Locus 222

Sequence ID 2R_DroMel_CAF1
Location 1,560,042 – 1,560,199
Length 157
Max. P 0.999836
window494 window495 window496 window497

overview

Window 4

Location 1,560,042 – 1,560,159
Length 117
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 87.82
Mean single sequence MFE -33.44
Consensus MFE -30.40
Energy contribution -29.76
Covariance contribution -0.64
Combinations/Pair 1.22
Mean z-score -1.49
Structure conservation index 0.91
SVM decision value 0.60
SVM RNA-class probability 0.795350
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1560042 117 + 20766785
---CUUUCCUAACAUCACCUUUCGGUGCCAUAAAAGUUUUGCGGUUAACAAAAUUGAAACGGCGCACGACGCCCACAAAUCGCUAGCGUACGAGCCCGCAGGGCCACAUUUGUUAACCGC
---............((((....)))).............((((((((((((........((((.....))))......(((........)))((((...))))....)))))))))))) ( -31.90)
>DroSec_CAF1 9782 117 + 1
---CUUUUCUAACAUCGCCUUUCGGCGCCAUAAAAGUUUUGCGGUUAACAAAAUUGAAACGGCGCACGACGCCCACAAAUCGCGAGCGUGCGAGCCCGCAGGGCCAUAUUUGUUAACCGC
---(((((.......((((....))))....)))))....((((((((((((..((......((((((.(((.........)))..)))))).((((...))))))..)))))))))))) ( -40.00)
>DroSim_CAF1 11279 120 + 1
AUCCCUUCCUAACAUCGCCUUUCGGUGCCAUAAAAGUUUUGCGGUUAACAAAAUUGAAACGGCGCACGACGCCCACAAAUCGCGAGCGUACGAGCCCGCAGGGCCAUAUUUGUUAACCGC
...............((((....)))).............((((((((((((..((....((((.....))))........(((.((......)).))).....))..)))))))))))) ( -33.60)
>DroEre_CAF1 10178 116 + 1
---CCUUU-GGGCCUCACCUUUCGGUGCUAUAAAAGUUAUGCGGUGAACAAAAUGGAAACGGCGCACGACGCCCACAAAUCGCAAACCUACGAGCCCGCAGGGCCAUAUUUGUUAGCCGC
---.((((-.(((...(((....))))))...))))....(((((.((((((((((....((((.....)))).............(((.((....)).))).)))).)))))).))))) ( -33.30)
>DroYak_CAF1 16342 117 + 1
---CUUUCCGAGCCUUACCUUUAAGUGCCAUAAAAGUUUUGCGGUUAACAAAAUUACAAAGGCGCACGAUGCCCACAAAUCGCGAACUUACGAGCUCACAGGGCCAUAUUUGUUAACCGC
---......(.((((((....)))).)))...........((((((((((((......(((...(.((((........)))).)..)))..(.(((.....))))...)))))))))))) ( -28.40)
>consensus
___CUUUCCUAACAUCACCUUUCGGUGCCAUAAAAGUUUUGCGGUUAACAAAAUUGAAACGGCGCACGACGCCCACAAAUCGCGAGCGUACGAGCCCGCAGGGCCAUAUUUGUUAACCGC
...............((((....)))).............((((((((((((........((((.....))))......(((........)))((((...))))....)))))))))))) (-30.40 = -29.76 +  -0.64)

alignment

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secondary structure

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Window 5

Location 1,560,042 – 1,560,159
Length 117
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 87.82
Mean single sequence MFE -47.58
Consensus MFE -41.68
Energy contribution -42.64
Covariance contribution 0.96
Combinations/Pair 1.19
Mean z-score -3.49
Structure conservation index 0.88
SVM decision value 4.21
SVM RNA-class probability 0.999836
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1560042 117 - 20766785
GCGGUUAACAAAUGUGGCCCUGCGGGCUCGUACGCUAGCGAUUUGUGGGCGUCGUGCGCCGUUUCAAUUUUGUUAACCGCAAAACUUUUAUGGCACCGAAAGGUGAUGUUAGGAAAG---
((((((((((((..(((....((((((.((.(((((.((.....)).))))))).)).)))).)))..))))))))))))....(((((....((((....)))).......)))))--- ( -48.70)
>DroSec_CAF1 9782 117 - 1
GCGGUUAACAAAUAUGGCCCUGCGGGCUCGCACGCUCGCGAUUUGUGGGCGUCGUGCGCCGUUUCAAUUUUGUUAACCGCAAAACUUUUAUGGCGCCGAAAGGCGAUGUUAGAAAAG---
((((((((((((..(((....((((((.((.((((((((.....)))))))))).)).)))).)))..)))))))))))).....(((((...((((....))))....)))))...--- ( -54.10)
>DroSim_CAF1 11279 120 - 1
GCGGUUAACAAAUAUGGCCCUGCGGGCUCGUACGCUCGCGAUUUGUGGGCGUCGUGCGCCGUUUCAAUUUUGUUAACCGCAAAACUUUUAUGGCACCGAAAGGCGAUGUUAGGAAGGGAU
((((((((((((..(((....((((((.((.((((((((.....)))))))))).)).)))).)))..))))))))))))....(((((.(((((((....))...))))).)))))... ( -52.80)
>DroEre_CAF1 10178 116 - 1
GCGGCUAACAAAUAUGGCCCUGCGGGCUCGUAGGUUUGCGAUUUGUGGGCGUCGUGCGCCGUUUCCAUUUUGUUCACCGCAUAACUUUUAUAGCACCGAAAGGUGAGGCCC-AAAGG---
((((..((((((.((((....((((((.((.(.(((..(.....)..))).))).)).))))..))))))))))..))))....((((.....((((....))))......-)))).--- ( -42.80)
>DroYak_CAF1 16342 117 - 1
GCGGUUAACAAAUAUGGCCCUGUGAGCUCGUAAGUUCGCGAUUUGUGGGCAUCGUGCGCCUUUGUAAUUUUGUUAACCGCAAAACUUUUAUGGCACUUAAAGGUAAGGCUCGGAAAG---
((((((((((((....((((((((((((....))))))))......))))....((((....))))..))))))))))))....(((((..(((.((((....)))))))..)))))--- ( -39.50)
>consensus
GCGGUUAACAAAUAUGGCCCUGCGGGCUCGUACGCUCGCGAUUUGUGGGCGUCGUGCGCCGUUUCAAUUUUGUUAACCGCAAAACUUUUAUGGCACCGAAAGGUGAUGUUAGGAAAG___
((((((((((((..(((....((((((.((.((((((((.....)))))))))).)).)))).)))..))))))))))))....(((((.(((((((....)))...)))).)))))... (-41.68 = -42.64 +   0.96)

alignment

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secondary structure

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dotplot

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Window 6

Location 1,560,079 – 1,560,199
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.00
Mean single sequence MFE -38.92
Consensus MFE -33.72
Energy contribution -33.68
Covariance contribution -0.04
Combinations/Pair 1.12
Mean z-score -2.12
Structure conservation index 0.87
SVM decision value 2.31
SVM RNA-class probability 0.992111
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1560079 120 + 20766785
GCGGUUAACAAAAUUGAAACGGCGCACGACGCCCACAAAUCGCUAGCGUACGAGCCCGCAGGGCCACAUUUGUUAACCGCCUGCACUUGACUAUCAUACGUUUAUGAUGUUUGAGCACAA
((((((((((((........((((.....))))......(((........)))((((...))))....)))))))))))).((..((..(.(((((((....))))))).)..))..)). ( -37.20)
>DroSec_CAF1 9819 120 + 1
GCGGUUAACAAAAUUGAAACGGCGCACGACGCCCACAAAUCGCGAGCGUGCGAGCCCGCAGGGCCAUAUUUGUUAACCGCUUGCACUUGACUAUCAUACGUUUAUGAUGUUUGGGCACAA
((((((((((((..((......((((((.(((.........)))..)))))).((((...))))))..)))))))))))).(((.((.(((.((((((....))))))))).)))))... ( -45.70)
>DroSim_CAF1 11319 120 + 1
GCGGUUAACAAAAUUGAAACGGCGCACGACGCCCACAAAUCGCGAGCGUACGAGCCCGCAGGGCCAUAUUUGUUAACCGCCUGCACUUGACUAUCAUACGUUUAUGAUGUUUGGGCACAA
((((((((((((..((....((((.....))))........(((.((......)).))).....))..)))))))))))).(((.((.(((.((((((....))))))))).)))))... ( -40.80)
>DroEre_CAF1 10214 120 + 1
GCGGUGAACAAAAUGGAAACGGCGCACGACGCCCACAAAUCGCAAACCUACGAGCCCGCAGGGCCAUAUUUGUUAGCCGCCUGCACUUGACUAUCAUGCGUUUAUGAUGUUUGGGCUCUU
(((((.........(....)((((.....)))).....)))))........(((((((((((((...........))..)))))....(((.((((((....))))))))).)))))).. ( -38.40)
>DroYak_CAF1 16379 120 + 1
GCGGUUAACAAAAUUACAAAGGCGCACGAUGCCCACAAAUCGCGAACUUACGAGCUCACAGGGCCAUAUUUGUUAACCGCUCGCACUUGUCUACCAUACGGUUAUGAUGUUUCUGCUCGU
((((((((((((......(((...(.((((........)))).)..)))..(.(((.....))))...))))))))))))..(((..((((.(((....)))...))))....))).... ( -32.50)
>consensus
GCGGUUAACAAAAUUGAAACGGCGCACGACGCCCACAAAUCGCGAGCGUACGAGCCCGCAGGGCCAUAUUUGUUAACCGCCUGCACUUGACUAUCAUACGUUUAUGAUGUUUGGGCACAA
((((((((((((........((((.....))))......(((........)))((((...))))....))))))))))))..((....(((.((((((....)))))))))...)).... (-33.72 = -33.68 +  -0.04)

alignment

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secondary structure

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dotplot

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Window 7

Location 1,560,079 – 1,560,199
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 90.00
Mean single sequence MFE -43.98
Consensus MFE -36.02
Energy contribution -37.30
Covariance contribution 1.28
Combinations/Pair 1.12
Mean z-score -2.52
Structure conservation index 0.82
SVM decision value 2.42
SVM RNA-class probability 0.993690
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1560079 120 - 20766785
UUGUGCUCAAACAUCAUAAACGUAUGAUAGUCAAGUGCAGGCGGUUAACAAAUGUGGCCCUGCGGGCUCGUACGCUAGCGAUUUGUGGGCGUCGUGCGCCGUUUCAAUUUUGUUAACCGC
(((..((...((((((((....)))))).))..))..)))((((((((((((..(((....((((((.((.(((((.((.....)).))))))).)).)))).)))..)))))))))))) ( -46.20)
>DroSec_CAF1 9819 120 - 1
UUGUGCCCAAACAUCAUAAACGUAUGAUAGUCAAGUGCAAGCGGUUAACAAAUAUGGCCCUGCGGGCUCGCACGCUCGCGAUUUGUGGGCGUCGUGCGCCGUUUCAAUUUUGUUAACCGC
(((..(....((((((((....)))))).))...)..)))((((((((((((..(((....((((((.((.((((((((.....)))))))))).)).)))).)))..)))))))))))) ( -49.00)
>DroSim_CAF1 11319 120 - 1
UUGUGCCCAAACAUCAUAAACGUAUGAUAGUCAAGUGCAGGCGGUUAACAAAUAUGGCCCUGCGGGCUCGUACGCUCGCGAUUUGUGGGCGUCGUGCGCCGUUUCAAUUUUGUUAACCGC
(((..(....((((((((....)))))).))...)..)))((((((((((((..(((....((((((.((.((((((((.....)))))))))).)).)))).)))..)))))))))))) ( -48.50)
>DroEre_CAF1 10214 120 - 1
AAGAGCCCAAACAUCAUAAACGCAUGAUAGUCAAGUGCAGGCGGCUAACAAAUAUGGCCCUGCGGGCUCGUAGGUUUGCGAUUUGUGGGCGUCGUGCGCCGUUUCCAUUUUGUUCACCGC
..((((((....(((((......)))))........(((((..((((.......)))))))))))))))...(((..((((..((..((((.(....).))))..))..))))..))).. ( -41.10)
>DroYak_CAF1 16379 120 - 1
ACGAGCAGAAACAUCAUAACCGUAUGGUAGACAAGUGCGAGCGGUUAACAAAUAUGGCCCUGUGAGCUCGUAAGUUCGCGAUUUGUGGGCAUCGUGCGCCUUUGUAAUUUUGUUAACCGC
....(((.....((((((....)))))).......)))..((((((((((((....((((((((((((....))))))))......))))....((((....))))..)))))))))))) ( -35.10)
>consensus
UUGUGCCCAAACAUCAUAAACGUAUGAUAGUCAAGUGCAGGCGGUUAACAAAUAUGGCCCUGCGGGCUCGUACGCUCGCGAUUUGUGGGCGUCGUGCGCCGUUUCAAUUUUGUUAACCGC
.((..(......((((((....))))))......)..)).((((((((((((..(((....((((((.((.((((((((.....)))))))))).)).)))).)))..)))))))))))) (-36.02 = -37.30 +   1.28)

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 09:32:53 2006