Locus 794

Sequence ID 3L_DroMel_CAF1
Location 2,370,211 – 2,370,337
Length 126
Max. P 0.999894
window1222 window1223 window1224 window1225

overview

Window 2

Location 2,370,211 – 2,370,305
Length 94
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 78.59
Mean single sequence MFE -29.62
Consensus MFE -20.70
Energy contribution -22.32
Covariance contribution 1.61
Combinations/Pair 1.21
Mean z-score -1.07
Structure conservation index 0.70
SVM decision value 0.02
SVM RNA-class probability 0.544632
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2370211 94 + 23771897
CACUUUCUCUAAGUGUAAGUCUGGAUCUGGUCCUAAGUUCCA--UUGCC---UCCCGCCCCUUCCUUUAUGGU-UUUUUGAGCAGCUGCAUGAGGGGCGG-----------
(((((.....)))))......((((.((.......)).))))--.....---..(((((((((((.....)).-.......((....))..)))))))))----------- ( -27.50)
>DroSec_CAF1 118906 93 + 1
CACUUUCUCUAAGUGUAAGUCUGGAUCUGGUCCUAAGACCCA--UUGCC---UCCCGCCCCUUCCUUUAUGGU-U-UUUGAGCAGCUGCAUGAGGGGCGG-----------
(((((.....))))).......((....((((....))))..--...))---..(((((((((((.....)).-.-.....((....))..)))))))))----------- ( -28.90)
>DroSim_CAF1 119989 93 + 1
CACUUUCUCUAAGUGUAAGUCUGGAUCUGGUCCUAAGACCCA--UUGCC---UCCCGCCCCUUCCUUUAUGGU-U-UUUGAGCAGCUGCAUGAGGGGCGG-----------
(((((.....))))).......((....((((....))))..--...))---..(((((((((((.....)).-.-.....((....))..)))))))))----------- ( -28.90)
>DroEre_CAF1 126225 93 + 1
UACUUUCUUCAAGUGUAAGCCUGGAUCUGGUCCUAAGAUCCA--UUGCC---UCCCGCCCCUUCCUU-AUGGUUU-UUUGAGCAGCUGCAGGAGAGGCGG-----------
(((((.....)))))...((((((((((.......)))))).--....(---(((.((..((..(((-(......-..)))).))..)).))))))))..----------- ( -26.30)
>DroYak_CAF1 123403 93 + 1
UACUUCCUCCAAGUGUAAGCCUGGAUCUGGUCCUAAGAUCCA--UUGCC---UCCCGCCCCUUCCUUUAUGGU-U-UCUGAGCAGCUGUAGGUGGGGCGG-----------
(((((.....)))))...((.(((((((.......)))))))--..)).---..(((((((..(((..(((((-(-.......))))))))).)))))))----------- ( -31.30)
>DroAna_CAF1 113552 104 + 1
CCUUUUCUCACGGUGUGCCCCUGGGAUGGGACCUAAGAUCCCGCCUGCAUCUCCCCGCCCCACCCUUC------U-UCUGAGCAGCUUUUUGGGGGGCGAUGGAGUAGGAU
(((...(((..((.((((....(((.(((((.......))))))))))))..)).((((((.((....------.-.((....))......))))))))...))).))).. ( -34.80)
>consensus
CACUUUCUCUAAGUGUAAGCCUGGAUCUGGUCCUAAGAUCCA__UUGCC___UCCCGCCCCUUCCUUUAUGGU_U_UUUGAGCAGCUGCAUGAGGGGCGG___________
..............((((...(((((((.......)))))))..))))......(((((((((((.....)).........((....))..)))))))))........... (-20.70 = -22.32 +   1.61)

alignment

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secondary structure

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Window 3

Location 2,370,211 – 2,370,305
Length 94
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 78.59
Mean single sequence MFE -31.93
Consensus MFE -18.80
Energy contribution -19.30
Covariance contribution 0.50
Combinations/Pair 1.25
Mean z-score -2.06
Structure conservation index 0.59
SVM decision value 0.88
SVM RNA-class probability 0.873489
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2370211 94 - 23771897
-----------CCGCCCCUCAUGCAGCUGCUCAAAAA-ACCAUAAAGGAAGGGGCGGGA---GGCAA--UGGAACUUAGGACCAGAUCCAGACUUACACUUAGAGAAAGUG
-----------((((((((...((....)).......-.((.....)).))))))))((---(....--((((.((.......)).))))..))).(((((.....))))) ( -27.50)
>DroSec_CAF1 118906 93 - 1
-----------CCGCCCCUCAUGCAGCUGCUCAAA-A-ACCAUAAAGGAAGGGGCGGGA---GGCAA--UGGGUCUUAGGACCAGAUCCAGACUUACACUUAGAGAAAGUG
-----------((((((((...((....)).....-.-.((.....)).))))))))((---(....--(((((((.......)))))))..))).(((((.....))))) ( -31.50)
>DroSim_CAF1 119989 93 - 1
-----------CCGCCCCUCAUGCAGCUGCUCAAA-A-ACCAUAAAGGAAGGGGCGGGA---GGCAA--UGGGUCUUAGGACCAGAUCCAGACUUACACUUAGAGAAAGUG
-----------((((((((...((....)).....-.-.((.....)).))))))))((---(....--(((((((.......)))))))..))).(((((.....))))) ( -31.50)
>DroEre_CAF1 126225 93 - 1
-----------CCGCCUCUCCUGCAGCUGCUCAAA-AAACCAU-AAGGAAGGGGCGGGA---GGCAA--UGGAUCUUAGGACCAGAUCCAGGCUUACACUUGAAGAAAGUA
-----------(((((((((((.............-.......-.))).)))))))).(---(((..--(((((((.......))))))).))))..((((.....)))). ( -30.80)
>DroYak_CAF1 123403 93 - 1
-----------CCGCCCCACCUACAGCUGCUCAGA-A-ACCAUAAAGGAAGGGGCGGGA---GGCAA--UGGAUCUUAGGACCAGAUCCAGGCUUACACUUGGAGGAAGUA
-----------(((((((........((....)).-.-.((.....))..))))))).(---(((..--(((((((.......))))))).))))..((((.....)))). ( -30.00)
>DroAna_CAF1 113552 104 - 1
AUCCUACUCCAUCGCCCCCCAAAAAGCUGCUCAGA-A------GAAGGGUGGGGCGGGGAGAUGCAGGCGGGAUCUUAGGUCCCAUCCCAGGGGCACACCGUGAGAAAAGG
..(((.((((.(((((((((......((....)).-.------....)).)))))))))))........(((((.....))))).((.((.((.....)).)).))..))) ( -40.30)
>consensus
___________CCGCCCCUCAUGCAGCUGCUCAAA_A_ACCAUAAAGGAAGGGGCGGGA___GGCAA__UGGAUCUUAGGACCAGAUCCAGACUUACACUUAGAGAAAGUG
...........(((((((((...........................)).)))))))............(((((((.......)))))))..................... (-18.80 = -19.30 +   0.50)

alignment

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secondary structure

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dotplot

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Window 4

Location 2,370,245 – 2,370,337
Length 92
Sequences 5
Columns 94
Reading direction forward
Mean pairwise identity 91.04
Mean single sequence MFE -36.04
Consensus MFE -33.68
Energy contribution -33.76
Covariance contribution 0.08
Combinations/Pair 1.08
Mean z-score -2.00
Structure conservation index 0.93
SVM decision value 2.97
SVM RNA-class probability 0.997950
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2370245 92 + 23771897
AAGUUCCAUUGCCUCCCGCCCCUUCCUUUAUGGU-UUUUUGAGCAGCUGCAUGAGGGGCGGGGAGUA-CAACGAGGUGGACUCCUUGUGGCUGU
..........((((((((((((((((.....)).-.......((....))..)))))))))))....-..((((((......)))))))))... ( -36.10)
>DroSec_CAF1 118940 90 + 1
AAGACCCAUUGCCUCCCGCCCCUUCCUUUAUGGU-U-UUUGAGCAGCUGCAUGAGGGGCGGGGUGGACCAACGAGGUGGACUCCUUGUGGCU--
..........(((..(((((((.(((((((((((-(-.......)))..))))))))).)))))))....((((((......))))))))).-- ( -36.30)
>DroSim_CAF1 120023 90 + 1
AAGACCCAUUGCCUCCCGCCCCUUCCUUUAUGGU-U-UUUGAGCAGCUGCAUGAGGGGCGGGGUGGACCAACGAGGUGGACUCCUUGUGGCU--
..........(((..(((((((.(((((((((((-(-.......)))..))))))))).)))))))....((((((......))))))))).-- ( -36.30)
>DroEre_CAF1 126259 89 + 1
AAGAUCCAUUGCCUCCCGCCCCUUCCUU-AUGGUUU-UUUGAGCAGCUGCAGGAGAGGCGGGGUGU-CCAACAAGGUGGACUCCUUGUGGCU--
..........((((((((((..(((((.-..((((.-.......))))..))))).)))))))...-...((((((......))))))))).-- ( -31.00)
>DroYak_CAF1 123437 89 + 1
AAGAUCCAUUGCCUCCCGCCCCUUCCUUUAUGGU-U-UCUGAGCAGCUGUAGGUGGGGCGGGGAGU-CCAACGAGGUGGACUCCUUGUGGCA--
.........((((..(((((((..(((..(((((-(-.......))))))))).)))))))(((((-(((......))))))))....))))-- ( -40.50)
>consensus
AAGAUCCAUUGCCUCCCGCCCCUUCCUUUAUGGU_U_UUUGAGCAGCUGCAUGAGGGGCGGGGUGUACCAACGAGGUGGACUCCUUGUGGCU__
..........((((((((((((((((.....)).........((....))..))))))))))).......((((((......)))))))))... (-33.68 = -33.76 +   0.08)

alignment

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secondary structure

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dotplot

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Window 5

Location 2,370,245 – 2,370,337
Length 92
Sequences 5
Columns 94
Reading direction reverse
Mean pairwise identity 91.04
Mean single sequence MFE -35.00
Consensus MFE -31.66
Energy contribution -31.54
Covariance contribution -0.12
Combinations/Pair 1.10
Mean z-score -2.87
Structure conservation index 0.90
SVM decision value 4.42
SVM RNA-class probability 0.999894
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2370245 92 - 23771897
ACAGCCACAAGGAGUCCACCUCGUUG-UACUCCCCGCCCCUCAUGCAGCUGCUCAAAAA-ACCAUAAAGGAAGGGGCGGGAGGCAAUGGAACUU
...(((((((.(((.....))).)))-)....(((((((((...((....)).......-.((.....)).))))))))).))).......... ( -35.20)
>DroSec_CAF1 118940 90 - 1
--AGCCACAAGGAGUCCACCUCGUUGGUCCACCCCGCCCCUCAUGCAGCUGCUCAAA-A-ACCAUAAAGGAAGGGGCGGGAGGCAAUGGGUCUU
--.(((.(((.(((.....))).)))......(((((((((...((....)).....-.-.((.....)).))))))))).))).......... ( -34.30)
>DroSim_CAF1 120023 90 - 1
--AGCCACAAGGAGUCCACCUCGUUGGUCCACCCCGCCCCUCAUGCAGCUGCUCAAA-A-ACCAUAAAGGAAGGGGCGGGAGGCAAUGGGUCUU
--.(((.(((.(((.....))).)))......(((((((((...((....)).....-.-.((.....)).))))))))).))).......... ( -34.30)
>DroEre_CAF1 126259 89 - 1
--AGCCACAAGGAGUCCACCUUGUUGG-ACACCCCGCCUCUCCUGCAGCUGCUCAAA-AAACCAU-AAGGAAGGGGCGGGAGGCAAUGGAUCUU
--.(((.......(((((......)))-))..((((((((((((.............-.......-.))).))))))))).))).......... ( -33.50)
>DroYak_CAF1 123437 89 - 1
--UGCCACAAGGAGUCCACCUCGUUGG-ACUCCCCGCCCCACCUACAGCUGCUCAGA-A-ACCAUAAAGGAAGGGGCGGGAGGCAAUGGAUCUU
--((((....((((((((......)))-)))))(((((((........((....)).-.-.((.....))..)))))))..))))......... ( -37.70)
>consensus
__AGCCACAAGGAGUCCACCUCGUUGGUACACCCCGCCCCUCAUGCAGCUGCUCAAA_A_ACCAUAAAGGAAGGGGCGGGAGGCAAUGGAUCUU
...(((.(((.(((.....))).)))......((((((((....((....)).........((.....))..)))))))).))).......... (-31.66 = -31.54 +  -0.12)

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 09:51:24 2006