Locus 4806

Sequence ID 3R_DroMel_CAF1
Location 12,563,299 – 12,563,406
Length 107
Max. P 0.990900
window7881 window7882

overview

Window 1

Location 12,563,299 – 12,563,406
Length 107
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 75.37
Mean single sequence MFE -22.07
Consensus MFE -13.60
Energy contribution -14.02
Covariance contribution 0.42
Combinations/Pair 1.18
Mean z-score -1.90
Structure conservation index 0.62
SVM decision value 1.34
SVM RNA-class probability 0.944242
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12563299 107 + 27905053
CGUUUUAAUUGAAUAA----CUUAA--------CUGUUUCUUACUUUUUUCUGUGUGAAUUUGGGUGGUAAUUUGAAGGG-GCCUAUCUCAACGCCCUCCAAAUUUAUCACCCCAAUCGU
.......((((.....----.....--------....(((.(((........))).)))...(((((((((((((..(((-((..........))))).)))).)))))))))))))... ( -24.30)
>DroSec_CAF1 52172 107 + 1
CAUUUUAGUUGAAUAA----CUUUA--------CUGUUUCUUACUUUUUUCUGUGUAAAUUUGGGUGGUACUUUGAAGGG-GCCUAUCUCAACGCCCUCCAAAUUUAUCACCCCAAUCGU
.......((((.....----.....--------.......((((..........))))....((((((((..((...(((-((..........)))))...))..))))))))))))... ( -21.00)
>DroSim_CAF1 52136 102 + 1
CACUUUACUAGAAUAA----C-------------UGUUUCUUACUUUUUUCUGUGUGAAUUUGGGUGGUACUUUGAAGGG-GCCUAUCUCAACGCCCUCCAAAUUUAUCACCCCAAUCGU
...((((((((((...----.-------------.((.....))....))))).)))))...((((((((..((...(((-((..........)))))...))..))))))))....... ( -25.10)
>DroEre_CAF1 50105 106 + 1
UAUAUUGUUUUAAUAA----CCUAA--------UUGUUUC-UACUUUUCUCUGUGUGAAUUUGGGUGGUACUUUGAAGGG-GCCUAUCUCAACGCCCUCCAAAUUUAUCACCCCAAUCGU
................----....(--------(((.(((-(((........))).)))...((((((((..((...(((-((..........)))))...))..))))))))))))... ( -21.40)
>DroYak_CAF1 49961 103 + 1
CAUAUUUAUUUUAUAA----CUUAC--------UU---AC-UACUUCUUUCUGUGUGAAUUUGGGUGGUACUUUGAAGGG-GCCUAUCUCAACGCCCUCCAAAUUUAUCACCCCAAUCGU
................----.....--------((---((-.((........))))))....((((((((..((...(((-((..........)))))...))..))))))))....... ( -21.40)
>DroAna_CAF1 51359 103 + 1
UAUAUUGAUAUAGUAAGUCCCAUAUUUGUUGCUCUGUUUCUAAUGUU-----------------UUGUUUUUUUGAAGGGCGCUUUUAUCGGCCUCCUUCGGAUUUAUCACACCAAUCGU
...((((.....((((((((.(((((.(..((...))..).))))).-----------------..........((((((.(((......))).)))))))))))))).....))))... ( -19.20)
>consensus
CAUAUUAAUUGAAUAA____CUUAA________CUGUUUCUUACUUUUUUCUGUGUGAAUUUGGGUGGUACUUUGAAGGG_GCCUAUCUCAACGCCCUCCAAAUUUAUCACCCCAAUCGU
..............................................................((((((((.((((.((((.(..........).)))).))))..))))))))....... (-13.60 = -14.02 +   0.42)

alignment

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secondary structure

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dotplot

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Window 2

Location 12,563,299 – 12,563,406
Length 107
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 75.37
Mean single sequence MFE -25.20
Consensus MFE -18.53
Energy contribution -19.42
Covariance contribution 0.89
Combinations/Pair 1.12
Mean z-score -2.61
Structure conservation index 0.74
SVM decision value 2.24
SVM RNA-class probability 0.990900
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12563299 107 - 27905053
ACGAUUGGGGUGAUAAAUUUGGAGGGCGUUGAGAUAGGC-CCCUUCAAAUUACCACCCAAAUUCACACAGAAAAAAGUAAGAAACAG--------UUAAG----UUAUUCAAUUAAAACG
..((((((((((...(((((((((((.(((......)))-)))))))))))..)))))...(((..((........))..))).)))--------))...----................ ( -28.00)
>DroSec_CAF1 52172 107 - 1
ACGAUUGGGGUGAUAAAUUUGGAGGGCGUUGAGAUAGGC-CCCUUCAAAGUACCACCCAAAUUUACACAGAAAAAAGUAAGAAACAG--------UAAAG----UUAUUCAACUAAAAUG
...(((((((((.....(((((((((.(((......)))-)))))))))....)))))...(((((..........)))))...)))--------)..((----((....))))...... ( -26.30)
>DroSim_CAF1 52136 102 - 1
ACGAUUGGGGUGAUAAAUUUGGAGGGCGUUGAGAUAGGC-CCCUUCAAAGUACCACCCAAAUUCACACAGAAAAAAGUAAGAAACA-------------G----UUAUUCUAGUAAAGUG
..((((((((((.....(((((((((.(((......)))-)))))))))....)))))...(((..((........))..))).))-------------)----)).............. ( -26.50)
>DroEre_CAF1 50105 106 - 1
ACGAUUGGGGUGAUAAAUUUGGAGGGCGUUGAGAUAGGC-CCCUUCAAAGUACCACCCAAAUUCACACAGAGAAAAGUA-GAAACAA--------UUAGG----UUAUUAAAACAAUAUA
..((((((((((.....(((((((((.(((......)))-)))))))))....)))))...(((.....))).......-....)))--------))...----................ ( -26.00)
>DroYak_CAF1 49961 103 - 1
ACGAUUGGGGUGAUAAAUUUGGAGGGCGUUGAGAUAGGC-CCCUUCAAAGUACCACCCAAAUUCACACAGAAAGAAGUA-GU---AA--------GUAAG----UUAUAAAAUAAAUAUG
..((...(((((.....(((((((((.(((......)))-)))))))))....)))))....))...............-..---..--------.....----................ ( -24.50)
>DroAna_CAF1 51359 103 - 1
ACGAUUGGUGUGAUAAAUCCGAAGGAGGCCGAUAAAAGCGCCCUUCAAAAAAACAA-----------------AACAUUAGAAACAGAGCAACAAAUAUGGGACUUACUAUAUCAAUAUA
...(((((((((.(((.((((((((..((........))..)))))..........-----------------..(((...................)))))).))).)))))))))... ( -19.91)
>consensus
ACGAUUGGGGUGAUAAAUUUGGAGGGCGUUGAGAUAGGC_CCCUUCAAAGUACCACCCAAAUUCACACAGAAAAAAGUAAGAAACAG________UUAAG____UUAUUAAAUUAAAAUG
.......(((((.....(((((((((.(((......))).)))))))))....))))).............................................................. (-18.53 = -19.42 +   0.89)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:39:21 2006