Locus 1187

Sequence ID 3R_DroMel_CAF1
Location 3,578,439 – 3,578,571
Length 132
Max. P 0.999936
window1940 window1941 window1942 window1943

overview

Window 0

Location 3,578,439 – 3,578,533
Length 94
Sequences 5
Columns 94
Reading direction forward
Mean pairwise identity 97.66
Mean single sequence MFE -33.14
Consensus MFE -31.84
Energy contribution -31.72
Covariance contribution -0.12
Combinations/Pair 1.07
Mean z-score -3.22
Structure conservation index 0.96
SVM decision value 4.67
SVM RNA-class probability 0.999936
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3578439 94 + 27905053
GAAACGAACCUGCACGUGGCUAACAAAACUGUUGGCCACUUUUUAGCAGAAAAGCGGUAAAUUUAUGGCUGUUGCUGGCAGCAUUUGCGUGCCA
...........((((((((((((((....))))))))))......(((((..(((.(((....))).)))((((....)))).))))))))).. ( -35.00)
>DroSec_CAF1 29374 94 + 1
GAAACAAACCUGCACGUGGCUAACAAAACUGCUGGCCACUUUUUAGCAGAAAAGCGGCAAAUUUAUGGCUGUUGCUGGCAGCAUUUGCGUGCCA
.........((((..(((((((.((....)).)))))))......))))...(((((((..........)))))))((((((....)).)))). ( -29.60)
>DroSim_CAF1 29856 94 + 1
GAAACAAACCUGCACGUGGCUAACAAAACUGUUGGCCACUUUUUAGCAGAAAAGCGGCAAAUUUAUGGCUGUUGCUGGCAGCAUUUGCGUGCCA
.........((((..((((((((((....))))))))))......))))...(((((((..........)))))))((((((....)).)))). ( -33.80)
>DroEre_CAF1 34731 94 + 1
GAAACGAACCUGCACGUGGCUAACAAAACUGUUGGCCACUUUUUAGCAGAAAAGCGGCAAAUUUAUGACUGUUGCUGGCAGCAUUUGCGUGCCA
.........((((..((((((((((....))))))))))......))))...(((((((..........)))))))((((((....)).)))). ( -33.80)
>DroYak_CAF1 21609 94 + 1
GAAACGAACCUGCACGUGGCUAACAAAACUGUUGGCCACUUUUUAGCAGAAAAGCGGCAAAUUUAUGGCUGUUGUUGGCAGCAUUUGCGUGCCA
..(((....((((..((((((((((....))))))))))......))))...((((((.........)))))))))((((((....)).)))). ( -33.50)
>consensus
GAAACGAACCUGCACGUGGCUAACAAAACUGUUGGCCACUUUUUAGCAGAAAAGCGGCAAAUUUAUGGCUGUUGCUGGCAGCAUUUGCGUGCCA
.........((((..((((((((((....))))))))))......))))...(((((((..........)))))))((((((....)).)))). (-31.84 = -31.72 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 1

Location 3,578,439 – 3,578,533
Length 94
Sequences 5
Columns 94
Reading direction reverse
Mean pairwise identity 97.66
Mean single sequence MFE -28.94
Consensus MFE -26.68
Energy contribution -26.36
Covariance contribution -0.32
Combinations/Pair 1.08
Mean z-score -2.37
Structure conservation index 0.92
SVM decision value 3.20
SVM RNA-class probability 0.998730
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3578439 94 - 27905053
UGGCACGCAAAUGCUGCCAGCAACAGCCAUAAAUUUACCGCUUUUCUGCUAAAAAGUGGCCAACAGUUUUGUUAGCCACGUGCAGGUUCGUUUC
(((((.((....)))))))..(((((((...........((......))......(((((.(((......))).))))).....)))).))).. ( -26.90)
>DroSec_CAF1 29374 94 - 1
UGGCACGCAAAUGCUGCCAGCAACAGCCAUAAAUUUGCCGCUUUUCUGCUAAAAAGUGGCCAGCAGUUUUGUUAGCCACGUGCAGGUUUGUUUC
(((((.((....)))))))((....)).(((((((((((((......))......(((((.(((......))).)))))).))))))))))... ( -31.20)
>DroSim_CAF1 29856 94 - 1
UGGCACGCAAAUGCUGCCAGCAACAGCCAUAAAUUUGCCGCUUUUCUGCUAAAAAGUGGCCAACAGUUUUGUUAGCCACGUGCAGGUUUGUUUC
(((((.((....)))))))((....)).(((((((((((((......))......(((((.(((......))).)))))).))))))))))... ( -31.20)
>DroEre_CAF1 34731 94 - 1
UGGCACGCAAAUGCUGCCAGCAACAGUCAUAAAUUUGCCGCUUUUCUGCUAAAAAGUGGCCAACAGUUUUGUUAGCCACGUGCAGGUUCGUUUC
(((((.((....))))))).........(..((((((((((......))......(((((.(((......))).)))))).)))))))..)... ( -27.70)
>DroYak_CAF1 21609 94 - 1
UGGCACGCAAAUGCUGCCAACAACAGCCAUAAAUUUGCCGCUUUUCUGCUAAAAAGUGGCCAACAGUUUUGUUAGCCACGUGCAGGUUCGUUUC
(((((.((....))))))).........(..((((((((((......))......(((((.(((......))).)))))).)))))))..)... ( -27.70)
>consensus
UGGCACGCAAAUGCUGCCAGCAACAGCCAUAAAUUUGCCGCUUUUCUGCUAAAAAGUGGCCAACAGUUUUGUUAGCCACGUGCAGGUUCGUUUC
(((((.((....)))))))...........((((..(((((......))......(((((.(((......))).))))).....)))..)))). (-26.68 = -26.36 +  -0.32)

alignment

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secondary structure

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dotplot

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Window 2

Location 3,578,453 – 3,578,571
Length 118
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 90.84
Mean single sequence MFE -43.30
Consensus MFE -34.56
Energy contribution -35.45
Covariance contribution 0.89
Combinations/Pair 1.17
Mean z-score -3.56
Structure conservation index 0.80
SVM decision value 1.55
SVM RNA-class probability 0.963028
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3578453 118 + 27905053
CGUGGCUAACAAAACUGUUGGCCACUUUUUAGCAGAAAAGCGGUAAAUUUAUGGCUGUUGCUGGCAGCAUUUGCGUGCCAGCAACUUUUUGGGC-ACUC-CUCCACCUGGAAAAAGACGA
.((((((((((....))))))))))((((((((((((((((.(((....))).)))((((((((((((....)).))))))))))))))))((.-....-..))..)))))))....... ( -46.70)
>DroSec_CAF1 29388 118 + 1
CGUGGCUAACAAAACUGCUGGCCACUUUUUAGCAGAAAAGCGGCAAAUUUAUGGCUGUUGCUGGCAGCAUUUGCGUGCCAGCAACUUUUUGGCC-ACUC-CUCCACCUGGAAAAAGACGA
.((((((((...........(((.((((((....)))))).)))............((((((((((((....)).))))))))))...))))))-))..-.(((....)))......... ( -44.90)
>DroSim_CAF1 29870 118 + 1
CGUGGCUAACAAAACUGUUGGCCACUUUUUAGCAGAAAAGCGGCAAAUUUAUGGCUGUUGCUGGCAGCAUUUGCGUGCCAGCAACUUUUUGGGC-ACUC-CCCCACCUGGAAAAAGACGA
(((((((((((....)))))))).((((((..(((...(((.(........).)))((((((((((((....)).))))))))))....((((.-....-.)))).))).))))))))). ( -46.00)
>DroEre_CAF1 34745 118 + 1
CGUGGCUAACAAAACUGUUGGCCACUUUUUAGCAGAAAAGCGGCAAAUUUAUGACUGUUGCUGGCAGCAUUUGCGUGCCAGCAACUUUUUGGGC-UCUC-CUCCACCUGGAAGAAGACGA
.((((((((((....)))))))))).....(((.(((((((((((......)).)))(((((((((((....)).)))))))))))))))..))-).((-.(((....))).))...... ( -44.20)
>DroYak_CAF1 21623 118 + 1
CGUGGCUAACAAAACUGUUGGCCACUUUUUAGCAGAAAAGCGGCAAAUUUAUGGCUGUUGUUGGCAGCAUUUGCGUGCCAGCAACUUUUUGGGC-ACUC-CUCCACCUGGAAAAAGACGU
.((((((((((....))))))))))......((.((((((((((.........))))(((((((((((....)).)))))))))))))))..))-....-.(((....)))......... ( -42.30)
>DroAna_CAF1 25208 114 + 1
CGUGGCAAACAAAACUGUUGGCCACUUUUUAGCAGAAGAACGGCAAAUUUAUGGCC------GCCAGCAUUUGCGUGUUGGCAACUUUUUUGGAUACCGGAAGCACCUGGAAAAAGAUGA
.(((((.((((....)))).))))).......(((((((..(((.........)))------((((((((....))))))))...)))))))....((((......)))).......... ( -35.70)
>consensus
CGUGGCUAACAAAACUGUUGGCCACUUUUUAGCAGAAAAGCGGCAAAUUUAUGGCUGUUGCUGGCAGCAUUUGCGUGCCAGCAACUUUUUGGGC_ACUC_CUCCACCUGGAAAAAGACGA
(((((((((((....)))))))).((((((..(((......(((.........)))((((((((((((....)).)))))))))).....................))).))))))))). (-34.56 = -35.45 +   0.89)

alignment

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secondary structure

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dotplot

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Window 3

Location 3,578,453 – 3,578,571
Length 118
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 90.84
Mean single sequence MFE -42.17
Consensus MFE -31.19
Energy contribution -32.83
Covariance contribution 1.64
Combinations/Pair 1.14
Mean z-score -3.48
Structure conservation index 0.74
SVM decision value 0.34
SVM RNA-class probability 0.696196
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3578453 118 - 27905053
UCGUCUUUUUCCAGGUGGAG-GAGU-GCCCAAAAAGUUGCUGGCACGCAAAUGCUGCCAGCAACAGCCAUAAAUUUACCGCUUUUCUGCUAAAAAGUGGCCAACAGUUUUGUUAGCCACG
.............((..(((-((((-(........((((((((((.((....)))))))))))).....((....)).))))))))..)).....(((((.(((......))).))))). ( -42.90)
>DroSec_CAF1 29388 118 - 1
UCGUCUUUUUCCAGGUGGAG-GAGU-GGCCAAAAAGUUGCUGGCACGCAAAUGCUGCCAGCAACAGCCAUAAAUUUGCCGCUUUUCUGCUAAAAAGUGGCCAGCAGUUUUGUUAGCCACG
.............((..(((-((((-(((......((((((((((.((....))))))))))))....(......)))))))))))..)).....(((((.(((......))).))))). ( -49.60)
>DroSim_CAF1 29870 118 - 1
UCGUCUUUUUCCAGGUGGGG-GAGU-GCCCAAAAAGUUGCUGGCACGCAAAUGCUGCCAGCAACAGCCAUAAAUUUGCCGCUUUUCUGCUAAAAAGUGGCCAACAGUUUUGUUAGCCACG
.............((..(..-((((-(........((((((((((.((....)))))))))))).((.........)))))))..)..)).....(((((.(((......))).))))). ( -45.40)
>DroEre_CAF1 34745 118 - 1
UCGUCUUCUUCCAGGUGGAG-GAGA-GCCCAAAAAGUUGCUGGCACGCAAAUGCUGCCAGCAACAGUCAUAAAUUUGCCGCUUUUCUGCUAAAAAGUGGCCAACAGUUUUGUUAGCCACG
..(..(((((((....))))-))).-.).......((((((((((.((....))))))))))))...............((......))......(((((.(((......))).))))). ( -44.10)
>DroYak_CAF1 21623 118 - 1
ACGUCUUUUUCCAGGUGGAG-GAGU-GCCCAAAAAGUUGCUGGCACGCAAAUGCUGCCAACAACAGCCAUAAAUUUGCCGCUUUUCUGCUAAAAAGUGGCCAACAGUUUUGUUAGCCACG
.............((..(((-((((-(........((((.(((((.((....))))))).)))).((.........))))))))))..)).....(((((.(((......))).))))). ( -38.80)
>DroAna_CAF1 25208 114 - 1
UCAUCUUUUUCCAGGUGCUUCCGGUAUCCAAAAAAGUUGCCAACACGCAAAUGCUGGC------GGCCAUAAAUUUGCCGUUCUUCUGCUAAAAAGUGGCCAACAGUUUUGUUUGCCACG
.(((((......))))).....((((..(((((..(((((((.((......)).))))------((((((......((.(.....).))......)))))))))..)))))..))))... ( -32.20)
>consensus
UCGUCUUUUUCCAGGUGGAG_GAGU_GCCCAAAAAGUUGCUGGCACGCAAAUGCUGCCAGCAACAGCCAUAAAUUUGCCGCUUUUCUGCUAAAAAGUGGCCAACAGUUUUGUUAGCCACG
....(((.((((....)))).)))...........((((((((((.((....))))))))))))...............((......))......(((((.(((......))).))))). (-31.19 = -32.83 +   1.64)

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 10:03:08 2006