Locus 5086

Sequence ID X_DroMel_CAF1
Location 13,296,404 – 13,296,560
Length 156
Max. P 0.909475
window8271 window8272 window8273

overview

Window 1

Location 13,296,404 – 13,296,520
Length 116
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 78.18
Mean single sequence MFE -22.74
Consensus MFE -8.93
Energy contribution -9.54
Covariance contribution 0.61
Combinations/Pair 1.05
Mean z-score -1.99
Structure conservation index 0.39
SVM decision value 0.23
SVM RNA-class probability 0.646327
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13296404 116 - 22224390
CGUUAUCGUUACACGGUAUUCAUUACACUAACGAUGUUUGCAUUGUGCAAUGCUAGAACAACUAUAGCAGCGAAUAU----AUCACAUUGAUAUAAUAGUAGUAAUUAAUGAAACUUUAG
...(((((.....)))))(((((((.((((((((((....))))))((..(((((.........)))))))...(((----(((.....))))))....))))...)))))))....... ( -24.10)
>DroSec_CAF1 11655 112 - 1
CGUUAUCGUUACACGGUAUUCAUUACACUAACGAUGUUUGCAUUGUGCAAUGUUAGAACAAUUAUAGCAGCGUAUAU----AUCACAUUGAUAUAAUA-UAGUAAUGAAUGAAAC---AG
.(((((((.....))))(((((((((....((((((....))))))((..(((((.........)))))))...(((----(((.....))))))...-..)))))))))..)))---.. ( -24.50)
>DroSim_CAF1 5562 112 - 1
CGUUAUCGUUACACGGUAUUCAUUACACUAACGAUGUUUGCAUUGUGCAAUGUUAAAACAACUAUAGCAGCGUAUAU----AUCACAUUGAUAUAAUA-UAGUAAUGAAUGAAAC---AG
.(((((((.....))))(((((((((....((((((....))))))((..(((((.........)))))))...(((----(((.....))))))...-..)))))))))..)))---.. ( -23.70)
>DroEre_CAF1 6568 91 - 1
CGUUAUCGUAACACGGUAUUCAUUACGCUAACGAUGUUUGCAUUGU-------UACAAUAAUUAUAGAAGUG-AUA------UAAUAUUGU---A---------AUUAAUGAGAC---AG
(((((.(((((...........))))).))))).(((((.((((((-------(((((((.(((((......-.))------)))))))))---)---------).)))))))))---). ( -22.10)
>DroYak_CAF1 5815 103 - 1
CGUUAUCGUUACACGGUAUUCAUUACACUAACGAUGUUUGCAUUGU-------UCGAAUAAUUCUACAAGUGCAUAUAUCUAUCACAUUGAUUUAACA-C----AUUUAUGUGA-----A
...(((((.....)))))..............(((((.((((((..-------..((.....))....)))))).)))))..((((((.(((......-.----))).))))))-----. ( -19.30)
>consensus
CGUUAUCGUUACACGGUAUUCAUUACACUAACGAUGUUUGCAUUGUGCAAUG_UAGAACAAUUAUAGCAGCGUAUAU____AUCACAUUGAUAUAAUA_UAGUAAUUAAUGAAAC___AG
...(((((.....)))))((((((......((((((....))))))...................................(((.....)))...............))))))....... ( -8.93 =  -9.54 +   0.61)

alignment

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secondary structure

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dotplot

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Window 2

Location 13,296,443 – 13,296,560
Length 117
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 88.09
Mean single sequence MFE -27.16
Consensus MFE -20.44
Energy contribution -20.84
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -2.15
Structure conservation index 0.75
SVM decision value 0.95
SVM RNA-class probability 0.887700
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13296443 117 + 22224390
---AUAUUCGCUGCUAUAGUUGUUCUAGCAUUGCACAAUGCAAACAUCGUUAGUGUAAUGAAUACCGUGUAACGAUAACGCAUUAUCGUAACCAAUGUGACCAUGUUUGCAAACGAAGCA
---...((((((((((.........)))))..))....(((((((((.((((((((.....)))).(.((.(((((((....))))))).)))....)))).)))))))))...)))... ( -28.20)
>DroSec_CAF1 11690 117 + 1
---AUAUACGCUGCUAUAAUUGUUCUAACAUUGCACAAUGCAAACAUCGUUAGUGUAAUGAAUACCGUGUAACGAUAACGAUUUAUCGUAACCAAUGUGACCAUGUUUGCAAACGAAGCA
---......(((......(((((.(.......).)))))((((((((.((((((((.....)))).(.((.(((((((....))))))).)))....)))).))))))))......))). ( -26.30)
>DroSim_CAF1 5597 117 + 1
---AUAUACGCUGCUAUAGUUGUUUUAACAUUGCACAAUGCAAACAUCGUUAGUGUAAUGAAUACCGUGUAACGAUAACGCUUUAUCGUUACCAAUGUGACCAUGUUUGCAAACGAAGCA
---......(((((.((.((((...)))))).))....(((((((((.((((((((.....)))).(.((((((((((....)))))))))))....)))).))))))))).....))). ( -30.70)
>DroEre_CAF1 6591 108 + 1
----UAU-CACUUCUAUAAUUAUUGUA-------ACAAUGCAAACAUCGUUAGCGUAAUGAAUACCGUGUUACGAUAACGCUUUAUCGUAACCAAUGUGACCAUGUUUGCAAACGAAGCA
----...-..((((((((.....))))-------....(((((((((.((((.(((.(((.....)))((((((((((....))))))))))..))))))).)))))))))...)))).. ( -27.20)
>DroYak_CAF1 5845 113 + 1
GAUAUAUGCACUUGUAGAAUUAUUCGA-------ACAAUGCAAACAUCGUUAGUGUAAUGAAUACCGUGUAACGAUAACGCUUUAUCGUAACCAAUGUGACCAUGUUCGCAAGCGAAGCA
......((((.((((.((.....))..-------))))))))....(((((.(((..(((..(((...((.(((((((....))))))).))....)))..)))...))).))))).... ( -23.40)
>consensus
___AUAUACGCUGCUAUAAUUGUUCUA_CAUUGCACAAUGCAAACAUCGUUAGUGUAAUGAAUACCGUGUAACGAUAACGCUUUAUCGUAACCAAUGUGACCAUGUUUGCAAACGAAGCA
......................................(((((((((.((((((((.....)))).(.((.(((((((....))))))).)))....)))).)))))))))......... (-20.44 = -20.84 +   0.40)

alignment

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secondary structure

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dotplot

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Window 3

Location 13,296,443 – 13,296,560
Length 117
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 88.09
Mean single sequence MFE -28.46
Consensus MFE -22.84
Energy contribution -22.40
Covariance contribution -0.44
Combinations/Pair 1.10
Mean z-score -1.95
Structure conservation index 0.80
SVM decision value 1.07
SVM RNA-class probability 0.909475
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13296443 117 - 22224390
UGCUUCGUUUGCAAACAUGGUCACAUUGGUUACGAUAAUGCGUUAUCGUUACACGGUAUUCAUUACACUAACGAUGUUUGCAUUGUGCAAUGCUAGAACAACUAUAGCAGCGAAUAU---
...(((((.(((((((((.((.......((.(((((((....))))))).))...(((.....)))....)).)))))))))........(((((.........))))))))))...--- ( -29.60)
>DroSec_CAF1 11690 117 - 1
UGCUUCGUUUGCAAACAUGGUCACAUUGGUUACGAUAAAUCGUUAUCGUUACACGGUAUUCAUUACACUAACGAUGUUUGCAUUGUGCAAUGUUAGAACAAUUAUAGCAGCGUAUAU---
.........(((((((((.((.......((.(((((((....))))))).))...(((.....)))....)).))))))))).(((((..(((((.........)))))..))))).--- ( -27.70)
>DroSim_CAF1 5597 117 - 1
UGCUUCGUUUGCAAACAUGGUCACAUUGGUAACGAUAAAGCGUUAUCGUUACACGGUAUUCAUUACACUAACGAUGUUUGCAUUGUGCAAUGUUAAAACAACUAUAGCAGCGUAUAU---
.........(((((((((.((.......((((((((((....))))))))))...(((.....)))....)).))))))))).(((((..(((((.........)))))..))))).--- ( -30.90)
>DroEre_CAF1 6591 108 - 1
UGCUUCGUUUGCAAACAUGGUCACAUUGGUUACGAUAAAGCGUUAUCGUAACACGGUAUUCAUUACGCUAACGAUGUUUGCAUUGU-------UACAAUAAUUAUAGAAGUG-AUA----
.(((((...(((((((((.((.......((((((((((....))))))))))...(((.....)))....)).)))))))))((((-------....)))).....))))).-...---- ( -29.40)
>DroYak_CAF1 5845 113 - 1
UGCUUCGCUUGCGAACAUGGUCACAUUGGUUACGAUAAAGCGUUAUCGUUACACGGUAUUCAUUACACUAACGAUGUUUGCAUUGU-------UCGAAUAAUUCUACAAGUGCAUAUAUC
.....((((((((((((..((.((((((((.(((((((....))))))).))...(((.....))).....))))))..))..)))-------)))..........))))))........ ( -24.70)
>consensus
UGCUUCGUUUGCAAACAUGGUCACAUUGGUUACGAUAAAGCGUUAUCGUUACACGGUAUUCAUUACACUAACGAUGUUUGCAUUGUGCAAUG_UAGAACAAUUAUAGCAGCGUAUAU___
.(((.(...(((((((((.((.......((.(((((((....))))))).))...(((.....)))....)).)))))))))((((...........)))).....).)))......... (-22.84 = -22.40 +  -0.44)

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 11:39:48 2006