Locus 3584

Sequence ID 3R_DroMel_CAF1
Location 9,680,361 – 9,680,470
Length 109
Max. P 0.783636
window5779 window5780

overview

Window 9

Location 9,680,361 – 9,680,470
Length 109
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 77.79
Mean single sequence MFE -29.81
Consensus MFE -19.78
Energy contribution -20.87
Covariance contribution 1.09
Combinations/Pair 1.33
Mean z-score -1.48
Structure conservation index 0.66
SVM decision value 0.56
SVM RNA-class probability 0.783636
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9680361 109 + 27905053
AAUAAAUAAACG---------AAU--UACUUAUUACAAAUCAUCUGUGGUUCGACCAUGGUAUUCGGGUAUCCAGGUGACCAUCAUUUCGGUCAUGUCGAAGACUGCGAAUGCUUUGCAG
..........((---------(((--(((................))))))))..((.(((((((((((.((.(.((((((........)))))).).))..))).)))))))).))... ( -28.79)
>DroSec_CAF1 4593 109 + 1
AAUAAAUAAACG---------AAU--UACUUAUUGCAAAUCAUCUGUGGUUCGACCAUGGUAUUCGGGUAUCCAGGUGACCACCAUUUCGGUCAUAUCGAAAACUGCAAAUGCUUUGCAG
............---------...--.......((((((.(((.((..((((((((.((((((....))).)))))(((((........)))))..))))..))..)).))).)))))). ( -28.50)
>DroSim_CAF1 3670 109 + 1
AAUAAAUAAACG---------AAU--UACUUAUUGCAAAUCAUCUGUGGUUCGACCAUGGUAUUCGGGUAUCCAGGUGACCAUCAUUUCGGUCAUGUCGAAGACUGCAAAUGCUUUGCAG
............---------...--.......((((((.(((.((..(((((((..((((((....))).))).((((((........)))))))))))..))..)).))).)))))). ( -30.80)
>DroEre_CAF1 4382 118 + 1
AAAAAAUACAUCAAAUUGGGCAAU--UACUUAUUGCAAAUCAUCGGUAGUUCGGCCAUGGAACUCGGGUAUCCAGGUGACCAUCAUUUCGGUCAUGUCGAACACCUCCAACGCUUUGCAA
...............(((((((((--.....)))))........(((.(((((((..((((((....)).)))).((((((........)))))))))))))))).)))).......... ( -33.00)
>DroYak_CAF1 3875 118 + 1
GAUAAAUAAAUAAAAUUGGGCAAU--UACUUAUUGCAACUCAUCGGUAGUUCGGCCGUGGAACUCGGGUAUCCUGGUGACCAUCAUUUCGGUCAUGUCAAAGCACUCCAACGCUUUGCAG
...................(((((--.....)))))...(((.((((......)))))))....((((...))))((((((........))))))(.((((((........))))))).. ( -27.20)
>DroAna_CAF1 3637 103 + 1
-----------------GGGAAAUCUAAUGUGCCGCGUAUCUUCGGAGGUUCGUCCACGAUACUCGGGUAUCCAGGUGACCAUCAUUUCGGUCAUGUCGAAGACCUCGAACGCCUCGCAG
-----------------...........((((..((((....(((.(((((..((.(((((((....)))))...((((((........)))))))).)).))))))))))))..)))). ( -30.60)
>consensus
AAUAAAUAAACG_________AAU__UACUUAUUGCAAAUCAUCGGUGGUUCGACCAUGGUACUCGGGUAUCCAGGUGACCAUCAUUUCGGUCAUGUCGAAGACCGCAAACGCUUUGCAG
................................(((((((.(...(((((((((((...(((((....)))))...((((((........)))))))))))..))))))...).))))))) (-19.78 = -20.87 +   1.09)

alignment

Postscript

secondary structure

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dotplot

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Window 0

Location 9,680,361 – 9,680,470
Length 109
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 77.79
Mean single sequence MFE -29.20
Consensus MFE -20.89
Energy contribution -20.20
Covariance contribution -0.69
Combinations/Pair 1.34
Mean z-score -1.22
Structure conservation index 0.72
SVM decision value 0.43
SVM RNA-class probability 0.735027
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 9680361 109 - 27905053
CUGCAAAGCAUUCGCAGUCUUCGACAUGACCGAAAUGAUGGUCACCUGGAUACCCGAAUACCAUGGUCGAACCACAGAUGAUUUGUAAUAAGUA--AUU---------CGUUUAUUUAUU
.((((((.(((..(..((..(((((.((((((......))))))..(((....))).........)))))))..)..))).))))))(((((((--(..---------...)))))))). ( -24.20)
>DroSec_CAF1 4593 109 - 1
CUGCAAAGCAUUUGCAGUUUUCGAUAUGACCGAAAUGGUGGUCACCUGGAUACCCGAAUACCAUGGUCGAACCACAGAUGAUUUGCAAUAAGUA--AUU---------CGUUUAUUUAUU
.((((((.((((((..((..((((..((((((......))))))(((((((......)).))).))))))))..)))))).))))))(((((((--(..---------...)))))))). ( -28.60)
>DroSim_CAF1 3670 109 - 1
CUGCAAAGCAUUUGCAGUCUUCGACAUGACCGAAAUGAUGGUCACCUGGAUACCCGAAUACCAUGGUCGAACCACAGAUGAUUUGCAAUAAGUA--AUU---------CGUUUAUUUAUU
.((((((.((((((..((..(((((.((((((......))))))..(((....))).........)))))))..)))))).))))))(((((((--(..---------...)))))))). ( -29.80)
>DroEre_CAF1 4382 118 - 1
UUGCAAAGCGUUGGAGGUGUUCGACAUGACCGAAAUGAUGGUCACCUGGAUACCCGAGUUCCAUGGCCGAACUACCGAUGAUUUGCAAUAAGUA--AUUGCCCAAUUUGAUGUAUUUUUU
(((((((.((((((.((((((((...((((((......))))))..))))))))..(((((.......))))).)))))).)))))))......--........................ ( -33.50)
>DroYak_CAF1 3875 118 - 1
CUGCAAAGCGUUGGAGUGCUUUGACAUGACCGAAAUGAUGGUCACCAGGAUACCCGAGUUCCACGGCCGAACUACCGAUGAGUUGCAAUAAGUA--AUUGCCCAAUUUUAUUUAUUUAUC
..((((..((((((((((((.((...((((((......))))))...((....))......)).)))...))).))))))..))))((((((((--(..........))))))))).... ( -29.40)
>DroAna_CAF1 3637 103 - 1
CUGCGAGGCGUUCGAGGUCUUCGACAUGACCGAAAUGAUGGUCACCUGGAUACCCGAGUAUCGUGGACGAACCUCCGAAGAUACGCGGCACAUUAGAUUUCCC-----------------
(((((...(.(((((((((.((.((.((((((......))))))....(((((....))))))).)).).)))).)))))...)))))...............----------------- ( -29.70)
>consensus
CUGCAAAGCAUUCGAAGUCUUCGACAUGACCGAAAUGAUGGUCACCUGGAUACCCGAAUACCAUGGUCGAACCACAGAUGAUUUGCAAUAAGUA__AUU_________CGUUUAUUUAUU
.((((((.((((((.....((((...((((((......))))))(((((((......)).))).)).))))...)))))).))))))................................. (-20.89 = -20.20 +  -0.69)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:05:09 2006