Locus 6636

Sequence ID 3R_DroMel_CAF1
Location 17,443,459 – 17,443,594
Length 135
Max. P 0.992710
window10804 window10805 window10806

overview

Window 4

Location 17,443,459 – 17,443,563
Length 104
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 80.03
Mean single sequence MFE -22.18
Consensus MFE -11.80
Energy contribution -11.68
Covariance contribution -0.12
Combinations/Pair 1.12
Mean z-score -1.88
Structure conservation index 0.53
SVM decision value 0.01
SVM RNA-class probability 0.536855
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17443459 104 + 27905053
-ACUCAGCAUUUUGGUCACUCUAAUUACGAGCUCCAAAAUAAAAUAAAAAACAGCACUGUCAUGACUUUUUGACAACCGCUGAAAGUGUGGUGUCCACCAU---------------ACAU
-..((((((((((((...(((.......)))..))))))).................(((((........)))))...)))))..(((((((....)))))---------------)).. ( -30.30)
>DroSec_CAF1 44950 104 + 1
-GCUCAGCAUUUUGGUCACUCUAAUUACGAGCUCCAAAAUAAUAUAAAAAACAGCAGUGUCAUGCCUUUUUGACAACCACUGAAAAUGUGGUGUCCAACAU---------------ACAU
-.......(((((((...(((.......)))..))))))).......((((..(((......)))..))))((((.((((.......))))))))......---------------.... ( -20.50)
>DroSim_CAF1 42152 104 + 1
-GCUCAGCAUUUUGGUCACUCUAAUUACGAGCUCCAAAAUAAUAUAAAAAACAGCAGUGUCAUGCCAUUUUGACAACCCCUGAAAAUGUGGUGUCCAACAU---------------ACAU
-..((((.(((((((...(((.......)))..))))))).................(((((........)))))....))))..(((((((.....)).)---------------)))) ( -18.50)
>DroEre_CAF1 44374 119 + 1
AGCUCAGCUAUUUGGUCACACUAAUUACGAGCUCCAAAAUAAAAUC-AAAACUGCACUGUCAUGACUUUUUGACAAAUGCUGAAAAUGUGGUGUUCAACUUAGUUGUUAAUUAAACACGU
....((((((.((((.....))))....((((.(((........((-(.....(((.(((((........)))))..)))))).....))).))))....)))))).............. ( -20.22)
>DroYak_CAF1 44834 119 + 1
UGCACAGCUAA-UGGUCACUCUAACUACGAGCUCCAAAAUAAAAUUGAAAACUGCAAUGUCAUGACUUUUUGACAAACACUAAAAUUAUGGUGUCCAACUUAGUUGUUAAUUAAACACGU
...((((((((-(((.((((.(((......((.....................))..(((((........)))))..........))).)))).)))..))))))))............. ( -21.40)
>consensus
_GCUCAGCAUUUUGGUCACUCUAAUUACGAGCUCCAAAAUAAAAUAAAAAACAGCACUGUCAUGACUUUUUGACAACCACUGAAAAUGUGGUGUCCAACAU_______________ACAU
............(((.((((.((.......((.....................))..(((((........)))))...........)).)))).)))....................... (-11.80 = -11.68 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 5

Location 17,443,498 – 17,443,594
Length 96
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 74.98
Mean single sequence MFE -18.99
Consensus MFE -9.94
Energy contribution -10.66
Covariance contribution 0.72
Combinations/Pair 1.12
Mean z-score -2.45
Structure conservation index 0.52
SVM decision value 2.35
SVM RNA-class probability 0.992710
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17443498 96 + 27905053
AAAAUAAAAAACAGCACUGUCAUGACUUUUUGACAACCGCUGAAAGUGUGGUGUCCACCAU---------------ACAUUAAA-AA--------ACAACACAUUUUCCAAAGUAUAACU
...........((((..(((((........)))))...))))...(((((((....)))))---------------))......-..--------......................... ( -20.20)
>DroSec_CAF1 44989 97 + 1
AAUAUAAAAAACAGCAGUGUCAUGCCUUUUUGACAACCACUGAAAAUGUGGUGUCCAACAU---------------ACAUUAAAAAA--------ACAACACAUUUUCCAAAGUAUAACU
.................(((((........)))))...((((((((((((.(((.......---------------...........--------))).)))))))))...)))...... ( -14.77)
>DroSim_CAF1 42191 97 + 1
AAUAUAAAAAACAGCAGUGUCAUGCCAUUUUGACAACCCCUGAAAAUGUGGUGUCCAACAU---------------ACAUUAAAAAA--------ACAACACAUUUUCCAAAGUAUAACU
.............((..(((((........)))))......(((((((((.(((.......---------------...........--------))).)))))))))....))...... ( -14.77)
>DroEre_CAF1 44414 118 + 1
AAAAUC-AAAACUGCACUGUCAUGACUUUUUGACAAAUGCUGAAAAUGUGGUGUUCAACUUAGUUGUUAAUUAAACACGUUAAAAAAGGGCGUAGACCACACAUUUUCCAA-AAAUGAUU
..((((-(.....(((.(((((........)))))..))).(((((((((.((.((......(((........)))(((((.......))))).)).)))))))))))...-...))))) ( -25.60)
>DroYak_CAF1 44873 119 + 1
AAAAUUGAAAACUGCAAUGUCAUGACUUUUUGACAAACACUAAAAUUAUGGUGUCCAACUUAGUUGUUAAUUAAACACGUUAAAAAAGGGCGUAAACAAC-CGUUUUCCAACAAAUGAUU
..((((((.(((((...(((((........))))).((((((......))))))......))))).))))))......(((..((((.((.........)-).))))..)))........ ( -19.60)
>consensus
AAAAUAAAAAACAGCACUGUCAUGACUUUUUGACAACCACUGAAAAUGUGGUGUCCAACAU_______________ACAUUAAAAAA________ACAACACAUUUUCCAAAGUAUAACU
.................(((((........)))))......(((((((((.(((.........................................))).)))))))))............ ( -9.94 = -10.66 +   0.72)

alignment

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secondary structure

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dotplot

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Window 6

Location 17,443,498 – 17,443,594
Length 96
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 74.98
Mean single sequence MFE -24.26
Consensus MFE -12.24
Energy contribution -13.04
Covariance contribution 0.80
Combinations/Pair 1.24
Mean z-score -2.08
Structure conservation index 0.50
SVM decision value 1.21
SVM RNA-class probability 0.930424
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17443498 96 - 27905053
AGUUAUACUUUGGAAAAUGUGUUGU--------UU-UUUAAUGU---------------AUGGUGGACACCACACUUUCAGCGGUUGUCAAAAAGUCAUGACAGUGCUGUUUUUUAUUUU
...(((((.(((((((((.....))--------))-))))).))---------------)))((((...)))).....(((((.(.((((........))))).)))))........... ( -21.30)
>DroSec_CAF1 44989 97 - 1
AGUUAUACUUUGGAAAAUGUGUUGU--------UUUUUUAAUGU---------------AUGUUGGACACCACAUUUUCAGUGGUUGUCAAAAAGGCAUGACACUGCUGUUUUUUAUAUU
............(((((((((.(((--------((..(......---------------..)..))))).)))))))))((..((.((((........))))))..))............ ( -22.60)
>DroSim_CAF1 42191 97 - 1
AGUUAUACUUUGGAAAAUGUGUUGU--------UUUUUUAAUGU---------------AUGUUGGACACCACAUUUUCAGGGGUUGUCAAAAUGGCAUGACACUGCUGUUUUUUAUAUU
.(....((((..(((((((((.(((--------((..(......---------------..)..))))).)))))))))..))))...)(((((((((......)))))))))....... ( -22.90)
>DroEre_CAF1 44414 118 - 1
AAUCAUUU-UUGGAAAAUGUGUGGUCUACGCCCUUUUUUAACGUGUUUAAUUAACAACUAAGUUGAACACCACAUUUUCAGCAUUUGUCAAAAAGUCAUGACAGUGCAGUUUU-GAUUUU
(((((...-...(((((((((.(((....)))..........((((((((((........))))))))))))))))))).(((((.((((........))))))))).....)-)))).. ( -31.20)
>DroYak_CAF1 44873 119 - 1
AAUCAUUUGUUGGAAAACG-GUUGUUUACGCCCUUUUUUAACGUGUUUAAUUAACAACUAAGUUGGACACCAUAAUUUUAGUGUUUGUCAAAAAGUCAUGACAUUGCAGUUUUCAAUUUU
........(((((((((.(-((.......))).)))))))))((((((((((........))))))))))...........(((.(((((........)))))..)))............ ( -23.30)
>consensus
AGUUAUACUUUGGAAAAUGUGUUGU________UUUUUUAAUGU_______________AUGUUGGACACCACAUUUUCAGCGGUUGUCAAAAAGUCAUGACACUGCUGUUUUUUAUUUU
............(((((((((.(((.........................................))).))))))))).(((((.((((........)))))))))............. (-12.24 = -13.04 +   0.80)

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 12:26:31 2006