Locus 5351

Sequence ID 2R_DroMel_CAF1
Location 17,290,329 – 17,290,471
Length 142
Max. P 0.987030
window8552 window8553 window8554

overview

Window 2

Location 17,290,329 – 17,290,448
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 89.87
Mean single sequence MFE -17.16
Consensus MFE -15.11
Energy contribution -15.80
Covariance contribution 0.69
Combinations/Pair 1.10
Mean z-score -2.54
Structure conservation index 0.88
SVM decision value 2.06
SVM RNA-class probability 0.987030
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17290329 119 - 20766785
CAAUUUUCGCACUUAAUUAUAAGCAACUCCAGCUGCCAAUUGCAGCAAAACAAACAAAAAACAAGCAAAAACAGGACACUGCACAGAAA-AAUGUGAAAAUACCAAAAAAAAAAUAAUUU
..(((((((((....................(((((.....))))).........................(((....)))........-..)))))))))................... ( -18.40)
>DroSec_CAF1 14693 117 - 1
CAAUUUUCGCACUUAAUUAUAAGCAACUCCAGCUGCCAAUUGCAGCAAAACAAACAA-AAACAAGCAAAAACAGGGCACUGCGCAGAAAAAAUGUUAAAAUACCAAAUUAAAAAG--UUA
...(((((((.((((....))))........(((((.....)))))...........-......)).....(((....)))....))))).........................--... ( -15.60)
>DroSim_CAF1 16402 117 - 1
CAAUUUUCGCACUUAAUUAUAAGCAACUCCAGCUGCCAAUUGCAGCAAAACAAACAA-AAACAAGCAAAAACAGGACACUGCACAGAAAAGAUGUGAAAUUACCAAAAUAAAAAU--UUU
....((((((((((........(((..(((.(((((.....)))))...........-......(......).)))...)))......))).)))))))................--... ( -17.84)
>DroEre_CAF1 10447 116 - 1
CAAUUUUCGCACUUAAUUAUAAGCAAGCCCAGCUGCCAAUUGCAGCAAAGCAAACAA-AAAGCAGCAAAAACAGGACAAUGCACUGAAAAAUUGUUGAAAUACCAAAAUAAAAG---UUU
....((((((.((((....))))...((...(((((.....)))))...))......-...))...........((((((..........))))))))))..............---... ( -16.80)
>consensus
CAAUUUUCGCACUUAAUUAUAAGCAACUCCAGCUGCCAAUUGCAGCAAAACAAACAA_AAACAAGCAAAAACAGGACACUGCACAGAAAAAAUGUGAAAAUACCAAAAUAAAAAU__UUU
..(((((((((...........(((..(((.(((((.....)))))..................(......).)))...)))..........)))))))))................... (-15.11 = -15.80 +   0.69)

alignment

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secondary structure

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dotplot

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Window 3

Location 17,290,368 – 17,290,471
Length 103
Sequences 4
Columns 103
Reading direction forward
Mean pairwise identity 94.63
Mean single sequence MFE -29.73
Consensus MFE -27.38
Energy contribution -26.88
Covariance contribution -0.50
Combinations/Pair 1.10
Mean z-score -1.72
Structure conservation index 0.92
SVM decision value 0.70
SVM RNA-class probability 0.825317
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17290368 103 + 20766785
AGUGUCCUGUUUUUGCUUGUUUUUUGUUUGUUUUGCUGCAAUUGGCAGCUGGAGUUGCUUAUAAUUAAGUGCGAAAAUUGGCCACAGACUCGAGUGGAGUCCC
.(((.((.((((((((..............((..(((((.....)))))..))...(((((....))))))))))))).)).))).(((((.....))))).. ( -32.00)
>DroSec_CAF1 14731 102 + 1
AGUGCCCUGUUUUUGCUUGUUU-UUGUUUGUUUUGCUGCAAUUGGCAGCUGGAGUUGCUUAUAAUUAAGUGCGAAAAUUGGCCACAGGUUCGAGUGGAGUCCC
.(((.((.((((((((......-.......((..(((((.....)))))..))...(((((....))))))))))))).)).))).(((((.....))).)). ( -27.90)
>DroSim_CAF1 16440 102 + 1
AGUGUCCUGUUUUUGCUUGUUU-UUGUUUGUUUUGCUGCAAUUGGCAGCUGGAGUUGCUUAUAAUUAAGUGCGAAAAUUGGCCACAGGUUCGAGUGGAGUCGC
.(((.((.((((((((......-.......((..(((((.....)))))..))...(((((....))))))))))))).)).))).(..((.....))..).. ( -28.30)
>DroEre_CAF1 10484 102 + 1
AUUGUCCUGUUUUUGCUGCUUU-UUGUUUGCUUUGCUGCAAUUGGCAGCUGGGCUUGCUUAUAAUUAAGUGCGAAAAUUGGCCACAGGUUCGAGUGGAGUCCC
.....((.((((((((.((((.-..((..(((..(((((.....)))))..)))..))........)))))))))))).))((((........))))...... ( -30.70)
>consensus
AGUGUCCUGUUUUUGCUUGUUU_UUGUUUGUUUUGCUGCAAUUGGCAGCUGGAGUUGCUUAUAAUUAAGUGCGAAAAUUGGCCACAGGUUCGAGUGGAGUCCC
.(((.((.((((((((..............((..(((((.....)))))..))...(((((....))))))))))))).)).))).(((((.....))))).. (-27.38 = -26.88 +  -0.50)

alignment

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secondary structure

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dotplot

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Window 4

Location 17,290,368 – 17,290,471
Length 103
Sequences 4
Columns 103
Reading direction reverse
Mean pairwise identity 94.63
Mean single sequence MFE -20.77
Consensus MFE -17.65
Energy contribution -17.65
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.08
Structure conservation index 0.85
SVM decision value 0.74
SVM RNA-class probability 0.839442
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17290368 103 - 20766785
GGGACUCCACUCGAGUCUGUGGCCAAUUUUCGCACUUAAUUAUAAGCAACUCCAGCUGCCAAUUGCAGCAAAACAAACAAAAAACAAGCAAAAACAGGACACU
.((((((.....))))))(((.((..((((.((.((((....))))........(((((.....)))))..................)).))))..)).))). ( -24.00)
>DroSec_CAF1 14731 102 - 1
GGGACUCCACUCGAACCUGUGGCCAAUUUUCGCACUUAAUUAUAAGCAACUCCAGCUGCCAAUUGCAGCAAAACAAACAA-AAACAAGCAAAAACAGGGCACU
(((......)))......(((.((..((((.((.((((....))))........(((((.....)))))...........-......)).))))..)).))). ( -20.40)
>DroSim_CAF1 16440 102 - 1
GCGACUCCACUCGAACCUGUGGCCAAUUUUCGCACUUAAUUAUAAGCAACUCCAGCUGCCAAUUGCAGCAAAACAAACAA-AAACAAGCAAAAACAGGACACU
.(((......)))..(((((.((........((............)).......(((((.....)))))...........-......))....)))))..... ( -18.50)
>DroEre_CAF1 10484 102 - 1
GGGACUCCACUCGAACCUGUGGCCAAUUUUCGCACUUAAUUAUAAGCAAGCCCAGCUGCCAAUUGCAGCAAAGCAAACAA-AAAGCAGCAAAAACAGGACAAU
(((.((((((........)))).........((............)).))))).(((((...((((......))))....-...))))).............. ( -20.20)
>consensus
GGGACUCCACUCGAACCUGUGGCCAAUUUUCGCACUUAAUUAUAAGCAACUCCAGCUGCCAAUUGCAGCAAAACAAACAA_AAACAAGCAAAAACAGGACACU
......((((........))))((..((((.((.((((....))))........(((((.....)))))..................)).))))..))..... (-17.65 = -17.65 +   0.00)

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 11:42:53 2006