Locus 8209

Sequence ID 3R_DroMel_CAF1
Location 22,036,675 – 22,036,824
Length 149
Max. P 0.990053
window13211 window13212 window13213 window13214

overview

Window 1

Location 22,036,675 – 22,036,792
Length 117
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 94.79
Mean single sequence MFE -38.70
Consensus MFE -34.98
Energy contribution -36.14
Covariance contribution 1.16
Combinations/Pair 1.06
Mean z-score -1.49
Structure conservation index 0.90
SVM decision value 1.24
SVM RNA-class probability 0.935229
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22036675 117 + 27905053
UCGGCUCAAAUUGCAACUUUUGAUUAGCACUCUGAUGUAAUAAUCAACUUUGGGCCACAAAUCCUGCCGUGGCAUUUGCUGGGCAGGAAAAGCGGUGCGGCUGGCAUUUUGUGGGGC
..((((((((.........(((((((..((......))..))))))).))))))))((((((((((((.((((....)))))))))))......((((.....)))))))))..... ( -37.40)
>DroSec_CAF1 34912 117 + 1
UCGGCUCAAAUUGCAACUUUUGAUUAGCACUCUGAUGUAAUAAUCAACUUUGGGCCACAAAUCCUGCCGUGGCAUUUGCUGGGCAGGAAAAGCGGUGCGGCUGGCAUUGUGUGGGGC
..((((((((.........(((((((..((......))..))))))).)))))))).....(((((((.((((....)))))))))))...(((((((.....)))))))....... ( -40.00)
>DroSim_CAF1 27203 117 + 1
UCGGCUCAAAUUGCAACUUUUGAUUAGCACUCUGAUGUAAUAAUCAACUUUGGGCCACAAAUCCUGCCGUGGCAUUUGCUGGGCAGGAAAAGCGGUGCGGCUGGCAUUGAGUGGGGC
((.((((((..(((.....(((((((..((......))..))))))).....((((.....(((((((.((((....)))))))))))...((...)))))).))))))))).)).. ( -41.10)
>DroEre_CAF1 28931 117 + 1
UCGGCCCAAAUUGCAACUUUUGAUUAGCACUCUGAUGUAAUAAUCAACUUUGGGCCACAAAUCCUGCCAUGGCAUUUGCCGGGCAGGAAAAGCGUUGCUGUUGGCAUUGUGAGGGGC
...((((...(..(((...(((((((..((......))..)))))))......((((....(((((((.((((....)))))))))))..(((...)))..)))).)))..).)))) ( -43.80)
>DroYak_CAF1 36606 117 + 1
UCGGCACAAAUUGCAACUUUUGAUUAGCACUCUGAUGUAAUAAUCAACUUUGGGCCACAAAUCCUGCCGUCGAAUUUGCUGGGCAGGAAAAGCGGUACGGCUGGCAUUGUGAGUGGU
(((.(((((....(((...(((((((..((......))..)))))))..))).(((.....(((((((.............)))))))..(((......)))))).)))))..))). ( -31.22)
>consensus
UCGGCUCAAAUUGCAACUUUUGAUUAGCACUCUGAUGUAAUAAUCAACUUUGGGCCACAAAUCCUGCCGUGGCAUUUGCUGGGCAGGAAAAGCGGUGCGGCUGGCAUUGUGUGGGGC
..((((((((.........(((((((..((......))..))))))).)))))))).....(((((((.((((....)))))))))))...(((((((.....)))))))....... (-34.98 = -36.14 +   1.16)

alignment

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secondary structure

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dotplot

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Window 2

Location 22,036,675 – 22,036,792
Length 117
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 94.79
Mean single sequence MFE -35.38
Consensus MFE -29.88
Energy contribution -29.96
Covariance contribution 0.08
Combinations/Pair 1.06
Mean z-score -2.21
Structure conservation index 0.84
SVM decision value 2.19
SVM RNA-class probability 0.990053
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22036675 117 - 27905053
GCCCCACAAAAUGCCAGCCGCACCGCUUUUCCUGCCCAGCAAAUGCCACGGCAGGAUUUGUGGCCCAAAGUUGAUUAUUACAUCAGAGUGCUAAUCAAAAGUUGCAAUUUGAGCCGA
......((((.(((.(((.(..((((...(((((((..((....))...)))))))...))))..)....(((((((.(((......))).)))))))..)))))).))))...... ( -34.70)
>DroSec_CAF1 34912 117 - 1
GCCCCACACAAUGCCAGCCGCACCGCUUUUCCUGCCCAGCAAAUGCCACGGCAGGAUUUGUGGCCCAAAGUUGAUUAUUACAUCAGAGUGCUAAUCAAAAGUUGCAAUUUGAGCCGA
............((((((((((.......(((((((..((....))...)))))))..)))))).(((..(((((((.(((......))).)))))))...))).....)).))... ( -32.20)
>DroSim_CAF1 27203 117 - 1
GCCCCACUCAAUGCCAGCCGCACCGCUUUUCCUGCCCAGCAAAUGCCACGGCAGGAUUUGUGGCCCAAAGUUGAUUAUUACAUCAGAGUGCUAAUCAAAAGUUGCAAUUUGAGCCGA
......((((((((.(((.(..((((...(((((((..((....))...)))))))...))))..)....(((((((.(((......))).)))))))..))))))..))))).... ( -35.50)
>DroEre_CAF1 28931 117 - 1
GCCCCUCACAAUGCCAACAGCAACGCUUUUCCUGCCCGGCAAAUGCCAUGGCAGGAUUUGUGGCCCAAAGUUGAUUAUUACAUCAGAGUGCUAAUCAAAAGUUGCAAUUUGGGCCGA
...........(((.....)))..((...(((((((.(((....)))..)))))))...))((((((((.(((((((.(((......))).))))))).........)))))))).. ( -41.00)
>DroYak_CAF1 36606 117 - 1
ACCACUCACAAUGCCAGCCGUACCGCUUUUCCUGCCCAGCAAAUUCGACGGCAGGAUUUGUGGCCCAAAGUUGAUUAUUACAUCAGAGUGCUAAUCAAAAGUUGCAAUUUGUGCCGA
......((((((((.(((.(..((((...(((((((...(......)..)))))))...))))..)....(((((((.(((......))).)))))))..))))))..))))).... ( -33.50)
>consensus
GCCCCACACAAUGCCAGCCGCACCGCUUUUCCUGCCCAGCAAAUGCCACGGCAGGAUUUGUGGCCCAAAGUUGAUUAUUACAUCAGAGUGCUAAUCAAAAGUUGCAAUUUGAGCCGA
............(((((..(((((((...(((((((..((....))...)))))))...)))).......(((((((.(((......))).)))))))....)))...))).))... (-29.88 = -29.96 +   0.08)

alignment

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secondary structure

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dotplot

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Window 3

Location 22,036,715 – 22,036,824
Length 109
Sequences 5
Columns 110
Reading direction forward
Mean pairwise identity 93.24
Mean single sequence MFE -33.00
Consensus MFE -26.72
Energy contribution -27.32
Covariance contribution 0.60
Combinations/Pair 1.12
Mean z-score -1.70
Structure conservation index 0.81
SVM decision value 0.74
SVM RNA-class probability 0.836791
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22036715 109 + 27905053
UAAUCAACUUUGGGCCACAAAUCCUGCCGUGGCAUUUGCUGGGCAGGAAAAGCGGUGCGGCUGGCAUUUUGUGGGGC-GUUCAUAAAUACAUAUUAUUGACUGAAUGAAG
..............((((((((((((((.((((....)))))))))))......((((.....)))))))))))..(-(((((..((((.....))))...))))))... ( -33.30)
>DroSec_CAF1 34952 109 + 1
UAAUCAACUUUGGGCCACAAAUCCUGCCGUGGCAUUUGCUGGGCAGGAAAAGCGGUGCGGCUGGCAUUGUGUGGGGC-AUUCAUAAAUACAUAUUAUUGACUGAAUAAAG
.......(((((..((((...(((((((.((((....)))))))))))...(((((((.....)))))))))))...-.((((..((((.....))))...))))))))) ( -33.40)
>DroSim_CAF1 27243 109 + 1
UAAUCAACUUUGGGCCACAAAUCCUGCCGUGGCAUUUGCUGGGCAGGAAAAGCGGUGCGGCUGGCAUUGAGUGGGGC-AUUCAUAAAUACAUAUUAUUGACUGAAUGAAG
..............((((...(((((((.((((....)))))))))))....((((((.....)))))).))))..(-(((((..((((.....))))...))))))... ( -34.60)
>DroEre_CAF1 28971 110 + 1
UAAUCAACUUUGGGCCACAAAUCCUGCCAUGGCAUUUGCCGGGCAGGAAAAGCGUUGCUGUUGGCAUUGUGAGGGGCAAUUCAUAAAUACAUAUUAUUGAGUGAAUGAAG
.......((((..(((.....(((((((.((((....)))))))))))...(((.(((.....))).)))....))).((((((.((((.....))))..)))))))))) ( -34.10)
>DroYak_CAF1 36646 109 + 1
UAAUCAACUUUGGGCCACAAAUCCUGCCGUCGAAUUUGCUGGGCAGGAAAAGCGGUACGGCUGGCAUUGUGAGUGGU-AUUCAUAAAUACAUAUUAUUCACUGAAUGAAG
...(((.......(((.....(((((((.............)))))))..(((......))))))...(((((((((-((..........)))))))))))....))).. ( -29.62)
>consensus
UAAUCAACUUUGGGCCACAAAUCCUGCCGUGGCAUUUGCUGGGCAGGAAAAGCGGUGCGGCUGGCAUUGUGUGGGGC_AUUCAUAAAUACAUAUUAUUGACUGAAUGAAG
.......((((..(((.....(((((((.((((....)))))))))))...(((((((.....)))))))....))).(((((..((((.....))))...))))))))) (-26.72 = -27.32 +   0.60)

alignment

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secondary structure

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dotplot

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Window 4

Location 22,036,715 – 22,036,824
Length 109
Sequences 5
Columns 110
Reading direction reverse
Mean pairwise identity 93.24
Mean single sequence MFE -27.82
Consensus MFE -22.98
Energy contribution -23.62
Covariance contribution 0.64
Combinations/Pair 1.04
Mean z-score -2.09
Structure conservation index 0.83
SVM decision value 1.78
SVM RNA-class probability 0.976892
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22036715 109 - 27905053
CUUCAUUCAGUCAAUAAUAUGUAUUUAUGAAC-GCCCCACAAAAUGCCAGCCGCACCGCUUUUCCUGCCCAGCAAAUGCCACGGCAGGAUUUGUGGCCCAAAGUUGAUUA
........(((((((.....((((((.((...-....))..))))))..((((((.......(((((((..((....))...)))))))..)))))).....))))))). ( -28.50)
>DroSec_CAF1 34952 109 - 1
CUUUAUUCAGUCAAUAAUAUGUAUUUAUGAAU-GCCCCACACAAUGCCAGCCGCACCGCUUUUCCUGCCCAGCAAAUGCCACGGCAGGAUUUGUGGCCCAAAGUUGAUUA
........(((((((.....(((((....)))-))..............((((((.......(((((((..((....))...)))))))..)))))).....))))))). ( -28.40)
>DroSim_CAF1 27243 109 - 1
CUUCAUUCAGUCAAUAAUAUGUAUUUAUGAAU-GCCCCACUCAAUGCCAGCCGCACCGCUUUUCCUGCCCAGCAAAUGCCACGGCAGGAUUUGUGGCCCAAAGUUGAUUA
...((((((...((((.....))))..)))))-)......(((((....((((((.......(((((((..((....))...)))))))..)))))).....)))))... ( -30.00)
>DroEre_CAF1 28971 110 - 1
CUUCAUUCACUCAAUAAUAUGUAUUUAUGAAUUGCCCCUCACAAUGCCAACAGCAACGCUUUUCCUGCCCGGCAAAUGCCAUGGCAGGAUUUGUGGCCCAAAGUUGAUUA
..........(((((..((((....))))....(((........(((.....)))..((...(((((((.(((....)))..)))))))...))))).....)))))... ( -26.30)
>DroYak_CAF1 36646 109 - 1
CUUCAUUCAGUGAAUAAUAUGUAUUUAUGAAU-ACCACUCACAAUGCCAGCCGUACCGCUUUUCCUGCCCAGCAAAUUCGACGGCAGGAUUUGUGGCCCAAAGUUGAUUA
....(((((.((((((.....)))))))))))-..............((((.(..((((...(((((((...(......)..)))))))...))))..)...)))).... ( -25.90)
>consensus
CUUCAUUCAGUCAAUAAUAUGUAUUUAUGAAU_GCCCCACACAAUGCCAGCCGCACCGCUUUUCCUGCCCAGCAAAUGCCACGGCAGGAUUUGUGGCCCAAAGUUGAUUA
........(((((((.............................(((.....)))((((...(((((((..((....))...)))))))...))))......))))))). (-22.98 = -23.62 +   0.64)

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 13:05:24 2006