Multiple sequence alignment - TraesCS4B01G159500

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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 TraesCS4B01G159500 chr4B 100.000 2141 0 0 1 2141 308696712 308698852 0 3954
1 TraesCS4B01G159500 chr5D 97.484 1431 34 2 1 1430 503218460 503219889 0 2442
2 TraesCS4B01G159500 chr5D 97.135 1431 39 2 1 1430 503277984 503276555 0 2414
3 TraesCS4B01G159500 chr5D 97.065 1431 40 2 1 1430 6189182 6190611 0 2409
4 TraesCS4B01G159500 chr5D 88.730 701 72 6 1431 2128 194559621 194558925 0 850
5 TraesCS4B01G159500 chr5D 88.559 708 68 10 1428 2128 187768303 187769004 0 846
6 TraesCS4B01G159500 chr3B 97.484 1431 34 2 1 1430 201527266 201528695 0 2442
7 TraesCS4B01G159500 chr3B 91.335 704 60 1 1433 2136 351079962 351080664 0 961
8 TraesCS4B01G159500 chr1A 97.484 1431 34 2 1 1430 554512490 554513919 0 2442
9 TraesCS4B01G159500 chr3A 97.414 1431 33 3 1 1430 672909765 672908338 0 2435
10 TraesCS4B01G159500 chr3D 97.402 1424 34 3 8 1430 589279295 589277874 0 2422
11 TraesCS4B01G159500 chr3D 88.652 705 67 10 1431 2128 14100832 14100134 0 846
12 TraesCS4B01G159500 chrUn 97.135 1431 39 2 1 1430 346596252 346594823 0 2414
13 TraesCS4B01G159500 chrUn 88.604 702 73 6 1431 2128 115905280 115905978 0 846
14 TraesCS4B01G159500 chr6D 97.065 1431 40 2 1 1430 168255168 168256597 0 2409
15 TraesCS4B01G159500 chr2D 88.730 701 71 7 1431 2128 271097038 271096343 0 850
16 TraesCS4B01G159500 chr7D 88.604 702 73 7 1430 2128 336370268 336369571 0 846
17 TraesCS4B01G159500 chr7D 88.445 701 72 9 1431 2128 330696156 330696850 0 837
18 TraesCS4B01G159500 chr1D 88.462 702 72 8 1431 2128 177356524 177355828 0 839


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 TraesCS4B01G159500 chr4B 308696712 308698852 2140 False 3954 3954 100.000 1 2141 1 chr4B.!!$F1 2140
1 TraesCS4B01G159500 chr5D 503218460 503219889 1429 False 2442 2442 97.484 1 1430 1 chr5D.!!$F3 1429
2 TraesCS4B01G159500 chr5D 503276555 503277984 1429 True 2414 2414 97.135 1 1430 1 chr5D.!!$R2 1429
3 TraesCS4B01G159500 chr5D 6189182 6190611 1429 False 2409 2409 97.065 1 1430 1 chr5D.!!$F1 1429
4 TraesCS4B01G159500 chr5D 194558925 194559621 696 True 850 850 88.730 1431 2128 1 chr5D.!!$R1 697
5 TraesCS4B01G159500 chr5D 187768303 187769004 701 False 846 846 88.559 1428 2128 1 chr5D.!!$F2 700
6 TraesCS4B01G159500 chr3B 201527266 201528695 1429 False 2442 2442 97.484 1 1430 1 chr3B.!!$F1 1429
7 TraesCS4B01G159500 chr3B 351079962 351080664 702 False 961 961 91.335 1433 2136 1 chr3B.!!$F2 703
8 TraesCS4B01G159500 chr1A 554512490 554513919 1429 False 2442 2442 97.484 1 1430 1 chr1A.!!$F1 1429
9 TraesCS4B01G159500 chr3A 672908338 672909765 1427 True 2435 2435 97.414 1 1430 1 chr3A.!!$R1 1429
10 TraesCS4B01G159500 chr3D 589277874 589279295 1421 True 2422 2422 97.402 8 1430 1 chr3D.!!$R2 1422
11 TraesCS4B01G159500 chr3D 14100134 14100832 698 True 846 846 88.652 1431 2128 1 chr3D.!!$R1 697
12 TraesCS4B01G159500 chrUn 346594823 346596252 1429 True 2414 2414 97.135 1 1430 1 chrUn.!!$R1 1429
13 TraesCS4B01G159500 chrUn 115905280 115905978 698 False 846 846 88.604 1431 2128 1 chrUn.!!$F1 697
14 TraesCS4B01G159500 chr6D 168255168 168256597 1429 False 2409 2409 97.065 1 1430 1 chr6D.!!$F1 1429
15 TraesCS4B01G159500 chr2D 271096343 271097038 695 True 850 850 88.730 1431 2128 1 chr2D.!!$R1 697
16 TraesCS4B01G159500 chr7D 336369571 336370268 697 True 846 846 88.604 1430 2128 1 chr7D.!!$R1 698
17 TraesCS4B01G159500 chr7D 330696156 330696850 694 False 837 837 88.445 1431 2128 1 chr7D.!!$F1 697
18 TraesCS4B01G159500 chr1D 177355828 177356524 696 True 839 839 88.462 1431 2128 1 chr1D.!!$R1 697

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
928 929 0.523335 GCGCTTTAACCATTCAGCCG 60.523 55.0 0.0 0.0 0.0 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2044 2052 1.204941 CCACGAAGGGGTAAGTGAGAG 59.795 57.143 0.0 0.0 36.79 3.2 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
144 145 5.029807 TGTATGCATTTCGATTAGGGTCA 57.970 39.130 3.54 0.0 0.00 4.02
217 218 6.946229 AATCTATTTTACAGTATAGGCGCG 57.054 37.500 0.00 0.0 0.00 6.86
299 300 1.431488 CGGTGCCGTCCATGAATCAG 61.431 60.000 1.93 0.0 34.35 2.90
308 309 5.239306 GCCGTCCATGAATCAGATTATTTCA 59.761 40.000 0.00 0.0 34.18 2.69
335 336 6.547510 GGATTGGATTTAACTTGCCTGTCTAT 59.452 38.462 0.00 0.0 0.00 1.98
498 499 3.117550 TGCATTGTATGGCCCAGAATAGT 60.118 43.478 0.00 0.0 0.00 2.12
838 839 4.591072 GGATAGAGAGCCAGTTCCAATAGT 59.409 45.833 0.00 0.0 0.00 2.12
928 929 0.523335 GCGCTTTAACCATTCAGCCG 60.523 55.000 0.00 0.0 0.00 5.52
951 952 3.459227 TGGATGCTTAACAGGGATCATCA 59.541 43.478 0.00 0.0 34.04 3.07
1253 1255 6.322201 CCTAGTTGGCATTGATAACAAGGATT 59.678 38.462 1.20 0.0 39.71 3.01
1478 1480 1.040646 TGTCAAGAGTCTGTTCGGCT 58.959 50.000 0.00 0.0 0.00 5.52
1582 1584 7.068348 GGATGGTATACTACTTGACACTTCTCA 59.932 40.741 2.25 0.0 0.00 3.27
1583 1585 7.770366 TGGTATACTACTTGACACTTCTCAA 57.230 36.000 2.25 0.0 0.00 3.02
1609 1611 3.244526 TGCATGCATAGGTATTGTCGGAT 60.245 43.478 18.46 0.0 0.00 4.18
1622 1624 1.134367 TGTCGGATCTTCACGGATGTC 59.866 52.381 0.00 0.0 0.00 3.06
1779 1781 4.711949 CCGCCAAGGAGCTGCACT 62.712 66.667 8.35 0.0 45.00 4.40
1805 1807 0.106268 TGGCCAACAACATCAGTGGT 60.106 50.000 0.61 0.0 31.62 4.16
1806 1808 1.143889 TGGCCAACAACATCAGTGGTA 59.856 47.619 0.61 0.0 29.65 3.25
1851 1853 2.594303 CCGTGCCTCACCAAAGCA 60.594 61.111 0.00 0.0 0.00 3.91
1894 1896 4.796231 ATCCGGCAGCGACGACAC 62.796 66.667 0.00 0.0 35.20 3.67
1921 1923 2.977772 CCAAAGTTTGGCCACTTCAA 57.022 45.000 21.39 0.0 45.17 2.69
2136 2144 8.449397 CAAATATCATAGCTCATTCTTAGGTGC 58.551 37.037 0.00 0.0 0.00 5.01
2137 2145 5.822132 ATCATAGCTCATTCTTAGGTGCT 57.178 39.130 0.00 0.0 38.33 4.40
2138 2146 5.620738 TCATAGCTCATTCTTAGGTGCTT 57.379 39.130 0.00 0.0 36.45 3.91
2139 2147 5.994250 TCATAGCTCATTCTTAGGTGCTTT 58.006 37.500 0.00 0.0 36.45 3.51
2140 2148 5.819379 TCATAGCTCATTCTTAGGTGCTTTG 59.181 40.000 0.00 0.0 36.45 2.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 5.597430 TCCTATATCAATGGGAAATGCCA 57.403 39.130 0.00 0.00 39.63 4.92
103 104 8.203485 TGCATACATTTGTCTCATACACTATGA 58.797 33.333 0.00 0.00 42.56 2.15
144 145 9.529823 TCTGGTAGAATCGTAACCATAGAATAT 57.470 33.333 5.80 0.00 42.23 1.28
206 207 1.811359 GAGGTCATACGCGCCTATACT 59.189 52.381 5.73 0.00 31.89 2.12
217 218 1.903183 GCATAGAGGGGGAGGTCATAC 59.097 57.143 0.00 0.00 0.00 2.39
308 309 5.025453 ACAGGCAAGTTAAATCCAATCCAT 58.975 37.500 0.00 0.00 0.00 3.41
321 322 3.073274 GGAACCATAGACAGGCAAGTT 57.927 47.619 0.00 0.00 0.00 2.66
928 929 3.281727 TGATCCCTGTTAAGCATCCAC 57.718 47.619 0.00 0.00 0.00 4.02
996 997 8.342634 TCTCGGGATATTTTCGATTTCATTTTC 58.657 33.333 0.00 0.00 32.32 2.29
1016 1017 1.806542 CCGAATATTTGCCATCTCGGG 59.193 52.381 0.40 0.00 41.61 5.14
1170 1172 7.508977 TCCTTTGATAACCAAGGTCATTCTTTT 59.491 33.333 3.22 0.00 35.94 2.27
1450 1452 2.676839 CAGACTCTTGACATGGTGATGC 59.323 50.000 0.00 0.00 32.14 3.91
1478 1480 3.694566 AGTAGATGTCGCATGTGTCACTA 59.305 43.478 8.36 9.21 0.00 2.74
1582 1584 2.260844 ATACCTATGCATGCACGCTT 57.739 45.000 25.37 9.96 0.00 4.68
1583 1585 1.875514 CAATACCTATGCATGCACGCT 59.124 47.619 25.37 10.39 0.00 5.07
1585 1587 2.096762 CGACAATACCTATGCATGCACG 60.097 50.000 25.37 16.91 0.00 5.34
1609 1611 1.095600 CTCCTCGACATCCGTGAAGA 58.904 55.000 0.00 0.00 39.75 2.87
1622 1624 1.739562 GTGCTTGCACTCCTCCTCG 60.740 63.158 17.36 0.00 0.00 4.63
1673 1675 1.745115 CTTCGGCCATCGCTTCCAA 60.745 57.895 2.24 0.00 39.05 3.53
1683 1685 2.970639 CTCCGTCTTCTTCGGCCA 59.029 61.111 2.24 0.00 46.49 5.36
1685 1687 1.517475 GAGCTCCGTCTTCTTCGGC 60.517 63.158 0.87 0.00 46.49 5.54
1687 1689 0.179150 CAGGAGCTCCGTCTTCTTCG 60.179 60.000 26.95 4.67 42.08 3.79
1703 1705 2.512515 GGCCGCTGTAGCTTCAGG 60.513 66.667 20.39 8.19 39.32 3.86
1779 1781 2.088423 GATGTTGTTGGCCATCCGTTA 58.912 47.619 6.09 0.00 33.00 3.18
1805 1807 3.536917 CTGGCGCCGGATGTCCTA 61.537 66.667 32.31 2.65 0.00 2.94
1835 1837 2.639286 GTGCTTTGGTGAGGCACG 59.361 61.111 0.00 0.00 44.91 5.34
1837 1839 2.594303 CCGTGCTTTGGTGAGGCA 60.594 61.111 0.00 0.00 0.00 4.75
1843 1845 4.397348 GGATGTCCGTGCTTTGGT 57.603 55.556 0.00 0.00 0.00 3.67
1885 1887 2.624264 GGTGTGTTGTGTCGTCGC 59.376 61.111 0.00 0.00 0.00 5.19
2044 2052 1.204941 CCACGAAGGGGTAAGTGAGAG 59.795 57.143 0.00 0.00 36.79 3.20
2117 2125 6.057627 CAAAGCACCTAAGAATGAGCTATG 57.942 41.667 0.00 0.00 0.00 2.23


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

AutoCloner maintained by Alex Coulton.