Locus 1294

Sequence ID 2R_DroMel_CAF1
Location 5,036,263 – 5,036,500
Length 237
Max. P 0.988795
window2242 window2243 window2244 window2245

overview

Window 2

Location 5,036,263 – 5,036,368
Length 105
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 80.35
Mean single sequence MFE -24.04
Consensus MFE -16.25
Energy contribution -16.58
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.54
Structure conservation index 0.68
SVM decision value -0.04
SVM RNA-class probability 0.511127
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5036263 105 + 20766785
-------CAUCCUAUAUAUAUAUAUAUAACAAUCAGAGAGCAAACGAACCCA-AUUGGAAGGGCUAACCAUCUAUAAUCGG-------CUAUAUACCGAUAAAGAUAUAGACGGCUGGCC
-------.....((((((....)))))).....................((.-...))...(((((.((.(((((((((((-------.......))))).....)))))).)).))))) ( -20.60)
>DroEre_CAF1 16357 101 + 1
-----UGCAUCCUAUA------UAUAAAACAAUCAGAGAGCAAACGAUCCCG-AUUGGAAGGGCUAACCGUCUAUAAGCGG-------CUAUAUACCGAUUAAGAUAUAGACGGCUGGCC
-----...........------.......(((((.(.((........))).)-))))....(((((.(((((((((..(((-------.......))).......))))))))).))))) ( -26.50)
>DroYak_CAF1 16494 112 + 1
GAAUCAGCAUCCUAUA------UAUA--ACAAUCAGAGAGCAAACGACCCCAAAUUGGAAGGGCUAACCGUCUAUAACCGAUAUUGUACGAUAUAGCGAUGAAGAUAUAGACGGCUGGCC
......((.((((...------....--......)).))))........((.....))...(((((.(((((((((..(..((((((........))))))..).))))))))).))))) ( -25.02)
>consensus
______GCAUCCUAUA______UAUA_AACAAUCAGAGAGCAAACGAACCCA_AUUGGAAGGGCUAACCGUCUAUAACCGG_______CUAUAUACCGAUAAAGAUAUAGACGGCUGGCC
.................................................((.....))...(((((.(((((((((.............................))))))))).))))) (-16.25 = -16.58 +   0.33)

alignment

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secondary structure

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dotplot

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Window 3

Location 5,036,263 – 5,036,368
Length 105
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 80.35
Mean single sequence MFE -30.90
Consensus MFE -23.17
Energy contribution -23.67
Covariance contribution 0.50
Combinations/Pair 1.07
Mean z-score -2.60
Structure conservation index 0.75
SVM decision value 2.14
SVM RNA-class probability 0.988795
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5036263 105 - 20766785
GGCCAGCCGUCUAUAUCUUUAUCGGUAUAUAG-------CCGAUUAUAGAUGGUUAGCCCUUCCAAU-UGGGUUCGUUUGCUCUCUGAUUGUUAUAUAUAUAUAUAUAGGAUG-------
(((.(((((((((((.....((((((.....)-------)))))))))))))))).)))..(((...-.((((......)))).........((((((....)))))))))..------- ( -32.70)
>DroEre_CAF1 16357 101 - 1
GGCCAGCCGUCUAUAUCUUAAUCGGUAUAUAG-------CCGCUUAUAGACGGUUAGCCCUUCCAAU-CGGGAUCGUUUGCUCUCUGAUUGUUUUAUA------UAUAGGAUGCA-----
(((.(((((((((((.......((((.....)-------)))..))))))))))).)))....((((-(((((........)).))))))).......------...........----- ( -31.30)
>DroYak_CAF1 16494 112 - 1
GGCCAGCCGUCUAUAUCUUCAUCGCUAUAUCGUACAAUAUCGGUUAUAGACGGUUAGCCCUUCCAAUUUGGGGUCGUUUGCUCUCUGAUUGU--UAUA------UAUAGGAUGCUGAUUC
((....))......(((..((((.((((((...(((..(((((...((((((....(((((........)))))))))))....))))))))--...)------)))))))))..))).. ( -28.70)
>consensus
GGCCAGCCGUCUAUAUCUUAAUCGGUAUAUAG_______CCGAUUAUAGACGGUUAGCCCUUCCAAU_UGGGAUCGUUUGCUCUCUGAUUGUU_UAUA______UAUAGGAUGC______
(((.(((((((((((.....(((((..............)))))))))))))))).)))..(((.....(((........)))...........(((((....))))))))......... (-23.17 = -23.67 +   0.50)

alignment

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secondary structure

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dotplot

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Window 4

Location 5,036,296 – 5,036,408
Length 112
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 88.89
Mean single sequence MFE -36.23
Consensus MFE -28.70
Energy contribution -29.37
Covariance contribution 0.67
Combinations/Pair 1.06
Mean z-score -2.23
Structure conservation index 0.79
SVM decision value 0.34
SVM RNA-class probability 0.693878
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5036296 112 - 20766785
ACAAACUGGUUGAUGCAGAGGAAAGCGUUAAAUGCAAAUCGGCCAGCCGUCUAUAUCUUUAUCGGUAUAUAG-------CCGAUUAUAGAUGGUUAGCCCUUCCAAU-UGGGUUCGUUUG
.(((((.((((((((((...((.....))...))))..))))))(((((((((((.....((((((.....)-------))))))))))))))))(((((.......-.))))).))))) ( -38.90)
>DroEre_CAF1 16386 111 - 1
ACA-ACUGGUUGAUGCAGAGGAAAGCGUUAAAUGCAGAUCGGCCAGCCGUCUAUAUCUUAAUCGGUAUAUAG-------CCGCUUAUAGACGGUUAGCCCUUCCAAU-CGGGAUCGUUUG
...-.(((((((.((((...((.....))...))))((..(((.(((((((((((.......((((.....)-------)))..))))))))))).)))..))))))-)))......... ( -36.30)
>DroYak_CAF1 16526 119 - 1
ACA-ACUGGUUGAUGCAGAGGAAAGCGUUAAAUGCAGAUCGGCCAGCCGUCUAUAUCUUCAUCGCUAUAUCGUACAAUAUCGGUUAUAGACGGUUAGCCCUUCCAAUUUGGGGUCGUUUG
...-.((((((((((((...((.....))...))))..))))))))(((((((((.....((((.(((........))).)))))))))))))...(((((........)))))...... ( -33.50)
>consensus
ACA_ACUGGUUGAUGCAGAGGAAAGCGUUAAAUGCAGAUCGGCCAGCCGUCUAUAUCUUAAUCGGUAUAUAG_______CCGAUUAUAGACGGUUAGCCCUUCCAAU_UGGGAUCGUUUG
.....(((.(((((((........)))))))...)))...(((.(((((((((((.....(((((..............)))))))))))))))).)))..(((.....)))........ (-28.70 = -29.37 +   0.67)

alignment

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secondary structure

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dotplot

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Window 5

Location 5,036,408 – 5,036,500
Length 92
Sequences 3
Columns 92
Reading direction forward
Mean pairwise identity 95.65
Mean single sequence MFE -16.57
Consensus MFE -15.32
Energy contribution -15.10
Covariance contribution -0.22
Combinations/Pair 1.04
Mean z-score -1.96
Structure conservation index 0.92
SVM decision value 0.53
SVM RNA-class probability 0.772177
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5036408 92 + 20766785
CGCGUAGGGAGAAGAUAAGACACCAAGUAUUAUAUAUACAAUAUACAACAUAUAUGAUAAUAAAGUGGAUAUUCUUAGAAGAUCUAGGCUAA
.((.((((...((((.....(((....((((((((((............)))))))))).....))).....))))......)))).))... ( -17.70)
>DroEre_CAF1 16497 92 + 1
CGCGUAGGGAGAAGAAAUGACACCAAGUAUUAUACAAACAAUAUACAACAUAUAUGAUAAUAAAGUGGAUACUCUUAGAAGACCUAGGCUAA
.((.((((...((((.....(((....((((((.......(((((.....))))).))))))..))).....))))......)))).))... ( -15.70)
>DroYak_CAF1 16645 92 + 1
CGCGUAGGGAGAAGAAAAGACACCAAGUAUUAUACAAACAAUAUACAACAUAUAUGAUAAUAAAGUGGAUACUCUUAGAAGACCUAGGCUAA
.((.((((...((((..(..(((....((((((.......(((((.....))))).))))))..)))..)..))))......)))).))... ( -16.30)
>consensus
CGCGUAGGGAGAAGAAAAGACACCAAGUAUUAUACAAACAAUAUACAACAUAUAUGAUAAUAAAGUGGAUACUCUUAGAAGACCUAGGCUAA
.((.((((...((((.....(((....((((((.......(((((.....))))).))))))..))).....))))......)))).))... (-15.32 = -15.10 +  -0.22)

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 10:01:20 2006