Locus 5996

Sequence ID 2R_DroMel_CAF1
Location 18,846,997 – 18,847,169
Length 172
Max. P 0.966972
window9614 window9615 window9616 window9617 window9618

overview

Window 4

Location 18,846,997 – 18,847,106
Length 109
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 80.86
Mean single sequence MFE -25.02
Consensus MFE -17.78
Energy contribution -18.00
Covariance contribution 0.22
Combinations/Pair 1.10
Mean z-score -1.96
Structure conservation index 0.71
SVM decision value 0.77
SVM RNA-class probability 0.846648
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18846997 109 - 20766785
GGAAUCACUCGACACCUCAAUAAAUAUUGAGAGUGUCAGCCACUUGAUGCUAAUGCAAAUUCGACUCGCCUAAGUCAUGUAACCCAUGUCCAUGUCCAUGCCCAUGC-CC
.((((.....(((((((((((....)))))).)))))..........(((....))).))))((((......))))........((((..(((....)))..)))).-.. ( -26.10)
>DroPse_CAF1 26619 98 - 1
GGCACUCCUCGACACCUCUAUAAAUAUUGAGAGUGUCAGGCACUUGAUGCUAAUGCAAAUUCAGUCCGC--------UGCCAGCCAUGUCCGUAAC----CCCAUGCCUC
((((......((((((((..........))).))))).(((......(((....)))....(((....)--------))...)))...........----....)))).. ( -25.80)
>DroSim_CAF1 21210 109 - 1
GGAAUCACUCGACACCUCAAUAAAUAUUGAGAGUGUCAGCCACUUGAUGCUAAUGCAAAUUCGACUCGCCUAAGUCAUGUAACCCAUGUCCAUGCCCAUGCCCAUGC-CC
.((((.....(((((((((((....)))))).)))))..........(((....))).))))((((......))))........((((..(((....)))..)))).-.. ( -26.10)
>DroEre_CAF1 24844 97 - 1
GGAAUCACUCGACACCUCAAUAAAUAUUGAGAGUGUCAGCCACUUGAUGCUAAUGCAAAUUCGACUCGCCUAAGUCAUGUAACCCAUGUCCAU------------GU-CC
(((.......(((((((((((....)))))).)))))..........(((....))).....((((......))))............)))..------------..-.. ( -22.80)
>DroYak_CAF1 21303 97 - 1
GGAAUCACUCGACACCUCAAUAAAUAUUGAGAGUGUCAGCCACUUGAUGCUAAUGCAAAUUCGACUUGCCUAAGUCAUGUAACCCAUGUCCAU------------GC-CC
(((.......(((((((((((....)))))).)))))..........(((....))).....(((((....)))))............)))..------------..-.. ( -23.50)
>DroPer_CAF1 26757 98 - 1
GGCACUCCUCGACACCUCUAUAAAUAUUGAGAGUGUCAGGCACUUGAUGCUAAUGCAAAUUCAGUCCGC--------UGCCAGCCAUGUCCGUAAC----CCCAUGCCUC
((((......((((((((..........))).))))).(((......(((....)))....(((....)--------))...)))...........----....)))).. ( -25.80)
>consensus
GGAAUCACUCGACACCUCAAUAAAUAUUGAGAGUGUCAGCCACUUGAUGCUAAUGCAAAUUCGACUCGCCUAAGUCAUGUAACCCAUGUCCAU__C____CCCAUGC_CC
(((.......(((((((((((....)))))).)))))......(((((((....)))...))))........................)))................... (-17.78 = -18.00 +   0.22)

alignment

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secondary structure

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Window 5

Location 18,847,036 – 18,847,146
Length 110
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 86.82
Mean single sequence MFE -32.15
Consensus MFE -25.68
Energy contribution -25.18
Covariance contribution -0.50
Combinations/Pair 1.24
Mean z-score -2.28
Structure conservation index 0.80
SVM decision value 0.38
SVM RNA-class probability 0.713520
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18847036 110 + 20766785
G-------GCGAGUCGAAUUUGCAUUAGCAUCAAGUGGCUGACACUCUCAAUAUUUAUUGAGGUGUCGAGUGAUUCCAUUUCGAUGAUUGCUUAUCGAUUUAAUGGAAAUUAACCAU
(-------(..(((((....(((....))).....)))))(((((.((((((....)))))))))))......((((((((((((((....)))))))...))))))).....)).. ( -33.90)
>DroPse_CAF1 26648 109 + 1
--------GCGGACUGAAUUUGCAUUAGCAUCAAGUGCCUGACACUCUCAAUAUUUAUAGAGGUGUCGAGGAGUGCCAUUUCGAUGAUUGCUUAUCGAUUUAGUGGGAAUUAGCCAU
--------..((.((((.(((.(((((((((......((((((((.(((..........)))))))).))).))))....(((((((....)))))))..))))).))))))))).. ( -31.90)
>DroEre_CAF1 24871 110 + 1
G-------GCGAGUCGAAUUUGCAUUAGCAUCAAGUGGCUGACACUCUCAAUAUUUAUUGAGGUGUCGAGUGAUUCCAUUUCGAUGAUUGCUUAUCGAUUUAAUGGAAAUUAACCAU
(-------(..(((((....(((....))).....)))))(((((.((((((....)))))))))))......((((((((((((((....)))))))...))))))).....)).. ( -33.90)
>DroYak_CAF1 21330 110 + 1
G-------GCAAGUCGAAUUUGCAUUAGCAUCAAGUGGCUGACACUCUCAAUAUUUAUUGAGGUGUCGAGUGAUUCCAUUUCGAUGAUUGCUUAUCGAUUUAAUGGAAAUUAACCAU
(-------(..(((((....(((....))).....)))))(((((.((((((....)))))))))))......((((((((((((((....)))))))...))))))).....)).. ( -33.80)
>DroAna_CAF1 20687 117 + 1
GCCAAAUGGAGAAUCGAAUUUGCAUUAGCAUCAAGUGGCUGAAACUCUCUCUGUUUAUCGAGGUGGCGAGCAGUUCCAUUCCGAUGAUUGCUUAUCGAUUUAAUCGAAAUAAGCAGC
...(((((((((...(......).(((((........))))).....)))))))))((((..((((.........))))..))))..((((((((((((...)))))..))))))). ( -27.50)
>DroPer_CAF1 26786 109 + 1
--------GCGGACUGAAUUUGCAUUAGCAUCAAGUGCCUGACACUCUCAAUAUUUAUAGAGGUGUCGAGGAGUGCCAUUUCGAUGAUUGCUUAUCGAUUUAGUGGGAAUUAGCCAU
--------..((.((((.(((.(((((((((......((((((((.(((..........)))))))).))).))))....(((((((....)))))))..))))).))))))))).. ( -31.90)
>consensus
G_______GCGAAUCGAAUUUGCAUUAGCAUCAAGUGGCUGACACUCUCAAUAUUUAUUGAGGUGUCGAGUAAUUCCAUUUCGAUGAUUGCUUAUCGAUUUAAUGGAAAUUAACCAU
..........(((((((....(((....(((((((((((((((((.(((..........)))))))).))).....))))).))))..)))...))))))).((((.......)))) (-25.68 = -25.18 +  -0.50)

alignment

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secondary structure

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dotplot

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Window 6

Location 18,847,036 – 18,847,146
Length 110
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 86.82
Mean single sequence MFE -28.25
Consensus MFE -21.23
Energy contribution -22.23
Covariance contribution 1.00
Combinations/Pair 1.12
Mean z-score -2.84
Structure conservation index 0.75
SVM decision value 0.30
SVM RNA-class probability 0.677659
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18847036 110 - 20766785
AUGGUUAAUUUCCAUUAAAUCGAUAAGCAAUCAUCGAAAUGGAAUCACUCGACACCUCAAUAAAUAUUGAGAGUGUCAGCCACUUGAUGCUAAUGCAAAUUCGACUCGC-------C
.(((((...(((((((...(((((.(....).))))))))))))......(((((((((((....)))))).)))))))))).(((((((....)))...)))).....-------. ( -31.90)
>DroPse_CAF1 26648 109 - 1
AUGGCUAAUUCCCACUAAAUCGAUAAGCAAUCAUCGAAAUGGCACUCCUCGACACCUCUAUAAAUAUUGAGAGUGUCAGGCACUUGAUGCUAAUGCAAAUUCAGUCCGC--------
..((((((((..((.....(((((.(....).)))))..((((((.(((.((((((((..........))).)))))))).....).))))).))..)))).))))...-------- ( -24.30)
>DroEre_CAF1 24871 110 - 1
AUGGUUAAUUUCCAUUAAAUCGAUAAGCAAUCAUCGAAAUGGAAUCACUCGACACCUCAAUAAAUAUUGAGAGUGUCAGCCACUUGAUGCUAAUGCAAAUUCGACUCGC-------C
.(((((...(((((((...(((((.(....).))))))))))))......(((((((((((....)))))).)))))))))).(((((((....)))...)))).....-------. ( -31.90)
>DroYak_CAF1 21330 110 - 1
AUGGUUAAUUUCCAUUAAAUCGAUAAGCAAUCAUCGAAAUGGAAUCACUCGACACCUCAAUAAAUAUUGAGAGUGUCAGCCACUUGAUGCUAAUGCAAAUUCGACUUGC-------C
.(((((...(((((((...(((((.(....).))))))))))))......(((((((((((....)))))).)))))))))).(((((((....)))...)))).....-------. ( -31.90)
>DroAna_CAF1 20687 117 - 1
GCUGCUUAUUUCGAUUAAAUCGAUAAGCAAUCAUCGGAAUGGAACUGCUCGCCACCUCGAUAAACAGAGAGAGUUUCAGCCACUUGAUGCUAAUGCAAAUUCGAUUCUCCAUUUGGC
((((((((..(((((...))))))))))....((((((.(((....((((.....(((........))).)))).....))).....(((....)))..)))))).........))) ( -25.20)
>DroPer_CAF1 26786 109 - 1
AUGGCUAAUUCCCACUAAAUCGAUAAGCAAUCAUCGAAAUGGCACUCCUCGACACCUCUAUAAAUAUUGAGAGUGUCAGGCACUUGAUGCUAAUGCAAAUUCAGUCCGC--------
..((((((((..((.....(((((.(....).)))))..((((((.(((.((((((((..........))).)))))))).....).))))).))..)))).))))...-------- ( -24.30)
>consensus
AUGGCUAAUUUCCAUUAAAUCGAUAAGCAAUCAUCGAAAUGGAACCACUCGACACCUCAAUAAAUAUUGAGAGUGUCAGCCACUUGAUGCUAAUGCAAAUUCGACUCGC_______C
.(((((...(((((((...(((((.(....).))))))))))))......((((((((..........))).)))))))))).(((((((....)))...))))............. (-21.23 = -22.23 +   1.00)

alignment

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secondary structure

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dotplot

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Window 7

Location 18,847,066 – 18,847,169
Length 103
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 78.50
Mean single sequence MFE -29.20
Consensus MFE -20.68
Energy contribution -20.93
Covariance contribution 0.25
Combinations/Pair 1.12
Mean z-score -2.37
Structure conservation index 0.71
SVM decision value 1.60
SVM RNA-class probability 0.966972
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18847066 103 + 20766785
GCUGACACUCUCAAUAUUUAUUGAGGUGUCGAGUGAUUCCAUUUCGAUGAUUGCUUAUCGAUUUAAUGGAAAUUAACCAUCACAACA-----------------AUUACCCAGUCAAGUG
((((((((.((((((....)))))))))))..((((((((((((((((((....)))))))...))))))........)))))....-----------------............))). ( -29.20)
>DroPse_CAF1 26677 120 + 1
CCUGACACUCUCAAUAUUUAUAGAGGUGUCGAGGAGUGCCAUUUCGAUGAUUGCUUAUCGAUUUAGUGGGAAUUAGCCAUAACCAUAACCAUAGCAGUACUGUUAUUAAUCACUCAAGUG
.(((((((.(((..........)))))))).))(((((((((((((((((....)))))))...))))).....................((((((....))))))....)))))..... ( -29.40)
>DroSec_CAF1 21015 103 + 1
GCUGACACUCUCAAUAUUUAUUGAGGUGUCGAGUGAUUCCAUUUCGAUGAUUGCUUAUCGAUUUAAUGGAAAUUAACCAUCACCACA-----------------AUUACCCAGUCAAGUG
((((((((.((((((....)))))))))))(.((((((((((((((((((....)))))))...))))))........))))))...-----------------............))). ( -28.80)
>DroEre_CAF1 24901 103 + 1
GCUGACACUCUCAAUAUUUAUUGAGGUGUCGAGUGAUUCCAUUUCGAUGAUUGCUUAUCGAUUUAAUGGAAAUUAACCAUCACAGCA-----------------AUUACCCGCUCAAGUG
((((((((.((((((....)))))))))))..((((((((((((((((((....)))))))...))))))........)))))))).-----------------......(((....))) ( -31.90)
>DroAna_CAF1 20724 103 + 1
GCUGAAACUCUCUCUGUUUAUCGAGGUGGCGAGCAGUUCCAUUCCGAUGAUUGCUUAUCGAUUUAAUCGAAAUAAGCAGCAAUAGUA-----------------AUUAUCCGCUGGAGCG
((((..((.(((..........)))))..).))).((((((..(.(((((((((((((((((...)))))..))))).((....)))-----------------)))))).).)))))). ( -26.50)
>DroPer_CAF1 26815 120 + 1
CCUGACACUCUCAAUAUUUAUAGAGGUGUCGAGGAGUGCCAUUUCGAUGAUUGCUUAUCGAUUUAGUGGGAAUUAGCCAUAACCAUAACCAUAGCAGUACUGUUAUUAAUCACUCGAGUG
.(((((((.(((..........)))))))).))(((((((((((((((((....)))))))...))))).....................((((((....))))))....)))))..... ( -29.40)
>consensus
GCUGACACUCUCAAUAUUUAUUGAGGUGUCGAGUAAUUCCAUUUCGAUGAUUGCUUAUCGAUUUAAUGGAAAUUAACCAUAACAACA_________________AUUACCCACUCAAGUG
((((((((.(((..........)))))))).)))..((((((((((((((....)))))))...)))))))................................................. (-20.68 = -20.93 +   0.25)

alignment

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secondary structure

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dotplot

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Window 8

Location 18,847,066 – 18,847,169
Length 103
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 78.50
Mean single sequence MFE -27.03
Consensus MFE -15.72
Energy contribution -16.75
Covariance contribution 1.03
Combinations/Pair 1.05
Mean z-score -1.84
Structure conservation index 0.58
SVM decision value 0.51
SVM RNA-class probability 0.762875
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18847066 103 - 20766785
CACUUGACUGGGUAAU-----------------UGUUGUGAUGGUUAAUUUCCAUUAAAUCGAUAAGCAAUCAUCGAAAUGGAAUCACUCGACACCUCAAUAAAUAUUGAGAGUGUCAGC
.........(((((((-----------------..(....)..)))...(((((((...(((((.(....).))))))))))))..))))(((((((((((....)))))).)))))... ( -27.80)
>DroPse_CAF1 26677 120 - 1
CACUUGAGUGAUUAAUAACAGUACUGCUAUGGUUAUGGUUAUGGCUAAUUCCCACUAAAUCGAUAAGCAAUCAUCGAAAUGGCACUCCUCGACACCUCUAUAAAUAUUGAGAGUGUCAGG
.....(((((...............(((((((......))))))).........(((..(((((.(....).)))))..))))))))...((((((((..........))).)))))... ( -26.80)
>DroSec_CAF1 21015 103 - 1
CACUUGACUGGGUAAU-----------------UGUGGUGAUGGUUAAUUUCCAUUAAAUCGAUAAGCAAUCAUCGAAAUGGAAUCACUCGACACCUCAAUAAAUAUUGAGAGUGUCAGC
.........(((((((-----------------..(....)..)))...(((((((...(((((.(....).))))))))))))..))))(((((((((((....)))))).)))))... ( -28.00)
>DroEre_CAF1 24901 103 - 1
CACUUGAGCGGGUAAU-----------------UGCUGUGAUGGUUAAUUUCCAUUAAAUCGAUAAGCAAUCAUCGAAAUGGAAUCACUCGACACCUCAAUAAAUAUUGAGAGUGUCAGC
......(((((....)-----------------))))(((((........((((((...(((((.(....).))))))))))))))))..(((((((((((....)))))).)))))... ( -29.70)
>DroAna_CAF1 20724 103 - 1
CGCUCCAGCGGAUAAU-----------------UACUAUUGCUGCUUAUUUCGAUUAAAUCGAUAAGCAAUCAUCGGAAUGGAACUGCUCGCCACCUCGAUAAACAGAGAGAGUUUCAGC
.(((((((((.(((..-----------------...)))))))(((((..(((((...)))))))))).......))).(((((((.(((..................)))))))))))) ( -22.77)
>DroPer_CAF1 26815 120 - 1
CACUCGAGUGAUUAAUAACAGUACUGCUAUGGUUAUGGUUAUGGCUAAUUCCCACUAAAUCGAUAAGCAAUCAUCGAAAUGGCACUCCUCGACACCUCUAUAAAUAUUGAGAGUGUCAGG
.....(((((...............(((((((......))))))).........(((..(((((.(....).)))))..))))))))...((((((((..........))).)))))... ( -27.10)
>consensus
CACUUGAGUGGGUAAU_________________UAUGGUGAUGGCUAAUUUCCAUUAAAUCGAUAAGCAAUCAUCGAAAUGGAACCACUCGACACCUCAAUAAAUAUUGAGAGUGUCAGC
.................................................(((((((...(((((.(....).))))))))))))......((((((((..........))).)))))... (-15.72 = -16.75 +   1.03)

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 11:59:59 2006