Locus 5957

Sequence ID 2R_DroMel_CAF1
Location 18,774,014 – 18,774,129
Length 115
Max. P 0.995331
window9556 window9557

overview

Window 6

Location 18,774,014 – 18,774,129
Length 115
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 77.46
Mean single sequence MFE -28.55
Consensus MFE -15.32
Energy contribution -15.64
Covariance contribution 0.32
Combinations/Pair 1.10
Mean z-score -1.88
Structure conservation index 0.54
SVM decision value 0.37
SVM RNA-class probability 0.707560
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18774014 115 + 20766785
AG-ACCACCCACCCAGCCACUCCGCCGCCGGAGUGCCACGCCCACGUA-CGCACACUAACACAGUCAAGCG--AGGGCGCUGUUUUGCAGUCAACAUAAUUUAACUACUUUUAUGGGCA
..-........(((((.(((((((....))))))).)..((((.(((.-.((...........))...)))--.))))((((.....))))......................)))).. ( -29.70)
>DroSec_CAF1 136778 114 + 1
AGGAAAAGCCACCCAGCCAC--CGCCCCCGGAGUGCCACGCCCACGUA-CGCACACUAACACAGUCAUGCG--AGGGCGCUGUUUUGCAGUCAACAUAAUUUAACUACUUUUAUGGGCA
.((....((......))..)--)((((..((((((....((((.((((-.(.((.........))).))))--.))))((((.....))))..............))))))...)))). ( -28.30)
>DroEre_CAF1 137860 100 + 1
--------------GCCAAC--CGCCCCCGCAGUGCCACGCCCUCGCA-CGCACACCAACACACUCAUGCG--AGGGCGCUGUUUUUCAGUCAACAUAAUUUAACUACUUUUAUGGGCA
--------------......--.((((....((((....(((((((((-..................))))--)))))((((.....))))..............)))).....)))). ( -29.07)
>DroYak_CAF1 139069 108 + 1
AA-CCC-----ACCACCCAC--CGCCACCGCAGUGCCACGCCCUCGCA-CGCACACUAACACACUCAUGCG--AGGGCGCUGUUUUGCAGUCAACAUAAUUUAACUACUUUUAUGGGCA
..-...-----.........--.(((...((((.((..((((((((((-..................))))--))))))..)).))))......(((((...........)))))))). ( -32.97)
>DroAna_CAF1 136702 111 + 1
UGU---AACCAACAUGCCAC--GCCCCCC---GCCCUAUGCCUCCUCUGGCCACACUCACACAGUCGUGGAUACUGGCGCUGUUUUUCAGUCAACAUAAUUUAACUACUUUUAUGGGCA
...---..............--((((...---(((....(((......)))((((((.....))).)))......)))((((.....)))).......................)))). ( -22.70)
>consensus
AG____A_CCAACCAGCCAC__CGCCCCCGCAGUGCCACGCCCACGCA_CGCACACUAACACAGUCAUGCG__AGGGCGCUGUUUUGCAGUCAACAUAAUUUAACUACUUUUAUGGGCA
..................................(((..((((......((((..............))))...))))((((.....))))...(((((...........)))))))). (-15.32 = -15.64 +   0.32)

alignment

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secondary structure

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dotplot

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Window 7

Location 18,774,014 – 18,774,129
Length 115
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 77.46
Mean single sequence MFE -43.14
Consensus MFE -22.60
Energy contribution -24.16
Covariance contribution 1.56
Combinations/Pair 1.12
Mean z-score -2.74
Structure conservation index 0.52
SVM decision value 2.56
SVM RNA-class probability 0.995331
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18774014 115 - 20766785
UGCCCAUAAAAGUAGUUAAAUUAUGUUGACUGCAAAACAGCGCCCU--CGCUUGACUGUGUUAGUGUGCG-UACGUGGGCGUGGCACUCCGGCGGCGGAGUGGCUGGGUGGGUGGU-CU
.((((((....((((((((......))))))))....((((((((.--(((...((((...))))..)))-.....))))....(((((((....))))))))))).))))))...-.. ( -47.10)
>DroSec_CAF1 136778 114 - 1
UGCCCAUAAAAGUAGUUAAAUUAUGUUGACUGCAAAACAGCGCCCU--CGCAUGACUGUGUUAGUGUGCG-UACGUGGGCGUGGCACUCCGGGGGCG--GUGGCUGGGUGGCUUUUCCU
.(((((.....((((((((......))))))))....((.((((((--(((((....))))..(.((((.-((((....)))))))).).)))))))--.))..))))).......... ( -43.80)
>DroEre_CAF1 137860 100 - 1
UGCCCAUAAAAGUAGUUAAAUUAUGUUGACUGAAAAACAGCGCCCU--CGCAUGAGUGUGUUGGUGUGCG-UGCGAGGGCGUGGCACUGCGGGGGCG--GUUGGC--------------
.((((......(((((.......((((........))))(((((((--((((((.(..(....)..).))-)))))))))))...)))))..)))).--......-------------- ( -40.60)
>DroYak_CAF1 139069 108 - 1
UGCCCAUAAAAGUAGUUAAAUUAUGUUGACUGCAAAACAGCGCCCU--CGCAUGAGUGUGUUAGUGUGCG-UGCGAGGGCGUGGCACUGCGGUGGCG--GUGGGUGGU-----GGG-UU
.((((((....((((((((......))))))))...((.(((((((--((((((.(..(....)..).))-)))))))))))..((((((....)))--))).)).))-----)))-). ( -51.50)
>DroAna_CAF1 136702 111 - 1
UGCCCAUAAAAGUAGUUAAAUUAUGUUGACUGAAAAACAGCGCCAGUAUCCACGACUGUGUGAGUGUGGCCAGAGGAGGCAUAGGGC---GGGGGGC--GUGGCAUGUUGGUU---ACA
.((((.......(((((((......)))))))........((((......(((.(((.....))))))(((......)))....)))---)..))))--(((((......)))---)). ( -32.70)
>consensus
UGCCCAUAAAAGUAGUUAAAUUAUGUUGACUGCAAAACAGCGCCCU__CGCAUGACUGUGUUAGUGUGCG_UGCGAGGGCGUGGCACUCCGGGGGCG__GUGGCUGGGUGG_U____CU
.((((......((((((((......))))))))......((((((...(((((.(((.....))))))))......))))))..........))))....................... (-22.60 = -24.16 +   1.56)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:59:01 2006