Locus 3331

Sequence ID 3R_DroMel_CAF1
Location 8,952,129 – 8,952,324
Length 195
Max. P 0.594006
window5367 window5368 window5369

overview

Window 7

Location 8,952,129 – 8,952,219
Length 90
Sequences 6
Columns 95
Reading direction forward
Mean pairwise identity 82.24
Mean single sequence MFE -38.05
Consensus MFE -23.76
Energy contribution -23.27
Covariance contribution -0.50
Combinations/Pair 1.31
Mean z-score -1.89
Structure conservation index 0.62
SVM decision value 0.08
SVM RNA-class probability 0.572288
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8952129 90 + 27905053
CUUGUCCGCCAGCGAGGAGCUAUAGAAUUGCUGGCAGCGUUGCUGU-----UGCAGUUCCCGCGCUUGUAGAUUGUGCAGCGGGGAGCUGUAGGG
.....((((((((((....(....)..))))))))...........-----((((((((((.((((.(((.....))))))))))))))))))). ( -39.70)
>DroVir_CAF1 92388 91 + 1
--UGUCCGCCAGGGAGGCACUGUAGAACUGUAGCUUCUGCUGCU--CGCGCUGCAGUUCACGUGCCUGCAAAUUGUGCAGCGGCGAGCUGUAUGG
--......((..(.((((((.((.((((((((((....((....--.)))))))))))))))))))).).....(((((((.....))))))))) ( -39.30)
>DroSec_CAF1 74145 90 + 1
CUUGUCCGCCAGCGAGGAGCUAUAGAACUGCUGGCAGCGUUGCUGU-----UGCAGUUCCCGCGCUUGCAGAUUGUGCAGCGGGGAGCUGUAGGG
.....((((((((.((...(....)..))))))))...........-----((((((((((.((((.(((.....))))))))))))))))))). ( -40.80)
>DroEre_CAF1 79520 90 + 1
UCUGUCCGCCAGAGAGGAGCUGUAGAAUUGCUGGCAGCGUUGCUGU-----UGCAGUUCGCGCGCUUGUAGAUUGUGCAGCGGGGAGCUGUAGGG
((((.....)))).(.(((((((.(((((((.((((((...)))))-----))))))))))).)))).)....(.((((((.....)))))).). ( -31.80)
>DroYak_CAF1 80515 90 + 1
CUUGUCCGCCAGCGAGGAGCUGUAGAAUUGCUGGCAGCGCUGCUGU-----UGCAGUUCGCGCGCUUGUAGAUUGUGCAGCGGGGAGCUGUAGGG
.....((..((((.....((((((.((((((.(((.(((((((...-----.))))..)))..))).))).))).)))))).....))))..)). ( -36.70)
>DroMoj_CAF1 98604 91 + 1
--UGUCCGCUAGAGAAGCGCUGUAGAACUGCAGCUUCUGUUGCU--CGCGCUGCAGCUCACGUGCCUGCAGAUUGUGCAGCGGGGAGCUGUAGGG
--....((((.....))))........((((((((((((((((.--((..(((((((......).))))))..)).))))).))))))))))).. ( -40.00)
>consensus
CUUGUCCGCCAGCGAGGAGCUGUAGAACUGCUGGCAGCGUUGCUGU_____UGCAGUUCACGCGCUUGCAGAUUGUGCAGCGGGGAGCUGUAGGG
.....(((((((...((..(....)..)).)))))................((((((((.(.(((.((((.....))))))).))))))))))). (-23.76 = -23.27 +  -0.50)

alignment

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secondary structure

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dotplot

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Window 8

Location 8,952,219 – 8,952,324
Length 105
Sequences 6
Columns 105
Reading direction forward
Mean pairwise identity 75.57
Mean single sequence MFE -39.48
Consensus MFE -24.62
Energy contribution -23.23
Covariance contribution -1.38
Combinations/Pair 1.50
Mean z-score -1.29
Structure conservation index 0.62
SVM decision value 0.12
SVM RNA-class probability 0.594006
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8952219 105 + 27905053
UGCUUCUCUCCGCGUGCUGUGGUGCCACUUUUGCAGGCGAGCCGGAUCACCGCCAUUGGAGUUCACAGAUCCCUGAUAGUGCAGGAAGCUGUGCGCAUCAUCGGU
..........(((.(((.(((....)))....))).))).(((((....(((....))).((.(((((...((((......))))...))))).))....))))) ( -34.10)
>DroPse_CAF1 79092 102 + 1
CGCCUCGCGGCGGGUGCUGUGGUGCCAUUUCUGGAGCCGUGCAGGAUCUGCUG---UGCUGCCUGCAGAUCCCUGAUAGUUCAGGAAGCUGUGGGCGUCGUCGCU
.((..((((((((((.(((((((.(((....))).)))..)))).))))))))---))..(((..(((...(((((....)))))...)))..)))......)). ( -49.80)
>DroWil_CAF1 77541 105 + 1
AGCCUCUCGUCUGGUACUGUGAUGCCAUUUCUGUAGUCGGGCCGGAUCUGCUGGAUGAUUGCCACUAGAUCCUUGAUAAUGCAAAAAACUAUGUCCAUCAUCACU
.(((........)))...((((((.((....)).....((((.(((((((.(((.......))).)))))))(((......)))........))))..)))))). ( -25.10)
>DroYak_CAF1 80605 105 + 1
AGCUUCUCGCCGCGUGCUGUGGUGCCACUUUUGCAGGCGAGCCGGAUCUCCCCCAUUGGAGUUCACAGAUCCCUGAUAGUGCAGGAAGCUGUGCGCAUCAUCCGU
.....(((((((((....(((....)))...))).)))))).(((((.(((......)))((.(((((...((((......))))...))))).))...))))). ( -38.30)
>DroAna_CAF1 79514 105 + 1
CGCCUCUCUUCGAGUGCUGUGAUGCCACUUUUGCAGGCGGGCCGGAUCCGUCGAAUUAGAGUUGACGGAUCCCUGAUAGUGCAGGAAGCUGUGCACAUCAUCACU
.(((((.....))).)).((((((((.((......)).))...(((((((((((.......)))))))))))......(..(((....)))..)....)))))). ( -39.80)
>DroPer_CAF1 80344 102 + 1
CGCCUCGCGGCGGGUGCUGUGGUGCCAUUUCUGGAGCCGUGCAGGAUCUGCUG---UGCUGCCUGCAGAUCCCUGAUAGUUCAGGAAGCUGUGGGCGUCGUCGCU
.((..((((((((((.(((((((.(((....))).)))..)))).))))))))---))..(((..(((...(((((....)))))...)))..)))......)). ( -49.80)
>consensus
CGCCUCUCGCCGGGUGCUGUGGUGCCACUUCUGCAGGCGAGCCGGAUCUGCUG_AUUGGAGCCCACAGAUCCCUGAUAGUGCAGGAAGCUGUGCGCAUCAUCGCU
.....((((((.......(((....))).......))))))..(((((((...............))))))).((((.(((((.(....).)))))))))..... (-24.62 = -23.23 +  -1.38)

alignment

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secondary structure

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dotplot

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Window 9

Location 8,952,219 – 8,952,324
Length 105
Sequences 6
Columns 105
Reading direction reverse
Mean pairwise identity 75.57
Mean single sequence MFE -37.27
Consensus MFE -17.90
Energy contribution -17.38
Covariance contribution -0.52
Combinations/Pair 1.32
Mean z-score -1.79
Structure conservation index 0.48
SVM decision value 0.04
SVM RNA-class probability 0.553745
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8952219 105 - 27905053
ACCGAUGAUGCGCACAGCUUCCUGCACUAUCAGGGAUCUGUGAACUCCAAUGGCGGUGAUCCGGCUCGCCUGCAAAAGUGGCACCACAGCACGCGGAGAGAAGCA
........(((.(((((.((((((......)))))).)))))..((((...(.(((....))).)..((.(((....(((....))).))).))))))....))) ( -36.50)
>DroPse_CAF1 79092 102 - 1
AGCGACGACGCCCACAGCUUCCUGAACUAUCAGGGAUCUGCAGGCAGCA---CAGCAGAUCCUGCACGGCUCCAGAAAUGGCACCACAGCACCCGCCGCGAGGCG
.........(((..(((.(((((((....))))))).)))..))).((.---..((((...))))..((..(((....)))..))...))...((((....)))) ( -40.30)
>DroWil_CAF1 77541 105 - 1
AGUGAUGAUGGACAUAGUUUUUUGCAUUAUCAAGGAUCUAGUGGCAAUCAUCCAGCAGAUCCGGCCCGACUACAGAAAUGGCAUCACAGUACCAGACGAGAGGCU
..((((((((.(.(......).).)))))))).((((((..(((.......)))..))))))(((((((...((....))...))...((.....))..).)))) ( -24.60)
>DroYak_CAF1 80605 105 - 1
ACGGAUGAUGCGCACAGCUUCCUGCACUAUCAGGGAUCUGUGAACUCCAAUGGGGGAGAUCCGGCUCGCCUGCAAAAGUGGCACCACAGCACGCGGCGAGAAGCU
.(((((......(((((.((((((......)))))).)))))..((((......))))))))).((((((.((....(((....))).....))))))))..... ( -42.10)
>DroAna_CAF1 79514 105 - 1
AGUGAUGAUGUGCACAGCUUCCUGCACUAUCAGGGAUCCGUCAACUCUAAUUCGACGGAUCCGGCCCGCCUGCAAAAGUGGCAUCACAGCACUCGAAGAGAGGCG
.(((((((((((((........))))).)))..(((((((((...........))))))))).....(((.((....)))))))))).((.(((.....))))). ( -39.80)
>DroPer_CAF1 80344 102 - 1
AGCGACGACGCCCACAGCUUCCUGAACUAUCAGGGAUCUGCAGGCAGCA---CAGCAGAUCCUGCACGGCUCCAGAAAUGGCACCACAGCACCCGCCGCGAGGCG
.........(((..(((.(((((((....))))))).)))..))).((.---..((((...))))..((..(((....)))..))...))...((((....)))) ( -40.30)
>consensus
AGCGAUGAUGCGCACAGCUUCCUGCACUAUCAGGGAUCUGUAAACACCAAU_CAGCAGAUCCGGCACGCCUGCAAAAAUGGCACCACAGCACCCGACGAGAGGCG
................((((((((......)))((((((.................))))))....((((..((....))((......))....)))).))))). (-17.90 = -17.38 +  -0.52)

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 10:58:36 2006