Locus 2618

Sequence ID 3R_DroMel_CAF1
Location 7,074,229 – 7,074,331
Length 102
Max. P 0.833991
window4261 window4262

overview

Window 1

Location 7,074,229 – 7,074,331
Length 102
Sequences 6
Columns 116
Reading direction forward
Mean pairwise identity 78.33
Mean single sequence MFE -22.32
Consensus MFE -12.59
Energy contribution -13.03
Covariance contribution 0.45
Combinations/Pair 1.07
Mean z-score -2.02
Structure conservation index 0.56
SVM decision value 0.73
SVM RNA-class probability 0.833991
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7074229 102 + 27905053
CACUGCACUUGGCU------UAGUGCAACACUCUUAAGUCUAAGCAAUUACACUAGGUAUCC-CCAACCUUGUGUCCGAAAUGUUAACUUUUCGC-------GAUUGUGGUCCUUU
.((..((.((((((------(((.((...........))))))))....((((.((((....-...)))).)))).(((((........))))))-------)).))..))..... ( -22.90)
>DroGri_CAF1 11539 115 + 1
UCUUGCACUUGUCUUCCCGCAAGUACAACACUCUCAAGUCUAAGCAAUUACACUAGGUAUCC-CCAACCUUGUGUCCGAAAUGUUGUUUUUUACUGAUUUCUGAUUUUCCUUCUUU
..(((.((((((......)))))).)))...((..(((((.(((((((.((((.((((....-...)))).)))).......)))))))......)))))..))............ ( -19.20)
>DroEre_CAF1 7514 102 + 1
CACUGCACUUGGUU------AAGUGCAACACUCUUAAGUCUAAGCAAUUACACUAGGUAUCC-CCAACCUUGUGUCCGAAAUGUUUACUUUUCGC-------GAUUUUUGUCCUUU
...(((((((....------))))))).....(..(((((.........((((.((((....-...)))).)))).(((((........))))).-------)))))..)...... ( -20.60)
>DroYak_CAF1 7837 102 + 1
CACUGCACUCGGUU------GAGUGCAACACUCUUAAGUCUAAGCAAUUACACUAGGUAUCC-CCAACCUUGUGUCCGAAAUGUUUACUUUUCGC-------GAUUUUGGUCCUUA
...(((((((....------))))))).....((.(((((.........((((.((((....-...)))).)))).(((((........))))).-------))))).))...... ( -23.70)
>DroMoj_CAF1 10231 111 + 1
UCUUGCACUUGUCUUCCCGCAAGUACAACACUCUUAAGUCUAAGCAAUUACACUAGGUAUCC-CCAACCUUGUGACCGAAAUACU---UUGUAAU-AUCUUUGAUUUGAGUCAUUU
..(((.((((((......)))))).)))....((((((((.(((..(((((((.((((....-...)))).)))..((((....)---)))))))-..))).))))))))...... ( -21.60)
>DroAna_CAF1 9119 97 + 1
UCCUGCACUUGUGUGCCCGCAAGUGCAACACUCUUAAGUCUAAGCAAUUACACUAGGUAUCCCCCAACCUUGUGUCCGAAAUGUUUUCUU-------------------GUCCUAU
...((((((((((....)))))))))).......((((...(((((.((((((.((((........)))).))))...)).))))).)))-------------------)...... ( -25.90)
>consensus
CACUGCACUUGGCU______AAGUGCAACACUCUUAAGUCUAAGCAAUUACACUAGGUAUCC_CCAACCUUGUGUCCGAAAUGUUUACUUUUCGC_______GAUUUUGGUCCUUU
...(((((((..........)))))))......................((((.((((........)))).))))......................................... (-12.59 = -13.03 +   0.45)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 7,074,229 – 7,074,331
Length 102
Sequences 6
Columns 116
Reading direction reverse
Mean pairwise identity 78.33
Mean single sequence MFE -24.02
Consensus MFE -17.22
Energy contribution -16.88
Covariance contribution -0.33
Combinations/Pair 1.15
Mean z-score -1.00
Structure conservation index 0.72
SVM decision value 0.01
SVM RNA-class probability 0.540877
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7074229 102 - 27905053
AAAGGACCACAAUC-------GCGAAAAGUUAACAUUUCGGACACAAGGUUGG-GGAUACCUAGUGUAAUUGCUUAGACUUAAGAGUGUUGCACUA------AGCCAAGUGCAGUG
.......(((..((-------.(((((.(....).)))))))(((..((((.(-(....))(((((((((..((((....))))...)))))))))------))))..)))..))) ( -24.60)
>DroGri_CAF1 11539 115 - 1
AAAGAAGGAAAAUCAGAAAUCAGUAAAAAACAACAUUUCGGACACAAGGUUGG-GGAUACCUAGUGUAAUUGCUUAGACUUGAGAGUGUUGUACUUGCGGGAAGACAAGUGCAAGA
....(((.((.....(((((..((.....))...)))))..((((.((((...-....)))).))))..)).))).............((((((((((.....).))))))))).. ( -21.80)
>DroEre_CAF1 7514 102 - 1
AAAGGACAAAAAUC-------GCGAAAAGUAAACAUUUCGGACACAAGGUUGG-GGAUACCUAGUGUAAUUGCUUAGACUUAAGAGUGUUGCACUU------AACCAAGUGCAGUG
...(.((.....((-------.(((((.(....).))))))).....((((((-(....)))((((((((..((((....))))...)))))))).------))))..)).).... ( -22.40)
>DroYak_CAF1 7837 102 - 1
UAAGGACCAAAAUC-------GCGAAAAGUAAACAUUUCGGACACAAGGUUGG-GGAUACCUAGUGUAAUUGCUUAGACUUAAGAGUGUUGCACUC------AACCGAGUGCAGUG
............((-------.(((((.(....).)))))))(((..((((((-(....)).((((((((..((((....))))...)))))))))------))))..)))..... ( -24.80)
>DroMoj_CAF1 10231 111 - 1
AAAUGACUCAAAUCAAAGAU-AUUACAA---AGUAUUUCGGUCACAAGGUUGG-GGAUACCUAGUGUAAUUGCUUAGACUUAAGAGUGUUGUACUUGCGGGAAGACAAGUGCAAGA
.....((((...((.(((..-((((((.---.((((..((..(....)..)).-.).)))....))))))..))).)).....)))).((((((((((.....).))))))))).. ( -25.40)
>DroAna_CAF1 9119 97 - 1
AUAGGAC-------------------AAGAAAACAUUUCGGACACAAGGUUGGGGGAUACCUAGUGUAAUUGCUUAGACUUAAGAGUGUUGCACUUGCGGGCACACAAGUGCAGGA
.((((.(-------------------(((((.....)))..((((.((((........)))).))))..)))))))............(((((((((.(....).))))))))).. ( -25.10)
>consensus
AAAGGACCAAAAUC_______GCGAAAAGUAAACAUUUCGGACACAAGGUUGG_GGAUACCUAGUGUAAUUGCUUAGACUUAAGAGUGUUGCACUU______AGACAAGUGCAGGA
.........................................((((.((((........)))).))))....((((........)))).((((((((..........)))))))).. (-17.22 = -16.88 +  -0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:40:39 2006