Locus 2315

Sequence ID 3R_DroMel_CAF1
Location 6,582,999 – 6,583,164
Length 165
Max. P 0.951174
window3739 window3740 window3741 window3742

overview

Window 9

Location 6,582,999 – 6,583,101
Length 102
Sequences 5
Columns 102
Reading direction reverse
Mean pairwise identity 81.91
Mean single sequence MFE -28.40
Consensus MFE -16.16
Energy contribution -16.96
Covariance contribution 0.80
Combinations/Pair 1.10
Mean z-score -2.07
Structure conservation index 0.57
SVM decision value 0.30
SVM RNA-class probability 0.678259
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6582999 102 - 27905053
UAGCAGAUCUAGUUAUGGUCUGGAUCUGUAGAUUGGGCUUAUCUGCAAUCUCACUUAACGCCUCGUCAUCGUGAUCGUGACGUGGCUAUCUCUGAACACAAA
..((((((((((.......))))))))))((((((.(......).))))))........(((.(((((.((....))))))).)))................ ( -32.40)
>DroSec_CAF1 662 96 - 1
------AUCUAGAUCUGGUCUGGAUCUUCAGAUUGCGCUUAUCUGGCAGCUCACUUAACGCCUCGUCAUCGUGAUCGUGACGUGGCUAUCUCUGCACACAAA
------((((((((...))))))))...((((..(((((.....))).)).........(((.(((((.((....))))))).)))....))))........ ( -26.80)
>DroSim_CAF1 616 96 - 1
------AUCUAGAUCUGGUCUGGAUCUUCAGAUUGCGCUUAUCUGGCAGCUCACUUAACGCCUCGUCAUCGUGAUCGUGACGUGGCUAUCUCUGCACACAAA
------((((((((...))))))))...((((..(((((.....))).)).........(((.(((((.((....))))))).)))....))))........ ( -26.80)
>DroEre_CAF1 632 85 - 1
-----------------AUGUGGAUCUGUAGAUUGGGCUUAUCUGACAGCUCACCUAACGCCUAGUCAUCGUGAUCGUGACGUGGUUAUCUCUGCUCACAAA
-----------------.....((((((..(((((((((((..(((....)))..))).))))))))..)).))))((((.(..(......)..)))))... ( -24.90)
>DroYak_CAF1 634 85 - 1
-----------------ACGUGGAUCUGUAGACUGGGCUUAUCUGACAGCUCACUUAACGCCUAGUCAUCGUGAUCGUGACGUGGCUAUCGCUGCUCACAAA
-----------------.....((((((..(((((((((((..(((....)))..))).))))))))..)).))))((((.(..((....))..)))))... ( -31.10)
>consensus
______AUCUAG_U_UGGUCUGGAUCUGUAGAUUGGGCUUAUCUGACAGCUCACUUAACGCCUCGUCAUCGUGAUCGUGACGUGGCUAUCUCUGCACACAAA
............................((((.((((((........))))))......(((.(((((.((....))))))).)))....))))........ (-16.16 = -16.96 +   0.80)

alignment

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secondary structure

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dotplot

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Window 0

Location 6,583,026 – 6,583,141
Length 115
Sequences 3
Columns 115
Reading direction reverse
Mean pairwise identity 86.10
Mean single sequence MFE -31.90
Consensus MFE -22.80
Energy contribution -22.80
Covariance contribution 0.00
Combinations/Pair 1.06
Mean z-score -2.24
Structure conservation index 0.71
SVM decision value 0.33
SVM RNA-class probability 0.691045
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6583026 115 - 27905053
GAUCUAGAUCUGGUUUUGAUCUGCAGAUAAUGCUUGGAGAUAGCAGAUCUAGUUAUGGUCUGGAUCUGUAGAUUGGGCUUAUCUGCAAUCUCACUUAACGCCUCGUCAUCGUGAU
.....(((((.......)))))((((((((.(((..(.....((((((((((.......))))))))))...)..)))))))))))....((((...(((...)))....)))). ( -37.30)
>DroSec_CAF1 689 101 - 1
GAUCUAGAUCUGGUUUUGAUCUGUAGAUAAUG--------------AUCUAGAUCUGGUCUGGAUCUUCAGAUUGCGCUUAUCUGGCAGCUCACUUAACGCCUCGUCAUCGUGAU
((((((((((.(((((.((((..........)--------------))).))))).)))))))))).((((((.(((((.....))).((.........))...)).))).))). ( -29.20)
>DroSim_CAF1 643 101 - 1
GAUCUAGAUCUGGUUUUGAUCUGUAGAUAAUG--------------AUCUAGAUCUGGUCUGGAUCUUCAGAUUGCGCUUAUCUGGCAGCUCACUUAACGCCUCGUCAUCGUGAU
((((((((((.(((((.((((..........)--------------))).))))).)))))))))).((((((.(((((.....))).((.........))...)).))).))). ( -29.20)
>consensus
GAUCUAGAUCUGGUUUUGAUCUGUAGAUAAUG______________AUCUAGAUCUGGUCUGGAUCUUCAGAUUGCGCUUAUCUGGCAGCUCACUUAACGCCUCGUCAUCGUGAU
((((((((((.(((((.(((..........................))).))))).)))))))))).((((((.......))))))....((((...(((...)))....)))). (-22.80 = -22.80 +   0.00)

alignment

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secondary structure

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dotplot

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Window 1

Location 6,583,066 – 6,583,164
Length 98
Sequences 3
Columns 98
Reading direction forward
Mean pairwise identity 83.57
Mean single sequence MFE -20.22
Consensus MFE -12.02
Energy contribution -12.69
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -3.86
Structure conservation index 0.59
SVM decision value 1.41
SVM RNA-class probability 0.951174
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6583066 98 + 27905053
CAAUCUACAGAUCCAGACCAUAACUAGAUCUGCUAUCUCCAAGCAUUAUCUGCAGAUCAAAACCAGAUCUAGAUCUGCUAUCUCCAAGCACUAUCUGU
......((((((..((.......(((((((((..........(((.....)))..........)))))))))...((((.......)))))))))))) ( -21.35)
>DroSec_CAF1 729 84 + 1
CAAUCUGAAGAUCCAGACCAGAUCUAGAU--------------CAUUAUCUACAGAUCAAAACCAGAUCUAGAUCUGCUAUGUCCGAGCACCAUCUGA
.............((((..((((((((((--------------(.....................)))))))))))(((.......)))....)))). ( -19.70)
>DroSim_CAF1 683 84 + 1
CAAUCUGAAGAUCCAGACCAGAUCUAGAU--------------CAUUAUCUACAGAUCAAAACCAGAUCUAGAUCUGCUAUCUCCAAGCACCAUCUGA
.............((((..((((((((((--------------(.....................)))))))))))(((.......)))....)))). ( -19.60)
>consensus
CAAUCUGAAGAUCCAGACCAGAUCUAGAU______________CAUUAUCUACAGAUCAAAACCAGAUCUAGAUCUGCUAUCUCCAAGCACCAUCUGA
.............((((..((((((((((.....................................))))))))))(((.......)))....)))). (-12.02 = -12.69 +   0.67)

alignment

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secondary structure

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dotplot

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Window 2

Location 6,583,066 – 6,583,164
Length 98
Sequences 3
Columns 98
Reading direction reverse
Mean pairwise identity 83.57
Mean single sequence MFE -28.90
Consensus MFE -17.90
Energy contribution -18.57
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -3.41
Structure conservation index 0.62
SVM decision value 1.38
SVM RNA-class probability 0.948269
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6583066 98 - 27905053
ACAGAUAGUGCUUGGAGAUAGCAGAUCUAGAUCUGGUUUUGAUCUGCAGAUAAUGCUUGGAGAUAGCAGAUCUAGUUAUGGUCUGGAUCUGUAGAUUG
....................(((((((((((((.......(((((((..................))))))).......)))))))))))))...... ( -30.01)
>DroSec_CAF1 729 84 - 1
UCAGAUGGUGCUCGGACAUAGCAGAUCUAGAUCUGGUUUUGAUCUGUAGAUAAUG--------------AUCUAGAUCUGGUCUGGAUCUUCAGAUUG
...((.(((.(.(((((....((((((((((((..((((........))))...)--------------)))))))))))))))))))).))...... ( -27.50)
>DroSim_CAF1 683 84 - 1
UCAGAUGGUGCUUGGAGAUAGCAGAUCUAGAUCUGGUUUUGAUCUGUAGAUAAUG--------------AUCUAGAUCUGGUCUGGAUCUUCAGAUUG
...........((((((((..((((.((((((((((.((..(((....)))...)--------------).)))))))))))))).)))))))).... ( -29.20)
>consensus
UCAGAUGGUGCUUGGAGAUAGCAGAUCUAGAUCUGGUUUUGAUCUGUAGAUAAUG______________AUCUAGAUCUGGUCUGGAUCUUCAGAUUG
........((((.......))))((((((((((.(((((.(((..........................))).))))).))))))))))......... (-17.90 = -18.57 +   0.67)

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 10:32:20 2006