Locus 3698

Sequence ID 3L_DroMel_CAF1
Location 10,764,427 – 10,764,545
Length 118
Max. P 0.895282
window5774 window5775

overview

Window 4

Location 10,764,427 – 10,764,545
Length 118
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 89.05
Mean single sequence MFE -24.76
Consensus MFE -19.86
Energy contribution -20.14
Covariance contribution 0.28
Combinations/Pair 1.08
Mean z-score -1.88
Structure conservation index 0.80
SVM decision value 0.99
SVM RNA-class probability 0.895282
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10764427 118 + 23771897
GCUCGACUCCUCAUCCAACUACUUCCAUACUUCCAGUGAUUCUCACGCCCCACCAGCUGCGUC-UUCGGAGGCUCUUCUUUCUUCUCCCCAUCACUGGAGACACUGCGUUCGUUGGCUU
..............(((((............(((((((((......((.......)).((.((-....)).)).................)))))))))(((.....))).)))))... ( -25.90)
>DroSec_CAF1 98135 116 + 1
GCU--ACUCCUCAUCCAACUGCUUCCAUACUUCCAGUGAUUCUCCCCCACCACCAGCUGCGUC-UUCGGGGGCCUUUCUUUCUUCUCCCCAUCAUUGGAGACACUGCGUUCGUUGGCUU
...--...............(((..(..((...(((((.....(((((...(((....).)).-...)))))...........(((((........)))))))))).))..)..))).. ( -24.00)
>DroSim_CAF1 101012 116 + 1
GCU--ACUCCUCAUCCAACUACUUCCAUACUUCCAGUGAUUCUCCCGCACCACCAGCUGCGUC-UUCGGGGGCCUUUCUUUCUUCUCCCCAUCAUUGGAGACACUGCGUUCGUUGGCUU
...--.........(((((............(((((((((.....((((.(....).))))..-...(((((.............))))))))))))))(((.....))).)))))... ( -26.82)
>DroEre_CAF1 103075 108 + 1
GCCA--CUCUUCAUCCAACUAC--------UUUCAGCGAUUCUCCCGCCCCACCAGCUGCUUC-UUCGGGGGCCUUUCUUUCUUCUCCCCAUCAUUGGAGACACUGCGUUCGUUGGCUU
....--........(((((...--------.....(((.......)))...(((((..(((((-....)))))..........(((((........)))))..))).))..)))))... ( -23.50)
>DroYak_CAF1 114135 117 + 1
GCCACACUCUUCAUCCAACUACUAC--UUCUUCCAGUGAUUCUCCCGCCCCACCAGCUGCUUCAUUUGGGGGCCUUUCUUUCUUCUCCCCAUCAUUGGAGACACUGCGUUCGUUGGCUU
..............(((((....((--......(((((........(((((..(((.((...)).))))))))..........(((((........)))))))))).))..)))))... ( -23.60)
>consensus
GCU__ACUCCUCAUCCAACUACUUCCAUACUUCCAGUGAUUCUCCCGCCCCACCAGCUGCGUC_UUCGGGGGCCUUUCUUUCUUCUCCCCAUCAUUGGAGACACUGCGUUCGUUGGCUU
..............(((((............(((((((((......((.......))..........(((((.............))))))))))))))(((.....))).)))))... (-19.86 = -20.14 +   0.28)

alignment

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secondary structure

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dotplot

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Window 5

Location 10,764,427 – 10,764,545
Length 118
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 89.05
Mean single sequence MFE -32.67
Consensus MFE -23.34
Energy contribution -23.46
Covariance contribution 0.12
Combinations/Pair 1.12
Mean z-score -1.72
Structure conservation index 0.71
SVM decision value -0.00
SVM RNA-class probability 0.531574
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10764427 118 - 23771897
AAGCCAACGAACGCAGUGUCUCCAGUGAUGGGGAGAAGAAAGAAGAGCCUCCGAA-GACGCAGCUGGUGGGGCGUGAGAAUCACUGGAAGUAUGGAAGUAGUUGGAUGAGGAGUCGAGC
...(((((..((...(((((((((....)))((((.............))))..)-)))))..(..((((..(....)..))))..)..........)).))))).............. ( -34.72)
>DroSec_CAF1 98135 116 - 1
AAGCCAACGAACGCAGUGUCUCCAAUGAUGGGGAGAAGAAAGAAAGGCCCCCGAA-GACGCAGCUGGUGGUGGGGGAGAAUCACUGGAAGUAUGGAAGCAGUUGGAUGAGGAGU--AGC
...(((((.....(((((((((((....)))))).............((((((..-..(((.....))).)))))).....)))))......((....))))))).........--... ( -33.60)
>DroSim_CAF1 101012 116 - 1
AAGCCAACGAACGCAGUGUCUCCAAUGAUGGGGAGAAGAAAGAAAGGCCCCCGAA-GACGCAGCUGGUGGUGCGGGAGAAUCACUGGAAGUAUGGAAGUAGUUGGAUGAGGAGU--AGC
...(((((.....((((((((((.....(((((...............)))))..-..((((.(....).)))))))))..)))))....(((....)))))))).........--... ( -33.06)
>DroEre_CAF1 103075 108 - 1
AAGCCAACGAACGCAGUGUCUCCAAUGAUGGGGAGAAGAAAGAAAGGCCCCCGAA-GAAGCAGCUGGUGGGGCGGGAGAAUCGCUGAAA--------GUAGUUGGAUGAAGAG--UGGC
...(((((..((.(((((((((((....))))))............(((((...(-(......))...)))))........)))))...--------)).)))))........--.... ( -31.90)
>DroYak_CAF1 114135 117 - 1
AAGCCAACGAACGCAGUGUCUCCAAUGAUGGGGAGAAGAAAGAAAGGCCCCCAAAUGAAGCAGCUGGUGGGGCGGGAGAAUCACUGGAAGAA--GUAGUAGUUGGAUGAAGAGUGUGGC
..((((....((......((((((((..(((((...............)))))..........(..((((..(....)..))))..).....--......)))))).))...)).)))) ( -30.06)
>consensus
AAGCCAACGAACGCAGUGUCUCCAAUGAUGGGGAGAAGAAAGAAAGGCCCCCGAA_GACGCAGCUGGUGGGGCGGGAGAAUCACUGGAAGUAUGGAAGUAGUUGGAUGAGGAGU__AGC
...(((((....((.(((((((....))(((((...............)))))...))))).)).(((((..(....)..)))))...............))))).............. (-23.34 = -23.46 +   0.12)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:04:34 2006