Locus 288

Sequence ID 3R_DroMel_CAF1
Location 1,109,513 – 1,109,648
Length 135
Max. P 0.880913
window489 window490 window491

overview

Window 9

Location 1,109,513 – 1,109,622
Length 109
Sequences 5
Columns 109
Reading direction forward
Mean pairwise identity 83.41
Mean single sequence MFE -30.24
Consensus MFE -17.99
Energy contribution -20.92
Covariance contribution 2.93
Combinations/Pair 1.06
Mean z-score -2.35
Structure conservation index 0.59
SVM decision value 0.58
SVM RNA-class probability 0.788862
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1109513 109 + 27905053
AUAUGUUAGCCACUGUCGGAACAUUAUGUUAACAGCACUGUUAAGCGUGUUUCGAACAACAGGUCUAGUGUUGGGACACUAUGUUUCUUCAACAUGUUGCUCGGAGCAU
..((((((((.(((((.(((((((..((((..((((((((....((.((((......)))).)).)))))))).))))..)))))))....))).)).)))...))))) ( -28.80)
>DroSec_CAF1 43204 109 + 1
AUAUGUUAGCCACUGUCGGAACAUUAUGUUUACAGCGCUGUUAAGCGUGUUUCAAACAACAGGUCUAGUGUUGAGACACCAUGUUUCUGCAACAUGUUGCUAGGAGCAU
........((..(((..(((((((..(((((.((((((((....((.((((......)))).)).)))))))))))))..))))))).((((....)))))))..)).. ( -32.00)
>DroSim_CAF1 43092 109 + 1
AUAUGUUAGCCACUGUCGGAACAUUAUGUUAACAGCGCUGUUAAGCGUGUUUCAAACAACAGGUCAAGUGUUGAGACACCAUGUUUCUGCAACAUGUUGCUAGGAGCAU
...(((((((...(((....)))....)))))))..(((....)))(((((((((...((.......)).))))))))).((((((((((((....)))).)))))))) ( -31.40)
>DroEre_CAF1 44171 91 + 1
AUAUGUUAGCCACUGUUUGUACAUUAUGUUAGCAGCGCUGUUAA--------------ACAGACCUAGUGUUGAGACACCAUGUUUCU-CAACAUGUUGCUAGGAG---
..((((.(((....)))...))))..(.((((((((.(((....--------------.))).....(((((((((.((...)).)))-)))))))))))))).).--- ( -24.20)
>DroYak_CAF1 64548 103 + 1
UUAUGAUUGCCACUGUUGGUACAUUAUGUUAGCAACGCUGUUAAUCGUGUUU-----AACAG-UCUAGUGUUGAGAAACUUUGUUUCUGCAACAUGUUGCUAGGAUUAU
.(((((((((((....))))).))))))((((((((((((((((......))-----)))))-)...((((((((((((...)))))).))))))))))))))...... ( -34.80)
>consensus
AUAUGUUAGCCACUGUCGGAACAUUAUGUUAACAGCGCUGUUAAGCGUGUUUC_AACAACAGGUCUAGUGUUGAGACACCAUGUUUCUGCAACAUGUUGCUAGGAGCAU
...(.(((((.(((((.(((((((..((((..((((((((....((.((((......)))).)).)))))))).))))..)))))))....))).)).))))).).... (-17.99 = -20.92 +   2.93) 

alignment

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secondary structure

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dotplot

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Window 0

Location 1,109,513 – 1,109,622
Length 109
Sequences 5
Columns 109
Reading direction reverse
Mean pairwise identity 83.41
Mean single sequence MFE -24.82
Consensus MFE -14.00
Energy contribution -15.36
Covariance contribution 1.36
Combinations/Pair 1.10
Mean z-score -2.02
Structure conservation index 0.56
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1109513 109 - 27905053
AUGCUCCGAGCAACAUGUUGAAGAAACAUAGUGUCCCAACACUAGACCUGUUGUUCGAAACACGCUUAACAGUGCUGUUAACAUAAUGUUCCGACAGUGGCUAACAUAU
..(((.(((((((((((((.....))))((((((....))))))....)))))))))................(((((((((.....)))..)))))))))........ ( -26.70)
>DroSec_CAF1 43204 109 - 1
AUGCUCCUAGCAACAUGUUGCAGAAACAUGGUGUCUCAACACUAGACCUGUUGUUUGAAACACGCUUAACAGCGCUGUAAACAUAAUGUUCCGACAGUGGCUAACAUAU
..(((...(((..((((((.....))))))((((.((((((.((....)).)).)))).)))))))....)))(((((.(((.....)))...)))))........... ( -25.70)
>DroSim_CAF1 43092 109 - 1
AUGCUCCUAGCAACAUGUUGCAGAAACAUGGUGUCUCAACACUUGACCUGUUGUUUGAAACACGCUUAACAGCGCUGUUAACAUAAUGUUCCGACAGUGGCUAACAUAU
..(((...(((..((((((.....))))))((((.(((((((.......).)).)))).)))))))....)))(((((((((.....)))..))))))........... ( -25.80)
>DroEre_CAF1 44171 91 - 1
---CUCCUAGCAACAUGUUG-AGAAACAUGGUGUCUCAACACUAGGUCUGU--------------UUAACAGCGCUGCUAACAUAAUGUACAAACAGUGGCUAACAUAU
---....((((....(((((-((..((.((((((....)))))).))...)--------------)))))).(((((...((.....)).....)))))))))...... ( -19.70)
>DroYak_CAF1 64548 103 - 1
AUAAUCCUAGCAACAUGUUGCAGAAACAAAGUUUCUCAACACUAGA-CUGUU-----AAACACGAUUAACAGCGUUGCUAACAUAAUGUACCAACAGUGGCAAUCAUAA
.......(((((((.(((((.((((((...)))))))))))...(.-(((((-----((......))))))))))))))).....(((..(((....)))....))).. ( -26.20)
>consensus
AUGCUCCUAGCAACAUGUUGCAGAAACAUGGUGUCUCAACACUAGACCUGUUGUU_GAAACACGCUUAACAGCGCUGUUAACAUAAUGUUCCGACAGUGGCUAACAUAU
.......((((.(((((((((((.....((((((....))))))...((((((.............))))))..)))).)))))..(((....))))).))))...... (-14.00 = -15.36 +   1.36) 

alignment

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secondary structure

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dotplot

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Window 1

Location 1,109,552 – 1,109,648
Length 96
Sequences 5
Columns 97
Reading direction forward
Mean pairwise identity 78.94
Mean single sequence MFE -25.70
Consensus MFE -15.58
Energy contribution -17.38
Covariance contribution 1.80
Combinations/Pair 1.25
Mean z-score -2.06
Structure conservation index 0.61
SVM decision value 0.92
SVM RNA-class probability 0.880913
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1109552 96 + 27905053
GUUAAGCGUGUUUCGAACAACAGGUCUAGUGUUGGGACACUAUGUUUCU-UCAACAUGUUGCUCGGAGCAUUCCAACUCGAAGUUGCGUAUACGUAA
.....(((((((((((.(((((....((((((....))))))((((...-..))))))))).)))))))....((((.....)))).....)))).. ( -25.10)
>DroSec_CAF1 43243 96 + 1
GUUAAGCGUGUUUCAAACAACAGGUCUAGUGUUGAGACACCAUGUUUCU-GCAACAUGUUGCUAGGAGCAUUCCAACUCGAAGUUGCGUAUACGUAA
(((..(.(((((((((...((.......)).))))))))))((((((((-((((....)))).))))))))...)))......(((((....))))) ( -25.80)
>DroSim_CAF1 43131 96 + 1
GUUAAGCGUGUUUCAAACAACAGGUCAAGUGUUGAGACACCAUGUUUCU-GCAACAUGUUGCUAGGAGCAUUCCAACUCGAAGUUUCGUAUACGUAA
...(((((((((((((...((.......)).))))))))).((((((((-((((....)))).))))))))...........))))........... ( -23.60)
>DroYak_CAF1 64587 90 + 1
GUUAAUCGUGUUU-----AACAG-UCUAGUGUUGAGAAACUUUGUUUCU-GCAACAUGUUGCUAGGAUUAUUCCAACUAGAAGUUGCGUAUGCGUAA
(((((......))-----)))..-((((((((((((((((...))))))-.)))).........(((....))).))))))..(((((....))))) ( -23.70)
>DroAna_CAF1 41386 88 + 1
---------AGUUUAAACAACAGGUCUACUAACUGGCCAACAUGUUGCUGGCAGCAUGUUGCCAGCAACAUUCUGACUUAACAUUGCGUAUACGUAA
---------.(((....((...((((........))))...(((((((((((((....)))))))))))))..))....))).(((((....))))) ( -30.30)
>consensus
GUUAAGCGUGUUUCAAACAACAGGUCUAGUGUUGAGACACCAUGUUUCU_GCAACAUGUUGCUAGGAGCAUUCCAACUCGAAGUUGCGUAUACGUAA
.......(((((((((...((.......)).))))))))).((((((((.((((....)))).))))))))............(((((....))))) (-15.58 = -17.38 +   1.80) 

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:39:32 2006