Locus 5860

Sequence ID X_DroMel_CAF1
Location 15,122,259 – 15,122,389
Length 130
Max. P 0.854054
window9512 window9513

overview

Window 2

Location 15,122,259 – 15,122,352
Length 93
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 77.45
Mean single sequence MFE -21.34
Consensus MFE -7.68
Energy contribution -9.44
Covariance contribution 1.76
Combinations/Pair 1.04
Mean z-score -1.87
Structure conservation index 0.36
SVM decision value 0.06
SVM RNA-class probability 0.563419
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15122259 93 - 22224390
AAAAUAUAGAAAACGGAUUU-UGCAGUUUUGCCAUCAGAGCUGCUGGCUGUA--------------------CACGGCCAAAU-----AUAA-CAUUUUUUAGUAAUUACAUAUUUGCAC
......(((((((.(.....-.(((((((((....)))))))))((((((..--------------------..))))))...-----....-).)))))))((((........)))).. ( -24.20)
>DroSec_CAF1 33914 97 - 1
AAAAUAUAGAAAACGGAUUU-UGCAGUUUUGCCAUCAGAGCUGC-GGCUGUA--------------------CACGGCCAAAUACUAUAUAA-AAUUUUUUAGUAAUUACAUAUUUGCAC
...((((((...........-.(((((((((....)))))))))-(((((..--------------------..))))).....))))))..-.........((((........)))).. ( -26.00)
>DroEre_CAF1 40872 90 - 1
AAAAUAUAGAAAACGGAUUU-CGCAGU--UGCCACCAGAGCUGC-GACUGCA--------------------CACGCCCAAAU-----AUAA-AAUUUUGUAGUAAUUACAUAUUUGCUC
..............((....-.(((((--(((..........))-)))))).--------------------....))(((((-----((..-((((.......))))..)))))))... ( -16.30)
>DroYak_CAF1 41463 92 - 1
AAAAUAUAGAAAACGGAUUU-UGUAGU-UUGCCAUCAGAGCUGC-GGCUGCA--------------------CACGGCCAAAU-----AUAAAAAUUUUUUAGUAAUUACAUGUUUGCAC
......(((((((.......-.(((((-((.......)))))))-(((((..--------------------..)))))....-----.......)))))))((((........)))).. ( -18.30)
>DroPer_CAF1 87542 112 - 1
AAAAUAUAGAAAACAGAUUUUUGUAGU-UCGCCGCCUCCGCCGC-AGACGCAGACGCAGUCACUGCCACUGCCACUGCCAAAC-----ACGC-AUUUUUUUAGUAAUUACAUAUUUGCAC
.............(((((...((((((-((((.((....)).))-....((((..(((((.......)))))..)))).....-----....-.........).))))))).)))))... ( -21.90)
>consensus
AAAAUAUAGAAAACGGAUUU_UGCAGU_UUGCCAUCAGAGCUGC_GGCUGCA____________________CACGGCCAAAU_____AUAA_AAUUUUUUAGUAAUUACAUAUUUGCAC
......(((((((.........(((((.(((....))).))))).(((((........................)))))................)))))))((((........)))).. ( -7.68 =  -9.44 +   1.76)

alignment

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secondary structure

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dotplot

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Window 3

Location 15,122,293 – 15,122,389
Length 96
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 74.40
Mean single sequence MFE -31.01
Consensus MFE -7.18
Energy contribution -6.94
Covariance contribution -0.24
Combinations/Pair 1.19
Mean z-score -1.86
Structure conservation index 0.23
SVM decision value 0.80
SVM RNA-class probability 0.854054
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15122293 96 - 22224390
CAUU---UGUGGGGCCCUUUGUGGGGCCUCAUUAUGCUGGAAAAUAUAGAAAACGGAUUU-UGCAGUUUUGCCAUCAGAGCUGCUGGCUGUA--------------------CACGGCCA
(((.---.((((((((((....)))))))))).)))(((..............)))....-.(((((((((....))))))))).(((((..--------------------..))))). ( -37.94)
>DroSec_CAF1 33953 91 - 1
CAUU---UGU---GCCCUUUGUGGGGCCUCAUUAUGCUG-AAAAUAUAGAAAACGGAUUU-UGCAGUUUUGCCAUCAGAGCUGC-GGCUGUA--------------------CACGGCCA
.(((---(((---(((((....))))).(((......))-)...........))))))..-.(((((((((....)))))))))-(((((..--------------------..))))). ( -30.00)
>DroEre_CAF1 40906 89 - 1
CAGU---GGG---GCCCUUUGUGA-GCCUCAUUAUGCUGGAAAAUAUAGAAAACGGAUUU-CGCAGU--UGCCACCAGAGCUGC-GACUGCA--------------------CACGCCCA
.(((---(((---((.(.....).-))))))))..((((.........((((.....)))-)(((((--(((..........))-)))))).--------------------)).))... ( -25.80)
>DroYak_CAF1 41498 90 - 1
CCGU---UGG---GCCCUUUGUGA-GCCUCAUUAUGCUGGAAAAUAUAGAAAACGGAUUU-UGUAGU-UUGCCAUCAGAGCUGC-GGCUGCA--------------------CACGGCCA
....---..(---(((...(((((-(((.((...((.((((((.(((((((......)))-)))).)-)).))).))....)).-)))).))--------------------)).)))). ( -27.70)
>DroPer_CAF1 87576 117 - 1
CCGUCUCUUUACGAUCCUUUGUGG-GUCUCAUUAUGGUGAAAAAUAUAGAAAACAGAUUUUUGUAGU-UCGCCGCCUCCGCCGC-AGACGCAGACGCAGUCACUGCCACUGCCACUGCCA
..(((((.....(((((.....))-))).......((((((...((((((((.....)))))))).)-))))).........).-))))((((..(((((.......)))))..)))).. ( -33.60)
>consensus
CAGU___UGU___GCCCUUUGUGG_GCCUCAUUAUGCUGGAAAAUAUAGAAAACGGAUUU_UGCAGU_UUGCCAUCAGAGCUGC_GGCUGCA____________________CACGGCCA
....................(((........(((((.(....).))))).............(((((...((.......)).....))))).....................)))..... ( -7.18 =  -6.94 +  -0.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:58:10 2006