Locus 3724

Sequence ID 2L_DroMel_CAF1
Location 10,848,379 – 10,848,627
Length 248
Max. P 0.990411
window5865 window5866 window5867 window5868

overview

Window 5

Location 10,848,379 – 10,848,496
Length 117
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 75.24
Mean single sequence MFE -29.63
Consensus MFE -19.57
Energy contribution -20.18
Covariance contribution 0.61
Combinations/Pair 1.14
Mean z-score -1.24
Structure conservation index 0.66
SVM decision value 0.37
SVM RNA-class probability 0.707506
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10848379 117 - 22407834
--U-AUUGCAUAUUUAAUUAAAAAUCGUCAGAAACAAGAACGGCAAGUUCAAGGUUGCCUACGGCCAUGAGAACGUCAAGGCCGAUUCGGAUGUGAACAUUGAUCUGAAGGGCCCCUUGA
--.-.((((..((((......))))((((........).)))))))..((((((..((((.(((((.(((.....))).))))).(((((((..........))))))))))).)))))) ( -32.50)
>DroVir_CAF1 114104 89 - 1
-------------------------------CAACAAGAACGGCAAGUUCAAGGUUGCGUACGGUCAUGAGAAUGUCAAGGCCGAUUCGGAUGUCAAUAUUGACCUGAAGGGUCCCUUGA
-------------------------------...((((...((((..((((.(..((....))..).))))..))))..((((..(((((..((((....))))))))).)))).)))). ( -25.20)
>DroPse_CAF1 82830 107 - 1
--C-ACU----------UUCUUUCCGAACAGAAACAAGAACGGCAAGUUCAAGGUUGGCUUCGGCCACGAAUACGUGAAAGCCGAUUCGGACGUCAACAUUGAUCUGAAGGGUCCCUUGA
--.-.((----------(((..(((((((........((((.....))))..(((((((....)))(((....)))...))))).)))))).((((....))))..)))))......... ( -28.70)
>DroYak_CAF1 84608 120 - 1
ACUAACUUGUAGUACUCUUCAUCUCCAUCAGAAACAAGAACGGCAAGUUCAAGGUUGCCUACGGCCAUGAGAACGUCAAGGCCGAUUCGGAUGUGAACAUUGAUCUGAAGGGCCCCUUGA
....((((((.((..((((..(((.....)))...)))))).))))))((((((..((((.(((((.(((.....))).))))).(((((((..........))))))))))).)))))) ( -37.80)
>DroMoj_CAF1 117317 89 - 1
-------------------------------CAACAAGAACGGCAAGUUCAAGGUUUCGUACGGUCAUGAGAAUGUCAAGGCCGAUUCGGAUGUCAACAUUGACCUGAAGGGUCCCUUGA
-------------------------------......((((.....))))((((..((...(((((.(((.....))).))))).(((((..((((....))))))))).))..)))).. ( -24.90)
>DroPer_CAF1 82650 107 - 1
--C-ACU----------UUCUUUCCGAACAGAAACAAGAACGGCAAGUUCAAGGUUGGCUUCGGCCACGAAUACGUGAAAGCCGAUUCGGACGUCAACAUUGAUCUGAAGGGUCCCUUGA
--.-.((----------(((..(((((((........((((.....))))..(((((((....)))(((....)))...))))).)))))).((((....))))..)))))......... ( -28.70)
>consensus
____ACU__________UUC_U__C_A_CAGAAACAAGAACGGCAAGUUCAAGGUUGCCUACGGCCAUGAGAACGUCAAGGCCGAUUCGGAUGUCAACAUUGAUCUGAAGGGUCCCUUGA
..................................((((...(((...((((.(((((....))))).))))...)))..((((..(((((..((((....))))))))).)))).)))). (-19.57 = -20.18 +   0.61)

alignment

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secondary structure

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dotplot

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Window 6

Location 10,848,496 – 10,848,587
Length 91
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 70.04
Mean single sequence MFE -24.73
Consensus MFE -15.70
Energy contribution -15.70
Covariance contribution 0.00
Combinations/Pair 1.12
Mean z-score -2.14
Structure conservation index 0.63
SVM decision value 2.21
SVM RNA-class probability 0.990411
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10848496 91 + 22407834
------------------UUAAUUA-----UUCUGCAGUGAACA-UAUAUGUAAUAACAUGUGAUCCUUACCCAGACUGAGGAGCAAAGUUGCCCUCCAGGGACAGCUUCAGACC
------------------.......-----...(((........-(((((((....))))))).((((((.......)))))))))(((((((((....))).))))))...... ( -22.90)
>DroSec_CAF1 81886 91 + 1
------------------UUAUUUA-----UUCUGCAGGGAACA-CAUAUGUAAUAACAUGUGAUCCUUACCCAGACUGAGGAGCGAAGUUGCCCUCCAGGGACAGCUUCAGACC
------------------...((((-----.((((.(((((...-(((((((....))))))).)))))...)))).))))....((((((((((....))).)))))))..... ( -29.70)
>DroSim_CAF1 88990 87 + 1
------------------UUA---------UUCUGCAGAGAACA-CAUAUGUAAUAACAUCUGAUCCUUACCCAGACUGAGGAGCGAAGUUGCCCUCCAGGGACAGCUUCAGACC
------------------...---------.(((((........-((.((((....)))).)).((((((.......))))))))((((((((((....))).)))))))))).. ( -25.20)
>DroEre_CAF1 82887 103 + 1
UUGAACUACUGAAUAAUAUGAAUUA-----UU-CGCAGAUAAAAUAAAAUGUAUC------UAUUUCUUACCCAGACUGGGGAGCGAAGUUGCCCUCCAGGGACAGCUUCAGACC
..........(((((((....))))-----))-)(((((((..........))))------)........(((.....)))..))((((((((((....))).)))))))..... ( -27.70)
>DroYak_CAF1 84767 112 + 1
UUUAACUAUUUAAUUAUAUAAAUGACUAUUUU-UGCGGUUAUAAGAAUAUGCAAUAACU--UUGUUCUUACCCAGACUGGGGAGCGAAGUUGCCCUCCAGGGACAGCUUCAGACC
......((((((......))))))........-...((((.((((((((..........--.))))))))(((.....)))....((((((((((....))).))))))).)))) ( -27.40)
>DroAna_CAF1 93289 81 + 1
------------------UUAAAAA-------CUAUAAACAAUA-GAUAGCUACUAA--------UCUUACCCAGACUGGGGAGCGAAGUUGCCCUCCAGCGACAGCUUCAGACC
------------------.......-------((((.....)))-).......(((.--------(((.....))).)))(((((...(((((......))))).)))))..... ( -15.50)
>consensus
__________________UUAAUUA_____UUCUGCAGAGAACA_AAUAUGUAAUAACA__UGAUCCUUACCCAGACUGAGGAGCGAAGUUGCCCUCCAGGGACAGCUUCAGACC
................................................................((((((.......))))))..((((((((((....))).)))))))..... (-15.70 = -15.70 +   0.00)

alignment

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secondary structure

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dotplot

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Window 7

Location 10,848,508 – 10,848,627
Length 119
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 85.50
Mean single sequence MFE -39.80
Consensus MFE -31.94
Energy contribution -32.30
Covariance contribution 0.36
Combinations/Pair 1.11
Mean z-score -2.41
Structure conservation index 0.80
SVM decision value 0.66
SVM RNA-class probability 0.813164
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10848508 119 + 22407834
CAGUGAACA-UAUAUGUAAUAACAUGUGAUCCUUACCCAGACUGAGGAGCAAAGUUGCCCUCCAGGGACAGCUUCAGACCCUCGAGGAGCUGAUCCUGGACAGCAACCUCGGUGAACAGC
((.(((...-(((((((....))))))).((((((.......)))))).....(((((..(((((((.(((((((.(.....)..))))))).)))))))..))))).))).))...... ( -41.70)
>DroSec_CAF1 81898 119 + 1
CAGGGAACA-CAUAUGUAAUAACAUGUGAUCCUUACCCAGACUGAGGAGCGAAGUUGCCCUCCAGGGACAGCUUCAGACCCUCGAGGAGCUGAUCCUGGACAGCAACCUCGGUGAACAGG
.(((((...-(((((((....))))))).))))).......(((...(.(((.(((((..(((((((.(((((((.(.....)..))))))).)))))))..))))).))).)...))). ( -46.90)
>DroSim_CAF1 88998 119 + 1
CAGAGAACA-CAUAUGUAAUAACAUCUGAUCCUUACCCAGACUGAGGAGCGAAGUUGCCCUCCAGGGACAGCUUCAGACCCUCGAGGAGCUGAUCUUGGACAGCAACCUCGGUGAACAGG
.......((-(..................((((((.......)))))).(((.(((((..(((((((.(((((((.(.....)..))))))).)))))))..))))).))))))...... ( -39.10)
>DroEre_CAF1 82916 114 + 1
CAGAUAAAAUAAAAUGUAUC------UAUUUCUUACCCAGACUGGGGAGCGAAGUUGCCCUCCAGGGACAGCUUCAGACCCUCGAGGAGCUGAUCCUGGACAGCAACCUCGGUGAACAGC
.(((((..........))))------)..(((...(((.....))).(.(((.(((((..(((((((.(((((((.(.....)..))))))).)))))))..))))).))).)))).... ( -39.80)
>DroYak_CAF1 84801 118 + 1
CGGUUAUAAGAAUAUGCAAUAACU--UUGUUCUUACCCAGACUGGGGAGCGAAGUUGCCCUCCAGGGACAGCUUCAGACCCUCGAGGAGCUGAUCCUGGACAGCAACCUCGGUGAACAGC
.((((((...........))))))--((((((...(((.....))).(.(((.(((((..(((((((.(((((((.(.....)..))))))).)))))))..))))).))).))))))). ( -44.90)
>DroAna_CAF1 93299 111 + 1
UAAACAAUA-GAUAGCUACUAA--------UCUUACCCAGACUGGGGAGCGAAGUUGCCCUCCAGCGACAGCUUCAGACCCUCCAACAGCUGAUCCUGAACAGCAACCUCGGUGAAGAGG
.........-....(((.....--------.........(.((((((.(((....))).)))))))..(((..((((............))))..)))...)))..((((......)))) ( -26.40)
>consensus
CAGAGAACA_AAUAUGUAAUAACA__UGAUCCUUACCCAGACUGAGGAGCGAAGUUGCCCUCCAGGGACAGCUUCAGACCCUCGAGGAGCUGAUCCUGGACAGCAACCUCGGUGAACAGC
.............................((((((.......)))))).(((.(((((..(((((((.(((((((..........))))))).)))))))..))))).)))......... (-31.94 = -32.30 +   0.36)

alignment

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secondary structure

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dotplot

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Window 8

Location 10,848,508 – 10,848,627
Length 119
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 85.50
Mean single sequence MFE -43.67
Consensus MFE -36.99
Energy contribution -37.13
Covariance contribution 0.14
Combinations/Pair 1.16
Mean z-score -2.45
Structure conservation index 0.85
SVM decision value 1.14
SVM RNA-class probability 0.921289
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10848508 119 - 22407834
GCUGUUCACCGAGGUUGCUGUCCAGGAUCAGCUCCUCGAGGGUCUGAAGCUGUCCCUGGAGGGCAACUUUGCUCCUCAGUCUGGGUAAGGAUCACAUGUUAUUACAUAUA-UGUUCACUG
((((.....((((((((((.((((((..(((((..(((......))))))))..)))))).)))))))))).....)))).......((((..((((((........)))-))))).)). ( -42.50)
>DroSec_CAF1 81898 119 - 1
CCUGUUCACCGAGGUUGCUGUCCAGGAUCAGCUCCUCGAGGGUCUGAAGCUGUCCCUGGAGGGCAACUUCGCUCCUCAGUCUGGGUAAGGAUCACAUGUUAUUACAUAUG-UGUUCCCUG
.(((.....((((((((((.((((((..(((((..(((......))))))))..)))))).)))))))))).....))).........(((.(((((((......)))))-)).)))... ( -50.00)
>DroSim_CAF1 88998 119 - 1
CCUGUUCACCGAGGUUGCUGUCCAAGAUCAGCUCCUCGAGGGUCUGAAGCUGUCCCUGGAGGGCAACUUCGCUCCUCAGUCUGGGUAAGGAUCAGAUGUUAUUACAUAUG-UGUUCUCUG
.......(((((((..((((........)))).))))(((((..(((((.(((((.....))))).))))).)))))......))).(((((((.((((....)))).))-.)))))... ( -38.50)
>DroEre_CAF1 82916 114 - 1
GCUGUUCACCGAGGUUGCUGUCCAGGAUCAGCUCCUCGAGGGUCUGAAGCUGUCCCUGGAGGGCAACUUCGCUCCCCAGUCUGGGUAAGAAAUA------GAUACAUUUUAUUUUAUCUG
((((.....((((((((((.((((((..(((((..(((......))))))))..)))))).)))))))))).....))))..((((((..((((------((.....)))))))))))). ( -44.70)
>DroYak_CAF1 84801 118 - 1
GCUGUUCACCGAGGUUGCUGUCCAGGAUCAGCUCCUCGAGGGUCUGAAGCUGUCCCUGGAGGGCAACUUCGCUCCCCAGUCUGGGUAAGAACAA--AGUUAUUGCAUAUUCUUAUAACCG
..(((((..((((((((((.((((((..(((((..(((......))))))))..)))))).))))))))))...(((.....)))...))))).--.(((((...........))))).. ( -46.80)
>DroAna_CAF1 93299 111 - 1
CCUCUUCACCGAGGUUGCUGUUCAGGAUCAGCUGUUGGAGGGUCUGAAGCUGUCGCUGGAGGGCAACUUCGCUCCCCAGUCUGGGUAAGA--------UUAGUAGCUAUC-UAUUGUUUA
..((((...((((((((((.(((((((.(((((.(..(.....)..)))))))).))))).))))))))))...(((.....))).))))--------.((((((....)-))))).... ( -39.50)
>consensus
CCUGUUCACCGAGGUUGCUGUCCAGGAUCAGCUCCUCGAGGGUCUGAAGCUGUCCCUGGAGGGCAACUUCGCUCCCCAGUCUGGGUAAGAAUCA__UGUUAUUACAUAUG_UGUUCUCUG
...((((..((((((((((.((((((..(((((..(((......))))))))..)))))).))))))))))...(((.....)))...))))............................ (-36.99 = -37.13 +   0.14)

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 10:59:31 2006