研究/陸上植物の葉緑体とシアノバクテリアのrbcLの塩基配列の違い

提供: 広島大学デジタル自然史博物館 植物
移動: 案内検索

陸上植物の葉緑体とシアノバクテリアのrbcLの塩基配列の違いの例

AB029384
Hypnum plumaeforme ハイゴケ(陸上植物,セン類)
LC003311
Sisymbrium orientale イヌカキネガラシ(陸上植物,双子葉植物,アブラナ科)
AY221516
Synechococcus sp. シネココッカス属の一種(シアノバクテリア)
AB075910
Fischerella muscicola フィッシャーエラ属の一種(シアノバクテリア)


MAFFT-L-INS-i Result

CLUSTAL format alignment by MAFFT (v7.408)


AB029384|AB0293 atgtcaccacaaacggagactaaagcaggtgttggatttaaagctggtgttaaagattac
LC003311|LC0033 -----------------------------tgttggattcaaagctggtgttaaagagtat
AY221516|AY2215 ------------------------------------------------------------
AB075910|AB0759 ------------------------------------------------------------
                                                                            

AB029384|AB0293 agattaacttattacactccagattatcagactacagcaactgatattttagcagcattt
LC003311|LC0033 aaattgacttattatactcctgaatatgaaaccaaggatactgatatcttggcagcattc
AY221516|AY2215 ------------------------------------------------------------
AB075910|AB0759 ------------------------------------------------------------
                                                                            

AB029384|AB0293 cgaatgactcctcaaccaggagtacccgctgaagaggcgggagctgcagtagctgcggaa
LC003311|LC0033 cgagtaactcctcaacccggagttccacctgaagaagcaggggctgcagtagctgctgaa
AY221516|AY2215 ------------------------------------------------------------
AB075910|AB0759 ------------------------------------------------------------
                                                                            

AB029384|AB0293 tcctccactggtacatggaccactgtttggactgatggacttaccagtcttgatcgttat
LC003311|LC0033 tcttctactggtacatggacaactgtgtggaccgatgggcttaccagccttgatcgttac
AY221516|AY2215 ------------------------------------------------------------
AB075910|AB0759 --------------------taccgtatggactgacttgctaaccgacctagatcgctac
                                                                            

AB029384|AB0293 aaaggacgatgctatgatcttgaagcagttcctggagaagagaatcaatatattgcttat
LC003311|LC0033 aaaggacgatgctaccacatcgagcccgttccaggagaagaaactcaatttattgcgtat
AY221516|AY2215 ------------------attgagccggttcctggcgaagagaaccagtatttctgcttc
AB075910|AB0759 aaaggtcgttgttacgatatcgaacccgttcgtggcgaggacaaccagtacattgcttac
                                   *.**. * ****  ** **.** * .**.* . *.   * .

AB029384|AB0293 gttgcttacccattagatttatttgaagaaggttctgttaccaatttatttacttctatt
LC003311|LC0033 gtagcttaccccttagacctttttgaagaagggtcggttactaacatgtttacctcgatt
AY221516|AY2215 gtcgcctacccgctggatctcttcgaggaaggctcagttaccaacatgctcacctcgatt
AB075910|AB0759 gtagcttatcctctagacttgtttgaggaaggctctgtaaccaacatgttgacctcaatt
                ** **.**.** .*.**..* **.**.***** ** ** **.**. *..* **.** ***

AB029384|AB0293 gttggtaatgtttttggatttaaagctttacgagctttacgtctagaagatttacgtatt
LC003311|LC0033 gtaggtaatgtatttgggttcaaagccctggctgctctacgtctagaggatctgcgaatc
AY221516|AY2215 gtgggcaatgtcttcggcttcaaggccttgaaggcgctgcggctggaggacttgcgtatt
AB075910|AB0759 gtcggtaacgtattcggtttcaaagctttacgggcgctgcgtctggaagacttgcggatt
                ** **.**.** **.** **.**.**..*.   ** .*.** **.**.**..*.** **.

AB029384|AB0293 cctccagcttattccaaaactttccaaggcccacctcatggtattcaagttgaaagagat
LC003311|LC0033 cctcctgcttatactaaaactttccagggaccacctcatggtatccaagttgaaagagat
AY221516|AY2215 cccgtagcctacttgaagaccttccagggccctccccacggtatccaggtagagcgggat
AB075910|AB0759 ccagttgcttacctcaagactttccaaggccctccccacggtatccaagttgagcgtgac
                **  . **.**. . **.**.*****.** ** **.**.*****.**.** **. * **.

AB029384|AB0293 aaattaaacaaatatggtcgtccattattaggatgtactattaagccaaaattgggttta
LC003311|LC0033 aaattgaacaagtatggacgtcccctattaggatgtactattaaacctaaattgggatta
AY221516|AY2215 aagctgaacaagtatggtcgtccactgctgggctgcaccatcaagcccaagctaggcctt
AB075910|AB0759 aaattaaacaaatacggtcgtcctttgttgggttgtaccattaagcccaaactcggtttg
                **..*.*****.**.** ***** .*..*.** **.**.**.**.** **..* ** .* 

AB029384|AB0293 tctgctaaaaactatggtagagctgtatatgaatgtcttcgtggtggacttgatttcaca
LC003311|LC0033 tccgcgaagaactatggtagagcagtttatgaatgtctacgtggtggacttgattttacc
AY221516|AY2215 tccgccaaaaactacgggcgggctgtgtacgaagcgctgcggggtgggctggactttacc
AB075910|AB0759 tctgcgaaaaactacggacgtgcagtatacgagtgcttgcgcggtggtttggacttcacc
                **.** **.*****.**  * ** ** **.**.   .* ** ***** .* **.**.** 

AB029384|AB0293 aaagatgatgaaaacgtaaattctcaaccttttatgcgttggagagatcgtttcttattt
LC003311|LC0033 aaagatgatgagaatgtgaactcccaaccatttatgcgttggagagaccgtttcttattt
AY221516|AY2215 aaagacgacgaaaacgtcaactcccagcccttcatgcgttggcgggatcgctacctgttt
AB075910|AB0759 aaagacgacgaaaatatcaactcccagcctttccaacgttggcgcgatcgcttcctgttt
                *****.**.**.**..* **.**.**.** **.  .****** * **.**.* *.*.***

AB029384|AB0293 gtagctgaagctatctacaaatctcaatctgaaacaggtgaaattaaaggacattattta
LC003311|LC0033 tgtgccgaagctatttataaatcacaggctgaaacaggtgaaatcaaagggcattatttg
AY221516|AY2215 gtcatggaagcggtccataaagcgcaggcagaaaccggcgagatcaaggggcactacctg
AB075910|AB0759 gtagctgatgccattcacaaagcccaagcagaaacaggcgaaatcaaaggtcactaccta
                   .. ** ** .*..*.*** * **. * ***** **.**.**.**.** **.**..*.

AB029384|AB0293 aatgctaccgcaggtacatgtgaagaaatgatgaaaagagctcagtttgctagagaatta
LC003311|LC0033 aatgctactgcgggtacatgcgaagaaatgatcaaaagagctgtatttgccagagaattg
AY221516|AY2215 aacgtgacggcgcccacctgcgaggagatgttcaagcgggcggagtttgctaaggagatt
AB075910|AB0759 aacgttaccgctcctacctgcgaagaaatgatgaaacgggcagagttcgctaaagaactc
                **.*. ** **   .** **.**.**.*** * **. *.**   .**.**.*..**. * 

AB029384|AB0293 ggcatgcctattgtcatgcacgactatttgacaggtggttttactgcaaatactagtttg
LC003311|LC0033 ggagttcctatcgtaatgcatgactacttaacagggggattcaccgcaaatactagtttg
AY221516|AY2215 ggtgcccccatcatcatgcatgactacctcaccgccggctttacggccaacaccagtctg
AB075910|AB0759 aagatgcctatcatcatgcatgactacttgaccgcaggtttcaccgccaatacaactttg
                .. .. **.**..* *****.*****..* ** *  ** **.** ** **.** * *.**

AB029384|AB0293 gctcattactgtcgtgataatggcttgctccttcatattcaccgtgcaatgcatgcagtt
LC003311|LC0033 gctcattattgccgagataatggcctacttcttcacatccaccgtgcaatgcacgctgtt
AY221516|AY2215 gccaagtggtgccgcgacaacggcattctgctgcacatccaccgcgccatgcacgcggtg
AB075910|AB0759 gctagatggtgtcgcgacaacggtatattgctccacattcaccgagcaatgcacgcggta
                **. . *. **.** **.**.**. * .* ** **.**.***** ** *****.** ** 

AB029384|AB0293 attgaccgacaaaaaattcatggtatgcatttccgtgtattagctaaagcattacgttta
LC003311|LC0033 attgatagacagaagaatcatggtatgcacttccgtgtactagctaaagctttacgtcta
AY221516|AY2215 attgaccggcagaaaaaccacggcatccacttccgggtgctggccaagtgcctgcgcatg
AB075910|AB0759 attgaccgtcaaaagaaccatggtatccacttccgcgttttggctaagactctgcggatg
                *****. * **.**.* .**.**.** **.***** ** .*.**.**.   .*.**  *.

AB029384|AB0293 tccggtggagaccatattcacgctggtactgtagtaggtaaacttgaaggagaacgtcaa
LC003311|LC0033 tctggtggagatcatgttcacgcgggtacagtagtaggtaaacttgaaggagacagagag
AY221516|AY2215 tcgggtggcgaccacctgcatgccggtacggtggtgggcaagctggaaggcgaccgcgcc
AB075910|AB0759 tctggtggagaccatattcacactggtacggtggtcggtaagctagagggtgagcgcggt
                ** ***** **.**. * **..* ***** **.** **.**.** **.** **  *    

AB029384|AB0293 gtaactttaggttttgttgatctacttcgcgatgattatattgagaaagatagaagccgt
LC003311|LC0033 tcaactttgggttttgttgatttactgcgcgatgattatgttgaaaaagaccgaagccgt
AY221516|AY2215 atcaccatgggctttgtggatctcatgcgagaaaactacgttgaggcggatcgttcccgc
AB075910|AB0759 attacaatgggcttcgttgacctactgcgcgaaaactatgttgagcaagacaaatctcgc
                 . **  *.**.**.** **..*  * ** ** .*.**..****.  .**. .   .**.

AB029384|AB0293 ggtatttatttcactcaagagtgggtttctttaccaggtgttttacctgtagcttctggt
LC003311|LC0033 ggtatctttttcactcaagattgggtctcactaccaggtgttctacctgtggcttctggg
AY221516|AY2215 ggcattttcttcacccaagattgggcttccatgccgggggtgatgccagtggcttccggt
AB075910|AB0759 ggtatttactttacccaagattgggcttctatgcctggtgtaatggctgttgcttctggt
                **.**.* .**.**.***** ****..**  *.** ** **  *. * ** *****.** 

AB029384|AB0293 ggtattcacgtttggcatatgccagcattaactgaaatctttggagatgattctgtatta
LC003311|LC0033 ggtattcacgtttggcatatgcctgctttgaccgagatctttggagatgattccgtacta
AY221516|AY2215 gggatccacgtttggcacatgcccatactggtggagctcttcggggacgacgctgtgctg
AB075910|AB0759 ggtatccacgtatggcacatgccagcattggtagaaatctttggtgatgattccgtactg
                ** **.***** *****.***** .. .*... **. ****.** **.**. *.**..*.

AB029384|AB0293 cagtttggtggaggaactttaggtcacccttggggtaatgcacctggagcagttgctaat
LC003311|LC0033 caattcggtggcggaactttaggccacccttggggaaatgcaccgggtgccgtagctaac
AY221516|AY2215 cagtttggtggcggaaccctaggtcacccctgggggaacgctccaggcgcgacggccaac
AB075910|AB0759 caattcggtggtggtacactcggtcacccctggggtaacgctcctggtgcaaccgcaaac
                **.**.***** ** ** .* **.*****.***** **.** ** ** ** .. ** **.

AB029384|AB0293 agagttgccgtagaagcctgtgtacaagctcgtaatgaaggacgtgatcttgctcgcgaa
LC003311|LC0033 cgagtagctc--------------------------------------------------
AY221516|AY2215 cgggtggctctggaggcctgcatccaggcccgcaatgaaggccgagatctgattcgcgag
AB075910|AB0759 cgtgttgctttggaagcttgtattcaagctcgtaacgaaggtcgcaacttggctcgcgaa
                 * ** **.                                                   

AB029384|AB0293 ggtaatgaaattattcgtgaagctactaaatggagtcccgaattagctgcggcttgtgaa
LC003311|LC0033 ------------------------------------------------------------
AY221516|AY2215 ggcaacgacatcatccgcgaagcagccaagtggtcgccagaactggcc------------
AB075910|AB0759 ggtaacgacgttatccgtgaagctgctaagtggtctcctgaattggctgctgcttgcgaa
                                                                            

AB029384|AB0293 gtttggaaagaaattaaatttgaatttgatacaattgatactatataa
LC003311|LC0033 ------------------------------------------------
AY221516|AY2215 ------------------------------------------------
AB075910|AB0759 cta---------------------------------------------
                                                                

Method
L-INS-i (Probably most accurate, very slow)

% mafft --inputorder --auto input 

References:
   Katoh et al. (2002) describes FFT-NS-1, FFT-NS-2 and FFT-NS-i.
   Katoh et al. (2005) describes G-INS-i, L-INS-i, E-INS-i and Mafft-homologs.
   Katoh and Toh (2008) describes Q-INS-i.
   Katoh and Frith (2012) describes *-fragment.
   Q-INS-i uses the McCaskill routine from the Vienna RNA package (Hofacker et al. 2003) and MXSCARNA (Tabei et al. 2008).
   Kuraku et al. (2013) outlines this web service.
   Katoh and Standley (2016) describes the VSM technique (--unalignlevel x).
   Yamada et al. (2016) explains how to build large MSAs.

MAFFT home:
   https://mafft.cbrc.jp/alignment/software/


id = .1811052315165160391eixq4t2nGQWgyVTmhlsfnormal, posted at Mon Nov 5 23:15:55 JST 2018
4 nucleotide sequences, 1428-1110 sites
This file will be removed after 96 hours.

FASTA形式

>AB029384|AB029384.1 Hypnum plumaeforme chloroplast rbcL gene for ribulose 1,5-bisphosphate carboxylase/oxygenase large subunit, complete cds.
atgtcaccacaaacggagactaaagcaggtgttggatttaaagctggtgttaaagattac
agattaacttattacactccagattatcagactacagcaactgatattttagcagcattt
cgaatgactcctcaaccaggagtacccgctgaagaggcgggagctgcagtagctgcggaa
tcctccactggtacatggaccactgtttggactgatggacttaccagtcttgatcgttat
aaaggacgatgctatgatcttgaagcagttcctggagaagagaatcaatatattgcttat
gttgcttacccattagatttatttgaagaaggttctgttaccaatttatttacttctatt
gttggtaatgtttttggatttaaagctttacgagctttacgtctagaagatttacgtatt
cctccagcttattccaaaactttccaaggcccacctcatggtattcaagttgaaagagat
aaattaaacaaatatggtcgtccattattaggatgtactattaagccaaaattgggttta
tctgctaaaaactatggtagagctgtatatgaatgtcttcgtggtggacttgatttcaca
aaagatgatgaaaacgtaaattctcaaccttttatgcgttggagagatcgtttcttattt
gtagctgaagctatctacaaatctcaatctgaaacaggtgaaattaaaggacattattta
aatgctaccgcaggtacatgtgaagaaatgatgaaaagagctcagtttgctagagaatta
ggcatgcctattgtcatgcacgactatttgacaggtggttttactgcaaatactagtttg
gctcattactgtcgtgataatggcttgctccttcatattcaccgtgcaatgcatgcagtt
attgaccgacaaaaaattcatggtatgcatttccgtgtattagctaaagcattacgttta
tccggtggagaccatattcacgctggtactgtagtaggtaaacttgaaggagaacgtcaa
gtaactttaggttttgttgatctacttcgcgatgattatattgagaaagatagaagccgt
ggtatttatttcactcaagagtgggtttctttaccaggtgttttacctgtagcttctggt
ggtattcacgtttggcatatgccagcattaactgaaatctttggagatgattctgtatta
cagtttggtggaggaactttaggtcacccttggggtaatgcacctggagcagttgctaat
agagttgccgtagaagcctgtgtacaagctcgtaatgaaggacgtgatcttgctcgcgaa
ggtaatgaaattattcgtgaagctactaaatggagtcccgaattagctgcggcttgtgaa
gtttggaaagaaattaaatttgaatttgatacaattgatactatataa
>LC003311|LC003311.1 Sisymbrium orientale chloroplast rbcL gene for ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit, partial cds, specimen_voucher: HIRO:HIRO-MY 94863.
-----------------------------tgttggattcaaagctggtgttaaagagtat
aaattgacttattatactcctgaatatgaaaccaaggatactgatatcttggcagcattc
cgagtaactcctcaacccggagttccacctgaagaagcaggggctgcagtagctgctgaa
tcttctactggtacatggacaactgtgtggaccgatgggcttaccagccttgatcgttac
aaaggacgatgctaccacatcgagcccgttccaggagaagaaactcaatttattgcgtat
gtagcttaccccttagacctttttgaagaagggtcggttactaacatgtttacctcgatt
gtaggtaatgtatttgggttcaaagccctggctgctctacgtctagaggatctgcgaatc
cctcctgcttatactaaaactttccagggaccacctcatggtatccaagttgaaagagat
aaattgaacaagtatggacgtcccctattaggatgtactattaaacctaaattgggatta
tccgcgaagaactatggtagagcagtttatgaatgtctacgtggtggacttgattttacc
aaagatgatgagaatgtgaactcccaaccatttatgcgttggagagaccgtttcttattt
tgtgccgaagctatttataaatcacaggctgaaacaggtgaaatcaaagggcattatttg
aatgctactgcgggtacatgcgaagaaatgatcaaaagagctgtatttgccagagaattg
ggagttcctatcgtaatgcatgactacttaacagggggattcaccgcaaatactagtttg
gctcattattgccgagataatggcctacttcttcacatccaccgtgcaatgcacgctgtt
attgatagacagaagaatcatggtatgcacttccgtgtactagctaaagctttacgtcta
tctggtggagatcatgttcacgcgggtacagtagtaggtaaacttgaaggagacagagag
tcaactttgggttttgttgatttactgcgcgatgattatgttgaaaaagaccgaagccgt
ggtatctttttcactcaagattgggtctcactaccaggtgttctacctgtggcttctggg
ggtattcacgtttggcatatgcctgctttgaccgagatctttggagatgattccgtacta
caattcggtggcggaactttaggccacccttggggaaatgcaccgggtgccgtagctaac
cgagtagctc--------------------------------------------------
------------------------------------------------------------
------------------------------------------------
>AY221516|AY221516.1 Synechococcus sp. OH28 ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) gene, partial cds.
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------attgagccggttcctggcgaagagaaccagtatttctgcttc
gtcgcctacccgctggatctcttcgaggaaggctcagttaccaacatgctcacctcgatt
gtgggcaatgtcttcggcttcaaggccttgaaggcgctgcggctggaggacttgcgtatt
cccgtagcctacttgaagaccttccagggccctccccacggtatccaggtagagcgggat
aagctgaacaagtatggtcgtccactgctgggctgcaccatcaagcccaagctaggcctt
tccgccaaaaactacgggcgggctgtgtacgaagcgctgcggggtgggctggactttacc
aaagacgacgaaaacgtcaactcccagcccttcatgcgttggcgggatcgctacctgttt
gtcatggaagcggtccataaagcgcaggcagaaaccggcgagatcaaggggcactacctg
aacgtgacggcgcccacctgcgaggagatgttcaagcgggcggagtttgctaaggagatt
ggtgcccccatcatcatgcatgactacctcaccgccggctttacggccaacaccagtctg
gccaagtggtgccgcgacaacggcattctgctgcacatccaccgcgccatgcacgcggtg
attgaccggcagaaaaaccacggcatccacttccgggtgctggccaagtgcctgcgcatg
tcgggtggcgaccacctgcatgccggtacggtggtgggcaagctggaaggcgaccgcgcc
atcaccatgggctttgtggatctcatgcgagaaaactacgttgaggcggatcgttcccgc
ggcattttcttcacccaagattgggcttccatgccgggggtgatgccagtggcttccggt
gggatccacgtttggcacatgcccatactggtggagctcttcggggacgacgctgtgctg
cagtttggtggcggaaccctaggtcacccctgggggaacgctccaggcgcgacggccaac
cgggtggctctggaggcctgcatccaggcccgcaatgaaggccgagatctgattcgcgag
ggcaacgacatcatccgcgaagcagccaagtggtcgccagaactggcc------------
------------------------------------------------
>AB075910|AB075910.1 Fischerella muscicola UTEX 1829 rbcL gene for ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit, partial cds.
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
--------------------taccgtatggactgacttgctaaccgacctagatcgctac
aaaggtcgttgttacgatatcgaacccgttcgtggcgaggacaaccagtacattgcttac
gtagcttatcctctagacttgtttgaggaaggctctgtaaccaacatgttgacctcaatt
gtcggtaacgtattcggtttcaaagctttacgggcgctgcgtctggaagacttgcggatt
ccagttgcttacctcaagactttccaaggccctccccacggtatccaagttgagcgtgac
aaattaaacaaatacggtcgtcctttgttgggttgtaccattaagcccaaactcggtttg
tctgcgaaaaactacggacgtgcagtatacgagtgcttgcgcggtggtttggacttcacc
aaagacgacgaaaatatcaactcccagcctttccaacgttggcgcgatcgcttcctgttt
gtagctgatgccattcacaaagcccaagcagaaacaggcgaaatcaaaggtcactaccta
aacgttaccgctcctacctgcgaagaaatgatgaaacgggcagagttcgctaaagaactc
aagatgcctatcatcatgcatgactacttgaccgcaggtttcaccgccaatacaactttg
gctagatggtgtcgcgacaacggtatattgctccacattcaccgagcaatgcacgcggta
attgaccgtcaaaagaaccatggtatccacttccgcgttttggctaagactctgcggatg
tctggtggagaccatattcacactggtacggtggtcggtaagctagagggtgagcgcggt
attacaatgggcttcgttgacctactgcgcgaaaactatgttgagcaagacaaatctcgc
ggtatttactttacccaagattgggcttctatgcctggtgtaatggctgttgcttctggt
ggtatccacgtatggcacatgccagcattggtagaaatctttggtgatgattccgtactg
caattcggtggtggtacactcggtcacccctggggtaacgctcctggtgcaaccgcaaac
cgtgttgctttggaagcttgtattcaagctcgtaacgaaggtcgcaacttggctcgcgaa
ggtaacgacgttatccgtgaagctgctaagtggtctcctgaattggctgctgcttgcgaa
cta---------------------------------------------