Locus 2172

Sequence ID 2L_DroMel_CAF1
Location 5,868,951 – 5,869,082
Length 131
Max. P 0.961230
window3506 window3507 window3508

overview

Window 6

Location 5,868,951 – 5,869,042
Length 91
Sequences 5
Columns 91
Reading direction forward
Mean pairwise identity 80.69
Mean single sequence MFE -20.04
Consensus MFE -12.36
Energy contribution -13.64
Covariance contribution 1.28
Combinations/Pair 1.05
Mean z-score -2.33
Structure conservation index 0.62
SVM decision value 1.23
SVM RNA-class probability 0.933540
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5868951 91 + 22407834
CCCAGAAAGUCCUACAUUUCUUCCGCCACUCUUUCGCCACUAAGCGAAAAAUUUAAGCAAAGUGAUACAUCUUACUUCUGGGUGAGUUGUA
(((((((.................((.....((((((......)))))).......))...((((......)))))))))))......... ( -17.90)
>DroSec_CAF1 58731 91 + 1
CCCACAAAGUCCCACAUUCCAUCCGCCACUUUUUCGCCACUAAGCGAAAAAUUUAAGCAAAGUGAUACAUAUUACUUCUGGGUGAGUUGUA
...((((...((((..........((...((((((((......)))))))).....)).(((((((....))))))).))))....)))). ( -20.50)
>DroSim_CAF1 59575 91 + 1
CCCACAGAGUCCUACAUUCCAUCCGCCACUUUUUCGCCACUAAGCGAAAAAUUUAAGCAAAGUGAUACAUAUUACUUCUGGGUGAGUUGUA
............((((...(((((((...((((((((......)))))))).....)).(((((((....)))))))..)))))...)))) ( -20.80)
>DroEre_CAF1 82862 74 + 1
CC----------CACAA------CCCCACA-CUCCGCCAGCAAGCGAAAAAUUUAAGCAAAGUGAUACAUAUUACUUUCGGGCGCGUUGUA
..----------.((((------((((...-...(((......)))..........(.((((((((....))))))))))))...))))). ( -16.40)
>DroYak_CAF1 84102 82 + 1
CC---------UUACAUUUCUUCCGCCACUUUUUCGCCAGUAAGCGAAAAGUUUAGGCAAAGUGAUACAUAUUACUUUUGGGUGAAUUGUA
..---------.((((.(((.((((((..((((((((......))))))))....)))((((((((....)))))))).))).))).)))) ( -24.60)
>consensus
CCCA_A_AGUCCUACAUUCCAUCCGCCACUUUUUCGCCACUAAGCGAAAAAUUUAAGCAAAGUGAUACAUAUUACUUCUGGGUGAGUUGUA
.......................((((..((((((((......))))))))........(((((((....)))))))...))))....... (-12.36 = -13.64 +   1.28)

alignment

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secondary structure

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dotplot

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Window 7

Location 5,868,951 – 5,869,042
Length 91
Sequences 5
Columns 91
Reading direction reverse
Mean pairwise identity 80.69
Mean single sequence MFE -25.86
Consensus MFE -15.30
Energy contribution -15.46
Covariance contribution 0.16
Combinations/Pair 1.28
Mean z-score -2.54
Structure conservation index 0.59
SVM decision value 1.52
SVM RNA-class probability 0.961230
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5868951 91 - 22407834
UACAACUCACCCAGAAGUAAGAUGUAUCACUUUGCUUAAAUUUUUCGCUUAGUGGCGAAAGAGUGGCGGAAGAAAUGUAGGACUUUCUGGG
.........(((((((((...((((.((..((((((....(((((((((....)))))))))..)))))).)).))))...)).))))))) ( -29.40)
>DroSec_CAF1 58731 91 - 1
UACAACUCACCCAGAAGUAAUAUGUAUCACUUUGCUUAAAUUUUUCGCUUAGUGGCGAAAAAGUGGCGGAUGGAAUGUGGGACUUUGUGGG
.........(((((((((..(((((.(((.((((((....(((((((((....)))))))))..))))))))).)))))..))))).)))) ( -29.90)
>DroSim_CAF1 59575 91 - 1
UACAACUCACCCAGAAGUAAUAUGUAUCACUUUGCUUAAAUUUUUCGCUUAGUGGCGAAAAAGUGGCGGAUGGAAUGUAGGACUCUGUGGG
.........((((((.((..(((((.(((.((((((....(((((((((....)))))))))..))))))))).)))))..)))))).)). ( -29.40)
>DroEre_CAF1 82862 74 - 1
UACAACGCGCCCGAAAGUAAUAUGUAUCACUUUGCUUAAAUUUUUCGCUUGCUGGCGGAG-UGUGGGG------UUGUG----------GG
.....(((((((..((((((..((...))..)))))).....(((((((....)))))))-....)))------.))))----------.. ( -19.20)
>DroYak_CAF1 84102 82 - 1
UACAAUUCACCCAAAAGUAAUAUGUAUCACUUUGCCUAAACUUUUCGCUUACUGGCGAAAAAGUGGCGGAAGAAAUGUAA---------GG
((((.(((..((.(((((.((....)).)))))(((...((((((((((....)))).)))))))))))..))).)))).---------.. ( -21.40)
>consensus
UACAACUCACCCAGAAGUAAUAUGUAUCACUUUGCUUAAAUUUUUCGCUUAGUGGCGAAAAAGUGGCGGAAGAAAUGUAGGACU_U_UGGG
((((..((..((.(((((..........)))))(((....(((((((((....)))))))))..)))))..))..))))............ (-15.30 = -15.46 +   0.16)

alignment

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secondary structure

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dotplot

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Window 8

Location 5,868,962 – 5,869,082
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.33
Mean single sequence MFE -30.30
Consensus MFE -23.74
Energy contribution -24.10
Covariance contribution 0.36
Combinations/Pair 1.19
Mean z-score -1.44
Structure conservation index 0.78
SVM decision value 0.01
SVM RNA-class probability 0.539438
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5868962 120 - 22407834
CGCAUGUUGUUAAAGGAUCCAUCUUCGACCUCAUCUAAUAUACAACUCACCCAGAAGUAAGAUGUAUCACUUUGCUUAAAUUUUUCGCUUAGUGGCGAAAGAGUGGCGGAAGAAAUGUAG
.((((.........(....).(((((((...(((((....(((..((.....))..))))))))..))....((((....(((((((((....)))))))))..))))))))).)))).. ( -25.60)
>DroSec_CAF1 58742 120 - 1
CGCAUGUUGUUGAAGGAUCCAUCUUCGACCUCAUCUAAAAUACAACUCACCCAGAAGUAAUAUGUAUCACUUUGCUUAAAUUUUUCGCUUAGUGGCGAAAAAGUGGCGGAUGGAAUGUGG
(((((...((((((((.....)))))))).((((((.................(((((.((....)).)))))(((....(((((((((....)))))))))..))))))))).))))). ( -31.60)
>DroSim_CAF1 59586 120 - 1
CGCAUGUUGUUGAAGGAUCCAUCUUCGACCUCAUCUAAUAUACAACUCACCCAGAAGUAAUAUGUAUCACUUUGCUUAAAUUUUUCGCUUAGUGGCGAAAAAGUGGCGGAUGGAAUGUAG
.(.(((..((((((((.....))))))))..)))).....((((..(((.((.(((((.((....)).)))))(((....(((((((((....)))))))))..))))).)))..)))). ( -30.90)
>DroEre_CAF1 82864 112 - 1
CGGAUGUUGUUGAAGGAUCCAUCUUCGACCUCAUCUAAUAUACAACGCGCCCGAAAGUAAUAUGUAUCACUUUGCUUAAAUUUUUCGCUUGCUGGCGGAG-UGUGGGG------UUGUG-
.(((((..((((((((.....))))))))..)))))....((((((...((((.((((((..((...))..)))))).....(((((((....)))))))-..)))))------)))))- ( -32.60)
>DroYak_CAF1 84104 120 - 1
CGCAUGUUGUUGAAGGAUCCAUCUUCGACCUCAUCUAAUAUACAAUUCACCCAAAAGUAAUAUGUAUCACUUUGCCUAAACUUUUCGCUUACUGGCGAAAAAGUGGCGGAAGAAAUGUAA
.(.(((..((((((((.....))))))))..)))).....((((.(((..((.(((((.((....)).)))))(((...((((((((((....)))).)))))))))))..))).)))). ( -30.80)
>consensus
CGCAUGUUGUUGAAGGAUCCAUCUUCGACCUCAUCUAAUAUACAACUCACCCAGAAGUAAUAUGUAUCACUUUGCUUAAAUUUUUCGCUUAGUGGCGAAAAAGUGGCGGAAGAAAUGUAG
.(.(((..((((((((.....))))))))..)))).....((((..((..((.(((((..........)))))(((....(((((((((....)))))))))..)))))..))..)))). (-23.74 = -24.10 +   0.36)

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 10:21:24 2006