Locus 5194

Sequence ID 2R_DroMel_CAF1
Location 16,877,869 – 16,877,961
Length 92
Max. P 0.999860
window8303 window8304

overview

Window 3

Location 16,877,869 – 16,877,961
Length 92
Sequences 4
Columns 98
Reading direction forward
Mean pairwise identity 74.22
Mean single sequence MFE -27.30
Consensus MFE -20.09
Energy contribution -20.90
Covariance contribution 0.81
Combinations/Pair 1.00
Mean z-score -2.84
Structure conservation index 0.74
SVM decision value 4.28
SVM RNA-class probability 0.999860
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16877869 92 + 20766785
ACUGCGGAGUGCCAGGACCACAGUGAAGACCGACCUCAAACUGGUCCUGUACCCCG------UCCGCCGUCGAUUUCCUCACUCCGUAGCAUCAAUCC
.((((((((((.((((((((...(((.(......))))...)))))))).....((------.(....).)).......))))))))))......... ( -31.70)
>DroSec_CAF1 28223 77 + 1
ACUGCGGAGUGCCAGGACCACAGUGAAGACCGACCACAAACUGGUCCUGUCCCCCACU---------------------CACUCCGGACCAUCAAUCC
....(((((((.((((((((..(((.........)))....)))))))).........---------------------)))))))............ ( -23.70)
>DroSim_CAF1 28531 94 + 1
ACUGCGGAGUGCCAGGACCACAGUGAAGACCGACCUCAAACUGGUCCUGUCUCCCACU----CCCUCCGCCGAUUUGCUCACUCCGGACCAUCAAUCC
....(((((((...(((....((((.((((.((((.......))))..))))..))))----...)))((......)).)))))))............ ( -28.10)
>DroEre_CAF1 28591 80 + 1
ACUGCGGAGUGCCAGGACCACAGUGAAGACCAACCUCAAACUGGUCCUGUCC------UCCGUCCUCCGUCGAUUUCCUCACUCA------------C
...((((((.(.((((((((...(((.(......))))...)))))))).))------)))))......................------------. ( -25.70)
>consensus
ACUGCGGAGUGCCAGGACCACAGUGAAGACCGACCUCAAACUGGUCCUGUCCCCCA______UCCUCCGUCGAUUUCCUCACUCCGGACCAUCAAUCC
....(((((((.((((((((...(((.(.....).)))...))))))))...............(......).......)))))))............ (-20.09 = -20.90 +   0.81)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 16,877,869 – 16,877,961
Length 92
Sequences 4
Columns 98
Reading direction reverse
Mean pairwise identity 74.22
Mean single sequence MFE -32.98
Consensus MFE -24.98
Energy contribution -25.85
Covariance contribution 0.87
Combinations/Pair 1.00
Mean z-score -1.64
Structure conservation index 0.76
SVM decision value 1.18
SVM RNA-class probability 0.927148
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16877869 92 - 20766785
GGAUUGAUGCUACGGAGUGAGGAAAUCGACGGCGGA------CGGGGUACAGGACCAGUUUGAGGUCGGUCUUCACUGUGGUCCUGGCACUCCGCAGU
........(((.(((((((.....(((..((.....------)).))).((((((((...(((((.....)))))...)))))))).))))))).))) ( -35.20)
>DroSec_CAF1 28223 77 - 1
GGAUUGAUGGUCCGGAGUG---------------------AGUGGGGGACAGGACCAGUUUGUGGUCGGUCUUCACUGUGGUCCUGGCACUCCGCAGU
((((.....))))......---------------------.((((((..((((((((....((((.......))))..))))))))...))))))... ( -31.90)
>DroSim_CAF1 28531 94 - 1
GGAUUGAUGGUCCGGAGUGAGCAAAUCGGCGGAGGG----AGUGGGAGACAGGACCAGUUUGAGGUCGGUCUUCACUGUGGUCCUGGCACUCCGCAGU
((((.....))))((((((......((.((......----.)).))...((((((((...(((((.....)))))...)))))))).))))))..... ( -35.50)
>DroEre_CAF1 28591 80 - 1
G------------UGAGUGAGGAAAUCGACGGAGGACGGA------GGACAGGACCAGUUUGAGGUUGGUCUUCACUGUGGUCCUGGCACUCCGCAGU
(------------((((((......((..((.....))..------)).((((((((...(((((.....)))))...)))))))).)))).)))... ( -29.30)
>consensus
GGAUUGAUGGUCCGGAGUGAGGAAAUCGACGGAGGA______UGGGGGACAGGACCAGUUUGAGGUCGGUCUUCACUGUGGUCCUGGCACUCCGCAGU
............(((((((......((......))..............((((((((...(((((.....)))))...)))))))).))))))).... (-24.98 = -25.85 +   0.87)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:38:53 2006