Multiple sequence alignment - TraesCS7B01G461200

Loading Multiple Alignment...

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 TraesCS7B01G461200 chr7B 100.000 2549 0 0 1 2549 718489041 718486493 0 4708
1 TraesCS7B01G461200 chr7B 96.281 1990 64 6 567 2549 621924191 621926177 0 3256
2 TraesCS7B01G461200 chr7B 95.760 566 23 1 2 567 718753396 718752832 0 911
3 TraesCS7B01G461200 chr2B 96.825 1984 59 4 567 2549 543889471 543887491 0 3312
4 TraesCS7B01G461200 chr2B 96.673 1984 62 4 567 2549 544319642 544317662 0 3295
5 TraesCS7B01G461200 chr2B 95.960 2005 73 6 552 2549 596962052 596964055 0 3247
6 TraesCS7B01G461200 chr5B 96.482 1990 62 5 566 2549 269389471 269391458 0 3280
7 TraesCS7B01G461200 chr5B 96.438 1993 64 4 561 2548 446193261 446191271 0 3280
8 TraesCS7B01G461200 chr1B 96.429 1988 64 5 567 2549 663786494 663788479 0 3271
9 TraesCS7B01G461200 chr1B 96.425 1986 63 7 568 2549 490563562 490561581 0 3267
10 TraesCS7B01G461200 chr3B 96.420 1983 66 4 568 2549 129332737 129330759 0 3264
11 TraesCS7B01G461200 chr7D 94.561 570 26 2 2 567 621337206 621337774 0 876
12 TraesCS7B01G461200 chr5D 93.158 570 34 2 2 567 425442241 425442809 0 832
13 TraesCS7B01G461200 chr5D 92.782 568 33 5 5 566 107934749 107934184 0 815
14 TraesCS7B01G461200 chr3D 93.146 569 34 2 2 566 275847386 275847953 0 830
15 TraesCS7B01G461200 chr3D 92.619 569 38 1 2 566 53210066 53209498 0 815
16 TraesCS7B01G461200 chr2D 92.970 569 36 1 2 566 326065654 326066222 0 826
17 TraesCS7B01G461200 chr4D 92.970 569 35 2 2 566 226593613 226593046 0 824
18 TraesCS7B01G461200 chr1D 92.619 569 38 1 2 566 307795504 307794936 0 815


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 TraesCS7B01G461200 chr7B 718486493 718489041 2548 True 4708 4708 100.000 1 2549 1 chr7B.!!$R1 2548
1 TraesCS7B01G461200 chr7B 621924191 621926177 1986 False 3256 3256 96.281 567 2549 1 chr7B.!!$F1 1982
2 TraesCS7B01G461200 chr7B 718752832 718753396 564 True 911 911 95.760 2 567 1 chr7B.!!$R2 565
3 TraesCS7B01G461200 chr2B 543887491 543889471 1980 True 3312 3312 96.825 567 2549 1 chr2B.!!$R1 1982
4 TraesCS7B01G461200 chr2B 544317662 544319642 1980 True 3295 3295 96.673 567 2549 1 chr2B.!!$R2 1982
5 TraesCS7B01G461200 chr2B 596962052 596964055 2003 False 3247 3247 95.960 552 2549 1 chr2B.!!$F1 1997
6 TraesCS7B01G461200 chr5B 269389471 269391458 1987 False 3280 3280 96.482 566 2549 1 chr5B.!!$F1 1983
7 TraesCS7B01G461200 chr5B 446191271 446193261 1990 True 3280 3280 96.438 561 2548 1 chr5B.!!$R1 1987
8 TraesCS7B01G461200 chr1B 663786494 663788479 1985 False 3271 3271 96.429 567 2549 1 chr1B.!!$F1 1982
9 TraesCS7B01G461200 chr1B 490561581 490563562 1981 True 3267 3267 96.425 568 2549 1 chr1B.!!$R1 1981
10 TraesCS7B01G461200 chr3B 129330759 129332737 1978 True 3264 3264 96.420 568 2549 1 chr3B.!!$R1 1981
11 TraesCS7B01G461200 chr7D 621337206 621337774 568 False 876 876 94.561 2 567 1 chr7D.!!$F1 565
12 TraesCS7B01G461200 chr5D 425442241 425442809 568 False 832 832 93.158 2 567 1 chr5D.!!$F1 565
13 TraesCS7B01G461200 chr5D 107934184 107934749 565 True 815 815 92.782 5 566 1 chr5D.!!$R1 561
14 TraesCS7B01G461200 chr3D 275847386 275847953 567 False 830 830 93.146 2 566 1 chr3D.!!$F1 564
15 TraesCS7B01G461200 chr3D 53209498 53210066 568 True 815 815 92.619 2 566 1 chr3D.!!$R1 564
16 TraesCS7B01G461200 chr2D 326065654 326066222 568 False 826 826 92.970 2 566 1 chr2D.!!$F1 564
17 TraesCS7B01G461200 chr4D 226593046 226593613 567 True 824 824 92.970 2 566 1 chr4D.!!$R1 564
18 TraesCS7B01G461200 chr1D 307794936 307795504 568 True 815 815 92.619 2 566 1 chr1D.!!$R1 564

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
652 657 1.144913 TGCTCAGTTTTGCCCCTAGTT 59.855 47.619 0.0 0.0 0.0 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1974 1984 1.533469 CGGTCTTGGGTTCGAGTCCT 61.533 60.0 8.28 0.0 32.56 3.85 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
47 48 6.325596 GTGAAATTGAGGAGGAAGTTTATGC 58.674 40.000 0.00 0.0 0.00 3.14
246 247 7.893302 AGGGTTAATGGACAATTATTTCTGTGA 59.107 33.333 0.00 0.0 30.74 3.58
281 282 9.418839 TGTGGATGATATCATATTTGGTTCAAA 57.581 29.630 18.19 0.0 35.82 2.69
497 498 2.037772 CCATGCCTACTAGTGGACATCC 59.962 54.545 7.98 0.0 33.53 3.51
588 593 4.034410 TGGGTTAATTATCCTTTTGCCCC 58.966 43.478 11.51 0.0 32.94 5.80
652 657 1.144913 TGCTCAGTTTTGCCCCTAGTT 59.855 47.619 0.00 0.0 0.00 2.24
768 774 5.226396 CCAATTTTATTCAGACCGTTGCAA 58.774 37.500 0.00 0.0 0.00 4.08
866 872 4.953868 CGGTGACCACGGCGACAA 62.954 66.667 16.62 0.0 0.00 3.18
926 932 2.432300 GGCGGTGGGAAGCTAGCTA 61.432 63.158 19.70 0.0 0.00 3.32
1006 1012 1.067250 GCTCCGAGCTCCATGTCTC 59.933 63.158 13.42 0.0 38.45 3.36
1068 1075 1.609061 CGTGTGGAGATGCCTGTCTTT 60.609 52.381 0.00 0.0 37.63 2.52
1070 1077 1.271543 TGTGGAGATGCCTGTCTTTGG 60.272 52.381 0.00 0.0 37.63 3.28
1077 1084 2.732289 GCCTGTCTTTGGCTTTCCA 58.268 52.632 0.00 0.0 46.38 3.53
1078 1085 1.260544 GCCTGTCTTTGGCTTTCCAT 58.739 50.000 0.00 0.0 46.38 3.41
1171 1178 2.771943 AGCGAGAATGGGGTAAGAATCA 59.228 45.455 0.00 0.0 0.00 2.57
1228 1235 2.083774 GCAATCGGTTGATCTGTTCCA 58.916 47.619 13.85 0.0 37.53 3.53
1239 1246 4.080687 TGATCTGTTCCATGTTCATGCAA 58.919 39.130 7.21 0.0 0.00 4.08
1974 1984 0.749649 ACAAAAATTGGTGCGGCTGA 59.250 45.000 0.00 0.0 34.12 4.26
2156 2168 4.388499 GCGGCTGGGGACTCGAAA 62.388 66.667 0.00 0.0 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
218 219 9.762381 ACAGAAATAATTGTCCATTAACCCTTA 57.238 29.630 0.00 0.00 30.78 2.69
285 286 7.889873 TCCAAACTTTTCACTAAAATGAGGA 57.110 32.000 0.00 0.00 34.18 3.71
497 498 4.938226 GGTTTCCATCCTTAGTCAAGTCAG 59.062 45.833 0.00 0.00 0.00 3.51
588 593 1.827344 TGAGCAGATGGACACCACTAG 59.173 52.381 0.00 0.00 35.80 2.57
879 885 3.063084 ACTCTCTCGCCGTGGTCC 61.063 66.667 0.00 0.00 0.00 4.46
926 932 4.415150 CACTGCCGCACCCTCCAT 62.415 66.667 0.00 0.00 0.00 3.41
1070 1077 3.451894 CCCGGCACCATGGAAAGC 61.452 66.667 21.47 18.44 0.00 3.51
1171 1178 3.056891 CACGAAAATGGTGCAATTACCCT 60.057 43.478 0.00 0.00 40.09 4.34
1239 1246 2.298163 CCAAAGAAAGAAGCATGCCACT 59.702 45.455 15.66 11.31 0.00 4.00
1447 1454 5.193679 GGGTATTGGTAGTGCTTGATCTTT 58.806 41.667 0.00 0.00 0.00 2.52
1662 1670 5.749462 TCTGAATTCCTCATTTCTTCTCCC 58.251 41.667 2.27 0.00 32.14 4.30
1974 1984 1.533469 CGGTCTTGGGTTCGAGTCCT 61.533 60.000 8.28 0.00 32.56 3.85


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

AutoCloner maintained by Alex Coulton.