Multiple sequence alignment - TraesCS5B01G002200

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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 TraesCS5B01G002200 chr5B 100.000 2549 0 0 1 2549 3450773 3448225 0 4708
1 TraesCS5B01G002200 chr7A 96.067 1983 42 10 599 2549 701581938 701583916 0 3197
2 TraesCS5B01G002200 chr7A 95.791 1948 77 3 602 2549 36946200 36948142 0 3138
3 TraesCS5B01G002200 chr2A 96.156 1951 67 6 602 2549 744582029 744583974 0 3181
4 TraesCS5B01G002200 chr2A 95.801 1953 69 7 602 2549 677958469 677956525 0 3140
5 TraesCS5B01G002200 chr2A 94.262 1952 99 9 602 2549 677413606 677411664 0 2972
6 TraesCS5B01G002200 chr2A 92.625 1966 118 20 598 2549 213959521 213957569 0 2802
7 TraesCS5B01G002200 chr2A 94.600 537 29 0 602 1138 695806752 695806216 0 832
8 TraesCS5B01G002200 chr1B 96.191 1943 54 7 602 2541 645321437 645323362 0 3160
9 TraesCS5B01G002200 chr1B 97.671 601 14 0 1 601 673013069 673012469 0 1033
10 TraesCS5B01G002200 chr1B 97.338 601 16 0 1 601 402954750 402955350 0 1022
11 TraesCS5B01G002200 chr7D 94.373 1955 89 14 602 2549 63995390 63997330 0 2981
12 TraesCS5B01G002200 chr3D 94.166 1954 95 14 602 2549 475106681 475108621 0 2959
13 TraesCS5B01G002200 chr3A 91.730 1959 112 11 599 2549 120653862 120655778 0 2675
14 TraesCS5B01G002200 chr6B 97.667 600 14 0 2 601 44700425 44699826 0 1031
15 TraesCS5B01G002200 chr6B 97.338 601 15 1 1 601 25136029 25135430 0 1020
16 TraesCS5B01G002200 chr6B 97.185 604 13 4 1 601 690516220 690515618 0 1018
17 TraesCS5B01G002200 chr4B 97.504 601 14 1 1 601 62992833 62993432 0 1026
18 TraesCS5B01G002200 chr4B 97.338 601 16 0 1 601 605989973 605990573 0 1022
19 TraesCS5B01G002200 chr4B 97.171 601 17 0 1 601 92747541 92748141 0 1016
20 TraesCS5B01G002200 chr3B 97.504 601 13 2 1 601 777900884 777901482 0 1026


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 TraesCS5B01G002200 chr5B 3448225 3450773 2548 True 4708 4708 100.000 1 2549 1 chr5B.!!$R1 2548
1 TraesCS5B01G002200 chr7A 701581938 701583916 1978 False 3197 3197 96.067 599 2549 1 chr7A.!!$F2 1950
2 TraesCS5B01G002200 chr7A 36946200 36948142 1942 False 3138 3138 95.791 602 2549 1 chr7A.!!$F1 1947
3 TraesCS5B01G002200 chr2A 744582029 744583974 1945 False 3181 3181 96.156 602 2549 1 chr2A.!!$F1 1947
4 TraesCS5B01G002200 chr2A 677956525 677958469 1944 True 3140 3140 95.801 602 2549 1 chr2A.!!$R3 1947
5 TraesCS5B01G002200 chr2A 677411664 677413606 1942 True 2972 2972 94.262 602 2549 1 chr2A.!!$R2 1947
6 TraesCS5B01G002200 chr2A 213957569 213959521 1952 True 2802 2802 92.625 598 2549 1 chr2A.!!$R1 1951
7 TraesCS5B01G002200 chr2A 695806216 695806752 536 True 832 832 94.600 602 1138 1 chr2A.!!$R4 536
8 TraesCS5B01G002200 chr1B 645321437 645323362 1925 False 3160 3160 96.191 602 2541 1 chr1B.!!$F2 1939
9 TraesCS5B01G002200 chr1B 673012469 673013069 600 True 1033 1033 97.671 1 601 1 chr1B.!!$R1 600
10 TraesCS5B01G002200 chr1B 402954750 402955350 600 False 1022 1022 97.338 1 601 1 chr1B.!!$F1 600
11 TraesCS5B01G002200 chr7D 63995390 63997330 1940 False 2981 2981 94.373 602 2549 1 chr7D.!!$F1 1947
12 TraesCS5B01G002200 chr3D 475106681 475108621 1940 False 2959 2959 94.166 602 2549 1 chr3D.!!$F1 1947
13 TraesCS5B01G002200 chr3A 120653862 120655778 1916 False 2675 2675 91.730 599 2549 1 chr3A.!!$F1 1950
14 TraesCS5B01G002200 chr6B 44699826 44700425 599 True 1031 1031 97.667 2 601 1 chr6B.!!$R2 599
15 TraesCS5B01G002200 chr6B 25135430 25136029 599 True 1020 1020 97.338 1 601 1 chr6B.!!$R1 600
16 TraesCS5B01G002200 chr6B 690515618 690516220 602 True 1018 1018 97.185 1 601 1 chr6B.!!$R3 600
17 TraesCS5B01G002200 chr4B 62992833 62993432 599 False 1026 1026 97.504 1 601 1 chr4B.!!$F1 600
18 TraesCS5B01G002200 chr4B 605989973 605990573 600 False 1022 1022 97.338 1 601 1 chr4B.!!$F3 600
19 TraesCS5B01G002200 chr4B 92747541 92748141 600 False 1016 1016 97.171 1 601 1 chr4B.!!$F2 600
20 TraesCS5B01G002200 chr3B 777900884 777901482 598 False 1026 1026 97.504 1 601 1 chr3B.!!$F1 600

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
54 56 0.108089 GGAGAGGAAAACGAGAGGCC 60.108 60.0 0.00 0.0 0.0 5.19 F
691 695 0.250597 GTTTTGCCCCTAGTCCGTGT 60.251 55.0 0.00 0.0 0.0 4.49 F
963 1008 0.978146 GGAAGCTAGCTGTGGAGGGA 60.978 60.0 20.16 0.0 0.0 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1119 1164 3.838903 AGAACGGACTATTCTGGTTCCTT 59.161 43.478 11.22 0.0 36.56 3.36 R
1494 1540 4.245660 CCAGTGCGATTACCATACCTATG 58.754 47.826 0.00 0.0 0.00 2.23 R
2250 2310 4.913154 TGTATACCTTCCTTCCCTACCT 57.087 45.455 0.00 0.0 0.00 3.08 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
54 56 0.108089 GGAGAGGAAAACGAGAGGCC 60.108 60.000 0.00 0.0 0.00 5.19
264 266 6.116126 AGAACAAAGGTATCAATCCAGTAGC 58.884 40.000 0.00 0.0 0.00 3.58
273 275 1.066858 CAATCCAGTAGCAGACCACGT 60.067 52.381 0.00 0.0 0.00 4.49
474 478 8.980596 GGAGATTGATATGATGAGAATAGACCT 58.019 37.037 0.00 0.0 0.00 3.85
667 671 0.659957 GCCCTCAGATGCGAATTGTC 59.340 55.000 0.00 0.0 0.00 3.18
670 674 2.636830 CCTCAGATGCGAATTGTCCTT 58.363 47.619 0.00 0.0 0.00 3.36
691 695 0.250597 GTTTTGCCCCTAGTCCGTGT 60.251 55.000 0.00 0.0 0.00 4.49
727 731 1.289380 GAACTCTGCCGTCTCCGTT 59.711 57.895 0.00 0.0 0.00 4.44
853 857 1.048601 TTGAGAAGAGAGCCGTTGGT 58.951 50.000 0.00 0.0 0.00 3.67
908 912 1.363807 CACGGTGACAGAGAGCACA 59.636 57.895 0.74 0.0 36.76 4.57
912 916 2.048784 TGACAGAGAGCACAGCGC 60.049 61.111 0.00 0.0 42.91 5.92
963 1008 0.978146 GGAAGCTAGCTGTGGAGGGA 60.978 60.000 20.16 0.0 0.00 4.20
1119 1164 1.070134 CGAAGGGTTTCTCAGACACCA 59.930 52.381 12.23 0.0 34.39 4.17
1132 1177 3.907474 TCAGACACCAAGGAACCAGAATA 59.093 43.478 0.00 0.0 0.00 1.75
1494 1540 5.938438 TTTGCAAATACTTTTGGGCATTC 57.062 34.783 8.05 0.0 42.09 2.67
2077 2133 3.093057 ACGCCAGGTGCCAAAATAAATA 58.907 40.909 0.00 0.0 36.24 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 56 6.207928 TCTCGCATTACATTATTTGCCATTG 58.792 36.000 0.00 0.00 0.00 2.82
245 247 5.396884 GGTCTGCTACTGGATTGATACCTTT 60.397 44.000 0.00 0.00 0.00 3.11
264 266 1.961277 GGGACTTGCACGTGGTCTG 60.961 63.158 18.88 1.93 0.00 3.51
273 275 1.972198 CAGGTACGAGGGACTTGCA 59.028 57.895 0.00 0.00 45.68 4.08
474 478 0.912487 AGTGAAACCTATGGCCCCGA 60.912 55.000 0.00 0.00 37.80 5.14
667 671 2.679930 CGGACTAGGGGCAAAACTAAGG 60.680 54.545 0.00 0.00 0.00 2.69
670 674 1.276989 CACGGACTAGGGGCAAAACTA 59.723 52.381 0.00 0.00 0.00 2.24
839 843 2.147387 ACCCACCAACGGCTCTCTT 61.147 57.895 0.00 0.00 0.00 2.85
895 899 2.048784 GCGCTGTGCTCTCTGTCA 60.049 61.111 5.84 0.00 41.73 3.58
912 916 1.987704 CTCTCTCTCGCCGTGGTCAG 61.988 65.000 0.00 0.00 0.00 3.51
1119 1164 3.838903 AGAACGGACTATTCTGGTTCCTT 59.161 43.478 11.22 0.00 36.56 3.36
1494 1540 4.245660 CCAGTGCGATTACCATACCTATG 58.754 47.826 0.00 0.00 0.00 2.23
1700 1749 6.640518 AGAGCTGCATTTCATTGATCAAAAT 58.359 32.000 13.09 5.13 0.00 1.82
2250 2310 4.913154 TGTATACCTTCCTTCCCTACCT 57.087 45.455 0.00 0.00 0.00 3.08


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

AutoCloner maintained by Alex Coulton.