Locus 3102

Sequence ID 3L_DroMel_CAF1
Location 8,981,333 – 8,981,449
Length 116
Max. P 0.993720
window4834 window4835 window4836 window4837

overview

Window 4

Location 8,981,333 – 8,981,424
Length 91
Sequences 4
Columns 91
Reading direction forward
Mean pairwise identity 91.53
Mean single sequence MFE -25.30
Consensus MFE -21.33
Energy contribution -22.57
Covariance contribution 1.25
Combinations/Pair 1.00
Mean z-score -2.00
Structure conservation index 0.84
SVM decision value 0.98
SVM RNA-class probability 0.893224
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8981333 91 + 23771897
UUCCUCGAGCAAUUUGUGCAUGCUGUAUGCCUUCCAUUUGCCUGUCCUCGCCGAAUACAUAAUUCGGCGUGGUUUUGCCUUUGGUUUCGGU
....(((((........(((((...)))))...(((...((....((.((((((((.....)))))))).))....))...))).))))). ( -25.20)
>DroSec_CAF1 20440 88 + 1
UU---CCAGCAAUUUGUGCAUGCUGCAUGCCUUCCUUUUGCCUGUCCUCGCCGAAUACAUAAUUCGGCGUGGUUCUGCCUUUGGUUUCGGU
..---.(((((.........)))))...(((..((....((....((.((((((((.....)))))))).))....))....))....))) ( -25.40)
>DroSim_CAF1 21054 91 + 1
UUCCUCCAGCAAUUUGUGCAUGCUGCAUGCCUUCCAUUUGCCUGUCCUCGCCGAAUACAUAAUUCGGCGUGGUUCUGCCUUUGGUUUCGGU
......(((((.........)))))...(((..(((...((....((.((((((((.....)))))))).))....))...)))....))) ( -27.10)
>DroEre_CAF1 20852 85 + 1
UU---CCAGCAAUUUGUG--UGCCGCAUGCG-UCCAUUUGCCCGUCCUCGCCGAAUACAUAAUUCGGCUUGGUUUUGCCUUUGGUUUCGGU
..---...((((..((..--(((.....)))-..)).))))(((.((..(((((((.....)))))))..((.....))...))...))). ( -23.50)
>consensus
UU___CCAGCAAUUUGUGCAUGCUGCAUGCCUUCCAUUUGCCUGUCCUCGCCGAAUACAUAAUUCGGCGUGGUUCUGCCUUUGGUUUCGGU
......(((((.........)))))...(((..(((...((....((.((((((((.....)))))))).))....))...)))....))) (-21.33 = -22.57 +   1.25)

alignment

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secondary structure

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Window 5

Location 8,981,333 – 8,981,424
Length 91
Sequences 4
Columns 91
Reading direction reverse
Mean pairwise identity 91.53
Mean single sequence MFE -26.88
Consensus MFE -24.11
Energy contribution -24.67
Covariance contribution 0.56
Combinations/Pair 1.05
Mean z-score -2.90
Structure conservation index 0.90
SVM decision value 2.42
SVM RNA-class probability 0.993720
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8981333 91 - 23771897
ACCGAAACCAAAGGCAAAACCACGCCGAAUUAUGUAUUCGGCGAGGACAGGCAAAUGGAAGGCAUACAGCAUGCACAAAUUGCUCGAGGAA
.((....(((...((....((.((((((((.....)))))))).))....))...)))...((((.....)))).............)).. ( -26.80)
>DroSec_CAF1 20440 88 - 1
ACCGAAACCAAAGGCAGAACCACGCCGAAUUAUGUAUUCGGCGAGGACAGGCAAAAGGAAGGCAUGCAGCAUGCACAAAUUGCUGG---AA
.(((...((....((....((.((((((((.....)))))))).))....))....))...(((((...))))).........)))---.. ( -26.70)
>DroSim_CAF1 21054 91 - 1
ACCGAAACCAAAGGCAGAACCACGCCGAAUUAUGUAUUCGGCGAGGACAGGCAAAUGGAAGGCAUGCAGCAUGCACAAAUUGCUGGAGGAA
.((....(((...((....((.((((((((.....)))))))).))....))...)))......(.(((((.........))))).))).. ( -29.80)
>DroEre_CAF1 20852 85 - 1
ACCGAAACCAAAGGCAAAACCAAGCCGAAUUAUGUAUUCGGCGAGGACGGGCAAAUGGA-CGCAUGCGGCA--CACAAAUUGCUGG---AA
.......(((...((....((..(((((((.....)))))))..))....))...))).-....(.(((((--.......))))).---). ( -24.20)
>consensus
ACCGAAACCAAAGGCAAAACCACGCCGAAUUAUGUAUUCGGCGAGGACAGGCAAAUGGAAGGCAUGCAGCAUGCACAAAUUGCUGG___AA
.......(((...((....((.((((((((.....)))))))).))....))...)))........(((((.........)))))...... (-24.11 = -24.67 +   0.56)

alignment

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secondary structure

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dotplot

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Window 6

Location 8,981,350 – 8,981,449
Length 99
Sequences 5
Columns 99
Reading direction forward
Mean pairwise identity 82.71
Mean single sequence MFE -27.60
Consensus MFE -18.40
Energy contribution -21.36
Covariance contribution 2.96
Combinations/Pair 1.08
Mean z-score -2.23
Structure conservation index 0.67
SVM decision value 0.92
SVM RNA-class probability 0.882548
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8981350 99 + 23771897
GCAUGCUGUAUGCCUUCCAUUUGCCUGUCCUCGCCGAAUACAUAAUUCGGCGUGGUUUUGCCUUUGGUUUCGGUUUCAUACAUAUCUCCCGCAUGCGAG
((((((((((((((..(((...((....((.((((((((.....)))))))).))....))...)))....))...))))))........))))))... ( -34.80)
>DroSec_CAF1 20454 99 + 1
GCAUGCUGCAUGCCUUCCUUUUGCCUGUCCUCGCCGAAUACAUAAUUCGGCGUGGUUCUGCCUUUGGUUUCGGUUUCAUACAUAUCUCCCGCAUGCGAG
((((((((...(((..((....((....((.((((((((.....)))))))).))....))....))....)))..))............))))))... ( -29.40)
>DroSim_CAF1 21071 99 + 1
GCAUGCUGCAUGCCUUCCAUUUGCCUGUCCUCGCCGAAUACAUAAUUCGGCGUGGUUCUGCCUUUGGUUUCGGUUUCAUACAAAUCUCCCGCAUGCGAG
((((((..........(((...((....((.((((((((.....)))))))).))....))...)))....(((((.....)))))....))))))... ( -31.70)
>DroEre_CAF1 20866 92 + 1
G--UGCCGCAUGCG-UCCAUUUGCCCGUCCUCGCCGAAUACAUAAUUCGGCUUGGUUUUGCCUUUGGUUUCGGUUUCAU----AUCUCCCGCAUGCGAG
.--...((((((((-.(((...((....((..(((((((.....)))))))..))....))...)))....(((.....----)))...)))))))).. ( -31.30)
>DroYak_CAF1 21518 76 + 1
-------------------CUCACCCUUCCCCACCGCAUACAUAAUUCGGCUUGGUUUUGCCUUUGGUUUCGGUUUCAU----AUCUCCCGCAUGCGCG
-------------------...............(((((.........(((........)))........(((......----.....))).))))).. ( -10.80)
>consensus
GCAUGCUGCAUGCCUUCCAUUUGCCUGUCCUCGCCGAAUACAUAAUUCGGCGUGGUUUUGCCUUUGGUUUCGGUUUCAUACA_AUCUCCCGCAUGCGAG
......(((((((...(((...((....((.((((((((.....)))))))).))....))...)))....((...............))))))))).. (-18.40 = -21.36 +   2.96)

alignment

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secondary structure

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dotplot

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Window 7

Location 8,981,350 – 8,981,449
Length 99
Sequences 5
Columns 99
Reading direction reverse
Mean pairwise identity 82.71
Mean single sequence MFE -30.44
Consensus MFE -22.06
Energy contribution -24.54
Covariance contribution 2.48
Combinations/Pair 1.09
Mean z-score -2.81
Structure conservation index 0.72
SVM decision value 2.12
SVM RNA-class probability 0.988544
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8981350 99 - 23771897
CUCGCAUGCGGGAGAUAUGUAUGAAACCGAAACCAAAGGCAAAACCACGCCGAAUUAUGUAUUCGGCGAGGACAGGCAAAUGGAAGGCAUACAGCAUGC
...((((((........((((((...((....(((...((....((.((((((((.....)))))))).))....))...)))..)))))))))))))) ( -34.20)
>DroSec_CAF1 20454 99 - 1
CUCGCAUGCGGGAGAUAUGUAUGAAACCGAAACCAAAGGCAGAACCACGCCGAAUUAUGUAUUCGGCGAGGACAGGCAAAAGGAAGGCAUGCAGCAUGC
...((((((........((((((...((....((....((....((.((((((((.....)))))))).))....))....))..)))))))))))))) ( -32.50)
>DroSim_CAF1 21071 99 - 1
CUCGCAUGCGGGAGAUUUGUAUGAAACCGAAACCAAAGGCAGAACCACGCCGAAUUAUGUAUUCGGCGAGGACAGGCAAAUGGAAGGCAUGCAGCAUGC
...((((((........((((((...((....(((...((....((.((((((((.....)))))))).))....))...)))..)))))))))))))) ( -34.20)
>DroEre_CAF1 20866 92 - 1
CUCGCAUGCGGGAGAU----AUGAAACCGAAACCAAAGGCAAAACCAAGCCGAAUUAUGUAUUCGGCGAGGACGGGCAAAUGGA-CGCAUGCGGCA--C
.(((((((((((....----......))....(((...((....((..(((((((.....)))))))..))....))...))).-)))))))))..--. ( -34.60)
>DroYak_CAF1 21518 76 - 1
CGCGCAUGCGGGAGAU----AUGAAACCGAAACCAAAGGCAAAACCAAGCCGAAUUAUGUAUGCGGUGGGGAAGGGUGAG-------------------
..(((((((((.....----......)).........(((........))).......)))))))...............------------------- ( -16.70)
>consensus
CUCGCAUGCGGGAGAU_UGUAUGAAACCGAAACCAAAGGCAAAACCACGCCGAAUUAUGUAUUCGGCGAGGACAGGCAAAUGGAAGGCAUGCAGCAUGC
...((((((((...............))....(((...((....((.((((((((.....)))))))).))....))...)))...))))))....... (-22.06 = -24.54 +   2.48)

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 10:49:34 2006