Locus 2435

Sequence ID 3R_DroMel_CAF1
Location 6,771,639 – 6,771,799
Length 160
Max. P 0.994414
window3972 window3973 window3974

overview

Window 2

Location 6,771,639 – 6,771,759
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 99.67
Mean single sequence MFE -42.96
Consensus MFE -41.36
Energy contribution -41.56
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.45
Structure conservation index 0.96
SVM decision value 0.58
SVM RNA-class probability 0.789406
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6771639 120 + 27905053
CUGUGCUGCAUGCGAGGCGGGCACAACAAGUUAAUUACGGAGGCAUGCAACUCACAGUUGCCGCCAUAAAUUGUGCGGGCUUGGGGGACCCAACUUGAUGUGCAGCGUUUAAUGAGUGUG
....((((((((((((..(((..(..((((((...(((((.(((..(((((.....))))).))).....)))))..))))))..)..)))..)))).)))))))).............. ( -43.40)
>DroSec_CAF1 35893 120 + 1
CUGUGCUGCAUGCGAGGCGGGCACAACAAGUUAAUUACGGAGGCAUGCAACUCACAGUUGCCGCCAUAAAUUGUGCGGGCUUGGGCGACCCAACUUGAUGUGCAGCGUUUAAUGAGUGUG
....((((((((((((((..((((((...((.....))...(((..(((((.....))))).))).....))))))..))(((((...))))))))).)))))))).............. ( -41.20)
>DroSim_CAF1 40452 120 + 1
CUGUGCUGCAUGCGAGGCGGGCACAACAAGUUAAUUACGGAGGCAUGCAACUCACAGUUGCCGCCAUAAAUUGUGCGGGCUUGGGGGACCCAACUUGAUGUGCAGCGUUUAAUGAGUGUG
....((((((((((((..(((..(..((((((...(((((.(((..(((((.....))))).))).....)))))..))))))..)..)))..)))).)))))))).............. ( -43.40)
>DroEre_CAF1 20895 120 + 1
CUGUGCUGCAUGCGAGGCGGGCACAACAAGUUAAUUACGGAGGCAUGCAACUCACAGUUGCCGCCAUAAAUUGUGCGGGCUUGGGGGACCCAACUUGAUGUGCAGCGUUUAAUGAGUGUG
....((((((((((((..(((..(..((((((...(((((.(((..(((((.....))))).))).....)))))..))))))..)..)))..)))).)))))))).............. ( -43.40)
>DroYak_CAF1 32990 120 + 1
CUGUGCUGCAUGCGAGGCGGGCACAACAAGUUAAUUACGGAGGCAUGCAACUCACAGUUGCCGCCAUAAAUUGUGCGGGCUUGGGGGACCCAACUUGAUGUGCAGCGUUUAAUGAGUGUG
....((((((((((((..(((..(..((((((...(((((.(((..(((((.....))))).))).....)))))..))))))..)..)))..)))).)))))))).............. ( -43.40)
>consensus
CUGUGCUGCAUGCGAGGCGGGCACAACAAGUUAAUUACGGAGGCAUGCAACUCACAGUUGCCGCCAUAAAUUGUGCGGGCUUGGGGGACCCAACUUGAUGUGCAGCGUUUAAUGAGUGUG
....((((((((((((..(((..(..((((((...(((((.(((..(((((.....))))).))).....)))))..))))))..)..)))..)))).)))))))).............. (-41.36 = -41.56 +   0.20)

alignment

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secondary structure

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dotplot

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Window 3

Location 6,771,639 – 6,771,759
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 99.67
Mean single sequence MFE -37.41
Consensus MFE -37.41
Energy contribution -37.41
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.04
Structure conservation index 1.00
SVM decision value 2.48
SVM RNA-class probability 0.994414
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6771639 120 - 27905053
CACACUCAUUAAACGCUGCACAUCAAGUUGGGUCCCCCAAGCCCGCACAAUUUAUGGCGGCAACUGUGAGUUGCAUGCCUCCGUAAUUAACUUGUUGUGCCCGCCUCGCAUGCAGCACAG
..............((((((.......(((((...)))))((..(((((((((((((.((((..(((.....))))))).)))))).......)))))))..))......)))))).... ( -37.41)
>DroSec_CAF1 35893 120 - 1
CACACUCAUUAAACGCUGCACAUCAAGUUGGGUCGCCCAAGCCCGCACAAUUUAUGGCGGCAACUGUGAGUUGCAUGCCUCCGUAAUUAACUUGUUGUGCCCGCCUCGCAUGCAGCACAG
..............((((((.......(((((...)))))((..(((((((((((((.((((..(((.....))))))).)))))).......)))))))..))......)))))).... ( -37.41)
>DroSim_CAF1 40452 120 - 1
CACACUCAUUAAACGCUGCACAUCAAGUUGGGUCCCCCAAGCCCGCACAAUUUAUGGCGGCAACUGUGAGUUGCAUGCCUCCGUAAUUAACUUGUUGUGCCCGCCUCGCAUGCAGCACAG
..............((((((.......(((((...)))))((..(((((((((((((.((((..(((.....))))))).)))))).......)))))))..))......)))))).... ( -37.41)
>DroEre_CAF1 20895 120 - 1
CACACUCAUUAAACGCUGCACAUCAAGUUGGGUCCCCCAAGCCCGCACAAUUUAUGGCGGCAACUGUGAGUUGCAUGCCUCCGUAAUUAACUUGUUGUGCCCGCCUCGCAUGCAGCACAG
..............((((((.......(((((...)))))((..(((((((((((((.((((..(((.....))))))).)))))).......)))))))..))......)))))).... ( -37.41)
>DroYak_CAF1 32990 120 - 1
CACACUCAUUAAACGCUGCACAUCAAGUUGGGUCCCCCAAGCCCGCACAAUUUAUGGCGGCAACUGUGAGUUGCAUGCCUCCGUAAUUAACUUGUUGUGCCCGCCUCGCAUGCAGCACAG
..............((((((.......(((((...)))))((..(((((((((((((.((((..(((.....))))))).)))))).......)))))))..))......)))))).... ( -37.41)
>consensus
CACACUCAUUAAACGCUGCACAUCAAGUUGGGUCCCCCAAGCCCGCACAAUUUAUGGCGGCAACUGUGAGUUGCAUGCCUCCGUAAUUAACUUGUUGUGCCCGCCUCGCAUGCAGCACAG
..............((((((.......(((((...)))))((..(((((((((((((.((((..(((.....))))))).)))))).......)))))))..))......)))))).... (-37.41 = -37.41 +   0.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 6,771,679 – 6,771,799
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.62
Mean single sequence MFE -28.28
Consensus MFE -28.20
Energy contribution -28.20
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.65
Structure conservation index 1.00
SVM decision value 2.15
SVM RNA-class probability 0.989073
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6771679 120 - 27905053
CCCCUCUCCUAAUUUAUCCCGCUUUCCUGGCCAACAUUUGCACACUCAUUAAACGCUGCACAUCAAGUUGGGUCCCCCAAGCCCGCACAAUUUAUGGCGGCAACUGUGAGUUGCAUGCCU
............................(((.......((((.((((((.....(((((.(((.(((((((((.......))))....)))))))))))))....)))))))))).))). ( -28.20)
>DroSec_CAF1 35933 116 - 1
----CCUCCUAAUUUAUUCCGCUUUCCUGGCCAACAUUUGCACACUCAUUAAACGCUGCACAUCAAGUUGGGUCGCCCAAGCCCGCACAAUUUAUGGCGGCAACUGUGAGUUGCAUGCCU
----........................(((.......((((.((((((.....(((((.(((.((((((.((.((....))..)).))))))))))))))....)))))))))).))). ( -28.60)
>DroSim_CAF1 40492 116 - 1
----CCUCCUAAUUUAUCCCGCUUUCCUGGCCAACAUUUGCACACUCAUUAAACGCUGCACAUCAAGUUGGGUCCCCCAAGCCCGCACAAUUUAUGGCGGCAACUGUGAGUUGCAUGCCU
----........................(((.......((((.((((((.....(((((.(((.(((((((((.......))))....)))))))))))))....)))))))))).))). ( -28.20)
>DroEre_CAF1 20935 116 - 1
----CCUCCUAAUUUAUCCCGCUUUCCUGGCCAACAUUUGCACACUCAUUAAACGCUGCACAUCAAGUUGGGUCCCCCAAGCCCGCACAAUUUAUGGCGGCAACUGUGAGUUGCAUGCCU
----........................(((.......((((.((((((.....(((((.(((.(((((((((.......))))....)))))))))))))....)))))))))).))). ( -28.20)
>DroYak_CAF1 33030 116 - 1
----CCUCCUAAUUUAUCCCGCUUUCCUGGCCAACAUUUGCACACUCAUUAAACGCUGCACAUCAAGUUGGGUCCCCCAAGCCCGCACAAUUUAUGGCGGCAACUGUGAGUUGCAUGCCU
----........................(((.......((((.((((((.....(((((.(((.(((((((((.......))))....)))))))))))))....)))))))))).))). ( -28.20)
>consensus
____CCUCCUAAUUUAUCCCGCUUUCCUGGCCAACAUUUGCACACUCAUUAAACGCUGCACAUCAAGUUGGGUCCCCCAAGCCCGCACAAUUUAUGGCGGCAACUGUGAGUUGCAUGCCU
............................(((.......((((.((((((.....(((((.(((.(((((((((.......))))....)))))))))))))....)))))))))).))). (-28.20 = -28.20 +  -0.00)

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 10:36:00 2006