Locus 212

Sequence ID 3R_DroMel_CAF1
Location 879,265 – 879,418
Length 153
Max. P 0.926944
window377 window378

overview

Window 7

Location 879,265 – 879,379
Length 114
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 80.69
Mean single sequence MFE -29.62
Consensus MFE -20.59
Energy contribution -20.03
Covariance contribution -0.56
Combinations/Pair 1.15
Mean z-score -2.12
Structure conservation index 0.70
SVM decision value 1.18
SVM RNA-class probability 0.926944
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 879265 114 + 27905053
UCAUAAUAAAAAAAGUGCAAUAAAAAACACGCAAUGACCAAG-----UGACUGCAGUCGGUGCAUCUCCG-GCUGCAUAAUUAAUUCACCUUACUGCAUCCCUCAGCCAUCUCCGGCUGC
..............(((((.(((....(((...........)-----))..(((((((((.......)))-)))))).............))).)))))....(((((......))))). ( -29.40)
>DroSec_CAF1 47270 114 + 1
NNNNNNNNNNNNNNNNNN-NNNACAGACAUGCAAUGACCAAG-----UGACUGCAGUCGGUGCAUCUCCGGGCUGCAUAAUUAAUUCACCUUACUGCAGACCUCAGCCAUCUCCGGCUGC
..................-......((.(((((.((((...(-----(....)).)))).))))).)).(((((((((((..........))).))))).)))(((((......))))). ( -25.00)
>DroSim_CAF1 46472 113 + 1
UCAUAAUAAAAAAAGGGC-AUUACAGACACGCAAUGACCAAG-----UGACUGCAGUCGGUGCAUCUCCG-GCUGCAUAAUUAAUUCACCUUACUGCAGCCCUCAGCCAUCUCCGGCUGC
.............(((((-....(((.(((...........)-----))..(((((((((.......)))-))))))................)))..)))))(((((......))))). ( -34.40)
>DroEre_CAF1 46384 118 + 1
UCAUAAUAAAAACAGGGC-AUUAAACACACGCAAUGGCCAUUUGGACCGACUGCAGUCGGCGCAUCUCCG-GCUGCAUAAUUAAUUCACCUUACUGUAUUCCUCGGCCAGCUCCGGCUGC
....((((.....((((.-(((((..........(((((....)).)))..(((((((((.......)))-))))))...))))).).))).....))))...(((((......))))). ( -29.70)
>consensus
UCAUAAUAAAAAAAGGGC_AUUAAAGACACGCAAUGACCAAG_____UGACUGCAGUCGGUGCAUCUCCG_GCUGCAUAAUUAAUUCACCUUACUGCAGCCCUCAGCCAUCUCCGGCUGC
..............................(((.(((..............(((((((((.......))).)))))).............))).)))......(((((......))))). (-20.59 = -20.03 +  -0.56)

alignment

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secondary structure

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dotplot

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Window 8

Location 879,305 – 879,418
Length 113
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 90.84
Mean single sequence MFE -38.56
Consensus MFE -29.95
Energy contribution -29.58
Covariance contribution -0.38
Combinations/Pair 1.06
Mean z-score -1.66
Structure conservation index 0.78
SVM decision value 0.19
SVM RNA-class probability 0.625072
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 879305 113 + 27905053
AG-----UGACUGCAGUCGGUGCAUCUCCG-GCUGCAUAAUUAAUUCACCUUACUGCAUCCCUCAGCCAUCUCCGGCUGCAGUG-CCAUCUACCGGGCCAGAGGUCAAUUAAGUGCUUUG
((-----(.(((((((((((.......)))-))))))...((((((.(((((((((((.......(((......)))))))))(-((........)))..))))).)))))))))))... ( -37.71)
>DroSec_CAF1 47309 115 + 1
AG-----UGACUGCAGUCGGUGCAUCUCCGGGCUGCAUAAUUAAUUCACCUUACUGCAGACCUCAGCCAUCUCCGGCUGCAGCGGCCACCUACCGGGCCAGAGGUCAAUUAAGUGCUUUG
((-----(.(((((((((((.......)).)))))))...((((((.(((((.((((((.((..((....))..)))))))).((((........)))).))))).)))))))))))... ( -38.90)
>DroSim_CAF1 46511 113 + 1
AG-----UGACUGCAGUCGGUGCAUCUCCG-GCUGCAUAAUUAAUUCACCUUACUGCAGCCCUCAGCCAUCUCCGGCUGCAGCG-CCACCUACCGGGCCAGAGGUCAAUUAAGUGCUUUG
((-----(.(((((((((((.......)))-))))))...((((((.(((((.((((((((.............)))))))).(-((........)))..))))).)))))))))))... ( -41.52)
>DroEre_CAF1 46423 118 + 1
UUUGGACCGACUGCAGUCGGCGCAUCUCCG-GCUGCAUAAUUAAUUCACCUUACUGUAUUCCUCGGCCAGCUCCGGCUGCAGCG-CCAUCUACCGGGCCAGAGGUCAAUUAAGUGUGUUG
.......((((.((((((((.......)))-)))))(((.((((((.(((((.........(((((((......))))).)).(-((........)))..))))).)))))).))))))) ( -36.10)
>consensus
AG_____UGACUGCAGUCGGUGCAUCUCCG_GCUGCAUAAUUAAUUCACCUUACUGCAGCCCUCAGCCAUCUCCGGCUGCAGCG_CCACCUACCGGGCCAGAGGUCAAUUAAGUGCUUUG
...........(((((((((.......))).))))))...((((((.(((((...((....(((((((......))))).))...((.......))))..))))).))))))........ (-29.95 = -29.58 +  -0.38)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:37:41 2006