Locus 4004

Sequence ID 3R_DroMel_CAF1
Location 10,912,982 – 10,913,105
Length 123
Max. P 0.999086
window6418 window6419 window6420

overview

Window 8

Location 10,912,982 – 10,913,080
Length 98
Sequences 4
Columns 107
Reading direction forward
Mean pairwise identity 78.86
Mean single sequence MFE -23.38
Consensus MFE -18.73
Energy contribution -19.10
Covariance contribution 0.37
Combinations/Pair 1.06
Mean z-score -2.88
Structure conservation index 0.80
SVM decision value 3.36
SVM RNA-class probability 0.999086
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10912982 98 + 27905053
----CCGCCUGGGGAAACCCCCCAUGUCCCCCCCCCCUUCCUUUAACCG-----CACACGCAUAAUUUAUUAUAAUUUUGACAUUGAACGAGUUCAAUGUCGACACU
----.....(((((.....)))))((((....................(-----(....))..................(((((((((....))))))))))))).. ( -24.60)
>DroSec_CAF1 183496 87 + 1
----CCGCCGGGGGAAACCCCCCCU----------------UUGAACCGCCGCACACACGCAUAAUUUAUUAUAAUUUUGACAUUGAACGAGUUCAAUGUCGACGCC
----.....((((....))))....----------------.......((.((......))................(((((((((((....))))))))))).)). ( -26.20)
>DroSim_CAF1 186329 87 + 1
----CCGCCGGGGCAAACCCCCCCU----------------UUGAACCACCGCACACACGCAUAAUUUAUUAUAAUUUUGACAUUGAACGAGUUCAAUGUCGACGCC
----..((.((((....))))....----------------..........((......))................(((((((((((....))))))))))).)). ( -21.50)
>DroEre_CAF1 182994 86 + 1
CCCCCCGCCGCCGGAGAAACCCCCU----------------UGGAGCCG-----CACACGCAUAAUUUAUUAUAAUUUUGACAUUGAACGAGUUCAAUGUCGACGCC
......((.(((.(((.......))----------------).).)).)-----)....((((((....))))....(((((((((((....))))))))))).)). ( -21.20)
>consensus
____CCGCCGGGGGAAACCCCCCCU________________UUGAACCG_____CACACGCAUAAUUUAUUAUAAUUUUGACAUUGAACGAGUUCAAUGUCGACGCC
.........(((((.....))))).....................................................(((((((((((....))))))))))).... (-18.73 = -19.10 +   0.37)

alignment

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secondary structure

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dotplot

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Window 9

Location 10,912,982 – 10,913,080
Length 98
Sequences 4
Columns 107
Reading direction reverse
Mean pairwise identity 78.86
Mean single sequence MFE -28.02
Consensus MFE -23.14
Energy contribution -23.33
Covariance contribution 0.19
Combinations/Pair 1.11
Mean z-score -1.49
Structure conservation index 0.83
SVM decision value 0.40
SVM RNA-class probability 0.722588
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10912982 98 - 27905053
AGUGUCGACAUUGAACUCGUUCAAUGUCAAAAUUAUAAUAAAUUAUGCGUGUG-----CGGUUAAAGGAAGGGGGGGGGGACAUGGGGGGUUUCCCCAGGCGG----
..(((((((((((((....))))))))).................(((....)-----))..............((((..((.......))..)))).)))).---- ( -28.50)
>DroSec_CAF1 183496 87 - 1
GGCGUCGACAUUGAACUCGUUCAAUGUCAAAAUUAUAAUAAAUUAUGCGUGUGUGCGGCGGUUCAA----------------AGGGGGGGUUUCCCCCGGCGG----
.((((((((((((((....)))))))))..................(((....)))))).......----------------.(((((.....))))).))..---- ( -29.60)
>DroSim_CAF1 186329 87 - 1
GGCGUCGACAUUGAACUCGUUCAAUGUCAAAAUUAUAAUAAAUUAUGCGUGUGUGCGGUGGUUCAA----------------AGGGGGGGUUUGCCCCGGCGG----
..(((((((((((((....)))))))))............((((((.(((....)))))))))...----------------....((((....)))))))).---- ( -27.90)
>DroEre_CAF1 182994 86 - 1
GGCGUCGACAUUGAACUCGUUCAAUGUCAAAAUUAUAAUAAAUUAUGCGUGUG-----CGGCUCCA----------------AGGGGGUUUCUCCGGCGGCGGGGGG
((.((((((((((((....)))))))))..................((....)-----)))).)).----------------........((((((....)))))). ( -26.10)
>consensus
GGCGUCGACAUUGAACUCGUUCAAUGUCAAAAUUAUAAUAAAUUAUGCGUGUG_____CGGUUCAA________________AGGGGGGGUUUCCCCCGGCGG____
..(((((((((((((....))))))))).......................................................(((((.....)))))))))..... (-23.14 = -23.33 +   0.19)

alignment

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secondary structure

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dotplot

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Window 0

Location 10,913,008 – 10,913,105
Length 97
Sequences 6
Columns 102
Reading direction reverse
Mean pairwise identity 80.40
Mean single sequence MFE -25.98
Consensus MFE -16.20
Energy contribution -16.20
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.49
Structure conservation index 0.62
SVM decision value 1.07
SVM RNA-class probability 0.910813
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10913008 97 - 27905053
GCUGGGCUGUCGUCUACUUGCAUAUAGUGUCGACAUUGAACUCGUUCAAUGUCAAAAUUAUAAUAAAUUAUGCGUGUG-----CGGUUAAAGGAAGGGGGGG
((((.((...(((.((.((...((((((...(((((((((....)))))))))...))))))...)).)).))).)).-----))))............... ( -23.30)
>DroSec_CAF1 183517 91 - 1
GCUGGGCUGUCGUCUACUUGCAUAUGGCGUCGACAUUGAACUCGUUCAAUGUCAAAAUUAUAAUAAAUUAUGCGUGUGUGCGGCGGUUCAA-----------
..(((((((((((.(((.((((((.(....)(((((((((....)))))))))...............)))))).))).))))))))))).----------- ( -34.10)
>DroSim_CAF1 186350 91 - 1
GCUGGGCUGUUGUCUACUUGCAUAUGGCGUCGACAUUGAACUCGUUCAAUGUCAAAAUUAUAAUAAAUUAUGCGUGUGUGCGGUGGUUCAA-----------
..(((((..((((.(((.((((((.(....)(((((((((....)))))))))...............)))))).))).))))..))))).----------- ( -29.20)
>DroEre_CAF1 183019 79 - 1
GGC-------UGUCUACUUGCAUAUGGCGUCGACAUUGAACUCGUUCAAUGUCAAAAUUAUAAUAAAUUAUGCGUGUG-----CGGCUCCA-----------
(((-------(((.(((..(((((.(....)(((((((((....)))))))))...............)))))))).)-----)))))...----------- ( -22.70)
>DroYak_CAF1 190391 86 - 1
GGCUGUCGGCUGUCUACUUGCAUAUAGCGUCGACAUUGAACUCGUUCAAUGUCAAAAUUAUAAUAAAUUAUGCGUGUG-----CGGCUCCA-----------
((..((((........)..((((((.((((.(((((((((....)))))))))..((((......)))))))))))))-----)))).)).----------- ( -23.70)
>DroAna_CAF1 181470 77 - 1
-----AGCGUCGUCUACUUGCAUAC--CAUCGACAUUGAACUCGUUCAAUGUCAAAAUUAUAAUAAAUUAUGCGUGUG-----UGGAUG-------------
-----.....(((((((.(((((..--....(((((((((....)))))))))..((((......)))))))))...)-----))))))------------- ( -22.90)
>consensus
GCUGGGCUGUCGUCUACUUGCAUAUGGCGUCGACAUUGAACUCGUUCAAUGUCAAAAUUAUAAUAAAUUAUGCGUGUG_____CGGUUCAA___________
..............(((.(((((........(((((((((....)))))))))..((((......))))))))).)))........................ (-16.20 = -16.20 +  -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 11:15:41 2006