Locus 7673

Sequence ID 3R_DroMel_CAF1
Location 20,560,820 – 20,560,916
Length 96
Max. P 0.909226
window12378 window12379

overview

Window 8

Location 20,560,820 – 20,560,916
Length 96
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 81.62
Mean single sequence MFE -26.55
Consensus MFE -16.70
Energy contribution -16.40
Covariance contribution -0.30
Combinations/Pair 1.36
Mean z-score -2.98
Structure conservation index 0.63
SVM decision value 1.06
SVM RNA-class probability 0.909226
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20560820 96 + 27905053
--------GU-AUGC-UGCAAUCAUUGUUUAUGCAAAU-UGGCAUAAAUAAGCAGGCAAA--GCA---AACAAGCUCAAAAGCUGCUCAGAUAAUGCCACAAAAUGGAGCUU
--------..-..((-(.((....((((((((((....-..))))))))))...((((..--...---....((((....))))..........))))......)).))).. ( -24.31)
>DroVir_CAF1 15802 106 + 1
-----GUAGU-AUACUUGAAAUCACUGUUUAUGCAAAUUUGGCAUAACUAAGUAAGCAUACUGCAUGCAACAAGCUCAAAAGCUGUUUAGGUAAUGCCGUAACGUUGGGCUU
-----(((((-((.(((......(((..((((((.......))))))...)))))).))))))).......((((((((....((((..((.....))..)))))))))))) ( -25.00)
>DroPse_CAF1 16450 97 + 1
--------GUUCUGC-UGCAAUCAUUGUUUAUGCAAAU-UGGCAUAAAUAAGCAAGCGGA--GCA---AACAAGCUCGAAAGCUGCUCAGAUAAUGCCGCAAAACGAAGCUU
--------(((((((-(((.....((((((((((....-..)))))))))))).))))))--)).---...(((((((...((.((.........)).))....)).))))) ( -31.00)
>DroWil_CAF1 20553 108 + 1
AAAAGAGAGCAUCGC-AGCAAUCAUUGUUUAUGCAAAU-UGGCAUAAAUAAACAAGCGAA--GCAUAAAACAAGCUCAAAAGCUGCUCAGAUAAUGCCACACACUGGAGCUU
......((((...((-(((.....((((((((((....-..))))))))))......((.--((.........))))....)))))..........(((.....))).)))) ( -25.80)
>DroAna_CAF1 15843 96 + 1
--------GU-AUGC-UGCAAUCAUUGUUUAUGCAAAU-UGGCAUAAAUAAGCAGGCAAC--ACA---AACAAGCUCAAAAGCUGCUCAGAUAAUGCCACAAAAUGAAGCUU
--------..-..((-(.((....((((((((((....-..))))))))))...((((..--...---....((((....))))..........))))......)).))).. ( -22.21)
>DroPer_CAF1 16333 97 + 1
--------GUUCUGC-UGCAAUCAUUGUUUAUGCAAAU-UGGCAUAAAUAAGCAAGCGGA--GCA---AACAAGCUCGAAAGCUGCUCAGAUAAUGCCGCAAAACGAAGCUU
--------(((((((-(((.....((((((((((....-..)))))))))))).))))))--)).---...(((((((...((.((.........)).))....)).))))) ( -31.00)
>consensus
________GU_AUGC_UGCAAUCAUUGUUUAUGCAAAU_UGGCAUAAAUAAGCAAGCAAA__GCA___AACAAGCUCAAAAGCUGCUCAGAUAAUGCCACAAAAUGAAGCUU
........((.((((.(((.....((((((((((.......))))))))))))).))))...)).......(((((((......((.........)).......)).))))) (-16.70 = -16.40 +  -0.30)

alignment

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secondary structure

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dotplot

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Window 9

Location 20,560,820 – 20,560,916
Length 96
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 81.62
Mean single sequence MFE -27.20
Consensus MFE -17.00
Energy contribution -16.45
Covariance contribution -0.55
Combinations/Pair 1.29
Mean z-score -2.67
Structure conservation index 0.63
SVM decision value 0.84
SVM RNA-class probability 0.864751
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20560820 96 - 27905053
AAGCUCCAUUUUGUGGCAUUAUCUGAGCAGCUUUUGAGCUUGUU---UGC--UUUGCCUGCUUAUUUAUGCCA-AUUUGCAUAAACAAUGAUUGCA-GCAU-AC--------
..((.........((((((....((((((((....((((.....---.))--)).).)))))))...))))))-...((((...........))))-))..-..-------- ( -26.20)
>DroVir_CAF1 15802 106 - 1
AAGCCCAACGUUACGGCAUUACCUAAACAGCUUUUGAGCUUGUUGCAUGCAGUAUGCUUACUUAGUUAUGCCAAAUUUGCAUAAACAGUGAUUUCAAGUAU-ACUAC-----
..((.(((((((..((.....))..)))((((....)))).))))...))((((((((((((...((((((.......))))))..))))......)))))-)))..----- ( -22.30)
>DroPse_CAF1 16450 97 - 1
AAGCUUCGUUUUGCGGCAUUAUCUGAGCAGCUUUCGAGCUUGUU---UGC--UCCGCUUGCUUAUUUAUGCCA-AUUUGCAUAAACAAUGAUUGCA-GCAGAAC--------
.......((((((((((((....((((((((....((((.....---.))--)).)).))))))...))))).-...((((...........))))-)))))))-------- ( -32.00)
>DroWil_CAF1 20553 108 - 1
AAGCUCCAGUGUGUGGCAUUAUCUGAGCAGCUUUUGAGCUUGUUUUAUGC--UUCGCUUGUUUAUUUAUGCCA-AUUUGCAUAAACAAUGAUUGCU-GCGAUGCUCUCUUUU
.((((((((((((.(((((.....((((((((....))).))))).))))--).))).......(((((((..-....)))))))........)))-).)).)))....... ( -27.40)
>DroAna_CAF1 15843 96 - 1
AAGCUUCAUUUUGUGGCAUUAUCUGAGCAGCUUUUGAGCUUGUU---UGU--GUUGCCUGCUUAUUUAUGCCA-AUUUGCAUAAACAAUGAUUGCA-GCAU-AC--------
..(((.((..((((((((.(((..((((((((....))).))))---)))--).)))).......((((((..-....))))))))))....)).)-))..-..-------- ( -23.30)
>DroPer_CAF1 16333 97 - 1
AAGCUUCGUUUUGCGGCAUUAUCUGAGCAGCUUUCGAGCUUGUU---UGC--UCCGCUUGCUUAUUUAUGCCA-AUUUGCAUAAACAAUGAUUGCA-GCAGAAC--------
.......((((((((((((....((((((((....((((.....---.))--)).)).))))))...))))).-...((((...........))))-)))))))-------- ( -32.00)
>consensus
AAGCUCCAUUUUGCGGCAUUAUCUGAGCAGCUUUUGAGCUUGUU___UGC__UUCGCUUGCUUAUUUAUGCCA_AUUUGCAUAAACAAUGAUUGCA_GCAU_AC________
...........((((((((....((((((((......((.........)).....)).))))))...)))))......(((...........)))..)))............ (-17.00 = -16.45 +  -0.55)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:51:40 2006