Locus 10129

Sequence ID 3R_DroMel_CAF1
Location 27,173,534 – 27,173,669
Length 135
Max. P 0.950086
window16122 window16123 window16124

overview

Window 2

Location 27,173,534 – 27,173,629
Length 95
Sequences 4
Columns 101
Reading direction reverse
Mean pairwise identity 92.54
Mean single sequence MFE -23.55
Consensus MFE -20.26
Energy contribution -20.70
Covariance contribution 0.44
Combinations/Pair 1.12
Mean z-score -1.37
Structure conservation index 0.86
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27173534 95 - 27905053
GGGGCAA-AUAAAAACAAAGCUGGCUGAAAUGGAAAAUAAGAAGUGAGUCCGAGUCGCCGGCAAUGGGGGUCAGGUCAGAUGCUGGAAAUGAUGCU-----
..((((.-...........((((((.((..((((..((.....))...))))..))))))))..(.((.(((......))).)).)......))))----- ( -24.40)
>DroSec_CAF1 70062 96 - 1
GGGGCAAAAUAAAAACAAAGCUGGCUGAAAUGGAAAAUAAGAAGCGAGUCCGAGUCGCCGCCAAUGGGGGUCAGGUCAGAUGCUGGAAAUGAUGCU-----
..((((............(((...((((..((........((..((....))..))(((.((...)).)))))..))))..)))........))))----- ( -20.25)
>DroSim_CAF1 72942 96 - 1
GGGGCAAAAUAAAAACAAAGCCCGCUGAAAUGGAAAAUAAGAAGCGAGUCCGAGUCGCCGGCAAUGGGGGUCAGGUCAGAUGCUGGAAAUGAUGCU-----
.((((..............))))((((...(....).......((((.......))))))))....((.((((..((((...))))...)))).))----- ( -20.84)
>DroEre_CAF1 70832 100 - 1
GGAGCAA-AUAAAAACAAAGCUGGCUGAAAUGGAAAAUAAGAAGUGAGUCCGAGUCGUCGGCAAUGGGGGUCAGGUCAGAUGCUGGAGCUGAUGCUCGACU
.((((..-...........((((((.((..((((..((.....))...))))..)))))))).......(((((.((........)).))))))))).... ( -28.70)
>consensus
GGGGCAA_AUAAAAACAAAGCUGGCUGAAAUGGAAAAUAAGAAGCGAGUCCGAGUCGCCGGCAAUGGGGGUCAGGUCAGAUGCUGGAAAUGAUGCU_____
..((((.............((((((.((..((((..((.....))...))))..))))))))..(.((.(((......))).)).)......))))..... (-20.26 = -20.70 +   0.44)

alignment

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secondary structure

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Window 3

Location 27,173,569 – 27,173,669
Length 100
Sequences 5
Columns 108
Reading direction forward
Mean pairwise identity 87.05
Mean single sequence MFE -27.30
Consensus MFE -17.82
Energy contribution -19.22
Covariance contribution 1.40
Combinations/Pair 1.10
Mean z-score -2.52
Structure conservation index 0.65
SVM decision value 0.46
SVM RNA-class probability 0.746640
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27173569 100 + 27905053
CCGGCGACUCGGACUCACUUCUUAUUUU-------CCAUUUCAGCCAGCUUUGUUUUUAU-UUGCCCCUCCAAGGGCAAUAAGCUGGCAUUUCUUGUUAGCCGCCUUG
.(((((((..(((..............)-------))......((((((((.........-((((((......)))))).)))))))).......))).))))..... ( -30.84)
>DroSec_CAF1 70097 101 + 1
GCGGCGACUCGGACUCGCUUCUUAUUUU-------CCAUUUCAGCCAGCUUUGUUUUUAUUUUGCCCCUCCAAGGGCAAUAAGCUGGCGUUUCUUGUUAGCCGCCUUG
((((((((..(((..............)-------))......((((((((..........((((((......)))))).)))))))).......))).))))).... ( -34.24)
>DroSim_CAF1 72977 101 + 1
CCGGCGACUCGGACUCGCUUCUUAUUUU-------CCAUUUCAGCGGGCUUUGUUUUUAUUUUGCCCCUCCAAGGGCAAUAAGCUGGCGUUUCUUGUUAGCCGCCUUG
.(((((((..(((..((((.((((((.(-------((.((..((.((((...((....))...))))))..))))).))))))..))))..))).))).))))..... ( -30.60)
>DroEre_CAF1 70872 100 + 1
CCGACGACUCGGACUCACUUCUUAUUUU-------CCAUUUCAGCCAGCUUUGUUUUUAU-UUGCUCCUGCAAGGGCAAUAAGCUGGCGUUUCUUGUUAGCCGCCUUG
((((....))))................-------........((((((((((((....(-((((....)))))))))..)))))))).................... ( -23.10)
>DroYak_CAF1 73766 94 + 1
-------------CUCACUUCUUAUUUUCCAUUUUCCAUUUCAGGCAGCUUUGUUUUUAC-UUACUCCUGCAAGGGCAAUAAGCUGGCGUUUCUUGUUAGCCGCCUUG
-------------.............................((((((((((((((((.(-........).)))))))..)))))(((...........))))))).. ( -17.70)
>consensus
CCGGCGACUCGGACUCACUUCUUAUUUU_______CCAUUUCAGCCAGCUUUGUUUUUAU_UUGCCCCUCCAAGGGCAAUAAGCUGGCGUUUCUUGUUAGCCGCCUUG
..((((.....................................((((((((..........((((((......)))))).))))))))(((.......)))))))... (-17.82 = -19.22 +   1.40)

alignment

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secondary structure

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dotplot

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Window 4

Location 27,173,569 – 27,173,669
Length 100
Sequences 5
Columns 108
Reading direction reverse
Mean pairwise identity 87.05
Mean single sequence MFE -31.12
Consensus MFE -20.58
Energy contribution -22.94
Covariance contribution 2.36
Combinations/Pair 1.12
Mean z-score -3.42
Structure conservation index 0.66
SVM decision value 1.40
SVM RNA-class probability 0.950086
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27173569 100 - 27905053
CAAGGCGGCUAACAAGAAAUGCCAGCUUAUUGCCCUUGGAGGGGCAA-AUAAAAACAAAGCUGGCUGAAAUGG-------AAAAUAAGAAGUGAGUCCGAGUCGCCGG
...(((((((..........((((((((.(((((((....)))))))-.........)))))))).....(((-------(..((.....))...))))))))))).. ( -37.30)
>DroSec_CAF1 70097 101 - 1
CAAGGCGGCUAACAAGAAACGCCAGCUUAUUGCCCUUGGAGGGGCAAAAUAAAAACAAAGCUGGCUGAAAUGG-------AAAAUAAGAAGCGAGUCCGAGUCGCCGC
...(((((((..........((((((((.(((((((....)))))))..........)))))))).....(((-------(..............))))))))))).. ( -36.14)
>DroSim_CAF1 72977 101 - 1
CAAGGCGGCUAACAAGAAACGCCAGCUUAUUGCCCUUGGAGGGGCAAAAUAAAAACAAAGCCCGCUGAAAUGG-------AAAAUAAGAAGCGAGUCCGAGUCGCCGG
...(((((((.....((..(((...((((((..((((..((((((..............)))).))..)).))-------..))))))..)))..))..))))))).. ( -33.04)
>DroEre_CAF1 70872 100 - 1
CAAGGCGGCUAACAAGAAACGCCAGCUUAUUGCCCUUGCAGGAGCAA-AUAAAAACAAAGCUGGCUGAAAUGG-------AAAAUAAGAAGUGAGUCCGAGUCGUCGG
...(((((((..........((((((((.((((((.....)).))))-.........)))))))).....(((-------(..((.....))...))))))))))).. ( -30.10)
>DroYak_CAF1 73766 94 - 1
CAAGGCGGCUAACAAGAAACGCCAGCUUAUUGCCCUUGCAGGAGUAA-GUAAAAACAAAGCUGCCUGAAAUGGAAAAUGGAAAAUAAGAAGUGAG-------------
..((((((((.....(......).(((((((.((......)))))))-))........)))))))).............................------------- ( -19.00)
>consensus
CAAGGCGGCUAACAAGAAACGCCAGCUUAUUGCCCUUGGAGGGGCAA_AUAAAAACAAAGCUGGCUGAAAUGG_______AAAAUAAGAAGUGAGUCCGAGUCGCCGG
...(((((((..........((((((((.(((((((....)))))))..........))))))))..........................((....))))))))).. (-20.58 = -22.94 +   2.36)

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 13:49:31 2006