Locus 7867

Sequence ID 3R_DroMel_CAF1
Location 21,057,172 – 21,057,308
Length 136
Max. P 0.989265
window12673 window12674 window12675

overview

Window 3

Location 21,057,172 – 21,057,282
Length 110
Sequences 4
Columns 114
Reading direction forward
Mean pairwise identity 88.54
Mean single sequence MFE -33.50
Consensus MFE -27.29
Energy contribution -27.85
Covariance contribution 0.56
Combinations/Pair 1.09
Mean z-score -3.22
Structure conservation index 0.81
SVM decision value 2.16
SVM RNA-class probability 0.989265
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21057172 110 + 27905053
UCAUCCAUAUAA-AAUAGGUAUGAAGAUCAGUCUGUUAUACCCUCAUGGACUUAAAGAGUAUAUAGACAACAGCAGCCACUGAAGACGGUGGCAAUGUUUUUGUUU---UUGUU
...(((((....-....((((((((((....))).)))))))...)))))..........(((.((((((.(((((((((((....)))))))..)))).))))))---.))). ( -28.20)
>DroSec_CAF1 10544 111 + 1
UCAUCCAUAUGAAAAUAGGUAUGCAGAUCAGUCUGUUAUACCCUCAUGGACUUAAAGAGUAUAUAGACAACAGCAGCCACUGAAGACGGUGGCAAUGUUUUUGUUG---UUGUU
...(((((((....)))((((((((((....)))).))))))....))))...............(((((((((((((((((....)))))))........)))))---))))) ( -35.00)
>DroSim_CAF1 9751 110 + 1
UCAUCCAUAUGA-AAUAGGUAUGCAGAUCAGUCUGUUAUACCCUCAUGGACUUAAAGAGUAUAUAGACAACAGCAGCCACUGAAGACGGUGGCAAUGUUUUUGUUG---UUGUU
...((((..(((-....((((((((((....)))).)))))).)))))))...............(((((((((((((((((....)))))))........)))))---))))) ( -34.60)
>DroYak_CAF1 10064 108 + 1
UCUUCCAUAUAA-AAUGGGUAUGCAGAUCGGUCUAGCAUACCUCUAUGGAUUCAAAGAGU-----CACAACAGCAGCCACUGAAGACGGUGGCAAUGCUUUUGUUUUUGUUGUU
...((((((...-...(((((((((((....))).)))))))).))))))....((.((.-----.((((.(((((((((((....)))))))..)))).))))..)).))... ( -36.20)
>consensus
UCAUCCAUAUAA_AAUAGGUAUGCAGAUCAGUCUGUUAUACCCUCAUGGACUUAAAGAGUAUAUAGACAACAGCAGCCACUGAAGACGGUGGCAAUGUUUUUGUUG___UUGUU
...(((((((....)))((((((((((....)))).))))))....))))...............(((((.(((((((((((....)))))))..)))).)))))......... (-27.29 = -27.85 +   0.56)

alignment

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secondary structure

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Window 4

Location 21,057,172 – 21,057,282
Length 110
Sequences 4
Columns 114
Reading direction reverse
Mean pairwise identity 88.54
Mean single sequence MFE -27.00
Consensus MFE -19.92
Energy contribution -20.18
Covariance contribution 0.25
Combinations/Pair 1.11
Mean z-score -2.29
Structure conservation index 0.74
SVM decision value 0.87
SVM RNA-class probability 0.871750
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21057172 110 - 27905053
AACAA---AAACAAAAACAUUGCCACCGUCUUCAGUGGCUGCUGUUGUCUAUAUACUCUUUAAGUCCAUGAGGGUAUAACAGACUGAUCUUCAUACCUAUU-UUAUAUGGAUGA
.....---.......((((..(((((.(....).)))))...))))((((.(((((((((.........)))))))))..))))......((((.((....-......)))))) ( -24.10)
>DroSec_CAF1 10544 111 - 1
AACAA---CAACAAAAACAUUGCCACCGUCUUCAGUGGCUGCUGUUGUCUAUAUACUCUUUAAGUCCAUGAGGGUAUAACAGACUGAUCUGCAUACCUAUUUUCAUAUGGAUGA
.((((---((.((........(((((.(....).))))))).))))))...............((((((((((((((..((((....)))).))))))....)))..))))).. ( -25.50)
>DroSim_CAF1 9751 110 - 1
AACAA---CAACAAAAACAUUGCCACCGUCUUCAGUGGCUGCUGUUGUCUAUAUACUCUUUAAGUCCAUGAGGGUAUAACAGACUGAUCUGCAUACCUAUU-UCAUAUGGAUGA
.((((---((.((........(((((.(....).))))))).))))))...............((((((((((((((..((((....)))).))))))...-)))..))))).. ( -25.90)
>DroYak_CAF1 10064 108 - 1
AACAACAAAAACAAAAGCAUUGCCACCGUCUUCAGUGGCUGCUGUUGUG-----ACUCUUUGAAUCCAUAGAGGUAUGCUAGACCGAUCUGCAUACCCAUU-UUAUAUGGAAGA
.....((((.((((.((((..(((((.(....).))))))))).)))).-----....))))..((((((..(((((((.(((....))))))))))....-...))))))... ( -32.50)
>consensus
AACAA___AAACAAAAACAUUGCCACCGUCUUCAGUGGCUGCUGUUGUCUAUAUACUCUUUAAGUCCAUGAGGGUAUAACAGACUGAUCUGCAUACCUAUU_UCAUAUGGAUGA
...............((((..(((((.(....).)))))...)))).................(((((((.((((((..((((....)))).)))))).......))))))).. (-19.92 = -20.18 +   0.25)

alignment

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secondary structure

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Window 5

Location 21,057,209 – 21,057,308
Length 99
Sequences 5
Columns 106
Reading direction forward
Mean pairwise identity 78.29
Mean single sequence MFE -29.68
Consensus MFE -15.07
Energy contribution -15.99
Covariance contribution 0.92
Combinations/Pair 1.20
Mean z-score -2.37
Structure conservation index 0.51
SVM decision value 1.43
SVM RNA-class probability 0.953498
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21057209 99 + 27905053
UACCCUCAUGGACUUAAAGAGUAUAUAGA-CAACAGCAGCCACUGAAGACGGUGGCAAUGUUUUUGUUU---UUGUUUCCUUGGUUCCGGUAUUUUCGAG---CGA
..(.(((..(((.((((.(((.(((.(((-(((.(((((((((((....)))))))..)))).))))))---.)))))).)))).)))((.....)))))---.). ( -27.70)
>DroSec_CAF1 10582 99 + 1
UACCCUCAUGGACUUAAAGAGUAUAUAGA-CAACAGCAGCCACUGAAGACGGUGGCAAUGUUUUUGUUG---UUGUUUCCUUGGUUCCGGUAUUUUUGAG---CCA
........(((.((((((((......(((-(((((((((((((((....)))))))........)))))---))))))((........))..))))))))---))) ( -29.90)
>DroSim_CAF1 9788 99 + 1
UACCCUCAUGGACUUAAAGAGUAUAUAGA-CAACAGCAGCCACUGAAGACGGUGGCAAUGUUUUUGUUG---UUGUUUCCUUGGUUCCGGUAUUUUUGAG---CCA
........(((.((((((((......(((-(((((((((((((((....)))))))........)))))---))))))((........))..))))))))---))) ( -29.90)
>DroYak_CAF1 10101 97 + 1
UACCUCUAUGGAUUCAAAGAGU-----CA-CAACAGCAGCCACUGAAGACGGUGGCAAUGCUUUUGUUUUUGUUGUUUCCUUGGUUCCGGUAUUUUUGAG---CCA
.........(((..(((.(((.-----.(-(((.(((((((((((....)))))))..)))).)))).))).)))..))).((((((..(....)..)))---))) ( -30.50)
>DroAna_CAF1 9332 91 + 1
------------CUCAAAGGGUAUGCAGAAGGACAACAACCACUAAAGGCGGUUGAAAAGUUCUUGUUG---UUGUUUCCUUGGUUCCGGAACACCGGGACUACUA
------------....(((((...((((((((((..(((((.(.....).)))))....)))))).)))---)....)))))((((((((....)))))))).... ( -30.40)
>consensus
UACCCUCAUGGACUUAAAGAGUAUAUAGA_CAACAGCAGCCACUGAAGACGGUGGCAAUGUUUUUGUUG___UUGUUUCCUUGGUUCCGGUAUUUUUGAG___CCA
........((((.((((.(((.........(((.(((((((((((....)))))))..)))).)))..........))).)))).))))................. (-15.07 = -15.99 +   0.92)

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 12:56:43 2006