Locus 101

Sequence ID	2R_DroMel_CAF1
Location	1,347,653 – 1,347,803
Length	150
Max. P	0.595986

overview

Window 1

Location	1,347,653 – 1,347,770
Length	117
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	86.52
Mean single sequence MFE	-32.45
Consensus MFE	-20.86
Energy contribution	-22.55
Covariance contribution	1.69
Combinations/Pair	1.08
Mean z-score	-1.85
Structure conservation index	0.64
SVM decision value	0.10
SVM RNA-class probability	0.585475
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1347653 117 - 20766785
UCCCAGUACCAGCUGACUUAACGUUGGCACAAAUCAAAGGUUAUCAUAGCCCAUCAGUCCAUCAUCCCGGACUGAAGGUUGGACCCGCAC--CUUUCACUGAGCACAAAG-CCCCCGCCC
...((((....((..((.....))..)).......((((((.....(((((..(((((((........))))))).))))).......))--)))).)))).((.....)-)........ ( -31.00)
>DroSec_CAF1 65967 118 - 1
UUCAUGUAGCAGCUGACUUAACGUUGGCACAAAUCAAAGGUUAUCAUAGCCCUUCAGUCCAUCAUCCUGGACUGAACGGUGGAGCCGUUCCGCUUCCACUGAGCACAAUG-CCC-CGCCC
....(((.((.((..((.....))..))..........(((((...))))).(((((((((......)))))))))(((((((((......)).))))))).)))))...-...-..... ( -37.20)
>DroSim_CAF1 44124 117 - 1
UUCAUGUAGCAACUGACUUAACGUUGGCACAAAUCAAAGGUUAUCAUAGCCCAUCAGUCCAUCAUCCUGGACUGAACGGUGGAGCCGUUCCACUUCCACUGAGCACAAUG-CCC-CGCC-
.(((.((....))))).....(((((((..........(((((...)))))..((((((((......)))))))).((((((((.........)))))))).)).)))))-...-....- ( -30.70)
>DroYak_CAF1 34517 117 - 1
UUCAUGAACCAGCUGACAUAACGUAGGCACAAAUCAAAGGUUAUCAUAGUCAAUCAGUCCGUUAUCCUGGACUGAAGGUUGGAGGCGCAC--UUUCCACUGUGCACAAAGACCC-CGCCC
........((((((((((((((.(.............).)))))....)))..((((((((......)))))))).)))))).(((((((--........)))).....(....-)))). ( -30.92)
>consensus
UUCAUGUACCAGCUGACUUAACGUUGGCACAAAUCAAAGGUUAUCAUAGCCCAUCAGUCCAUCAUCCUGGACUGAACGGUGGAGCCGCAC__CUUCCACUGAGCACAAAG_CCC_CGCCC
...........((((((.....))))))..........(((............((((((((......)))))))).((((((((.........))))))))...............))). (-20.86 = -22.55 +   1.69)

alignment

secondary structure

dotplot

Window 2

Location	1,347,690 – 1,347,803
Length	113
Sequences	4
Columns	113
Reading direction	forward
Mean pairwise identity	85.84
Mean single sequence MFE	-31.98
Consensus MFE	-21.48
Energy contribution	-24.72
Covariance contribution	3.25
Combinations/Pair	1.09
Mean z-score	-1.66
Structure conservation index	0.67
SVM decision value	0.13
SVM RNA-class probability	0.595986
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1347690 113 + 20766785
AACCUUCAGUCCGGGAUGAUGGACUGAUGGGCUAUGAUAACCUUUGAUUUGUGCCAACGUUAAGUCAGCUGGUACUGGGAAAUGAUACCAAGCUUUUGACGAACGGGUCUAAG
..((.((((((((......)))))))).))...........(((.(((((((.....(((((((..(((((((((........).)))).))))))))))).))))))).))) ( -34.50)
>DroSec_CAF1 66005 113 + 1
ACCGUUCAGUCCAGGAUGAUGGACUGAAGGGCUAUGAUAACCUUUGAUUUGUGCCAACGUUAAGUCAGCUGCUACAUGAAAGUGAUACCAAGCUUUUGACGAACGAGUCUAAG
.((.(((((((((......))))))))).))..........(((.(((((((.....(((((((..((((..(((((....))).))...))))))))))).))))))).))) ( -36.30)
>DroSim_CAF1 44161 113 + 1
ACCGUUCAGUCCAGGAUGAUGGACUGAUGGGCUAUGAUAACCUUUGAUUUGUGCCAACGUUAAGUCAGUUGCUACAUGAAAGUGAUACCCAGCUUUUGACGAACGAGUCUAAG
.((((.(((((((......)))))))))))...........(((.(((((((.....(((((((..(((((...(((....))).....)))))))))))).))))))).))) ( -33.60)
>DroYak_CAF1 34554 103 + 1
AACCUUCAGUCCAGGAUAACGGACUGAUUGACUAUGAUAACCUUUGAUUUGUGCCUACGUUAUGUCAGCUGGUUCAUGAAAAUGAUACCAAACUU-UGACGAGC---------
..(..(((((((........)))))))..)............................(((.((((((.((((((((....)))).))))....)-))))))))--------- ( -23.50)
>consensus
AACCUUCAGUCCAGGAUGAUGGACUGAUGGGCUAUGAUAACCUUUGAUUUGUGCCAACGUUAAGUCAGCUGCUACAUGAAAAUGAUACCAAGCUUUUGACGAACGAGUCUAAG
.....((((((((......))))))))..(((...(((........)))...)))..(((((((..(((((((((((....))).)))).)))))))))))............ (-21.48 = -24.72 +   3.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:27:10 2006