Locus 8245

Sequence ID 3L_DroMel_CAF1
Location 21,657,410 – 21,657,548
Length 138
Max. P 0.871225
window13483 window13484 window13485

overview

Window 3

Location 21,657,410 – 21,657,528
Length 118
Sequences 4
Columns 119
Reading direction forward
Mean pairwise identity 82.09
Mean single sequence MFE -36.31
Consensus MFE -22.05
Energy contribution -23.30
Covariance contribution 1.25
Combinations/Pair 1.17
Mean z-score -2.34
Structure conservation index 0.61
SVM decision value 0.87
SVM RNA-class probability 0.871225
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21657410 118 + 23771897
CCACAGCGCCUGCAGAUGCCACCGCUGCUCAGAG-AGCUCGGUUCGCAUGCAGUGCGGGGCUUGCCAUAAAAAAUAUUGGCCACCUUAAUGUAAGUGGCUUAUAAAUUUGUGCACAAGC
((...((((.((((..(((.((((..((((...)-))).))))..))))))))))).))(((((.((((((...(((.((((((..........)))))).)))..))))))..))))) ( -42.10)
>DroEre_CAF1 33648 116 + 1
GCACAACGCCUGCAGAUGCCACCGCUGCUCAG---AGCUCAGUUCGCAUGCAGUGCGGUAUUUGCCAUAAAAAAUAUUGGCCACCUUAAUGUAAGUGGCUUAUAAAUUUGUGCACAAGC
((((((.....(((((((((..((((((...(---(((...))))....)))))).))))))))).........(((.((((((..........)))))).)))...))))))...... ( -41.20)
>DroYak_CAF1 42786 116 + 1
CCACAACGCUUGCAGAUGCCACCGCUGCUCAG---AGCUCAGUUCGCUUCCAGUGCGGUAUUUGCCAUAAAAAAUAUUGGCCACCUUAAUGUAAGUGGCUUAUAAAUUUGUGCACAAGC
.......(((((((((((((..(((((....(---(((.......)))).))))).)))))))))((((((...(((.((((((..........)))))).)))..))))))...)))) ( -34.50)
>DroAna_CAF1 33800 104 + 1
------------UGGAUCCCA--ACUGCUUGGCGACGAUCGGUUCGCAUGCAGUGUGCCGUUUGCCAUAAAA-AUAAUUGCCGCCUUAAUGUAAGUGGCUUAUAAAUUUGUGCACAAAC
------------.((......--(((((...((((........))))..)))))...))(((((.((((((.-......(((((..........))))).......))))))..))))) ( -27.44)
>consensus
CCACAACGCCUGCAGAUGCCACCGCUGCUCAG___AGCUCAGUUCGCAUGCAGUGCGGUAUUUGCCAUAAAAAAUAUUGGCCACCUUAAUGUAAGUGGCUUAUAAAUUUGUGCACAAGC
...........(((((((((..((((((.....................)))))).)))))))))((((((...(((.((((((..........)))))).)))..))))))....... (-22.05 = -23.30 +   1.25)

alignment

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secondary structure

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dotplot

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Window 4

Location 21,657,448 – 21,657,548
Length 100
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 73.59
Mean single sequence MFE -26.37
Consensus MFE -14.17
Energy contribution -14.28
Covariance contribution 0.11
Combinations/Pair 1.13
Mean z-score -1.60
Structure conservation index 0.54
SVM decision value 0.30
SVM RNA-class probability 0.677020
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21657448 100 + 23771897
CGGUUCGCAUGCAGUGCGGGGCUUGCCAUAAAAAAUAUUGGCCACCUUAAUGUAAGUGGCUUAUAAAUUUGUGCACAAGCCCAGACCAUUUAUGGCCAAC--------------------
.(((((((((...)))))(((((((.((((((...(((.((((((..........)))))).)))..))))))..))))))).)))).............-------------------- ( -34.10)
>DroVir_CAF1 20138 83 + 1
--GU----------UGUACCA-UGGCCAUAAA-AAUAUUUGCCGCCUUAAUGUGAGUGGCUUAUAAAUUUG--CACAAACGC-GACCAUAUAUAGCAUUU--------------------
--((----------((((..(-(((.......-..(((..((((((.......).)))))..)))...(((--(......))-)))))).))))))....-------------------- ( -19.40)
>DroEre_CAF1 33684 100 + 1
CAGUUCGCAUGCAGUGCGGUAUUUGCCAUAAAAAAUAUUGGCCACCUUAAUGUAAGUGGCUUAUAAAUUUGUGCACAAGCCCAGGCCAUUUAUGGCCAUC--------------------
......((((...))))(((.(.(((.(((((...(((.((((((..........)))))).)))..)))))))).).)))..(((((....)))))...-------------------- ( -27.50)
>DroYak_CAF1 42822 100 + 1
CAGUUCGCUUCCAGUGCGGUAUUUGCCAUAAAAAAUAUUGGCCACCUUAAUGUAAGUGGCUUAUAAAUUUGUGCACAAGCCCAAGCCAUUUAUGGCCAUC--------------------
......((((...(((((((....)))(((((...(((.((((((..........)))))).)))..)))))))))))))....((((....))))....-------------------- ( -25.10)
>DroMoj_CAF1 22976 83 + 1
--GU----------UGCGCCA-UGGCCAUAAA-AAUAUUUGCCGCCUUAAUGUGAGUGGCUUAUAAAUUUG--CACAAACGC-GACCAUAUAUAGCGGCU--------------------
--((----------(((...(-(((.......-..(((..((((((.......).)))))..)))...(((--(......))-)))))).....))))).-------------------- ( -20.20)
>DroAna_CAF1 33825 119 + 1
CGGUUCGCAUGCAGUGUGCCGUUUGCCAUAAAA-AUAAUUGCCGCCUUAAUGUAAGUGGCUUAUAAAUUUGUGCACAAACCCAGACCAUUUAUGGCCAUGUGGCGGAGCCAGGGCGAGGG
((((.(((.....))).))))((((((......-......(((((.....(((((((((((......((((....))))...)).))))))))).....)))))(....)..)))))).. ( -31.90)
>consensus
C_GUUCGCAUGCAGUGCGCCAUUUGCCAUAAAAAAUAUUGGCCACCUUAAUGUAAGUGGCUUAUAAAUUUGUGCACAAACCCAGACCAUUUAUGGCCAUC____________________
........................((((((((...(((..(((((.(((...))))))))..)))..((((....)))).........))))))))........................ (-14.17 = -14.28 +   0.11)

alignment

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secondary structure

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dotplot

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Window 5

Location 21,657,448 – 21,657,548
Length 100
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 73.59
Mean single sequence MFE -27.08
Consensus MFE -14.31
Energy contribution -14.48
Covariance contribution 0.17
Combinations/Pair 1.18
Mean z-score -1.79
Structure conservation index 0.53
SVM decision value 0.72
SVM RNA-class probability 0.833073
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21657448 100 - 23771897
--------------------GUUGGCCAUAAAUGGUCUGGGCUUGUGCACAAAUUUAUAAGCCACUUACAUUAAGGUGGCCAAUAUUUUUUAUGGCAAGCCCCGCACUGCAUGCGAACCG
--------------------...(((((....))))).((((((((.((.(((..(((..(((((((......)))))))..)))...))).))))))))))((((.....))))..... ( -34.40)
>DroVir_CAF1 20138 83 - 1
--------------------AAAUGCUAUAUAUGGUC-GCGUUUGUG--CAAAUUUAUAAGCCACUCACAUUAAGGCGGCAAAUAUU-UUUAUGGCCA-UGGUACA----------AC--
--------------------..........(((((((-(((....))--)(((..(((..(((.((........)).)))..)))..-)))..)))))-)).....----------..-- ( -16.70)
>DroEre_CAF1 33684 100 - 1
--------------------GAUGGCCAUAAAUGGCCUGGGCUUGUGCACAAAUUUAUAAGCCACUUACAUUAAGGUGGCCAAUAUUUUUUAUGGCAAAUACCGCACUGCAUGCGAACUG
--------------------....(((((((((((((..((((((((........))))))))((((......)))))))))......))))))))......((((.....))))..... ( -31.70)
>DroYak_CAF1 42822 100 - 1
--------------------GAUGGCCAUAAAUGGCUUGGGCUUGUGCACAAAUUUAUAAGCCACUUACAUUAAGGUGGCCAAUAUUUUUUAUGGCAAAUACCGCACUGGAAGCGAACUG
--------------------....(((((((((((((..((((((((........))))))))((((......)))))))))......))))))))......(((.......)))..... ( -28.10)
>DroMoj_CAF1 22976 83 - 1
--------------------AGCCGCUAUAUAUGGUC-GCGUUUGUG--CAAAUUUAUAAGCCACUCACAUUAAGGCGGCAAAUAUU-UUUAUGGCCA-UGGCGCA----------AC--
--------------------.((.(((....((((((-(((....))--)(((..(((..(((.((........)).)))..)))..-)))..)))))-)))))).----------..-- ( -19.90)
>DroAna_CAF1 33825 119 - 1
CCCUCGCCCUGGCUCCGCCACAUGGCCAUAAAUGGUCUGGGUUUGUGCACAAAUUUAUAAGCCACUUACAUUAAGGCGGCAAUUAU-UUUUAUGGCAAACGGCACACUGCAUGCGAACCG
...((((....((...(((.....((((((((.....((((((((....))))))))...(((.(((......))).)))......-.))))))))....))).....))..)))).... ( -31.70)
>consensus
____________________GAUGGCCAUAAAUGGUCUGGGCUUGUGCACAAAUUUAUAAGCCACUUACAUUAAGGCGGCAAAUAUUUUUUAUGGCAAAUGCCGCACUGCAUGCGAAC_G
........................((((((((..(((..((((((((........)))))))).(((.....)))..)))........))))))))........................ (-14.31 = -14.48 +   0.17)

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 13:10:23 2006