Locus 4389

Sequence ID 3R_DroMel_CAF1
Location 11,607,745 – 11,607,877
Length 132
Max. P 0.971941
window7171 window7172 window7173

overview

Window 1

Location 11,607,745 – 11,607,852
Length 107
Sequences 5
Columns 107
Reading direction forward
Mean pairwise identity 95.70
Mean single sequence MFE -29.88
Consensus MFE -25.58
Energy contribution -25.50
Covariance contribution -0.08
Combinations/Pair 1.08
Mean z-score -1.93
Structure conservation index 0.86
SVM decision value 1.68
SVM RNA-class probability 0.971941
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11607745 107 + 27905053
ACGGAGCGUACGAAAAAUGCAAUUUUAAUUAGCCAGACGUGCGACAAACGCACGUAGAACGCAUAACCGCAAGAUGGUGCUGCAAUUAGGCGAACCCAUCCGAAUCC
.((((((((.......))))...........(((..(((((((.....))))))).....(((..((((.....))))..))).....))).......))))..... ( -31.60)
>DroSec_CAF1 137652 107 + 1
GCGAAGCGUACGAAAAAUGCAAUUUUAAUUAGCCAGACGUGCGACAAACGCACGUAGAACGCAUAACCGCAAGAUGGUGCUGCAAUUAGGCGAACCCAUCCGAAUCG
(((..((((.......))))...........((...(((((((.....))))))).....)).....)))..(((((((((.......))))...)))))....... ( -27.60)
>DroSim_CAF1 145801 107 + 1
ACGAAGCGUACGAAAAAUGCAAUUUUAAUUAGCCAGACGUGCGACAAACGCACGUAGAACGCAUAACCGCAAGAUGGUGCUGCAAUUAGGCGAACCCAUCCGAAUCG
.(((.((((.......))))...........(((..(((((((.....))))))).....(((..((((.....))))..))).....))).............))) ( -27.20)
>DroYak_CAF1 139131 107 + 1
ACGGAGCGUACGAAAAAUGCAAUUUUAAUUAGCCAGACGUGCGACAAACGCACGUAGAACGCAUAACCGCAAGAUGGUGCUGCAAUUAGGCGAAUCCAUACGAAUCG
..(((((((.......))))...........(((..(((((((.....))))))).....(((..((((.....))))..))).....)))...))).......... ( -29.60)
>DroAna_CAF1 229061 107 + 1
GGGAAGCGUUCGAAAAAUGCAAUUUUAAUUAGCCAGACGUGCGACAAACGCACGUAGAACGCAUAACCGCAAGAUGGCGCUGCAAUUAGGCGAACCCAUCAGGAUCC
.(((.((((((.......(((((....))).))...(((((((.....))))))).))))))....((....(((((((((.......))))...))))).)).))) ( -33.40)
>consensus
ACGAAGCGUACGAAAAAUGCAAUUUUAAUUAGCCAGACGUGCGACAAACGCACGUAGAACGCAUAACCGCAAGAUGGUGCUGCAAUUAGGCGAACCCAUCCGAAUCG
.(((.((((.......))))...........(((..(((((((.....))))))).....(((..((((.....))))..))).....))).............))) (-25.58 = -25.50 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 2

Location 11,607,745 – 11,607,852
Length 107
Sequences 5
Columns 107
Reading direction reverse
Mean pairwise identity 95.70
Mean single sequence MFE -32.68
Consensus MFE -26.24
Energy contribution -26.56
Covariance contribution 0.32
Combinations/Pair 1.07
Mean z-score -1.75
Structure conservation index 0.80
SVM decision value 0.39
SVM RNA-class probability 0.716730
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11607745 107 - 27905053
GGAUUCGGAUGGGUUCGCCUAAUUGCAGCACCAUCUUGCGGUUAUGCGUUCUACGUGCGUUUGUCGCACGUCUGGCUAAUUAAAAUUGCAUUUUUCGUACGCUCCGU
(((..((((((((((.((......))))).))))).(((((..(((((((..(((((((.....)))))))..))).(((....)))))))...))))))).))).. ( -32.80)
>DroSec_CAF1 137652 107 - 1
CGAUUCGGAUGGGUUCGCCUAAUUGCAGCACCAUCUUGCGGUUAUGCGUUCUACGUGCGUUUGUCGCACGUCUGGCUAAUUAAAAUUGCAUUUUUCGUACGCUUCGC
(((..((((((((((.((......))))).))))).(((((..(((((((..(((((((.....)))))))..))).(((....)))))))...)))))))..))). ( -32.80)
>DroSim_CAF1 145801 107 - 1
CGAUUCGGAUGGGUUCGCCUAAUUGCAGCACCAUCUUGCGGUUAUGCGUUCUACGUGCGUUUGUCGCACGUCUGGCUAAUUAAAAUUGCAUUUUUCGUACGCUUCGU
(((..((((((((((.((......))))).))))).(((((..(((((((..(((((((.....)))))))..))).(((....)))))))...)))))))..))). ( -33.00)
>DroYak_CAF1 139131 107 - 1
CGAUUCGUAUGGAUUCGCCUAAUUGCAGCACCAUCUUGCGGUUAUGCGUUCUACGUGCGUUUGUCGCACGUCUGGCUAAUUAAAAUUGCAUUUUUCGUACGCUCCGU
((...((((((((...((.(((((((((.......))))))))).))(((..(((((((.....)))))))..))).................))))))))...)). ( -31.30)
>DroAna_CAF1 229061 107 - 1
GGAUCCUGAUGGGUUCGCCUAAUUGCAGCGCCAUCUUGCGGUUAUGCGUUCUACGUGCGUUUGUCGCACGUCUGGCUAAUUAAAAUUGCAUUUUUCGAACGCUUCCC
((((((....))))))...(((((((((.......))))))))).((((((.(((((((.....)))))))...((...........)).......))))))..... ( -33.50)
>consensus
CGAUUCGGAUGGGUUCGCCUAAUUGCAGCACCAUCUUGCGGUUAUGCGUUCUACGUGCGUUUGUCGCACGUCUGGCUAAUUAAAAUUGCAUUUUUCGUACGCUUCGU
......(((((((((.((......))))).)))))).((((....((((.(.(((((((.....)))))))...((...........)).......).)))).)))) (-26.24 = -26.56 +   0.32)

alignment

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secondary structure

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dotplot

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Window 3

Location 11,607,777 – 11,607,877
Length 100
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 77.06
Mean single sequence MFE -25.92
Consensus MFE -17.90
Energy contribution -17.82
Covariance contribution -0.08
Combinations/Pair 1.06
Mean z-score -1.23
Structure conservation index 0.69
SVM decision value 0.41
SVM RNA-class probability 0.724904
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11607777 100 + 27905053
CCAGACGUGCGACAAACGCACGUAGAACGCAUAACCGCAAGAUGGUGCUGCAAUUAGGCG-----AACCCAUCCGAAUCCGAAUCAGAGUACGAAUCCGUAGCAG---------
....(((((((.....))))))).............((..(((((((((.......))))-----...)))))................((((....))))))..--------- ( -23.80)
>DroPse_CAF1 169276 97 + 1
GCAAACGUGCGACAAACGCACGUAGAAGGCAUAACCACAAGAUGGCGCUGCAAUUAGGCGAAACGAACCCAUCAGGAACGUUACCAGAGU--GACUCCA---------------
((..(((((((.....))))))).....))..........(((((((((.......))))........))))).(((..(((((....))--)))))).--------------- ( -27.30)
>DroSim_CAF1 145833 100 + 1
CCAGACGUGCGACAAACGCACGUAGAACGCAUAACCGCAAGAUGGUGCUGCAAUUAGGCG-----AACCCAUCCGAAUCGGAAUCAGAGUACGAAUCCGUAGCAG---------
(((.(((((((.....))))))).....((......))....)))((((((.....((..-----...)).........(((.((.......)).))))))))).--------- ( -27.60)
>DroYak_CAF1 139163 96 + 1
CCAGACGUGCGACAAACGCACGUAGAACGCAUAACCGCAAGAUGGUGCUGCAAUUAGGCG-----AAUCCAUACGAAUCGGAAUCCGAAUCC-------------AUUCCGAGU
....(((((((.....))))))).....((((...(....)...))))(((......)))-----............(((((((........-------------))))))).. ( -26.00)
>DroAna_CAF1 229093 98 + 1
CCAGACGUGCGACAAACGCACGUAGAACGCAUAACCGCAAGAUGGCGCUGCAAUUAGGCG-----AACCCAUCAGGAUCCUGACCC-CGUACC-GUCCAUACCCU---------
....(((((((.....))))))).....((......))..(((((((((.......))))-----......((((....))))...-....))-)))........--------- ( -26.40)
>DroPer_CAF1 170590 97 + 1
GCAAACGUGCGACAAACGCACGUAGAAGGCAUAACCACAAGAUGGCGCUGCAAUUAGGCGAAACGAACCCAUCAGGAACGUUACCAGAAU--GACUCCA---------------
((..(((((((.....))))))).....))..........(((((((((.......))))........))))).(((..((((......)--)))))).--------------- ( -24.40)
>consensus
CCAGACGUGCGACAAACGCACGUAGAACGCAUAACCGCAAGAUGGCGCUGCAAUUAGGCG_____AACCCAUCAGAAUCGGAACCAGAGUACGAAUCCA_______________
....(((((((.....))))))).................(((((((((.......))))........)))))......................................... (-17.90 = -17.82 +  -0.08)

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 11:27:56 2006