Multiple sequence alignment - TraesCS7B01G396200

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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 TraesCS7B01G396200 chr7B 100.000 2240 0 0 1 2240 663096932 663094693 0.000000e+00 4137.0
1 TraesCS7B01G396200 chr7B 98.259 2240 39 0 1 2240 662729407 662731646 0.000000e+00 3921.0
2 TraesCS7B01G396200 chr2A 98.795 2241 26 1 1 2240 726903962 726901722 0.000000e+00 3988.0
3 TraesCS7B01G396200 chr5D 98.394 2241 33 3 1 2240 503247765 503250003 0.000000e+00 3936.0
4 TraesCS7B01G396200 chr3D 98.349 2241 35 2 1 2240 589261034 589258795 0.000000e+00 3932.0
5 TraesCS7B01G396200 chr3B 98.304 2241 37 1 1 2240 201572294 201570054 0.000000e+00 3927.0
6 TraesCS7B01G396200 chr3B 98.125 2240 40 2 1 2240 201542013 201544250 0.000000e+00 3903.0
7 TraesCS7B01G396200 chr3B 96.886 1092 34 0 24 1115 757834128 757833037 0.000000e+00 1829.0
8 TraesCS7B01G396200 chr3B 97.108 1072 29 1 1171 2240 757832794 757831723 0.000000e+00 1807.0
9 TraesCS7B01G396200 chr3B 98.913 552 5 1 1387 1937 201547868 201547317 0.000000e+00 985.0
10 TraesCS7B01G396200 chr3B 98.204 334 6 0 990 1323 733064477 733064810 3.210000e-163 584.0
11 TraesCS7B01G396200 chr3B 97.500 240 6 0 1291 1530 257576632 257576871 5.760000e-111 411.0
12 TraesCS7B01G396200 chr3B 98.876 178 2 0 2063 2240 201547856 201548033 3.590000e-83 318.0
13 TraesCS7B01G396200 chr3B 93.689 206 5 3 1904 2109 32745351 32745154 3.620000e-78 302.0
14 TraesCS7B01G396200 chr3B 86.282 277 20 4 928 1202 169829162 169829422 3.640000e-73 285.0
15 TraesCS7B01G396200 chr3B 98.734 158 2 0 1171 1328 687455801 687455958 4.710000e-72 281.0
16 TraesCS7B01G396200 chr3B 92.617 149 11 0 1596 1744 47547651 47547503 4.850000e-52 215.0
17 TraesCS7B01G396200 chr3B 95.455 110 5 0 2131 2240 416932814 416932923 2.290000e-40 176.0
18 TraesCS7B01G396200 chr3B 96.907 97 3 0 903 999 636830463 636830367 1.780000e-36 163.0
19 TraesCS7B01G396200 chr3B 94.000 100 6 0 1499 1598 636817944 636817845 3.850000e-33 152.0
20 TraesCS7B01G396200 chr3B 97.260 73 2 0 1775 1847 132251676 132251604 8.400000e-25 124.0
21 TraesCS7B01G396200 chr3B 100.000 44 0 0 1878 1921 21185307 21185264 5.130000e-12 82.4
22 TraesCS7B01G396200 chr3B 100.000 37 0 0 251 287 636818442 636818478 3.990000e-08 69.4
23 TraesCS7B01G396200 chr3B 96.970 33 1 0 76 108 654318821 654318853 3.110000e-04 56.5


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 TraesCS7B01G396200 chr7B 663094693 663096932 2239 True 4137.0 4137 100.0000 1 2240 1 chr7B.!!$R1 2239
1 TraesCS7B01G396200 chr7B 662729407 662731646 2239 False 3921.0 3921 98.2590 1 2240 1 chr7B.!!$F1 2239
2 TraesCS7B01G396200 chr2A 726901722 726903962 2240 True 3988.0 3988 98.7950 1 2240 1 chr2A.!!$R1 2239
3 TraesCS7B01G396200 chr5D 503247765 503250003 2238 False 3936.0 3936 98.3940 1 2240 1 chr5D.!!$F1 2239
4 TraesCS7B01G396200 chr3D 589258795 589261034 2239 True 3932.0 3932 98.3490 1 2240 1 chr3D.!!$R1 2239
5 TraesCS7B01G396200 chr3B 201570054 201572294 2240 True 3927.0 3927 98.3040 1 2240 1 chr3B.!!$R6 2239
6 TraesCS7B01G396200 chr3B 201542013 201548033 6020 False 2110.5 3903 98.5005 1 2240 2 chr3B.!!$F8 2239
7 TraesCS7B01G396200 chr3B 757831723 757834128 2405 True 1818.0 1829 96.9970 24 2240 2 chr3B.!!$R9 2216
8 TraesCS7B01G396200 chr3B 201547317 201547868 551 True 985.0 985 98.9130 1387 1937 1 chr3B.!!$R5 550

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
137 138 0.613777 CCTTAGAGGGAAGCAACCGT 59.386 55.000 0.0 0.0 0.0 4.83 F
763 764 2.030628 CGGGCGACTGTTTACCAAAAAT 60.031 45.455 0.0 0.0 0.0 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1011 1012 1.078426 GGTGCAGGTAGTCCGCATT 60.078 57.895 0.0 0.0 41.91 3.56 R
1598 1786 1.553690 ATGCTCTAACGCCCACACCT 61.554 55.000 0.0 0.0 0.00 4.00 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
56 57 1.386533 CCCTTGCGCTGAAGATGAAT 58.613 50.000 9.73 0.00 0.00 2.57
137 138 0.613777 CCTTAGAGGGAAGCAACCGT 59.386 55.000 0.00 0.00 0.00 4.83
401 402 2.112279 AAGGACACAAGGTGACCCTA 57.888 50.000 12.93 0.00 46.34 3.53
686 687 5.469757 AAGGAACTCGGCAAAATAGCCCT 62.470 47.826 0.00 0.00 46.91 5.19
763 764 2.030628 CGGGCGACTGTTTACCAAAAAT 60.031 45.455 0.00 0.00 0.00 1.82
845 846 3.714798 AGGTCAAGGAAGTTGGTGAACTA 59.285 43.478 0.00 0.00 41.87 2.24
1011 1012 5.408299 CGGTGAAATAGACATGTCTGTGAAA 59.592 40.000 33.76 17.12 40.71 2.69
1153 1154 1.898472 CCCGAGCCATCAGTGAGATAT 59.102 52.381 0.00 0.00 34.43 1.63
1164 1165 6.014413 CCATCAGTGAGATATCACTCTGGAAT 60.014 42.308 28.83 14.05 46.96 3.01
1166 1167 7.517614 TCAGTGAGATATCACTCTGGAATAC 57.482 40.000 19.90 4.36 46.96 1.89
1263 1451 0.250989 CCCAAAAGGTAACGGAGGCA 60.251 55.000 0.00 0.00 46.39 4.75
1538 1726 4.597032 CAAGGGTTGGGCTGTTCA 57.403 55.556 0.00 0.00 0.00 3.18
1598 1786 3.130516 GTGAGACAGTTCGGTCCATATCA 59.869 47.826 0.02 0.00 38.59 2.15
1829 2017 2.227089 GACAGCGACGGGTTCTCCAT 62.227 60.000 0.00 0.00 34.36 3.41
2185 6158 1.087501 GCCTTTCCTCGTTCATGGTC 58.912 55.000 0.00 0.00 0.00 4.02
2207 6180 2.628178 CGATATTCTGGTGTCCTAGGCA 59.372 50.000 2.96 2.51 0.00 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 2.505982 GCAGATCGCTTAGCCCCA 59.494 61.111 0.00 0.0 37.77 4.96
137 138 4.367023 CGTCGACCCCCGCTTTCA 62.367 66.667 10.58 0.0 38.37 2.69
209 210 1.152419 AACCTTGGGTTTTCGGGGG 60.152 57.895 0.00 0.0 44.33 5.40
229 230 0.036388 GTGGATGAACCTTGCGGAGA 60.036 55.000 0.00 0.0 39.86 3.71
401 402 3.465966 ACCCCTTCTTACCCTGAAAAAGT 59.534 43.478 0.00 0.0 0.00 2.66
686 687 1.272807 CCCCTTCTCCCGAAGTTACA 58.727 55.000 1.92 0.0 44.12 2.41
763 764 0.242825 CGACTTTGCGGAGACCTGTA 59.757 55.000 0.00 0.0 0.00 2.74
845 846 2.044946 GCCGGCTTCCCTGTCATT 60.045 61.111 22.15 0.0 0.00 2.57
1011 1012 1.078426 GGTGCAGGTAGTCCGCATT 60.078 57.895 0.00 0.0 41.91 3.56
1153 1154 2.820728 TCCGAGGTATTCCAGAGTGA 57.179 50.000 0.00 0.0 35.89 3.41
1164 1165 4.091549 ACACAAGGTTAGAATCCGAGGTA 58.908 43.478 0.00 0.0 0.00 3.08
1166 1167 3.056107 TGACACAAGGTTAGAATCCGAGG 60.056 47.826 0.00 0.0 0.00 4.63
1263 1451 1.250840 GCCCGAGGAAACCTTTGCAT 61.251 55.000 0.00 0.0 31.76 3.96
1538 1726 3.531538 CTCACGTACTGCATTAATGGGT 58.468 45.455 17.02 0.0 0.00 4.51
1598 1786 1.553690 ATGCTCTAACGCCCACACCT 61.554 55.000 0.00 0.0 0.00 4.00
1712 1900 3.118445 GCTTTCAGCAGTTATCCTCTCCT 60.118 47.826 0.00 0.0 41.89 3.69
2185 6158 2.028930 GCCTAGGACACCAGAATATCGG 60.029 54.545 14.75 0.0 0.00 4.18
2207 6180 3.189606 TGGATTGGTGTGGTTCCTCTAT 58.810 45.455 0.00 0.0 0.00 1.98


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

AutoCloner maintained by Alex Coulton.