Locus 1790

Sequence ID 3R_DroMel_CAF1
Location 5,117,653 – 5,117,811
Length 158
Max. P 0.877614
window2948 window2949 window2950

overview

Window 8

Location 5,117,653 – 5,117,771
Length 118
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.77
Mean single sequence MFE -28.22
Consensus MFE -23.88
Energy contribution -23.76
Covariance contribution -0.12
Combinations/Pair 1.09
Mean z-score -1.28
Structure conservation index 0.85
SVM decision value -0.01
SVM RNA-class probability 0.527684
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5117653 118 + 27905053
GUGUUUGUUUGUUUGC--UGCCUUUUGUUCGCUUGUAGUGGUGCUGAUUGUGUUUGCAAAAAUUGUCAACAUUAUUUCAUUCUCAGACACGUUGAAGUAUGAAAGGAAUUAACAAAUACU
(((((((((.(((...--..(((((..(..((((...(((...((((..(((((.(((.....))).)))))..........)))).)))....)))))..)))))))).))))))))). ( -26.20)
>DroSec_CAF1 19250 120 + 1
GUGUUUGUUUGUUUGCUUUGCCUUUUGUUCGCUUGUAGUGGUGCUGAUUGUGUUUGCAAAAAUUGUCAACAUUAUUUCAUUCUCAGCCACGUUGAAGUAUGAAAGGAAUUAACAAAUACU
(((((((((.(((.......(((((..(..((((...(((((..(((..(((((.(((.....))).)))))....)))......)))))....)))))..)))))))).))))))))). ( -28.61)
>DroSim_CAF1 19825 118 + 1
GUGUUUGUUUGUUUGC--UGCCUUUUGUUCGCUUGUAGUGGUGCUGAUUGUGUUUGCAAAAAUUGUCAACAUUAUUUCAUUCUCAGCCACGUUGAAGUAUGAAAGGAAUUAACAAAUACU
(((((((((.(((...--..(((((..(..((((...(((((..(((..(((((.(((.....))).)))))....)))......)))))....)))))..)))))))).))))))))). ( -29.20)
>DroEre_CAF1 20725 115 + 1
-UG--GGUGUGUUUGC--UGCUUUUUGUUCGCUUGUAGUGGUGCUGAUUGUGUUUGCGAAAAUUGUCAACAUUAUUUCAUUCUCAGCCACGUUGAAGUAUGAAAAGAAUUAACAAAUACU
-..--...(((((((.--..(((((..(..((((...(((((..(((..(((((.((((...)))).)))))....)))......)))))....)))))..)))))......))))))). ( -24.50)
>DroYak_CAF1 20698 116 + 1
GUG--GGUGUGUUUGC--UGCCUUUUGUUCGCUUGUAGUGGUGCUGAUUGUGUUUGCGAAAAUUGUCAACAUUAUUUCAUUCUCAGCCACGUUGAAGCAUGAAAGGCAUUAACAAAUACU
...--...(((((((.--(((((((..(..((((...(((((..(((..(((((.((((...)))).)))))....)))......)))))....)))))..)))))))....))))))). ( -32.60)
>consensus
GUGUUUGUUUGUUUGC__UGCCUUUUGUUCGCUUGUAGUGGUGCUGAUUGUGUUUGCAAAAAUUGUCAACAUUAUUUCAUUCUCAGCCACGUUGAAGUAUGAAAGGAAUUAACAAAUACU
......(((((((.......(((((..(..((((...(((((..(((..(((((.((((...)))).)))))....)))......)))))....)))))..)))))....)))))))... (-23.88 = -23.76 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 9

Location 5,117,691 – 5,117,811
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.17
Mean single sequence MFE -25.05
Consensus MFE -23.12
Energy contribution -23.56
Covariance contribution 0.44
Combinations/Pair 1.03
Mean z-score -1.12
Structure conservation index 0.92
SVM decision value 0.12
SVM RNA-class probability 0.592317
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5117691 120 + 27905053
GUGCUGAUUGUGUUUGCAAAAAUUGUCAACAUUAUUUCAUUCUCAGACACGUUGAAGUAUGAAAGGAAUUAACAAAUACUUACAGCAGACAUUGCCUGCAGAAUUUUAGUUUUUGCAAAU
(((((((..(((((.(((.....))).)))))..........)))).)))((((((((((...............)))))).))))..........(((((((.......)))))))... ( -23.86)
>DroSec_CAF1 19290 120 + 1
GUGCUGAUUGUGUUUGCAAAAAUUGUCAACAUUAUUUCAUUCUCAGCCACGUUGAAGUAUGAAAGGAAUUAACAAAUACUUACAGCAGACAUUGCCUGCAGAAUUUUAGUUUUUGUAAAU
.(((((...(((((((.......((....))...((((((.((((((...)))).)).))))))........)))))))...))))).........(((((((.......)))))))... ( -23.50)
>DroSim_CAF1 19863 120 + 1
GUGCUGAUUGUGUUUGCAAAAAUUGUCAACAUUAUUUCAUUCUCAGCCACGUUGAAGUAUGAAAGGAAUUAACAAAUACUUACAGCAGACAUUGCCUGCAGAAUUUUAGUUUUUGCAAAA
.(((((...(((((((.......((....))...((((((.((((((...)))).)).))))))........)))))))...))))).........(((((((.......)))))))... ( -25.50)
>DroEre_CAF1 20760 120 + 1
GUGCUGAUUGUGUUUGCGAAAAUUGUCAACAUUAUUUCAUUCUCAGCCACGUUGAAGUAUGAAAAGAAUUAACAAAUACUUACAGCAAACAUGGCCUGCACAAUUUUAGUUAUUGCACAU
((((.(.(..(((((((((......)).......((((((.((((((...)))).)).))))))....................)))))))..).).))))................... ( -25.70)
>DroYak_CAF1 20734 120 + 1
GUGCUGAUUGUGUUUGCGAAAAUUGUCAACAUUAUUUCAUUCUCAGCCACGUUGAAGCAUGAAAGGCAUUAACAAAUACUUACAGCAAACAUUGCCUGCAGAAGUUUAGUUUUUGCACAU
.(((((...(((((((..((...((((.......((((((.((((((...)))).)).))))))))))))..)))))))...))))).........((((((((.....))))))))... ( -26.71)
>consensus
GUGCUGAUUGUGUUUGCAAAAAUUGUCAACAUUAUUUCAUUCUCAGCCACGUUGAAGUAUGAAAGGAAUUAACAAAUACUUACAGCAGACAUUGCCUGCAGAAUUUUAGUUUUUGCAAAU
.(((((...(((((((.......((....))...((((((.((((((...)))).)).))))))........)))))))...))))).........(((((((.......)))))))... (-23.12 = -23.56 +   0.44)

alignment

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secondary structure

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dotplot

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Window 0

Location 5,117,691 – 5,117,811
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.17
Mean single sequence MFE -24.74
Consensus MFE -22.20
Energy contribution -22.56
Covariance contribution 0.36
Combinations/Pair 1.03
Mean z-score -1.41
Structure conservation index 0.90
SVM decision value 0.90
SVM RNA-class probability 0.877614
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5117691 120 - 27905053
AUUUGCAAAAACUAAAAUUCUGCAGGCAAUGUCUGCUGUAAGUAUUUGUUAAUUCCUUUCAUACUUCAACGUGUCUGAGAAUGAAAUAAUGUUGACAAUUUUUGCAAACACAAUCAGCAC
.((((((((((..........((((((...)))))).........((((((((...((((((.((.((.......)))).))))))....))))))))))))))))))............ ( -26.50)
>DroSec_CAF1 19290 120 - 1
AUUUACAAAAACUAAAAUUCUGCAGGCAAUGUCUGCUGUAAGUAUUUGUUAAUUCCUUUCAUACUUCAACGUGGCUGAGAAUGAAAUAAUGUUGACAAUUUUUGCAAACACAAUCAGCAC
.....................((((((...))))))((((((...((((((((...((((((.((.((.......)))).))))))....))))))))..)))))).............. ( -22.40)
>DroSim_CAF1 19863 120 - 1
UUUUGCAAAAACUAAAAUUCUGCAGGCAAUGUCUGCUGUAAGUAUUUGUUAAUUCCUUUCAUACUUCAACGUGGCUGAGAAUGAAAUAAUGUUGACAAUUUUUGCAAACACAAUCAGCAC
.((((((((((..........((((((...)))))).........((((((((...((((((.((.((.......)))).))))))....))))))))))))))))))............ ( -26.40)
>DroEre_CAF1 20760 120 - 1
AUGUGCAAUAACUAAAAUUGUGCAGGCCAUGUUUGCUGUAAGUAUUUGUUAAUUCUUUUCAUACUUCAACGUGGCUGAGAAUGAAAUAAUGUUGACAAUUUUCGCAAACACAAUCAGCAC
.((..((((.......))))..)).....(((((((.(.(((...((((((((...((((((.((.((.......)))).))))))....)))))))).))))))))))).......... ( -25.00)
>DroYak_CAF1 20734 120 - 1
AUGUGCAAAAACUAAACUUCUGCAGGCAAUGUUUGCUGUAAGUAUUUGUUAAUGCCUUUCAUGCUUCAACGUGGCUGAGAAUGAAAUAAUGUUGACAAUUUUCGCAAACACAAUCAGCAC
..((((.........(((((.((((((...)))))).).))))..(((((((((..((((((..((((.......)))).))))))...)))))))))..................)))) ( -23.40)
>consensus
AUUUGCAAAAACUAAAAUUCUGCAGGCAAUGUCUGCUGUAAGUAUUUGUUAAUUCCUUUCAUACUUCAACGUGGCUGAGAAUGAAAUAAUGUUGACAAUUUUUGCAAACACAAUCAGCAC
...(((...............((((((...))))))((((((...((((((((...((((((..((((.......)))).))))))....))))))))..))))))..........))). (-22.20 = -22.56 +   0.36)

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 10:19:36 2006