Multiple sequence alignment - TraesCS2D01G098800

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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 TraesCS2D01G098800 chr2D 100.000 3083 0 0 1 3083 51132945 51129863 0.000000e+00 5694.0
1 TraesCS2D01G098800 chr2D 83.396 1066 173 3 849 1912 51254357 51255420 0.000000e+00 985.0
2 TraesCS2D01G098800 chr2D 88.679 53 6 0 2212 2264 51157797 51157745 7.140000e-07 65.8
3 TraesCS2D01G098800 chr2B 95.878 1310 53 1 849 2158 79670672 79669364 0.000000e+00 2119.0
4 TraesCS2D01G098800 chr2B 90.400 125 10 1 2155 2277 79668008 79667884 2.460000e-36 163.0
5 TraesCS2D01G098800 chr2B 82.000 150 22 3 1915 2063 80202659 80202804 4.170000e-24 122.0
6 TraesCS2D01G098800 chr2A 96.913 1166 34 1 849 2012 52426820 52425655 0.000000e+00 1953.0
7 TraesCS2D01G098800 chr2A 83.208 1066 175 3 849 1912 52757727 52758790 0.000000e+00 974.0
8 TraesCS2D01G098800 chr2A 90.566 53 5 0 2212 2264 52570769 52570717 1.530000e-08 71.3
9 TraesCS2D01G098800 chr7D 98.124 853 15 1 1 853 119007404 119006553 0.000000e+00 1485.0
10 TraesCS2D01G098800 chr7D 85.660 1060 143 4 861 1918 79359955 79358903 0.000000e+00 1107.0
11 TraesCS2D01G098800 chr7D 84.874 1071 159 3 849 1918 76398018 76399086 0.000000e+00 1077.0
12 TraesCS2D01G098800 chr3A 95.878 849 35 0 1 849 737862516 737863364 0.000000e+00 1375.0
13 TraesCS2D01G098800 chr3D 97.622 799 18 1 2286 3083 18901195 18901993 0.000000e+00 1369.0
14 TraesCS2D01G098800 chr4B 95.545 853 38 0 1 853 4705211 4706063 0.000000e+00 1365.0
15 TraesCS2D01G098800 chr6D 97.372 799 20 1 2286 3083 17329585 17328787 0.000000e+00 1358.0
16 TraesCS2D01G098800 chr6D 100.000 47 0 0 806 852 144029085 144029131 1.520000e-13 87.9
17 TraesCS2D01G098800 chr1A 93.774 787 48 1 2286 3071 58387328 58386542 0.000000e+00 1181.0
18 TraesCS2D01G098800 chr7A 86.686 1059 138 3 861 1918 82154562 82153506 0.000000e+00 1171.0
19 TraesCS2D01G098800 chr7A 84.422 1072 163 4 849 1918 80314981 80316050 0.000000e+00 1051.0
20 TraesCS2D01G098800 chr3B 84.608 1072 160 5 849 1918 703923249 703924317 0.000000e+00 1061.0
21 TraesCS2D01G098800 chr3B 92.453 53 3 1 800 851 783451620 783451568 1.190000e-09 75.0
22 TraesCS2D01G098800 chr5A 94.419 663 34 2 2286 2947 641419608 641418948 0.000000e+00 1016.0
23 TraesCS2D01G098800 chr5A 90.566 53 4 1 798 849 611830465 611830413 5.520000e-08 69.4
24 TraesCS2D01G098800 chr4A 83.805 778 102 9 97 853 3273084 3273858 0.000000e+00 717.0
25 TraesCS2D01G098800 chr6B 93.750 48 3 0 806 853 678346646 678346693 4.260000e-09 73.1
26 TraesCS2D01G098800 chr6B 95.455 44 2 0 806 849 33013011 33012968 1.530000e-08 71.3


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 TraesCS2D01G098800 chr2D 51129863 51132945 3082 True 5694 5694 100.000 1 3083 1 chr2D.!!$R1 3082
1 TraesCS2D01G098800 chr2D 51254357 51255420 1063 False 985 985 83.396 849 1912 1 chr2D.!!$F1 1063
2 TraesCS2D01G098800 chr2B 79667884 79670672 2788 True 1141 2119 93.139 849 2277 2 chr2B.!!$R1 1428
3 TraesCS2D01G098800 chr2A 52425655 52426820 1165 True 1953 1953 96.913 849 2012 1 chr2A.!!$R1 1163
4 TraesCS2D01G098800 chr2A 52757727 52758790 1063 False 974 974 83.208 849 1912 1 chr2A.!!$F1 1063
5 TraesCS2D01G098800 chr7D 119006553 119007404 851 True 1485 1485 98.124 1 853 1 chr7D.!!$R2 852
6 TraesCS2D01G098800 chr7D 79358903 79359955 1052 True 1107 1107 85.660 861 1918 1 chr7D.!!$R1 1057
7 TraesCS2D01G098800 chr7D 76398018 76399086 1068 False 1077 1077 84.874 849 1918 1 chr7D.!!$F1 1069
8 TraesCS2D01G098800 chr3A 737862516 737863364 848 False 1375 1375 95.878 1 849 1 chr3A.!!$F1 848
9 TraesCS2D01G098800 chr3D 18901195 18901993 798 False 1369 1369 97.622 2286 3083 1 chr3D.!!$F1 797
10 TraesCS2D01G098800 chr4B 4705211 4706063 852 False 1365 1365 95.545 1 853 1 chr4B.!!$F1 852
11 TraesCS2D01G098800 chr6D 17328787 17329585 798 True 1358 1358 97.372 2286 3083 1 chr6D.!!$R1 797
12 TraesCS2D01G098800 chr1A 58386542 58387328 786 True 1181 1181 93.774 2286 3071 1 chr1A.!!$R1 785
13 TraesCS2D01G098800 chr7A 82153506 82154562 1056 True 1171 1171 86.686 861 1918 1 chr7A.!!$R1 1057
14 TraesCS2D01G098800 chr7A 80314981 80316050 1069 False 1051 1051 84.422 849 1918 1 chr7A.!!$F1 1069
15 TraesCS2D01G098800 chr3B 703923249 703924317 1068 False 1061 1061 84.608 849 1918 1 chr3B.!!$F1 1069
16 TraesCS2D01G098800 chr5A 641418948 641419608 660 True 1016 1016 94.419 2286 2947 1 chr5A.!!$R2 661
17 TraesCS2D01G098800 chr4A 3273084 3273858 774 False 717 717 83.805 97 853 1 chr4A.!!$F1 756

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
939 961 1.337260 GGTGATAGTAGCATCGCTGGG 60.337 57.143 0.0 0.0 40.1 4.45 F
1626 1651 1.073722 CTGCTGGCTCCTTGGTGAA 59.926 57.895 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1903 1928 0.108585 TTCTTCTCTTTGCCCACGCT 59.891 50.0 0.00 0.0 35.36 5.07 R
3052 4441 2.196997 AATACCGCTCAGCCCAGCAA 62.197 55.0 5.41 0.0 39.62 3.91 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
39 40 3.068873 GTCAAACAGGGGTTGCATAACAA 59.931 43.478 0.00 0.00 38.58 2.83
877 899 2.287915 AGTACAAGCTCAAAGTTGCACG 59.712 45.455 0.00 0.00 0.00 5.34
939 961 1.337260 GGTGATAGTAGCATCGCTGGG 60.337 57.143 0.00 0.00 40.10 4.45
969 991 2.414691 GCTTTGCGAGGACAATTTCTCC 60.415 50.000 0.00 0.00 0.00 3.71
1626 1651 1.073722 CTGCTGGCTCCTTGGTGAA 59.926 57.895 0.00 0.00 0.00 3.18
2081 2106 1.853114 GCTCCAGCGCCATCATCATG 61.853 60.000 2.29 0.00 0.00 3.07
2086 2111 1.162181 AGCGCCATCATCATGAACGG 61.162 55.000 2.29 6.24 32.80 4.44
2089 2114 1.667236 GCCATCATCATGAACGGTGA 58.333 50.000 9.70 4.95 30.57 4.02
2117 2142 2.632512 GGTGACATGGGTGGATGTTTTT 59.367 45.455 0.00 0.00 36.67 1.94
2118 2143 3.306019 GGTGACATGGGTGGATGTTTTTC 60.306 47.826 0.00 0.00 36.67 2.29
2122 2147 4.959723 ACATGGGTGGATGTTTTTCTTTG 58.040 39.130 0.00 0.00 32.38 2.77
2138 2163 3.138304 TCTTTGTCCATGTTCACTTCCG 58.862 45.455 0.00 0.00 0.00 4.30
2169 3553 5.478233 CAGTATTATTACTGTTGCGCCAA 57.522 39.130 4.18 0.00 46.84 4.52
2186 3570 7.971183 TGCGCCAACATAAATACTATATGAA 57.029 32.000 4.18 0.00 35.28 2.57
2219 3603 2.267426 TCGTTATGATTCACTGGTGCG 58.733 47.619 0.00 0.00 0.00 5.34
2224 3608 5.640732 GTTATGATTCACTGGTGCGAAATT 58.359 37.500 0.00 0.00 0.00 1.82
2233 3617 5.240623 TCACTGGTGCGAAATTTCAAGTTAT 59.759 36.000 17.99 0.00 0.00 1.89
2277 3663 8.407832 TGAGTGATTGATAATACAAATTGCTGG 58.592 33.333 0.00 0.00 33.44 4.85
2278 3664 8.297470 AGTGATTGATAATACAAATTGCTGGT 57.703 30.769 0.00 0.00 33.44 4.00
2279 3665 8.192774 AGTGATTGATAATACAAATTGCTGGTG 58.807 33.333 0.00 0.00 33.44 4.17
2280 3666 7.436080 GTGATTGATAATACAAATTGCTGGTGG 59.564 37.037 0.00 0.00 33.44 4.61
2281 3667 7.341512 TGATTGATAATACAAATTGCTGGTGGA 59.658 33.333 0.00 0.00 33.44 4.02
2282 3668 6.449635 TGATAATACAAATTGCTGGTGGAC 57.550 37.500 0.00 0.00 0.00 4.02
2283 3669 3.848272 AATACAAATTGCTGGTGGACG 57.152 42.857 0.00 0.00 0.00 4.79
2284 3670 2.552599 TACAAATTGCTGGTGGACGA 57.447 45.000 0.00 0.00 0.00 4.20
2380 3766 2.039137 GGACCTTCCCTCCTCGGT 59.961 66.667 0.00 0.00 0.00 4.69
2418 3804 4.357947 TCGCGCCTCAACTTCGCT 62.358 61.111 0.00 0.00 45.87 4.93
2635 4023 0.736636 CGTGGATACTCCTGTGCGTA 59.263 55.000 0.00 0.00 37.46 4.42
2896 4285 2.671070 AGGCGTGCCTGCTATTGT 59.329 55.556 13.68 0.00 46.22 2.71
2919 4308 1.895707 GCAGCTGCCAACACTCTGT 60.896 57.895 28.76 0.00 34.31 3.41
2927 4316 3.736483 AACACTCTGTTGCTGCCG 58.264 55.556 0.00 0.00 39.45 5.69
3020 4409 2.959357 GCAACTGCCAGAGTGCGAC 61.959 63.158 0.00 0.00 34.02 5.19
3048 4437 3.574952 TGGTTGTGCCAGCTAGGT 58.425 55.556 0.00 0.00 43.61 3.08
3052 4441 0.890996 GTTGTGCCAGCTAGGTTGCT 60.891 55.000 17.69 0.00 45.18 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 1.843368 CAGCCCTGTCATCCATTTGT 58.157 50.000 0.00 0.00 0.00 2.83
350 351 2.464459 ATAGGCTGCAAAGCGCGTC 61.464 57.895 8.43 0.00 46.97 5.19
389 390 2.499289 AGTGCAAGGAGAGATGATTCGT 59.501 45.455 0.00 0.00 0.00 3.85
400 401 0.879765 CAAAGGAGCAGTGCAAGGAG 59.120 55.000 19.20 0.00 0.00 3.69
900 922 2.166870 ACCATCGTAATTGCAGTACCGA 59.833 45.455 5.77 5.77 0.00 4.69
939 961 1.012841 CCTCGCAAAGCAGGATCTTC 58.987 55.000 0.00 0.00 31.74 2.87
969 991 4.620982 GGATTTTGGACTGTTGAACCTTG 58.379 43.478 0.00 0.00 0.00 3.61
1423 1448 2.045926 GGCAGACTTGATGGCGGT 60.046 61.111 0.00 0.00 33.23 5.68
1626 1651 1.000896 AATGGTTGCTAGGCCGCTT 60.001 52.632 0.00 0.00 0.00 4.68
1903 1928 0.108585 TTCTTCTCTTTGCCCACGCT 59.891 50.000 0.00 0.00 35.36 5.07
2086 2111 1.227999 CCATGTCACCACACGGTCAC 61.228 60.000 0.00 0.00 44.71 3.67
2096 2121 1.923356 AAACATCCACCCATGTCACC 58.077 50.000 0.00 0.00 35.87 4.02
2105 2130 4.664150 TGGACAAAGAAAAACATCCACC 57.336 40.909 0.00 0.00 31.30 4.61
2117 2142 3.138304 CGGAAGTGAACATGGACAAAGA 58.862 45.455 0.00 0.00 0.00 2.52
2118 2143 3.138304 TCGGAAGTGAACATGGACAAAG 58.862 45.455 0.00 0.00 0.00 2.77
2122 2147 2.699954 ACATCGGAAGTGAACATGGAC 58.300 47.619 0.00 0.00 0.00 4.02
2201 3585 4.678509 TTTCGCACCAGTGAATCATAAC 57.321 40.909 0.99 0.00 43.23 1.89
2214 3598 3.300590 CGCATAACTTGAAATTTCGCACC 59.699 43.478 13.34 0.00 0.00 5.01
2219 3603 7.253321 GGTTCGAATCGCATAACTTGAAATTTC 60.253 37.037 11.41 11.41 0.00 2.17
2224 3608 3.997681 TGGTTCGAATCGCATAACTTGAA 59.002 39.130 0.00 0.00 0.00 2.69
2233 3617 1.476488 TCATCTCTGGTTCGAATCGCA 59.524 47.619 0.00 0.00 0.00 5.10
2279 3665 3.808656 GGTCGTCGGAGGTCGTCC 61.809 72.222 1.16 1.16 42.85 4.79
2280 3666 2.745492 AGGTCGTCGGAGGTCGTC 60.745 66.667 0.00 0.00 40.32 4.20
2281 3667 2.745492 GAGGTCGTCGGAGGTCGT 60.745 66.667 0.00 0.00 40.32 4.34
2282 3668 3.862402 CGAGGTCGTCGGAGGTCG 61.862 72.222 7.05 0.00 45.58 4.79
2896 4285 2.515757 TGTTGGCAGCTGCGACAA 60.516 55.556 31.81 27.15 43.26 3.18
2919 4308 4.641645 CTGGTCCACCGGCAGCAA 62.642 66.667 0.00 0.00 39.43 3.91
3048 4437 2.987547 GCTCAGCCCAGCAAGCAA 60.988 61.111 8.54 0.00 38.72 3.91
3052 4441 2.196997 AATACCGCTCAGCCCAGCAA 62.197 55.000 5.41 0.00 39.62 3.91


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

AutoCloner maintained by Alex Coulton.