Locus 8369

Sequence ID 3L_DroMel_CAF1
Location 21,976,074 – 21,976,166
Length 92
Max. P 0.889626
window13688 window13689

overview

Window 8

Location 21,976,074 – 21,976,166
Length 92
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 78.75
Mean single sequence MFE -27.10
Consensus MFE -16.96
Energy contribution -18.48
Covariance contribution 1.52
Combinations/Pair 1.18
Mean z-score -1.73
Structure conservation index 0.63
SVM decision value 0.27
SVM RNA-class probability 0.663796
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21976074 92 + 23771897
--------------UGACAGCGUCAUCAAAACUGAUGUCACAAGAUGGA------------GAUGGAGAUGAAGAUGACGAGCAGCAGCAGAAGGGGAAUGCCCCUAAAACUGCUGGC
--------------......(((((((........((((.(......).------------))))........)))))))..((((((....(((((....)))))....)))))).. ( -28.39)
>DroSec_CAF1 102704 98 + 1
--------------UGACAGCGUCAUCAAAACUGAUGUCACAAGAUGGAGACGGA------GAUGGAGAUGAAGAUGACGAGCAGCGGCAGAAGGGGAAUGCCCCUAAAACUGCUGGC
--------------......(((((((.....(.((.((......((....))..------....)).)).).)))))))..((((((....(((((....)))))....)))))).. ( -30.80)
>DroSim_CAF1 102952 98 + 1
--------------UGACAGCGUCAUCAAAACUGAUGUCACAAGAUGGAGACGGA------GAUGGAGAUGAAGAUGACGAGCAGCGGCAGAAGGGGAAUGCCCCUAAAACUGCUGGC
--------------......(((((((.....(.((.((......((....))..------....)).)).).)))))))..((((((....(((((....)))))....)))))).. ( -30.80)
>DroYak_CAF1 119484 104 + 1
--------------UGACAGCGUCAUCAAAACUGAUGUCACAAGAUGAAGAUGAAGAUGAAGAUGAAGAUGAAGAUGACGAGCAGCGGCAGAAGGAGAAUUCCCCUAAAACUGCUGGC
--------------......(((((((....((...(((....)))..))((....))...............)))))))..((((((....(((.(....).)))....)))))).. ( -20.00)
>DroAna_CAF1 106726 105 + 1
CACCGAACUUCCCUCGACGGCUCCACCAAAACUUAUGUCACACGACG---AUGUU------GAUGGAGAUG---AUGACGAGCAGGAGAAGAAAAGAAUUUCUCCUAAAA-UGCUGGC
..(((.......((((.((.(((((.(((......((((....))))---...))------).)))))...---.)).)))).((((((((.......))))))))....-...))). ( -25.50)
>consensus
______________UGACAGCGUCAUCAAAACUGAUGUCACAAGAUGGAGACGGA______GAUGGAGAUGAAGAUGACGAGCAGCGGCAGAAGGGGAAUGCCCCUAAAACUGCUGGC
....................(((((((.........(((....)))(....).....................)))))))..((((((....(((((....)))))....)))))).. (-16.96 = -18.48 +   1.52)

alignment

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secondary structure

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dotplot

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Window 9

Location 21,976,074 – 21,976,166
Length 92
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 78.75
Mean single sequence MFE -25.58
Consensus MFE -17.18
Energy contribution -17.42
Covariance contribution 0.24
Combinations/Pair 1.25
Mean z-score -1.93
Structure conservation index 0.67
SVM decision value 0.96
SVM RNA-class probability 0.889626
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21976074 92 - 23771897
GCCAGCAGUUUUAGGGGCAUUCCCCUUCUGCUGCUGCUCGUCAUCUUCAUCUCCAUC------------UCCAUCUUGUGACAUCAGUUUUGAUGACGCUGUCA--------------
(((((((((...(((((....)))))...)))))))...((((((..........((------------.(......).))..........)))))))).....-------------- ( -28.05)
>DroSec_CAF1 102704 98 - 1
GCCAGCAGUUUUAGGGGCAUUCCCCUUCUGCCGCUGCUCGUCAUCUUCAUCUCCAUC------UCCGUCUCCAUCUUGUGACAUCAGUUUUGAUGACGCUGUCA--------------
((.(((.((...(((((....)))))...)).)))))..(.((.(.(((((.....(------(..(((.(......).)))...))....))))).).)).).-------------- ( -23.90)
>DroSim_CAF1 102952 98 - 1
GCCAGCAGUUUUAGGGGCAUUCCCCUUCUGCCGCUGCUCGUCAUCUUCAUCUCCAUC------UCCGUCUCCAUCUUGUGACAUCAGUUUUGAUGACGCUGUCA--------------
((.(((.((...(((((....)))))...)).)))))..(.((.(.(((((.....(------(..(((.(......).)))...))....))))).).)).).-------------- ( -23.90)
>DroYak_CAF1 119484 104 - 1
GCCAGCAGUUUUAGGGGAAUUCUCCUUCUGCCGCUGCUCGUCAUCUUCAUCUUCAUCUUCAUCUUCAUCUUCAUCUUGUGACAUCAGUUUUGAUGACGCUGUCA--------------
((((((.((...(((((....)))))...)).))))...((((((.....((......((((...............))))....))....)))))))).....-------------- ( -21.86)
>DroAna_CAF1 106726 105 - 1
GCCAGCA-UUUUAGGAGAAAUUCUUUUCUUCUCCUGCUCGUCAU---CAUCUCCAUC------AACAU---CGUCGUGUGACAUAAGUUUUGGUGGAGCCGUCGAGGGAAGUUCGGUG
((((((.-...((((((((.........))))))))((((.(..---...(((((((------((.((---.(((....)))....)).)))))))))..).))))....))).))). ( -30.20)
>consensus
GCCAGCAGUUUUAGGGGCAUUCCCCUUCUGCCGCUGCUCGUCAUCUUCAUCUCCAUC______UCCAUCUCCAUCUUGUGACAUCAGUUUUGAUGACGCUGUCA______________
((.((((((...(((((....)))))......)))))).))....................................(((.((((......)))).)))................... (-17.18 = -17.42 +   0.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:13:39 2006