 1555.0
5 TraesCS6B01G005900 chr2B 94.063 539 20 1 1317 1843 769995038 769995576 0.000000e+00 808.0
6 TraesCS6B01G005900 chr2B 96.480 483 16 1 1858 2339 769995735 769996217 0.000000e+00 797.0
7 TraesCS6B01G005900 chr2B 86.426 582 53 8 1279 1838 200710547 200709970 4.270000e-172 614.0
8 TraesCS6B01G005900 chr2B 88.032 493 43 4 1742 2234 200709948 200709472 9.380000e-159 569.0
9 TraesCS6B01G005900 chr2B 82.105 475 57 10 1890 2339 679646626 679646155 4.720000e-102 381.0
10 TraesCS6B01G005900 chr7D 96.849 1333 38 4 1 1332 633359744 633358415 0.000000e+00 2226.0
11 TraesCS6B01G005900 chr7D 94.747 533 16 1 1323 1843 633358377 633357845 0.000000e+00 819.0
12 TraesCS6B01G005900 chr7D 91.514 601 39 10 1742 2339 633357828 633357237 0.000000e+00 817.0
13 TraesCS6B01G005900 chr7D 92.683 41 1 2 1858 1897 633357845 633357806 9.030000e-05 58.4
14 TraesCS6B01G005900 chr3B 91.353 1619 103 23 1 1605 744535949 744534354 0.000000e+00 2180.0
15 TraesCS6B01G005900 chr5D 94.122 1225 66 3 1 1221 74187567 74188789 0.000000e+00 1858.0
16 TraesCS6B01G005900 chr5D 88.889 1278 140 2 2 1278 385494705 385493429 0.000000e+00 1572.0
17 TraesCS6B01G005900 chr5D 89.610 1232 125 3 2 1233 357884352 357885580 0.000000e+00 1563.0
18 TraesCS6B01G005900 chr5D 85.381 643 61 11 1280 1896 74198337 74198972 9.120000e-179 636.0
19 TraesCS6B01G005900 chr5D 80.731 602 78 19 1758 2339 385492495 385491912 3.570000e-118 435.0
20 TraesCS6B01G005900 chr5D 84.198 424 46 5 1739 2160 74198933 74199337 2.180000e-105 392.0
21 TraesCS6B01G005900 chr5D 90.625 160 13 2 2156 2314 74209622 74209780 6.550000e-51 211.0
22 TraesCS6B01G005900 chr5D 86.164 159 21 1 2130 2288 387258051 387258208 1.110000e-38 171.0
23 TraesCS6B01G005900 chr5D 95.192 104 4 1 1223 1326 74198214 74198316 1.860000e-36 163.0
24 TraesCS6B01G005900 chr1A 95.371 1145 50 3 1 1145 577422583 577421442 0.000000e+00 1818.0
25 TraesCS6B01G005900 chr1A 91.002 589 35 12 1754 2339 577400317 577399744 0.000000e+00 778.0
26 TraesCS6B01G005900 chr1A 93.258 534 22 5 1323 1843 577400996 577400464 0.000000e+00 774.0
27 TraesCS6B01G005900 chr1A 97.895 190 4 0 1140 1329 577401227 577401038 1.730000e-86 329.0
28 TraesCS6B01G005900 chr1A 92.157 102 8 0 1742 1843 577400447 577400346 6.740000e-31 145.0
29 TraesCS6B01G005900 chr1A 92.500 40 1 2 1858 1896 577400464 577400426 3.250000e-04 56.5
30 TraesCS6B01G005900 chr7A 87.895 1297 152 5 2 1298 483750173 483748882 0.000000e+00 1520.0
31 TraesCS6B01G005900 chr6A 82.297 209 26 7 2117 2324 428630278 428630476 1.110000e-38 171.0


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 TraesCS6B01G005900 chr6B 4276106 4278444 2338 False 4320.000000 4320 100.000000 1 2339 1 chr6B.!!$F1 2338
1 TraesCS6B01G005900 chr7B 689854580 689857014 2434 True 2045.500000 3256 97.615000 3 2339 2 chr7B.!!$R1 2336
2 TraesCS6B01G005900 chr2B 769993674 769996217 2543 False 1292.333333 2272 96.020667 1 2339 3 chr2B.!!$F1 2338
3 TraesCS6B01G005900 chr2B 679646155 679648703 2548 True 968.000000 1555 85.379500 2 2339 2 chr2B.!!$R2 2337
4 TraesCS6B01G005900 chr2B 200709472 200710547 1075 True 591.500000 614 87.229000 1279 2234 2 chr2B.!!$R1 955
5 TraesCS6B01G005900 chr7D 633357237 633359744 2507 True 980.100000 2226 93.948250 1 2339 4 chr7D.!!$R1 2338
6 TraesCS6B01G005900 chr3B 744534354 744535949 1595 True 2180.000000 2180 91.353000 1 1605 1 chr3B.!!$R1 1604
7 TraesCS6B01G005900 chr5D 74187567 74188789 1222 False 1858.000000 1858 94.122000 1 1221 1 chr5D.!!$F1 1220
8 TraesCS6B01G005900 chr5D 357884352 357885580 1228 False 1563.000000 1563 89.610000 2 1233 1 chr5D.!!$F3 1231
9 TraesCS6B01G005900 chr5D 385491912 385494705 2793 True 1003.500000 1572 84.810000 2 2339 2 chr5D.!!$R1 2337
10 TraesCS6B01G005900 chr5D 74198214 74199337 1123 False 397.000000 636 88.257000 1223 2160 3 chr5D.!!$F5 937
11 TraesCS6B01G005900 chr1A 577421442 577422583 1141 True 1818.000000 1818 95.371000 1 1145 1 chr1A.!!$R1 1144
12 TraesCS6B01G005900 chr1A 577399744 577401227 1483 True 416.500000 778 93.362400 1140 2339 5 chr1A.!!$R2 1199
13 TraesCS6B01G005900 chr7A 483748882 483750173 1291 True 1520.000000 1520 87.895000 2 1298 1 chr7A.!!$R1 1296

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
668 674 1.216678 TCAGGAACAAAGGGCCAAAGA 59.783 47.619 6.18 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2110 3059 1.826385 ATGTGAGGTTAGCAGTTGGC 58.174 50.0 0.0 0.0 45.3 4.52 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
668 674 1.216678 TCAGGAACAAAGGGCCAAAGA 59.783 47.619 6.18 0.00 0.00 2.52
686 692 6.618811 CCAAAGATCAGAAGTTTCATGGAAG 58.381 40.000 0.00 0.00 0.00 3.46
690 696 7.862512 AGATCAGAAGTTTCATGGAAGAATC 57.137 36.000 0.00 0.00 0.00 2.52
719 725 6.183360 CCCAGTGCTTTTAAGAAGTTGAAGAA 60.183 38.462 0.00 0.00 0.00 2.52
740 746 2.393271 AGCATAGCAAGGACACAGTC 57.607 50.000 0.00 0.00 0.00 3.51
762 768 3.053693 CCATGGAGGTACTTTGGAATGGA 60.054 47.826 5.56 0.00 41.55 3.41
988 994 8.556213 TTATGAACACTATTTGGAACCTGTAC 57.444 34.615 0.00 0.00 0.00 2.90
1106 1112 8.531362 AATAATGATAGGAGGAGGGAAGAAAT 57.469 34.615 0.00 0.00 0.00 2.17
1481 2052 1.946768 GAACTGTGCCAAGTACTGCAA 59.053 47.619 9.29 1.08 39.57 4.08
1752 2373 6.776094 GTTGTAAACTGAGATGCTATCAACC 58.224 40.000 0.00 0.00 45.32 3.77
2109 3058 8.088365 GCACTTTTTCCTACCAAAATAACTCAT 58.912 33.333 0.00 0.00 0.00 2.90
2110 3059 9.410556 CACTTTTTCCTACCAAAATAACTCATG 57.589 33.333 0.00 0.00 0.00 3.07
2173 3143 3.562182 AGGAAAACACCTACCACAAAGG 58.438 45.455 0.00 0.00 38.65 3.11
2305 3275 0.473755 ATGACCAGACACAGGCACAA 59.526 50.000 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 6.719370 TGAACCCTAACTTCAGTGCATTAAAT 59.281 34.615 0.00 0.00 0.00 1.40
84 89 1.055040 ACAGCTCTCCTTTCACAGCT 58.945 50.000 0.00 0.00 43.16 4.24
668 674 6.095160 GCAGATTCTTCCATGAAACTTCTGAT 59.905 38.462 12.61 0.00 34.81 2.90
686 692 1.260544 AAAAGCACTGGGGCAGATTC 58.739 50.000 0.00 0.00 35.18 2.52
690 696 1.909700 TCTTAAAAGCACTGGGGCAG 58.090 50.000 0.00 0.00 37.52 4.85
719 725 4.065321 GACTGTGTCCTTGCTATGCTAT 57.935 45.455 0.00 0.00 0.00 2.97
740 746 3.053693 TCCATTCCAAAGTACCTCCATGG 60.054 47.826 4.97 4.97 42.93 3.66
988 994 1.962807 TGGCCACATTTCTTCACCTTG 59.037 47.619 0.00 0.00 0.00 3.61
1106 1112 6.368779 TTTTGCTAGGCTTAGGTTTCTCTA 57.631 37.500 4.88 0.00 0.00 2.43
1448 1953 3.256631 GGCACAGTTCCAAATGATCTTGT 59.743 43.478 0.00 0.00 0.00 3.16
1503 2074 3.151554 TGTGCATTTGCTGATGACTTCT 58.848 40.909 3.94 0.00 42.66 2.85
1752 2373 4.445052 TGCTTGAAATTTGACTGCATTTCG 59.555 37.500 0.00 0.00 40.77 3.46
2110 3059 1.826385 ATGTGAGGTTAGCAGTTGGC 58.174 50.000 0.00 0.00 45.30 4.52
2173 3143 3.383620 TGTGGTGATGGTTTTCATTGC 57.616 42.857 0.00 0.00 35.97 3.56


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

AutoCloner maintained by Alex Coulton.