Locus 774

Sequence ID 3R_DroMel_CAF1
Location 2,680,018 – 2,680,159
Length 141
Max. P 0.984981
window1231 window1232 window1233 window1234

overview

Window 1

Location 2,680,018 – 2,680,120
Length 102
Sequences 5
Columns 102
Reading direction forward
Mean pairwise identity 84.37
Mean single sequence MFE -24.29
Consensus MFE -15.82
Energy contribution -16.10
Covariance contribution 0.28
Combinations/Pair 1.15
Mean z-score -3.26
Structure conservation index 0.65
SVM decision value 1.87
SVM RNA-class probability 0.980951
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2680018 102 + 27905053
GAACAUAAUAUUUUUUUUUAGAGAAUAUCUUAACUAUGUUGCGAAGUAUUCCGACAUUACAUUGCAUUUGCAACAUUUACUGCAAUGUAUCUGAAACAGUGU
...............(((((((.............((((((.((.....))))))))(((((((((..............))))))))))))))))...... ( -18.24)
>DroSec_CAF1 39563 100 + 1
GAACACAAUAUUUU--UUUAAAGAAUAUCUUAACCAUGUUGCGAAGUAUUGCAACAUUACAUUGCAUUUGCAACAUUGCCUGCAAUGUAUCUGAAACAGUGU
..((((.(((((((--.....))))))).......(((((((((....)))))))))(((((((((...(((....))).))))))))).........)))) ( -25.50)
>DroSim_CAF1 32723 100 + 1
GAACACAAUAUUUU--UUUAAAGAAUAUCUUAACAAUGUUGCGAAGUAUUGCAACAUUACAUUGCAUUUGCAACAUUGCCUGCAAUGUAUCUGAAACAGUGU
..((((.(((((((--.....)))))))......((((((((((....))))))))))((((((((...(((....))).))))))))..........)))) ( -25.80)
>DroEre_CAF1 33440 95 + 1
AUACACAUUU-------UUUAAGAAUAUAUUAAAAAUGUUGCAAAGCAUUGCAACUGUACAUUGCAUUUGCAACAUGUGCUGCAAUGUAUCUGAAACAGUGU
..((((..((-------(((((.......)))))))((((.((..((((((((...(((((((((....)))..))))))))))))))...)).)))))))) ( -25.20)
>DroYak_CAF1 40025 100 + 1
GUACACAAUUUCUU-UCUUAAACAAUAUAUUAACAAUGUUGCAAAGUGUUGCAAGUGUAAAUUGCAUUUGCAACAUUU-AUGCAAUGUAUCUGAAACAAUGU
..............-....................(((((((((((((((((((((((.....)))))))))))))))-.)))))))).............. ( -26.70)
>consensus
GAACACAAUAUUUU__UUUAAAGAAUAUCUUAACAAUGUUGCGAAGUAUUGCAACAUUACAUUGCAUUUGCAACAUUUCCUGCAAUGUAUCUGAAACAGUGU
..((((...............................(((((((....)))))))..(((((((((..............))))))))).........)))) (-15.82 = -16.10 +   0.28) 

alignment

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secondary structure

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Window 2

Location 2,680,018 – 2,680,120
Length 102
Sequences 5
Columns 102
Reading direction reverse
Mean pairwise identity 84.37
Mean single sequence MFE -23.10
Consensus MFE -13.64
Energy contribution -14.52
Covariance contribution 0.88
Combinations/Pair 1.06
Mean z-score -2.78
Structure conservation index 0.59
SVM decision value 0.86
SVM RNA-class probability 0.869476
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2680018 102 - 27905053
ACACUGUUUCAGAUACAUUGCAGUAAAUGUUGCAAAUGCAAUGUAAUGUCGGAAUACUUCGCAACAUAGUUAAGAUAUUCUCUAAAAAAAAAUAUUAUGUUC
...(((...))).((((((((((((.....)))...))))))))).....(((((((((.((......)).))).))))))..................... ( -16.40)
>DroSec_CAF1 39563 100 - 1
ACACUGUUUCAGAUACAUUGCAGGCAAUGUUGCAAAUGCAAUGUAAUGUUGCAAUACUUCGCAACAUGGUUAAGAUAUUCUUUAAA--AAAAUAUUGUGUUC
((((.........(((((((((.(((....)))...)))))))))(((((((........)))))))...................--........)))).. ( -25.70)
>DroSim_CAF1 32723 100 - 1
ACACUGUUUCAGAUACAUUGCAGGCAAUGUUGCAAAUGCAAUGUAAUGUUGCAAUACUUCGCAACAUUGUUAAGAUAUUCUUUAAA--AAAAUAUUGUGUUC
((((.........(((((((((.(((....)))...)))))))))(((((((........)))))))...................--........)))).. ( -25.10)
>DroEre_CAF1 33440 95 - 1
ACACUGUUUCAGAUACAUUGCAGCACAUGUUGCAAAUGCAAUGUACAGUUGCAAUGCUUUGCAACAUUUUUAAUAUAUUCUUAAA-------AAAUGUGUAU
((((..(((.(((((((((((((((.....)))...)))))))))..(((((((....))))))).............))).)))-------....)))).. ( -26.00)
>DroYak_CAF1 40025 100 - 1
ACAUUGUUUCAGAUACAUUGCAU-AAAUGUUGCAAAUGCAAUUUACACUUGCAACACUUUGCAACAUUGUUAAUAUAUUGUUUAAGA-AAGAAAUUGUGUAC
((((.(((((.......(((((.-...((((((((.((.......)).))))))))...)))))..((.((((........)))).)-).))))).)))).. ( -22.30)
>consensus
ACACUGUUUCAGAUACAUUGCAGGAAAUGUUGCAAAUGCAAUGUAAUGUUGCAAUACUUCGCAACAUUGUUAAGAUAUUCUUUAAA__AAAAUAUUGUGUUC
((((.........(((((((((..............)))))))))..(((((........)))))...............................)))).. (-13.64 = -14.52 +   0.88) 

alignment

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secondary structure

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dotplot

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Window 3

Location 2,680,040 – 2,680,159
Length 119
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 91.43
Mean single sequence MFE -34.57
Consensus MFE -27.32
Energy contribution -26.96
Covariance contribution -0.36
Combinations/Pair 1.10
Mean z-score -2.57
Structure conservation index 0.79
SVM decision value 1.99
SVM RNA-class probability 0.984981
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2680040 119 + 27905053
GAAUAUCUUAACUAUGUUGCGAAGUAUUCCGACAUUACAUUGCAUUUGCAACAUUUACUGCAAUGUAUCUGAAACAGUGUUGCUGUAAGGACCGCUGCAAGCAGUGCAUCCUGCUCUGC
................((((..(((..(((..((.(((((((((..............)))))))))..))..((((.....))))..)))..)))))))((((.((.....)).)))) ( -29.04)
>DroSec_CAF1 39583 119 + 1
GAAUAUCUUAACCAUGUUGCGAAGUAUUGCAACAUUACAUUGCAUUUGCAACAUUGCCUGCAAUGUAUCUGAAACAGUGUUGCUGUAAGGACCGCUGCAAGCAGUGCAUCCUGCUCUGC
.............(((((((((....)))))))))(((((((((...(((....))).)))))))))......((((.....)))).((((.(((((....)))))..))))....... ( -35.10)
>DroSim_CAF1 32743 119 + 1
GAAUAUCUUAACAAUGUUGCGAAGUAUUGCAACAUUACAUUGCAUUUGCAACAUUGCCUGCAAUGUAUCUGAAACAGUGUUGCUGUAAGGACCGCUGCAAGCAGUGCAUCCUGCUCUGC
............((((((((((....))))))))))((((((((...(((....))).)))))))).......((((.....)))).((((.(((((....)))))..))))....... ( -35.40)
>DroEre_CAF1 33455 119 + 1
GAAUAUAUUAAAAAUGUUGCAAAGCAUUGCAACUGUACAUUGCAUUUGCAACAUGUGCUGCAAUGUAUCUGAAACAGUGUUGCUGUAAGGACCGCUGCAAGCAGUGCAUCCUGCUAUAG
...............(((((((....))))))).((((((((((...(((.....))))))))))))).....((((.....)))).((((.(((((....)))))..))))....... ( -34.10)
>DroYak_CAF1 40046 118 + 1
CAAUAUAUUAACAAUGUUGCAAAGUGUUGCAAGUGUAAAUUGCAUUUGCAACAUUU-AUGCAAUGUAUCUGAAACAAUGUUGCUGUAAGGACCGCUGCAAGCAGUGCAUCCUGCUCUGC
...((((.((((((((((((((((((((((((((((.....)))))))))))))))-.))))))))...........))))).))))((((.(((((....)))))..))))....... ( -39.20)
>consensus
GAAUAUCUUAACAAUGUUGCGAAGUAUUGCAACAUUACAUUGCAUUUGCAACAUUUCCUGCAAUGUAUCUGAAACAGUGUUGCUGUAAGGACCGCUGCAAGCAGUGCAUCCUGCUCUGC
.............((((((((((....(((((.......))))))))))))))).....((((..(..........)..)))).(((.(((.(((((....)))))..))))))..... (-27.32 = -26.96 +  -0.36) 

alignment

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secondary structure

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dotplot

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Window 4

Location 2,680,040 – 2,680,159
Length 119
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 91.43
Mean single sequence MFE -33.80
Consensus MFE -25.66
Energy contribution -26.10
Covariance contribution 0.44
Combinations/Pair 1.10
Mean z-score -2.46
Structure conservation index 0.76
SVM decision value 1.28
SVM RNA-class probability 0.939766
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2680040 119 - 27905053
GCAGAGCAGGAUGCACUGCUUGCAGCGGUCCUUACAGCAACACUGUUUCAGAUACAUUGCAGUAAAUGUUGCAAAUGCAAUGUAAUGUCGGAAUACUUCGCAACAUAGUUAAGAUAUUC
(((.(((((......)))))))).(((((((..((((.....))))......((((((((((((.....)))...))))))))).....))).....)))).................. ( -29.80)
>DroSec_CAF1 39583 119 - 1
GCAGAGCAGGAUGCACUGCUUGCAGCGGUCCUUACAGCAACACUGUUUCAGAUACAUUGCAGGCAAUGUUGCAAAUGCAAUGUAAUGUUGCAAUACUUCGCAACAUGGUUAAGAUAUUC
(((.(((((......)))))))).((((........(((((((((...))).(((((((((.(((....)))...))))))))).))))))......)))).................. ( -37.64)
>DroSim_CAF1 32743 119 - 1
GCAGAGCAGGAUGCACUGCUUGCAGCGGUCCUUACAGCAACACUGUUUCAGAUACAUUGCAGGCAAUGUUGCAAAUGCAAUGUAAUGUUGCAAUACUUCGCAACAUUGUUAAGAUAUUC
(((.(((((......)))))))).((((........(((((((((...))).(((((((((.(((....)))...))))))))).))))))......)))).................. ( -37.64)
>DroEre_CAF1 33455 119 - 1
CUAUAGCAGGAUGCACUGCUUGCAGCGGUCCUUACAGCAACACUGUUUCAGAUACAUUGCAGCACAUGUUGCAAAUGCAAUGUACAGUUGCAAUGCUUUGCAACAUUUUUAAUAUAUUC
((..((((((.((((((((.....))))).......))).).)))))..)).((((((((((((.....)))...)))))))))..(((((((....)))))))............... ( -33.51)
>DroYak_CAF1 40046 118 - 1
GCAGAGCAGGAUGCACUGCUUGCAGCGGUCCUUACAGCAACAUUGUUUCAGAUACAUUGCAU-AAAUGUUGCAAAUGCAAUUUACACUUGCAACACUUUGCAACAUUGUUAAUAUAUUG
(((.(((((......))))))))(((..........((((...(((.......)))))))..-.((((((((((((((((.......)))))....))))))))))))))......... ( -30.40)
>consensus
GCAGAGCAGGAUGCACUGCUUGCAGCGGUCCUUACAGCAACACUGUUUCAGAUACAUUGCAGGAAAUGUUGCAAAUGCAAUGUAAUGUUGCAAUACUUCGCAACAUUGUUAAGAUAUUC
(((.(((((......)))))))).((((........(((((.(((...))).(((((((((..............)))))))))..)))))......)))).................. (-25.66 = -26.10 +   0.44) 

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 09:51:47 2006