Locus 6564

Sequence ID 2L_DroMel_CAF1
Location 18,464,875 – 18,465,010
Length 135
Max. P 0.987309
window10468 window10469 window10470 window10471

overview

Window 8

Location 18,464,875 – 18,464,978
Length 103
Sequences 5
Columns 103
Reading direction forward
Mean pairwise identity 91.65
Mean single sequence MFE -31.06
Consensus MFE -24.44
Energy contribution -24.92
Covariance contribution 0.48
Combinations/Pair 1.14
Mean z-score -1.72
Structure conservation index 0.79
SVM decision value 0.56
SVM RNA-class probability 0.781968
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18464875 103 + 22407834
GCAGAAAGAGCUCAGUGUAUUGCAUAAUUUCGUGCAACUCCCACAAACAUAGGCGUUUUUGAUCUGUCUGUGUGUAGGUUCCUCGCUCUGCAUGUGUAUGCGU
(((((..(((....(((..((((((......))))))....)))..(((((((((.........)))))))))........)))..)))))((((....)))) ( -27.50)
>DroSec_CAF1 19311 103 + 1
GCACAAAGAGUUCAGCGUAUUGCAUAAUUUCGUGCAACUCCAACACACAUAGACGCUUUUGAUCUGUCUGUGUGUAGGUUCCUCGCUCUGCAUGUGUAUGCGA
(((((.(((((..(((...((((((......)))))).......(((((((((((.........)))))))))))..)))....)))))...)))))...... ( -29.50)
>DroSim_CAF1 19720 103 + 1
GCACAAAGAGUUCAGCGUAUUGCAUAAUUUCGUGCAACUCCAACACACAUAGGCGCUUUUGAUCUGUCUGUGUGUAGGUUCCUCGCUCUGCAUGUGUAUGCGU
(((((.(((((..(((...((((((......)))))).......(((((((((((.........)))))))))))..)))....)))))...)))))...... ( -28.90)
>DroEre_CAF1 19159 103 + 1
GCACAAAGAGCUUAGCGUAUUGCAUAAUUUCGUGCAACUCCCACACAGAUAGGCGCUUCUGAUCUGUCUGCGUGUAGGUUCCUCGCUCUGCAUGUGUAUGCGU
(((((.(((((..........((((......))))((((..(((.((((((((((....)).)))))))).)))..))))....)))))...)))))...... ( -33.20)
>DroYak_CAF1 19423 103 + 1
GUACUAAGAGCUUAGCGUAUUGCAUAAUUUUGUGCAACUCCCACACACAUAGGCGCUUUUGGCCUGUCUGUGUGGAGGUUCCUCGUUCUGCAUGUGUAUGCAU
......(((((..........(((((....)))))(((..(((((((.((((((.(....))))))).)))))))..)))....)))))((((....)))).. ( -36.20)
>consensus
GCACAAAGAGCUCAGCGUAUUGCAUAAUUUCGUGCAACUCCCACACACAUAGGCGCUUUUGAUCUGUCUGUGUGUAGGUUCCUCGCUCUGCAUGUGUAUGCGU
(((((.(((((........((((((......))))))..((...(((((((((((.........))))))))))).))......)))))...)))))...... (-24.44 = -24.92 +   0.48)

alignment

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secondary structure

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dotplot

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Window 9

Location 18,464,875 – 18,464,978
Length 103
Sequences 5
Columns 103
Reading direction reverse
Mean pairwise identity 91.65
Mean single sequence MFE -28.32
Consensus MFE -23.84
Energy contribution -24.92
Covariance contribution 1.08
Combinations/Pair 1.07
Mean z-score -1.61
Structure conservation index 0.84
SVM decision value 0.93
SVM RNA-class probability 0.883604
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18464875 103 - 22407834
ACGCAUACACAUGCAGAGCGAGGAACCUACACACAGACAGAUCAAAAACGCCUAUGUUUGUGGGAGUUGCACGAAAUUAUGCAAUACACUGAGCUCUUUCUGC
..((((....))))(((((..((..((((((.(((....(........).....))).)))))).((((((........))))))...))..)))))...... ( -26.20)
>DroSec_CAF1 19311 103 - 1
UCGCAUACACAUGCAGAGCGAGGAACCUACACACAGACAGAUCAAAAGCGUCUAUGUGUGUUGGAGUUGCACGAAAUUAUGCAAUACGCUGAACUCUUUGUGC
..((((....))))...(((((((.((.(((((((...((((.......)))).))))))).)).((((((........)))))).........))))))).. ( -28.60)
>DroSim_CAF1 19720 103 - 1
ACGCAUACACAUGCAGAGCGAGGAACCUACACACAGACAGAUCAAAAGCGCCUAUGUGUGUUGGAGUUGCACGAAAUUAUGCAAUACGCUGAACUCUUUGUGC
..((((....))))...(((((((.((.(((((((....(........).....))))))).)).((((((........)))))).........))))))).. ( -25.80)
>DroEre_CAF1 19159 103 - 1
ACGCAUACACAUGCAGAGCGAGGAACCUACACGCAGACAGAUCAGAAGCGCCUAUCUGUGUGGGAGUUGCACGAAAUUAUGCAAUACGCUAAGCUCUUUGUGC
..(((((.....((..((((.....((..((((((((.((...........)).)))))))))).((((((........)))))).))))..))....))))) ( -29.70)
>DroYak_CAF1 19423 103 - 1
AUGCAUACACAUGCAGAACGAGGAACCUCCACACAGACAGGCCAAAAGCGCCUAUGUGUGUGGGAGUUGCACAAAAUUAUGCAAUACGCUAAGCUCUUAGUAC
.(((((....)))))......(.(((..(((((((.(.(((((....).)))).).)))))))..))).).................(((((....))))).. ( -31.30)
>consensus
ACGCAUACACAUGCAGAGCGAGGAACCUACACACAGACAGAUCAAAAGCGCCUAUGUGUGUGGGAGUUGCACGAAAUUAUGCAAUACGCUGAGCUCUUUGUGC
..((((....))))...(((((((.((((((((((...((...........)).)))))))))).((((((........)))))).........))))))).. (-23.84 = -24.92 +   1.08)

alignment

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secondary structure

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dotplot

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Window 0

Location 18,464,908 – 18,465,010
Length 102
Sequences 5
Columns 102
Reading direction forward
Mean pairwise identity 92.84
Mean single sequence MFE -35.02
Consensus MFE -27.20
Energy contribution -26.88
Covariance contribution -0.32
Combinations/Pair 1.19
Mean z-score -1.75
Structure conservation index 0.78
SVM decision value 0.40
SVM RNA-class probability 0.722016
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18464908 102 + 22407834
GCAACUCCCACAAACAUAGGCGUUUUUGAUCUGUCUGUGUGUAGGUUCCUCGCUCUGCAUGUGUAUGCGUGUGUGGCAUUGGCUUUGAUUGUGUGUAGGAGC
....((((((((((((((((((.........)))))))))((..((.((.(((.(.((((....))))).))).)).))..)).....)))))....)))). ( -27.90)
>DroSec_CAF1 19344 102 + 1
GCAACUCCAACACACAUAGACGCUUUUGAUCUGUCUGUGUGUAGGUUCCUCGCUCUGCAUGUGUAUGCGAGUGUGGCAUUGGCUUUGAUUGUGUGUAGGAGC
....((((.(((((((..((.(((..(((((((.(.....)))))).((.(((((.((((....))))))))).))))..))).))...))))))).)))). ( -35.70)
>DroSim_CAF1 19753 102 + 1
GCAACUCCAACACACAUAGGCGCUUUUGAUCUGUCUGUGUGUAGGUUCCUCGCUCUGCAUGUGUAUGCGUGUGUGACAUUGGCUUUGAUUGUGUGUAGGAGC
....((((.(((((((..((.(((..((.((.....(.(((.((....))))).).((((((....))))))..))))..))).))...))))))).)))). ( -31.00)
>DroEre_CAF1 19192 101 + 1
GCAACUCCCACACAGAUAGGCGCUUCUGAUCUGUCUGCGUGUAGGUUCCUCGCUCUGCAUGUGUAUGCGUGUGUGGCAUUGGCU-UGUUUGUGUGUAGGAGC
....(((((((((((((((((......((((((.(.....)))))))....(((..((((((....))))))..)))....)))-))))))))))..)))). ( -36.90)
>DroYak_CAF1 19456 102 + 1
GCAACUCCCACACACAUAGGCGCUUUUGGCCUGUCUGUGUGGAGGUUCCUCGUUCUGCAUGUGUAUGCAUGUGUGGCAUUGGCUUUGCUUGUGUGUGGGAGC
....((((((((((((.((((.(....)))))(((.((((.(((....))).....(((((((....))))))).)))).)))......)))))))))))). ( -43.60)
>consensus
GCAACUCCCACACACAUAGGCGCUUUUGAUCUGUCUGUGUGUAGGUUCCUCGCUCUGCAUGUGUAUGCGUGUGUGGCAUUGGCUUUGAUUGUGUGUAGGAGC
....((((.(((((((..((.(((..((.((.....(.(((.((....))))).).(((..((....))..)))))))..))).))...))))))).)))). (-27.20 = -26.88 +  -0.32)

alignment

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secondary structure

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dotplot

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Window 1

Location 18,464,908 – 18,465,010
Length 102
Sequences 5
Columns 102
Reading direction reverse
Mean pairwise identity 92.84
Mean single sequence MFE -27.99
Consensus MFE -22.98
Energy contribution -23.78
Covariance contribution 0.80
Combinations/Pair 1.08
Mean z-score -2.29
Structure conservation index 0.82
SVM decision value 2.07
SVM RNA-class probability 0.987309
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18464908 102 - 22407834
GCUCCUACACACAAUCAAAGCCAAUGCCACACACGCAUACACAUGCAGAGCGAGGAACCUACACACAGACAGAUCAAAAACGCCUAUGUUUGUGGGAGUUGC
(((((((((.(((.....................((((....))))((.(((((....)).......((....)).....))))).))).)))))))))... ( -22.90)
>DroSec_CAF1 19344 102 - 1
GCUCCUACACACAAUCAAAGCCAAUGCCACACUCGCAUACACAUGCAGAGCGAGGAACCUACACACAGACAGAUCAAAAGCGUCUAUGUGUGUUGGAGUUGC
(((((.(((((((.............((.(.(((((((....)))).))).).))...........((((...........)))).))))))).)))))... ( -28.80)
>DroSim_CAF1 19753 102 - 1
GCUCCUACACACAAUCAAAGCCAAUGUCACACACGCAUACACAUGCAGAGCGAGGAACCUACACACAGACAGAUCAAAAGCGCCUAUGUGUGUUGGAGUUGC
(((((.(((((((......((...((((......((((....))))...(.(((....)).).)...))))........)).....))))))).)))))... ( -25.30)
>DroEre_CAF1 19192 101 - 1
GCUCCUACACACAAACA-AGCCAAUGCCACACACGCAUACACAUGCAGAGCGAGGAACCUACACGCAGACAGAUCAGAAGCGCCUAUCUGUGUGGGAGUUGC
(((((((((((......-.((...((........((((....))))...(((.(.......).)))........))...)).......)))))))))))... ( -26.04)
>DroYak_CAF1 19456 102 - 1
GCUCCCACACACAAGCAAAGCCAAUGCCACACAUGCAUACACAUGCAGAACGAGGAACCUCCACACAGACAGGCCAAAAGCGCCUAUGUGUGUGGGAGUUGC
(((((((((((((((....((....(((.....(((((....)))))....(((....)))..........))).....))..)).)))))))))))))... ( -36.90)
>consensus
GCUCCUACACACAAUCAAAGCCAAUGCCACACACGCAUACACAUGCAGAGCGAGGAACCUACACACAGACAGAUCAAAAGCGCCUAUGUGUGUGGGAGUUGC
(((((((((((((.....................((((....))))((.(((((....)).......(......).....))))).)))))))))))))... (-22.98 = -23.78 +   0.80)

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 12:14:16 2006