Locus 4657

Sequence ID	2L_DroMel_CAF1
Location	13,344,743 – 13,344,873
Length	130
Max. P	0.948564

overview

Window 2

Location	13,344,743 – 13,344,845
Length	102
Sequences	4
Columns	107
Reading direction	forward
Mean pairwise identity	87.64
Mean single sequence MFE	-29.40
Consensus MFE	-26.24
Energy contribution	-26.18
Covariance contribution	-0.06
Combinations/Pair	1.03
Mean z-score	-1.55
Structure conservation index	0.89
SVM decision value	0.46
SVM RNA-class probability	0.746048
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13344743 102 + 22407834
UUGGAGUCGAGAGUGCGC---CCGGCC--ACCUCAUAUGCUCGCAUACUUGUACACUCGCCUCUGAACAACUGUACAAAUGUACAAAUGUACAAAUGUACUCCGGUG
(..(((.((((.((((..---..((..--.))...((((....))))...)))).)))).)))..)((....(((((..(((((....)))))..)))))....)). ( -29.10)
>DroSec_CAF1 57028 96 + 1
UUGGAGUCGAGAGUGCGC---CCGGCCUCACCUCAUAUGCUCGCAUACUUGUACACUCGCCUCUGAACAACUGUACAAAUGU--------ACAAUUGUACUCCGGUG
(..(((.((((.((((..---..((.....))...((((....))))...)))).)))).)))..)((((.(((((....))--------))).))))......... ( -27.10)
>DroSim_CAF1 57369 96 + 1
UUGGAGCCGGGAGUGCGC---GCGGCCUCACCUCAUAUGCUCGCAUACUUGUACACUCGCCUCUGAACAACUGUACAAAUGU--------ACAAAUGUACUCCGGUG
.....((((((((((..(---(.((.....)).).((((....))))...)..)))))........(((..(((((....))--------)))..)))...))))). ( -26.90)
>DroYak_CAF1 57602 105 + 1
UUGGAGUCGAGAGUGCGCCUCCUGGCC--ACCUCAUAUGCUCGCAUACGUGUACACUCGCCUCUGAACGAAUGUACAAAUGUAGAAAUGUACAAAUGUACUCCAGUG
(((((((((((.(((.(((....))))--)))))((((..((((((...((((((.(((........))).)))))).)))).)).))))......).))))))).. ( -34.50)
>consensus
UUGGAGUCGAGAGUGCGC___CCGGCC__ACCUCAUAUGCUCGCAUACUUGUACACUCGCCUCUGAACAACUGUACAAAUGU________ACAAAUGUACUCCGGUG
(..(((.((((.((((.......((.....))...((((....))))...)))).)))).)))..)((....(((((..((((......))))..)))))....)). (-26.24 = -26.18 +  -0.06)

alignment

secondary structure

dotplot

Window 3

Location	13,344,743 – 13,344,845
Length	102
Sequences	4
Columns	107
Reading direction	reverse
Mean pairwise identity	87.64
Mean single sequence MFE	-35.73
Consensus MFE	-27.99
Energy contribution	-28.17
Covariance contribution	0.19
Combinations/Pair	1.03
Mean z-score	-2.42
Structure conservation index	0.78
SVM decision value	1.38
SVM RNA-class probability	0.948564
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13344743 102 - 22407834
CACCGGAGUACAUUUGUACAUUUGUACAUUUGUACAGUUGUUCAGAGGCGAGUGUACAAGUAUGCGAGCAUAUGAGGU--GGCCGG---GCGCACUCUCGACUCCAA
....((((((((..(((((....)))))..)))))....(((.(((((((..((..((.(((((....)))))....)--)..)).---.))).)))).)))))).. ( -36.00)
>DroSec_CAF1 57028 96 - 1
CACCGGAGUACAAUUGU--------ACAUUUGUACAGUUGUUCAGAGGCGAGUGUACAAGUAUGCGAGCAUAUGAGGUGAGGCCGG---GCGCACUCUCGACUCCAA
....(((((((((((((--------((....))))))))))..(((((((.((.(((..(((((....)))))...)))..))...---.))).))))..))))).. ( -33.90)
>DroSim_CAF1 57369 96 - 1
CACCGGAGUACAUUUGU--------ACAUUUGUACAGUUGUUCAGAGGCGAGUGUACAAGUAUGCGAGCAUAUGAGGUGAGGCCGC---GCGCACUCCCGGCUCCAA
....(((((...(((((--------(.(((((((((.((((......)))).))))))))).)))))).......((.(((((...---..)).))))).))))).. ( -34.70)
>DroYak_CAF1 57602 105 - 1
CACUGGAGUACAUUUGUACAUUUCUACAUUUGUACAUUCGUUCAGAGGCGAGUGUACACGUAUGCGAGCAUAUGAGGU--GGCCAGGAGGCGCACUCUCGACUCCAA
...((((((.(...((((......))))..(((((((((((......))))))))))).(((((....)))))(((((--((((....))).))).)))))))))). ( -38.30)
>consensus
CACCGGAGUACAUUUGU________ACAUUUGUACAGUUGUUCAGAGGCGAGUGUACAAGUAUGCGAGCAUAUGAGGU__GGCCGG___GCGCACUCUCGACUCCAA
....((((((((..((((......))))..)))))....(((.(((((((.........(((((....)))))..((.....))......))).)))).)))))).. (-27.99 = -28.17 +   0.19)

alignment

secondary structure

dotplot

Window 4

Location	13,344,767 – 13,344,873
Length	106
Sequences	4
Columns	109
Reading direction	forward
Mean pairwise identity	88.65
Mean single sequence MFE	-25.43
Consensus MFE	-19.88
Energy contribution	-20.25
Covariance contribution	0.38
Combinations/Pair	1.00
Mean z-score	-1.96
Structure conservation index	0.78
SVM decision value	0.74
SVM RNA-class probability	0.838954
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13344767 106 + 22407834
-ACCUCAUAUGCUCGCAUACUUGUACACUCGCCUCUGAACAACUGUACAAAUGUACAAAUGUACAAAUGUACUCCGGUGGACUACACU--GCUGCCACCUGGCGCCUCC
-......((((....))))..........((((...........(((((..(((((....)))))..)))))...(((((.(......--...)))))).))))..... ( -25.60)
>DroSec_CAF1 57053 101 + 1
CACCUCAUAUGCUCGCAUACUUGUACACUCGCCUCUGAACAACUGUACAAAUGU--------ACAAUUGUACUCCGGUGGACUACACCGGGCUGCCACCUGGCGCCACC
.......((((....))))...................((((.(((((....))--------))).))))....(((((.....)))))(((.(((....))))))... ( -27.90)
>DroSim_CAF1 57394 101 + 1
CACCUCAUAUGCUCGCAUACUUGUACACUCGCCUCUGAACAACUGUACAAAUGU--------ACAAAUGUACUCCGGUGGACUACACCGCGCUGCCACCUGGCGCCACC
..........((.(((......(((((.(((....))).....(((((....))--------)))..)))))...((((.....)))))))..(((....))))).... ( -23.70)
>DroYak_CAF1 57629 106 + 1
-ACCUCAUAUGCUCGCAUACGUGUACACUCGCCUCUGAACGAAUGUACAAAUGUAGAAAUGUACAAAUGUACUCCAGUGGACUACUAC--GCUGCCACCUGGCGCCACC
-.........((..((.....((((((.(((........))).))))))...((((....((((....))))(((...)))...))))--)).(((....))))).... ( -24.50)
>consensus
_ACCUCAUAUGCUCGCAUACUUGUACACUCGCCUCUGAACAACUGUACAAAUGU________ACAAAUGUACUCCGGUGGACUACACC__GCUGCCACCUGGCGCCACC
.......((((....))))..........((((...........(((((..((((......))))..)))))...(((((.(...........)))))).))))..... (-19.88 = -20.25 +   0.38)

alignment

secondary structure

dotplot

Window 5

Location	13,344,767 – 13,344,873
Length	106
Sequences	4
Columns	109
Reading direction	reverse
Mean pairwise identity	88.65
Mean single sequence MFE	-36.23
Consensus MFE	-29.06
Energy contribution	-29.25
Covariance contribution	0.19
Combinations/Pair	1.03
Mean z-score	-2.08
Structure conservation index	0.80
SVM decision value	1.00
SVM RNA-class probability	0.897574
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13344767 106 - 22407834
GGAGGCGCCAGGUGGCAGC--AGUGUAGUCCACCGGAGUACAUUUGUACAUUUGUACAUUUGUACAGUUGUUCAGAGGCGAGUGUACAAGUAUGCGAGCAUAUGAGGU-
....(((((....))).((--(..(((.(((...))).)))((((((((((((((...((((.((....)).)))).)))))))))))))).)))..)).........- ( -36.20)
>DroSec_CAF1 57053 101 - 1
GGUGGCGCCAGGUGGCAGCCCGGUGUAGUCCACCGGAGUACAAUUGU--------ACAUUUGUACAGUUGUUCAGAGGCGAGUGUACAAGUAUGCGAGCAUAUGAGGUG
((..(((((.(((....))).)))))...))(((...(((...((((--------(.(((((((((.((((......)))).))))))))).)))))...)))..))). ( -37.80)
>DroSim_CAF1 57394 101 - 1
GGUGGCGCCAGGUGGCAGCGCGGUGUAGUCCACCGGAGUACAUUUGU--------ACAUUUGUACAGUUGUUCAGAGGCGAGUGUACAAGUAUGCGAGCAUAUGAGGUG
....(((((....))).))((.(((((.(((...))).)))))((((--------(.(((((((((.((((......)))).))))))))).))))))).......... ( -35.30)
>DroYak_CAF1 57629 106 - 1
GGUGGCGCCAGGUGGCAGC--GUAGUAGUCCACUGGAGUACAUUUGUACAUUUCUACAUUUGUACAUUCGUUCAGAGGCGAGUGUACACGUAUGCGAGCAUAUGAGGU-
.((((..((((.(((..((--......))))))))).((((....))))....))))...(((((((((((......)))))))))))((((((....))))))....- ( -35.60)
>consensus
GGUGGCGCCAGGUGGCAGC__GGUGUAGUCCACCGGAGUACAUUUGU________ACAUUUGUACAGUUGUUCAGAGGCGAGUGUACAAGUAUGCGAGCAUAUGAGGU_
(((((((((....))).((.....)).).)))))...(((((..((((......))))..))))).....((((...((..(((((....)))))..))...))))... (-29.06 = -29.25 +   0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:23:53 2006