Locus 4188

Sequence ID X_DroMel_CAF1
Location 10,995,667 – 10,995,867
Length 200
Max. P 0.999281
window6879 window6880 window6881 window6882 window6883

overview

Window 9

Location 10,995,667 – 10,995,787
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 79.97
Mean single sequence MFE -26.24
Consensus MFE -19.68
Energy contribution -20.24
Covariance contribution 0.56
Combinations/Pair 1.25
Mean z-score -3.46
Structure conservation index 0.75
SVM decision value 3.39
SVM RNA-class probability 0.999129
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10995667 120 + 22224390
UUCAAUAUUUUUCCAACGUGCAUCCUUAUCCAUCAAUCUCAACCUCAUUUGUGAUUGAAAUGUAUUCCCUUUUUUGCUCAGUGCUUGUGGUCAUUAGCGUUUUUAAUGGCCAUUAGCACC
.................(.(((....(((...((((((.(((......))).))))))...)))..........))).).(((((.(((((((((((.....))))))))))).))))). ( -28.74)
>DroSec_CAF1 7896 120 + 1
UUCAAUAUUUUCCCAAAGUGCGUCCUUAUCCAUCAAUACCAACCUCAAUUGUAAUUGAAAUGUAUUCCCUGUUUUGAUCAGUGCUAAUGGCCAUUAUCGUUUUUGAUGGCCAUUAGCACC
.((((.((........(((((((.........(((((..(((......)))..))))).)))))))....)).))))...((((((((((((((((.......)))))))))))))))). ( -31.20)
>DroSim_CAF1 9420 120 + 1
UUCAAUACUUUCCCAACGUGCGUCCUUAUCCAUCCAUACCAACCCCAAUUGUAAUUGAAAUGUAUUCUCUGUUUUGCUCAGUGCUAAUGGUCAUUAUCGUUUUUGAUGGCCAUUAGCACC
...(((((((((......((((...........................))))...)))).)))))..............((((((((((((((((.......)))))))))))))))). ( -27.03)
>DroEre_CAF1 7084 112 + 1
UUUAAUAUUUUCCCUCCGUGCGUC-UUACCCAUC-------ACCUCAUAUUUAAUUAAUAUGCAUACCUUUUUUGGCUCAGUGCUUUUGGCCAUGAGUGGUUUUCAUUGCCAUUAGCACC
..................((.(((-.........-------....((((((.....))))))............))).))(((((..((((.(((((.....))))).))))..))))). ( -24.41)
>DroYak_CAF1 7943 112 + 1
UUCCAUAUUU-ACCUCCGUGCGUCCUUACCCACC-------ACCUCAAUUUUAAUUAAUAUAUAUACCCUAUUUUGCUCUGUGCUUCUGGCCAUAAGCGGUUUUAAUGGCCAUUAGCACC
..........-......(((.((........)))-------)).....................................(((((..(((((((...........)))))))..))))). ( -19.80)
>consensus
UUCAAUAUUUUCCCAACGUGCGUCCUUAUCCAUC_AU__CAACCUCAAUUGUAAUUGAAAUGUAUUCCCUGUUUUGCUCAGUGCUUAUGGCCAUUAGCGUUUUUAAUGGCCAUUAGCACC
................................................................................(((((.(((((((((((.....))))))))))).))))). (-19.68 = -20.24 +   0.56)

alignment

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secondary structure

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dotplot

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Window 0

Location 10,995,667 – 10,995,787
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 79.97
Mean single sequence MFE -27.43
Consensus MFE -14.60
Energy contribution -16.00
Covariance contribution 1.40
Combinations/Pair 1.10
Mean z-score -2.11
Structure conservation index 0.53
SVM decision value 0.53
SVM RNA-class probability 0.771799
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10995667 120 - 22224390
GGUGCUAAUGGCCAUUAAAAACGCUAAUGACCACAAGCACUGAGCAAAAAAGGGAAUACAUUUCAAUCACAAAUGAGGUUGAGAUUGAUGGAUAAGGAUGCACGUUGGAAAAAUAUUGAA
((((((..(((.(((((.......))))).)))..))))))..(((.............(((((((((........))))))))).............)))................... ( -24.27)
>DroSec_CAF1 7896 120 - 1
GGUGCUAAUGGCCAUCAAAAACGAUAAUGGCCAUUAGCACUGAUCAAAACAGGGAAUACAUUUCAAUUACAAUUGAGGUUGGUAUUGAUGGAUAAGGACGCACUUUGGGAAAAUAUUGAA
(((((((((((((((...........)))))))))))))))..((((..((...(((((((((((((....))))))))..)))))..))..(((((.....)))))........)))). ( -34.20)
>DroSim_CAF1 9420 120 - 1
GGUGCUAAUGGCCAUCAAAAACGAUAAUGACCAUUAGCACUGAGCAAAACAGAGAAUACAUUUCAAUUACAAUUGGGGUUGGUAUGGAUGGAUAAGGACGCACGUUGGGAAAGUAUUGAA
(((((((((((.(((...........))).))))))))))).............(((((.((((.....((((..(.(((..(((......)))..))).)..)))).)))))))))... ( -28.40)
>DroEre_CAF1 7084 112 - 1
GGUGCUAAUGGCAAUGAAAACCACUCAUGGCCAAAAGCACUGAGCCAAAAAAGGUAUGCAUAUUAAUUAAAUAUGAGGU-------GAUGGGUAA-GACGCACGGAGGGAAAAUAUUAAA
((((((..((((.((((.......)))).))))..))))))..(((......)))...((((((.....))))))..((-------(.((.....-..)))))................. ( -24.90)
>DroYak_CAF1 7943 112 - 1
GGUGCUAAUGGCCAUUAAAACCGCUUAUGGCCAGAAGCACAGAGCAAAAUAGGGUAUAUAUAUUAAUUAAAAUUGAGGU-------GGUGGGUAAGGACGCACGGAGGU-AAAUAUGGAA
.(((((..(((((((...........)))))))..))))).............((((.(((.(((((....)))))...-------.(((.((....)).)))....))-).)))).... ( -25.40)
>consensus
GGUGCUAAUGGCCAUCAAAAACGCUAAUGGCCAUAAGCACUGAGCAAAAAAGGGAAUACAUUUCAAUUACAAUUGAGGUUG__AU_GAUGGAUAAGGACGCACGUUGGGAAAAUAUUGAA
((((((..(((((((...........)))))))..))))))..................((((((((....))))))))......................................... (-14.60 = -16.00 +   1.40)

alignment

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secondary structure

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Window 1

Location 10,995,707 – 10,995,827
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 80.85
Mean single sequence MFE -28.96
Consensus MFE -19.68
Energy contribution -20.24
Covariance contribution 0.56
Combinations/Pair 1.25
Mean z-score -3.05
Structure conservation index 0.68
SVM decision value 2.63
SVM RNA-class probability 0.995953
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10995707 120 + 22224390
AACCUCAUUUGUGAUUGAAAUGUAUUCCCUUUUUUGCUCAGUGCUUGUGGUCAUUAGCGUUUUUAAUGGCCAUUAGCACCUGUGCAGCUUCCACCUAACAAUCCCAGCCACACCUAAUGU
.....((((((((..((...(((..........((((.(((((((.(((((((((((.....))))))))))).)))).))).))))..........)))....))..))))...)))). ( -31.25)
>DroSec_CAF1 7936 120 + 1
AACCUCAAUUGUAAUUGAAAUGUAUUCCCUGUUUUGAUCAGUGCUAAUGGCCAUUAUCGUUUUUGAUGGCCAUUAGCACCUGUGCUGAUUCCACCUAACAAUCCCAGCCACGCCUAAUGU
....(((((....)))))......................((((((((((((((((.......))))))))))))))))..((((((.................))).)))......... ( -32.73)
>DroSim_CAF1 9460 120 + 1
AACCCCAAUUGUAAUUGAAAUGUAUUCUCUGUUUUGCUCAGUGCUAAUGGUCAUUAUCGUUUUUGAUGGCCAUUAGCACCUGUGCUGAUUCCACCUAACAAUCCCAGCCACGCCUAAAAU
........(((..((((..................((.((((((((((((((((((.......))))))))))))))).))).))((....)).....))))..)))............. ( -30.30)
>DroEre_CAF1 7117 116 + 1
-ACCUCAUAUUUAAUUAAUAUGCAUACCUUUUUUGGCUCAGUGCUUUUGGCCAUGAGUGGUUUUCAUUGCCAUUAGCACCUGUG---CUUCCACCUCACAAUCACCGAAACACUUAAUGU
-....((((((.....))))))........((((((....(((((..((((.(((((.....))))).))))..))))).((((---.........))))....)))))).......... ( -26.80)
>DroYak_CAF1 7976 116 + 1
-ACCUCAAUUUUAAUUAAUAUAUAUACCCUAUUUUGCUCUGUGCUUCUGGCCAUAAGCGGUUUUAAUGGCCAUUAGCACCUGUG---AUUCCACCUCACAAUUAGCUAGACACUUAAUGU
-..................................(((..(((((..(((((((...........)))))))..))))).((((---(.......)))))...))).............. ( -23.70)
>consensus
AACCUCAAUUGUAAUUGAAAUGUAUUCCCUGUUUUGCUCAGUGCUUAUGGCCAUUAGCGUUUUUAAUGGCCAUUAGCACCUGUGC_GAUUCCACCUAACAAUCCCAGCCACACCUAAUGU
........................................(((((.(((((((((((.....))))))))))).)))))......................................... (-19.68 = -20.24 +   0.56)

alignment

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secondary structure

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dotplot

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Window 2

Location 10,995,707 – 10,995,827
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 80.85
Mean single sequence MFE -31.07
Consensus MFE -17.87
Energy contribution -17.79
Covariance contribution -0.08
Combinations/Pair 1.24
Mean z-score -2.01
Structure conservation index 0.58
SVM decision value 0.39
SVM RNA-class probability 0.715505
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10995707 120 - 22224390
ACAUUAGGUGUGGCUGGGAUUGUUAGGUGGAAGCUGCACAGGUGCUAAUGGCCAUUAAAAACGCUAAUGACCACAAGCACUGAGCAAAAAAGGGAAUACAUUUCAAUCACAAAUGAGGUU
((.(((..((((..((..((.((...........(((...((((((..(((.(((((.......))))).)))..))))))..)))...........))))..))..))))..))).)). ( -31.05)
>DroSec_CAF1 7936 120 - 1
ACAUUAGGCGUGGCUGGGAUUGUUAGGUGGAAUCAGCACAGGUGCUAAUGGCCAUCAAAAACGAUAAUGGCCAUUAGCACUGAUCAAAACAGGGAAUACAUUUCAAUUACAAUUGAGGUU
.........(((.(((.((((.....(((.......))).(((((((((((((((...........)))))))))))))))))))....)))....)))((((((((....)))))))). ( -35.70)
>DroSim_CAF1 9460 120 - 1
AUUUUAGGCGUGGCUGGGAUUGUUAGGUGGAAUCAGCACAGGUGCUAAUGGCCAUCAAAAACGAUAAUGACCAUUAGCACUGAGCAAAACAGAGAAUACAUUUCAAUUACAAUUGGGGUU
.........(((.(((.((((.(.....).)))).((...(((((((((((.(((...........))).)))))))))))..))....)))....)))((..((((....))))..)). ( -30.50)
>DroEre_CAF1 7117 116 - 1
ACAUUAAGUGUUUCGGUGAUUGUGAGGUGGAAG---CACAGGUGCUAAUGGCAAUGAAAACCACUCAUGGCCAAAAGCACUGAGCCAAAAAAGGUAUGCAUAUUAAUUAAAUAUGAGGU-
.......(((((((.(...........).))))---))).((((((..((((.((((.......)))).))))..))))))..(((......)))...((((((.....))))))....- ( -30.00)
>DroYak_CAF1 7976 116 - 1
ACAUUAAGUGUCUAGCUAAUUGUGAGGUGGAAU---CACAGGUGCUAAUGGCCAUUAAAACCGCUUAUGGCCAGAAGCACAGAGCAAAAUAGGGUAUAUAUAUUAAUUAAAAUUGAGGU-
..............(((..((((((.......)---)))))(((((..(((((((...........)))))))..)))))..)))..................................- ( -28.10)
>consensus
ACAUUAGGUGUGGCUGGGAUUGUUAGGUGGAAUC_GCACAGGUGCUAAUGGCCAUCAAAAACGCUAAUGGCCAUAAGCACUGAGCAAAAAAGGGAAUACAUUUCAAUUACAAUUGAGGUU
.................(((((....(((...........((((((..(((((((...........)))))))..))))))...............)))....)))))............ (-17.87 = -17.79 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 3

Location 10,995,747 – 10,995,867
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 79.20
Mean single sequence MFE -34.61
Consensus MFE -22.52
Energy contribution -24.68
Covariance contribution 2.16
Combinations/Pair 1.24
Mean z-score -3.48
Structure conservation index 0.65
SVM decision value 3.48
SVM RNA-class probability 0.999281
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10995747 120 + 22224390
GUGCUUGUGGUCAUUAGCGUUUUUAAUGGCCAUUAGCACCUGUGCAGCUUCCACCUAACAAUCCCAGCCACACCUAAUGUGACACUCACGUUCUUGUCGUCAUUAGGAUCCAGUGCAGAU
(((((.(((((((((((.....))))))))))).)))))(((..(.(((................)))....((((((((((((..........))))).))))))).....)..))).. ( -40.59)
>DroSec_CAF1 7976 120 + 1
GUGCUAAUGGCCAUUAUCGUUUUUGAUGGCCAUUAGCACCUGUGCUGAUUCCACCUAACAAUCCCAGCCACGCCUAAUGUGACACUCACGCUCUUGCCAUCAUUAGGAUCCAAUACAGAU
((((((((((((((((.......))))))))))))))))((((((((.................))))....(((((((((.....)))((....))....)))))).......)))).. ( -42.43)
>DroSim_CAF1 9500 120 + 1
GUGCUAAUGGUCAUUAUCGUUUUUGAUGGCCAUUAGCACCUGUGCUGAUUCCACCUAACAAUCCCAGCCACGCCUAAAAUGACACUCACGCUCUUGCCAUCANNNNNNNNNNNNNNNNNN
((((((((((((((((.......))))))))))))))))..((((((.................))).)))..................((....))....................... ( -29.13)
>DroEre_CAF1 7156 117 + 1
GUGCUUUUGGCCAUGAGUGGUUUUCAUUGCCAUUAGCACCUGUG---CUUCCACCUCACAAUCACCGAAACACUUAAUGUGACACUCACGCUCUUUCCACCAUUAGGAUCCCGUGCAGAU
(((((..((((.(((((.....))))).))))..)))))(((..---(..............................(((.....)))......(((.......)))....)..))).. ( -30.70)
>DroYak_CAF1 8015 117 + 1
GUGCUUCUGGCCAUAAGCGGUUUUAAUGGCCAUUAGCACCUGUG---AUUCCACCUCACAAUUAGCUAGACACUUAAUGUGACACUCACGCUCUUGCCACCAUUAGGAUCCCGUGCAGAU
(((((..(((((((...........)))))))..)))))(((((---..(((...(((((.((((........))))))))).......((....))........))).....))))).. ( -30.20)
>consensus
GUGCUUAUGGCCAUUAGCGUUUUUAAUGGCCAUUAGCACCUGUGC_GAUUCCACCUAACAAUCCCAGCCACACCUAAUGUGACACUCACGCUCUUGCCAUCAUUAGGAUCCAGUGCAGAU
(((((.(((((((((((.....))))))))))).)))))(((((.....(((..........................(((.....)))((....))........))).....))))).. (-22.52 = -24.68 +   2.16)

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 11:18:40 2006