Locus 1626

Sequence ID	3R_DroMel_CAF1
Location	4,719,516 – 4,719,650
Length	134
Max. P	0.755080

overview

Window 7

Location	4,719,516 – 4,719,618
Length	102
Sequences	6
Columns	116
Reading direction	forward
Mean pairwise identity	82.52
Mean single sequence MFE	-23.98
Consensus MFE	-14.75
Energy contribution	-14.64
Covariance contribution	-0.11
Combinations/Pair	1.09
Mean z-score	-2.11
Structure conservation index	0.62
SVM decision value	0.12
SVM RNA-class probability	0.594463
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4719516 102 + 27905053
CUCACUUGUUUAUGUCGACUUAGGCC-AGCCACAUUUGGUCAAAAGCAAAUUUGUUAUUUAACAAUUU---GCAAUUUCCAA-------UGCAAUGCGAUC---CAUUGCAAUGCG
......................((((-((......))))))....(((((((.(((....))))))))---)).........-------.(((.(((((..---..))))).))). ( -22.60)
>DroPse_CAF1 91365 116 + 1
GCUAGUUGUUUAUGUCGACUUAGCCCCCAUCAUUUAUGGUCAAACACAAAUUUGUUAUUUAACAAUUUUGACCAUUUUCCAACGCCAAUUGCAAUGCGAUACCCAAUUGCAAUGCA
((((((((.......)))).))))...........(((((((((.......(((((....))))).)))))))))..............((((.((((((.....)))))).)))) ( -26.00)
>DroEre_CAF1 68420 103 + 1
CUCAGUUGUUUAUGUCGACUUAGGCC-AACCGCUUUUGGUCAAAAGCAAAUUUGUUAUUUAACAAUUU---GCAAUUUCCAA------CUGCAAUGCGAUC---CAUUGCAAUGCG
...(((((........((((.((((.-....))))..))))....(((((((.(((....))))))))---))......)))------))(((.(((((..---..))))).))). ( -27.40)
>DroYak_CAF1 67988 102 + 1
CUCAGUUGUUUAUGUCGACUUAGGCU-AACCGCUUUUGGUCAAAAGCAAAUUUGUUAUUUAACAAUUU---GCAAUUUCCAA-------UGCAAUGCGAUC---CAUUGCAAUGCG
....((((........((((.((((.-....))))..))))....(((((((.(((....))))))))---))......)))-------)(((.(((((..---..))))).))). ( -25.00)
>DroAna_CAF1 64827 102 + 1
GUCGGUUGUUUAUGUCGACUUAGGCC-AACCGAUUAUGGUCAAUAGCAAAUUUGUUAUUUAACAAUUU---CCAAUUUCCAA-------UGCAAUGCGAUC---CAUUGCAAUGCU
((((((((.....(((......))))-)))))))..((...(((((((....)))))))...))....---........((.-------(((((((.....---))))))).)).. ( -23.30)
>DroPer_CAF1 90476 116 + 1
GCUAGUUGUUUAUGUCGACUUAGCCCCCAUCAUUUAUGGUCAAACACAAAUUUGUUAUUUAACAAUUUUUCCCAUUUUCCGACGCCAAUUGCAAUGCGAUACCCAAUUGCAAUGCA
...(((((....(((((.........((((.....))))........(((.(((((....))))).)))..........))))).)))))(((.((((((.....)))))).))). ( -19.60)
>consensus
CUCAGUUGUUUAUGUCGACUUAGGCC_AACCACUUAUGGUCAAAAGCAAAUUUGUUAUUUAACAAUUU___CCAAUUUCCAA_______UGCAAUGCGAUC___CAUUGCAAUGCG
...(((((.......)))))................(((............(((((....))))).............))).........(((.((((((.....)))))).))). (-14.75 = -14.64 +  -0.11)

alignment

secondary structure

dotplot

Window 8

Location	4,719,554 – 4,719,650
Length	96
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	83.39
Mean single sequence MFE	-23.65
Consensus MFE	-15.32
Energy contribution	-15.35
Covariance contribution	0.03
Combinations/Pair	1.09
Mean z-score	-2.88
Structure conservation index	0.65
SVM decision value	0.49
SVM RNA-class probability	0.755080
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4719554 96 + 27905053
UCAAAAGCAAAUUUGUUAUUUAACAAUUU---GCAAUUUCCAA-------UGCAAUGCGAUC---CAUUGCAAUGCGAUGCGUGUAAAUGUUAUAACCCAAUUUGAC--------AA
......(((((((.((((..(((((.(((---(((...((((.-------(((((((.....---))))))).)).))....)))))))))))))))..)))))).)--------.. ( -23.00)
>DroPse_CAF1 91404 117 + 1
UCAAACACAAAUUUGUUAUUUAACAAUUUUGACCAUUUUCCAACGCCAAUUGCAAUGCGAUACCCAAUUGCAAUGCAAUGCGUGUAAAUGUUAGAAGCCAAUUUGACAAUUGGACAA
.......((((.(((((....))))).)))).......((((((((..((((((.((((((.....)))))).)))))))))).....(((((((......)))))))..))))... ( -30.50)
>DroSec_CAF1 64620 96 + 1
UCAAAAGCAAAUUUGUUAUUUAACAAUUA---GCAAUUGCCAA-------UGCAAUGCGAUC---CAUUGCAAUGCGAUGCGUGUAAAUGCUAUAAGCCAAUUUGAC--------AA
(((((.((....(((((....))))).((---(((.((((((.-------((((.(((((..---..))))).)))).))...)))).)))))...))...))))).--------.. ( -22.10)
>DroEre_CAF1 68458 97 + 1
UCAAAAGCAAAUUUGUUAUUUAACAAUUU---GCAAUUUCCAA------CUGCAAUGCGAUC---CAUUGCAAUGCGAUGCGUGUAAAUGUUAUAAGCCAAUUUGAC--------AA
......(((((((.(((...(((((.(((---(((...((((.------.(((((((.....---))))))).)).))....)))))))))))..))).)))))).)--------.. ( -22.40)
>DroAna_CAF1 64865 96 + 1
UCAAUAGCAAAUUUGUUAUUUAACAAUUU---CCAAUUUCCAA-------UGCAAUGCGAUC---CAUUGCAAUGCUAUGCGUGUAAAUGUUAUAAGCCAAUUUGAC--------AA
......(((((((.(((...(((((....---...........-------(((((((.....---)))))))((((...)))).....)))))..))).)))))).)--------.. ( -17.30)
>DroPer_CAF1 90515 117 + 1
UCAAACACAAAUUUGUUAUUUAACAAUUUUUCCCAUUUUCCGACGCCAAUUGCAAUGCGAUACCCAAUUGCAAUGCAAUGCGUGUAAAUGUUAGAAGCCAAUUUGACAAUUGGACAA
............(((((....)))))(((((..(((((....((((..((((((.((((((.....)))))).))))))))))..)))))..)))))((((((....)))))).... ( -26.60)
>consensus
UCAAAAGCAAAUUUGUUAUUUAACAAUUU___CCAAUUUCCAA_______UGCAAUGCGAUC___CAUUGCAAUGCGAUGCGUGUAAAUGUUAUAAGCCAAUUUGAC________AA
.......((((((.(((.................................((((.((((((.....)))))).))))..((((....))))....))).))))))............ (-15.32 = -15.35 +   0.03)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:15:10 2006