Locus 3777

Sequence ID 3R_DroMel_CAF1
Location 10,244,518 – 10,244,608
Length 90
Max. P 0.669356
window6051 window6052

overview

Window 1

Location 10,244,518 – 10,244,608
Length 90
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 74.89
Mean single sequence MFE -35.73
Consensus MFE -21.71
Energy contribution -21.27
Covariance contribution -0.44
Combinations/Pair 1.21
Mean z-score -1.40
Structure conservation index 0.61
SVM decision value 0.29
SVM RNA-class probability 0.669356
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10244518 90 + 27905053
GCUCACGUUGGCCUGGCUCAGCCUCUGCCUGGCGAUUUAUUGCGGCGGUGGCCA------------------------UGGCC------AUGGCAAUGUGGUCCUAUCUUUGCCACCAUC
..((((((((.(((((((..(((.(((((..((((....))))))))).)))..------------------------.))))------).))))))))))................... ( -36.10)
>DroVir_CAF1 118809 99 + 1
GCUCACGCUCGCCUGGCUUUGUGUCUGCCUGGCGAUUUAUUGUAGCGGCGGCUU------UGCCA---------ACAACGGCC------GAGGCAAUGUGGUCUUAUCUUUGCCACCAUC
(((((...(((((.(((.........))).))))).....)).)))((.(((..------.(((.---------.....))).------(((((......)))))......))).))... ( -33.10)
>DroPse_CAF1 110339 114 + 1
ACUCACGCUCGCCUGGCUCAGCGUCUGCCUGGCGAUUUAUUGCGGCGGCGGCCACAGCUACAGCCACGGCCACAGCCACGGCC------ACGGCAAUGUGGUCCUAUCUUUGCCACCAUC
......(((((((.(((.........))).)))))......))((.(((((((...((....))...))))........((((------(((....)))))))........))).))... ( -42.30)
>DroWil_CAF1 115597 81 + 1
GCUAACGCUUGCCUGGCUAUGUGUCUGCUUGGCGAUUUAUUGCGGCG---------------------------------GCC------AUGGCAAUGUGGUCUUAUCUUUGCCACCAUC
((....)).......((((((.(.(((((..((((....))))))))---------------------------------)))------)))))...(((((.........))))).... ( -23.90)
>DroMoj_CAF1 111372 99 + 1
ACUCACGCUCGCCUGGCUCUGGGUCUGCCUGGCGAUUUAUUGUAGCGGAGGCUU------UGCCA---------ACAACGGCC------AAGGCAAUGUGGUCUUAUCUUUGCCACCAUC
.(((.((((((((.(((.........))).))))).........))))))((((------((((.---------.....)).)------)))))...(((((.........))))).... ( -34.00)
>DroPer_CAF1 113024 114 + 1
ACUCACGCUCGCCUGGCUCAGCGUCUGCCUGGCGAUUUAUUGCGGCGGCGGCCA------CAGCCACAGCCACAGCCACGGCCACGGCCACGGCAAUGUGGUCCUAUCUUUGCCACCAUC
......(((((((.(((.........))).)))))......))((.((((((..------..)))...(((((((((..(((....)))..)))..)))))).........))).))... ( -45.00)
>consensus
ACUCACGCUCGCCUGGCUCAGCGUCUGCCUGGCGAUUUAUUGCGGCGGCGGCCA_________C___________C_ACGGCC______AAGGCAAUGUGGUCCUAUCUUUGCCACCAUC
.....((((((((.(((.........))).)))).........)))).................................(((........)))...(((((.........))))).... (-21.71 = -21.27 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 2

Location 10,244,518 – 10,244,608
Length 90
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 74.89
Mean single sequence MFE -37.24
Consensus MFE -21.33
Energy contribution -21.38
Covariance contribution 0.06
Combinations/Pair 1.14
Mean z-score -1.39
Structure conservation index 0.57
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10244518 90 - 27905053
GAUGGUGGCAAAGAUAGGACCACAUUGCCAU------GGCCA------------------------UGGCCACCGCCGCAAUAAAUCGCCAGGCAGAGGCUGAGCCAGGCCAACGUGAGC
.((((((((((.(.........).)))))))------((((.------------------------(((((((((((((........))..)))...)).)).))))))))..))).... ( -30.10)
>DroVir_CAF1 118809 99 - 1
GAUGGUGGCAAAGAUAAGACCACAUUGCCUC------GGCCGUUGU---------UGGCA------AAGCCGCCGCUACAAUAAAUCGCCAGGCAGACACAAAGCCAGGCGAGCGUGAGC
..(((((((........(((.((...((...------.)).)).))---------)(((.------..)))))))))).......(((((.(((.........))).)))))((....)) ( -33.20)
>DroPse_CAF1 110339 114 - 1
GAUGGUGGCAAAGAUAGGACCACAUUGCCGU------GGCCGUGGCUGUGGCCGUGGCUGUAGCUGUGGCCGCCGCCGCAAUAAAUCGCCAGGCAGACGCUGAGCCAGGCGAGCGUGAGU
(.(((((((.......((.(......)))..------(((((..((((..((....))..))))..)))))))))))))......(((((.(((.........))).)))))((....)) ( -54.50)
>DroWil_CAF1 115597 81 - 1
GAUGGUGGCAAAGAUAAGACCACAUUGCCAU------GGC---------------------------------CGCCGCAAUAAAUCGCCAAGCAGACACAUAGCCAGGCAAGCGUUAGC
(((((((((........).)))).(((((.(------(((---------------------------------.((.((........))...)).(...)...))))))))).))))... ( -18.00)
>DroMoj_CAF1 111372 99 - 1
GAUGGUGGCAAAGAUAAGACCACAUUGCCUU------GGCCGUUGU---------UGGCA------AAGCCUCCGCUACAAUAAAUCGCCAGGCAGACCCAGAGCCAGGCGAGCGUGAGU
....(((((........).)))).(((((((------(((..((((---------((...------.(((....))).))))))...))))(((.........)))))))))((....)) ( -29.40)
>DroPer_CAF1 113024 114 - 1
GAUGGUGGCAAAGAUAGGACCACAUUGCCGUGGCCGUGGCCGUGGCUGUGGCUGUGGCUG------UGGCCGCCGCCGCAAUAAAUCGCCAGGCAGACGCUGAGCCAGGCGAGCGUGAGU
(.(((((((.......((.(((((..((((..((((..((....))..))))..))))))------)))))))))))))......(((((.(((.........))).)))))((....)) ( -58.21)
>consensus
GAUGGUGGCAAAGAUAAGACCACAUUGCCAU______GGCCGU_G___________G_________UGGCCGCCGCCGCAAUAAAUCGCCAGGCAGACGCAGAGCCAGGCGAGCGUGAGC
....(((((...(((........)))(((........)))..................................)))))......(((((.(((.........))).)))))((....)) (-21.33 = -21.38 +   0.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:09:48 2006