Locus 5540

Sequence ID 3L_DroMel_CAF1
Location 15,213,908 – 15,214,032
Length 124
Max. P 0.587402
window8755 window8756

overview

Window 5

Location 15,213,908 – 15,213,998
Length 90
Sequences 6
Columns 101
Reading direction forward
Mean pairwise identity 79.30
Mean single sequence MFE -14.42
Consensus MFE -10.09
Energy contribution -10.45
Covariance contribution 0.36
Combinations/Pair 1.06
Mean z-score -1.07
Structure conservation index 0.70
SVM decision value -0.04
SVM RNA-class probability 0.512513
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15213908 90 + 23771897
UUUAUUUUCCA-------CCGAUUCU---CUUCUGUGGCUUU-UUUGCGUUAACGUUUUAAUUGAUCGCUUUCAGUUAUAAACAAGUUGGCUUUUGAUUUA
........(((-------(.((....---..)).))))....-.....(((((((((((((((((......))))))).))))..)))))).......... ( -17.10)
>DroVir_CAF1 93032 79 + 1
-------GUUG-------CUGUUGUUGUU-----GUUUU--U-UUUGCGUUAACGUUUUAAUUGAUCGCUUUCAGUUAUAAACAAGUUGGCUUUUGAUUUA
-------...(-------((...((((.(-----((...--.-...))).))))(((((((((((......))))))).)))).....))).......... ( -12.90)
>DroSec_CAF1 103415 79 + 1
------UUUCA-------CCGAUU--------CUGUGGCUUU-UUUGCGUUAACGUUUUAAUUGAUCGCUUUCAGUUAUAAACAAGUUGGCUUUUGAUUUA
------...((-------(.....--------..)))((...-...))(((((((((((((((((......))))))).))))..)))))).......... ( -13.60)
>DroSim_CAF1 110779 77 + 1
------UUCCA-------CAAAUU--------CUGAGGCUU--UUUGCGUCAAAGUUAUAAUAGAUCGCAUUCAGUUAUAAACAAGUUGGCUGUUGAU-UA
------.....-------..((((--------.(((.((..--...)).))).))))......(((((....((((((.........)))))).))))-). ( -13.30)
>DroYak_CAF1 108081 85 + 1
-----UUUCCA-------CCGAUUCU---CUGCUGUGGCUUU-UUUGCGUUAACGUUUUAAUUGAUCGCUUUCAGUUAUAAACAAGUUGGCUUUUGAUUUA
-----...(((-------(.(.....---...).))))....-.....(((((((((((((((((......))))))).))))..)))))).......... ( -14.70)
>DroAna_CAF1 98266 92 + 1
------UUUCUCCGAUUUCUGAUUCU---CGGCUGUGGCUUUUUUUGCGUUAACGUUUUAAUUGAUCGCUUUCAGUUAUAAACAAGUUGGCUUUUGAUUUA
------.....((((..........)---))).....((.......))(((((((((((((((((......))))))).))))..)))))).......... ( -14.90)
>consensus
______UUCCA_______CCGAUUCU______CUGUGGCUUU_UUUGCGUUAACGUUUUAAUUGAUCGCUUUCAGUUAUAAACAAGUUGGCUUUUGAUUUA
................................................(((((((((((((((((......))))))).))))..)))))).......... (-10.09 = -10.45 +   0.36)

alignment

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secondary structure

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dotplot

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Window 6

Location 15,213,926 – 15,214,032
Length 106
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 81.78
Mean single sequence MFE -24.43
Consensus MFE -18.56
Energy contribution -19.08
Covariance contribution 0.53
Combinations/Pair 1.04
Mean z-score -1.34
Structure conservation index 0.76
SVM decision value 0.11
SVM RNA-class probability 0.587402
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15213926 106 + 23771897
U-----CUUCUGUGGC--UUUUUUGCGUUAACGUUUUAAUUGAUCGCUUUCAGUUAUAAACAAGUUGGCUUUUGAUUUAUGAGCGCGUGCGUGCAGCAGCGACAGAGAA-AAA-----A
.-----.((((((.((--(.....(((((((((((((((((((......))))))).))))..)))))).............((((....)))).))))).))))))..-...-----. ( -29.40)
>DroVir_CAF1 93043 96 + 1
UGUU-------GUUUU----UUUUGCGUUAACGUUUUAAUUGAUCGCUUUCAGUUAUAAACAAGUUGGCUUUUGAUUUAUGAGCGCGUGCGUGCA---GCGACAGAA----AA-----A
....-------.((((----(.(((((((((((((((((((((......))))))).))))..)))))).............((((....)))).---)))).))))----).-----. ( -22.80)
>DroPse_CAF1 91529 104 + 1
--------UCUUU--A--UUUUUUGCGUUAACAUUUUAAUUGAUCGCUUUCAGUUAUAAACAAGUUGGCUUUUGAUUUAUGAGCGCGUGCGUGCA---GCGACAGAAAAAAAAAUUCAA
--------.....--.--(((((((((((..(((...(((..(..(((..(............)..)))..)..))).))).((((....)))))---))).))))))).......... ( -19.90)
>DroGri_CAF1 99373 108 + 1
UGUUUUAUUUUGUUGCUUUUUUUUGCGUUAACGUUUUAAUUGAUCGCUUUCAGUUAUAAACAAGUUGGCUUUUGAUUUAUGAGCGCGUGCGUGCA---GCGACAGAA---AAA-----A
.......((((((((((.........(((((((((((((((((......))))))).))))..)))))).............((((....)))))---)))))))))---...-----. ( -28.10)
>DroSim_CAF1 110790 100 + 1
---------CUGAGGC--UU-UUUGCGUCAAAGUUAUAAUAGAUCGCAUUCAGUUAUAAACAAGUUGGCUGUUGAU-UAUGAGCGCGAGCGUGCAGCCGCGACAGAGAA-AAA-----A
---------.(((.((--..-...)).)))...(((((((.((......)).))))))).........((((((..-..((.((....))...))....))))))....-...-----. ( -23.80)
>DroMoj_CAF1 97352 100 + 1
UGUU-------GUUUUUAUUUUUUGCGUUAACGUUUUAAUUGAUCGCUUUCAGUUAUAAACAAGUUGGCUUUUGAUUUAUGAGCGCGUGCGUGCA---GCGACAGAA----AA-----A
((((-------(((............(((((((((((((((((......))))))).))))..)))))).............((((....)))))---))))))...----..-----. ( -22.60)
>consensus
U________CUGUUGC__UUUUUUGCGUUAACGUUUUAAUUGAUCGCUUUCAGUUAUAAACAAGUUGGCUUUUGAUUUAUGAGCGCGUGCGUGCA___GCGACAGAA___AAA_____A
......................(((((((((((((((((((((......))))))).))))..)))))).............((((....))))....))))................. (-18.56 = -19.08 +   0.53)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:52:48 2006