Locus 3292

Sequence ID 3R_DroMel_CAF1
Location 8,818,729 – 8,818,869
Length 140
Max. P 0.995553
window5312 window5313 window5314

overview

Window 2

Location 8,818,729 – 8,818,849
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.33
Mean single sequence MFE -39.53
Consensus MFE -33.44
Energy contribution -34.20
Covariance contribution 0.76
Combinations/Pair 1.17
Mean z-score -2.33
Structure conservation index 0.85
SVM decision value 2.59
SVM RNA-class probability 0.995553
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8818729 120 + 27905053
AUCCUUAUAGCCAUCGCCGCGAUUGUAAAAGUCCAACUGCUUCCACUUGAAGACCUCAAUCAUGGGAUCUCCAUCUGCAGAGAUUAGCAAUUGGAACCCUGAGAUUGCGCACAGGAGCAG
.((((....((....))(((((((.......(((((.((((.(((.((((.....))))...)))((((((........)))))))))).))))).......)))))))...)))).... ( -31.04)
>DroSec_CAF1 238725 120 + 1
AUCCUUAUAGCCAUCGCCGCGAUUGUAAAAGUCCAGUUGCUUCCACUUGAAGACCUCAAUCAUGGGAUCUCCAUCUGCGGAGAUUAGCAGUUGGAAACCUGCGAUUGCGCAGAGGAGCAG
.(((((...((....))((((((((((....((((..((((.(((.((((.....))))...)))(((((((......)))))))))))..))))....))))))))))..))))).... ( -42.20)
>DroSim_CAF1 257001 120 + 1
AUCCUUAUAGCCAUCGCCGCGAUUGUAAAAGUCCAGUUGCUUCCACUUGAAGACCUCAAUCAUGGGAUCUCCAUCUGCGGAGAUUAGCAGUUGGAAACCUGCGAUUGCGCAGAGGAGCAG
.(((((...((....))((((((((((....((((..((((.(((.((((.....))))...)))(((((((......)))))))))))..))))....))))))))))..))))).... ( -42.20)
>DroEre_CAF1 258968 120 + 1
AUCCAUAUAGUCAUCUCCGCGGUUGUAAAAGUCCAGCUGCUUCCACUUGAAAACCUCUAUCAUAGGAUCUCCGUCUGCCGAGAUUAGCAGUUGGAAACCUGCAAUUGCGCAGAUGAGCAG
..........((((((.((((((((((....(((((((((((((...(((.........)))..)))((((.(....).))))..))))))))))....)))))))))).)))))).... ( -43.90)
>DroYak_CAF1 252036 120 + 1
AUCCAUAUAGCCAUCCUUGCCAUUGUAAAAGUCCAGCUGCUUCCACUUGAAGACCUCUAUCAUGGGAUCUCCAUCUGCGGAGAUUAGCAAGUGGAGCCCUGCGAUUGCGCAGAGGAGCAG
.........((..(((((.....(((...(((((((..(((.(((((((....((........))(((((((......)))))))..)))))))))).))).))))..)))))))))).. ( -38.30)
>consensus
AUCCUUAUAGCCAUCGCCGCGAUUGUAAAAGUCCAGCUGCUUCCACUUGAAGACCUCAAUCAUGGGAUCUCCAUCUGCGGAGAUUAGCAGUUGGAAACCUGCGAUUGCGCAGAGGAGCAG
.........(((.((..((((((((((....(((((((((((((...(((.........)))..)))(((((......)))))..))))))))))....))))))))))..)).).)).. (-33.44 = -34.20 +   0.76)

alignment

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secondary structure

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dotplot

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Window 3

Location 8,818,729 – 8,818,849
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.33
Mean single sequence MFE -39.28
Consensus MFE -30.18
Energy contribution -30.98
Covariance contribution 0.80
Combinations/Pair 1.21
Mean z-score -1.63
Structure conservation index 0.77
SVM decision value 0.21
SVM RNA-class probability 0.637287
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8818729 120 - 27905053
CUGCUCCUGUGCGCAAUCUCAGGGUUCCAAUUGCUAAUCUCUGCAGAUGGAGAUCCCAUGAUUGAGGUCUUCAAGUGGAAGCAGUUGGACUUUUACAAUCGCGGCGAUGGCUAUAAGGAU
....((((..(((.......(((((.(((((((((....((..(...((((((((.((....)).)))))))).)..))))))))))))))))......)))(((....)))...)))). ( -37.72)
>DroSec_CAF1 238725 120 - 1
CUGCUCCUCUGCGCAAUCGCAGGUUUCCAACUGCUAAUCUCCGCAGAUGGAGAUCCCAUGAUUGAGGUCUUCAAGUGGAAGCAACUGGACUUUUACAAUCGCGGCGAUGGCUAUAAGGAU
....((((....((.(((((.((((((((.((((........)))).)))))))).(.((((((((((((.....((....))...))))))...)))))).)))))).))....)))). ( -40.20)
>DroSim_CAF1 257001 120 - 1
CUGCUCCUCUGCGCAAUCGCAGGUUUCCAACUGCUAAUCUCCGCAGAUGGAGAUCCCAUGAUUGAGGUCUUCAAGUGGAAGCAACUGGACUUUUACAAUCGCGGCGAUGGCUAUAAGGAU
....((((....((.(((((.((((((((.((((........)))).)))))))).(.((((((((((((.....((....))...))))))...)))))).)))))).))....)))). ( -40.20)
>DroEre_CAF1 258968 120 - 1
CUGCUCAUCUGCGCAAUUGCAGGUUUCCAACUGCUAAUCUCGGCAGACGGAGAUCCUAUGAUAGAGGUUUUCAAGUGGAAGCAGCUGGACUUUUACAACCGCGGAGAUGACUAUAUGGAU
....((((((.(((.(((..((((((((..(((((......)))))..))))).)))..)))...((((.....(((((((........)))))))))))))).)))))).......... ( -38.80)
>DroYak_CAF1 252036 120 - 1
CUGCUCCUCUGCGCAAUCGCAGGGCUCCACUUGCUAAUCUCCGCAGAUGGAGAUCCCAUGAUAGAGGUCUUCAAGUGGAAGCAGCUGGACUUUUACAAUGGCAAGGAUGGCUAUAUGGAU
....(((.(((((....)))))((((...((((((((((((((....)))))))....((.(((((((((...((((....)).))))))))))))).)))))))...))))....))). ( -39.50)
>consensus
CUGCUCCUCUGCGCAAUCGCAGGUUUCCAACUGCUAAUCUCCGCAGAUGGAGAUCCCAUGAUUGAGGUCUUCAAGUGGAAGCAGCUGGACUUUUACAAUCGCGGCGAUGGCUAUAAGGAU
((((..(((((((....))))))).((((.(((((....(((((...((((((((.(......).)))))))).)))))))))).))))...........))))................ (-30.18 = -30.98 +   0.80)

alignment

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secondary structure

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dotplot

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Window 4

Location 8,818,769 – 8,818,869
Length 100
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 83.01
Mean single sequence MFE -33.14
Consensus MFE -25.02
Energy contribution -26.66
Covariance contribution 1.64
Combinations/Pair 1.09
Mean z-score -1.53
Structure conservation index 0.75
SVM decision value 0.01
SVM RNA-class probability 0.538927
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8818769 100 - 27905053
--------------------AAAUGUUAUCGCUGGACGUUCUGCUCCUGUGCGCAAUCUCAGGGUUCCAAUUGCUAAUCUCUGCAGAUGGAGAUCCCAUGAUUGAGGUCUUCAAGUGGAA
--------------------........(((((((((.....((......)).(((((...((((((((.((((........)))).)))))..)))..)))))..))))...))))).. ( -28.10)
>DroSec_CAF1 238765 120 - 1
GUUUUUAAACGAAGCUAUAUAAAUGUUAUCGCUGGAGGUUCUGCUCCUCUGCGCAAUCGCAGGUUUCCAACUGCUAAUCUCCGCAGAUGGAGAUCCCAUGAUUGAGGUCUUCAAGUGGAA
..........((((((.............(((.(((((.......))))))))((((((..((((((((.((((........)))).)))))).))..)))))).)).))))........ ( -35.60)
>DroSim_CAF1 257041 113 - 1
-------AACGAAGCCAUAUAAAUGUUAUCGCUGGAGGUUCUGCUCCUCUGCGCAAUCGCAGGUUUCCAACUGCUAAUCUCCGCAGAUGGAGAUCCCAUGAUUGAGGUCUUCAAGUGGAA
-------...((((((.............(((.(((((.......))))))))((((((..((((((((.((((........)))).)))))).))..)))))).)).))))........ ( -38.20)
>DroEre_CAF1 259008 113 - 1
GUUU-----CAUAUACA--UAAAUGUUAUCGCUGAAGUUUCUGCUCAUCUGCGCAAUUGCAGGUUUCCAACUGCUAAUCUCGGCAGACGGAGAUCCUAUGAUAGAGGUUUUCAAGUGGAA
....-----........--.........(((((((((..((((.(((((((((....)))))((((((..(((((......)))))..))))))...))))))))..))))..))))).. ( -30.10)
>DroYak_CAF1 252076 120 - 1
GUGUUUAAACAAAGCCAUAAAAAUGUUAUCGCUGCACGUUCUGCUCCUCUGCGCAAUCGCAGGGCUCCACUUGCUAAUCUCCGCAGAUGGAGAUCCCAUGAUAGAGGUCUUCAAGUGGAA
((((........(((.((((.....)))).))))))).(((..((((((((((....))).((((((((.((((........)))).)))))..))).....)))))......))..))) ( -33.70)
>consensus
GU_U___AACAAAGCCAUAUAAAUGUUAUCGCUGGAGGUUCUGCUCCUCUGCGCAAUCGCAGGUUUCCAACUGCUAAUCUCCGCAGAUGGAGAUCCCAUGAUUGAGGUCUUCAAGUGGAA
............................(((((.((((.(((((......)).((((((..((((((((.((((........)))).))))))))...))))))))).)))).))))).. (-25.02 = -26.66 +   1.64)

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 10:57:43 2006