# STOCKHOLM 1.0
#=GF ID mtDNA_ssA
#=GF AC RF01853
#=GF DE Mitochondrial DNA control region secondary structure A
#=GF AU Moore B; 0000-0002-4074-1933
#=GF GA 40.0
#=GF NC 39.9
#=GF TC 40.0
#=GF SE Gardner PP;
#=GF SS Published; PMID:18845547
#=GF TP Gene; antisense;
#=GF BM cmbuild -F CM SEED
#=GF CB cmcalibrate --mpi CM
#=GF SM cmsearch --cpu 4 --verbose --nohmmonly -T 35.31 -Z 2958934 CM SEQDB
#=GF DR SO; 0005836; regulatory_region;
#=GF RN [1]
#=GF RM 18845547
#=GF RT Evidence for variable selective pressures at a large secondary structure
#=GF RT of the human mitochondrial DNA control region.
#=GF RA Pereira F, Soares P, Carneiro J, Pereira L, Richards MB, Samuels DC,
#=GF RA Amorim A
#=GF RL Mol Biol Evol. 2008;25:2759-2770.
#=GF WK MtDNA_control_region
#=GF SQ 53

AY966398.1/1-104           --CUU-UCAUGGGGAAGC-AG--A---UUUGGGUACC-ACC--CAAGUA---UUGA-CUCACCCAUCAACA-AC--CGCC-AUGUAUUUCGUACAUUA-CUGCCAGCCACCAUGAAUAUUGUACG
AY595133.1/1-106           UUCUU-UCAUGGGGAAGC-AG--A---UUUGGGUACC-ACC--CAAGUA---UUGA-CUCACCCAUCAACA-AC--CGUU-AUGUAUUUCGUACAUUA-CUGCUAGCCACCAUGAAUAUUGUACA
AY005559.1/5-110           UUCUU-UCAUGGGGAAGC-AG--A---UUUGGGUACC-ACC--CAAGUA---UUGA-NUUACCCAUCAACA-AC--CGCU-AUGUAUUUCGUACAUUA-CUGCCAGCCACCAUGAAUAUUGCACG
DQ145833.1/1-106           UUCUU-UCAUGGGGAAGC-AG--A---UUUGGGUGCC-ACC--CAAGUA---UUGA-CUCACCCAUCAACA-AC--CGCU-AUGUAUCUCGUACAUUA-CUGCCAGCCACCAUGAAUAUCGUACG
AY957299.1/18-123          GUUCU-UUAUGGGGAAGC-AG--A---UUUGGGUACC-ACC--CAAGUA---UUGA-CUCACCCAUCAACA-AC--CGCU-AUGUAUUUCGUACAUUA-CUGCCAGCCACCAUGAAUAUUGUACG
AY210520.1/2-107           UUCUU-KSRUGGGGAAGC-AG--A---UUUGGGUACC-ACC--CAAGUA---UUGA-CUCACCCAUCAACA-AC--CGCU-AUGUAUUUCGUACAUUA-CUGCCAGCCACCAUGAAUAUUGUACG
AY398125.1/1-106           UUCUU-UCAUGGGGAAGC-AG--A---UUUGGGUACC-ACC--CAAGUA---UUGA-CUCACCCAUCAACA-AC--CGCU-AUGUACUUCGUACAUUA-UUGCCAGUCACCAUGAAUAUUGUACG
AF392313.1/24-129          UUCUU-UCAUGGGGAAGC-AG--A---UUUGGGUACC-ACC--CAAGUA---UUGA-CUCACCCAUCAACA-AC--CGCU-AUGUAUUUCGUACAUUA-CUGNCAGCCACCAUGAUUAUUGUNCG
AF011222.1/2-107           UUCUU-UCAUGGGGGAGC-AG--A---UUUGGGUACC-ACC--CAAGUA---UUGA-CUCACCCAUCAGCA-AC--CGCU-AUGUAUCUCGUACAUUA-CUGUUAGUUACCAUGAAUAUUGUACA
D38113.1/15442-15546       UUCUU-UCAUGGGGAAGC-AA--A---UUUAGGUACC-ACC--UAAGUA---CUGG-CUCAUUCAUUA-CA-AC--CGCU-AUGUAUUUCGUACAUUA-CUGCCAGCCACCAUGAAUAUCGUACA
AM392418.1/441-546         UUCUU-UCAUGGGGAGGC-AA--A---UUUGGGUACC-ACC--CAAGUA---UUGG-CUAACCCAUCAAUA-AU--UAUC-AUGUAUGUCGUGCAUUC-CUGCCAGACACCAUGAAUAAUGCACA
U84319.1/1-105             UUCUU-UCAUGGGGAAGC-AA--A---UUUAAGUACC-ACC--UAAGUA---UUGG-CUUAUUCAUUA-CA-AC--CACU-AUGUAUUUCGUACAUUA-CUGCUAGCCACCAUGAAUAUUGUACA
AJ812285.1/1-106           UUCUU-UCAUGGGGAGAC-AA--A---UUUGGGUGCC-ACC--CAAGUA---UUAG-CUAACCCACCAACA-AU--UGUC-AUGUAUAUCGUGCAUUA-CUGCUAGCCACCAUGAAUAAUAUACA
AF240457.1/17-122          UUCUU-UCAUGGGGAGAC-AA--A---UUUGGGUACC-ACC--CAAGUA---UUAG-CUAACCCACCAAUA-AU--UGUU-AUGUAUGUCGUGCAUUA-CUGCCAGUCACCAUGAAUAAUAUACA
AF089820.1/1-106           UUCUU-UCAUGGGGAGAC-GA--A---UUUGGGUGCC-ACC--CAAGUA---UUAG-UUAACCCACCAAUA-AU--UGUC-AUGUAUGUCGUGCAUUA-CUGCCAGCCACCAUGAAUAAUGUACA
AJ586555.1/1-105           UUCUU-UCAUGGGGAAGC-AA--A---UUUAAGUGCC-ACC--CAAGUA---UUGG-CUCAUUCACUA-UA-AC--CGCU-AUGUAUUUCGUACAUUA-CUGCCAGCCACCAUGAAUAUUAUAUA
DQ367568.1/10-114          UUCUU-UCAUGGGGAGGC-AA--G---UUUAAGUACC-ACC--UAAGUA---UUAG-CCUAUUCAUUA-CA-AC--CGCU-AUGUAUUUCGUACAUUA-CUGCCAGCCACCAUGAAUAUCGUACA
AY126678.1/1-101           ----U-UCAUGGGGAAGC-AA--A---UUUAAGUACC-ACC--UAAGUA---UUAG-CUUAUUCAUUA-CA-AC--CGCU-AUGUAUUUCGUACAUUA-CUGCCAGCCACCAUGAAUAUUGUACA
AY079509.1/1-106           UUCUU-UCAUGGGGAGAC-AA--A---UUUGGGUACC-ACC--CAAGUA---UUAG-CUAACCCAUCAAUA-AU--UAUC-AUGUAUAUCGUGCAUCA-CUGCCAGACACCAUGAAUAAUGUACG
AADA01019444.1/1181-1288   UAUUU-UCAUGAGGAGGC-AA--U---UUUGGGUACU-ACC--CAAGUA---UCGA-CCCACCCCCCUACG-ACAAUUCC-AUGUAUAUCGUGCAUUA-CUGCUAGCCACCAUGAAUAUUACAUA
D38115.1/15473-15575       UUCUU-UCAUGGGGGAUC-AG--A---UUUGGGUACC-ACC--CCAGUA--------CCGACCCAUUUCCA-GC--GGCCUAUGUAUUUCGUACAUUC-CUGCCAGCCAACAUGAAUAUCACCCA
X97707.1/15484-15586       UUCUU-UCAUGGGGGACC-AG--A---UUUGGGUGCC-ACC--CCAGUA--------CUGACCCAUUUCUA-AC--GGCCUAUGUAUUUCGUACAUUC-CUGCUAGCCAACAUGAAUAUCACCCA
D38114.1/15447-15549       UUCUU-UCAUGGGGAGAC-AA--A---UUUGGGUACU-ACC----AGUA---UUAG-CUAACCCA-UCAUA-AU--UAUC-AUGUAUGUCGUGCAUUA-CUGCCAGACACCAUGAAUAAUGUACA
AF338873.1/498-602         UAUUC-UCAUGUGGAAGC-UG--U---UUUGAGUACA-ACC--CCAGUA---UUAA-CCUGUUCUUCCACA-AC--C-CU-AUGUACUUCGUACAUUA-CUGCUAGCCCCCAUGAAUAUCGUACA
EF363489.1/1-105           UAUUC-UCAUGUGGAGGC-UG--U---UUUGAGUACA-ACC--CCAGUA---UUAA-CCCGUUCUCUCACA-AC--U-CU-AUGUACUUCGUACAUUA-CUGCCAGUCCCCAUGAAUAUUGUACA
AANU01037963.1/1241-1138   GUAUU-CUAUG-GGGUGCAAG--C---UUUAAGUGCA-ACU--UAAGUA---CUAA-UUUAUUUAUCAG---AC--CCUU-AUGUAAUUUGUGCAUUA-CUGCUAGCCAACAUGAAUGUUAUAUA
AF311725.1/1-104           UAUUC-UCGUGUGGAAGU-AA--U---UUUGGGUACA-ACC--CCAGUA---UCGA-UCUAUCCC-CUAUA-AU--UUU--AUGUACUUCGUACAUUA-CUGCUAGCCCCCAUGGAUAUUGUACA
AY661547.1/79-183          GUAUU-CUAUG-GGGUGCAAG--C---UUUAAAUGCA-ACU--UAAGUA---CUAA-UUUAUU--UUAGCACAC--CCUU-AUGUAAAUCGUGCAUUA-CUGCUAGCCAACAUGAAUAUUAUAUA
AF338877.1/498-602         UAUUC-UCAUGUGGAAGC-GG--U---UUUGAGUACGGACC--CAG-UA---CCAA-CCCACCC-UCCCCC-AA--CUCU-AUGUACUUCGUACAUUA-CUGCCAGCCCCCAUGAAUAUUGUACA
AF311722.1/1-104           UAUUC-UCAUGUGGAAGC-UG--U---UUUGAGUACA-ACC--CUAGUACAACCCA-UUUUCCCAUG-----AC--CUU--AUGUACUUCGUACAUUA-CUGCUAGUCCCCAUGAAUAUUGUACA
AANU01130438.1/6303-6200   GUAUU-CUAUG-GGGUGC-AA--A--CUUUAAAUGCA-ACU--UAAGUA---CUAA-UUAUUUUAUCAG---AC--CCUU-AUGUAAAUCAUGCAUUA-CUGCUAGCCAACAUGAAUAUUACAUA
AANU01020701.1/941-838     GUCUU-UUAUG-GUAUGCAAG--C---UUUAAAUGCA-ACU--UAAGUA---UUAA-ACAUUUCAAUAA---AC--UUUU-AUGUAAAUCGUGCAUUA-CUGUUAGCCAACAUGAAUACUAUAUA
AANU01062068.1/156-257     ---UU-CUUUGGGGUGAA-AG--C---UUUAAAUGUA-ACU--UAAGUA---CUAA-UUUAUU--UUAACACAC--UCCU-AUGUAAUUCGUGCAUUA-CUGCUAGCCAACAUGAAUAUUAUAUA
AC187501.2/31050-30946     GUAUU-CUAUG-GGGUGCAAG--C---UUUAAAUGCA-ACU--UAAGUA---CUAA-UUUAUU--UUGUCAGAC--CCCC-AUGUAAAUGGUGCAUUA-CUGCUAGCCAACAUGAAUGUUAUAUA
DQ661674.1/395-291         GUAUU-CUAAGGGG--GC-AC--AACCACAAAGUACA-AUU--UAAGU----AUAA-CCUAAUC-UUAUAU-GC--CCCU-AUGUAAUUCGUGCAUUA-CUGCUAGUCACCAUGGAUAUUAUAUA
EU004480.1/1275-1379       GUAUU-CUAAGGGG--GC-AU--AACCAUAAAGUACA-AUU--UAAGUA---CGAU-CUAAUUUUAU--AU-GC--CCCU-AUGUAAUUCGUGCAUUA-CUGCUAGUCACCAUGGAUAUUAUAUA
AY397669.1/89-193          GUAUU-CUAAGGGG--GC-AU--AACCACAAAAUACA-AUU--UUAGUA---UAAU-CUAAUUUUAU--AU-GC--CCUU-AUGUAAUUCGUGCAUUA-CUGCUAGUCACCAUGGAUAUUAUAUA
AY682605.1/56-160          GUAUU-UUAUGUUGUACA-AG--C--CCCACAGUACA-ACC--UUAGCA---CUAG-CUAACUU-UUA-AU-GC--CACU-AUGUAAUUCGUGCAUUA-CUGCUAGCCAACAUGAAUAAUAUAUA
DQ355301.1/15466-15572     GCAUU-CUAUAGGGGUAC-AA--UC-CUUAAAGAUCA-ACU--UAAGUA---CUAA-UCCAAUU-UUAUGU-AC--CCCU-AUGUAAUUCGUGCAUUA-CUGCUUGUCACCAUGAAUAUUAUAUA
DQ373494.1/306-403         AUGUU-GUAUGA----GC-UU--C---AUAAGACA---GUC--CUAGUA---UUAA-CCUGCUCA-UAA-U-AC--UACU-AUGUAAUUCGUGCAUUA-CUGCUAGCCAACAUGUAUAAUAUAUA
AF376805.1/1-104           --AUU-UGAUGUUGGUGU-GA--AC-CUUACAAUACA-AUC--UUAGUA---CUAA-CUUGUUUCU-A-AU-GC--UACU-AUGUAAUUCGUGCAUUA-CUGCUAGCCAACAUGAAUAAUAUAUA
U88994.1/95-195            UUUAU-UGAUGGACUAGC-AA-------UGAAGU----ACU--UUGGAA---GUAU-GCAUAACAUUUCAA-AC--UUUU-AUGUAAUUUGUGCAUUA-AUGCUUAACCCCAUGAAUAAUAUAUA
U88999.1/94-198            CUCUA-UUAUUGGUGGAC-UAGCA---AUAAAGU----ACU--UUGCAA---GUAC-AUGCAACACUUCAA-AC--UUCU-AUGUAAUUAGUGCAUUA-UUGUUCAACCCCAUGAAUAAUAUAUA
AY048783.1/237-333         CUGUU-UUGUG-GACAUU-AA-CA---UGU-----CC-------GCGUA-----GGCAUAAUGUACC-AAG-AC-AUAUU-AUGUAUAUCGUACAUUAAUUGAUAGUCCCCAUGAAUAUUAAGUA
U89000.1/97-197            UUUAU-UGAUGGACUAGCGAU-GA---AGUACUUUAC-AAGCAUACGUA---G------CGUUUA---CAA-AC--UCCU-AUGUAAUUUGUGCAUUA-AUGCUUGC-CACAUGAAUAAUAUAUA
U88992.1/96-196            UUUAU-UGAUGGACUAGC-AA-------UGAAGU----ACU--UUGUAA---GUAU-GCAUAAUAUUUCAA-AC--UUUU-AUGUAAUUUGUGCAUUA-AUGCUUGGCCCCAUGAAUAAUAUAUA
DQ241236.1/84-184          CUUAU-UGAUGGACGAAC-AU-------CAAAGU----ACU--UUAUAA---GUAC-ACACAACAUCUCAA-UU--GGUU-AUGUAAUUAGUGCAUUA-UUGUUAAACCCCAUGAAUAAUGCACA
DQ241248.1/84-184          CUUAU-UGAUGGCUCAAC-AUUAA---AGUACUUUAC-AAG--UACAUA-----------UAAUAUUUAAA-UU--GGUU-AUGUAAUUAGUGCAUUA-AUGCUUAACCCCAUGAAUAAUGUACA
DQ241250.1/84-184          CUUAU-UGGUGGUUCAAC-AU-------UAAAGU----ACU--UUACAA---GUAC-AUAUAUUAUUUAAA-UU--GGUU-AUGUAAUUAGUGCAUUA-AUGUUUAACCCCAUGAAUAAUGUACA
U89008.1/99-199            AUUAU-UGGUGGACUAAC-GA-------UAAAGU----ACU--UUGCAG---GUAC-AUGCAACACCCCAA-AC--UUCU-AUGUAAUUAGUGCAUUA-UUGUUUAGCCCCACGAAUAAUACAUA
AY196756.1/84-184          UUUAU-UGAUGGACUAGC-AA-------UGAAGU----ACU--UUGCAA---GUAU-GCAUAACAUUUCAA-AU--UUUU-AUGUAAUUUGUGCAUUA-AUGUUUUGCCCCAUGAAUAAUACAUA
AACZ03060926.1/95317-95212 UUCUU-UCAUGGGGAAGC-AA--A---UUUGGGUACC-ACC--CAAGUA---UUGG-CUAACCCACCAACA-AC--CGCC-AUGUAUAUCGUGCAUUA-CUGCCAGCCACCAUGAAUAUUAUAUA
AACZ03034773.1/2787-2681   --UGUAUUCUGGUAAAGC-ACCCA---UUUGGGUAUA-ACC--CAAGUA---UUGACCUGCCCCAUUAAUA-AU--UUUC--UGUAUAUUGUGCAUUA-CUGCUAGCCAACAUGAAUAUUAUAUA
#=GC SS_cons               ::::(.((((((((--((.((..,...,<<<<<<___.>>>..>>><<-...<<<<.________>>>>--.>>..,,,,.<<<<<_____>>>>>,,.))))---))-))))))):::::::::
#=GC RF                    uUuUU.ucAUGgggaagC.Ag..a...UuuggGUaCa.ACc..caaguA...uuga.cUaauuCAucaaaA.ac..uucU.AUGuAaUUcGUgCAUUA.cUGcUAGccacCAUgaAUAuUaUAuA
//
