Locus 2681

Sequence ID 2R_DroMel_CAF1
Location 9,461,723 – 9,461,858
Length 135
Max. P 0.999985
window4411 window4412 window4413

overview

Window 1

Location 9,461,723 – 9,461,821
Length 98
Sequences 4
Columns 109
Reading direction forward
Mean pairwise identity 74.96
Mean single sequence MFE -23.62
Consensus MFE -13.84
Energy contribution -15.40
Covariance contribution 1.56
Combinations/Pair 1.12
Mean z-score -3.33
Structure conservation index 0.59
SVM decision value 4.23
SVM RNA-class probability 0.999842
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9461723 98 + 20766785
A-UUUAAAAAUUUUUU----------GCCACCACUGAAAUAUCAAGGGAUUUGAAAUCAUUCGUGAAGUUCCACCAGUUUGUAUAUGAUUUCAAAUCCAAAGAGAUUUC
.-..............----------.........(((((.((...((((((((((((((..(..((.(......).))..)..))))))))))))))...)).))))) ( -23.30)
>DroSec_CAF1 48528 108 + 1
A-UUUAAAAAUAAUAUAUCAAAUUGUGAUACCACUGAAAUAUCAAGGGAUUUGAAAUCAUUCGUGAAGUUCCAAAAGUUUGUAUAUGACUUCAAAUCCAAAGAGAUUUC
.-.............(((((.....))))).....(((((.((...(((((((((.((((..(..((.((....)).))..)..)))).)))))))))...)).))))) ( -22.30)
>DroSim_CAF1 58329 99 + 1
A-UUUAAAAAUAAUAUAUCAAAUUGUG---------AAAUAUCAAGGGAUUUGAAAUCAUGCGUGAAGUUGCACAAGUUUGUAUACGACUUCAAAUCCAAAGAUAUUUC
.-........................(---------(((((((...(((((((((.((.((((......))))...((......)))).)))))))))...)))))))) ( -23.70)
>DroYak_CAF1 49009 98 + 1
GAC-UAAAAAGACAAUAUCAAAUUGUGCUACCACUGAAACAUCAAGUGAUUUGAAAUCAUUC----------ACUAGUUUGUAAGUGACUUCAAAUCGCAUGAGAUUUC
...-.....(((((((.....))))).))......((((..(((.((((((((((.(((((.----------((......)).))))).)))))))))).)))..)))) ( -25.20)
>consensus
A_UUUAAAAAUAAUAUAUCAAAUUGUGCUACCACUGAAAUAUCAAGGGAUUUGAAAUCAUUCGUGAAGUUCCACAAGUUUGUAUAUGACUUCAAAUCCAAAGAGAUUUC
...................................(((((.((...(((((((((.(((((.(..((.(......).))..).))))).)))))))))...)).))))) (-13.84 = -15.40 +   1.56)

alignment

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secondary structure

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dotplot

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Window 2

Location 9,461,723 – 9,461,821
Length 98
Sequences 4
Columns 109
Reading direction reverse
Mean pairwise identity 74.96
Mean single sequence MFE -26.18
Consensus MFE -18.02
Energy contribution -18.21
Covariance contribution 0.19
Combinations/Pair 1.14
Mean z-score -3.89
Structure conservation index 0.69
SVM decision value 5.40
SVM RNA-class probability 0.999985
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9461723 98 - 20766785
GAAAUCUCUUUGGAUUUGAAAUCAUAUACAAACUGGUGGAACUUCACGAAUGAUUUCAAAUCCCUUGAUAUUUCAGUGGUGGC----------AAAAAAUUUUUAAA-U
(((((.((...((((((((((((((...(.....)((((....))))..))))))))))))))...)).))))).........----------..............-. ( -24.10)
>DroSec_CAF1 48528 108 - 1
GAAAUCUCUUUGGAUUUGAAGUCAUAUACAAACUUUUGGAACUUCACGAAUGAUUUCAAAUCCCUUGAUAUUUCAGUGGUAUCACAAUUUGAUAUAUUAUUUUUAAA-U
(((((.((...((((((((((((((..........(((........)))))))))))))))))...)).)))))....((((((.....))))))............-. ( -25.10)
>DroSim_CAF1 58329 99 - 1
GAAAUAUCUUUGGAUUUGAAGUCGUAUACAAACUUGUGCAACUUCACGCAUGAUUUCAAAUCCCUUGAUAUUU---------CACAAUUUGAUAUAUUAUUUUUAAA-U
((((((((...((((((((((((((..(((....)))((........))))))))))))))))...)))))))---------)........................-. ( -28.00)
>DroYak_CAF1 49009 98 - 1
GAAAUCUCAUGCGAUUUGAAGUCACUUACAAACUAGU----------GAAUGAUUUCAAAUCACUUGAUGUUUCAGUGGUAGCACAAUUUGAUAUUGUCUUUUUA-GUC
(((((.(((.(.((((((((((((.((((......))----------)).)))))))))))).).))).))))).(((....)))....................-... ( -27.50)
>consensus
GAAAUCUCUUUGGAUUUGAAGUCAUAUACAAACUUGUGGAACUUCACGAAUGAUUUCAAAUCCCUUGAUAUUUCAGUGGUAGCACAAUUUGAUAUAUUAUUUUUAAA_U
(((((.((...((((((((((((((........................))))))))))))))...)).)))))................................... (-18.02 = -18.21 +   0.19)

alignment

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secondary structure

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dotplot

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Window 3

Location 9,461,752 – 9,461,858
Length 106
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 78.26
Mean single sequence MFE -21.68
Consensus MFE -7.58
Energy contribution -7.74
Covariance contribution 0.16
Combinations/Pair 1.08
Mean z-score -1.99
Structure conservation index 0.35
SVM decision value 0.25
SVM RNA-class probability 0.651638
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9461752 106 - 20766785
CGCACGCGGUCCCUCAAAAUGUUGAAUCGAACUUAUAGAAAUCUCUUUGGAUUUGAAAU-----------CAUAUACAAACUGGUGGAACUUCACGAAUGAUUUCAAAUCCCUUGAU
......((((...((((....))))))))..............((...(((((((((((-----------(((...(.....)((((....))))..))))))))))))))...)). ( -21.50)
>DroSec_CAF1 48567 106 - 1
CGCAUGCGGUCCCUCAAAAUGUUGAAUCGAACUCUUAGAAAUCUCUUUGGAUUUGAAGU-----------CAUAUACAAACUUUUGGAACUUCACGAAUGAUUUCAAAUCCCUUGAU
......((((...((((....))))))))..............((...(((((((((((-----------(((..........(((........)))))))))))))))))...)). ( -19.00)
>DroSim_CAF1 58359 106 - 1
CGCAUGCGGUCCCUCAAAAUGUUGAAUCGAACUCUUAGAAAUAUCUUUGGAUUUGAAGU-----------CGUAUACAAACUUGUGCAACUUCACGCAUGAUUUCAAAUCCCUUGAU
..((((((((((.((((....))))..........((....)).....)))).((((((-----------.(((((......))))).))))))))))))...((((.....)))). ( -22.60)
>DroEre_CAF1 48605 103 - 1
CACA----GUCCCUCAAAAUGUUGAAUCGAACAUUUAGAAAUCUCUUUCGAUUUGAAAUCAGUCAUAAAUCACUUGCGAGCUACU----------GCAUGAUUUCAAAUCACUUGAU
....----.....((.(((((((......))))))).))..........((((((((((((((..((..((......))..))..----------)).))))))))))))....... ( -21.30)
>DroYak_CAF1 49048 92 - 1
CACA----GUCCCCCAAAAUGUUGAAUCGAACAUUUAGAAAUCUCAUGCGAUUUGAAGU-----------CACUUACAAACUAGU----------GAAUGAUUUCAAAUCACUUGAU
....----........(((((((......))))))).......(((.(.((((((((((-----------((.((((......))----------)).)))))))))))).).))). ( -24.00)
>consensus
CGCA_GCGGUCCCUCAAAAUGUUGAAUCGAACUUUUAGAAAUCUCUUUGGAUUUGAAGU___________CAUAUACAAACUAGUG_AACUUCACGAAUGAUUUCAAAUCCCUUGAU
...........................................((...(((((((((((.........................................)))))))))))...)). ( -7.58 =  -7.74 +   0.16)

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 10:36:13 2006