Locus 345

Sequence ID	2R_DroMel_CAF1
Location	2,283,593 – 2,283,686
Length	93
Max. P	0.957765

overview

Window 9

Location	2,283,593 – 2,283,686
Length	93
Sequences	6
Columns	118
Reading direction	forward
Mean pairwise identity	68.01
Mean single sequence MFE	-25.94
Consensus MFE	-8.13
Energy contribution	-9.47
Covariance contribution	1.33
Combinations/Pair	1.06
Mean z-score	-1.98
Structure conservation index	0.31
SVM decision value	0.40
SVM RNA-class probability	0.719624
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2283593 93 + 20766785
GGA-AUUUACUGCAAGUGGCAAGUGUAAUUUCCACCAUUGAUGCAAC-------UUCUGCAUCCGACC-UGAGCACAAAU-CGGAACCGGCUA--CUCGCAUUUU-------------
...-......(((.((((((..((((....((.......((((((..-------...)))))).....-.))))))....-((....))))))--)).)))....------------- ( -22.82)
>DroSec_CAF1 49711 93 + 1
GGA-AUUUACUGCAAGUGGCAAGUGUAAUUUCCACCAUUGAUGCAAC-------UUCUGCAUCCGACC-UGUGCACAAAU-CGGAAUCGACCA--CUUGCAUUUU-------------
...-......(((((((((...(((.......)))..((((((((..-------...))).(((((..-((....))..)-))))))))))))--))))))....------------- ( -26.70)
>DroSim_CAF1 50396 91 + 1
-----UUUACUGCAAGUGGCAAGUGUAAUUUCCACCAUUGAUGCAAC-------UUCUGCAUCCGACCNUGGGCACAAAUNCGGAACCGACCA--CUUGCAUUUU-------------
-----.....(((((((((...((((.....(((.....((((((..-------...))))))......))))))).....((....)).)))--))))))....------------- ( -28.00)
>DroEre_CAF1 50150 99 + 1
CGG-AUUUUCUGCAAGUGGCAAGUGUAAUUUCCGCCAUUGAUGCAGUCAAUGCAUCCUGCAUCCGACU-GG-GCUCAAAU-UGGCACCAAAUC--CUUGCAUUUU-------------
.((-((((..(((.((((((.............))))))(((.(((((.((((.....))))..))))-).-).))....-..)))..)))))--).........------------- ( -28.02)
>DroYak_CAF1 45485 93 + 1
GGA-ACUUGCUGCAAGUUGCAACUGUAAUUUCCGCUAUUGAUGCCAU-------UCCUGCAUCUGACU-UGGCCUCAAAU-UGGAACCGACUA--CUUGCAUUUU-------------
..(-(((((...))))))((((..((...(((((...((((.((((.-------((........))..-)))).))))..-)))))...))..--.)))).....------------- ( -21.00)
>DroPer_CAF1 51087 105 + 1
CCACAUUUACCGCAAGAGGCGAGUGCAAUAUCCGCCAUUGAUUGCGCCA---CAACUAACAUCCUCCU-GG--------C-UGGCAGUAAAUGAGGCUGCAGCCUGGAAACCAAACCC
((.(((((((.((....((((....((((.......))))....)))).---.......((.((....-))--------.-)))).)))))))((((....))))))........... ( -29.10)
>consensus
GGA_AUUUACUGCAAGUGGCAAGUGUAAUUUCCACCAUUGAUGCAAC_______UCCUGCAUCCGACC_UG_GCACAAAU_CGGAACCGACUA__CUUGCAUUUU_____________
...........((((((((.((......)).))))....((((((............)))))).................................)))).................. ( -8.13 =  -9.47 +   1.33)

alignment

secondary structure

dotplot

Window 0

Location	2,283,593 – 2,283,686
Length	93
Sequences	6
Columns	118
Reading direction	reverse
Mean pairwise identity	68.01
Mean single sequence MFE	-29.73
Consensus MFE	-15.09
Energy contribution	-15.12
Covariance contribution	0.03
Combinations/Pair	1.37
Mean z-score	-1.94
Structure conservation index	0.51
SVM decision value	1.48
SVM RNA-class probability	0.957765
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2283593 93 - 20766785
-------------AAAAUGCGAG--UAGCCGGUUCCG-AUUUGUGCUCA-GGUCGGAUGCAGAA-------GUUGCAUCAAUGGUGGAAAUUACACUUGCCACUUGCAGUAAAU-UCC
-------------....((((((--(.((.(((((((-(((((....))-)))).(((((((..-------.)))))))......)))......))).)).)))))))......-... ( -28.10)
>DroSec_CAF1 49711 93 - 1
-------------AAAAUGCAAG--UGGUCGAUUCCG-AUUUGUGCACA-GGUCGGAUGCAGAA-------GUUGCAUCAAUGGUGGAAAUUACACUUGCCACUUGCAGUAAAU-UCC
-------------....((((((--((((.((.((((-(((((....))-)))))))(((((..-------.)))))))...((((.......)))).))))))))))......-... ( -33.50)
>DroSim_CAF1 50396 91 - 1
-------------AAAAUGCAAG--UGGUCGGUUCCGNAUUUGUGCCCANGGUCGGAUGCAGAA-------GUUGCAUCAAUGGUGGAAAUUACACUUGCCACUUGCAGUAAA-----
-------------....((((((--((((.(((.....((((.((((........(((((((..-------.)))))))...)))).))))...))).)))))))))).....----- ( -30.20)
>DroEre_CAF1 50150 99 - 1
-------------AAAAUGCAAG--GAUUUGGUGCCA-AUUUGAGC-CC-AGUCGGAUGCAGGAUGCAUUGACUGCAUCAAUGGCGGAAAUUACACUUGCCACUUGCAGAAAAU-CCG
-------------.........(--(((((..(((..-..((((..-.(-(((((.((((.....))))))))))..))))((((((.........))))))...)))..))))-)). ( -30.60)
>DroYak_CAF1 45485 93 - 1
-------------AAAAUGCAAG--UAGUCGGUUCCA-AUUUGAGGCCA-AGUCAGAUGCAGGA-------AUGGCAUCAAUAGCGGAAAUUACAGUUGCAACUUGCAGCAAGU-UCC
-------------.........(--((((...((((.-..((((.((((-..((.......)).-------.)))).))))....))))))))).(((((.....)))))....-... ( -22.50)
>DroPer_CAF1 51087 105 - 1
GGGUUUGGUUUCCAGGCUGCAGCCUCAUUUACUGCCA-G--------CC-AGGAGGAUGUUAGUUG---UGGCGCAAUCAAUGGCGGAUAUUGCACUCGCCUCUUGCGGUAAAUGUGG
.(((((((...)))))))....((.((((((((((..-(--------((-(.((.........)).---)))).........(((((.........)))))....)))))))))).)) ( -33.50)
>consensus
_____________AAAAUGCAAG__UAGUCGGUUCCA_AUUUGUGC_CA_AGUCGGAUGCAGAA_______GUUGCAUCAAUGGCGGAAAUUACACUUGCCACUUGCAGUAAAU_UCC
.................((((((................................(((((((..........)))))))..((((((.........)))))))))))).......... (-15.09 = -15.12 +   0.03)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:36:02 2006