Multiple sequence alignment - TraesCS6B01G036700

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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 TraesCS6B01G036700 chr6B 100.000 6768 0 0 1 6768 21371782 21365015 0 12499
1 TraesCS6B01G036700 chr7A 98.573 6796 68 11 1 6768 624766405 624759611 0 11985
2 TraesCS6B01G036700 chr7A 98.163 6805 85 13 1 6768 634123087 634129888 0 11838
3 TraesCS6B01G036700 chr7A 92.286 1789 62 31 173 1929 636922327 636924071 0 2470
4 TraesCS6B01G036700 chr7A 90.858 1783 85 34 172 1929 299376458 299374729 0 2318
5 TraesCS6B01G036700 chr7A 85.526 988 94 32 953 1929 667398938 667397989 0 987
6 TraesCS6B01G036700 chr1B 98.366 6794 78 15 1 6768 637607124 637613910 0 11900
7 TraesCS6B01G036700 chr6A 98.236 6803 81 21 1 6768 480630554 480637352 0 11862
8 TraesCS6B01G036700 chr6A 98.306 6788 70 9 1 6768 570883168 570889930 0 11856
9 TraesCS6B01G036700 chr6A 98.163 6803 89 16 1 6768 87933827 87940628 0 11838
10 TraesCS6B01G036700 chr6A 98.475 6622 69 11 179 6768 12700532 12693911 0 11640
11 TraesCS6B01G036700 chr6A 98.410 4277 43 11 5 4260 591833227 591837499 0 7498
12 TraesCS6B01G036700 chr7B 98.205 6798 91 15 1 6768 666533833 666527037 0 11849
13 TraesCS6B01G036700 chr7B 98.176 6799 88 22 1 6768 194120429 194127222 0 11836
14 TraesCS6B01G036700 chr5A 98.174 5421 68 16 1 5396 396395838 396401252 0 9433
15 TraesCS6B01G036700 chr5A 98.391 4848 64 5 1928 6768 294228996 294233836 0 8508
16 TraesCS6B01G036700 chr5A 97.021 772 12 6 1 762 17444569 17445339 0 1288
17 TraesCS6B01G036700 chr2A 98.309 4850 71 9 1928 6768 389214722 389209875 0 8492
18 TraesCS6B01G036700 chr2A 94.406 1448 50 19 493 1930 614230791 614229365 0 2196
19 TraesCS6B01G036700 chr2A 96.653 717 12 7 1 706 389216846 389216131 0 1181
20 TraesCS6B01G036700 chr2A 86.994 938 82 27 996 1929 378369075 378369976 0 1020
21 TraesCS6B01G036700 chr4B 97.236 1954 27 13 1 1929 14719155 14717204 0 3284
22 TraesCS6B01G036700 chr4B 97.184 1953 26 13 1 1929 261499270 261497323 0 3275
23 TraesCS6B01G036700 chr4B 97.035 1956 29 14 1 1929 149733257 149731304 0 3264
24 TraesCS6B01G036700 chr2B 97.236 1954 27 13 1 1929 741902547 741904498 0 3284
25 TraesCS6B01G036700 chr2B 86.441 1003 90 31 939 1929 652838951 652837983 0 1057
26 TraesCS6B01G036700 chr4A 99.116 1583 10 4 1 1580 66557159 66555578 0 2843
27 TraesCS6B01G036700 chr4A 84.646 990 99 32 953 1929 527898432 527897483 0 937
28 TraesCS6B01G036700 chr5D 88.900 1000 64 30 939 1929 545963203 545964164 0 1188
29 TraesCS6B01G036700 chr1D 88.229 1011 64 31 929 1929 479062846 479063811 0 1157
30 TraesCS6B01G036700 chr1D 85.115 1001 97 34 939 1929 77359076 77358118 0 976
31 TraesCS6B01G036700 chr6D 86.241 1003 84 32 939 1929 318120756 318119796 0 1038
32 TraesCS6B01G036700 chr2D 85.900 1000 85 33 939 1929 525287448 525286496 0 1014


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 TraesCS6B01G036700 chr6B 21365015 21371782 6767 True 12499.0 12499 100.000 1 6768 1 chr6B.!!$R1 6767
1 TraesCS6B01G036700 chr7A 624759611 624766405 6794 True 11985.0 11985 98.573 1 6768 1 chr7A.!!$R2 6767
2 TraesCS6B01G036700 chr7A 634123087 634129888 6801 False 11838.0 11838 98.163 1 6768 1 chr7A.!!$F1 6767
3 TraesCS6B01G036700 chr7A 636922327 636924071 1744 False 2470.0 2470 92.286 173 1929 1 chr7A.!!$F2 1756
4 TraesCS6B01G036700 chr7A 299374729 299376458 1729 True 2318.0 2318 90.858 172 1929 1 chr7A.!!$R1 1757
5 TraesCS6B01G036700 chr7A 667397989 667398938 949 True 987.0 987 85.526 953 1929 1 chr7A.!!$R3 976
6 TraesCS6B01G036700 chr1B 637607124 637613910 6786 False 11900.0 11900 98.366 1 6768 1 chr1B.!!$F1 6767
7 TraesCS6B01G036700 chr6A 480630554 480637352 6798 False 11862.0 11862 98.236 1 6768 1 chr6A.!!$F2 6767
8 TraesCS6B01G036700 chr6A 570883168 570889930 6762 False 11856.0 11856 98.306 1 6768 1 chr6A.!!$F3 6767
9 TraesCS6B01G036700 chr6A 87933827 87940628 6801 False 11838.0 11838 98.163 1 6768 1 chr6A.!!$F1 6767
10 TraesCS6B01G036700 chr6A 12693911 12700532 6621 True 11640.0 11640 98.475 179 6768 1 chr6A.!!$R1 6589
11 TraesCS6B01G036700 chr6A 591833227 591837499 4272 False 7498.0 7498 98.410 5 4260 1 chr6A.!!$F4 4255
12 TraesCS6B01G036700 chr7B 666527037 666533833 6796 True 11849.0 11849 98.205 1 6768 1 chr7B.!!$R1 6767
13 TraesCS6B01G036700 chr7B 194120429 194127222 6793 False 11836.0 11836 98.176 1 6768 1 chr7B.!!$F1 6767
14 TraesCS6B01G036700 chr5A 396395838 396401252 5414 False 9433.0 9433 98.174 1 5396 1 chr5A.!!$F3 5395
15 TraesCS6B01G036700 chr5A 294228996 294233836 4840 False 8508.0 8508 98.391 1928 6768 1 chr5A.!!$F2 4840
16 TraesCS6B01G036700 chr5A 17444569 17445339 770 False 1288.0 1288 97.021 1 762 1 chr5A.!!$F1 761
17 TraesCS6B01G036700 chr2A 389209875 389216846 6971 True 4836.5 8492 97.481 1 6768 2 chr2A.!!$R2 6767
18 TraesCS6B01G036700 chr2A 614229365 614230791 1426 True 2196.0 2196 94.406 493 1930 1 chr2A.!!$R1 1437
19 TraesCS6B01G036700 chr2A 378369075 378369976 901 False 1020.0 1020 86.994 996 1929 1 chr2A.!!$F1 933
20 TraesCS6B01G036700 chr4B 14717204 14719155 1951 True 3284.0 3284 97.236 1 1929 1 chr4B.!!$R1 1928
21 TraesCS6B01G036700 chr4B 261497323 261499270 1947 True 3275.0 3275 97.184 1 1929 1 chr4B.!!$R3 1928
22 TraesCS6B01G036700 chr4B 149731304 149733257 1953 True 3264.0 3264 97.035 1 1929 1 chr4B.!!$R2 1928
23 TraesCS6B01G036700 chr2B 741902547 741904498 1951 False 3284.0 3284 97.236 1 1929 1 chr2B.!!$F1 1928
24 TraesCS6B01G036700 chr2B 652837983 652838951 968 True 1057.0 1057 86.441 939 1929 1 chr2B.!!$R1 990
25 TraesCS6B01G036700 chr4A 66555578 66557159 1581 True 2843.0 2843 99.116 1 1580 1 chr4A.!!$R1 1579
26 TraesCS6B01G036700 chr4A 527897483 527898432 949 True 937.0 937 84.646 953 1929 1 chr4A.!!$R2 976
27 TraesCS6B01G036700 chr5D 545963203 545964164 961 False 1188.0 1188 88.900 939 1929 1 chr5D.!!$F1 990
28 TraesCS6B01G036700 chr1D 479062846 479063811 965 False 1157.0 1157 88.229 929 1929 1 chr1D.!!$F1 1000
29 TraesCS6B01G036700 chr1D 77358118 77359076 958 True 976.0 976 85.115 939 1929 1 chr1D.!!$R1 990
30 TraesCS6B01G036700 chr6D 318119796 318120756 960 True 1038.0 1038 86.241 939 1929 1 chr6D.!!$R1 990
31 TraesCS6B01G036700 chr2D 525286496 525287448 952 True 1014.0 1014 85.900 939 1929 1 chr2D.!!$R1 990

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
454 459 3.600388 CCAGTTGCTCTACTTAGTTGGG 58.400 50.000 0.0 0.0 0.00 4.12 F
2071 2380 0.671781 GAGCGACCATCACAAGCAGT 60.672 55.000 0.0 0.0 0.00 4.40 F
2228 2537 0.472925 TCCTGGTGCAGTCCTACCAA 60.473 55.000 0.0 0.0 45.65 3.67 F
2366 2675 3.118112 ACAAGGATGCCACTAGGAGATTG 60.118 47.826 0.0 0.0 36.89 2.67 F
4984 5336 2.629656 GCAGCATCCACGGCAAACT 61.630 57.895 0.0 0.0 0.00 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2228 2537 2.057922 ACCATTTCAGAGGTCTGTGGT 58.942 47.619 12.72 12.72 42.49 4.16 R
4039 4363 1.663161 CCGCCGTCTCTTTCTTTTTGC 60.663 52.381 0.00 0.00 0.00 3.68 R
4984 5336 0.673985 CACTTCTGGACCACGTGAGA 59.326 55.000 19.30 9.01 0.00 3.27 R
5051 5403 2.485814 GCAACTTCACTCACCATCTTCC 59.514 50.000 0.00 0.00 0.00 3.46 R
5969 6334 1.376466 GGCCCTGAAGAACTGCTCA 59.624 57.895 0.00 0.00 0.00 4.26 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
229 232 7.159372 GGTGTTCAGAGATTTAAGTGGTTAGA 58.841 38.462 0.00 0.00 0.00 2.10
454 459 3.600388 CCAGTTGCTCTACTTAGTTGGG 58.400 50.000 0.00 0.00 0.00 4.12
1256 1425 2.778299 TGAGGTAAGTGGCATGTTGAC 58.222 47.619 0.00 0.00 0.00 3.18
1590 1811 5.351465 ACATTAGTTGGCATCTTGTAGTTCG 59.649 40.000 2.98 0.00 0.00 3.95
2071 2380 0.671781 GAGCGACCATCACAAGCAGT 60.672 55.000 0.00 0.00 0.00 4.40
2228 2537 0.472925 TCCTGGTGCAGTCCTACCAA 60.473 55.000 0.00 0.00 45.65 3.67
2366 2675 3.118112 ACAAGGATGCCACTAGGAGATTG 60.118 47.826 0.00 0.00 36.89 2.67
2513 2822 3.577805 ACTTTTCTAGCACCAACCACT 57.422 42.857 0.00 0.00 0.00 4.00
3154 3472 7.862372 CACAGTTTTACTAATCTTGTTGCACAT 59.138 33.333 0.00 0.00 0.00 3.21
3538 3859 4.371624 TTCTATTGGCTGGGATGTATGG 57.628 45.455 0.00 0.00 0.00 2.74
3641 3962 5.337578 AGGTTTTGTAGTTGCACATGTTT 57.662 34.783 0.00 0.00 0.00 2.83
4944 5296 5.772169 GGAATATTTAAAGCTGCTCCCAGAT 59.228 40.000 1.00 0.00 41.77 2.90
4984 5336 2.629656 GCAGCATCCACGGCAAACT 61.630 57.895 0.00 0.00 0.00 2.66
5051 5403 0.675633 CAGTTGCCTCAAACCAAGGG 59.324 55.000 0.00 0.00 34.26 3.95
5982 6347 2.156917 CTTGGCATGAGCAGTTCTTCA 58.843 47.619 0.00 0.00 44.61 3.02
6275 6640 2.597455 ACAGGGCTTTTAGTTGCACAT 58.403 42.857 0.00 0.00 34.58 3.21
6552 6922 9.562408 TTTTCTGTAAGTTTTTCCAAAACCTTT 57.438 25.926 8.20 1.51 33.52 3.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
376 381 1.672356 GTGATGCAGCCAACCGAGT 60.672 57.895 0.00 0.00 0.00 4.18
792 941 6.465439 AAGTTAAGTAAAGGCAACAAGCTT 57.535 33.333 0.00 0.00 44.79 3.74
1590 1811 5.567138 ACTATGAAAACATGCCAACTAGC 57.433 39.130 0.00 0.00 0.00 3.42
1968 2277 9.539825 TGAAAGCATTACACAAACATTAAACAT 57.460 25.926 0.00 0.00 0.00 2.71
2071 2380 2.106511 GCTGGTGATGCCCTTATCCTAA 59.893 50.000 0.00 0.00 36.04 2.69
2228 2537 2.057922 ACCATTTCAGAGGTCTGTGGT 58.942 47.619 12.72 12.72 42.49 4.16
2366 2675 4.154918 CCAGTTATGTTGAAAGCCTGTCTC 59.845 45.833 0.00 0.00 0.00 3.36
2513 2822 2.034687 GGGCTGAGCTTCAAGGCA 59.965 61.111 16.76 0.00 34.17 4.75
3154 3472 4.019771 TCCTACCAACTGATGCAACACATA 60.020 41.667 0.00 0.00 39.84 2.29
3475 3796 9.619316 GATACAAGTTTATGTATGCAAAACACA 57.381 29.630 12.22 5.26 44.44 3.72
3538 3859 7.871853 ACAAAAGTTATACATGTCCAACTGAC 58.128 34.615 20.00 5.43 44.72 3.51
3577 3898 8.046708 ACATACATCACAGCCAACTAAATTCTA 58.953 33.333 0.00 0.00 0.00 2.10
4039 4363 1.663161 CCGCCGTCTCTTTCTTTTTGC 60.663 52.381 0.00 0.00 0.00 3.68
4984 5336 0.673985 CACTTCTGGACCACGTGAGA 59.326 55.000 19.30 9.01 0.00 3.27
5051 5403 2.485814 GCAACTTCACTCACCATCTTCC 59.514 50.000 0.00 0.00 0.00 3.46
5969 6334 1.376466 GGCCCTGAAGAACTGCTCA 59.624 57.895 0.00 0.00 0.00 4.26
5982 6347 4.335647 CGTGCAAGAGGTGGCCCT 62.336 66.667 0.00 0.00 46.66 5.19
6658 7028 3.281727 TGTGGATCCCTTGCTGTAATC 57.718 47.619 9.90 0.00 0.00 1.75


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

AutoCloner maintained by Alex Coulton.