Multiple sequence alignment - TraesCS4B01G146500

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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 TraesCS4B01G146500 chr4B 100.000 2471 0 0 1 2471 209133142 209135612 0 4564
1 TraesCS4B01G146500 chr4B 93.472 674 28 14 1806 2471 209284034 209284699 0 987
2 TraesCS4B01G146500 chr4B 93.175 674 30 14 1806 2471 209062372 209061707 0 976
3 TraesCS4B01G146500 chr6A 98.626 2474 31 1 1 2471 64687536 64685063 0 4377
4 TraesCS4B01G146500 chr7A 98.139 2472 44 2 1 2471 60253095 60255565 0 4309
5 TraesCS4B01G146500 chr7B 95.353 2496 71 21 1 2471 52971624 52969149 0 3925
6 TraesCS4B01G146500 chr7B 95.043 1977 69 5 1 1974 139532984 139531034 0 3081
7 TraesCS4B01G146500 chrUn 98.642 2062 24 1 1 2058 86467995 86465934 0 3650
8 TraesCS4B01G146500 chrUn 98.117 903 14 1 1572 2471 449376047 449375145 0 1570
9 TraesCS4B01G146500 chr3A 98.231 1979 26 4 1 1974 633121761 633123735 0 3452
10 TraesCS4B01G146500 chr3A 93.304 672 30 13 1806 2471 633123605 633124267 0 977
11 TraesCS4B01G146500 chr1B 97.923 1974 41 0 1 1974 672580355 672578382 0 3419
12 TraesCS4B01G146500 chr1B 93.175 674 30 14 1806 2471 672578514 672577849 0 976
13 TraesCS4B01G146500 chr3D 94.397 2231 91 21 1 2229 523715700 523713502 0 3397
14 TraesCS4B01G146500 chr3D 95.630 595 22 2 1877 2471 399719059 399719649 0 952
15 TraesCS4B01G146500 chr6B 96.360 1978 60 6 1 1974 625629406 625627437 0 3243
16 TraesCS4B01G146500 chr6D 96.053 1900 68 3 1 1896 153925837 153923941 0 3086


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 TraesCS4B01G146500 chr4B 209133142 209135612 2470 False 4564.0 4564 100.0000 1 2471 1 chr4B.!!$F1 2470
1 TraesCS4B01G146500 chr4B 209284034 209284699 665 False 987.0 987 93.4720 1806 2471 1 chr4B.!!$F2 665
2 TraesCS4B01G146500 chr4B 209061707 209062372 665 True 976.0 976 93.1750 1806 2471 1 chr4B.!!$R1 665
3 TraesCS4B01G146500 chr6A 64685063 64687536 2473 True 4377.0 4377 98.6260 1 2471 1 chr6A.!!$R1 2470
4 TraesCS4B01G146500 chr7A 60253095 60255565 2470 False 4309.0 4309 98.1390 1 2471 1 chr7A.!!$F1 2470
5 TraesCS4B01G146500 chr7B 52969149 52971624 2475 True 3925.0 3925 95.3530 1 2471 1 chr7B.!!$R1 2470
6 TraesCS4B01G146500 chr7B 139531034 139532984 1950 True 3081.0 3081 95.0430 1 1974 1 chr7B.!!$R2 1973
7 TraesCS4B01G146500 chrUn 86465934 86467995 2061 True 3650.0 3650 98.6420 1 2058 1 chrUn.!!$R1 2057
8 TraesCS4B01G146500 chrUn 449375145 449376047 902 True 1570.0 1570 98.1170 1572 2471 1 chrUn.!!$R2 899
9 TraesCS4B01G146500 chr3A 633121761 633124267 2506 False 2214.5 3452 95.7675 1 2471 2 chr3A.!!$F1 2470
10 TraesCS4B01G146500 chr1B 672577849 672580355 2506 True 2197.5 3419 95.5490 1 2471 2 chr1B.!!$R1 2470
11 TraesCS4B01G146500 chr3D 523713502 523715700 2198 True 3397.0 3397 94.3970 1 2229 1 chr3D.!!$R1 2228
12 TraesCS4B01G146500 chr3D 399719059 399719649 590 False 952.0 952 95.6300 1877 2471 1 chr3D.!!$F1 594
13 TraesCS4B01G146500 chr6B 625627437 625629406 1969 True 3243.0 3243 96.3600 1 1974 1 chr6B.!!$R1 1973
14 TraesCS4B01G146500 chr6D 153923941 153925837 1896 True 3086.0 3086 96.0530 1 1896 1 chr6D.!!$R1 1895

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
628 629 1.538047 TCTGATGGTTGAGCCTTTGC 58.462 50.0 0.0 0.0 38.35 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1740 1758 0.883833 CAGAATTTTGCAGCTCCCGT 59.116 50.0 0.0 0.0 0.0 5.28 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
133 134 2.347731 GTTTTCAGCTCTAAGGTCCCG 58.652 52.381 0.00 0.00 0.00 5.14
236 237 9.533831 ACCTGATCTATTTGAACTTTAAACCAT 57.466 29.630 0.00 0.00 0.00 3.55
494 495 7.988937 AGAATGGAAGAATGCCCATAATACTA 58.011 34.615 0.00 0.00 41.98 1.82
628 629 1.538047 TCTGATGGTTGAGCCTTTGC 58.462 50.000 0.00 0.00 38.35 3.68
752 753 2.168496 CTTGTACTCGACTCTTCCCCA 58.832 52.381 0.00 0.00 0.00 4.96
814 815 4.340097 TCCAAACTCTTTCTCGTGTGACTA 59.660 41.667 0.00 0.00 0.00 2.59
1057 1065 7.535258 CACAATTTTTCTGGTTATGTCTTCTCG 59.465 37.037 0.00 0.00 0.00 4.04
1235 1248 3.256879 AGCACCGGTCTCTCATATATGTG 59.743 47.826 2.59 10.23 0.00 3.21
1248 1261 8.427902 TCTCATATATGTGCTCCAGTTTATCT 57.572 34.615 12.42 0.00 0.00 1.98
1456 1469 1.966451 GTTCCACACGGGCAAGGAG 60.966 63.158 0.00 0.00 36.21 3.69
1588 1604 5.279256 GCTTTTGGGGAGCAACAGTAATTAA 60.279 40.000 0.00 0.00 39.89 1.40
1630 1646 8.549731 CATACCAGTAGTAGGAGATACCATAGA 58.450 40.741 0.00 0.00 42.04 1.98
1681 1698 4.321675 GGACAATGCCACCTTAAATCGTTT 60.322 41.667 0.00 0.00 0.00 3.60
1740 1758 5.010213 CCTTTTGATTTAAACGTTCTCCCCA 59.990 40.000 0.00 0.00 0.00 4.96
2266 2439 1.938585 CCCCGCTCATATCTCCCTTA 58.061 55.000 0.00 0.00 0.00 2.69
2401 2574 2.497107 AACAAATGGATAGCATGCGC 57.503 45.000 13.01 0.00 38.99 6.09
2435 2608 5.525454 TCCTACCCTCAGTTGTAGTAAGA 57.475 43.478 0.00 0.00 34.04 2.10
2446 2619 7.896811 TCAGTTGTAGTAAGATGAGTGTGATT 58.103 34.615 0.00 0.00 0.00 2.57
2449 2622 6.510879 TGTAGTAAGATGAGTGTGATTCGT 57.489 37.500 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
133 134 1.398390 GGCCAACGATTGTGATGAGTC 59.602 52.381 0.00 0.00 0.00 3.36
236 237 5.183140 GCTGCTTATGTGAAAACTTCCCTTA 59.817 40.000 0.00 0.00 0.00 2.69
494 495 8.814038 ATTAGTGAGGTATTCTTCTGCATTTT 57.186 30.769 0.00 0.00 0.00 1.82
752 753 1.147817 AGCCTTTGTTGGGGAGTGATT 59.852 47.619 0.00 0.00 0.00 2.57
814 815 1.741706 CATCGCTCAAGAAAGCACCAT 59.258 47.619 0.00 0.00 42.62 3.55
1248 1261 5.338871 GGTCTTACACCATTGGGATACTTCA 60.339 44.000 7.78 0.00 45.98 3.02
1373 1386 7.180229 TGGAAGAAGTGTTATATGAGGACTTCA 59.820 37.037 16.02 0.00 43.25 3.02
1525 1541 7.006509 AGGTGGTACGTATCCTATAAAAGCTA 58.993 38.462 2.79 0.00 0.00 3.32
1630 1646 1.153756 CCACCCCAAAGCCAAGTCT 59.846 57.895 0.00 0.00 0.00 3.24
1681 1698 6.315393 GGCGAGTAAATGATGGAGACTAAAAA 59.685 38.462 0.00 0.00 0.00 1.94
1740 1758 0.883833 CAGAATTTTGCAGCTCCCGT 59.116 50.000 0.00 0.00 0.00 5.28
1752 1770 1.986210 GCTGCCCCTGCCAGAATTT 60.986 57.895 0.00 0.00 36.33 1.82
1828 1885 5.287674 TGAATCATCAGATGAACTCCCTC 57.712 43.478 17.24 7.78 43.50 4.30
2401 2574 1.004745 AGGGTAGGATTGGTTGCACAG 59.995 52.381 0.00 0.00 0.00 3.66
2435 2608 3.696548 TGCTCTCTACGAATCACACTCAT 59.303 43.478 0.00 0.00 0.00 2.90
2446 2619 4.457949 TGATACACACTTTGCTCTCTACGA 59.542 41.667 0.00 0.00 0.00 3.43


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

AutoCloner maintained by Alex Coulton.