Locus 10175

Sequence ID 3R_DroMel_CAF1
Location 27,304,198 – 27,304,331
Length 133
Max. P 0.976761
window16201 window16202 window16203 window16204

overview

Window 1

Location 27,304,198 – 27,304,291
Length 93
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 79.87
Mean single sequence MFE -25.82
Consensus MFE -14.36
Energy contribution -15.25
Covariance contribution 0.89
Combinations/Pair 1.12
Mean z-score -1.90
Structure conservation index 0.56
SVM decision value 0.16
SVM RNA-class probability 0.612681
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27304198 93 + 27905053
-UUCUUG------CAAGGGAUCCAUUUGGACACUUUUGAGA--------------------GCUGCAAUGAAAGUUCAUCGAUUUUACCUCACUUUUCACUUUCAUUGCAAGAGUGUUAA
-((((((------.((((..(((....)))..)))))))))--------------------).((((((((((((.......................)))))))))))).......... ( -22.50)
>DroSec_CAF1 9168 93 + 1
-UUCUUG------CAAGGGAUCCAUUUGGACACUUUUGAGA--------------------GAUGCAAUGAAAGUGCAGCGAUUUUACCUUACUUUUCACUUUCAUUGCAAGAGUGUUAA
-.(((..------((((((.(((....)))..))))))..)--------------------))(((((((((((((.((..(.......)..))...))))))))))))).......... ( -27.20)
>DroSim_CAF1 9591 93 + 1
-UUCUUG------CAAGGGAUCCAUUUGGACACUUUUGAGA--------------------GAUGCAAUGAAAGUGCAGAGAUUUUACCUUACUUUUCACUUUCAUUGCAAGAGUGUUAA
-.(((..------((((((.(((....)))..))))))..)--------------------))(((((((((((((.((((...........)))).))))))))))))).......... ( -30.60)
>DroEre_CAF1 9408 93 + 1
-UUCUUG------CAAGGGAUCCAUUUGGACAGUUUUGAGA--------------------GAUGCAAUGAAAGCGCAGCGAUUUUACAUCACUUUUCACUUUCAUUGCAAGAGUGUUAA
-.(((..------(((((..(((....)))...)))))..)--------------------))(((((((((((.(.((.(((.....))).))...).))))))))))).......... ( -23.50)
>DroYak_CAF1 5468 93 + 1
-AUCUGG------CAAGGGAUCCAUUUGGACAGCGAUGAGA--------------------GAUGCAAUGAAAGUGCAGCGAUUUUACCUCACUUUUCACUUUCAUUGCAAGAGUGUUAA
-...(((------((.....(((....)))..(((((((((--------------------(.((....(((((((.((.(......)))))))))))))))))))))).....))))). ( -24.00)
>DroAna_CAF1 10593 118 + 1
GAUCUCGGAGCAUCAGAGGAAUCAUUAGCAGAGGUUAAAGAGUUGUUCAGCCUCGUAUGUAGAUGCCACGAAAGUGCAGCGAUUUCA--GUGCUUUUCACUUUCCUUGCAAGCGUGUUAA
.........((....((((((.....((((((((((.((......)).))))))...((.(((((((((....)))..)).))))))--.)))).......))))))....))....... ( -27.10)
>consensus
_UUCUUG______CAAGGGAUCCAUUUGGACACUUUUGAGA____________________GAUGCAAUGAAAGUGCAGCGAUUUUACCUCACUUUUCACUUUCAUUGCAAGAGUGUUAA
..((((.........)))).(((....))).................................(((((((((((((.((.((.......)).))...))))))))))))).......... (-14.36 = -15.25 +   0.89)

alignment

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secondary structure

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Window 2

Location 27,304,198 – 27,304,291
Length 93
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 79.87
Mean single sequence MFE -27.03
Consensus MFE -18.33
Energy contribution -19.42
Covariance contribution 1.08
Combinations/Pair 1.10
Mean z-score -3.46
Structure conservation index 0.68
SVM decision value 1.78
SVM RNA-class probability 0.976761
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27304198 93 - 27905053
UUAACACUCUUGCAAUGAAAGUGAAAAGUGAGGUAAAAUCGAUGAACUUUCAUUGCAGC--------------------UCUCAAAAGUGUCCAAAUGGAUCCCUUG------CAAGAA-
.........(((((((((((((......(((.......)))....))))))))))))).--------------------(((...(((.((((....))))..))).------..))).- ( -23.10)
>DroSec_CAF1 9168 93 - 1
UUAACACUCUUGCAAUGAAAGUGAAAAGUAAGGUAAAAUCGCUGCACUUUCAUUGCAUC--------------------UCUCAAAAGUGUCCAAAUGGAUCCCUUG------CAAGAA-
..........(((((((((((((...((..(.......)..)).)))))))))))))..--------------------(((...(((.((((....))))..))).------..))).- ( -26.10)
>DroSim_CAF1 9591 93 - 1
UUAACACUCUUGCAAUGAAAGUGAAAAGUAAGGUAAAAUCUCUGCACUUUCAUUGCAUC--------------------UCUCAAAAGUGUCCAAAUGGAUCCCUUG------CAAGAA-
..........(((((((((((((...((..((((...)))))).)))))))))))))..--------------------(((...(((.((((....))))..))).------..))).- ( -24.90)
>DroEre_CAF1 9408 93 - 1
UUAACACUCUUGCAAUGAAAGUGAAAAGUGAUGUAAAAUCGCUGCGCUUUCAUUGCAUC--------------------UCUCAAAACUGUCCAAAUGGAUCCCUUG------CAAGAA-
..........(((((((((((((...((((((.....)))))).)))))))))))))((--------------------(..(((....((((....))))...)))------..))).- ( -32.10)
>DroYak_CAF1 5468 93 - 1
UUAACACUCUUGCAAUGAAAGUGAAAAGUGAGGUAAAAUCGCUGCACUUUCAUUGCAUC--------------------UCUCAUCGCUGUCCAAAUGGAUCCCUUG------CCAGAU-
..........(((((((((((((...(((((.......))))).)))))))))))))((--------------------(..((.....((((....))))....))------..))).- ( -29.80)
>DroAna_CAF1 10593 118 - 1
UUAACACGCUUGCAAGGAAAGUGAAAAGCAC--UGAAAUCGCUGCACUUUCGUGGCAUCUACAUACGAGGCUGAACAACUCUUUAACCUCUGCUAAUGAUUCCUCUGAUGCUCCGAGAUC
......(((((.......)))))....(((.--((....)).)))..(((((..(((((.......((((.((((......)))).)))).......((....)).)))))..))))).. ( -26.20)
>consensus
UUAACACUCUUGCAAUGAAAGUGAAAAGUAAGGUAAAAUCGCUGCACUUUCAUUGCAUC____________________UCUCAAAACUGUCCAAAUGGAUCCCUUG______CAAGAA_
..........(((((((((((((...(((...........))).)))))))))))))................................((((....))))................... (-18.33 = -19.42 +   1.08)

alignment

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secondary structure

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Window 3

Location 27,304,231 – 27,304,331
Length 100
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 84.88
Mean single sequence MFE -29.85
Consensus MFE -23.37
Energy contribution -24.15
Covariance contribution 0.78
Combinations/Pair 1.12
Mean z-score -2.42
Structure conservation index 0.78
SVM decision value 0.57
SVM RNA-class probability 0.786763
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27304231 100 + 27905053
A--------------------GCUGCAAUGAAAGUUCAUCGAUUUUACCUCACUUUUCACUUUCAUUGCAAGAGUGUUAACAAUUUGAGCGUGGCCCUAAUGAUGGCACAUGCAGGUUAC
(--------------------((((((((((((((.......................)))))))))))...................((((((((........))).))))).)))).. ( -25.40)
>DroSec_CAF1 9201 100 + 1
A--------------------GAUGCAAUGAAAGUGCAGCGAUUUUACCUUACUUUUCACUUUCAUUGCAAGAGUGUUAACAAUCUGAGCGUGGCUCUAAUGAUGGCUCAUGCAGGUUAC
.--------------------..(((((((((((((.((..(.......)..))...)))))))))))))(((.((....)).)))..((((((((........))).)))))....... ( -28.20)
>DroSim_CAF1 9624 100 + 1
A--------------------GAUGCAAUGAAAGUGCAGAGAUUUUACCUUACUUUUCACUUUCAUUGCAAGAGUGUUAACAAUCUGAGCGUGGCCCUAAUGAUGGCUCAUGCAGGUUAC
.--------------------..(((((((((((((.((((...........)))).)))))))))))))(((.((....)).)))..((((((((........))).)))))....... ( -33.60)
>DroEre_CAF1 9441 100 + 1
A--------------------GAUGCAAUGAAAGCGCAGCGAUUUUACAUCACUUUUCACUUUCAUUGCAAGAGUGUUAACAAUUUGAGCAUGGCCCUAAUGAUGGCUCAUGCAGGUUAC
.--------------------..(((((((((((.(.((.(((.....))).))...).)))))))))))..................((((((((........))).)))))....... ( -28.10)
>DroYak_CAF1 5501 100 + 1
A--------------------GAUGCAAUGAAAGUGCAGCGAUUUUACCUCACUUUUCACUUUCAUUGCAAGAGUGUUAACAAUUUGAGCAUGGCCCUAAUGAUGGCUCAUGCAGGUUAC
.--------------------..(((((((((((((.((.((.......)).))...)))))))))))))..................((((((((........))).)))))....... ( -30.80)
>DroAna_CAF1 10633 115 + 1
AGUUGUUCAGCCUCGUAUGUAGAUGCCACGAAAGUGCAGCGAUUUCA--GUGCUUUUCACUUUCCUUGCAAGCGUGUUAACAAUU---GCUUGGCCCUAAUGACGUCUCAUGCAGGUUAU
........(((((.(((((.(((((.((.(((((((.((((......--.))))...)))))))....(((((.((....))...---))))).......)).))))))))))))))).. ( -33.00)
>consensus
A____________________GAUGCAAUGAAAGUGCAGCGAUUUUACCUCACUUUUCACUUUCAUUGCAAGAGUGUUAACAAUUUGAGCGUGGCCCUAAUGAUGGCUCAUGCAGGUUAC
.......................(((((((((((((.((.((.......)).))...)))))))))))))..................((((((((........))).)))))....... (-23.37 = -24.15 +   0.78)

alignment

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secondary structure

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dotplot

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Window 4

Location 27,304,231 – 27,304,331
Length 100
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 84.88
Mean single sequence MFE -30.65
Consensus MFE -22.13
Energy contribution -23.05
Covariance contribution 0.92
Combinations/Pair 1.09
Mean z-score -3.22
Structure conservation index 0.72
SVM decision value 0.65
SVM RNA-class probability 0.812155
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27304231 100 - 27905053
GUAACCUGCAUGUGCCAUCAUUAGGGCCACGCUCAAAUUGUUAACACUCUUGCAAUGAAAGUGAAAAGUGAGGUAAAAUCGAUGAACUUUCAUUGCAGC--------------------U
.......((.((.(((........))))).)).................(((((((((((((......(((.......)))....))))))))))))).--------------------. ( -24.80)
>DroSec_CAF1 9201 100 - 1
GUAACCUGCAUGAGCCAUCAUUAGAGCCACGCUCAGAUUGUUAACACUCUUGCAAUGAAAGUGAAAAGUAAGGUAAAAUCGCUGCACUUUCAUUGCAUC--------------------U
.((((.....(((((..((....)).....)))))....)))).......(((((((((((((...((..(.......)..)).)))))))))))))..--------------------. ( -27.60)
>DroSim_CAF1 9624 100 - 1
GUAACCUGCAUGAGCCAUCAUUAGGGCCACGCUCAGAUUGUUAACACUCUUGCAAUGAAAGUGAAAAGUAAGGUAAAAUCUCUGCACUUUCAUUGCAUC--------------------U
.......((.((.(((........))))).))..(((.((....)).)))(((((((((((((...((..((((...)))))).)))))))))))))..--------------------. ( -27.70)
>DroEre_CAF1 9441 100 - 1
GUAACCUGCAUGAGCCAUCAUUAGGGCCAUGCUCAAAUUGUUAACACUCUUGCAAUGAAAGUGAAAAGUGAUGUAAAAUCGCUGCGCUUUCAUUGCAUC--------------------U
.......(((((.(((........))))))))..................(((((((((((((...((((((.....)))))).)))))))))))))..--------------------. ( -38.20)
>DroYak_CAF1 5501 100 - 1
GUAACCUGCAUGAGCCAUCAUUAGGGCCAUGCUCAAAUUGUUAACACUCUUGCAAUGAAAGUGAAAAGUGAGGUAAAAUCGCUGCACUUUCAUUGCAUC--------------------U
.......(((((.(((........))))))))..................(((((((((((((...(((((.......))))).)))))))))))))..--------------------. ( -36.90)
>DroAna_CAF1 10633 115 - 1
AUAACCUGCAUGAGACGUCAUUAGGGCCAAGC---AAUUGUUAACACGCUUGCAAGGAAAGUGAAAAGCAC--UGAAAUCGCUGCACUUUCGUGGCAUCUACAUACGAGGCUGAACAACU
....((((.((((....))))))))((((.((---((.(((....))).))))...(((((((...(((..--.......))).))))))).))))........................ ( -28.70)
>consensus
GUAACCUGCAUGAGCCAUCAUUAGGGCCACGCUCAAAUUGUUAACACUCUUGCAAUGAAAGUGAAAAGUAAGGUAAAAUCGCUGCACUUUCAUUGCAUC____________________U
.......((.((.(((........))))).))..................(((((((((((((...(((...........))).)))))))))))))....................... (-22.13 = -23.05 +   0.92)

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 13:50:41 2006