Locus 1183

Sequence ID 3L_DroMel_CAF1
Location 3,373,188 – 3,373,388
Length 200
Max. P 0.624763
window1850 window1851 window1852 window1853

overview

Window 0

Location 3,373,188 – 3,373,298
Length 110
Sequences 4
Columns 111
Reading direction reverse
Mean pairwise identity 96.38
Mean single sequence MFE -29.80
Consensus MFE -27.67
Energy contribution -28.18
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.46
Structure conservation index 0.93
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3373188 110 - 23771897
UACCCUAGUUUAGGGUAUUUUCGAAACGGCAGCAGCCGAAAAGUGCGACACAGCCGGCGUUGAAUGUGCCCUGAAGUUUUGUUUAUUUUCGGAGAUAAAAA-AAAAUGAAA
........((((((((((.(((((..((((.(..(((.....).))..)...))))...))))).)))))))))).((((((((........)))))))).-......... ( -29.60)
>DroSec_CAF1 40320 110 - 1
UACCCUCGUUUAGGGUAUUUUCGAAACGGCAGCAGCCGAAAAGUGCGACACAGCCGGCGUUGAAUGUGCCCUGAAGUUUUGUUUAUUUUCGGAGAUAAAAA-AAAGAGAAA
....(((.((((((((((.(((((..((((.(..(((.....).))..)...))))...))))).)))))))))).((((((((........)))))))).-...)))... ( -32.80)
>DroSim_CAF1 38049 111 - 1
UACCCUCGUUUAGGGUAUUUUCGAAACGGCAGCAGCCGAAAAGUGCGACACAGCCGGCGUUGAAUGUGCCCUGAAGUUUUGUUUAUUUUCGGAGAUAAAAAAAAAAAGAAA
.....((.((((((((((.(((((..((((.(..(((.....).))..)...))))...))))).)))))))))).((((((((........)))))))).......)).. ( -29.70)
>DroEre_CAF1 39771 110 - 1
UACCCUCGCUUAGGGUAUUUUCGAAACGGCAGCAGCCAAAAAGUGCGACACAGCCGGCGUUGAAUGUGCCCCGAAGUUUUGUUUAUUUUCGGAGAUAAAAA-AAGAAGAAA
....(((.....((((((.(((((..((((.(..(((.....).))..)...))))...))))).))))))(((((..........)))))))).......-......... ( -27.10)
>consensus
UACCCUCGUUUAGGGUAUUUUCGAAACGGCAGCAGCCGAAAAGUGCGACACAGCCGGCGUUGAAUGUGCCCUGAAGUUUUGUUUAUUUUCGGAGAUAAAAA_AAAAAGAAA
........((((((((((.(((((..((((.(..(((.....).))..)...))))...))))).)))))))))).((((((((........))))))))........... (-27.67 = -28.18 +   0.50)

alignment

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secondary structure

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Window 1

Location 3,373,258 – 3,373,377
Length 119
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 85.77
Mean single sequence MFE -27.50
Consensus MFE -22.30
Energy contribution -22.05
Covariance contribution -0.25
Combinations/Pair 1.20
Mean z-score -1.53
Structure conservation index 0.81
SVM decision value 0.19
SVM RNA-class probability 0.624763
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3373258 119 + 23771897
UUCGGCUGCUGCCGUUUCGAAAAUACCCUAAACUAGGGUAUGGAAGUUUGUCCUUAAUUUUGGUUCAUAAGAUCCUGGAUUAUAUACAUAUAUAUGGGCUUAAAACCAUAUUAUGUCAA-
..((((....))))........((((((((...))))))))(((......))).(((((..((.((....)).))..)))))...(((((.((((((........)))))))))))...- ( -31.50)
>DroSec_CAF1 40390 119 + 1
UUCGGCUGCUGCCGUUUCGAAAAUACCCUAAACGAGGGUAUUGAAGUUUGUCCCUAAUUUUGGUUCAUAAGAUCCUGGAUUAUAUACAUAUAUAUGGGCUUAAUACCAUAUCAUAUCAG-
..((((....))))((((((...((((((.....))))))))))))..(((...(((((..((.((....)).))..)))))...)))(((((((((........)))))).)))....- ( -28.30)
>DroSim_CAF1 38120 117 + 1
UUCGGCUGCUGCCGUUUCGAAAAUACCCUAAACGAGGGUAUUGAAGUUUGUCCCUAAUUUUGGUUCACAAGAUCCUGGAUUAUAUACAUAUAUAUGGGCUUAAU--CAUAUCAUAUCAG-
..((((....)))).......((((((((.....))))))))...((..((((...((((((.....))))))...)))).....))((((((((((......)--))))).))))...- ( -27.00)
>DroYak_CAF1 39149 119 + 1
UUUGGCUGCUGCCGUUUCGAAAAUACCCUAAACGAGGGUAUUCAAAUUUGUUCUUACCUUUGGU-CACUAGGUCCUUGAUUUUCUAUAUAAGUAUGUGCUAAAGAUCAUACUACUUUAGU
...(((....))).....((((((..((((..((((((((..((....))....))))))))..-...))))......))))))......((((((..(....)..))))))........ ( -23.20)
>consensus
UUCGGCUGCUGCCGUUUCGAAAAUACCCUAAACGAGGGUAUUGAAGUUUGUCCCUAAUUUUGGUUCACAAGAUCCUGGAUUAUAUACAUAUAUAUGGGCUUAAUACCAUAUCAUAUCAG_
..((((....)))).......((((((((.....))))))))...((..((((...((((((.....))))))...)))).....))....((((((........))))))......... (-22.30 = -22.05 +  -0.25)

alignment

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secondary structure

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dotplot

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Window 2

Location 3,373,258 – 3,373,377
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 85.77
Mean single sequence MFE -25.45
Consensus MFE -20.74
Energy contribution -21.30
Covariance contribution 0.56
Combinations/Pair 1.15
Mean z-score -1.45
Structure conservation index 0.81
SVM decision value 0.07
SVM RNA-class probability 0.567063
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3373258 119 - 23771897
-UUGACAUAAUAUGGUUUUAAGCCCAUAUAUAUGUAUAUAAUCCAGGAUCUUAUGAACCAAAAUUAAGGACAAACUUCCAUACCCUAGUUUAGGGUAUUUUCGAAACGGCAGCAGCCGAA
-...(((((((((((........)))))).)))))..........((.((....)).))........(((......)))((((((((...))))))))........((((....)))).. ( -28.90)
>DroSec_CAF1 40390 119 - 1
-CUGAUAUGAUAUGGUAUUAAGCCCAUAUAUAUGUAUAUAAUCCAGGAUCUUAUGAACCAAAAUUAGGGACAAACUUCAAUACCCUCGUUUAGGGUAUUUUCGAAACGGCAGCAGCCGAA
-(((((...((((((........))))))................((.((....)).))...)))))........(((((((((((.....))))))))...))).((((....)))).. ( -25.70)
>DroSim_CAF1 38120 117 - 1
-CUGAUAUGAUAUG--AUUAAGCCCAUAUAUAUGUAUAUAAUCCAGGAUCUUGUGAACCAAAAUUAGGGACAAACUUCAAUACCCUCGUUUAGGGUAUUUUCGAAACGGCAGCAGCCGAA
-...((((((((((--........))))).)))))......(((..(((.(((.....))).)))..))).....(((((((((((.....))))))))...))).((((....)))).. ( -24.40)
>DroYak_CAF1 39149 119 - 1
ACUAAAGUAGUAUGAUCUUUAGCACAUACUUAUAUAGAAAAUCAAGGACCUAGUG-ACCAAAGGUAAGAACAAAUUUGAAUACCCUCGUUUAGGGUAUUUUCGAAACGGCAGCAGCCAAA
.(((....((((((..........))))))....)))..........((((....-.....)))).........((((((((((((.....)))))))..)))))..(((....)))... ( -22.80)
>consensus
_CUGAUAUAAUAUGGUAUUAAGCCCAUAUAUAUGUAUAUAAUCCAGGAUCUUAUGAACCAAAAUUAAGGACAAACUUCAAUACCCUCGUUUAGGGUAUUUUCGAAACGGCAGCAGCCGAA
....(((((((((((........)))))).)))))..........((.((....)).))...................((((((((.....)))))))).......((((....)))).. (-20.74 = -21.30 +   0.56)

alignment

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secondary structure

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dotplot

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Window 3

Location 3,373,298 – 3,373,388
Length 90
Sequences 3
Columns 90
Reading direction reverse
Mean pairwise identity 87.12
Mean single sequence MFE -16.47
Consensus MFE -14.20
Energy contribution -13.43
Covariance contribution -0.77
Combinations/Pair 1.20
Mean z-score -1.65
Structure conservation index 0.86
SVM decision value 0.15
SVM RNA-class probability 0.609081
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3373298 90 - 23771897
GUUUUGAAAGGUUGACAUAAUAUGGUUUUAAGCCCAUAUAUAUGUAUAUAAUCCAGGAUCUUAUGAACCAAAAUUAAGGACAAACUUCCA
.........((...(((((((((((........)))))).))))).......)).((.((....)).))........(((......))). ( -15.20)
>DroSec_CAF1 40430 84 - 1
GUUCC------CUGAUAUGAUAUGGUAUUAAGCCCAUAUAUAUGUAUAUAAUCCAGGAUCUUAUGAACCAAAAUUAGGGACAAACUUCAA
..(((------(((((...((((((........))))))................((.((....)).))...)))))))).......... ( -18.40)
>DroSim_CAF1 38160 82 - 1
GUUCC------CUGAUAUGAUAUG--AUUAAGCCCAUAUAUAUGUAUAUAAUCCAGGAUCUUGUGAACCAAAAUUAGGGACAAACUUCAA
..(((------(((((.......(--((((.(..(((....)))..).)))))..((.((....)).))...)))))))).......... ( -15.80)
>consensus
GUUCC______CUGAUAUGAUAUGGUAUUAAGCCCAUAUAUAUGUAUAUAAUCCAGGAUCUUAUGAACCAAAAUUAGGGACAAACUUCAA
(((((.........(((((((((((........)))))).)))))..........((.((....)).)).......)))))......... (-14.20 = -13.43 +  -0.77)

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 10:01:27 2006