Locus 2334

Sequence ID 3L_DroMel_CAF1
Location 6,555,648 – 6,555,768
Length 120
Max. P 0.999737
window3606 window3607

overview

Window 6

Location 6,555,648 – 6,555,768
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 68.49
Mean single sequence MFE -28.77
Consensus MFE -10.15
Energy contribution -15.65
Covariance contribution 5.50
Combinations/Pair 1.00
Mean z-score -3.08
Structure conservation index 0.35
SVM decision value 1.06
SVM RNA-class probability 0.908947
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6555648 120 + 23771897
GAGAGAUUUCAAUAAAAAAAGUUGAAACUAACAGUGAAAUCUCUGAGGUGUUAAGCAACUUUUACGAAAGGGCCUUAACACCCUUGGGAUUUCUUUGUUACCUCUUUCAAGUUCUAUUUA
(((((((((((((.......))))))).((((((.((((((((...(((((((((...((((....))))...)))))))))...)))))))).))))))..))))))............ ( -38.60)
>DroSec_CAF1 18365 118 + 1
GAG-AAUUUCAAUGAAAAUA-UUCAUAUGAACUCUAAAAUCUGUGGGGUGUUAAGAUACUUCCACCAAAGGGUCUUAACACCCUUGGGAUUUCUUUGUUACCCUUUUCAAGUUCUAUUUA
.((-(((((..(((((....-)))))...(((....((((((..((((((((((((..(((......)))..))))))))))))..))))))....))).........)))))))..... ( -33.50)
>DroSim_CAF1 18434 115 + 1
----AGUUUCAAUAAAAAGA-UUCAGAUUAACACUAAAAUCUGGUGGGUGUUAAGAUACUCUUACCAAAGGGCCUUAACAACCUAGGGAUUUCUUUGUUACCCUUUUCAAGUUCUUUUUA
----........((((((((-.(((((((........))))))).(((((.((((.....)))).((((((.(((((......)))))...)))))).))))).........)))))))) ( -26.40)
>DroEre_CAF1 18561 94 + 1
AAG-G-UAAACAUAGGAAGA-UUCAGGAUAACACUGAAAACUGUAGGAUGUUGAGAAACUA------A--------AACACC---------UCGUUGUUACCCUUUUCAUGAUCCAUUCU
..(-(-....(((..((((.-(((((.......)))))(((...(((.((((.........------.--------))))))---------)....)))...))))..)))..))..... ( -16.60)
>consensus
GAG_AAUUUCAAUAAAAAGA_UUCAGAUUAACACUAAAAUCUGUGGGGUGUUAAGAAACUUUUACCAAAGGGCCUUAACACCCUUGGGAUUUCUUUGUUACCCUUUUCAAGUUCUAUUUA
............................(((((..(((((((..(((((((((((...(((......)))...)))))))))))..)))))))..))))).................... (-10.15 = -15.65 +   5.50)

alignment

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secondary structure

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dotplot

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Window 7

Location 6,555,648 – 6,555,768
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 68.49
Mean single sequence MFE -27.40
Consensus MFE -16.75
Energy contribution -20.56
Covariance contribution 3.81
Combinations/Pair 1.31
Mean z-score -2.58
Structure conservation index 0.61
SVM decision value 3.97
SVM RNA-class probability 0.999737
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6555648 120 - 23771897
UAAAUAGAACUUGAAAGAGGUAACAAAGAAAUCCCAAGGGUGUUAAGGCCCUUUCGUAAAAGUUGCUUAACACCUCAGAGAUUUCACUGUUAGUUUCAACUUUUUUUAUUGAAAUCUCUC
...............((((.(((((..((((((.(..((((((((((...((((....))))...))))))))))..).))))))..)))))(((((((.........))))))))))). ( -30.00)
>DroSec_CAF1 18365 118 - 1
UAAAUAGAACUUGAAAAGGGUAACAAAGAAAUCCCAAGGGUGUUAAGACCCUUUGGUGGAAGUAUCUUAACACCCCACAGAUUUUAGAGUUCAUAUGAA-UAUUUUCAUUGAAAUU-CUC
......((((((.(((((((............)))..(((((((((((..((((....))))..)))))))))))......)))).))))))..(((((-....))))).......-... ( -33.00)
>DroSim_CAF1 18434 115 - 1
UAAAAAGAACUUGAAAAGGGUAACAAAGAAAUCCCUAGGUUGUUAAGGCCCUUUGGUAAGAGUAUCUUAACACCCACCAGAUUUUAGUGUUAAUCUGAA-UCUUUUUAUUGAAACU----
((((((((.(((....))).(((((..((((((....((.((((((((..((((....))))..)))))))).))....))))))..))))).......-))))))))........---- ( -29.50)
>DroEre_CAF1 18561 94 - 1
AGAAUGGAUCAUGAAAAGGGUAACAACGA---------GGUGUU--------U------UAGUUUCUCAACAUCCUACAGUUUUCAGUGUUAUCCUGAA-UCUUCCUAUGUUUA-C-CUU
.....(((..((....(((((((((((.(---------((((((--------.------.........)))).)))...))......)))))))))..)-)..)))........-.-... ( -17.10)
>consensus
UAAAUAGAACUUGAAAAGGGUAACAAAGAAAUCCCAAGGGUGUUAAGGCCCUUUGGUAAAAGUAUCUUAACACCCCACAGAUUUCAGUGUUAAUCUGAA_UCUUUUUAUUGAAAUC_CUC
..(((((((.......(((.(((((..((((((....(((((((((((..((((....))))..)))))))))))....))))))..))))).))).......))))))).......... (-16.75 = -20.56 +   3.81)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:29:51 2006