Locus 30

Sequence ID 4_DroMel_CAF1
Location 273,082 – 273,233
Length 151
Max. P 0.940044
window50 window51 window52

overview

Window 0

Location 273,082 – 273,197
Length 115
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 73.20
Mean single sequence MFE -22.65
Consensus MFE -3.35
Energy contribution -2.51
Covariance contribution -0.84
Combinations/Pair 1.50
Mean z-score -2.00
Structure conservation index 0.15
SVM decision value 1.31
SVM RNA-class probability 0.940044
Prediction RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 273082 115 - 1281640
----CG-UGGCAAACAUGCCACAUUCUUGAAUAAUUCGCCAAUUAAAAUCAAACCAUUCAUUAUUUUAGUCUUGAAUUUAAAUAUAUGGUGUCAAUACAUUAGUGCAACUUCAUAUUUAA
----.(-(((((....)))))).....((((((...(((((.(((((.((((..(.............)..)))).))))).....)))))....(((....)))........)))))). ( -17.62)
>DroPse_CAF1 3578 118 - 1
GCGUCAUUUGU--AAAAUCAACGUGCUUGGAUUUUUCCUUCAACAAAAUUAGACCUAUAAUUUUGUUGAUUUUGAAUUUUAAUAUAUGUGUUCAACAUAUAAGCGCAACUUCAUUUUUGA
((((......(--((((((((.......(((....))).((((((((((((......))))))))))))..))).)))))).(((((((.....))))))).)))).............. ( -27.70)
>DroEre_CAF1 2932 115 - 1
----CG-UGGCAAACAUGCCACAUUUUCGGAUAAUUCGCCAAUUAAGAUCAAACCAAUCAUUAUUUUAGUCUUGAAUUUAAAUAUUUGGUGUCAGAAUAUAAGUGCAUCUUCAUACUUAA
----.(-(((((....))))))...(((.((.....(((((((((((.((((((.((........)).)).)))).)))))....)))))))).)))..((((((........)))))). ( -21.10)
>DroYak_CAF1 18376 115 - 1
----CG-UGGCAAAAAUGCCACAUUUUCGGAUAAUUCGCCAAUUAAGAUCAAACCAUUCAUUAUUUUAGUCUUAAAUUUAAGUAUAUGGUGUCAGAAUAUUAGUGCAGCUCCAUAUUUAA
----.(-(((((....))))))......(((.....(((.(((.........(((((....(((((.(((.....))).))))).)))))........))).)))....)))........ ( -19.93)
>DroPer_CAF1 5205 118 - 1
GCGUCAUUUGU--AAAAUCAACGUGCUUGGAUUUUUCCUUCAACAAAAUUAAACCUAUAAUUUUGUUGAUUUUGAAUUUUAAUAUAUGUGUUCAACAUAUAAGCGCAACUUCAUUUUUGA
((((......(--((((((((.......(((....))).((((((((((((......))))))))))))..))).)))))).(((((((.....))))))).)))).............. ( -26.90)
>consensus
____CG_UGGCAAAAAUGCCACAUUCUUGGAUAAUUCGCCAAUUAAAAUCAAACCAAUCAUUAUUUUAGUCUUGAAUUUAAAUAUAUGGUGUCAAAAUAUAAGUGCAACUUCAUAUUUAA
.......((((......))))......................((((((...................)))))).............................................. ( -3.35 =  -2.51 +  -0.84)

alignment

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secondary structure

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Window 1

Location 273,122 – 273,233
Length 111
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 69.08
Mean single sequence MFE -24.06
Consensus MFE -4.59
Energy contribution -5.79
Covariance contribution 1.20
Combinations/Pair 1.30
Mean z-score -1.79
Structure conservation index 0.19
SVM decision value -0.03
SVM RNA-class probability 0.518877
Prediction RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 273122 111 + 1281640
UAAAUUCAAGACUAAAAUAAUGAAUGGUUUGAUUUUAAUUGGCGAAUUAUUCAAGAAUGUGGCAUGUUUGCCA-CG----CGACAUGUUGCUUUAAUUCAUUUGUCUUUCACAGA----U
.......(((((........(((((((((((...........))))))))))).((((((((((....)))))-)(----(((....))))....))))....))))).......----. ( -28.40)
>DroPse_CAF1 3618 113 + 1
AAAAUUCAAAAUCAACAAAAUUAUAGGUCUAAUUUUGUUGAAGGAAAAAUCCAAGCACGUUGAUUUU--ACAAAUGACGCCGCCAUAUCGG-UCAAUACAAGCGUCUUGAAAUUG----C
.(((.((((..((((((((((((......)))))))))))).(((....))).......)))).)))--.(((..(((((.(((.....))-)........))))))))......----. ( -23.20)
>DroEre_CAF1 2972 115 + 1
UAAAUUCAAGACUAAAAUAAUGAUUGGUUUGAUCUUAAUUGGCGAAUUAUCCGAAAAUGUGGCAUGUUUGCCA-CG----AGACAUGUUGCUUUAAUUCAUUUGUCUUUCACAGAUACAU
........(((((((........))))))).((((.....(((((((.....(((...(..((((((((....-..----))))))))..).....))))))))))......)))).... ( -21.70)
>DroYak_CAF1 18416 111 + 1
UAAAUUUAAGACUAAAAUAAUGAAUGGUUUGAUCUUAAUUGGCGAAUUAUCCGAAAAUGUGGCAUUUUUGCCA-CG----AGACAUGUUGCUUUAAUUCAUUUGUCUUUCACAGA----U
.......(((((......((((((((((.((.((((..((((........))))....((((((....)))))-))----)))))....)))...))))))).))))).......----. ( -23.00)
>DroPer_CAF1 5245 113 + 1
AAAAUUCAAAAUCAACAAAAUUAUAGGUUUAAUUUUGUUGAAGGAAAAAUCCAAGCACGUUGAUUUU--ACAAAUGACGCCGCCAUAUCGG-UCAAUACAAGCGUCUUGAAAUUG----C
.(((.((((..((((((((((((......)))))))))))).(((....))).......)))).)))--.(((..(((((.(((.....))-)........))))))))......----. ( -24.00)
>consensus
UAAAUUCAAGACUAAAAUAAUGAUUGGUUUGAUUUUAAUUGGCGAAUUAUCCAAGAAUGUGGCAUUUUUGCCA_CG____CGACAUGUUGCUUUAAUUCAUUUGUCUUUCACAGA____U
........(((((((........)))))))....(((...(((((..............(((((....)))))..............))))).)))........................ ( -4.59 =  -5.79 +   1.20)

alignment

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secondary structure

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Window 2

Location 273,122 – 273,233
Length 111
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 69.08
Mean single sequence MFE -23.14
Consensus MFE -5.11
Energy contribution -3.35
Covariance contribution -1.76
Combinations/Pair 1.53
Mean z-score -1.87
Structure conservation index 0.22
SVM decision value 0.23
SVM RNA-class probability 0.642389
Prediction RNA

Download alignment: ClustalW | MAF

>4_DroMel_CAF1 273122 111 - 1281640
A----UCUGUGAAAGACAAAUGAAUUAAAGCAACAUGUCG----CG-UGGCAAACAUGCCACAUUCUUGAAUAAUUCGCCAAUUAAAAUCAAACCAUUCAUUAUUUUAGUCUUGAAUUUA
.----.......(((((....((((((...(((.((((.(----((-((.....))))).))))..)))..))))))......((((((.............)))))))))))....... ( -19.62)
>DroPse_CAF1 3618 113 - 1
G----CAAUUUCAAGACGCUUGUAUUGA-CCGAUAUGGCGGCGUCAUUUGU--AAAAUCAACGUGCUUGGAUUUUUCCUUCAACAAAAUUAGACCUAUAAUUUUGUUGAUUUUGAAUUUU
.----.........((((((((((((..-..))))))..)))))).....(--(((((((((((....(((....)))....))(((((((......)))))))))))))))))...... ( -27.40)
>DroEre_CAF1 2972 115 - 1
AUGUAUCUGUGAAAGACAAAUGAAUUAAAGCAACAUGUCU----CG-UGGCAAACAUGCCACAUUUUCGGAUAAUUCGCCAAUUAAGAUCAAACCAAUCAUUAUUUUAGUCUUGAAUUUA
...((((((.((((((((..((........))...)))))----.(-(((((....)))))).))).)))))).........(((((((.(((...........))).)))))))..... ( -21.90)
>DroYak_CAF1 18416 111 - 1
A----UCUGUGAAAGACAAAUGAAUUAAAGCAACAUGUCU----CG-UGGCAAAAAUGCCACAUUUUCGGAUAAUUCGCCAAUUAAGAUCAAACCAUUCAUUAUUUUAGUCUUAAAUUUA
(----((((.((((((((..((........))...)))))----.(-(((((....)))))).))).)))))..........(((((((.(((...........))).)))))))..... ( -20.20)
>DroPer_CAF1 5245 113 - 1
G----CAAUUUCAAGACGCUUGUAUUGA-CCGAUAUGGCGGCGUCAUUUGU--AAAAUCAACGUGCUUGGAUUUUUCCUUCAACAAAAUUAAACCUAUAAUUUUGUUGAUUUUGAAUUUU
.----.........((((((((((((..-..))))))..)))))).....(--(((((((((((....(((....)))....))(((((((......)))))))))))))))))...... ( -26.60)
>consensus
A____UCUGUGAAAGACAAAUGAAUUAAAGCAACAUGUCG____CG_UGGCAAAAAUGCCACAUUCUUGGAUAAUUCGCCAAUUAAAAUCAAACCAAUCAUUAUUUUAGUCUUGAAUUUA
.................(((((.......((.....)).........((((......))))))))).................((((((...................))))))...... ( -5.11 =  -3.35 +  -1.76)

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 09:31:58 2006