Locus 9777

Sequence ID 3R_DroMel_CAF1
Location 25,927,983 – 25,928,094
Length 111
Max. P 0.952872
window15617 window15618

overview

Window 7

Location 25,927,983 – 25,928,094
Length 111
Sequences 5
Columns 115
Reading direction forward
Mean pairwise identity 96.27
Mean single sequence MFE -39.84
Consensus MFE -38.24
Energy contribution -38.24
Covariance contribution -0.00
Combinations/Pair 1.07
Mean z-score -1.43
Structure conservation index 0.96
SVM decision value 1.43
SVM RNA-class probability 0.952872
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25927983 111 + 27905053
GCGCAUUUUCGGAGGCCUUCAAUUAAUAAUGUGAUGUAAGCCUCCUCCGCCACGAAAAGGGGCAGACCCACCGGUACCGA----UCGUCGGUUCUAACUGGUUGGGACUGGCCCG
(((.......((((((.....((((......))))....))))))..)))........(((.(((.(((((((((((((.----....))))....))))).)))).))).))). ( -41.90)
>DroSec_CAF1 53299 111 + 1
GCACAUUUUCGGAGACCUUCAAUUAAUAAUGUGAUGUAAGCCUCCUCCGCCACGAAAAGGGGCAGACCCACCGGUACCGA----UCGUCGGUUCUAACUGGUUGGGACUGGCCCG
.........(((((..(((..((((......))))..)))....))))).........(((.(((.(((((((((((((.----....))))....))))).)))).))).))). ( -36.50)
>DroSim_CAF1 54986 111 + 1
GCGCAUUUUCGGAGACCUUCAAUUAAUAAUGUGAUGUAAGCCUCCUCCGCCACGAAAAGGGGCAGACCCACCGGUACCGA----UCGUCGGUUCUAACUGGUUGGGACUGGCCCG
.........(((((..(((..((((......))))..)))....))))).........(((.(((.(((((((((((((.----....))))....))))).)))).))).))). ( -36.50)
>DroEre_CAF1 61940 115 + 1
GCGCAUUUUUGGAGGCCUUCAAUUAAUAAUGUGAUGUAAGCCUCCUCCGCCACGAAAAGGGGCAGAUCCACCGGUACCGAUGGAUCGUCGGUUCUAACUGGUUGGGACUGGCCCG
(((.......((((((.....((((......))))....))))))..)))........(((.(((.((((((((((((((((...)))))))....))))).)))).))).))). ( -43.50)
>DroYak_CAF1 62624 111 + 1
GCGCAUUUUUGGAGGCCUUCAAUUAAUAAUGUGAUGUAAGCCUCCUCCGCCACGAAAAGGGGCAGAUCCACCGGUGCCGA----UCGUCGGUUCUAACUGGUUGGGACUGGCCCG
(((.......((((((.....((((......))))....))))))..)))........(((.(((.(((((((((((((.----....))))....))))).)))).))).))). ( -40.80)
>consensus
GCGCAUUUUCGGAGGCCUUCAAUUAAUAAUGUGAUGUAAGCCUCCUCCGCCACGAAAAGGGGCAGACCCACCGGUACCGA____UCGUCGGUUCUAACUGGUUGGGACUGGCCCG
..........((((((.....((((......))))....)))))).............(((.(((.((((((((((((((.......)))))....))))).)))).))).))). (-38.24 = -38.24 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 8

Location 25,927,983 – 25,928,094
Length 111
Sequences 5
Columns 115
Reading direction reverse
Mean pairwise identity 96.27
Mean single sequence MFE -38.00
Consensus MFE -36.84
Energy contribution -37.04
Covariance contribution 0.20
Combinations/Pair 1.06
Mean z-score -1.16
Structure conservation index 0.97
SVM decision value 0.47
SVM RNA-class probability 0.747621
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25927983 111 - 27905053
CGGGCCAGUCCCAACCAGUUAGAACCGACGA----UCGGUACCGGUGGGUCUGCCCCUUUUCGUGGCGGAGGAGGCUUACAUCACAUUAUUAAUUGAAGGCCUCCGAAAAUGCGC
.(((.(((.((((.((.((....((((....----.)))))).)))))).))).)))........(((..((((((((.((.............)).)))))))).....))).. ( -41.42)
>DroSec_CAF1 53299 111 - 1
CGGGCCAGUCCCAACCAGUUAGAACCGACGA----UCGGUACCGGUGGGUCUGCCCCUUUUCGUGGCGGAGGAGGCUUACAUCACAUUAUUAAUUGAAGGUCUCCGAAAAUGUGC
.(((.(((.((((.((.((....((((....----.)))))).)))))).))).)))........(((..((((((((.((.............)).)))))))).....))).. ( -36.72)
>DroSim_CAF1 54986 111 - 1
CGGGCCAGUCCCAACCAGUUAGAACCGACGA----UCGGUACCGGUGGGUCUGCCCCUUUUCGUGGCGGAGGAGGCUUACAUCACAUUAUUAAUUGAAGGUCUCCGAAAAUGCGC
.(((.(((.((((.((.((....((((....----.)))))).)))))).))).)))........(((..((((((((.((.............)).)))))))).....))).. ( -38.72)
>DroEre_CAF1 61940 115 - 1
CGGGCCAGUCCCAACCAGUUAGAACCGACGAUCCAUCGGUACCGGUGGAUCUGCCCCUUUUCGUGGCGGAGGAGGCUUACAUCACAUUAUUAAUUGAAGGCCUCCAAAAAUGCGC
.(((.....)))............((...(((((((((....))))))))).(((.(.....).))))).((((((((.((.............)).)))))))).......... ( -39.32)
>DroYak_CAF1 62624 111 - 1
CGGGCCAGUCCCAACCAGUUAGAACCGACGA----UCGGCACCGGUGGAUCUGCCCCUUUUCGUGGCGGAGGAGGCUUACAUCACAUUAUUAAUUGAAGGCCUCCAAAAAUGCGC
.((((..((((..(((.((.....(((....----.))).)).)))))))..)))).........(((..((((((((.((.............)).)))))))).....))).. ( -33.82)
>consensus
CGGGCCAGUCCCAACCAGUUAGAACCGACGA____UCGGUACCGGUGGGUCUGCCCCUUUUCGUGGCGGAGGAGGCUUACAUCACAUUAUUAAUUGAAGGCCUCCGAAAAUGCGC
.(((.(((.((((.((.((....(((((.......))))))).)))))).))).)))........(((..((((((((.((.............)).)))))))).....))).. (-36.84 = -37.04 +   0.20)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:41:58 2006