Multiple sequence alignment - TraesCS6A01G074900

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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 TraesCS6A01G074900 chr6A 100.000 3907 0 0 1 3907 44182786 44186692 0.000000e+00 7215.0
1 TraesCS6A01G074900 chr6A 99.590 3907 16 0 1 3907 44091489 44095395 0.000000e+00 7127.0
2 TraesCS6A01G074900 chr6A 95.301 2426 99 9 1485 3907 43275187 43277600 0.000000e+00 3834.0
3 TraesCS6A01G074900 chr6A 82.201 309 28 16 848 1135 43274544 43274846 1.400000e-59 241.0
4 TraesCS6A01G074900 chr6A 88.889 54 2 3 1253 1304 399220872 399220821 3.260000e-06 63.9
5 TraesCS6A01G074900 chrUn 88.793 2427 190 45 539 2935 104628306 104625932 0.000000e+00 2900.0
6 TraesCS6A01G074900 chrUn 91.238 1575 101 19 1370 2933 104682675 104681127 0.000000e+00 2109.0
7 TraesCS6A01G074900 chrUn 89.457 1603 118 21 1345 2933 104799141 104797576 0.000000e+00 1977.0
8 TraesCS6A01G074900 chrUn 88.654 758 61 18 593 1337 104683416 104682671 0.000000e+00 900.0
9 TraesCS6A01G074900 chrUn 78.598 542 89 14 4 537 62345192 62345714 2.250000e-87 333.0
10 TraesCS6A01G074900 chrUn 78.599 514 86 10 4 511 51420705 51420210 6.300000e-83 318.0
11 TraesCS6A01G074900 chrUn 81.283 374 31 16 848 1203 104799601 104799249 2.310000e-67 267.0
12 TraesCS6A01G074900 chr6B 90.333 1500 94 21 1340 2825 77010801 77012263 0.000000e+00 1919.0
13 TraesCS6A01G074900 chr6B 85.926 1549 166 34 132 1650 77459752 77458226 0.000000e+00 1605.0
14 TraesCS6A01G074900 chr6B 92.274 1139 57 9 1658 2796 77458070 77456963 0.000000e+00 1587.0
15 TraesCS6A01G074900 chr6B 78.643 501 82 15 3 495 113678848 113678365 3.790000e-80 309.0
16 TraesCS6A01G074900 chr6B 83.766 308 25 9 848 1135 77010372 77010674 6.430000e-68 268.0
17 TraesCS6A01G074900 chr6B 93.182 44 1 2 1253 1294 677205990 677206033 3.260000e-06 63.9
18 TraesCS6A01G074900 chr6B 93.023 43 1 2 1253 1293 49828826 49828784 1.170000e-05 62.1
19 TraesCS6A01G074900 chr7B 77.377 999 195 17 2928 3905 622618082 622619070 7.330000e-157 564.0
20 TraesCS6A01G074900 chr7B 82.319 526 70 13 18 537 339619503 339618995 6.000000e-118 435.0
21 TraesCS6A01G074900 chr7B 76.923 390 67 11 4 387 720876187 720876559 2.380000e-47 200.0
22 TraesCS6A01G074900 chr5B 77.619 840 177 9 2924 3756 535046025 535045190 2.100000e-137 499.0
23 TraesCS6A01G074900 chr5B 90.909 44 2 2 1253 1294 654530327 654530284 1.520000e-04 58.4
24 TraesCS6A01G074900 chr6D 76.906 892 190 12 2928 3810 161792 162676 3.510000e-135 492.0
25 TraesCS6A01G074900 chr6D 81.481 540 77 11 8 539 428978244 428978768 4.670000e-114 422.0
26 TraesCS6A01G074900 chr6D 81.559 526 76 11 18 537 20135038 20134528 7.810000e-112 414.0
27 TraesCS6A01G074900 chr6D 72.410 917 218 26 2923 3811 62211843 62210934 3.870000e-65 259.0
28 TraesCS6A01G074900 chr6D 83.744 203 31 2 538 739 389333963 389333762 1.430000e-44 191.0
29 TraesCS6A01G074900 chr2A 75.475 999 216 17 2929 3905 27627267 27626276 9.890000e-126 460.0
30 TraesCS6A01G074900 chr2A 85.027 187 22 6 556 738 702195054 702195238 6.670000e-43 185.0
31 TraesCS6A01G074900 chr7D 81.853 529 69 16 18 537 136414859 136414349 1.680000e-113 420.0
32 TraesCS6A01G074900 chr7D 81.298 524 77 8 18 535 628134554 628135062 4.700000e-109 405.0
33 TraesCS6A01G074900 chr7D 78.598 542 87 15 4 537 105425808 105425288 8.090000e-87 331.0
34 TraesCS6A01G074900 chr7D 79.135 393 59 13 3 387 5079836 5079459 2.330000e-62 250.0
35 TraesCS6A01G074900 chr4D 81.250 528 75 17 18 537 428988518 428988007 4.700000e-109 405.0
36 TraesCS6A01G074900 chr3A 81.179 526 78 11 18 537 134257625 134257115 1.690000e-108 403.0
37 TraesCS6A01G074900 chr3D 78.930 598 120 6 2917 3510 612690926 612690331 6.080000e-108 401.0
38 TraesCS6A01G074900 chr3D 86.058 208 19 9 536 740 608540373 608540173 8.500000e-52 215.0
39 TraesCS6A01G074900 chr5D 80.220 546 81 15 1 537 318867902 318867375 6.120000e-103 385.0
40 TraesCS6A01G074900 chr7A 76.881 545 102 13 1 537 140745874 140745346 1.780000e-73 287.0
41 TraesCS6A01G074900 chr2B 76.493 519 94 10 23 535 90700694 90701190 1.390000e-64 257.0
42 TraesCS6A01G074900 chr1D 86.022 186 21 5 557 740 434612183 434612365 1.110000e-45 195.0
43 TraesCS6A01G074900 chr1D 81.683 202 31 4 538 738 45133157 45133353 3.120000e-36 163.0
44 TraesCS6A01G074900 chr1A 83.511 188 26 4 556 739 434422873 434422687 1.870000e-38 171.0
45 TraesCS6A01G074900 chr3B 82.126 207 28 8 538 739 172729495 172729697 6.710000e-38 169.0
46 TraesCS6A01G074900 chr3B 90.000 50 2 3 1253 1299 373620260 373620211 1.170000e-05 62.1
47 TraesCS6A01G074900 chr2D 95.082 61 3 0 2930 2990 580385735 580385675 3.210000e-16 97.1
48 TraesCS6A01G074900 chr5A 93.750 64 3 1 2927 2990 580557760 580557822 1.160000e-15 95.3
49 TraesCS6A01G074900 chr4A 90.909 44 2 2 1253 1294 722057014 722056971 1.520000e-04 58.4


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 TraesCS6A01G074900 chr6A 44182786 44186692 3906 False 7215.0 7215 100.0000 1 3907 1 chr6A.!!$F2 3906
1 TraesCS6A01G074900 chr6A 44091489 44095395 3906 False 7127.0 7127 99.5900 1 3907 1 chr6A.!!$F1 3906
2 TraesCS6A01G074900 chr6A 43274544 43277600 3056 False 2037.5 3834 88.7510 848 3907 2 chr6A.!!$F3 3059
3 TraesCS6A01G074900 chrUn 104625932 104628306 2374 True 2900.0 2900 88.7930 539 2935 1 chrUn.!!$R2 2396
4 TraesCS6A01G074900 chrUn 104681127 104683416 2289 True 1504.5 2109 89.9460 593 2933 2 chrUn.!!$R3 2340
5 TraesCS6A01G074900 chrUn 104797576 104799601 2025 True 1122.0 1977 85.3700 848 2933 2 chrUn.!!$R4 2085
6 TraesCS6A01G074900 chrUn 62345192 62345714 522 False 333.0 333 78.5980 4 537 1 chrUn.!!$F1 533
7 TraesCS6A01G074900 chr6B 77456963 77459752 2789 True 1596.0 1605 89.1000 132 2796 2 chr6B.!!$R3 2664
8 TraesCS6A01G074900 chr6B 77010372 77012263 1891 False 1093.5 1919 87.0495 848 2825 2 chr6B.!!$F2 1977
9 TraesCS6A01G074900 chr7B 622618082 622619070 988 False 564.0 564 77.3770 2928 3905 1 chr7B.!!$F1 977
10 TraesCS6A01G074900 chr7B 339618995 339619503 508 True 435.0 435 82.3190 18 537 1 chr7B.!!$R1 519
11 TraesCS6A01G074900 chr5B 535045190 535046025 835 True 499.0 499 77.6190 2924 3756 1 chr5B.!!$R1 832
12 TraesCS6A01G074900 chr6D 161792 162676 884 False 492.0 492 76.9060 2928 3810 1 chr6D.!!$F1 882
13 TraesCS6A01G074900 chr6D 428978244 428978768 524 False 422.0 422 81.4810 8 539 1 chr6D.!!$F2 531
14 TraesCS6A01G074900 chr6D 20134528 20135038 510 True 414.0 414 81.5590 18 537 1 chr6D.!!$R1 519
15 TraesCS6A01G074900 chr6D 62210934 62211843 909 True 259.0 259 72.4100 2923 3811 1 chr6D.!!$R2 888
16 TraesCS6A01G074900 chr2A 27626276 27627267 991 True 460.0 460 75.4750 2929 3905 1 chr2A.!!$R1 976
17 TraesCS6A01G074900 chr7D 136414349 136414859 510 True 420.0 420 81.8530 18 537 1 chr7D.!!$R3 519
18 TraesCS6A01G074900 chr7D 628134554 628135062 508 False 405.0 405 81.2980 18 535 1 chr7D.!!$F1 517
19 TraesCS6A01G074900 chr7D 105425288 105425808 520 True 331.0 331 78.5980 4 537 1 chr7D.!!$R2 533
20 TraesCS6A01G074900 chr4D 428988007 428988518 511 True 405.0 405 81.2500 18 537 1 chr4D.!!$R1 519
21 TraesCS6A01G074900 chr3A 134257115 134257625 510 True 403.0 403 81.1790 18 537 1 chr3A.!!$R1 519
22 TraesCS6A01G074900 chr3D 612690331 612690926 595 True 401.0 401 78.9300 2917 3510 1 chr3D.!!$R2 593
23 TraesCS6A01G074900 chr5D 318867375 318867902 527 True 385.0 385 80.2200 1 537 1 chr5D.!!$R1 536
24 TraesCS6A01G074900 chr7A 140745346 140745874 528 True 287.0 287 76.8810 1 537 1 chr7A.!!$R1 536

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
832 866 0.942962 GATCTGATGGGCTTTCGCAG 59.057 55.0 0.0 0.0 38.59 5.18 F
1166 1220 2.224079 CACATCTGGTCAAACTGGTTCG 59.776 50.0 0.0 0.0 0.00 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1797 2110 3.323979 GGGACTGAAACTGGAACTGTCTA 59.676 47.826 0.00 0.0 40.38 2.59 R
3174 3522 8.862325 ATATTGCTTGGAATATATGGAACGAA 57.138 30.769 5.73 0.0 28.55 3.85 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
70 74 3.031736 ACCACCTAGCGATGACTACAAT 58.968 45.455 0.0 0.0 0.00 2.71
832 866 0.942962 GATCTGATGGGCTTTCGCAG 59.057 55.000 0.0 0.0 38.59 5.18
1166 1220 2.224079 CACATCTGGTCAAACTGGTTCG 59.776 50.000 0.0 0.0 0.00 3.95
1425 1545 4.757149 AGAGTGACCGATTTTCTTTGGAAG 59.243 41.667 0.0 0.0 32.61 3.46
1797 2110 0.251341 CCACCCAGTTTAGCAAGGCT 60.251 55.000 0.0 0.0 43.41 4.58
3174 3522 4.142138 TGTTGGAAAACACGCCTATTTTGT 60.142 37.500 0.0 0.0 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
70 74 0.319900 GCTTCGAGGTGCTTCAGTGA 60.320 55.000 0.00 0.0 0.00 3.41
1166 1220 1.659954 CTCATAGACGCAGCTCGCC 60.660 63.158 5.63 0.0 43.23 5.54
1425 1545 6.948589 AGAGTTGGATAAAACCTTCTCCTAC 58.051 40.000 0.00 0.0 35.30 3.18
1797 2110 3.323979 GGGACTGAAACTGGAACTGTCTA 59.676 47.826 0.00 0.0 40.38 2.59
3174 3522 8.862325 ATATTGCTTGGAATATATGGAACGAA 57.138 30.769 5.73 0.0 28.55 3.85
3354 3702 1.548357 ATCACCTCTTGCTCGGCTGT 61.548 55.000 0.00 0.0 0.00 4.40


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

AutoCloner maintained by Alex Coulton.