Locus 1491

Sequence ID X_DroMel_CAF1
Location 4,422,012 – 4,422,205
Length 193
Max. P 0.999647
window2389 window2390 window2391 window2392

overview

Window 9

Location 4,422,012 – 4,422,131
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.98
Mean single sequence MFE -28.19
Consensus MFE -25.53
Energy contribution -26.65
Covariance contribution 1.12
Combinations/Pair 1.09
Mean z-score -1.30
Structure conservation index 0.91
SVM decision value 0.66
SVM RNA-class probability 0.816043
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4422012 119 - 22224390
CUGGUCGUAAAGCCCAUGGCAUUGAUCAUAAUCGAUGCCACAGGAUAAUAAACUCUAGGAAUGCACUGCAA-GUCCAUUGAUGACUGCAGCAGGUUCAUAAAAAGAUACUGAAAGUAUCA
((((........((..((((((((((....))))))))))..))..........))))((((...(((((.-(((.......))))))))...)))).......(((((.....))))). ( -34.77)
>DroSec_CAF1 24488 120 - 1
CUGGUCAUAAAGCCCAUGGCAUUGAUCAUAAUCGAUGCCACAGGAUAAUAAACUCUAGGAAUGCACUGCACUGUCCAUUGAUGACUGCAGCAGGUUCAUAAAAAGAUACUGAAAGAAUCA
..((((((....((..((((((((((....))))))))))..)).............(((.(((...)))...)))....))))))....(((..((.......))..)))......... ( -29.10)
>DroSim_CAF1 25800 120 - 1
CUGGUCGUAAAGCCCAUGGCAUUGAUCAUAAUCGAUGCCACAGGAUAAUAAACUCUAGGAAUGCACUGCACUGUCCAUUGAUGACUGCAGCAGGUUCAUAAAAAGAUACUGAAAGAAUCA
..((((((....((..((((((((((....))))))))))..)).............(((.(((...)))...)))....))))))....(((..((.......))..)))......... ( -28.70)
>DroEre_CAF1 25475 119 - 1
CUGGUCGUAAAGCCCAUGGCAUUGAUCAUAAUCGAAGGCGCAGGAUAAUAAACUCUAGGAAUGCACUGCAA-GUCCAUUGAAGGCUGCAGCAGGUUCAUAAAAAGAUUGGGAAAGAAUCG
(..(((.......((.((((.(((((....)))))..)).))))..............((((...(((((.-(((.......))))))))...)))).......)))..).......... ( -23.10)
>DroYak_CAF1 25056 119 - 1
CUGGUCGUAAAGCCCAUGGCAUUGAUCAUAAUCGAAGCCACAGGAUAAUAAACUCUAGGAAUGCACUGCAA-GUCCAUUGAAGACUGCAUCAGGUUCAUAAAAAGAUUCUGAAAAAAUCG
((((........((..((((.(((((....))))).))))..))..........))))((......((((.-(((.......)))))))((((..((.......))..)))).....)). ( -25.27)
>consensus
CUGGUCGUAAAGCCCAUGGCAUUGAUCAUAAUCGAUGCCACAGGAUAAUAAACUCUAGGAAUGCACUGCAA_GUCCAUUGAUGACUGCAGCAGGUUCAUAAAAAGAUACUGAAAGAAUCA
((((........((..((((((((((....))))))))))..))..........))))((((...(((((..(((.......))))))))...)))).......(((((.....))))). (-25.53 = -26.65 +   1.12)

alignment

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secondary structure

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Window 0

Location 4,422,052 – 4,422,166
Length 114
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.03
Mean single sequence MFE -38.86
Consensus MFE -33.72
Energy contribution -34.40
Covariance contribution 0.68
Combinations/Pair 1.05
Mean z-score -3.14
Structure conservation index 0.87
SVM decision value 3.83
SVM RNA-class probability 0.999647
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4422052 114 + 22224390
CAAUGGAC-UUGCAGUGCAUUCCUAGAGUUUAUUAUCCUGUGGCAUCGAUUAUGAUCAAUGCCAUGGGCUUUACGACCAGCAACUUGGAUCGUUAACUGGGAGUCCAUUAAACCG-----
.(((((((-((.((((....................((((((((((.(((....))).))))))))))....((((((((....)))).))))..)))).)))))))))......----- ( -41.30)
>DroSec_CAF1 24528 115 + 1
CAAUGGACAGUGCAGUGCAUUCCUAGAGUUUAUUAUCCUGUGGCAUCGAUUAUGAUCAAUGCCAUGGGCUUUAUGACCAGCAACUUGGAUCGUUAACUGGGAGUCCAUUAAACCG-----
.(((((((.((((...))))((((((..........((((((((((.(((....))).))))))))))....((((((((....)))).))))...)))))))))))))......----- ( -39.60)
>DroSim_CAF1 25840 115 + 1
CAAUGGACAGUGCAGUGCAUUCCUAGAGUUUAUUAUCCUGUGGCAUCGAUUAUGAUCAAUGCCAUGGGCUUUACGACCAGCAACUUGGAUCGUUAACUGGGAGUCCAUUAAACCG-----
.(((((((.((((...))))((((((..........((((((((((.(((....))).))))))))))....((((((((....)))).))))...)))))))))))))......----- ( -41.40)
>DroEre_CAF1 25515 114 + 1
CAAUGGAC-UUGCAGUGCAUUCCUAGAGUUUAUUAUCCUGCGCCUUCGAUUAUGAUCAAUGCCAUGGGCUUUACGACCAGCAACUUGGAUCGUUAACUGCGGGUCCAUUAAACCG-----
.(((((((-(((((((((..(((..(((((......((((.((.((.(((....))))).)))).))(((........)))))))))))..))..))))))))))))))......----- ( -34.10)
>DroYak_CAF1 25096 119 + 1
CAAUGGAC-UUGCAGUGCAUUCCUAGAGUUUAUUAUCCUGUGGCUUCGAUUAUGAUCAAUGCCAUGGGCUUUACGACCAGCAACUUGGAUCGUUAACUGGGAGUCCAUUAAACCGUAGCU
.(((((((-((.((((....................((((((((...(((....)))...))))))))....((((((((....)))).))))..)))).)))))))))........... ( -37.90)
>consensus
CAAUGGAC_UUGCAGUGCAUUCCUAGAGUUUAUUAUCCUGUGGCAUCGAUUAUGAUCAAUGCCAUGGGCUUUACGACCAGCAACUUGGAUCGUUAACUGGGAGUCCAUUAAACCG_____
.(((((((..(((...))).((((((..........((((((((((.(((....))).))))))))))....((((((((....)))).))))...)))))))))))))........... (-33.72 = -34.40 +   0.68)

alignment

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secondary structure

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dotplot

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Window 1

Location 4,422,052 – 4,422,166
Length 114
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.03
Mean single sequence MFE -34.06
Consensus MFE -29.88
Energy contribution -30.32
Covariance contribution 0.44
Combinations/Pair 1.03
Mean z-score -2.20
Structure conservation index 0.88
SVM decision value 2.74
SVM RNA-class probability 0.996739
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4422052 114 - 22224390
-----CGGUUUAAUGGACUCCCAGUUAACGAUCCAAGUUGCUGGUCGUAAAGCCCAUGGCAUUGAUCAUAAUCGAUGCCACAGGAUAAUAAACUCUAGGAAUGCACUGCAA-GUCCAUUG
-----.....(((((((((..((((..((((.(((......)))))))....((..((((((((((....))))))))))..))....................))))..)-)))))))) ( -37.20)
>DroSec_CAF1 24528 115 - 1
-----CGGUUUAAUGGACUCCCAGUUAACGAUCCAAGUUGCUGGUCAUAAAGCCCAUGGCAUUGAUCAUAAUCGAUGCCACAGGAUAAUAAACUCUAGGAAUGCACUGCACUGUCCAUUG
-----.....(((((((((((.((((....((((.....(((........)))...((((((((((....))))))))))..))))....))))...))).(((...)))..)))))))) ( -34.00)
>DroSim_CAF1 25840 115 - 1
-----CGGUUUAAUGGACUCCCAGUUAACGAUCCAAGUUGCUGGUCGUAAAGCCCAUGGCAUUGAUCAUAAUCGAUGCCACAGGAUAAUAAACUCUAGGAAUGCACUGCACUGUCCAUUG
-----.....(((((((((((.((((.((((.(((......)))))))....((..((((((((((....))))))))))..))......))))...))).(((...)))..)))))))) ( -35.30)
>DroEre_CAF1 25515 114 - 1
-----CGGUUUAAUGGACCCGCAGUUAACGAUCCAAGUUGCUGGUCGUAAAGCCCAUGGCAUUGAUCAUAAUCGAAGGCGCAGGAUAAUAAACUCUAGGAAUGCACUGCAA-GUCCAUUG
-----.....((((((((..(((((...((.(((.((.(.((((((.....(((...))).(((((....))))).))).))).).........)).))).)).)))))..-)))))))) ( -29.50)
>DroYak_CAF1 25096 119 - 1
AGCUACGGUUUAAUGGACUCCCAGUUAACGAUCCAAGUUGCUGGUCGUAAAGCCCAUGGCAUUGAUCAUAAUCGAAGCCACAGGAUAAUAAACUCUAGGAAUGCACUGCAA-GUCCAUUG
(((....)))(((((((((..((((..((((.(((......)))))))....((..((((.(((((....))))).))))..))....................))))..)-)))))))) ( -34.30)
>consensus
_____CGGUUUAAUGGACUCCCAGUUAACGAUCCAAGUUGCUGGUCGUAAAGCCCAUGGCAUUGAUCAUAAUCGAUGCCACAGGAUAAUAAACUCUAGGAAUGCACUGCAA_GUCCAUUG
..........((((((((...((((...((.(((.(((((((........)))((.((((((((((....))))))))))..))......))))...))).)).))))....)))))))) (-29.88 = -30.32 +   0.44)

alignment

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secondary structure

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Window 2

Location 4,422,091 – 4,422,205
Length 114
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.85
Mean single sequence MFE -31.78
Consensus MFE -28.98
Energy contribution -29.22
Covariance contribution 0.24
Combinations/Pair 1.09
Mean z-score -1.67
Structure conservation index 0.91
SVM decision value 1.93
SVM RNA-class probability 0.982960
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4422091 114 - 22224390
CAGGUUUUAUGUCUGACACGUUCUUUUAGCUACCUUCCU------CGGUUUAAUGGACUCCCAGUUAACGAUCCAAGUUGCUGGUCGUAAAGCCCAUGGCAUUGAUCAUAAUCGAUGCCA
..(((((((((........((((..((((..(((.....------.))))))).))))..(((((.(((.......)))))))).)))))))))..((((((((((....)))))))))) ( -34.50)
>DroSec_CAF1 24568 114 - 1
CAGGUUUUAUGUCUGACACGUUCUUUUGGCUACCUUCCU------CGGUUUAAUGGACUCCCAGUUAACGAUCCAAGUUGCUGGUCAUAAAGCCCAUGGCAUUGAUCAUAAUCGAUGCCA
..(((((((((........((((..((((..(((.....------.))))))).))))..(((((.(((.......)))))))).)))))))))..((((((((((....)))))))))) ( -34.50)
>DroSim_CAF1 25880 114 - 1
CAGGUUUUAUGUCUGACACGUUCUUUUGGCUACCUUCCU------CGGUUUAAUGGACUCCCAGUUAACGAUCCAAGUUGCUGGUCGUAAAGCCCAUGGCAUUGAUCAUAAUCGAUGCCA
..(((((((((........((((..((((..(((.....------.))))))).))))..(((((.(((.......)))))))).)))))))))..((((((((((....)))))))))) ( -34.10)
>DroEre_CAF1 25554 114 - 1
CAGGUUUUAUGUCUGACACGUUCUUUUAGCUACCUUCCU------CGGUUUAAUGGACCCGCAGUUAACGAUCCAAGUUGCUGGUCGUAAAGCCCAUGGCAUUGAUCAUAAUCGAAGGCG
..(((((((((.(......((((..((((..(((.....------.))))))).))))...((((.(((.......)))))))).)))))))))....((.(((((....)))))..)). ( -23.50)
>DroYak_CAF1 25135 120 - 1
CAGGUUUUAUGUCUGACACGUUCUUUUAGCUACGUUCCUUAGCUACGGUUUAAUGGACUCCCAGUUAACGAUCCAAGUUGCUGGUCGUAAAGCCCAUGGCAUUGAUCAUAAUCGAAGCCA
..(((((((((((((((.(((......(((((.......)))))))))))....))))..(((((.(((.......))))))))..))))))))..((((.(((((....))))).)))) ( -32.30)
>consensus
CAGGUUUUAUGUCUGACACGUUCUUUUAGCUACCUUCCU______CGGUUUAAUGGACUCCCAGUUAACGAUCCAAGUUGCUGGUCGUAAAGCCCAUGGCAUUGAUCAUAAUCGAUGCCA
..(((((((((........((((....((((...............))))....))))..(((((.(((.......)))))))).)))))))))..((((((((((....)))))))))) (-28.98 = -29.22 +   0.24)

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 10:10:54 2006