Multiple sequence alignment - TraesCS6D01G049200

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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 TraesCS6D01G049200 chr6D 100.000 2755 0 0 1 2755 23972062 23969308 0 5088
1 TraesCS6D01G049200 chr6D 97.880 849 16 1 1909 2755 23887016 23886168 0 1467
2 TraesCS6D01G049200 chr6D 97.757 847 19 0 1909 2755 152030480 152029634 0 1459
3 TraesCS6D01G049200 chr6D 97.757 847 19 0 1909 2755 217774704 217775550 0 1459
4 TraesCS6D01G049200 chr6D 97.757 847 19 0 1909 2755 226844404 226845250 0 1459
5 TraesCS6D01G049200 chr6D 97.535 852 20 1 1905 2755 471473373 471472522 0 1456
6 TraesCS6D01G049200 chr6D 97.203 858 22 2 1898 2755 149909421 149910276 0 1450
7 TraesCS6D01G049200 chr3D 97.092 963 26 2 948 1910 542835013 542835973 0 1622
8 TraesCS6D01G049200 chr3D 96.781 963 31 0 948 1910 478120715 478121677 0 1607
9 TraesCS6D01G049200 chr3D 96.573 963 33 0 948 1910 543499683 543500645 0 1596
10 TraesCS6D01G049200 chr3D 96.369 964 31 2 948 1910 68840858 68841818 0 1583
11 TraesCS6D01G049200 chr3D 94.198 948 53 2 1 946 291070493 291069546 0 1445
12 TraesCS6D01G049200 chr3D 93.882 948 52 4 1 946 347138514 347137571 0 1424
13 TraesCS6D01G049200 chr7D 96.989 963 29 0 948 1910 116648526 116649488 0 1618
14 TraesCS6D01G049200 chr7D 97.875 847 18 0 1909 2755 124562348 124563194 0 1465
15 TraesCS6D01G049200 chr7D 94.211 950 51 4 1 947 547191239 547192187 0 1447
16 TraesCS6D01G049200 chr7D 94.006 951 53 4 1 947 162784873 162785823 0 1437
17 TraesCS6D01G049200 chr2D 96.979 960 28 1 951 1909 634062739 634061780 0 1611
18 TraesCS6D01G049200 chr5D 96.388 969 32 3 948 1914 238122487 238123454 0 1592
19 TraesCS6D01G049200 chr5D 96.552 957 32 1 954 1910 350368467 350367512 0 1583
20 TraesCS6D01G049200 chr5D 97.875 847 18 0 1909 2755 467910169 467909323 0 1465
21 TraesCS6D01G049200 chr5D 94.093 948 53 3 1 946 214284064 214285010 0 1437
22 TraesCS6D01G049200 chr5D 93.895 950 54 4 1 946 214754738 214755687 0 1430
23 TraesCS6D01G049200 chr1A 96.262 963 36 0 948 1910 506522203 506523165 0 1580
24 TraesCS6D01G049200 chr1A 94.099 949 53 3 1 946 580998480 580997532 0 1439
25 TraesCS6D01G049200 chr1D 94.515 948 50 2 1 946 214109156 214108209 0 1461
26 TraesCS6D01G049200 chr1D 97.757 847 19 0 1909 2755 430358459 430357613 0 1459
27 TraesCS6D01G049200 chr1D 93.888 949 56 2 1 947 214100545 214099597 0 1430


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 TraesCS6D01G049200 chr6D 23969308 23972062 2754 True 5088 5088 100.000 1 2755 1 chr6D.!!$R2 2754
1 TraesCS6D01G049200 chr6D 23886168 23887016 848 True 1467 1467 97.880 1909 2755 1 chr6D.!!$R1 846
2 TraesCS6D01G049200 chr6D 152029634 152030480 846 True 1459 1459 97.757 1909 2755 1 chr6D.!!$R3 846
3 TraesCS6D01G049200 chr6D 217774704 217775550 846 False 1459 1459 97.757 1909 2755 1 chr6D.!!$F2 846
4 TraesCS6D01G049200 chr6D 226844404 226845250 846 False 1459 1459 97.757 1909 2755 1 chr6D.!!$F3 846
5 TraesCS6D01G049200 chr6D 471472522 471473373 851 True 1456 1456 97.535 1905 2755 1 chr6D.!!$R4 850
6 TraesCS6D01G049200 chr6D 149909421 149910276 855 False 1450 1450 97.203 1898 2755 1 chr6D.!!$F1 857
7 TraesCS6D01G049200 chr3D 542835013 542835973 960 False 1622 1622 97.092 948 1910 1 chr3D.!!$F3 962
8 TraesCS6D01G049200 chr3D 478120715 478121677 962 False 1607 1607 96.781 948 1910 1 chr3D.!!$F2 962
9 TraesCS6D01G049200 chr3D 543499683 543500645 962 False 1596 1596 96.573 948 1910 1 chr3D.!!$F4 962
10 TraesCS6D01G049200 chr3D 68840858 68841818 960 False 1583 1583 96.369 948 1910 1 chr3D.!!$F1 962
11 TraesCS6D01G049200 chr3D 291069546 291070493 947 True 1445 1445 94.198 1 946 1 chr3D.!!$R1 945
12 TraesCS6D01G049200 chr3D 347137571 347138514 943 True 1424 1424 93.882 1 946 1 chr3D.!!$R2 945
13 TraesCS6D01G049200 chr7D 116648526 116649488 962 False 1618 1618 96.989 948 1910 1 chr7D.!!$F1 962
14 TraesCS6D01G049200 chr7D 124562348 124563194 846 False 1465 1465 97.875 1909 2755 1 chr7D.!!$F2 846
15 TraesCS6D01G049200 chr7D 547191239 547192187 948 False 1447 1447 94.211 1 947 1 chr7D.!!$F4 946
16 TraesCS6D01G049200 chr7D 162784873 162785823 950 False 1437 1437 94.006 1 947 1 chr7D.!!$F3 946
17 TraesCS6D01G049200 chr2D 634061780 634062739 959 True 1611 1611 96.979 951 1909 1 chr2D.!!$R1 958
18 TraesCS6D01G049200 chr5D 238122487 238123454 967 False 1592 1592 96.388 948 1914 1 chr5D.!!$F3 966
19 TraesCS6D01G049200 chr5D 350367512 350368467 955 True 1583 1583 96.552 954 1910 1 chr5D.!!$R1 956
20 TraesCS6D01G049200 chr5D 467909323 467910169 846 True 1465 1465 97.875 1909 2755 1 chr5D.!!$R2 846
21 TraesCS6D01G049200 chr5D 214284064 214285010 946 False 1437 1437 94.093 1 946 1 chr5D.!!$F1 945
22 TraesCS6D01G049200 chr5D 214754738 214755687 949 False 1430 1430 93.895 1 946 1 chr5D.!!$F2 945
23 TraesCS6D01G049200 chr1A 506522203 506523165 962 False 1580 1580 96.262 948 1910 1 chr1A.!!$F1 962
24 TraesCS6D01G049200 chr1A 580997532 580998480 948 True 1439 1439 94.099 1 946 1 chr1A.!!$R1 945
25 TraesCS6D01G049200 chr1D 214108209 214109156 947 True 1461 1461 94.515 1 946 1 chr1D.!!$R2 945
26 TraesCS6D01G049200 chr1D 430357613 430358459 846 True 1459 1459 97.757 1909 2755 1 chr1D.!!$R3 846
27 TraesCS6D01G049200 chr1D 214099597 214100545 948 True 1430 1430 93.888 1 947 1 chr1D.!!$R1 946

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
948 954 0.489567 AGTCCAGGACTCCCTCAACT 59.51 55.0 17.31 0.0 38.71 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2491 2503 2.434702 GACAATAATCGGGACCACTCCT 59.565 50.0 0.0 0.0 36.68 3.69 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
172 174 7.651808 GGATGTGATCCGATGACAAATTTAAT 58.348 34.615 4.70 0.00 40.13 1.40
246 248 7.303182 TGAAGATCAAGTATCCACGGATATT 57.697 36.000 8.99 2.29 39.04 1.28
282 284 2.912956 AGCTTCCAAATCTGACCTGGTA 59.087 45.455 0.00 0.00 0.00 3.25
301 303 2.589540 CCAGGGGCGTTGCTATCA 59.410 61.111 0.00 0.00 0.00 2.15
696 701 5.151454 AGAAGCCTAGCCTGTATGACTATT 58.849 41.667 0.00 0.00 0.00 1.73
745 750 3.194968 CGCCCTCCGGTTTATATAGACAT 59.805 47.826 0.00 0.00 0.00 3.06
947 953 2.233305 TAGTCCAGGACTCCCTCAAC 57.767 55.000 26.42 0.00 42.40 3.18
948 954 0.489567 AGTCCAGGACTCCCTCAACT 59.510 55.000 17.31 0.00 38.71 3.16
949 955 1.717077 AGTCCAGGACTCCCTCAACTA 59.283 52.381 17.31 0.00 38.71 2.24
973 979 0.879765 CAAGCTAGCAGCAGCAAAGT 59.120 50.000 18.83 0.00 45.56 2.66
990 996 5.003804 GCAAAGTCAAAGAAGGATGGTAGA 58.996 41.667 0.00 0.00 0.00 2.59
1096 1102 0.111253 CAAGGGCTTCAAGGAGGTGT 59.889 55.000 0.00 0.00 0.00 4.16
1189 1195 3.165875 CACCTGAGGAAGTGGAGAAGTA 58.834 50.000 4.99 0.00 0.00 2.24
1216 1222 0.321122 CCAAGTGTCCAGGCTGAGAC 60.321 60.000 17.94 20.41 0.00 3.36
1340 1346 3.716353 TCATACTGTCCACCATTGCCTAT 59.284 43.478 0.00 0.00 0.00 2.57
1421 1429 3.137544 AGTTCCTCAACACACCCATACAA 59.862 43.478 0.00 0.00 34.60 2.41
1719 1728 3.240134 GAGTGCAAGCCCCTCGACA 62.240 63.158 0.00 0.00 0.00 4.35
1752 1761 0.179073 GTATGGCGCTGTCATGACCT 60.179 55.000 22.85 2.16 0.00 3.85
1857 1867 3.680786 CCGACGCTCACAGGGTGA 61.681 66.667 0.00 0.00 41.76 4.02
2215 2225 2.806745 CGTAGGCATTGGATCGGTGATT 60.807 50.000 0.00 0.00 0.00 2.57
2234 2244 6.261603 GGTGATTGAGAATTATGTCAGATGCA 59.738 38.462 0.00 0.00 29.52 3.96
2314 2326 4.637276 TGTAATGTAGGCATGTATTCCGG 58.363 43.478 0.00 0.00 35.15 5.14
2404 2416 3.586174 GGGGTCCTAACAGAAACTAAGGT 59.414 47.826 0.00 0.00 0.00 3.50
2491 2503 3.907474 TCCTCAAACTAAGGTCATCACCA 59.093 43.478 0.00 0.00 46.68 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
165 167 5.600696 GCCCCGATGAACATGAATTAAATT 58.399 37.500 0.00 0.00 0.00 1.82
172 174 0.461870 CTCGCCCCGATGAACATGAA 60.462 55.000 0.00 0.00 34.61 2.57
234 236 0.386858 CGTCGCGAATATCCGTGGAT 60.387 55.000 12.06 6.63 40.13 3.41
246 248 0.039798 AAGCTTGAACTACGTCGCGA 60.040 50.000 3.71 3.71 0.00 5.87
377 380 1.270305 TGACGCTGTCCAAGGAGAAAG 60.270 52.381 6.30 0.00 0.00 2.62
665 669 3.039011 CAGGCTAGGCTTCTAGGGTTAA 58.961 50.000 17.59 0.00 40.53 2.01
696 701 4.775253 TCCGGATGGCATATACTCATTACA 59.225 41.667 0.00 0.00 34.14 2.41
745 750 1.854939 TGTAACCCTAGATCCCTCCGA 59.145 52.381 0.00 0.00 0.00 4.55
947 953 2.538437 CTGCTGCTAGCTTGAGTGTAG 58.462 52.381 17.23 3.05 42.97 2.74
948 954 1.404717 GCTGCTGCTAGCTTGAGTGTA 60.405 52.381 17.23 0.00 42.97 2.90
949 955 0.673022 GCTGCTGCTAGCTTGAGTGT 60.673 55.000 17.23 0.00 42.97 3.55
973 979 5.186992 TGTTCGATCTACCATCCTTCTTTGA 59.813 40.000 0.00 0.00 0.00 2.69
990 996 2.485426 CTGCCACTTCATGTTGTTCGAT 59.515 45.455 0.00 0.00 0.00 3.59
1096 1102 1.862201 CTTCGCAACGGTGTTCAAGTA 59.138 47.619 0.66 0.00 0.00 2.24
1189 1195 1.842562 CCTGGACACTTGGATCCATCT 59.157 52.381 17.06 0.00 44.06 2.90
1340 1346 5.302360 AGTGTTGTTAGTTGCGATTAGGAA 58.698 37.500 0.00 0.00 0.00 3.36
1421 1429 3.951037 TGTGTTGCATCTGGTTGTAGTTT 59.049 39.130 0.00 0.00 0.00 2.66
1719 1728 1.511613 CCATACAGGTCAGGGTGGAT 58.488 55.000 0.00 0.00 0.00 3.41
1752 1761 2.978824 GTCGCTGAAGCCACCCTA 59.021 61.111 0.00 0.00 37.91 3.53
2137 2147 4.530710 TCCGTTGCTACTGTTACAATCT 57.469 40.909 0.00 0.00 0.00 2.40
2215 2225 6.408869 TGAACTGCATCTGACATAATTCTCA 58.591 36.000 0.00 0.00 0.00 3.27
2491 2503 2.434702 GACAATAATCGGGACCACTCCT 59.565 50.000 0.00 0.00 36.68 3.69


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

AutoCloner maintained by Alex Coulton.