Locus 10195

Sequence ID	3R_DroMel_CAF1
Location	27,357,390 – 27,357,526
Length	136
Max. P	0.999816

overview

Window 4

Location	27,357,390 – 27,357,488
Length	98
Sequences	5
Columns	106
Reading direction	forward
Mean pairwise identity	93.48
Mean single sequence MFE	-33.26
Consensus MFE	-29.76
Energy contribution	-29.32
Covariance contribution	-0.44
Combinations/Pair	1.10
Mean z-score	-2.74
Structure conservation index	0.89
SVM decision value	4.15
SVM RNA-class probability	0.999816
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27357390 98 + 27905053
GCCCA--UGACUGCGUGCUGCAGUUGCUCUGGGC------UCUUGGCUUUUUGAGUUUCCAUUGCUUGGCUUAAACCAGAGGACUUGACUUGGCCAAUUUGAUUUA
(((((--(((((((.....)))))))...)))))------..((((((..(..((((..(......(((......))))..))))..)...))))))......... ( -30.10)
>DroSec_CAF1 102840 104 + 1
GCCCA--UGACUGCGUGCUGCAGUUGCUCUGGGCUCUGGCUCUUGGCUUUUUGAGUUUCCAUUUCUUGGCUUAAACCAGAGGACUUGACUUGGUCAAUUUGAUUUA
(((((--(((((((.....)))))))...)))))(((((.....((((....(((.......)))..))))....))))).((((......))))........... ( -30.10)
>DroSim_CAF1 67037 98 + 1
GCCCA--UGACUGCGUGCUGCAGUUGCUCUGGGC------UCUUGGCUUUUUGAGUUUCCAUUGCUUAGCUUAAACCAGAGGACUUGACUUGGCCAAUUUGAUUUA
(((((--(((((((.....)))))))...)))))------..((((((..(..((..(((.(((.((......)).))).)))))..)...))))))......... ( -28.30)
>DroEre_CAF1 67266 100 + 1
GCCCAGGUGACUGCGUGCUGCAGUUGCUCUGGGC------UCUUGGCCUUUUAAGUUUCCAUUUCUUGGCUUAAGCCAGAAGACUUGACUUGGCCAAUUUGAUUUA
(((((((..(((((.....)))))..).))))))------..((((((..(((((((.....((((.(((....))))))))))))))...))))))......... ( -45.30)
>DroYak_CAF1 60190 98 + 1
GCCCA--UGACUGCGUGCUGCAGUUGCUCUGGGC------UCUUGGCCUUUUAAGUUUCCAUUUCUUGGCUUAAACCAGAGGACUUGACUUGGCCAAUUUGAUUUA
(((((--(((((((.....)))))))...)))))------..((((((..(((((((.....((((.((......)))))))))))))...))))))......... ( -32.50)
>consensus
GCCCA__UGACUGCGUGCUGCAGUUGCUCUGGGC______UCUUGGCUUUUUGAGUUUCCAUUUCUUGGCUUAAACCAGAGGACUUGACUUGGCCAAUUUGAUUUA
(((((..(((((((.....)))))))...)))))........((((((..(((((((..(......(((......))))..)))))))...))))))......... (-29.76 = -29.32 +  -0.44)

alignment

secondary structure

dotplot

Window 5

Location	27,357,390 – 27,357,488
Length	98
Sequences	5
Columns	106
Reading direction	reverse
Mean pairwise identity	93.48
Mean single sequence MFE	-29.36
Consensus MFE	-23.91
Energy contribution	-23.63
Covariance contribution	-0.28
Combinations/Pair	1.13
Mean z-score	-2.93
Structure conservation index	0.81
SVM decision value	2.73
SVM RNA-class probability	0.996683
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27357390 98 - 27905053
UAAAUCAAAUUGGCCAAGUCAAGUCCUCUGGUUUAAGCCAAGCAAUGGAAACUCAAAAAGCCAAGA------GCCCAGAGCAACUGCAGCACGCAGUCA--UGGGC
.........(((((.........(((.(((((....))).))....)))..........)))))..------(((((.....(((((.....)))))..--))))) ( -25.31)
>DroSec_CAF1 102840 104 - 1
UAAAUCAAAUUGACCAAGUCAAGUCCUCUGGUUUAAGCCAAGAAAUGGAAACUCAAAAAGCCAAGAGCCAGAGCCCAGAGCAACUGCAGCACGCAGUCA--UGGGC
.........(((((...)))))....((((((((..((........(....).......))...))))))))(((((.....(((((.....)))))..--))))) ( -28.66)
>DroSim_CAF1 67037 98 - 1
UAAAUCAAAUUGGCCAAGUCAAGUCCUCUGGUUUAAGCUAAGCAAUGGAAACUCAAAAAGCCAAGA------GCCCAGAGCAACUGCAGCACGCAGUCA--UGGGC
.........(((((.........(((..((.((......)).))..)))..........)))))..------(((((.....(((((.....)))))..--))))) ( -25.11)
>DroEre_CAF1 67266 100 - 1
UAAAUCAAAUUGGCCAAGUCAAGUCUUCUGGCUUAAGCCAAGAAAUGGAAACUUAAAAGGCCAAGA------GCCCAGAGCAACUGCAGCACGCAGUCACCUGGGC
.........((((((..........(((((((....))).))))..(....)......))))))..------((((((.(..(((((.....)))))..))))))) ( -37.00)
>DroYak_CAF1 60190 98 - 1
UAAAUCAAAUUGGCCAAGUCAAGUCCUCUGGUUUAAGCCAAGAAAUGGAAACUUAAAAGGCCAAGA------GCCCAGAGCAACUGCAGCACGCAGUCA--UGGGC
.........((((((((((....(((((((((....))).)))...))).))))....))))))..------(((((.....(((((.....)))))..--))))) ( -30.70)
>consensus
UAAAUCAAAUUGGCCAAGUCAAGUCCUCUGGUUUAAGCCAAGAAAUGGAAACUCAAAAAGCCAAGA______GCCCAGAGCAACUGCAGCACGCAGUCA__UGGGC
.........(((((.........(((.(((((....))).))....)))..........)))))........(((((.....(((((.....)))))....))))) (-23.91 = -23.63 +  -0.28)

alignment

secondary structure

dotplot

Window 6

Location	27,357,422 – 27,357,526
Length	104
Sequences	5
Columns	107
Reading direction	reverse
Mean pairwise identity	94.49
Mean single sequence MFE	-21.80
Consensus MFE	-19.11
Energy contribution	-18.75
Covariance contribution	-0.36
Combinations/Pair	1.13
Mean z-score	-1.45
Structure conservation index	0.88
SVM decision value	0.84
SVM RNA-class probability	0.863340
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27357422 104 - 27905053
CAACGAGGAAGAGACAAGUUCUCCGGCUAGCACAAACAUAAAUCAAAUUGGCCAAGUCAAGUCCUCUGGUUUAAGCCAAGCAAUGGAAACUCAAAAAGCCAAGA---
....(((((.((((.....)))).((((((.................))))))........)))))((((((..((...))...(....).....))))))...--- ( -21.83)
>DroSec_CAF1 102875 107 - 1
CAACGAGGAAGAGACAAGUUCUCUGGCUAGCACAAACAUAAAUCAAAUUGACCAAGUCAAGUCCUCUGGUUUAAGCCAAGAAAUGGAAACUCAAAAAGCCAAGAGCC
.................(((((.(((((...................(((((...))))).(((((((((....))).)))...))).........)))))))))). ( -21.10)
>DroSim_CAF1 67069 104 - 1
CAACGAGGAAGAGACAAGUUCUCCGGCUAGCACAAACAUAAAUCAAAUUGGCCAAGUCAAGUCCUCUGGUUUAAGCUAAGCAAUGGAAACUCAAAAAGCCAAGA---
....(((((.((((.....)))).((((((.................))))))........)))))((((((..((...))...(....).....))))))...--- ( -21.83)
>DroEre_CAF1 67300 104 - 1
CAACGAGGAAGAGACAAGUUCUCCGGCUAGCAUAGACAUAAAUCAAAUUGGCCAAGUCAAGUCUUCUGGCUUAAGCCAAGAAAUGGAAACUUAAAAGGCCAAGA---
...((..(((........)))..))......................((((((..........(((((((....))).))))..(....)......))))))..--- ( -22.50)
>DroYak_CAF1 60222 104 - 1
CAACGAGGAAGAGACAAGUUCUCCGGCUAGCACAAACAUAAAUCAAAUUGGCCAAGUCAAGUCCUCUGGUUUAAGCCAAGAAAUGGAAACUUAAAAGGCCAAGA---
....(((((.((((.....)))).((((((.................))))))........)))))((((((((((((.....)))...)))))...))))...--- ( -21.73)
>consensus
CAACGAGGAAGAGACAAGUUCUCCGGCUAGCACAAACAUAAAUCAAAUUGGCCAAGUCAAGUCCUCUGGUUUAAGCCAAGAAAUGGAAACUCAAAAAGCCAAGA___
....(((((.((((.....)))).((((((.................))))))........)))))((((((......(....)(....).....))))))...... (-19.11 = -18.75 +  -0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:51:09 2006