Locus 4896

Sequence ID X_DroMel_CAF1
Location 12,728,430 – 12,728,541
Length 111
Max. P 0.977750
window7990 window7991

overview

Window 0

Location 12,728,430 – 12,728,541
Length 111
Sequences 4
Columns 111
Reading direction forward
Mean pairwise identity 84.30
Mean single sequence MFE -27.45
Consensus MFE -14.77
Energy contribution -15.76
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -3.11
Structure conservation index 0.54
SVM decision value 0.51
SVM RNA-class probability 0.765794
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12728430 111 + 22224390
AGCACAAAACAGAACCGCACAGAACAGCACCGACACAAAUGCAGAUACAAAUGUGGAUGUAUCUUCGCAACAGCAUCAGUAUCUGAAUCUGUAUCUGUAUCUGUAACUGUG
........((((....((........))...........((((((((((.(((..(((........((....)).((((...)))))))..))).)))))))))).)))). ( -28.30)
>DroSec_CAF1 81095 105 + 1
AGCACAAAACAGAACCGCACAGAACAGCACCGACACAAAUGCAGAUACAAAUGUGGAUGUAUCUUCGCAGCAGCAGCAGUAUC------UGUAUCUGUAUCUGUAACUGUG
..((((..(((((...((........))......(((.((((((((((...((((((......))))))((....)).)))))------))))).))).)))))...)))) ( -30.70)
>DroEre_CAF1 79919 88 + 1
AGCACAAAACAGAA-----CAGAACAGCACCGACACAAAUUCAGAUACAAAUGUGGAUGUAUCUUCGCAUCAGCUUCA------------GU------AUCUGUAACUGUG
..............-----..............((((....(((((((....((.(((((......))))).))....------------))------)))))....)))) ( -18.60)
>DroYak_CAF1 84137 94 + 1
AGCACAAAACAGAG-----CAGAACAGCACCGACACAAAUGCAGAUACAAAUGUGGAUGUAUCUUCGCAUCAGCAUCU------------GUAUCUGUAUCUGUAACUGUG
........((((.(-----(......))......(((.(((((((((((.((((.(((((......))))).)))).)------------)))))))))).)))..)))). ( -32.20)
>consensus
AGCACAAAACAGAA_____CAGAACAGCACCGACACAAAUGCAGAUACAAAUGUGGAUGUAUCUUCGCAUCAGCAUCA____________GUAUCUGUAUCUGUAACUGUG
.................................((((..((((((((((..((((((......))))))...((................))...))))))))))..)))) (-14.77 = -15.76 +   1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 12,728,430 – 12,728,541
Length 111
Sequences 4
Columns 111
Reading direction reverse
Mean pairwise identity 84.30
Mean single sequence MFE -35.27
Consensus MFE -21.39
Energy contribution -23.70
Covariance contribution 2.31
Combinations/Pair 1.03
Mean z-score -4.03
Structure conservation index 0.61
SVM decision value 1.80
SVM RNA-class probability 0.977750
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12728430 111 - 22224390
CACAGUUACAGAUACAGAUACAGAUUCAGAUACUGAUGCUGUUGCGAAGAUACAUCCACAUUUGUAUCUGCAUUUGUGUCGGUGCUGUUCUGUGCGGUUCUGUUUUGUGCU
(((((..(((((.((.(.((((((..(((.(((((((((...(((..(((((((........))))))))))...)))))))))))).))))))).))))))).))))).. ( -42.10)
>DroSec_CAF1 81095 105 - 1
CACAGUUACAGAUACAGAUACA------GAUACUGCUGCUGCUGCGAAGAUACAUCCACAUUUGUAUCUGCAUUUGUGUCGGUGCUGUUCUGUGCGGUUCUGUUUUGUGCU
(((((..(((((((((((.(((------(.(((((.(((...(((..(((((((........))))))))))...))).)))))))))))))))....))))).))))).. ( -35.60)
>DroEre_CAF1 79919 88 - 1
CACAGUUACAGAU------AC------------UGAAGCUGAUGCGAAGAUACAUCCACAUUUGUAUCUGAAUUUGUGUCGGUGCUGUUCUG-----UUCUGUUUUGUGCU
(((((..(((((.------((------------.((((((((((((((((((((........)))))))....))))))))))....))).)-----)))))).))))).. ( -27.90)
>DroYak_CAF1 84137 94 - 1
CACAGUUACAGAUACAGAUAC------------AGAUGCUGAUGCGAAGAUACAUCCACAUUUGUAUCUGCAUUUGUGUCGGUGCUGUUCUG-----CUCUGUUUUGUGCU
(((((..(((((..((((.((------------((.((((((((((((((((((........)))))))....)))))))))))))))))))-----.))))).))))).. ( -35.50)
>consensus
CACAGUUACAGAUACAGAUAC____________UGAUGCUGAUGCGAAGAUACAUCCACAUUUGUAUCUGCAUUUGUGUCGGUGCUGUUCUG_____UUCUGUUUUGUGCU
(((((..(((((.........................(((((((((((((((((........)))))))....))))))))))(((((.....)))))))))).))))).. (-21.39 = -23.70 +   2.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:35:35 2006