Locus 8005

Sequence ID 3R_DroMel_CAF1
Location 21,469,749 – 21,469,839
Length 90
Max. P 0.907506
window12885 window12886

overview

Window 5

Location 21,469,749 – 21,469,839
Length 90
Sequences 4
Columns 92
Reading direction forward
Mean pairwise identity 87.55
Mean single sequence MFE -34.45
Consensus MFE -29.21
Energy contribution -31.02
Covariance contribution 1.81
Combinations/Pair 1.04
Mean z-score -1.76
Structure conservation index 0.85
SVM decision value 0.70
SVM RNA-class probability 0.827967
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21469749 90 + 27905053
--UGGGCCCCUCCGACCCCAAAACAGGUUCCUUCGACCAUGGCCAAAACGAUGGCCAAGUCUGGCGACCCGACAGCCUCGGCUGCUGGAGCC
--((((..(....)..)))).....((((((.(((.(((((((((......))))))....))))))...(.((((....))))).)))))) ( -32.80)
>DroSec_CAF1 76529 90 + 1
--UGGGCCCCCCCGAGCCCAAAACAGGUUCCUCCGACCAUGGCCAAAACGAUGGCCAAGUCUGGCGACCCGAGAGCCUCGGCUGCUGGAGCC
--(((((........))))).....((((((...(((..((((((......)))))).))).((((..(((((...))))).)))))))))) ( -37.80)
>DroSim_CAF1 61685 90 + 1
--UGGGCCCCCCCGAGCCCAAAACAGGUUCCACCGACCAUGGCCAAAACGAUGGCCAAGUCUGGCGACCCGAGAGCCUCGGCUGCUGGAGCC
--(((((........))))).....((((((...(((..((((((......)))))).))).((((..(((((...))))).)))))))))) ( -38.30)
>DroEre_CAF1 77692 79 + 1
GCUGGACCC----------AAAACAGGUUCCUUCGACCAUGGCCAAACCGAUGGCCAAGUCUGGCGACCCGAGAGCCUCGGC---CGGAGCC
.........----------......((((((.(((.(((((((((......))))))....)))))).(((((...))))).---.)))))) ( -28.90)
>consensus
__UGGGCCCCCCCGAGCCCAAAACAGGUUCCUCCGACCAUGGCCAAAACGAUGGCCAAGUCUGGCGACCCGAGAGCCUCGGCUGCUGGAGCC
..(((((........))))).....((((((...(((..((((((......)))))).))).(((...(((((...)))))..))))))))) (-29.21 = -31.02 +   1.81)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 21,469,749 – 21,469,839
Length 90
Sequences 4
Columns 92
Reading direction reverse
Mean pairwise identity 87.55
Mean single sequence MFE -42.18
Consensus MFE -34.91
Energy contribution -36.98
Covariance contribution 2.06
Combinations/Pair 1.03
Mean z-score -2.02
Structure conservation index 0.83
SVM decision value 1.05
SVM RNA-class probability 0.907506
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21469749 90 - 27905053
GGCUCCAGCAGCCGAGGCUGUCGGGUCGCCAGACUUGGCCAUCGUUUUGGCCAUGGUCGAAGGAACCUGUUUUGGGGUCGGAGGGGCCCA--
((((((..((((....))))((.(..(.(((((..((((((......)))))).((((....).)))...))))))..).))))))))..-- ( -42.20)
>DroSec_CAF1 76529 90 - 1
GGCUCCAGCAGCCGAGGCUCUCGGGUCGCCAGACUUGGCCAUCGUUUUGGCCAUGGUCGGAGGAACCUGUUUUGGGCUCGGGGGGGCCCA--
((((((.....(((((.(((.((((((.((.((((((((((......)))))).))))))..).)))))....)))))))).))))))..-- ( -45.10)
>DroSim_CAF1 61685 90 - 1
GGCUCCAGCAGCCGAGGCUCUCGGGUCGCCAGACUUGGCCAUCGUUUUGGCCAUGGUCGGUGGAACCUGUUUUGGGCUCGGGGGGGCCCA--
((((((.....(((((.(((.(((((((((.((((((((((......)))))).))))))))..)))))....)))))))).))))))..-- ( -47.90)
>DroEre_CAF1 77692 79 - 1
GGCUCCG---GCCGAGGCUCUCGGGUCGCCAGACUUGGCCAUCGGUUUGGCCAUGGUCGAAGGAACCUGUUUU----------GGGUCCAGC
(((....---)))(.(((((.(((((..((.((((((((((......)))))).))))...)).)))))....----------))))))... ( -33.50)
>consensus
GGCUCCAGCAGCCGAGGCUCUCGGGUCGCCAGACUUGGCCAUCGUUUUGGCCAUGGUCGAAGGAACCUGUUUUGGGCUCGGGGGGGCCCA__
((((((.....(((((.((..(((((..((.((((((((((......)))))).))))...)).)))))....)).))))).)))))).... (-34.91 = -36.98 +   2.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:00:09 2006