Locus 1359

Sequence ID 3R_DroMel_CAF1
Location 4,000,015 – 4,000,195
Length 180
Max. P 0.976670
window2230 window2231 window2232 window2233 window2234

overview

Window 0

Location 4,000,015 – 4,000,116
Length 101
Sequences 3
Columns 101
Reading direction reverse
Mean pairwise identity 100.00
Mean single sequence MFE -35.30
Consensus MFE -35.30
Energy contribution -35.30
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.09
Structure conservation index 1.00
SVM decision value 1.15
SVM RNA-class probability 0.922810
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4000015 101 - 27905053
GCUGUUGCUGCUGUUGUUGUGAUUUGUCUAACACAGCGAGCGGUCAGUUGGCCAUACAAAGAGUCCCGGACAGCGGCAUUCAUUAAUUUUGCAGCACCAGC
((((.((((((..((((((((..........))))))))..((((....)))).......((((.(((.....))).)))).........)))))).)))) ( -35.30)
>DroSec_CAF1 5647 101 - 1
GCUGUUGCUGCUGUUGUUGUGAUUUGUCUAACACAGCGAGCGGUCAGUUGGCCAUACAAAGAGUCCCGGACAGCGGCAUUCAUUAAUUUUGCAGCACCAGC
((((.((((((..((((((((..........))))))))..((((....)))).......((((.(((.....))).)))).........)))))).)))) ( -35.30)
>DroSim_CAF1 5705 101 - 1
GCUGUUGCUGCUGUUGUUGUGAUUUGUCUAACACAGCGAGCGGUCAGUUGGCCAUACAAAGAGUCCCGGACAGCGGCAUUCAUUAAUUUUGCAGCACCAGC
((((.((((((..((((((((..........))))))))..((((....)))).......((((.(((.....))).)))).........)))))).)))) ( -35.30)
>consensus
GCUGUUGCUGCUGUUGUUGUGAUUUGUCUAACACAGCGAGCGGUCAGUUGGCCAUACAAAGAGUCCCGGACAGCGGCAUUCAUUAAUUUUGCAGCACCAGC
((((.((((((..((((((((..........))))))))..((((....)))).......((((.(((.....))).)))).........)))))).)))) (-35.30 = -35.30 +   0.00)

alignment

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secondary structure

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dotplot

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Window 1

Location 4,000,052 – 4,000,155
Length 103
Sequences 3
Columns 103
Reading direction forward
Mean pairwise identity 100.00
Mean single sequence MFE -31.20
Consensus MFE -29.40
Energy contribution -29.40
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.59
Structure conservation index 0.94
SVM decision value 1.26
SVM RNA-class probability 0.937276
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4000052 103 + 27905053
ACUCUUUGUAUGGCCAACUGACCGCUCGCUGUGUUAGACAAAUCACAACAACAGCAGCAACAGCAACAUGUUGCUGCCGUGCGUAAGCUUUUGUCUCGCCUCC
...........(((........(((.....)))..(((((((........((.(((((((((......))))))))).))((....)).))))))).)))... ( -31.20)
>DroSec_CAF1 5684 103 + 1
ACUCUUUGUAUGGCCAACUGACCGCUCGCUGUGUUAGACAAAUCACAACAACAGCAGCAACAGCAACAUGUUGCUGCCGUGCGUAAGCUUUUGUCUCGCCUCC
...........(((........(((.....)))..(((((((........((.(((((((((......))))))))).))((....)).))))))).)))... ( -31.20)
>DroSim_CAF1 5742 103 + 1
ACUCUUUGUAUGGCCAACUGACCGCUCGCUGUGUUAGACAAAUCACAACAACAGCAGCAACAGCAACAUGUUGCUGCCGUGCGUAAGCUUUUGUCUCGCCUCC
...........(((........(((.....)))..(((((((........((.(((((((((......))))))))).))((....)).))))))).)))... ( -31.20)
>consensus
ACUCUUUGUAUGGCCAACUGACCGCUCGCUGUGUUAGACAAAUCACAACAACAGCAGCAACAGCAACAUGUUGCUGCCGUGCGUAAGCUUUUGUCUCGCCUCC
...........(((........(((.....)))..(((((((.....((.((.(((((((((......))))))))).))..)).....))))))).)))... (-29.40 = -29.40 +   0.00)

alignment

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secondary structure

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dotplot

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Window 2

Location 4,000,052 – 4,000,155
Length 103
Sequences 3
Columns 103
Reading direction reverse
Mean pairwise identity 100.00
Mean single sequence MFE -37.70
Consensus MFE -37.70
Energy contribution -37.70
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.61
Structure conservation index 1.00
SVM decision value 1.78
SVM RNA-class probability 0.976670
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4000052 103 - 27905053
GGAGGCGAGACAAAAGCUUACGCACGGCAGCAACAUGUUGCUGUUGCUGCUGUUGUUGUGAUUUGUCUAACACAGCGAGCGGUCAGUUGGCCAUACAAAGAGU
...(((.(((((((.((..(((.((((((((((((......))))))))))))))).))..)))))))....((((.........)))))))........... ( -37.70)
>DroSec_CAF1 5684 103 - 1
GGAGGCGAGACAAAAGCUUACGCACGGCAGCAACAUGUUGCUGUUGCUGCUGUUGUUGUGAUUUGUCUAACACAGCGAGCGGUCAGUUGGCCAUACAAAGAGU
...(((.(((((((.((..(((.((((((((((((......))))))))))))))).))..)))))))....((((.........)))))))........... ( -37.70)
>DroSim_CAF1 5742 103 - 1
GGAGGCGAGACAAAAGCUUACGCACGGCAGCAACAUGUUGCUGUUGCUGCUGUUGUUGUGAUUUGUCUAACACAGCGAGCGGUCAGUUGGCCAUACAAAGAGU
...(((.(((((((.((..(((.((((((((((((......))))))))))))))).))..)))))))....((((.........)))))))........... ( -37.70)
>consensus
GGAGGCGAGACAAAAGCUUACGCACGGCAGCAACAUGUUGCUGUUGCUGCUGUUGUUGUGAUUUGUCUAACACAGCGAGCGGUCAGUUGGCCAUACAAAGAGU
...(((.(((((((.((..(((.((((((((((((......))))))))))))))).))..)))))))....((((.........)))))))........... (-37.70 = -37.70 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 4,000,090 – 4,000,195
Length 105
Sequences 3
Columns 105
Reading direction forward
Mean pairwise identity 99.37
Mean single sequence MFE -29.10
Consensus MFE -27.83
Energy contribution -28.17
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.77
Structure conservation index 0.96
SVM decision value 1.59
SVM RNA-class probability 0.966108
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4000090 105 + 27905053
CAAAUCACAACAACAGCAGCAACAGCAACAUGUUGCUGCCGUGCGUAAGCUUUUGUCUCGCCUCCUGAUAUAAAUCGCAGUGGAGCUGUUUUUUGAUUUAACAAA
.((((((.((.(((((((((((((......))))))).(((((((......(((((.(((.....))).))))).)))).))).)))))).))))))))...... ( -29.60)
>DroSec_CAF1 5722 104 + 1
CAAAUCACAACAACAGCAGCAACAGCAACAUGUUGCUGCCGUGCGUAAGCUUUUGUCUCGCCUCCUGAUAUAAAUCGCAGUGGAGCU-UUUUUUGAUUUAACAAA
.((((((..(((((.(((((((((......))))))))).))((....))...)))...(((..(((..........)))..).)).-.....))))))...... ( -28.10)
>DroSim_CAF1 5780 105 + 1
CAAAUCACAACAACAGCAGCAACAGCAACAUGUUGCUGCCGUGCGUAAGCUUUUGUCUCGCCUCCUGAUAUAAAUCGCAGUGGAGCUGUUUUUUGAUUUAACAAA
.((((((.((.(((((((((((((......))))))).(((((((......(((((.(((.....))).))))).)))).))).)))))).))))))))...... ( -29.60)
>consensus
CAAAUCACAACAACAGCAGCAACAGCAACAUGUUGCUGCCGUGCGUAAGCUUUUGUCUCGCCUCCUGAUAUAAAUCGCAGUGGAGCUGUUUUUUGAUUUAACAAA
.((((((.((.(((((((((((((......))))))).(((((((......(((((.(((.....))).))))).)))).))).)))))).))))))))...... (-27.83 = -28.17 +   0.33)

alignment

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secondary structure

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dotplot

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Window 4

Location 4,000,090 – 4,000,195
Length 105
Sequences 3
Columns 105
Reading direction reverse
Mean pairwise identity 99.37
Mean single sequence MFE -32.37
Consensus MFE -31.53
Energy contribution -31.87
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.46
Structure conservation index 0.97
SVM decision value 1.46
SVM RNA-class probability 0.955577
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4000090 105 - 27905053
UUUGUUAAAUCAAAAAACAGCUCCACUGCGAUUUAUAUCAGGAGGCGAGACAAAAGCUUACGCACGGCAGCAACAUGUUGCUGUUGCUGCUGUUGUUGUGAUUUG
.....(((((((...((((((.....((((((....))).(.((((.........)))).)))).((((((((((......)))))))))))))))).))))))) ( -33.30)
>DroSec_CAF1 5722 104 - 1
UUUGUUAAAUCAAAAAA-AGCUCCACUGCGAUUUAUAUCAGGAGGCGAGACAAAAGCUUACGCACGGCAGCAACAUGUUGCUGUUGCUGCUGUUGUUGUGAUUUG
.....(((((((.....-.((..(.(((..........))))..))..((((...((....))((((((((((((......)))))))))))))))).))))))) ( -30.50)
>DroSim_CAF1 5780 105 - 1
UUUGUUAAAUCAAAAAACAGCUCCACUGCGAUUUAUAUCAGGAGGCGAGACAAAAGCUUACGCACGGCAGCAACAUGUUGCUGUUGCUGCUGUUGUUGUGAUUUG
.....(((((((...((((((.....((((((....))).(.((((.........)))).)))).((((((((((......)))))))))))))))).))))))) ( -33.30)
>consensus
UUUGUUAAAUCAAAAAACAGCUCCACUGCGAUUUAUAUCAGGAGGCGAGACAAAAGCUUACGCACGGCAGCAACAUGUUGCUGUUGCUGCUGUUGUUGUGAUUUG
.....(((((((...((((((.....((((((....))).(.((((.........)))).)))).((((((((((......)))))))))))))))).))))))) (-31.53 = -31.87 +   0.33)

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 10:07:58 2006