Locus 1398

Sequence ID 2R_DroMel_CAF1
Location 5,408,888 – 5,409,020
Length 132
Max. P 0.998121
window2394 window2395 window2396

overview

Window 4

Location 5,408,888 – 5,409,008
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.67
Mean single sequence MFE -34.26
Consensus MFE -30.20
Energy contribution -29.84
Covariance contribution -0.36
Combinations/Pair 1.23
Mean z-score -2.37
Structure conservation index 0.88
SVM decision value 3.01
SVM RNA-class probability 0.998121
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5408888 120 + 20766785
AAUAACCAACGCGCAUUUUGCGACUCCGAAAAAUGCCAAUGGGAACACAUUAAUCCCGAGGAGCAAACAAUAGACUUGGACUCUACCGAAAGUGAUGGACCAAGUCUGUCCUGCUUUGCC
.....((...(.(((((((.((....)).))))))))..(((((.........))))).)).(((((((((((((((((..((((((....).).))))))))))))))..)).))))). ( -37.30)
>DroSec_CAF1 10608 120 + 1
AAUAACCAACGAGCAUUUUGUGACUCCGAAAAAUGCCAAUGGGAACACAUUACUUCCGAGGAGCAAACAAUAGACUUGGACUCCACCGAAAGUGAUGGACCAAGUCUGUCCUGCUUUGCC
.....((...(.(((((((.((....)).))))))))....((((........))))..)).(((((((((((((((((..((((((....).).))))))))))))))..)).))))). ( -36.00)
>DroSim_CAF1 9105 120 + 1
AAUAACCAACGAGCAUUUUGUGACUCCGAAAAAUGCCAAUGGGAACACAUUACUUCCGAGGAGCAAACAAUAGACUUGGACUCCACCGAAAGUGAUGGACCAAGUCUGUCCUGCUUUGCC
.....((...(.(((((((.((....)).))))))))....((((........))))..)).(((((((((((((((((..((((((....).).))))))))))))))..)).))))). ( -36.00)
>DroEre_CAF1 10536 120 + 1
AACAACCAACGCGCAAUUUGCGACACCGAAAAUUGCCAGUGGGAACACAUUAAUCCCGAGGAGCAAACAAUAGACUUGGACACCAACGACAGCGAUGGACCAAGCCUGUCCUGCUUUGCC
.....((...(.(((((((.((....)).))))))))..(((((.........))))).)).(((((((((((.(((((...(((.((....)).))).))))).))))..)).))))). ( -32.20)
>DroYak_CAF1 9407 120 + 1
AAUAACCAACGGGCAAUUUGCGAAACUGAAAAAUGUCAUUGGGAGCACAUCAAUCCCGAGGAACAGACGAUAGACAUAGACGCCAACGAAAGCGAUGGACCAAGUCUGUCCUGCUUUGCC
...........(((((...(((................((((((.........))))))(((.(((((......(((...(((........))))))......))))))))))).))))) ( -29.80)
>consensus
AAUAACCAACGAGCAUUUUGCGACUCCGAAAAAUGCCAAUGGGAACACAUUAAUCCCGAGGAGCAAACAAUAGACUUGGACUCCACCGAAAGUGAUGGACCAAGUCUGUCCUGCUUUGCC
.....((...(.(((((((.((....)).))))))))..(((((.........))))).)).(((((((((((((((((..((((.((....)).))))))))))))))..)).))))). (-30.20 = -29.84 +  -0.36)

alignment

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secondary structure

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dotplot

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Window 5

Location 5,408,928 – 5,409,020
Length 92
Sequences 5
Columns 92
Reading direction forward
Mean pairwise identity 91.41
Mean single sequence MFE -25.64
Consensus MFE -21.70
Energy contribution -22.26
Covariance contribution 0.56
Combinations/Pair 1.12
Mean z-score -2.10
Structure conservation index 0.85
SVM decision value 2.12
SVM RNA-class probability 0.988535
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5408928 92 + 20766785
GGGAACACAUUAAUCCCGAGGAGCAAACAAUAGACUUGGACUCUACCGAAAGUGAUGGACCAAGUCUGUCCUGCUUUGCCAUACAAAAUCAG
((((.........))))(..(((((....((((((((((..((((((....).).))))))))))))))..)))))..)............. ( -27.70)
>DroSec_CAF1 10648 92 + 1
GGGAACACAUUACUUCCGAGGAGCAAACAAUAGACUUGGACUCCACCGAAAGUGAUGGACCAAGUCUGUCCUGCUUUGCCAUACAAAAUCAG
.((((........))))(..(((((....((((((((((..((((((....).).))))))))))))))..)))))..)............. ( -28.30)
>DroSim_CAF1 9145 92 + 1
GGGAACACAUUACUUCCGAGGAGCAAACAAUAGACUUGGACUCCACCGAAAGUGAUGGACCAAGUCUGUCCUGCUUUGCCAUACAAAAUCGG
.((((........))))(..(((((....((((((((((..((((((....).).))))))))))))))..)))))..)............. ( -28.30)
>DroEre_CAF1 10576 92 + 1
GGGAACACAUUAAUCCCGAGGAGCAAACAAUAGACUUGGACACCAACGACAGCGAUGGACCAAGCCUGUCCUGCUUUGCCAUACAAAAUCAG
((((.........))))(..(((((....((((.(((((...(((.((....)).))).))))).))))..)))))..)............. ( -22.70)
>DroYak_CAF1 9447 92 + 1
GGGAGCACAUCAAUCCCGAGGAACAGACGAUAGACAUAGACGCCAACGAAAGCGAUGGACCAAGUCUGUCCUGCUUUGCCAUACAGAAUCAG
((((.........)))).((((.(((((......(((...(((........))))))......))))))))).................... ( -21.20)
>consensus
GGGAACACAUUAAUCCCGAGGAGCAAACAAUAGACUUGGACUCCACCGAAAGUGAUGGACCAAGUCUGUCCUGCUUUGCCAUACAAAAUCAG
((((.........))))(..(((((....((((((((((..((((.((....)).))))))))))))))..)))))..)............. (-21.70 = -22.26 +   0.56)

alignment

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secondary structure

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dotplot

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Window 6

Location 5,408,928 – 5,409,020
Length 92
Sequences 5
Columns 92
Reading direction reverse
Mean pairwise identity 91.41
Mean single sequence MFE -26.74
Consensus MFE -24.48
Energy contribution -24.72
Covariance contribution 0.24
Combinations/Pair 1.24
Mean z-score -1.16
Structure conservation index 0.92
SVM decision value 0.11
SVM RNA-class probability 0.587825
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5408928 92 - 20766785
CUGAUUUUGUAUGGCAAAGCAGGACAGACUUGGUCCAUCACUUUCGGUAGAGUCCAAGUCUAUUGUUUGCUCCUCGGGAUUAAUGUGUUCCC
.((((((((...((((((.(((...((((((((.(((((......))).).).)))))))).)))))))))...)))))))).......... ( -25.60)
>DroSec_CAF1 10648 92 - 1
CUGAUUUUGUAUGGCAAAGCAGGACAGACUUGGUCCAUCACUUUCGGUGGAGUCCAAGUCUAUUGUUUGCUCCUCGGAAGUAAUGUGUUCCC
....(((((...((((((.(((...((((((((((((((......))))))..)))))))).)))))))))...)))))............. ( -28.80)
>DroSim_CAF1 9145 92 - 1
CCGAUUUUGUAUGGCAAAGCAGGACAGACUUGGUCCAUCACUUUCGGUGGAGUCCAAGUCUAUUGUUUGCUCCUCGGAAGUAAUGUGUUCCC
((((.((((.....))))(((((..((((((((((((((......))))))..))))))))....)))))...))))............... ( -29.10)
>DroEre_CAF1 10576 92 - 1
CUGAUUUUGUAUGGCAAAGCAGGACAGGCUUGGUCCAUCGCUGUCGUUGGUGUCCAAGUCUAUUGUUUGCUCCUCGGGAUUAAUGUGUUCCC
.((((((((...((((((.(((...((((((((.(((.((....)).)))...)))))))).)))))))))...)))))))).......... ( -27.90)
>DroYak_CAF1 9447 92 - 1
CUGAUUCUGUAUGGCAAAGCAGGACAGACUUGGUCCAUCGCUUUCGUUGGCGUCUAUGUCUAUCGUCUGUUCCUCGGGAUUGAUGUGCUCCC
..(((((((...((...((((((..((((.(((.....((((......)))).))).))))....)))))))).)))))))........... ( -22.30)
>consensus
CUGAUUUUGUAUGGCAAAGCAGGACAGACUUGGUCCAUCACUUUCGGUGGAGUCCAAGUCUAUUGUUUGCUCCUCGGGAUUAAUGUGUUCCC
.((((((((...((...((((((..((((((((.(((((......)))))...))))))))....)))))))).)))))))).......... (-24.48 = -24.72 +   0.24)

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 10:03:51 2006