Locus 1319

Sequence ID X_DroMel_CAF1
Location 3,931,217 – 3,931,312
Length 95
Max. P 0.584452
window2103 window2104

overview

Window 3

Location 3,931,217 – 3,931,312
Length 95
Sequences 6
Columns 97
Reading direction forward
Mean pairwise identity 83.06
Mean single sequence MFE -33.08
Consensus MFE -27.31
Energy contribution -27.28
Covariance contribution -0.03
Combinations/Pair 1.11
Mean z-score -1.31
Structure conservation index 0.83
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3931217 95 + 22224390
UCCUGGAAGCCGGUGGCACUGUGGAGCAGCACAAGGCCGCUGUGGCAGCAGCCACGGCCAUGAAGUUCGAUGGUAAGUACAU--UAUUUACUCCUCA
....(((.(((((((((..((((......))))..))))))(((((....))))))))..............(((((((...--))))))))))... ( -33.80)
>DroGri_CAF1 122822 84 + 1
UUUUGGAGGCCGGCGGCACCGUGGAACAGCACAAGGCCGCUGUGGCAGCUGCCACGGCUAUGAAAUUUGAUGGUAAGUCUCAAC-------------
.....(((((..(((((...(((......)))...)))((((((((....))))))))..............))..)))))...------------- ( -32.60)
>DroSec_CAF1 47705 95 + 1
UCCUGGAAGCCGGUGGCACGGUGGAGCAGCACAAGGCCGCUGUGGCAGCAGCCACGGCCAUGAAGUUCGAUGGUAAGUACAU--UAUUAACCCCUUA
....((..(((((((((...(((......)))...))))))(((((....)))))))).............(((.((((...--)))).)))))... ( -30.40)
>DroEre_CAF1 53925 87 + 1
UCCUGGAAGCCGGUGGCACUGUGGAGCAGCACAAGGCCGCUGUGGCAGCUGCCACGGCCAUGAAGUUCGAUGGUAAGUGCAU----------CAUUA
........(((((((((..((((......))))..))))))(((((....))))))))..........((((.......)))----------).... ( -31.80)
>DroYak_CAF1 52672 95 + 1
UCCUGGAAGCCGGUGGCACUGUGGAGCAGCACAAGGCUGCUGUGGCUGCUGCCACGGCCAUGAAGUUCGAUGGUAAGUACAU--AAUUUACUCAUUG
((.(((..(((...))).((((((((((((...((....))...)))))).))))))))).))....(((((((((((....--.)))))).))))) ( -34.50)
>DroAna_CAF1 40038 89 + 1
UCCUGGAAGCCGGCGGCACUGUGGAGCAGCACAAGGCCGCUGUGGCAGCUGCCACGGCCAUGAAAUUCGAUGGUAGGUUCA--------ACUCCCCA
....(((((((((((((..((((......))))..))))))(((((....))))).(((((........))))).))))..--------..)))... ( -35.40)
>consensus
UCCUGGAAGCCGGUGGCACUGUGGAGCAGCACAAGGCCGCUGUGGCAGCUGCCACGGCCAUGAAGUUCGAUGGUAAGUACAU_______ACUCCUUA
........(((((((((..((((......))))..))))))(((((....))))))))....................................... (-27.31 = -27.28 +  -0.03)

alignment

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secondary structure

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dotplot

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Window 4

Location 3,931,217 – 3,931,312
Length 95
Sequences 6
Columns 97
Reading direction reverse
Mean pairwise identity 83.06
Mean single sequence MFE -31.05
Consensus MFE -26.01
Energy contribution -25.43
Covariance contribution -0.58
Combinations/Pair 1.32
Mean z-score -1.42
Structure conservation index 0.84
SVM decision value 0.10
SVM RNA-class probability 0.584452
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3931217 95 - 22224390
UGAGGAGUAAAUA--AUGUACUUACCAUCGAACUUCAUGGCCGUGGCUGCUGCCACAGCGGCCUUGUGCUGCUCCACAGUGCCACCGGCUUCCAGGA
.((.(((((....--...)))))....))...(((...(((((((((.((((....((((((.....))))))...)))))))).)))))...))). ( -31.40)
>DroGri_CAF1 122822 84 - 1
-------------GUUGAGACUUACCAUCAAAUUUCAUAGCCGUGGCAGCUGCCACAGCGGCCUUGUGCUGUUCCACGGUGCCGCCGGCCUCCAAAA
-------------..(((((.((......)).)))))..((((((((....))))).(((((.(((((......))))).))))).)))........ ( -29.00)
>DroSec_CAF1 47705 95 - 1
UAAGGGGUUAAUA--AUGUACUUACCAUCGAACUUCAUGGCCGUGGCUGCUGCCACAGCGGCCUUGUGCUGCUCCACCGUGCCACCGGCUUCCAGGA
...((((((....--(((.......)))..)))))).((((((((((....)))))((((((.....)))))).....).))))((........)). ( -28.50)
>DroEre_CAF1 53925 87 - 1
UAAUG----------AUGCACUUACCAUCGAACUUCAUGGCCGUGGCAGCUGCCACAGCGGCCUUGUGCUGCUCCACAGUGCCACCGGCUUCCAGGA
...((----------(((.......)))))..(((...((((((((((.(((....((((((.....))))))...)))))))).)))))...))). ( -31.30)
>DroYak_CAF1 52672 95 - 1
CAAUGAGUAAAUU--AUGUACUUACCAUCGAACUUCAUGGCCGUGGCAGCAGCCACAGCAGCCUUGUGCUGCUCCACAGUGCCACCGGCUUCCAGGA
...((((((....--...))))))((...(((((...(((((((((.((((((.((((.....)))))))))))))).).))))..)).)))..)). ( -29.30)
>DroAna_CAF1 40038 89 - 1
UGGGGAGU--------UGAACCUACCAUCGAAUUUCAUGGCCGUGGCAGCUGCCACAGCGGCCUUGUGCUGCUCCACAGUGCCGCCGGCUUCCAGGA
..((((((--------((......((((.(.....)))))..(((((....))))).(((((.(((((......))))).))))))))))))).... ( -36.80)
>consensus
UAAGGAGU_______AUGUACUUACCAUCGAACUUCAUGGCCGUGGCAGCUGCCACAGCGGCCUUGUGCUGCUCCACAGUGCCACCGGCUUCCAGGA
................................(((...(((((((((.((((....((((((.....))))))...)))))))).)))))...))). (-26.01 = -25.43 +  -0.58)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:06:26 2006