Locus 957

Sequence ID 2R_DroMel_CAF1
Location 4,100,067 – 4,100,178
Length 111
Max. P 0.997104
window1705 window1706 window1707 window1708

overview

Window 5

Location 4,100,067 – 4,100,161
Length 94
Sequences 3
Columns 95
Reading direction forward
Mean pairwise identity 95.09
Mean single sequence MFE -30.30
Consensus MFE -28.45
Energy contribution -27.90
Covariance contribution -0.55
Combinations/Pair 1.18
Mean z-score -3.48
Structure conservation index 0.94
SVM decision value 2.08
SVM RNA-class probability 0.987398
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4100067 94 + 20766785
CACAAACGAUUUGUCCACUCAUGUUCAACCGAUAGACUGAACAGCCGGUCAUGUUCCGCCGUCCAAUUAGACGGCCACUUCGGUUGGCCAUACA-
....................(((..(((((((..(((((......))))).......((((((......))))))....)))))))..)))...- ( -30.70)
>DroSec_CAF1 4161 95 + 1
CACAAACGAUUUGUCCACUCAUGUUCAACCGAUCGACUGAACAGCCAGUCAUGUUCCGCCGCCCAAUUAGACGGCCACUUCGGUUGGCCAUACAU
....................(((..(((((((..(((((......))))).......((((.(......).))))....)))))))..))).... ( -26.50)
>DroSim_CAF1 4142 95 + 1
CACAAACGAUUUGUCCACUCAUGUUCAACCGAUCGGCUGAACAGCCGGUCAUGUUCCGCCGUCCAAUUAGACGGCCACUUCGGUUGACUAUACAU
....................(((.((((((((((((((....)))))))).......((((((......))))))......)))))).))).... ( -33.70)
>consensus
CACAAACGAUUUGUCCACUCAUGUUCAACCGAUCGACUGAACAGCCGGUCAUGUUCCGCCGUCCAAUUAGACGGCCACUUCGGUUGGCCAUACAU
....................(((.((((((((..(((((......))))).......((((((......))))))....)))))))).))).... (-28.45 = -27.90 +  -0.55)

alignment

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secondary structure

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dotplot

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Window 6

Location 4,100,067 – 4,100,161
Length 94
Sequences 3
Columns 95
Reading direction reverse
Mean pairwise identity 95.09
Mean single sequence MFE -35.17
Consensus MFE -31.84
Energy contribution -31.73
Covariance contribution -0.11
Combinations/Pair 1.07
Mean z-score -2.70
Structure conservation index 0.91
SVM decision value 1.32
SVM RNA-class probability 0.941441
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4100067 94 - 20766785
-UGUAUGGCCAACCGAAGUGGCCGUCUAAUUGGACGGCGGAACAUGACCGGCUGUUCAGUCUAUCGGUUGAACAUGAGUGGACAAAUCGUUUGUG
-..((((..(((((((....(((((((....))))))).(((((........)))))......)))))))..)))).(..(((.....)))..). ( -33.60)
>DroSec_CAF1 4161 95 - 1
AUGUAUGGCCAACCGAAGUGGCCGUCUAAUUGGGCGGCGGAACAUGACUGGCUGUUCAGUCGAUCGGUUGAACAUGAGUGGACAAAUCGUUUGUG
...((((..(((((((.((.(((((((....)))))))...)).(((((((....))))))).)))))))..)))).(..(((.....)))..). ( -36.00)
>DroSim_CAF1 4142 95 - 1
AUGUAUAGUCAACCGAAGUGGCCGUCUAAUUGGACGGCGGAACAUGACCGGCUGUUCAGCCGAUCGGUUGAACAUGAGUGGACAAAUCGUUUGUG
...(((..((((((((.((.(((((((....)))))))...)).....(((((....))))).))))))))..))).(..(((.....)))..). ( -35.90)
>consensus
AUGUAUGGCCAACCGAAGUGGCCGUCUAAUUGGACGGCGGAACAUGACCGGCUGUUCAGUCGAUCGGUUGAACAUGAGUGGACAAAUCGUUUGUG
...((((..(((((((.((.(((((((....)))))))...))......((((....))))..)))))))..)))).(..(((.....)))..). (-31.84 = -31.73 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 7

Location 4,100,082 – 4,100,178
Length 96
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 66.33
Mean single sequence MFE -28.40
Consensus MFE -18.24
Energy contribution -19.05
Covariance contribution 0.81
Combinations/Pair 1.32
Mean z-score -1.98
Structure conservation index 0.64
SVM decision value 2.80
SVM RNA-class probability 0.997104
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4100082 96 + 20766785
CACUCAUGUUCAACCGAUAGACUGAACAGCCGGUCAUGUUCCGCCGUCCAAUUAGACGGCCACUUCGGUUGGCCAUACA----------------------UAACGA--CGAGCACUUGA
..((((((..(((((((..(((((......))))).......((((((......))))))....)))))))..))).(.----------------------....).--.)))....... ( -31.00)
>DroSec_CAF1 4176 116 + 1
CACUCAUGUUCAACCGAUCGACUGAACAGCCAGUCAUGUUCCGCCGCCCAAUUAGACGGCCACUUCGGUUGGCCAUACAUAU--AUACAUUUGUAUCUGCAUAACGA--CGAGCACUUGG
..((((((..(((((((..(((((......))))).......((((.(......).))))....)))))))..))).((.((--(((....))))).))........--.)))....... ( -30.00)
>DroSim_CAF1 4157 118 + 1
CACUCAUGUUCAACCGAUCGGCUGAACAGCCGGUCAUGUUCCGCCGUCCAAUUAGACGGCCACUUCGGUUGACUAUACAUAUACAUACAUAUGUAUCUGCAUAACGA--CGAGCACUUGG
..(((....((((((((((((((....)))))))).......((((((......))))))......))))))..((((((((......))))))))...........--.)))....... ( -40.70)
>DroWil_CAF1 10336 88 + 1
CAAUCAUGUUAACUCAAUUGACUCC-------GUC-UGUUGCCCCCU-----U----GCGCAGAUCAGCAUAUUAUGCAUA---AUACA------------UAUCCAGCAAAGCACUUGA
.............((((.((.((..-------(((-(((.((.....-----.----))))))))..((....((((....---...))------------))....))..)))).)))) ( -11.90)
>consensus
CACUCAUGUUCAACCGAUCGACUGAACAGCCGGUCAUGUUCCGCCGUCCAAUUAGACGGCCACUUCGGUUGACCAUACAUA___AUACA____________UAACGA__CGAGCACUUGA
.....(((.((((((((..(((((......))))).......((((((......))))))....)))))))).)))............................................ (-18.24 = -19.05 +   0.81)

alignment

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secondary structure

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dotplot

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Window 8

Location 4,100,082 – 4,100,178
Length 96
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 66.33
Mean single sequence MFE -37.35
Consensus MFE -18.06
Energy contribution -19.88
Covariance contribution 1.81
Combinations/Pair 1.29
Mean z-score -2.65
Structure conservation index 0.48
SVM decision value 2.77
SVM RNA-class probability 0.996911
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4100082 96 - 20766785
UCAAGUGCUCG--UCGUUA----------------------UGUAUGGCCAACCGAAGUGGCCGUCUAAUUGGACGGCGGAACAUGACCGGCUGUUCAGUCUAUCGGUUGAACAUGAGUG
......(((((--((((((----------------------(((.(((....))).....(((((((....)))))))...)))))).))))((((((..(....)..)))))).)))). ( -35.40)
>DroSec_CAF1 4176 116 - 1
CCAAGUGCUCG--UCGUUAUGCAGAUACAAAUGUAU--AUAUGUAUGGCCAACCGAAGUGGCCGUCUAAUUGGGCGGCGGAACAUGACUGGCUGUUCAGUCGAUCGGUUGAACAUGAGUG
......(((((--(.((((((((.((((....))))--...))))))))(((((((.((.(((((((....)))))))...)).(((((((....))))))).)))))))...)))))). ( -45.70)
>DroSim_CAF1 4157 118 - 1
CCAAGUGCUCG--UCGUUAUGCAGAUACAUAUGUAUGUAUAUGUAUAGUCAACCGAAGUGGCCGUCUAAUUGGACGGCGGAACAUGACCGGCUGUUCAGCCGAUCGGUUGAACAUGAGUG
......(((((--(.((((((((.((((((....)))))).)))))).((((((((.((.(((((((....)))))))...)).....(((((....))))).)))))))))))))))). ( -48.40)
>DroWil_CAF1 10336 88 - 1
UCAAGUGCUUUGCUGGAUA------------UGUAU---UAUGCAUAAUAUGCUGAUCUGCGC----A-----AGGGGGCAACA-GAC-------GGAGUCAAUUGAGUUAACAUGAUUG
((((.((((((((((..((------------(((..---...)))))......((.(((.(..----.-----.).))))).))-).)-------)))).)).))))............. ( -19.90)
>consensus
CCAAGUGCUCG__UCGUUA____________UGUAU___UAUGUAUAGCCAACCGAAGUGGCCGUCUAAUUGGACGGCGGAACAUGACCGGCUGUUCAGUCGAUCGGUUGAACAUGAGUG
...........................................((((.((((((((....(((((((....))))))).(((((........)))))......)))))))).)))).... (-18.06 = -19.88 +   1.81)

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 09:52:45 2006