Locus 8136

Sequence ID 3R_DroMel_CAF1
Location 21,854,694 – 21,854,826
Length 132
Max. P 0.999948
window13085 window13086 window13087

overview

Window 5

Location 21,854,694 – 21,854,811
Length 117
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 79.63
Mean single sequence MFE -22.72
Consensus MFE -12.07
Energy contribution -13.15
Covariance contribution 1.08
Combinations/Pair 1.04
Mean z-score -1.90
Structure conservation index 0.53
SVM decision value 0.01
SVM RNA-class probability 0.540321
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21854694 117 - 27905053
CGAAUCCAGUCUUCCAGCUGAAGAAUCUUCUUCAGCAUCGACAUUGAAUCCUGUCUUCCA-CCAGCAACUUCUGCUGCAACGAAUCAUGUCUUCCAAUUGAAUCGUUAACAAUGUGAU
................((((((((....))))))))(((.((((((..............-.(((((.....))))).(((((.(((...........))).)))))..))))))))) ( -30.00)
>DroPse_CAF1 39114 92 - 1
CGAAUCCUGUCUUCCAAC-----------------CAACGACUACGAAUCCUGUCUUCCAACCAACAA---------CAACGAAUCAUGUCUUCCAAUUGACUCGUUCUAACUGUGAU
.((.((..(((.......-----------------....)))...)).))..................---------.(((((.(((...........))).)))))........... (  -7.10)
>DroSim_CAF1 31388 117 - 1
CGAAUCCAGUCUUCCAGCUGAGGAAUCUUCUUCAGCAUCGACAUUGAAUCCUGUCUUCCA-CCAGCAGCUUCUGCUGCAACGAAUCAUGUCUUCCAAUUGAAUCGUUAACCAUGUGAU
.(((..(((.......((((((((....)))))))).(((....)))...)))..)))((-(..(((((....)))))(((((.(((...........))).)))))......))).. ( -32.00)
>DroEre_CAF1 31907 117 - 1
CGAAUCCAGUCUUCCAGCUGAGGAAUACUCUUCAGCAUCGACAUUGAAUCCUGUCUUCCA-CCAGCAACUUCUGCUGCAACGAAUCAUGUCUUCCAAUUGAAUCGUUUACAAUGUGAU
................((((((((....))))))))(((.((((((..............-.(((((.....))))).(((((.(((...........))).)))))..))))))))) ( -29.30)
>DroYak_CAF1 35701 117 - 1
CGAAUCCAGUCUUCCAGCUGAGGAAUCUUCUUCAGCACCGACAUUGAAUCCUGUCUUCCA-CCAGCAACUUCUGUUGCAACGAAUCAAGUCUUCCAAUUGAAUCGUUAACCAUGUGAU
.(((..(((..(((..((((((((....)))))))).........)))..)))..)))((-(..(((((....)))))(((((.((((.........)))).)))))......))).. ( -30.50)
>DroPer_CAF1 39495 92 - 1
CGAAUCCUGUCUUCCAUU-----------------CAACGACUACGAAUCCUGUCUUCCAACCAACAA---------CAACGAAUCAUGUCUUCCAAUUGACUCGUUCUAACUGUGAU
.................(-----------------((..(((..........))).............---------.(((((.(((...........))).))))).......))). (  -7.40)
>consensus
CGAAUCCAGUCUUCCAGCUGAGGAAUCUUCUUCAGCAUCGACAUUGAAUCCUGUCUUCCA_CCAGCAACUUCUGCUGCAACGAAUCAUGUCUUCCAAUUGAAUCGUUAACAAUGUGAU
.((.((..(((.....((((((((....))))))))...)))...)).))............................(((((.(((...........))).)))))........... (-12.07 = -13.15 +   1.08)

alignment

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secondary structure

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dotplot

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Window 6

Location 21,854,732 – 21,854,826
Length 94
Sequences 5
Columns 94
Reading direction forward
Mean pairwise identity 96.81
Mean single sequence MFE -27.10
Consensus MFE -26.30
Energy contribution -25.98
Covariance contribution -0.32
Combinations/Pair 1.08
Mean z-score -1.68
Structure conservation index 0.97
SVM decision value 2.27
SVM RNA-class probability 0.991547
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21854732 94 + 27905053
UUGCAGCAGAAGUUGCUGGUGGAAGACAGGAUUCAAUGUCGAUGCUGAAGAAGAUUCUUCAGCUGGAAGACUGGAUUCGAUGUCGAUGAUGAUG
..(((((....)))))........(((((((((((..(((...((((((((....)))))))).....))))))))))..)))).......... ( -29.70)
>DroSec_CAF1 38319 94 + 1
UUGCAGCAGAAGUUGCUGGUGGAAGACAGGAUUCAAUGUCGAUGCUGAAGAAGAUUCCUCAGCUGGAAGACUGGAUUCGAUGUCGAUGAUGAUG
..(((((....)))))........(((((((((((..(((...(((((.((....)).))))).....))))))))))..)))).......... ( -25.60)
>DroSim_CAF1 31426 94 + 1
UUGCAGCAGAAGCUGCUGGUGGAAGACAGGAUUCAAUGUCGAUGCUGAAGAAGAUUCCUCAGCUGGAAGACUGGAUUCGAUGUCGAUGAUGAUG
..(((((....)))))........(((((((((((..(((...(((((.((....)).))))).....))))))))))..)))).......... ( -28.00)
>DroEre_CAF1 31945 94 + 1
UUGCAGCAGAAGUUGCUGGUGGAAGACAGGAUUCAAUGUCGAUGCUGAAGAGUAUUCCUCAGCUGGAAGACUGGAUUCGAUGUCGUUGAUGAUG
..(((((....)))))..((.((.(((((((((((..(((...(((((.(......).))))).....))))))))))..)))).)).)).... ( -25.90)
>DroYak_CAF1 35739 94 + 1
UUGCAACAGAAGUUGCUGGUGGAAGACAGGAUUCAAUGUCGGUGCUGAAGAAGAUUCCUCAGCUGGAAGACUGGAUUCGAUGUCGUUGAUGAUG
..(((((....)))))..((.((.(((((((((((..(((...(((((.((....)).))))).....))))))))))..)))).)).)).... ( -26.30)
>consensus
UUGCAGCAGAAGUUGCUGGUGGAAGACAGGAUUCAAUGUCGAUGCUGAAGAAGAUUCCUCAGCUGGAAGACUGGAUUCGAUGUCGAUGAUGAUG
..(((((....)))))........(((((((((((..(((...(((((.((....)).))))).....))))))))))..)))).......... (-26.30 = -25.98 +  -0.32)

alignment

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secondary structure

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dotplot

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Window 7

Location 21,854,732 – 21,854,826
Length 94
Sequences 5
Columns 94
Reading direction reverse
Mean pairwise identity 96.81
Mean single sequence MFE -23.92
Consensus MFE -22.78
Energy contribution -22.46
Covariance contribution -0.32
Combinations/Pair 1.08
Mean z-score -3.97
Structure conservation index 0.95
SVM decision value 4.77
SVM RNA-class probability 0.999948
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21854732 94 - 27905053
CAUCAUCAUCGACAUCGAAUCCAGUCUUCCAGCUGAAGAAUCUUCUUCAGCAUCGACAUUGAAUCCUGUCUUCCACCAGCAACUUCUGCUGCAA
..........((((..((.((..(((.....((((((((....))))))))...)))...)).)).))))......(((((.....)))))... ( -23.00)
>DroSec_CAF1 38319 94 - 1
CAUCAUCAUCGACAUCGAAUCCAGUCUUCCAGCUGAGGAAUCUUCUUCAGCAUCGACAUUGAAUCCUGUCUUCCACCAGCAACUUCUGCUGCAA
..........((((..((.((..(((.....((((((((....))))))))...)))...)).)).))))......(((((.....)))))... ( -22.70)
>DroSim_CAF1 31426 94 - 1
CAUCAUCAUCGACAUCGAAUCCAGUCUUCCAGCUGAGGAAUCUUCUUCAGCAUCGACAUUGAAUCCUGUCUUCCACCAGCAGCUUCUGCUGCAA
..........((((..((.((..(((.....((((((((....))))))))...)))...)).)).))))........(((((....))))).. ( -26.70)
>DroEre_CAF1 31945 94 - 1
CAUCAUCAACGACAUCGAAUCCAGUCUUCCAGCUGAGGAAUACUCUUCAGCAUCGACAUUGAAUCCUGUCUUCCACCAGCAACUUCUGCUGCAA
..........((((..((.((..(((.....((((((((....))))))))...)))...)).)).))))......(((((.....)))))... ( -22.90)
>DroYak_CAF1 35739 94 - 1
CAUCAUCAACGACAUCGAAUCCAGUCUUCCAGCUGAGGAAUCUUCUUCAGCACCGACAUUGAAUCCUGUCUUCCACCAGCAACUUCUGUUGCAA
..........((((..((.((..(((.....((((((((....))))))))...)))...)).)).))))........(((((....))))).. ( -24.30)
>consensus
CAUCAUCAUCGACAUCGAAUCCAGUCUUCCAGCUGAGGAAUCUUCUUCAGCAUCGACAUUGAAUCCUGUCUUCCACCAGCAACUUCUGCUGCAA
..........((((..((.((..(((.....((((((((....))))))))...)))...)).)).))))......(((((.....)))))... (-22.78 = -22.46 +  -0.32)

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 13:03:24 2006