Locus 2220

Sequence ID 3L_DroMel_CAF1
Location 6,131,798 – 6,131,894
Length 96
Max. P 0.904448
window3441 window3442

overview

Window 1

Location 6,131,798 – 6,131,894
Length 96
Sequences 4
Columns 96
Reading direction forward
Mean pairwise identity 86.81
Mean single sequence MFE -20.60
Consensus MFE -15.48
Energy contribution -16.85
Covariance contribution 1.37
Combinations/Pair 1.10
Mean z-score -1.43
Structure conservation index 0.75
SVM decision value 0.02
SVM RNA-class probability 0.542892
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6131798 96 + 23771897
UUUACAGAAAGUCAUUAGCUCGAUCAAGCUAAACGACAUAGUCCAAGCAACCCAAGCCGGUUGUACAGAAAUGGUAACCCAUUAUUAUGCUGAUGA
....(((...(((.((((((......))))))..)))(((((....((((((......)))))).....(((((....)))))))))).))).... ( -21.00)
>DroSec_CAF1 36512 93 + 1
UUUACAGAAAGGCAUCAGCUCGAUCAAGCUAACCGAAAUAGUCCAAGCAACCCAAGCCAA---GACAGAAAUGGUAACCCAUUAUUAUGCUGAUGA
............(((((((.....................(((...((.......))...---)))...(((((....))))).....))))))). ( -17.90)
>DroSim_CAF1 38220 96 + 1
UUUACAGAAAGUCACCAGCUUGAUUGAGCUGACCGAAAUAGUCCAAGCAACCCAAGCCGGUUGUACAGAAAUGGUAACCCAUUAUUAUGCUGAUGA
....(((....((..((((((....))))))...............((((((......))))))...))(((((....)))))......))).... ( -20.50)
>DroYak_CAF1 45347 91 + 1
-----AGAAAGUCAUCAGCUAGAUCAAGCUAAUCAAAAUAGUCGAAGCAACCCAAGCCGGUUGUAGAGAAGUGGUAACCCAUUAUUAUGCUGAUGA
-----......((((((((......................((...((((((......))))))...))(((((....))))).....)))))))) ( -23.00)
>consensus
UUUACAGAAAGUCAUCAGCUCGAUCAAGCUAACCGAAAUAGUCCAAGCAACCCAAGCCGGUUGUACAGAAAUGGUAACCCAUUAUUAUGCUGAUGA
............(((((((......................((...((((((......))))))...))(((((....))))).....))))))). (-15.48 = -16.85 +   1.37)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 6,131,798 – 6,131,894
Length 96
Sequences 4
Columns 96
Reading direction reverse
Mean pairwise identity 86.81
Mean single sequence MFE -25.68
Consensus MFE -20.42
Energy contribution -21.30
Covariance contribution 0.88
Combinations/Pair 1.16
Mean z-score -2.08
Structure conservation index 0.80
SVM decision value 1.04
SVM RNA-class probability 0.904448
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6131798 96 - 23771897
UCAUCAGCAUAAUAAUGGGUUACCAUUUCUGUACAACCGGCUUGGGUUGCUUGGACUAUGUCGUUUAGCUUGAUCGAGCUAAUGACUUUCUGUAAA
....(((......(((((....)))))((((..(((((......)))))..))))....((((((.(((((....)))))))))))...))).... ( -24.20)
>DroSec_CAF1 36512 93 - 1
UCAUCAGCAUAAUAAUGGGUUACCAUUUCUGUC---UUGGCUUGGGUUGCUUGGACUAUUUCGGUUAGCUUGAUCGAGCUGAUGCCUUUCUGUAAA
.(((((((.....(((((....)))))...(((---(.(((.......))).))))....((((((.....)))))))))))))............ ( -26.80)
>DroSim_CAF1 38220 96 - 1
UCAUCAGCAUAAUAAUGGGUUACCAUUUCUGUACAACCGGCUUGGGUUGCUUGGACUAUUUCGGUCAGCUCAAUCAAGCUGGUGACUUUCUGUAAA
(((((((((((..(((((....)))))..)))......((.((((((((.(((((....))))).))))))))))..))))))))........... ( -28.70)
>DroYak_CAF1 45347 91 - 1
UCAUCAGCAUAAUAAUGGGUUACCACUUCUCUACAACCGGCUUGGGUUGCUUCGACUAUUUUGAUUAGCUUGAUCUAGCUGAUGACUUUCU-----
((((((((.......(((....)))........(((((......)))))..(((((((.......))).))))....))))))))......----- ( -23.00)
>consensus
UCAUCAGCAUAAUAAUGGGUUACCAUUUCUGUACAACCGGCUUGGGUUGCUUGGACUAUUUCGGUUAGCUUGAUCGAGCUGAUGACUUUCUGUAAA
(((((((((((..(((((....)))))..)))......((.((((((((.(((((....))))).))))))))))..))))))))........... (-20.42 = -21.30 +   0.88)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:27:11 2006