Locus 4491

Sequence ID 3R_DroMel_CAF1
Location 11,898,535 – 11,898,724
Length 189
Max. P 0.985051
window7343 window7344 window7345

overview

Window 3

Location 11,898,535 – 11,898,655
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 93.11
Mean single sequence MFE -34.01
Consensus MFE -30.58
Energy contribution -31.22
Covariance contribution 0.64
Combinations/Pair 1.06
Mean z-score -2.04
Structure conservation index 0.90
SVM decision value 1.99
SVM RNA-class probability 0.985051
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11898535 120 + 27905053
UGCGCUGCUUCUUCUCGAGCAAAUUGUUGCGCGCAUUUUGCUCCUCGAGCAGCAUGCGCAGAUCGUUCAUCUCGUUGGUCAUCUUCUGUGCCUUGCGCUUCCAUUGGCCCACAACCUGAC
(((((((((.(((...(((((((.(((.....))).)))))))...))).)))).))))).............((.(((((......((((...))))......))))).))........ ( -38.90)
>DroGri_CAF1 4006 120 + 1
UGCGCUGCUUCUUCUCUAGCAAAUUGUUGCGUGCAUUUUGCUCCUCGAGCAGCAUGCGCAAGUCAUUCAUCUCGUUGGUCAUCUUUUGUGCCUUGCGUUUCCAUUGGCCCACAACCUGAC
(((((((((.(((....((((((.(((.....))).))))))....))).)))).))))).((((.......(((.(((((.....)).)))..))).......))))............ ( -33.04)
>DroEre_CAF1 3066 120 + 1
UGCGCUGCUUCUUCUCGAGCAAAUUGUUGCGCGCAUUUUGCUCCUCGAUUAACAUGCGCAGAUCGUUCAUCUCGUUGGUCAUCUUCUGUGCCUUGCGCUUCCAUUGGCCCACAACCUGAC
(((((((.((..((..(((((((.(((.....))).)))))))...))..)))).))))).............((.(((((......((((...))))......))))).))........ ( -31.80)
>DroWil_CAF1 3480 120 + 1
UGCGCUGCUUCUUCUCCAGCAAAUUGUUACGGGCAUUUUGCUCUUCGAGCAGCAUGCGCAAAUCAUUCAUCUCAUUGGUCAUCUUUUGUGCCUUGCGCUUCCAUUGGCCCACAACUUGAC
(((((((((.(((....((((((.(((.....))).))))))....))).)))).)))))......(((.......(((((......((((...))))......))))).......))). ( -34.74)
>DroMoj_CAF1 3417 120 + 1
UGCGCUGCUUCUUCUCCAGCAAAUUGUUUCGUGCAUUUUGCUCCUCGAGCAGCAUGCGCAAAUCAUUCAUCUCGUUGGUCAUCUUUUGAGCCUUGCGUUUCCAUUGGCCCACAACCUGAC
(((((((((.(((....((((((.(((.....))).))))))....))).)))).))))).............((.(((((........((...))........))))).))........ ( -32.39)
>DroPer_CAF1 3834 120 + 1
UGCGCUGCUUCUUCUCGAGCAAAUUGUUACGGGCAUUCUGCUCCUCGAGCAGCAUGCGCAGAUCGUUCAUCUCGUUUGUCAUCUUCUGUGCCUUGCGCUUCCAUUGGCCCACAACCUGGC
.(((((((((......(((((...(((.....)))...)))))...)))))))..(((((((.....((.......))......)))))))...))(((......)))(((.....))). ( -33.20)
>consensus
UGCGCUGCUUCUUCUCGAGCAAAUUGUUGCGCGCAUUUUGCUCCUCGAGCAGCAUGCGCAAAUCAUUCAUCUCGUUGGUCAUCUUCUGUGCCUUGCGCUUCCAUUGGCCCACAACCUGAC
(((((((((.(((....((((((.(((.....))).))))))....))).)))).)))))......(((....((.(((((......((((...))))......))))).))....))). (-30.58 = -31.22 +   0.64)

alignment

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secondary structure

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dotplot

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Window 4

Location 11,898,535 – 11,898,655
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 93.11
Mean single sequence MFE -34.53
Consensus MFE -30.66
Energy contribution -30.72
Covariance contribution 0.06
Combinations/Pair 1.06
Mean z-score -1.28
Structure conservation index 0.89
SVM decision value 0.19
SVM RNA-class probability 0.624183
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11898535 120 - 27905053
GUCAGGUUGUGGGCCAAUGGAAGCGCAAGGCACAGAAGAUGACCAACGAGAUGAACGAUCUGCGCAUGCUGCUCGAGGAGCAAAAUGCGCGCAACAAUUUGCUCGAGAAGAAGCAGCGCA
((((..((.((.(((..((....))...))).)).))..)))).....((((.....))))((((.((((.(((((...((.....))..((((....)))))))))....)))))))). ( -37.50)
>DroGri_CAF1 4006 120 - 1
GUCAGGUUGUGGGCCAAUGGAAACGCAAGGCACAAAAGAUGACCAACGAGAUGAAUGACUUGCGCAUGCUGCUCGAGGAGCAAAAUGCACGCAACAAUUUGCUAGAGAAGAAGCAGCGCA
.(((..(((((((((..((....))...))).((.....)).)).))))..)))......(((((.((((.(((....((((((.((.......)).)))))).)))....))))))))) ( -35.70)
>DroEre_CAF1 3066 120 - 1
GUCAGGUUGUGGGCCAAUGGAAGCGCAAGGCACAGAAGAUGACCAACGAGAUGAACGAUCUGCGCAUGUUAAUCGAGGAGCAAAAUGCGCGCAACAAUUUGCUCGAGAAGAAGCAGCGCA
((((..((.((.(((..((....))...))).)).))..)))).....((((.....))))((((.((((..((...(((((((.((.......)).)))))))..))...)))))))). ( -32.70)
>DroWil_CAF1 3480 120 - 1
GUCAAGUUGUGGGCCAAUGGAAGCGCAAGGCACAAAAGAUGACCAAUGAGAUGAAUGAUUUGCGCAUGCUGCUCGAAGAGCAAAAUGCCCGUAACAAUUUGCUGGAGAAGAAGCAGCGCA
.....(((((((((........(((((((.((.......................)).)))))))....(((((...)))))....))))))))).....((((.........))))... ( -29.70)
>DroMoj_CAF1 3417 120 - 1
GUCAGGUUGUGGGCCAAUGGAAACGCAAGGCUCAAAAGAUGACCAACGAGAUGAAUGAUUUGCGCAUGCUGCUCGAGGAGCAAAAUGCACGAAACAAUUUGCUGGAGAAGAAGCAGCGCA
((((..((.((((((..((....))...)))))).))..)))).................(((((.((((.(((....((((((.((.......)).)))))).)))....))))))))) ( -37.10)
>DroPer_CAF1 3834 120 - 1
GCCAGGUUGUGGGCCAAUGGAAGCGCAAGGCACAGAAGAUGACAAACGAGAUGAACGAUCUGCGCAUGCUGCUCGAGGAGCAGAAUGCCCGUAACAAUUUGCUCGAGAAGAAGCAGCGCA
((((((((((..(((..((....))...))).((.....)).............)))))))).))..(((((((...(((((((.((.......)).))))))).....).))))))... ( -34.50)
>consensus
GUCAGGUUGUGGGCCAAUGGAAGCGCAAGGCACAAAAGAUGACCAACGAGAUGAACGAUCUGCGCAUGCUGCUCGAGGAGCAAAAUGCACGCAACAAUUUGCUCGAGAAGAAGCAGCGCA
((((..((.((.(((..((....))...))).)).))..)))).................(((((.((((.(((....((((((.((.......)).)))))).)))....))))))))) (-30.66 = -30.72 +   0.06)

alignment

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secondary structure

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dotplot

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Window 5

Location 11,898,615 – 11,898,724
Length 109
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 74.82
Mean single sequence MFE -28.90
Consensus MFE -22.14
Energy contribution -22.42
Covariance contribution 0.28
Combinations/Pair 1.05
Mean z-score -1.20
Structure conservation index 0.77
SVM decision value 1.04
SVM RNA-class probability 0.904881
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11898615 109 - 27905053
-ACGGAAGUGUAAUAUG-----UUCCACCCCGCCAUUUCAGCUUUCCGAUGCCUACGAAGAAGUUGUGGAACAACGUCAGGUUGUGGGCCAAUGGAAGCGCAAGGCACAGAAGAU
-..((((..........-----)))).....(((......((((((....((((((((.((.((((.....)))).))...))))))))....))))))....)))......... ( -30.70)
>DroVir_CAF1 3868 105 - 1
-----UAACUUGAUCUGAGCUUUCCC-----ACAUUCGCAGCUAUCCGAUGCCUACGAGGAAGUUGAAGAACAACGUCAGGUUGUGGGCCAAUGGAAACGCAAGGCACAAAAGAU
-----...((((.....((((.....-----........)))).((((..((((((((.((.((((.....)))).))...))))))))...))))....))))........... ( -24.22)
>DroPse_CAF1 3929 98 - 1
------AUUGUAAUCCC-----UUUCU------GCUUGUAGCUUUCGGAUGCCUACGAGGAAGUUGAGGAGCAACGCCAGGUUGUGGGCCAAUGGAAGCGCAAGGCACAGAAGAU
------...........-----(((((------((((((.(((((((...((((((((((..((((.....)))).))...))))))))...))))))))))))...)))))).. ( -33.00)
>DroWil_CAF1 3560 98 - 1
------AUUUUACAAUG-----UUU------UCUUUUGCAGCUUUCCGAUGCCUACGAGGAAGUUGAAGAACAACGUCAAGUUGUGGGCCAAUGGAAGCGCAAGGCACAAAAGAU
------...........-----...------(((((((..((((((....((((((((.((.((((.....)))).))...))))))))....))))))((...)).))))))). ( -28.80)
>DroMoj_CAF1 3497 111 - 1
AGA--UAAUACAAACAUAACUUUUCCAUG--ACACUUUCAGCUUUCCGAUGCCUACGAAGAAGUUGAGGAACAACGUCAGGUUGUGGGCCAAUGGAAACGCAAGGCUCAAAAGAU
...--..............(((((((.((--(.....)))((((((((..((((((((.((.((((.....)))).))...))))))))...)))))).))..))...))))).. ( -26.90)
>DroAna_CAF1 20336 106 - 1
--UAGACCCUUAAUAAU-----UUCUAUCUUUGAA--ACAGCUUUCCGAUGCCUACGAAGAAGUUGAGGAGCAACGUCAAGUUGUGGGCCAAUGGAAGCGCAAGGCUCAGAAGAU
--..((.((((.....(-----(((.......)))--)..((((((((..((((((((.((.((((.....)))).))...))))))))...)))))).)))))).))....... ( -29.80)
>consensus
______AAUUUAAUAUG_____UUCCA____ACAAUUGCAGCUUUCCGAUGCCUACGAAGAAGUUGAGGAACAACGUCAGGUUGUGGGCCAAUGGAAGCGCAAGGCACAAAAGAU
........................................((((((((..((((((((.((.((((.....)))).))...))))))))...)))))).)).............. (-22.14 = -22.42 +   0.28)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:30:44 2006