Locus 728

Sequence ID 3R_DroMel_CAF1
Location 2,601,542 – 2,601,638
Length 96
Max. P 0.845945
window1146 window1147

overview

Window 6

Location 2,601,542 – 2,601,638
Length 96
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 67.70
Mean single sequence MFE -29.44
Consensus MFE -9.06
Energy contribution -10.82
Covariance contribution 1.76
Combinations/Pair 1.22
Mean z-score -2.07
Structure conservation index 0.31
SVM decision value 0.77
SVM RNA-class probability 0.845945
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2601542 96 + 27905053
AGUUUGUGCA------AACCUUUCCU--CCUUCCAGGACGCACGGCCGUAAGGA--------CGCCAGUGAAGCCCCACAAUAUCCUGGA-ACGGGUUAAGAAUGCAAACAAA
.((((((...------...(((..((--(.((((((((....((.((....)).--------))...(((......)))....)))))))-).)))..)))...))))))... ( -30.70)
>DroSim_CAF1 66159 104 + 1
AGUUUGUGCA------AGCCUUUCCU--CCUUCCAGGACGCAAGGACGCAAGGACGCCAGGACGCCAGUGAAGCCCCACAAUUUCCUGGA-AAGGGUUAAGAAUGCAAACAAA
.((((((...------(((((((..(--((((...(..(....)..)..)))))..((((((.....(((......)))....)))))).-)))))))......))))))... ( -30.90)
>DroEre_CAF1 69711 88 + 1
AGUUUGUGUA------AACCCUUCCU--CGUUCCA----------------GGACGCUAGGAAGCCAGUGAAGCCCCACAAUUUCCUGAA-ACGGGUUAAGAAUGCAAACAAA
.((((((((.------((((((((((--((((...----------------.))))..)))))..(((.((((........)))))))..-..)))))....))))))))... ( -24.80)
>DroYak_CAF1 68776 104 + 1
AGUUUGUGUA------AACCUUUUCU--CGUUCCACGACGUAAGUACGCAAGGACGCAAGGACUCCAGUGAAGCCCCACAAUUUCCUGGA-ACGAGUUAAGAAUGCAAACAAA
.((((((((.------...(((..((--((((((.((((....)).))..(((((....).......(((......)))....)))))))-)))))..))).))))))))... ( -33.40)
>DroMoj_CAF1 79153 97 + 1
CGUAUUUGCAGCUUAGAAGCAUUACGGGUAUUCCAGGAGCAGA-ACC-----------AG--CAGCAGUCGAGC--AGCCAUUUCCUGUGGCUGCGUUAAGGAUGCACACAAU
.((.(((((.(((....)))......((....))....)))))-...-----------..--..(((..(..((--((((((.....)))))))).....)..)))))..... ( -27.40)
>consensus
AGUUUGUGCA______AACCUUUCCU__CCUUCCAGGACGCAAGGACG_AAGGACGC_AGGACGCCAGUGAAGCCCCACAAUUUCCUGGA_ACGGGUUAAGAAUGCAAACAAA
.((...((((......(((((..........(((((((.............((...........)).(((......)))....)))))))...))))).....)))).))... ( -9.06 = -10.82 +   1.76)

alignment

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secondary structure

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dotplot

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Window 7

Location 2,601,542 – 2,601,638
Length 96
Sequences 5
Columns 113
Reading direction reverse
Mean pairwise identity 67.70
Mean single sequence MFE -32.92
Consensus MFE -6.42
Energy contribution -6.90
Covariance contribution 0.48
Combinations/Pair 1.33
Mean z-score -2.19
Structure conservation index 0.20
SVM decision value 0.55
SVM RNA-class probability 0.778266
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2601542 96 - 27905053
UUUGUUUGCAUUCUUAACCCGU-UCCAGGAUAUUGUGGGGCUUCACUGGCG--------UCCUUACGGCCGUGCGUCCUGGAAGG--AGGAAAGGUU------UGCACAAACU
(((((..(((..(((..(((.(-((((((((...(((.((((.....((..--------.))....)))).)))))))))))).)--.))..)))..------)))))))).. ( -33.60)
>DroSim_CAF1 66159 104 - 1
UUUGUUUGCAUUCUUAACCCUU-UCCAGGAAAUUGUGGGGCUUCACUGGCGUCCUGGCGUCCUUGCGUCCUUGCGUCCUGGAAGG--AGGAAAGGCU------UGCACAAACU
(((((..(((..(((..(((((-(((((((...((..(((...((..(((((....)))))..))...)))..))))))))))))--.))..)))..------)))))))).. ( -39.90)
>DroEre_CAF1 69711 88 - 1
UUUGUUUGCAUUCUUAACCCGU-UUCAGGAAAUUGUGGGGCUUCACUGGCUUCCUAGCGUCC----------------UGGAACG--AGGAAGGGUU------UACACAAACU
(((((.((.((((((..(((((-(((((((..(((.((((((.....)))))).)))..)))----------------)))))))--.)))))))).------)).))))).. ( -31.80)
>DroYak_CAF1 68776 104 - 1
UUUGUUUGCAUUCUUAACUCGU-UCCAGGAAAUUGUGGGGCUUCACUGGAGUCCUUGCGUCCUUGCGUACUUACGUCGUGGAACG--AGAAAAGGUU------UACACAAACU
...(((((...((((..(((((-((((.((......(((((((.....)))))))(((((....)))))......)).)))))))--))..))))..------....))))). ( -34.60)
>DroMoj_CAF1 79153 97 - 1
AUUGUGUGCAUCCUUAACGCAGCCACAGGAAAUGGCU--GCUCGACUGCUG--CU-----------GGU-UCUGCUCCUGGAAUACCCGUAAUGCUUCUAAGCUGCAAAUACG
...(((((((..((((..(((((((.......)))))--))..((..((((--(.-----------(((-(((......)))..))).)))..)).)))))).))))..))). ( -24.70)
>consensus
UUUGUUUGCAUUCUUAACCCGU_UCCAGGAAAUUGUGGGGCUUCACUGGCGUCCU_GCGUCCUU_CGGCCUUGCGUCCUGGAACG__AGGAAAGGUU______UGCACAAACU
...(((((..........((...(((((((....(((......))).((...........)).............)))))))......))....((........)).))))). ( -6.42 =  -6.90 +   0.48)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:50:19 2006