Locus 1116

Sequence ID 3L_DroMel_CAF1
Location 3,272,090 – 3,272,183
Length 93
Max. P 0.999500
window1732 window1733

overview

Window 2

Location 3,272,090 – 3,272,183
Length 93
Sequences 5
Columns 110
Reading direction forward
Mean pairwise identity 77.33
Mean single sequence MFE -41.07
Consensus MFE -31.90
Energy contribution -32.26
Covariance contribution 0.36
Combinations/Pair 1.19
Mean z-score -5.41
Structure conservation index 0.78
SVM decision value 3.01
SVM RNA-class probability 0.998116
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3272090 93 + 23771897
UU----UC-UGAAGCCAGCAAAGUU------------AUUUUGUGGCGCCAUCUACAUAACAGCUGCGGAAGUCUGAGCUUAUUCUGUAAGCUGUGUAGAUGGCGCUGCU
((----((-((....))).)))...------------.....(..(((((((((((((..(((..((....)))))(((((((...))))))))))))))))))))..). ( -39.60)
>DroSec_CAF1 2248 94 + 1
UU----UC-UGAAGCCUACCAAGUGU-----------UUGUUGUGGCGCCAUCUACAUAACAGAGGCGGAAGCCUGAGCUUAUUUUGUUAGCAGUGUAGAUGGCGCUGCU
..----..-..((((((....)).))-----------))...(..(((((((((((((.....((((....))))..(((.........))).)))))))))))))..). ( -40.60)
>DroSim_CAF1 2659 94 + 1
UU----UC-UGAAGCCUGAAAAGUUU-----------CUUUUGUGGCGCCAUCUACAUAACAGAGGCGGAAGCCUGAGCUUAUUUUGUUAGCUGUGUAGAUGGCGCUGCU
..----..-.(((((.(....)))))-----------)....(..(((((((((((((.....((((....)))).((((.........)))))))))))))))))..). ( -43.40)
>DroEre_CAF1 2230 99 + 1
UU----UCUUGAAGUCUGAGACUUUU-------UAAAAUGUUGUGGCGCCAUCUACAUAACAGCUGGCGAAGCCGAGGCUUAUUCAGUUAGCUGUGUAGAUGGCGCUGCU
..----....((((((...)))))).-------.........(..(((((((((((...(((((((((.((((....)))).....))))))))))))))))))))..). ( -45.70)
>DroYak_CAF1 2317 110 + 1
UUUUUUUUUCCAAGUCUGAAAAGCUUACUUCAAAAAAAUGUUGUGGCGCCAUCUACAUAACAUAGGCUGAAACUUAAGCUUAUUCAUUUAGCCGUGUAGGUGGCGCUGCU
...((((((..((((((....))...))))..))))))....(..(((((((((((((......(((((((...............))))))))))))))))))))..). ( -36.06)
>consensus
UU____UC_UGAAGCCUGAAAAGUUU___________AUGUUGUGGCGCCAUCUACAUAACAGAGGCGGAAGCCUGAGCUUAUUCUGUUAGCUGUGUAGAUGGCGCUGCU
..........................................(..(((((((((((((.....((((....))))..(((.........))).)))))))))))))..). (-31.90 = -32.26 +   0.36)

alignment

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secondary structure

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dotplot

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Window 3

Location 3,272,090 – 3,272,183
Length 93
Sequences 5
Columns 110
Reading direction reverse
Mean pairwise identity 77.33
Mean single sequence MFE -30.68
Consensus MFE -24.75
Energy contribution -25.07
Covariance contribution 0.32
Combinations/Pair 1.11
Mean z-score -3.82
Structure conservation index 0.81
SVM decision value 3.66
SVM RNA-class probability 0.999500
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3272090 93 - 23771897
AGCAGCGCCAUCUACACAGCUUACAGAAUAAGCUCAGACUUCCGCAGCUGUUAUGUAGAUGGCGCCACAAAAU------------AACUUUGCUGGCUUCA-GA----AA
(((.((((((((((((.((((((.....))))))(((.((.....)))))...))))))))))))((((((..------------...)))).)))))...-..----.. ( -30.90)
>DroSec_CAF1 2248 94 - 1
AGCAGCGCCAUCUACACUGCUAACAAAAUAAGCUCAGGCUUCCGCCUCUGUUAUGUAGAUGGCGCCACAACAA-----------ACACUUGGUAGGCUUCA-GA----AA
(((.((((((((((((..(((.........)))..((((....))))......)))))))))))).....(((-----------....)))....)))...-..----.. ( -29.70)
>DroSim_CAF1 2659 94 - 1
AGCAGCGCCAUCUACACAGCUAACAAAAUAAGCUCAGGCUUCCGCCUCUGUUAUGUAGAUGGCGCCACAAAAG-----------AAACUUUUCAGGCUUCA-GA----AA
(((.((((((((((((.((((.........)))).((((....))))......)))))))))))).......(-----------((....)))..)))...-..----.. ( -30.70)
>DroEre_CAF1 2230 99 - 1
AGCAGCGCCAUCUACACAGCUAACUGAAUAAGCCUCGGCUUCGCCAGCUGUUAUGUAGAUGGCGCCACAACAUUUUA-------AAAAGUCUCAGACUUCAAGA----AA
....((((((((((((.(((...(((...((((....))))...)))..))).))))))))))))............-------..(((((...))))).....----.. ( -33.60)
>DroYak_CAF1 2317 110 - 1
AGCAGCGCCACCUACACGGCUAAAUGAAUAAGCUUAAGUUUCAGCCUAUGUUAUGUAGAUGGCGCCACAACAUUUUUUUGAAGUAAGCUUUUCAGACUUGGAAAAAAAAA
....((((((.(((((..((....((((...........))))......))..))))).)))))).......(((((((.((((...........)))).)))))))... ( -28.50)
>consensus
AGCAGCGCCAUCUACACAGCUAACAGAAUAAGCUCAGGCUUCCGCCUCUGUUAUGUAGAUGGCGCCACAACAU___________AAACUUUUCAGGCUUCA_GA____AA
....((((((((((((.(((.........((((....))))........))).))))))))))))............................................. (-24.75 = -25.07 +   0.32)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:59:29 2006