Locus 6415

Sequence ID 2R_DroMel_CAF1
Location 20,054,075 – 20,054,215
Length 140
Max. P 0.973558
window10235 window10236 window10237 window10238

overview

Window 5

Location 20,054,075 – 20,054,177
Length 102
Sequences 4
Columns 116
Reading direction forward
Mean pairwise identity 85.61
Mean single sequence MFE -18.82
Consensus MFE -12.71
Energy contribution -13.71
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -1.66
Structure conservation index 0.68
SVM decision value 0.15
SVM RNA-class probability 0.605596
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20054075 102 + 20766785
CCUCAGUCGCAUCCCGUACACACCAC-------UCACCAUCCGCCAUAU-------UCCAUAUUCCAUAUAGCACGUACCAGAUCGGAAUCGGAGGAGAUCCUCCGCCGCAACUCU
....(((.((................-------......(((((.((((-------..........)))).)).(......)...)))..((((((....))))))..)).))).. ( -17.90)
>DroSec_CAF1 13856 103 + 1
CCUCAGUCGCAUCCCGUACACACCAC-------U------CUGCCAUAUUCCAUUCUCCAUAUUCCAUAUAGCACGUACCAGAUCGGAAUCGGAGGAGAUCCUCCUCCGCAACUCU
....(((.((...(((........((-------.------.(((.((((.................)))).))).)).......)))....(((((((...))))))))).))).. ( -19.89)
>DroSim_CAF1 14223 109 + 1
CCUCAGUCGCAUCCCGUACACACCAC-------UCACCAUCCGCCAUAUUCCAUUCUCCAUAUUCCAUAUAGCACGUACCAGAUCGGAAUCGGAGGAGAUCCUCCUCCGCAACUCU
....(((.((................-------..............(((((..(((.......................)))..))))).(((((((...))))))))).))).. ( -19.20)
>DroEre_CAF1 14122 112 + 1
CCUCAGUCGCAUCCCGUAUACACCACUCACCAUUCGCCAUUCGCCAUAUUCCCAU-UCCAUAUUCCAUCUAGCCCGUAGCAGAUCGGAAUCG---GAGAUCCUCCUCCGCAACUCU
....(((.((.............................................-.....(((((((((.((.....)))))).))))).(---(((......)))))).))).. ( -18.30)
>consensus
CCUCAGUCGCAUCCCGUACACACCAC_______UCACCAUCCGCCAUAUUCCAUU_UCCAUAUUCCAUAUAGCACGUACCAGAUCGGAAUCGGAGGAGAUCCUCCUCCGCAACUCU
....(((.((...................................................(((((...................))))).(((((((...))))))))).))).. (-12.71 = -13.71 +   1.00)

alignment

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secondary structure

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dotplot

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Window 6

Location 20,054,075 – 20,054,177
Length 102
Sequences 4
Columns 116
Reading direction reverse
Mean pairwise identity 85.61
Mean single sequence MFE -35.97
Consensus MFE -26.70
Energy contribution -28.26
Covariance contribution 1.56
Combinations/Pair 1.03
Mean z-score -2.72
Structure conservation index 0.74
SVM decision value 1.71
SVM RNA-class probability 0.973558
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20054075 102 - 20766785
AGAGUUGCGGCGGAGGAUCUCCUCCGAUUCCGAUCUGGUACGUGCUAUAUGGAAUAUGGA-------AUAUGGCGGAUGGUGA-------GUGGUGUGUACGGGAUGCGACUGAGG
..((((((((((((((....))))))...)).((((.(((((..((((........((..-------......))........-------))))..))))).)))))))))).... ( -36.39)
>DroSec_CAF1 13856 103 - 1
AGAGUUGCGGAGGAGGAUCUCCUCCGAUUCCGAUCUGGUACGUGCUAUAUGGAAUAUGGAGAAUGGAAUAUGGCAG------A-------GUGGUGUGUACGGGAUGCGACUGAGG
..(((((((((((((...))))))).......((((.(((((..((((.((..((((..........))))..)).------.-------))))..))))).)))))))))).... ( -39.60)
>DroSim_CAF1 14223 109 - 1
AGAGUUGCGGAGGAGGAUCUCCUCCGAUUCCGAUCUGGUACGUGCUAUAUGGAAUAUGGAGAAUGGAAUAUGGCGGAUGGUGA-------GUGGUGUGUACGGGAUGCGACUGAGG
..(((((((((((((...))))))).......((((.(((((..(((((((...(((.....)))...))).((.....))..-------))))..))))).)))))))))).... ( -36.50)
>DroEre_CAF1 14122 112 - 1
AGAGUUGCGGAGGAGGAUCUC---CGAUUCCGAUCUGCUACGGGCUAGAUGGAAUAUGGA-AUGGGAAUAUGGCGAAUGGCGAAUGGUGAGUGGUGUAUACGGGAUGCGACUGAGG
..((((((((((......)))---).((((((((..(((((..((((..((..((.((..-(((....)))..)).))..))..))))..)))))..)).)))))))))))).... ( -31.40)
>consensus
AGAGUUGCGGAGGAGGAUCUCCUCCGAUUCCGAUCUGGUACGUGCUAUAUGGAAUAUGGA_AAUGGAAUAUGGCGGAUGGUGA_______GUGGUGUGUACGGGAUGCGACUGAGG
..((((((((((((((....)))))...))).((((.(((((..((((.((..((((..........))))..))...............))))..))))).)))))))))).... (-26.70 = -28.26 +   1.56)

alignment

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secondary structure

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dotplot

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Window 7

Location 20,054,104 – 20,054,215
Length 111
Sequences 4
Columns 118
Reading direction forward
Mean pairwise identity 90.38
Mean single sequence MFE -28.40
Consensus MFE -23.64
Energy contribution -24.45
Covariance contribution 0.81
Combinations/Pair 1.04
Mean z-score -1.82
Structure conservation index 0.83
SVM decision value 0.71
SVM RNA-class probability 0.829427
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20054104 111 + 20766785
CCAUCCGCCAUAU-------UCCAUAUUCCAUAUAGCACGUACCAGAUCGGAAUCGGAGGAGAUCCUCCGCCGCAACUCUGGCUAAUUGAAAAGCAAUUGUGGCGCACUCAACUAGCA
.....((((((..-------......................(((((.(((...((((((....)))))))))....)))))..(((((.....)))))))))))............. ( -29.50)
>DroSec_CAF1 13883 114 + 1
----CUGCCAUAUUCCAUUCUCCAUAUUCCAUAUAGCACGUACCAGAUCGGAAUCGGAGGAGAUCCUCCUCCGCAACUCUGGCUAAUUGAAAAGCAAUUGUGGCGCACUCAACUAGCC
----.(((...(((((..(((.......................)))..))))).(((((((...)))))))))).....(((((.((((...((.......))....)))).))))) ( -28.10)
>DroSim_CAF1 14252 118 + 1
CCAUCCGCCAUAUUCCAUUCUCCAUAUUCCAUAUAGCACGUACCAGAUCGGAAUCGGAGGAGAUCCUCCUCCGCAACUCUGGCUAAUUGAAAAGCAAUUGUGGCGCACUCAACUAGCC
.....((((((...............................(((((.((((...(((((....)))))))))....)))))..(((((.....)))))))))))............. ( -29.00)
>DroEre_CAF1 14158 114 + 1
CCAUUCGCCAUAUUCCCAU-UCCAUAUUCCAUCUAGCCCGUAGCAGAUCGGAAUCG---GAGAUCCUCCUCCGCAACUCUGGCUAAUUGAAAAGCAAUUGUGGCGCACUCAACUAGCC
.....((((((....(((.-.....(((((((((.((.....)))))).)))))((---(((......)))))......)))..(((((.....)))))))))))............. ( -27.00)
>consensus
CCAUCCGCCAUAUUCCAUU_UCCAUAUUCCAUAUAGCACGUACCAGAUCGGAAUCGGAGGAGAUCCUCCUCCGCAACUCUGGCUAAUUGAAAAGCAAUUGUGGCGCACUCAACUAGCC
.....(((((((...............................((((.((((...(((((....)))))))))....))))(((........)))...)))))))............. (-23.64 = -24.45 +   0.81)

alignment

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secondary structure

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dotplot

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Window 8

Location 20,054,104 – 20,054,215
Length 111
Sequences 4
Columns 118
Reading direction reverse
Mean pairwise identity 90.38
Mean single sequence MFE -38.80
Consensus MFE -31.33
Energy contribution -32.58
Covariance contribution 1.25
Combinations/Pair 1.00
Mean z-score -1.91
Structure conservation index 0.81
SVM decision value 0.71
SVM RNA-class probability 0.830053
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20054104 111 - 20766785
UGCUAGUUGAGUGCGCCACAAUUGCUUUUCAAUUAGCCAGAGUUGCGGCGGAGGAUCUCCUCCGAUUCCGAUCUGGUACGUGCUAUAUGGAAUAUGGA-------AUAUGGCGGAUGG
.((((((((((.(((.......)))..))))))))))((((....(((((((((....))))))...))).)))).....((((((((..........-------))))))))..... ( -38.40)
>DroSec_CAF1 13883 114 - 1
GGCUAGUUGAGUGCGCCACAAUUGCUUUUCAAUUAGCCAGAGUUGCGGAGGAGGAUCUCCUCCGAUUCCGAUCUGGUACGUGCUAUAUGGAAUAUGGAGAAUGGAAUAUGGCAG----
(((((((((((.(((.......)))..)))))))))))(((....(((((((((....)))))...)))).)))......((((((((....(((.....)))..)))))))).---- ( -40.40)
>DroSim_CAF1 14252 118 - 1
GGCUAGUUGAGUGCGCCACAAUUGCUUUUCAAUUAGCCAGAGUUGCGGAGGAGGAUCUCCUCCGAUUCCGAUCUGGUACGUGCUAUAUGGAAUAUGGAGAAUGGAAUAUGGCGGAUGG
(((((((((((.(((.......)))..))))))))))).......((((((((...))))))))..((((........(((.((((((...))))))...)))........))))... ( -40.09)
>DroEre_CAF1 14158 114 - 1
GGCUAGUUGAGUGCGCCACAAUUGCUUUUCAAUUAGCCAGAGUUGCGGAGGAGGAUCUC---CGAUUCCGAUCUGCUACGGGCUAGAUGGAAUAUGGA-AUGGGAAUAUGGCGAAUGG
(((((((((((.(((.......)))..)))))))))))....((((((((......)))---).(((((.((((((.....)).))))))))).....-...........)))).... ( -36.30)
>consensus
GGCUAGUUGAGUGCGCCACAAUUGCUUUUCAAUUAGCCAGAGUUGCGGAGGAGGAUCUCCUCCGAUUCCGAUCUGGUACGUGCUAUAUGGAAUAUGGA_AAUGGAAUAUGGCGGAUGG
.((((((((((.(((.......)))..))))))))))((((....(((((((((....)))))...)))).))))......(((((((.................)))))))...... (-31.33 = -32.58 +   1.25)

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 12:10:28 2006