Locus 2055

Sequence ID 3L_DroMel_CAF1
Location 5,663,124 – 5,663,229
Length 105
Max. P 0.992358
window3203 window3204

overview

Window 3

Location 5,663,124 – 5,663,229
Length 105
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 76.08
Mean single sequence MFE -19.91
Consensus MFE -14.58
Energy contribution -15.06
Covariance contribution 0.48
Combinations/Pair 1.13
Mean z-score -2.25
Structure conservation index 0.73
SVM decision value 2.32
SVM RNA-class probability 0.992358
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5663124 105 + 23771897
UAUUUAAAGGCAAUUUGGGUGGCACAGCCUCCACAUCCG--GACGCAGCCUCAUCUGCAUCUGCAUCUACAUCUACAUCCA------CAUCCACA------UCCACAUCCUCAUCGCCU
.......((((.((..(((((.....((.(((......)--)).)).........(((....)))................------........------....)))))..)).)))) ( -20.80)
>DroSec_CAF1 35805 93 + 1
UAUUUAAAGGCAAUUUGGGUGGCACAGUCCCCACCUCCG--GCCGCAGCCACAUCUGCAUCUGCAUCUACAUCCUCA------------------------UCCACAUCCUCAUCGCCU
.......((((.....((((((........))))))..(--((....))).....(((....)))............------------------------..............)))) ( -19.50)
>DroSim_CAF1 36884 93 + 1
UAUUUAAAGGCAAUUUGGGUGGCACAGCCUCCACCUCCG--GCCGCAGCCACAUCUGCAUCUGCAUCUGCAUCUACA------------------------UCCACAUCCUCAUCGCCU
.......((((.((..(((((((.(.(((.........)--)).)..)))))...((((........))))......------------------------.......))..)).)))) ( -21.90)
>DroEre_CAF1 39059 111 + 1
UAUUUAAAGGCAAUUUGGGUGGCACAGCCUCCAUCUCCU--GCCGCAGCCUCAUCUGCAUCUGCAUUUACAUCCACAUCCACUUUCACAUCCACA------UCCACAUCCUCAUCGCCU
.......((((.((..((((((((..............)--)))((((......)))).....................................------.....))))..)).)))) ( -18.04)
>DroYak_CAF1 36526 107 + 1
UAUUUAAAGGCAAUUUGGGUGGCACAGCCUCCACCGCCUCAUCUGCAUCUGC------------AUCUACAUCUGCAGCCACAUUCACAUCCACAUCCACUUCCACAUCCUCAUCGCCU
.......((((......(((((........))))).......(((((..((.------------.....))..))))).....................................)))) ( -19.30)
>consensus
UAUUUAAAGGCAAUUUGGGUGGCACAGCCUCCACCUCCG__GCCGCAGCCACAUCUGCAUCUGCAUCUACAUCUACA_CCA______CAUCCACA______UCCACAUCCUCAUCGCCU
.......((((....((((.(((...)))))))...........((((......)))).........................................................)))) (-14.58 = -15.06 +   0.48)

alignment

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secondary structure

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dotplot

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Window 4

Location 5,663,124 – 5,663,229
Length 105
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 76.08
Mean single sequence MFE -31.50
Consensus MFE -20.62
Energy contribution -21.20
Covariance contribution 0.58
Combinations/Pair 1.24
Mean z-score -2.13
Structure conservation index 0.65
SVM decision value 1.78
SVM RNA-class probability 0.976761
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5663124 105 - 23771897
AGGCGAUGAGGAUGUGGA------UGUGGAUG------UGGAUGUAGAUGUAGAUGCAGAUGCAGAUGAGGCUGCGUC--CGGAUGUGGAGGCUGUGCCACCCAAAUUGCCUUUAAAUA
(((((((..((((.((((------((..(...------((..((((..(((....)))..))))..))...)..))))--)).))((((........))))))..)))))))....... ( -35.50)
>DroSec_CAF1 35805 93 - 1
AGGCGAUGAGGAUGUGGA------------------------UGAGGAUGUAGAUGCAGAUGCAGAUGUGGCUGCGGC--CGGAGGUGGGGACUGUGCCACCCAAAUUGCCUUUAAAUA
(((((((..((.......------------------------............(((....)))...(((((.(((((--(........)).)))))))))))..)))))))....... ( -27.90)
>DroSim_CAF1 36884 93 - 1
AGGCGAUGAGGAUGUGGA------------------------UGUAGAUGCAGAUGCAGAUGCAGAUGUGGCUGCGGC--CGGAGGUGGAGGCUGUGCCACCCAAAUUGCCUUUAAAUA
(((((((..((.......------------------------((((..(((....)))..))))...(((((.(((((--(.........)))))))))))))..)))))))....... ( -36.80)
>DroEre_CAF1 39059 111 - 1
AGGCGAUGAGGAUGUGGA------UGUGGAUGUGAAAGUGGAUGUGGAUGUAAAUGCAGAUGCAGAUGAGGCUGCGGC--AGGAGAUGGAGGCUGUGCCACCCAAAUUGCCUUUAAAUA
(((((((..((......(------(.((.((.((....((.((....)).))....)).)).)).))..(((.(((((--...........))))))))..))..)))))))....... ( -27.30)
>DroYak_CAF1 36526 107 - 1
AGGCGAUGAGGAUGUGGAAGUGGAUGUGGAUGUGAAUGUGGCUGCAGAUGUAGAU------------GCAGAUGCAGAUGAGGCGGUGGAGGCUGUGCCACCCAAAUUGCCUUUAAAUA
(((((((..((..((((........................(((((..(((....------------)))..))))).....(((((....))))).))))))..)))))))....... ( -30.00)
>consensus
AGGCGAUGAGGAUGUGGA______UGUGGAUG______UGG_UGUAGAUGUAGAUGCAGAUGCAGAUGAGGCUGCGGC__CGGAGGUGGAGGCUGUGCCACCCAAAUUGCCUUUAAAUA
(((((((..((...............................(((((.((((..(((....)))..)))).))))).........((((........))))))..)))))))....... (-20.62 = -21.20 +   0.58)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:23:19 2006