Locus 5780

Sequence ID 3L_DroMel_CAF1
Location 15,661,721 – 15,661,927
Length 206
Max. P 0.952944
window9181 window9182 window9183

overview

Window 1

Location 15,661,721 – 15,661,833
Length 112
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 78.43
Mean single sequence MFE -29.87
Consensus MFE -12.95
Energy contribution -14.23
Covariance contribution 1.28
Combinations/Pair 1.19
Mean z-score -2.47
Structure conservation index 0.43
SVM decision value 0.57
SVM RNA-class probability 0.783899
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15661721 112 + 23771897
UUUCAUUGACCGCUGAUCACGG-------ACCUGUGAUCACCAAUCACGGAUUGUGAAUCACGGCUUGCGAGAUAAAUAACUUUUAUUGCACUCGCAUAAAUGCAAUUUAUUCGCACCC
.........(((.(((((((((-------.((.(((((.....))))))).))))).)))))))..((((((.(((((..(.(((((.((....))))))).)..)))))))))))... ( -30.30)
>DroSec_CAF1 21533 112 + 1
UUUCAUUGAGCGCCGAUCACGG-------ACCUGUGAUCACCGAUCACGGAUUGUGAAUCACGGCUAGCGAGAUAAAUAACUUUUAUUGCACUCGCAUAAAUGCAAUUUAUUCGCACCC
...........((((.((((((-------.((.((((((...)))))))).))))))....))))..(((((.(((((..(.(((((.((....))))))).)..)))))))))).... ( -31.80)
>DroSim_CAF1 21504 112 + 1
UUUCAUUGACCGCCGAUCACGG-------ACCUGUGAUCACCGAUCACGGAUUGUGAAUCACGGCUAGCGAGAUAAAUAACUUUUAUUGCACUCGCAUAAAUGCAAUUUAUUCGCACCC
...........((((.((((((-------.((.((((((...)))))))).))))))....))))..(((((.(((((..(.(((((.((....))))))).)..)))))))))).... ( -31.80)
>DroEre_CAF1 21359 112 + 1
UUUCAUUGAUCACCGCUCACCG-------AUCGGCGAUCACUGAUCACGGAUUGCGAGUCACGGCUCGUGAGAAAAAUAACUUUUAUUGCACUCGCAUAAAUGCAAUUUAUUCGCACCC
..(((.(((((.(((.((...)-------).))).))))).)))....(((((((((((....))))(((((...((((.....))))...)))))......))))))).......... ( -31.60)
>DroYak_CAF1 21568 119 + 1
UUUCAUUGAUCACCGAUCACUGGUCACGGACCUGUGAUCACCGAUCACGGAUUGCGAGGCACUGGUCGUGAGAUAAAUAACUUUAAUGGCACUCGCAUAAAUGCAAUUUAUUCGCACCC
......(((((...((((((.((((...)))).))))))...))))).((..((((((((....(((....)))......(......))).))))))....(((.........))))). ( -35.60)
>DroAna_CAF1 80448 94 + 1
UUUCAAUGAACCACGAUCCCCG--------------AUCCCCUAUCGCCCAUAGU-----------CAUAAGAUAAAUUGCCUUUACGGCGCUCCCGUAUAUGCGAUUUAUUCGCAUUA
.....((((.....((((...)--------------)))..((((.....)))))-----------)))..((((((((((...(((((.....)))))...))))))))))....... ( -18.10)
>consensus
UUUCAUUGACCGCCGAUCACGG_______ACCUGUGAUCACCGAUCACGGAUUGUGAAUCACGGCUCGCGAGAUAAAUAACUUUUAUUGCACUCGCAUAAAUGCAAUUUAUUCGCACCC
..............((((((((.........))))))))..(((((...))))).............((((.((((((..(.(((((.((....))))))).)..)))))))))).... (-12.95 = -14.23 +   1.28)

alignment

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secondary structure

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dotplot

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Window 2

Location 15,661,721 – 15,661,833
Length 112
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 78.43
Mean single sequence MFE -35.12
Consensus MFE -20.88
Energy contribution -21.59
Covariance contribution 0.70
Combinations/Pair 1.32
Mean z-score -2.38
Structure conservation index 0.59
SVM decision value 1.39
SVM RNA-class probability 0.949420
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15661721 112 - 23771897
GGGUGCGAAUAAAUUGCAUUUAUGCGAGUGCAAUAAAAGUUAUUUAUCUCGCAAGCCGUGAUUCACAAUCCGUGAUUGGUGAUCACAGGU-------CCGUGAUCAGCGGUCAAUGAAA
((.(((((((((((.((.(((((((....)).))))).)).)))))).)))))..))(((...)))..((..((((((.(((((((....-------..))))))).))))))..)).. ( -36.20)
>DroSec_CAF1 21533 112 - 1
GGGUGCGAAUAAAUUGCAUUUAUGCGAGUGCAAUAAAAGUUAUUUAUCUCGCUAGCCGUGAUUCACAAUCCGUGAUCGGUGAUCACAGGU-------CCGUGAUCGGCGCUCAAUGAAA
((((((((((((((.((.(((((((....)).))))).)).)))))).))))..((((....((((...((((((((...)))))).)).-------..)))).))))))))....... ( -36.80)
>DroSim_CAF1 21504 112 - 1
GGGUGCGAAUAAAUUGCAUUUAUGCGAGUGCAAUAAAAGUUAUUUAUCUCGCUAGCCGUGAUUCACAAUCCGUGAUCGGUGAUCACAGGU-------CCGUGAUCGGCGGUCAAUGAAA
((((((((((((((.((.(((((((....)).))))).)).)))))).)))).....(((...))).)))).((((((.(((((((....-------..))))))).))))))...... ( -36.30)
>DroEre_CAF1 21359 112 - 1
GGGUGCGAAUAAAUUGCAUUUAUGCGAGUGCAAUAAAAGUUAUUUUUCUCACGAGCCGUGACUCGCAAUCCGUGAUCAGUGAUCGCCGAU-------CGGUGAGCGGUGAUCAAUGAAA
((((((((....(((((((((....)))))))))....(((((..(((....)))..))))))))).)))).((((((.((.(((((...-------.))))).)).))))))...... ( -39.20)
>DroYak_CAF1 21568 119 - 1
GGGUGCGAAUAAAUUGCAUUUAUGCGAGUGCCAUUAAAGUUAUUUAUCUCACGACCAGUGCCUCGCAAUCCGUGAUCGGUGAUCACAGGUCCGUGACCAGUGAUCGGUGAUCAAUGAAA
((((((((.....)))).....((((((.((...((((....))))....((.....)))))))))))))).((((((.(((((((.((((...)))).))))))).))))))...... ( -39.60)
>DroAna_CAF1 80448 94 - 1
UAAUGCGAAUAAAUCGCAUAUACGGGAGCGCCGUAAAGGCAAUUUAUCUUAUG-----------ACUAUGGGCGAUAGGGGAU--------------CGGGGAUCGUGGUUCAUUGAAA
..((((((.....)))))).(((((.....)))))...........((..(((-----------(((((((.((((.....))--------------))....)))))).)))).)).. ( -22.60)
>consensus
GGGUGCGAAUAAAUUGCAUUUAUGCGAGUGCAAUAAAAGUUAUUUAUCUCACGAGCCGUGAUUCACAAUCCGUGAUCGGUGAUCACAGGU_______CCGUGAUCGGCGAUCAAUGAAA
..(((.((.(((((.((.(((((((....)).))))).)).))))))).)))................((..((((((.(((((((.............))))))).))))))..)).. (-20.88 = -21.59 +   0.70)

alignment

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secondary structure

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dotplot

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Window 3

Location 15,661,833 – 15,661,927
Length 94
Sequences 5
Columns 102
Reading direction forward
Mean pairwise identity 92.59
Mean single sequence MFE -26.00
Consensus MFE -23.54
Energy contribution -23.14
Covariance contribution -0.40
Combinations/Pair 1.16
Mean z-score -1.54
Structure conservation index 0.91
SVM decision value 1.43
SVM RNA-class probability 0.952944
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15661833 94 + 23771897
UCACAUGUGGAUUUCUAGUUGGUUGUCGGUGAUUUGUUUACCCAUUCAAAUGGGUAUAACAAUAAUGAAGCACGGAAACGGACGGCGACUGCAA--------
...((..(((....)))..))(((((((.....((((((((((((....))))))).)))))..........((....))..))))))).....-------- ( -26.70)
>DroSec_CAF1 21645 94 + 1
UCACAUGUGGAUUUCUAGUUGGUUGUCGGUGAUUUGUUUACCCAUUCAAAUGGGUAUAACAAUAAUGAAGCACGGAAACGGACGGCAACUGCAA--------
...((..(((....)))..))(((((((.....((((((((((((....))))))).)))))..........((....))..))))))).....-------- ( -27.00)
>DroSim_CAF1 21616 94 + 1
UCACAUGUGGAUUUCUAGUUGGUUGUCGGUGAUUUGUUUACCCAUUCAAAUGGGUAUAACAAUAAUGAAGCACGGAAACGGACGGCGACUGCAA--------
...((..(((....)))..))(((((((.....((((((((((((....))))))).)))))..........((....))..))))))).....-------- ( -26.70)
>DroEre_CAF1 21471 94 + 1
UCACAUGUGGCUUUCUAGUUGGCUGUCGGUGAUUUGUUUACCCAUUAAAAUGGGCAUAAUAAUAAUGAAGCACGGAAAUGGACGGCAACUGCAA--------
...............((((((.(((((.((..(.(((((.(((((....)))))(((.......)))))))).)...)).)))))))))))...-------- ( -21.90)
>DroYak_CAF1 21687 102 + 1
UCACAUGUGGAUUUCUAGUUGGUUGUCGGUGAUUUGUUUACCCAUUCAAAUGGGUAUAAUAAUAAUGAAGCACGGAAGCGGACUGCAACUGCAAGUGCAUUG
.(((.((..(.....(((((.(((.((.(((.((..(((((((((....))))))).......))..)).))).))))).)))))...)..)).)))..... ( -27.71)
>consensus
UCACAUGUGGAUUUCUAGUUGGUUGUCGGUGAUUUGUUUACCCAUUCAAAUGGGUAUAACAAUAAUGAAGCACGGAAACGGACGGCAACUGCAA________
...............((((((.(((((......((((((((((((....))))))).)))))..........((....)))))))))))))........... (-23.54 = -23.14 +  -0.40)

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 11:59:44 2006