Locus 7419

Sequence ID 3L_DroMel_CAF1
Location 19,971,787 – 19,971,922
Length 135
Max. P 0.997583
window12052 window12053 window12054 window12055

overview

Window 2

Location 19,971,787 – 19,971,902
Length 115
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 77.14
Mean single sequence MFE -36.14
Consensus MFE -25.18
Energy contribution -27.46
Covariance contribution 2.28
Combinations/Pair 1.13
Mean z-score -1.45
Structure conservation index 0.70
SVM decision value 0.23
SVM RNA-class probability 0.645829
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19971787 115 + 23771897
GAAAUUCAGACA--GGACUCAGGCGCAGCACGAACAAAGCAAGCCGUUUAAUUUGCAUUGCAUUACCGUGUGGAGGACCCGCUAGGACCCUCCUCGUCCUGCGGAGGUCCUUGCCAU
............--.......(((...(((((......((((((.(......).)).)))).....))))).((((((((((.(((((.......))))))))..)))))))))).. ( -36.50)
>DroSec_CAF1 62792 96 + 1
GAAAUGCAGACA--GGACACAGGCGCAACACGAACA---------------UUUGCAUUGCAUUACCGUGUGGAGGACCCUCCAGGAC----CUCGUCCUGCGGAGGUCCUUGCCAU
............--.......(((...(((((....---------------..(((...)))....))))).(((((((..(((((((----...)))))).)..)))))))))).. ( -34.00)
>DroSim_CAF1 21301 111 + 1
GAAAUUCAGACA--GGACACAGGCGCAGCACGAACAAAGCGAGCCGUUUAAUUUGCAUUGCAUUACCGUGUGGAGGACCCUCCAGGAC----CUCGUCCUGCGGAGGUCCUUGCCAU
............--.......(((...(((((......((((((.(......).)).)))).....))))).(((((((..(((((((----...)))))).)..)))))))))).. ( -37.30)
>DroEre_CAF1 13780 101 + 1
A------UGGCAUUGUGCAAAUUC-------AGACAGAGCGAGCCGUUUAAUUUGCAUUGCAUUACCGUGUGGAGGACCCUCCAGGACU---UUCGUCCUGGCGAGGUCCUUGCCGC
.------..(((..(((((((((.-------((((.(......).))))))))))))))))......(((..((((((((.(((((((.---...))))))).).)))))))..))) ( -42.00)
>DroYak_CAF1 13823 106 + 1
G------CGACA--GAGCACAGGCCGAGCACGAACAAAGCGAGCCAUUUAAUUUGCAUUGCAUUACCGUGUGGAGAACCCUCCAGGACC---CUCGUCCUGCUGAGGUCCUUGCCAU
(------(....--..))...(((...(((((......((((((.(......).)).)))).....)))))(((....((((((((((.---...))))))..)))))))..))).. ( -30.90)
>consensus
GAAAU_CAGACA__GGACACAGGCGCAGCACGAACAAAGCGAGCCGUUUAAUUUGCAUUGCAUUACCGUGUGGAGGACCCUCCAGGAC____CUCGUCCUGCGGAGGUCCUUGCCAU
.....................(((...(((((..(((.(((((........))))).)))......))))).((((((((..((((((.......))))))..).)))))))))).. (-25.18 = -27.46 +   2.28)

alignment

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secondary structure

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dotplot

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Window 3

Location 19,971,787 – 19,971,902
Length 115
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 77.14
Mean single sequence MFE -40.22
Consensus MFE -27.84
Energy contribution -29.60
Covariance contribution 1.76
Combinations/Pair 1.09
Mean z-score -2.06
Structure conservation index 0.69
SVM decision value 1.60
SVM RNA-class probability 0.966933
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19971787 115 - 23771897
AUGGCAAGGACCUCCGCAGGACGAGGAGGGUCCUAGCGGGUCCUCCACACGGUAAUGCAAUGCAAAUUAAACGGCUUGCUUUGUUCGUGCUGCGCCUGAGUCC--UGUCUGAAUUUC
..((((.(((((..(((((.(((((((((..((....))..)))))(((.(((((.((...............))))))).))))))).)))))...).))))--))))........ ( -46.66)
>DroSec_CAF1 62792 96 - 1
AUGGCAAGGACCUCCGCAGGACGAG----GUCCUGGAGGGUCCUCCACACGGUAAUGCAAUGCAAA---------------UGUUCGUGUUGCGCCUGUGUCC--UGUCUGCAUUUC
..((((((((((..(.((((((...----)))))))..))))))..((((((...((((((((...---------------.....)))))))).))))))..--))))........ ( -37.60)
>DroSim_CAF1 21301 111 - 1
AUGGCAAGGACCUCCGCAGGACGAG----GUCCUGGAGGGUCCUCCACACGGUAAUGCAAUGCAAAUUAAACGGCUCGCUUUGUUCGUGCUGCGCCUGUGUCC--UGUCUGAAUUUC
..((((((((((..(.((((((...----)))))))..)))))).((((.(((...(((..(((((.............)))))...)))...)))))))...--))))........ ( -36.72)
>DroEre_CAF1 13780 101 - 1
GCGGCAAGGACCUCGCCAGGACGAA---AGUCCUGGAGGGUCCUCCACACGGUAAUGCAAUGCAAAUUAAACGGCUCGCUCUGUCU-------GAAUUUGCACAAUGCCA------U
(.((..(((((((..(((((((...---.))))))).))))))))).)..((((.((...((((((((..((((......))))..-------.)))))))))).)))).------. ( -45.20)
>DroYak_CAF1 13823 106 - 1
AUGGCAAGGACCUCAGCAGGACGAG---GGUCCUGGAGGGUUCUCCACACGGUAAUGCAAUGCAAAUUAAAUGGCUCGCUUUGUUCGUGCUCGGCCUGUGCUC--UGUCG------C
..(((((((((((...((((((...---.))))))..))))))).((((.(((...(((..(((((.............)))))...)))...)))))))...--)))).------. ( -34.92)
>consensus
AUGGCAAGGACCUCCGCAGGACGAG____GUCCUGGAGGGUCCUCCACACGGUAAUGCAAUGCAAAUUAAACGGCUCGCUUUGUUCGUGCUGCGCCUGUGUCC__UGUCUG_AUUUC
..(((((((((((...((((((.......))))))..))))))).((((.(((...(((..(((((.............)))))...)))...))))))).....))))........ (-27.84 = -29.60 +   1.76)

alignment

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secondary structure

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dotplot

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Window 4

Location 19,971,822 – 19,971,922
Length 100
Sequences 5
Columns 100
Reading direction forward
Mean pairwise identity 84.61
Mean single sequence MFE -34.82
Consensus MFE -29.86
Energy contribution -30.86
Covariance contribution 1.00
Combinations/Pair 1.12
Mean z-score -2.73
Structure conservation index 0.86
SVM decision value 2.69
SVM RNA-class probability 0.996392
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19971822 100 + 23771897
AGCAAGCCGUUUAAUUUGCAUUGCAUUACCGUGUGGAGGACCCGCUAGGACCCUCCUCGUCCUGCGGAGGUCCUUGCCAUCGAUAGGUGCAAUUACACUU
.(((((........)))))((((((((..((.(((((((((((((.(((((.......))))))))..))))))..))))))...))))))))....... ( -35.00)
>DroSec_CAF1 62826 82 + 1
--------------UUUGCAUUGCAUUACCGUGUGGAGGACCCUCCAGGAC----CUCGUCCUGCGGAGGUCCUUGCCAUCGAUAUGUGCAAUUACACGU
--------------.....(((((((...((.((((((((((..(((((((----...)))))).)..))))))..))))))....)))))))....... ( -32.50)
>DroSim_CAF1 21336 96 + 1
AGCGAGCCGUUUAAUUUGCAUUGCAUUACCGUGUGGAGGACCCUCCAGGAC----CUCGUCCUGCGGAGGUCCUUGCCAUCGAUAGGUGCACUUACACGU
.((((((.(......).)).)))).....(((((((((((((..(((((((----...)))))).)..)))))))((.(((....)))))...)))))). ( -36.50)
>DroEre_CAF1 13804 93 + 1
AGCGAGCCGUUUAAUUUGCAUUGCAUUACCGUGUGGAGGACCCUCCAGGACU---UUCGUCCUGGCGAGGUCCUUGCCGCCGAUAGGUGCAAUUAU----
.(((((........)))))((((((((..((.(((((((((((.(((((((.---...))))))).).))))))..))))))...))))))))...---- ( -41.30)
>DroYak_CAF1 13852 97 + 1
AGCGAGCCAUUUAAUUUGCAUUGCAUUACCGUGUGGAGAACCCUCCAGGACC---CUCGUCCUGCUGAGGUCCUUGCCAUCGAUAGGUGCAAUUAUACUU
.(((((........)))))((((((((..((.((((.....((((((((((.---...))))))..))))......))))))...))))))))....... ( -28.80)
>consensus
AGCGAGCCGUUUAAUUUGCAUUGCAUUACCGUGUGGAGGACCCUCCAGGAC____CUCGUCCUGCGGAGGUCCUUGCCAUCGAUAGGUGCAAUUACACGU
.(((((........)))))((((((((..((.(((((((((((..((((((.......))))))..).))))))..))))))...))))))))....... (-29.86 = -30.86 +   1.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 19,971,822 – 19,971,922
Length 100
Sequences 5
Columns 100
Reading direction reverse
Mean pairwise identity 84.61
Mean single sequence MFE -35.08
Consensus MFE -29.70
Energy contribution -30.14
Covariance contribution 0.44
Combinations/Pair 1.04
Mean z-score -2.90
Structure conservation index 0.85
SVM decision value 2.89
SVM RNA-class probability 0.997583
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19971822 100 - 23771897
AAGUGUAAUUGCACCUAUCGAUGGCAAGGACCUCCGCAGGACGAGGAGGGUCCUAGCGGGUCCUCCACACGGUAAUGCAAUGCAAAUUAAACGGCUUGCU
...((((.(((((..(((((.(((..((((((..((((((((.......))))).))))))))))))..))))).)))))))))................ ( -34.80)
>DroSec_CAF1 62826 82 - 1
ACGUGUAAUUGCACAUAUCGAUGGCAAGGACCUCCGCAGGACGAG----GUCCUGGAGGGUCCUCCACACGGUAAUGCAAUGCAAA--------------
...((((.(((((..(((((.(((..((((((..(.((((((...----)))))))..)))))))))..))))).)))))))))..-------------- ( -34.90)
>DroSim_CAF1 21336 96 - 1
ACGUGUAAGUGCACCUAUCGAUGGCAAGGACCUCCGCAGGACGAG----GUCCUGGAGGGUCCUCCACACGGUAAUGCAAUGCAAAUUAAACGGCUCGCU
...((((..((((..(((((.(((..((((((..(.((((((...----)))))))..)))))))))..))))).)))).))))................ ( -34.00)
>DroEre_CAF1 13804 93 - 1
----AUAAUUGCACCUAUCGGCGGCAAGGACCUCGCCAGGACGAA---AGUCCUGGAGGGUCCUCCACACGGUAAUGCAAUGCAAAUUAAACGGCUCGCU
----...((((((..((((((.((..(((((((..(((((((...---.))))))).))))))))).).))))).))))))................... ( -41.40)
>DroYak_CAF1 13852 97 - 1
AAGUAUAAUUGCACCUAUCGAUGGCAAGGACCUCAGCAGGACGAG---GGUCCUGGAGGGUUCUCCACACGGUAAUGCAAUGCAAAUUAAAUGGCUCGCU
.......((((((..(((((.(((..(((((((...((((((...---.))))))..))))))))))..))))).))))))................... ( -30.30)
>consensus
AAGUGUAAUUGCACCUAUCGAUGGCAAGGACCUCCGCAGGACGAG____GUCCUGGAGGGUCCUCCACACGGUAAUGCAAUGCAAAUUAAACGGCUCGCU
.......((((((..(((((.(((..(((((((...((((((.......))))))..))))))))))..))))).))))))................... (-29.70 = -30.14 +   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 12:46:35 2006