Locus 6559

Sequence ID 2R_DroMel_CAF1
Location 20,515,876 – 20,516,004
Length 128
Max. P 0.739006
window10441 window10442

overview

Window 1

Location 20,515,876 – 20,515,971
Length 95
Sequences 4
Columns 95
Reading direction forward
Mean pairwise identity 86.82
Mean single sequence MFE -21.48
Consensus MFE -15.09
Energy contribution -15.15
Covariance contribution 0.06
Combinations/Pair 1.22
Mean z-score -1.89
Structure conservation index 0.70
SVM decision value 0.44
SVM RNA-class probability 0.739006
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20515876 95 + 20766785
UCAGAUUGGUCUCGGGAGUGAGGCGUUCAGGAAUGCCUGAACAAAGACAGCGGAUAAGAAGAGCAUUAGCGCUGAAGAAGAGGGAAAAAAGAAAA
........((((((....))))))(((((((....))))))).....(((((..(((........))).)))))..................... ( -24.70)
>DroSec_CAF1 17485 94 + 1
UCAGAUUGGUCGCGGUAGUGAGGCAUUCAGGAAUGCCUGAACAAAGACAGCGGAUAAGAAGAGCAUUAGCGUCGAAGAAGAGAGAA-AAAGAGAU
((...(((..(((.((.((.(((((((....)))))))..))....)).)))..)))((...((....)).))))...........-........ ( -18.20)
>DroSim_CAF1 17453 94 + 1
UCAGAUUGGUCGCGGGAGUGAGGCAUUCAGGAAUGCCUGAACAAAGACAGCGGAUAAGAAGAGCAUUAGCGUCGAAGAAGAGAGAA-AAAGAGAA
((...((.(.(((....((.(((((((....)))))))..)).......((...........))....))).).))...)).....-........ ( -18.00)
>DroEre_CAF1 17563 95 + 1
CCAGAUUGGUCGGCGGAGUGGGGCAUGGAGGAAUGCCAGAACAGCGUCAGCGGAUAAGAAGAGCAUUAGCGCUGAAGAAGAGGGACAUAGGGGAG
((......(((.((...((..(((((......)))))...)).)).((((((..(((........))).))))))........))).....)).. ( -25.00)
>consensus
UCAGAUUGGUCGCGGGAGUGAGGCAUUCAGGAAUGCCUGAACAAAGACAGCGGAUAAGAAGAGCAUUAGCGCCGAAGAAGAGAGAA_AAAGAGAA
((...(((.((((....))))((((((....))))))....)))...(((((..(((........))).)))))................))... (-15.09 = -15.15 +   0.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 20,515,909 – 20,516,004
Length 95
Sequences 4
Columns 102
Reading direction reverse
Mean pairwise identity 84.82
Mean single sequence MFE -18.90
Consensus MFE -13.45
Energy contribution -13.32
Covariance contribution -0.12
Combinations/Pair 1.11
Mean z-score -1.45
Structure conservation index 0.71
SVM decision value -0.02
SVM RNA-class probability 0.521457
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20515909 95 - 20766785
------UUCGUGAACACGGUGGA-AAUGUGUUUACACCUCUUUUCUUUUUUCCCUCUUCUUCAGCGCUAAUGCUCUUCUUAUCCGCUGUCUUUGUUCAGGCA
------..(.(((((((((((((-...(((....))).........................((.((....)).)).....))))))))....))))).).. ( -19.50)
>DroSec_CAF1 17518 95 - 1
------UUCGUAAACACGGCGGAAAAUGUGUUUACACUUCAUCUCUUU-UUCUCUCUUCUUCGACGCUAAUGCUCUUCUUAUCCGCUGUCUUUGUUCAGGCA
------....((((.((((((((....(((....)))...........-.............((.((....))))......)))))))).))))........ ( -18.40)
>DroSim_CAF1 17486 95 - 1
------UUCGUAAACACGGUGGAAAAUGUGUUUACACUUCUUCUCUUU-UUCUCUCUUCUUCGACGCUAAUGCUCUUCUUAUCCGCUGUCUUUGUUCAGGCA
------....((((.((((((((....(((....)))...........-.............((.((....))))......)))))))).))))........ ( -16.50)
>DroEre_CAF1 17596 101 - 1
UGAGUAUUCGUAAACAUGGUGGCAA-AGUGUUUACACUUCCUCCCCUAUGUCCCUCUUCUUCAGCGCUAAUGCUCUUCUUAUCCGCUGACGCUGUUCUGGCA
.............((((((.((..(-((((....)))))...)).)))))).........((((((.(((........)))..)))))).(((.....))). ( -21.20)
>consensus
______UUCGUAAACACGGUGGAAAAUGUGUUUACACUUCUUCUCUUU_UUCCCUCUUCUUCAACGCUAAUGCUCUUCUUAUCCGCUGUCUUUGUUCAGGCA
.........((.(((((((((((....(((....)))............................((....))........)))))))....))))...)). (-13.45 = -13.32 +  -0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:13:48 2006