Locus 5024

Sequence ID	3L_DroMel_CAF1
Location	13,776,552 – 13,776,691
Length	139
Max. P	0.999883

overview

Window 1

Location	13,776,552 – 13,776,651
Length	99
Sequences	5
Columns	99
Reading direction	forward
Mean pairwise identity	91.00
Mean single sequence MFE	-28.54
Consensus MFE	-24.70
Energy contribution	-25.78
Covariance contribution	1.08
Combinations/Pair	1.07
Mean z-score	-3.62
Structure conservation index	0.87
SVM decision value	4.37
SVM RNA-class probability	0.999883
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13776552 99 + 23771897
UGUUUCGCUGAACAUAGUAAAACUAUUUUAACGUUUUGUGUCUGCUUAAAUUGUCUGAAUUUAUAGCGGUCAAUUUGAGCAGACAUAUAUAAGCCGCGC
.....(((((((.((((.....))))))))..(((((((((((((((((((((.(((.........))).)))))))))))))))))...)))).))). ( -31.70)
>DroSec_CAF1 23125 97 + 1
UGUUUCGCUGAACAUAGUAAAACUAUUUUAACGUUUUGUGUCUGCUUAAAUUGUCUGAAUUUAUAGCGGUCAAUUUGAGCACACAU--AUAAGCAGCGC
.....(((((...((((.....))))..........(((((.(((((((((((.(((.........))).))))))))))).))))--)....))))). ( -28.10)
>DroSim_CAF1 18859 97 + 1
UGUUUCGCUGAACAUAGUAAAACUAUUUUAACGUUUUGUGUCUGCUUAAAUUGUCUGAAUUUAUAGCGGUCAAUUUGAGCAGACAU--AUAAGCUGCGC
.....(((((((.((((.....))))))))..(((((((((((((((((((((.(((.........))).))))))))))))))))--).)))).))). ( -33.10)
>DroEre_CAF1 22614 97 + 1
UGUUUCGCUGAACAUAAUAAAACUAUUUUAACGUUUUGUGUCUGCUUAAAUUGUCUAUUUUUAUUGCGGUCAAUUUGAGCAGACAU--AUAAGCUACGC
(((((....)))))..................(((((((((((((((((((((.((...........)).))))))))))))))))--).))))..... ( -27.10)
>DroYak_CAF1 21383 97 + 1
UGUUUCGCUGAGCAUAGUAAAACUAUUUUAACGUUUUGUGUCUGCUUAAAUCAUCUGCUUUUAUUGCGGUCAAUUUGGUGGGACAU--CAAAGCUACGC
.((((..(((....)))..)))).........(((((((((((..((((((...((((.......))))...))))))..))))).--))))))..... ( -22.70)
>consensus
UGUUUCGCUGAACAUAGUAAAACUAUUUUAACGUUUUGUGUCUGCUUAAAUUGUCUGAAUUUAUAGCGGUCAAUUUGAGCAGACAU__AUAAGCUGCGC
.((((..(((....)))..)))).........((((.((((((((((((((((.(((.........))).))))))))))))))))....))))..... (-24.70 = -25.78 +   1.08)

alignment

secondary structure

dotplot

Window 2

Location	13,776,552 – 13,776,651
Length	99
Sequences	5
Columns	99
Reading direction	reverse
Mean pairwise identity	91.00
Mean single sequence MFE	-19.85
Consensus MFE	-15.57
Energy contribution	-16.01
Covariance contribution	0.44
Combinations/Pair	1.14
Mean z-score	-1.90
Structure conservation index	0.78
SVM decision value	0.87
SVM RNA-class probability	0.870459
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13776552 99 - 23771897
GCGCGGCUUAUAUAUGUCUGCUCAAAUUGACCGCUAUAAAUUCAGACAAUUUAAGCAGACACAAAACGUUAAAAUAGUUUUACUAUGUUCAGCGAAACA
.(((.....(((((((((((((.((((((....((........)).)))))).)))))))).(((((.........)))))..)))))...)))..... ( -22.00)
>DroSec_CAF1 23125 97 - 1
GCGCUGCUUAU--AUGUGUGCUCAAAUUGACCGCUAUAAAUUCAGACAAUUUAAGCAGACACAAAACGUUAAAAUAGUUUUACUAUGUUCAGCGAAACA
.(((((..(((--((((.((((.((((((....((........)).)))))).)))).))).(((((.........)))))..))))..)))))..... ( -22.10)
>DroSim_CAF1 18859 97 - 1
GCGCAGCUUAU--AUGUCUGCUCAAAUUGACCGCUAUAAAUUCAGACAAUUUAAGCAGACACAAAACGUUAAAAUAGUUUUACUAUGUUCAGCGAAACA
.(((.......--.((((((((.((((((....((........)).)))))).))))))))............((((.....)))).....)))..... ( -21.20)
>DroEre_CAF1 22614 97 - 1
GCGUAGCUUAU--AUGUCUGCUCAAAUUGACCGCAAUAAAAAUAGACAAUUUAAGCAGACACAAAACGUUAAAAUAGUUUUAUUAUGUUCAGCGAAACA
.(((.(..(((--(((((((((.((((((.................)))))).)))))))).(((((.........)))))..))))..).)))..... ( -19.53)
>DroYak_CAF1 21383 97 - 1
GCGUAGCUUUG--AUGUCCCACCAAAUUGACCGCAAUAAAAGCAGAUGAUUUAAGCAGACACAAAACGUUAAAAUAGUUUUACUAUGCUCAGCGAAACA
((..(((((((--.((((.....((((((.(.((.......)).).)))))).....))))))))........((((.....)))))))..))...... ( -14.40)
>consensus
GCGCAGCUUAU__AUGUCUGCUCAAAUUGACCGCUAUAAAUUCAGACAAUUUAAGCAGACACAAAACGUUAAAAUAGUUUUACUAUGUUCAGCGAAACA
.(((..........((((((((.((((((.................)))))).)))))))).(((((.........)))))..........)))..... (-15.57 = -16.01 +   0.44)

alignment

secondary structure

dotplot

Window 3

Location	13,776,571 – 13,776,691
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	87.88
Mean single sequence MFE	-30.80
Consensus MFE	-25.34
Energy contribution	-26.70
Covariance contribution	1.36
Combinations/Pair	1.10
Mean z-score	-2.94
Structure conservation index	0.82
SVM decision value	2.95
SVM RNA-class probability	0.997868
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13776571 120 + 23771897
AAACUAUUUUAACGUUUUGUGUCUGCUUAAAUUGUCUGAAUUUAUAGCGGUCAAUUUGAGCAGACAUAUAUAAGCCGCGCCAAAUUGCUUAGUUAGCUAAAUAAAAGAAAACUAAAUCUC
.............(((((((((((((((((((((.(((.........))).)))))))))))))))))...)))).(((......)))((((((..((.......))..))))))..... ( -31.90)
>DroSec_CAF1 23144 118 + 1
AAACUAUUUUAACGUUUUGUGUCUGCUUAAAUUGUCUGAAUUUAUAGCGGUCAAUUUGAGCACACAU--AUAAGCAGCGCCAAAUUGCUUAGUUAGCUGAAGAAAAGAAAACUAAAUCUC
.............(((((((((.(((((((((((.(((.........))).))))))))))).))))--).)))).(((......)))((((((..((.......))..))))))..... ( -28.70)
>DroSim_CAF1 18878 118 + 1
AAACUAUUUUAACGUUUUGUGUCUGCUUAAAUUGUCUGAAUUUAUAGCGGUCAAUUUGAGCAGACAU--AUAAGCUGCGCCAAAUUGCUUAGUUAGCUGAAGAAAAGAAAACUAAAUCUC
.............(((((((((((((((((((((.(((.........))).))))))))))))))))--).)))).(((......)))((((((..((.......))..))))))..... ( -34.20)
>DroEre_CAF1 22633 118 + 1
AAACUAUUUUAACGUUUUGUGUCUGCUUAAAUUGUCUAUUUUUAUUGCGGUCAAUUUGAGCAGACAU--AUAAGCUACGCGAAAUUGCUUAGUUAGCUGAAGAUAGAAAAACUAGCACUC
...(((((((...(((.(((((((((((((((((.((...........)).))))))))))))))))--)..(((((.(((....))).))))))))..))))))).............. ( -34.50)
>DroYak_CAF1 21402 118 + 1
AAACUAUUUUAACGUUUUGUGUCUGCUUAAAUCAUCUGCUUUUAUUGCGGUCAAUUUGGUGGGACAU--CAAAGCUACGCGCAAUGGCUCAGUUAGCCGAAGAAAAGAAAACUAGCACUG
.............(((((((((((..((((((...((((.......))))...))))))..))))).--)))))).....((..(((((.....)))))......((....)).)).... ( -24.70)
>consensus
AAACUAUUUUAACGUUUUGUGUCUGCUUAAAUUGUCUGAAUUUAUAGCGGUCAAUUUGAGCAGACAU__AUAAGCUGCGCCAAAUUGCUUAGUUAGCUGAAGAAAAGAAAACUAAAUCUC
.............(((((((((((((((((((((.(((.........))).)))))))))))))))).....(((((.((......)).))))).............)))))........ (-25.34 = -26.70 +   1.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:39:56 2006