Locus 3881

Sequence ID 3R_DroMel_CAF1
Location 10,552,585 – 10,552,716
Length 131
Max. P 0.951869
window6220 window6221 window6222

overview

Window 0

Location 10,552,585 – 10,552,695
Length 110
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 79.64
Mean single sequence MFE -27.32
Consensus MFE -19.13
Energy contribution -20.05
Covariance contribution 0.92
Combinations/Pair 1.17
Mean z-score -1.61
Structure conservation index 0.70
SVM decision value 0.64
SVM RNA-class probability 0.808784
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10552585 110 + 27905053
GUUCGUUGUCUAAUUGUAUU------AUUUGGCAAUUGCUGCCAACUCGACCGCCAUGGCGGAUUUCACAUAUUUAAGCGUUUUGGCCAUUUUACAACGGUCGCU---UAAUAAUGCUU
(..((((((..(((.((...------..((((((.....)))))).....((((....)))).......................)).)))..))))))..)((.---.......)).. ( -26.00)
>DroVir_CAF1 9016 93 + 1
-UUCG-UGCCUAUUUGUAUUACGGCUAUUUGGCAAUUGUUGCCACG-----------------UUUUGCAUUGCUCGGCGUUUUGGCCAU-UUACAGCACGCACU---CGCAAA---UA
-...(-(((.....((((....(((((...((((.....))))(((-----------------((..((...))..)))))..)))))..-.))))))))((...---.))...---.. ( -24.10)
>DroSec_CAF1 1688 110 + 1
GUUCGUUGUCUAAUUGUAUU------AUUUGGCAAUUGCUGCCAACUCGACCGCCAUGGCGGAUUUCACAUAUAUUGGCGUUUUGGCCAUUUUACAACGGUCGCU---UAAUAAUGCUU
(..((((((.....(((...------..((((((.....)))))).....((((....)))).....))).....((((......))))....))))))..)((.---.......)).. ( -29.20)
>DroSim_CAF1 1756 110 + 1
GUUCGUUGUCUAAUUGUAUU------AUUUGGCAAUUGCUGCCAACUCGACCGCCAUGGCGGAUUUCACAUAUUUUGGCGUUUUGGCCAUUUUACAACGAUCGCU---UAAUAAUGCUU
(.(((((((.....(((...------..((((((.....)))))).....((((....)))).....))).....((((......))))....))))))).)((.---.......)).. ( -30.10)
>DroEre_CAF1 10836 112 + 1
GUUCGCUGUCUAAUUGUAUU------AUUUGGCAAUUGCUGCCAACUCGACCGCCAUGGCGGAUUUCACAUAUUUUGGCGUUUUGGCCAU-UUACAACGAUCGCCUCCUAUUAACGCUC
....((.(((...(((((..------..((((((.....)))))).....((((....)))).............((((......)))).-.))))).))).))............... ( -25.80)
>DroYak_CAF1 10787 112 + 1
GUUCGUUGUCUAAUUGUAUU------AUUUGGCAAUUGCUGCCAACUCGACCGCCAUGGCGGUUUUCACGUAUUUCGCUGUUUUGGCCAA-UUACAACGAUCGCUCAAUAAUAAUGCUU
(.(((((((..(((((....------..((((((.....))))))...((((((....))))))............(((.....))))))-))))))))).)((...........)).. ( -28.70)
>consensus
GUUCGUUGUCUAAUUGUAUU______AUUUGGCAAUUGCUGCCAACUCGACCGCCAUGGCGGAUUUCACAUAUUUUGGCGUUUUGGCCAU_UUACAACGAUCGCU___UAAUAAUGCUU
..(((((((.....(((...........((((((.....)))))).....((((....)))).....)))......(((......))).....)))))))................... (-19.13 = -20.05 +   0.92)

alignment

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secondary structure

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dotplot

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Window 1

Location 10,552,585 – 10,552,695
Length 110
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 79.64
Mean single sequence MFE -28.80
Consensus MFE -20.83
Energy contribution -21.20
Covariance contribution 0.37
Combinations/Pair 1.28
Mean z-score -2.44
Structure conservation index 0.72
SVM decision value 1.42
SVM RNA-class probability 0.951869
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10552585 110 - 27905053
AAGCAUUAUUA---AGCGACCGUUGUAAAAUGGCCAAAACGCUUAAAUAUGUGAAAUCCGCCAUGGCGGUCGAGUUGGCAGCAAUUGCCAAAU------AAUACAAUUAGACAACGAAC
..(.((((((.---..((((((((.....(((((.....(((........)))......)))))))))))))...((((((...)))))))))------))).)............... ( -26.90)
>DroVir_CAF1 9016 93 - 1
UA---UUUGCG---AGUGCGUGCUGUAA-AUGGCCAAAACGCCGAGCAAUGCAAAA-----------------CGUGGCAACAAUUGCCAAAUAGCCGUAAUACAAAUAGGCA-CGAA-
((---((((..---..((((.(((((..-.((((......))))............-----------------..(((((.....))))).)))))))))...))))))....-....- ( -23.80)
>DroSec_CAF1 1688 110 - 1
AAGCAUUAUUA---AGCGACCGUUGUAAAAUGGCCAAAACGCCAAUAUAUGUGAAAUCCGCCAUGGCGGUCGAGUUGGCAGCAAUUGCCAAAU------AAUACAAUUAGACAACGAAC
..((.......---.))...((((((....((((......)))).....((((....((((....)))).....(((((((...)))))))..------..)))).....))))))... ( -29.00)
>DroSim_CAF1 1756 110 - 1
AAGCAUUAUUA---AGCGAUCGUUGUAAAAUGGCCAAAACGCCAAAAUAUGUGAAAUCCGCCAUGGCGGUCGAGUUGGCAGCAAUUGCCAAAU------AAUACAAUUAGACAACGAAC
..((.......---.))..(((((((....((((......)))).....((((....((((....)))).....(((((((...)))))))..------..)))).....))))))).. ( -30.60)
>DroEre_CAF1 10836 112 - 1
GAGCGUUAAUAGGAGGCGAUCGUUGUAA-AUGGCCAAAACGCCAAAAUAUGUGAAAUCCGCCAUGGCGGUCGAGUUGGCAGCAAUUGCCAAAU------AAUACAAUUAGACAGCGAAC
..((.((.....)).))..(((((((..-.((((......)))).....((((....((((....)))).....(((((((...)))))))..------..)))).....))))))).. ( -32.00)
>DroYak_CAF1 10787 112 - 1
AAGCAUUAUUAUUGAGCGAUCGUUGUAA-UUGGCCAAAACAGCGAAAUACGUGAAAACCGCCAUGGCGGUCGAGUUGGCAGCAAUUGCCAAAU------AAUACAAUUAGACAACGAAC
..((.(((....)))))..(((((((((-((((((((..(.(((.....)))....(((((....))))).)..))))).((....)).....------....)))))..))))))).. ( -30.50)
>consensus
AAGCAUUAUUA___AGCGAUCGUUGUAA_AUGGCCAAAACGCCAAAAUAUGUGAAAUCCGCCAUGGCGGUCGAGUUGGCAGCAAUUGCCAAAU______AAUACAAUUAGACAACGAAC
....................((((((....((((......)))).....((((....((((....)))).....(((((((...)))))))..........)))).....))))))... (-20.83 = -21.20 +   0.37)

alignment

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secondary structure

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dotplot

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Window 2

Location 10,552,618 – 10,552,716
Length 98
Sequences 5
Columns 101
Reading direction reverse
Mean pairwise identity 80.99
Mean single sequence MFE -24.60
Consensus MFE -16.92
Energy contribution -17.88
Covariance contribution 0.96
Combinations/Pair 1.19
Mean z-score -1.56
Structure conservation index 0.69
SVM decision value 0.03
SVM RNA-class probability 0.547290
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10552618 98 - 27905053
CGUAUGUAUGUAUGGCCAGAAAAGCAUUAUUA---AGCGACCGUUGUAAAAUGGCCAAAACGCUUAAAUAUGUGAAAUCCGCCAUGGCGGUCGAGUUGGCA
(((((....)))))(((((....((((..(((---((((.(((((....)))))......)))))))..)))).....((((....)))).....))))). ( -28.40)
>DroSec_CAF1 1721 90 - 1
CAA--------AUGGCCAGAGAAGCAUUAUUA---AGCGACCGUUGUAAAAUGGCCAAAACGCCAAUAUAUGUGAAAUCCGCCAUGGCGGUCGAGUUGGCA
...--------...(((((....((.......---.))((((((..(....((((......))))......(((.....))).)..))))))...))))). ( -26.90)
>DroSim_CAF1 1789 90 - 1
CGA--------AUGGCCAGAAAAGCAUUAUUA---AGCGAUCGUUGUAAAAUGGCCAAAACGCCAAAAUAUGUGAAAUCCGCCAUGGCGGUCGAGUUGGCA
...--------.((((((.....(((......---.........)))....))))))....(((((......(((...((((....)))))))..))))). ( -25.06)
>DroEre_CAF1 10869 90 - 1
----------UACGGGCACAAGAGCGUUAAUAGGAGGCGAUCGUUGUAA-AUGGCCAAAACGCCAAAAUAUGUGAAAUCCGCCAUGGCGGUCGAGUUGGCA
----------....(((((((((.((((.......)))).)).))))..-...))).....(((((......(((...((((....)))))))..))))). ( -23.40)
>DroYak_CAF1 10820 84 - 1
----------------CCAAAAAGCAUUAUUAUUGAGCGAUCGUUGUAA-UUGGCCAAAACAGCGAAAUACGUGAAAACCGCCAUGGCGGUCGAGUUGGCA
----------------((((...((.(((....)))))((((((..(..-..(((.......(((.....))).......))))..))))))...)))).. ( -19.24)
>consensus
C__________AUGGCCAGAAAAGCAUUAUUA___AGCGAUCGUUGUAAAAUGGCCAAAACGCCAAAAUAUGUGAAAUCCGCCAUGGCGGUCGAGUUGGCA
..............(((((....((...........))((((((..(....((((......))))......(((.....))).)..))))))...))))). (-16.92 = -17.88 +   0.96)

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 11:12:28 2006