Locus 1789

Sequence ID X_DroMel_CAF1
Location 4,937,936 – 4,938,063
Length 127
Max. P 0.881993
window2923 window2924

overview

Window 3

Location 4,937,936 – 4,938,037
Length 101
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 79.78
Mean single sequence MFE -36.00
Consensus MFE -21.76
Energy contribution -21.90
Covariance contribution 0.14
Combinations/Pair 1.12
Mean z-score -2.24
Structure conservation index 0.60
SVM decision value 0.92
SVM RNA-class probability 0.881993
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4937936 101 + 22224390
--GG----C--------UCACUUGAGGGUCACUCGCCAUGUUGGCUUAAUCGGUCAUUGGGCUUGUUAUACGGCUCAAUUAUGCC-CGUUUUGCCAUGUGGCGCAU---UU-GCCUCUGG
--((----(--------......(((.....)))(((((((.(((..(((.(((.((((((((........))))))))...)))-.)))..))))))))))....---..-)))..... ( -36.10)
>DroPse_CAF1 11789 114 + 1
--UGGGGGCCAAAACAUCCGUCCGUGGGUCAGUCGACAUGCUGGCUUAAUCGGUCAUUGGGCUUGUUAGACGGCUCAAUUAUGCCCCGUUUUGCCAUGUGGCGCAU---UU-CUCUCUCC
--..(((((..........(.((((((((((((......)))))))))..))).)((((((((........))))))))...))))).....(((....)))....---..-........ ( -37.40)
>DroEre_CAF1 12328 96 + 1
--GG----C--------UCACUUGAGGGUCACUCGCCAUGUUGGCUUAAUCGGUCAUUGGGCUUGUUAUACGGCUCAAUUAUGCC-CGUUUUGCCAUGUGGCGCAU---UU-GCC-----
--((----(--------((......)))))...((((((((.(((..(((.(((.((((((((........))))))))...)))-.)))..)))))))))))...---..-...----- ( -34.90)
>DroWil_CAF1 11544 104 + 1
--UU----G--------UUGUUUGGGGGUCACUCUCCAUGUUGGCUUAAUCGGUCAUUGGGCUUGUUAUACAGCUCAAUUAUGUC-CAUUUUGCCAUGUGGCGCACCCUUG-AGCUCUGC
--..----.--------..(((..(((((....(.((((((.(((..(((.((.(((((((((.(.....)))))))...))).)-))))..))))))))).).)))))..-)))..... ( -35.80)
>DroYak_CAF1 11746 101 + 1
--GG----C--------UCACUUGAGGGUCACUCGCCAUGUUGGCUUAAUCGGUCAUUGGGCUUGUUAUACGGCUCAAUUAUGCC-CGUUUUGCCAUGUGGCGCAU---UU-GCCUGUGG
--((----(--------......(((.....)))(((((((.(((..(((.(((.((((((((........))))))))...)))-.)))..))))))))))....---..-)))..... ( -36.10)
>DroAna_CAF1 11723 101 + 1
CAAG----U--------UCACUUUUAGGCCACUCGCCAUGUUGGCUUAAUCGGUCAUUGGGCUUGUUAUACGGCUCAAUUAUGGC-CAUUUGGCCAUGUGGUGCAU---GCAGCCAC---
....----.--------.........(((((..((((((((.((((.(((.((((((((((((........))))))...)))))-)))).))))))))))))..)---)..)))..--- ( -35.70)
>consensus
__GG____C________UCACUUGAGGGUCACUCGCCAUGUUGGCUUAAUCGGUCAUUGGGCUUGUUAUACGGCUCAAUUAUGCC_CGUUUUGCCAUGUGGCGCAU___UU_GCCUCUG_
.................................(((((((.((((..((..(((.((((((((........))))))))...)))...))..)))))))))))................. (-21.76 = -21.90 +   0.14)

alignment

Postscript

secondary structure

Postscript

dotplot

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Window 4

Location 4,937,962 – 4,938,063
Length 101
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 71.85
Mean single sequence MFE -25.18
Consensus MFE -14.53
Energy contribution -14.25
Covariance contribution -0.28
Combinations/Pair 1.13
Mean z-score -1.41
Structure conservation index 0.58
SVM decision value 0.30
SVM RNA-class probability 0.680600
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4937962 101 + 22224390
UUGGCUUAAUCGGUCAUUGGGCUUGUUAUACGGCUCAAUUAUGCC-CGUUUUGCCAUGUGGCGCAU---UU-GCCUCUGGCCCUCUGGUUA-CACCCCCCUCCCCAC-------------
.((((..(((.(((.((((((((........))))))))...)))-.)))..))))((((((.((.---..-(((...)))....))))))-)).............------------- ( -27.20)
>DroPse_CAF1 11827 93 + 1
CUGGCUUAAUCGGUCAUUGGGCUUGUUAGACGGCUCAAUUAUGCCCCGUUUUGCCAUGUGGCGCAU---UU-CUCUCUCCACCCCAC-UCACCCCUGG----------------------
.((((..(((.((.(((((((((........))))))...))).)).)))..)))).((((.(...---..-....).)))).(((.-.......)))---------------------- ( -20.30)
>DroSim_CAF1 3213 91 + 1
UUGGCUUAAUCGGUCAUUGGGCUUGUUAUACGGCUCAAUUAUGCC-CGUUUUGCCAUGUGGCGCAU---UU-GCCUCUGGCCCUCUG-UUA-CAACCC----------------------
.((((..(((.(((.((((((((........))))))))...)))-.)))..))))(((((((...---..-(((...)))....))-)))-))....---------------------- ( -27.10)
>DroEre_CAF1 12354 83 + 1
UUGGCUUAAUCGGUCAUUGGGCUUGUUAUACGGCUCAAUUAUGCC-CGUUUUGCCAUGUGGCGCAU---UU-GCC--------UCCG-GUC-CUCUGG----------------------
.((((..(((.(((.((((((((........))))))))...)))-.)))..))))...((((...---.)-)))--------.(((-(..-..))))---------------------- ( -26.10)
>DroWil_CAF1 11570 110 + 1
UUGGCUUAAUCGGUCAUUGGGCUUGUUAUACAGCUCAAUUAUGUC-CAUUUUGCCAUGUGGCGCACCCUUG-AGCUCUGCUCCUCC--UUC-CAACUC-----CCAAAACUUCCUGCUUC
.((((..(((.((.(((((((((.(.....)))))))...))).)-))))..)))).(..(.((.......-.)).)..)......--...-......-----................. ( -22.80)
>DroAna_CAF1 11751 84 + 1
UUGGCUUAAUCGGUCAUUGGGCUUGUUAUACGGCUCAAUUAUGGC-CAUUUGGCCAUGUGGUGCAU---GCAGCCAC---CCC----------AC--C----CCCAC-------------
.(((((.(((.((((((((((((........))))))...)))))-)))).))))).(((((....---...)))))---...----------..--.----.....------------- ( -27.60)
>consensus
UUGGCUUAAUCGGUCAUUGGGCUUGUUAUACGGCUCAAUUAUGCC_CGUUUUGCCAUGUGGCGCAU___UU_GCCUCUG_CCCUCCG_UUA_CACCCC______________________
.(((((.....)))))(((((((........)))))))..............(((....))).......................................................... (-14.53 = -14.25 +  -0.28)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:18:56 2006