Locus 157

Sequence ID 3R_DroMel_CAF1
Location 800,249 – 800,409
Length 160
Max. P 0.998353
window258 window259 window260 window261

overview

Window 8

Location 800,249 – 800,369
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 77.90
Mean single sequence MFE -32.10
Consensus MFE -25.91
Energy contribution -26.60
Covariance contribution 0.69
Combinations/Pair 1.12
Mean z-score -2.08
Structure conservation index 0.81
SVM decision value 1.83
SVM RNA-class probability 0.979343
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 800249 120 + 27905053
CUUGGAAAUUUCGAAGGCAUCGCGAUCGGCUUGGUAAAAUGGCCAAGCAAAUAUGCAGGAAACUUCACUUUCCUGCACUUUGUGCUCGGCCUGCCUACUACUAAUUUGUGUUUGGCACUU
..............((((..(((((...(((((((......))))))).....(((((((((......)))))))))..)))))....))))(((...(((......)))...))).... ( -39.40)
>DroSec_CAF1 38278 120 + 1
CUUGGAAACUUCGAAGGCAUGGCGAUCGACUUUGUAAAAUGGCCAAGCAAAUAUGCAGGAAACUUCACUUUCUUGCACUUUGUGCUCGGCCUGCCUACUACUAAUUUGUGUUUGGCACUU
...(....).....(((((..((((......)))).....((((.((((....(((((((((......))))))))).....)))).)))))))))...........(((.....))).. ( -35.40)
>DroEre_CAF1 21874 106 + 1
CUUGGCAUUU-GGGA-------------GAUUUGUAAAAUGGCCAGGCAAAUAUGCAGGAAACUUCACUUUCCUGCACUUUGUGCUCGGACUGCCUACUACUAAUUUGUGUUUGGCACUU
((.(((((..-((..-------------.((((((...........)))))).(((((((((......)))))))))))..))))).))..((((...(((......)))...))))... ( -29.80)
>DroYak_CAF1 27734 92 + 1
----------------------------AUUUUGUAAGAAGGCCAGGAAAAUAUGCAAGAAACUUCAGUUUCCAGCACUUUGUGCCCGGACUGCCUACUACUAAUUUGUGUUAGGCACUU
----------------------------............((((.((..((..(((..(((((....)))))..)))..))...)).)).))(((((.(((......))).))))).... ( -23.80)
>consensus
CUUGGAAAUU_CGAA_____________ACUUUGUAAAAUGGCCAAGCAAAUAUGCAGGAAACUUCACUUUCCUGCACUUUGUGCUCGGACUGCCUACUACUAAUUUGUGUUUGGCACUU
........................................((((.((((....(((((((((......))))))))).....)))).))))((((...(((......)))...))))... (-25.91 = -26.60 +   0.69)

alignment

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secondary structure

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dotplot

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Window 9

Location 800,249 – 800,369
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 77.90
Mean single sequence MFE -32.45
Consensus MFE -28.20
Energy contribution -29.32
Covariance contribution 1.12
Combinations/Pair 1.07
Mean z-score -2.59
Structure conservation index 0.87
SVM decision value 3.08
SVM RNA-class probability 0.998353
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 800249 120 - 27905053
AAGUGCCAAACACAAAUUAGUAGUAGGCAGGCCGAGCACAAAGUGCAGGAAAGUGAAGUUUCCUGCAUAUUUGCUUGGCCAUUUUACCAAGCCGAUCGCGAUGCCUUCGAAAUUUCCAAG
..(((.....))).........(.((((((((((((((.((.((((((((((......)))))))))).)))))))))))..........((.....))..))))).)............ ( -41.90)
>DroSec_CAF1 38278 120 - 1
AAGUGCCAAACACAAAUUAGUAGUAGGCAGGCCGAGCACAAAGUGCAAGAAAGUGAAGUUUCCUGCAUAUUUGCUUGGCCAUUUUACAAAGUCGAUCGCCAUGCCUUCGAAGUUUCCAAG
...((((.(..((......))..).))))(((((((((.((.(((((.((((......)))).))))).)))))))))))...........((((..((...))..)))).......... ( -34.70)
>DroEre_CAF1 21874 106 - 1
AAGUGCCAAACACAAAUUAGUAGUAGGCAGUCCGAGCACAAAGUGCAGGAAAGUGAAGUUUCCUGCAUAUUUGCCUGGCCAUUUUACAAAUC-------------UCCC-AAAUGCCAAG
..(((.....)))............((((.(((..((((...)))).)))..(((((((..((.(((....)))..))..))))))).....-------------....-...))))... ( -26.00)
>DroYak_CAF1 27734 92 - 1
AAGUGCCUAACACAAAUUAGUAGUAGGCAGUCCGGGCACAAAGUGCUGGAAACUGAAGUUUCUUGCAUAUUUUCCUGGCCUUCUUACAAAAU----------------------------
...((((((..((......))..))))))(.(((((...((.((((.((((((....)))))).)))).))..))))).)............---------------------------- ( -27.20)
>consensus
AAGUGCCAAACACAAAUUAGUAGUAGGCAGGCCGAGCACAAAGUGCAGGAAAGUGAAGUUUCCUGCAUAUUUGCCUGGCCAUUUUACAAAGC_____________UUCG_AAUUUCCAAG
...((((.(..((......))..).))))(((((((((.((.((((((((((......)))))))))).)))))))))))........................................ (-28.20 = -29.32 +   1.12)

alignment

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secondary structure

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dotplot

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Window 0

Location 800,289 – 800,409
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 93.89
Mean single sequence MFE -34.62
Consensus MFE -29.25
Energy contribution -30.00
Covariance contribution 0.75
Combinations/Pair 1.11
Mean z-score -1.50
Structure conservation index 0.84
SVM decision value -0.04
SVM RNA-class probability 0.511716
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 800289 120 + 27905053
GGCCAAGCAAAUAUGCAGGAAACUUCACUUUCCUGCACUUUGUGCUCGGCCUGCCUACUACUAAUUUGUGUUUGGCACUUGGCUGUAUCGCUUUUUGAAGUCUUCGCGCUGUUCGUGAUG
((((.((((....(((((((((......))))))))).....)))).))))((((...(((......)))...))))...((((.((........)).)))).(((((.....))))).. ( -39.20)
>DroSec_CAF1 38318 120 + 1
GGCCAAGCAAAUAUGCAGGAAACUUCACUUUCUUGCACUUUGUGCUCGGCCUGCCUACUACUAAUUUGUGUUUGGCACUUGGCUGUAUCGCUUUUUGAAGUCUUCGCGCUGUUCGUGAUG
((((.((((....(((((((((......))))))))).....)))).))))((((...(((......)))...))))...((((.((........)).)))).(((((.....))))).. ( -36.50)
>DroEre_CAF1 21900 119 + 1
GGCCAGGCAAAUAUGCAGGAAACUUCACUUUCCUGCACUUUGUGCUCGGACUGCCUACUACUAAUUUGUGUUUGGCACUUGGCUGUAUCG-UUUUUGAAGUCUUCGCGCUGUUCGUGAUG
(((((((((....(((((((((......))))))))).....)))).....((((...(((......)))...))))..)))))......-............(((((.....))))).. ( -33.90)
>DroYak_CAF1 27746 120 + 1
GGCCAGGAAAAUAUGCAAGAAACUUCAGUUUCCAGCACUUUGUGCCCGGACUGCCUACUACUAAUUUGUGUUAGGCACUUGGUUGUAUCUCUUUUUGAAGUCUUCGCGCUGUUCAUGAUA
...((.(((.....((..((((((((((..(((.((((...))))..))).((((((.(((......))).)))))).................))))))).)))..))..))).))... ( -28.90)
>consensus
GGCCAAGCAAAUAUGCAGGAAACUUCACUUUCCUGCACUUUGUGCUCGGACUGCCUACUACUAAUUUGUGUUUGGCACUUGGCUGUAUCGCUUUUUGAAGUCUUCGCGCUGUUCGUGAUG
((((.((((....(((((((((......))))))))).....)))).))))((((...(((......)))...))))...((((.((........)).)))).(((((.....))))).. (-29.25 = -30.00 +   0.75)

alignment

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secondary structure

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dotplot

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Window 1

Location 800,289 – 800,409
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 93.89
Mean single sequence MFE -32.59
Consensus MFE -27.69
Energy contribution -28.62
Covariance contribution 0.94
Combinations/Pair 1.09
Mean z-score -1.94
Structure conservation index 0.85
SVM decision value 0.68
SVM RNA-class probability 0.820522
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 800289 120 - 27905053
CAUCACGAACAGCGCGAAGACUUCAAAAAGCGAUACAGCCAAGUGCCAAACACAAAUUAGUAGUAGGCAGGCCGAGCACAAAGUGCAGGAAAGUGAAGUUUCCUGCAUAUUUGCUUGGCC
............(((..............))).....(((.(.(((.............))).).))).(((((((((.((.((((((((((......)))))))))).))))))))))) ( -38.26)
>DroSec_CAF1 38318 120 - 1
CAUCACGAACAGCGCGAAGACUUCAAAAAGCGAUACAGCCAAGUGCCAAACACAAAUUAGUAGUAGGCAGGCCGAGCACAAAGUGCAAGAAAGUGAAGUUUCCUGCAUAUUUGCUUGGCC
............(((..............))).....(((.(.(((.............))).).))).(((((((((.((.(((((.((((......)))).))))).))))))))))) ( -31.76)
>DroEre_CAF1 21900 119 - 1
CAUCACGAACAGCGCGAAGACUUCAAAAA-CGAUACAGCCAAGUGCCAAACACAAAUUAGUAGUAGGCAGUCCGAGCACAAAGUGCAGGAAAGUGAAGUUUCCUGCAUAUUUGCCUGGCC
.........(((.(((((((((((.....-.))....(((.(.(((.............))).).)))))))..........((((((((((......)))))))))).))))))))... ( -29.82)
>DroYak_CAF1 27746 120 - 1
UAUCAUGAACAGCGCGAAGACUUCAAAAAGAGAUACAACCAAGUGCCUAACACAAAUUAGUAGUAGGCAGUCCGGGCACAAAGUGCUGGAAACUGAAGUUUCUUGCAUAUUUUCCUGGCC
..(((.(((.(..((((((((((((..................((((((..((......))..)))))).(((((.(((...))))))))...)))))))).))))...).))).))).. ( -30.50)
>consensus
CAUCACGAACAGCGCGAAGACUUCAAAAAGCGAUACAGCCAAGUGCCAAACACAAAUUAGUAGUAGGCAGGCCGAGCACAAAGUGCAGGAAAGUGAAGUUUCCUGCAUAUUUGCCUGGCC
..((.((.....)).))..........................((((.(..((......))..).))))(((((((((.((.((((((((((......)))))))))).))))))))))) (-27.69 = -28.62 +   0.94)

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 09:35:16 2006