Locus 1475

Sequence ID 2R_DroMel_CAF1
Location 5,634,911 – 5,635,071
Length 160
Max. P 0.998830
window2511 window2512 window2513

overview

Window 1

Location 5,634,911 – 5,635,031
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.67
Mean single sequence MFE -24.43
Consensus MFE -22.87
Energy contribution -22.83
Covariance contribution -0.04
Combinations/Pair 1.12
Mean z-score -1.23
Structure conservation index 0.94
SVM decision value 0.58
SVM RNA-class probability 0.790364
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5634911 120 - 20766785
CUUAAAAAUACUCUUUAUGGCCAUUGAUUAAAACUGUCGGCGGCCAUAAAGAAAAGUUAAGCCAAAAUUAUAAAACGUAAUAUGAAGUGAAUGGAGCUACAGGUCUGAAAAUUAGCACGG
...........(((((((((((.(((((.......))))).)))))))))))...((((((((...(((((.....))))).((.(((.......))).))))).......))))).... ( -26.41)
>DroSec_CAF1 1619 120 - 1
CUUAAAAAUACUCUUUAUGGGCAUUGAUUAAAACUGUCGGCGGCCAUAAAGAAAAGUUAAGCCAAAAUUAUAAAGCGUAAUAUGAAGUGAAUGGAGCUACAGGUCUGAAAAUUAGCACGG
...........(((((((((.(.(((((.......))))).).)))))))))...((((((((...(((((.....))))).((.(((.......))).))))).......))))).... ( -21.81)
>DroSim_CAF1 1617 120 - 1
CUUAAAAAUACUCUUUAUGGCCAUUGAUUAAAACUGUCGGCGGCCAUAAAGAAAAGUUAAGCCAAAAUUAUAAAGCGUAAUAUGAAGUGAAUGGAGCUACAGGUCUGAAAAUUAGCACGG
...........(((((((((((.(((((.......))))).)))))))))))...((((((((...(((((.....))))).((.(((.......))).))))).......))))).... ( -26.41)
>DroEre_CAF1 1953 120 - 1
CUUAAAAAUACUCUUUAUGGCCAUUGAUUAAAAAUGUCGGCGGUCAUACAGAAAAGUUAAACCUAAAUUAUAAAGCGUAAUAUGAAGUGAAUGGAGCUACAGGUCUCGAAAUUAGCACGG
...........(((.(((((((.(((((.......))))).))))))).)))...(((((.......(((((........)))))........((((.....).)))....))))).... ( -19.70)
>DroYak_CAF1 1595 119 - 1
CUUAAAAAUACUCUUUAUGGCCAUUGAUUAAAACUGUCGGCGGCCAUAAAGAAAAGUUAAGCCUAAAUUA-AAAGCGUAAUAUAAAGUGAAUGGAGCCACAGGUCUGGAAAUUAGCACGG
(((((......(((((((((((.(((((.......))))).)))))))))))....))))).........-...............(((.......(((......))).......))).. ( -27.84)
>consensus
CUUAAAAAUACUCUUUAUGGCCAUUGAUUAAAACUGUCGGCGGCCAUAAAGAAAAGUUAAGCCAAAAUUAUAAAGCGUAAUAUGAAGUGAAUGGAGCUACAGGUCUGAAAAUUAGCACGG
...........(((((((((((.(((((.......))))).)))))))))))...((((((((....(((((........))))).(((........))).))).......))))).... (-22.87 = -22.83 +  -0.04)

alignment

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secondary structure

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dotplot

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Window 2

Location 5,634,951 – 5,635,071
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 87.16
Mean single sequence MFE -30.27
Consensus MFE -23.66
Energy contribution -24.38
Covariance contribution 0.72
Combinations/Pair 1.10
Mean z-score -3.61
Structure conservation index 0.78
SVM decision value 3.05
SVM RNA-class probability 0.998258
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5634951 120 + 20766785
UUACGUUUUAUAAUUUUGGCUUAACUUUUCUUUAUGGCCGCCGACAGUUUUAAUCAAUGGCCAUAAAGAGUAUUUUUAAGCCAAAUGAUGCUAAUUUUUUGGAAUUGAUAGCGCUAAUUU
...((((...((((((((((((((...(((((((((((((..((.........))..))))))))))))).....)))))))))......((((....)))))))))..))))....... ( -31.70)
>DroSec_CAF1 1659 97 + 1
UUACGCUUUAUAAUUUUGGCUUAACUUUUCUUUAUGGCCGCCGACAGUUUUAAUCAAUGCCCAUAAAGAGUAUUUUUAAGCCAAAUGAUGCUAA-----------------------UUU
....((.((((....(((((((((...((((((((((.((..((.........))..)).)))))))))).....))))))))))))).))...-----------------------... ( -23.20)
>DroSim_CAF1 1657 120 + 1
UUACGCUUUAUAAUUUUGGCUUAACUUUUCUUUAUGGCCGCCGACAGUUUUAAUCAAUGGCCAUAAAGAGUAUUUUUAAGCCAAAUGAUGCUAAUUUUUUGGAAUUGAUAGCGCUAAUUU
...((((...((((((((((((((...(((((((((((((..((.........))..))))))))))))).....)))))))))......((((....)))))))))..))))....... ( -34.10)
>DroEre_CAF1 1993 120 + 1
UUACGCUUUAUAAUUUAGGUUUAACUUUUCUGUAUGACCGCCGACAUUUUUAAUCAAUGGCCAUAAAGAGUAUUUUUAAGCCAAAUGAUGUUAAUUUAUGGGAAUUAAAAGCGCUAAUUU
...((((((.((((((.((((..((......))..)))).(((.........((((.((((..((((((...)))))).))))..)))).........)))))))))))))))....... ( -22.97)
>DroYak_CAF1 1635 118 + 1
UUACGCUUU-UAAUUUAGGCUUAACUUUUCUUUAUGGCCGCCGACAGUUUUAAUCAAUGGCCAUAAAGAGUAUUUUUAAGCCAAAUGAUGCUAAUUUGUA-UAAUUAAGAGCGCUAAUUU
...((((((-(((((..(((((((...(((((((((((((..((.........))..))))))))))))).....))))))).....((((......)))-))))))))))))....... ( -39.40)
>consensus
UUACGCUUUAUAAUUUUGGCUUAACUUUUCUUUAUGGCCGCCGACAGUUUUAAUCAAUGGCCAUAAAGAGUAUUUUUAAGCCAAAUGAUGCUAAUUUUUUGGAAUUAAUAGCGCUAAUUU
....((.(((....((((((((((...(((((((((((((..((.........))..))))))))))))).....))))))))))))).))............................. (-23.66 = -24.38 +   0.72)

alignment

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secondary structure

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dotplot

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Window 3

Location 5,634,951 – 5,635,071
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 87.16
Mean single sequence MFE -32.95
Consensus MFE -27.52
Energy contribution -28.36
Covariance contribution 0.84
Combinations/Pair 1.04
Mean z-score -5.57
Structure conservation index 0.84
SVM decision value 3.24
SVM RNA-class probability 0.998830
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5634951 120 - 20766785
AAAUUAGCGCUAUCAAUUCCAAAAAAUUAGCAUCAUUUGGCUUAAAAAUACUCUUUAUGGCCAUUGAUUAAAACUGUCGGCGGCCAUAAAGAAAAGUUAAGCCAAAAUUAUAAAACGUAA
......((((((...............))))....((((((((((......(((((((((((.(((((.......))))).)))))))))))....))))))))))..........)).. ( -36.26)
>DroSec_CAF1 1659 97 - 1
AAA-----------------------UUAGCAUCAUUUGGCUUAAAAAUACUCUUUAUGGGCAUUGAUUAAAACUGUCGGCGGCCAUAAAGAAAAGUUAAGCCAAAAUUAUAAAGCGUAA
...-----------------------.........((((((((((......(((((((((.(.(((((.......))))).).)))))))))....)))))))))).............. ( -28.30)
>DroSim_CAF1 1657 120 - 1
AAAUUAGCGCUAUCAAUUCCAAAAAAUUAGCAUCAUUUGGCUUAAAAAUACUCUUUAUGGCCAUUGAUUAAAACUGUCGGCGGCCAUAAAGAAAAGUUAAGCCAAAAUUAUAAAGCGUAA
......((((((...............))))....((((((((((......(((((((((((.(((((.......))))).)))))))))))....))))))))))........)).... ( -38.46)
>DroEre_CAF1 1993 120 - 1
AAAUUAGCGCUUUUAAUUCCCAUAAAUUAACAUCAUUUGGCUUAAAAAUACUCUUUAUGGCCAUUGAUUAAAAAUGUCGGCGGUCAUACAGAAAAGUUAAACCUAAAUUAUAAAGCGUAA
......((((((((((((........(((((...((((.......))))..(((.(((((((.(((((.......))))).))))))).)))...))))).....))))).))))))).. ( -24.32)
>DroYak_CAF1 1635 118 - 1
AAAUUAGCGCUCUUAAUUA-UACAAAUUAGCAUCAUUUGGCUUAAAAAUACUCUUUAUGGCCAUUGAUUAAAACUGUCGGCGGCCAUAAAGAAAAGUUAAGCCUAAAUUA-AAAGCGUAA
......(((((.((((((.-...((((.......))))(((((((......(((((((((((.(((((.......))))).)))))))))))....)))))))..)))))-).))))).. ( -37.40)
>consensus
AAAUUAGCGCUAUCAAUUCCAAAAAAUUAGCAUCAUUUGGCUUAAAAAUACUCUUUAUGGCCAUUGAUUAAAACUGUCGGCGGCCAUAAAGAAAAGUUAAGCCAAAAUUAUAAAGCGUAA
...................................((((((((((......(((((((((((.(((((.......))))).)))))))))))....)))))))))).............. (-27.52 = -28.36 +   0.84)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:05:46 2006