Locus 1799

Sequence ID X_DroMel_CAF1
Location 4,978,891 – 4,979,031
Length 140
Max. P 0.754188
window2935 window2936

overview

Window 5

Location 4,978,891 – 4,979,009
Length 118
Sequences 4
Columns 119
Reading direction forward
Mean pairwise identity 83.43
Mean single sequence MFE -24.15
Consensus MFE -14.95
Energy contribution -15.20
Covariance contribution 0.25
Combinations/Pair 1.14
Mean z-score -1.96
Structure conservation index 0.62
SVM decision value 0.27
SVM RNA-class probability 0.663501
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4978891 118 + 22224390
UUUUUGUUUGCCGUUGAAGAAAAGAAAACUUAAGAAAAGCAAAAUGUUCAGAAAGUUGUUGCAUUGUGUCAGAGUU-UGGACAAUGGUGCACGAUGGCGGUGGAAAAAUUGAACCAAAA
(((((..(((((((((..........(((((......(((.....)))....)))))..(((((..((((......-..))).)..))))))))))))))..)))))............ ( -24.80)
>DroSec_CAF1 44421 107 + 1
------UUUGCCGUGGAAGAUAGGAAAACUUAAGAAAAGCAAAAUGUUCAGAAAGUUGUUGCAUUGUGUCAGAGUU-UGAACAAUGGUGCACGAUGGCGGUGGAAAAAUUGAA-----A
------((..((((.(..(.((((....))))......(((...((((((((...(((.(((...))).)))..))-))))))....))).)..).))))..)).........-----. ( -22.80)
>DroEre_CAF1 49906 105 + 1
------UACCCCGGAGAAAAAAAGAAAACUUAGGAAAAGCAAAAUGUUCAGAAAGUUGUUGCAUUGUGUCAGAGUU-UGGACAAUGG--CACGAUGGCGGGGGAAAAAUUGAA-----A
------..(((((.............(((((..(((.(......).)))...)))))....((((((((((..((.-...))..)))--))))))).)))))...........-----. ( -27.10)
>DroYak_CAF1 46618 104 + 1
------UU--CCGGCAUAGAAAAGAAAACUUAAGAAAAGCUAAAUUUUCGGAAAGUUGUUGCAUUGUGUCAGAGUUUUGGACAAUGG--CAUGUUGGCGGUGGAAAAAUUGAU-----U
------((--(((.(...........(((((..(((((......)))))...)))))...((..(((((((..(((...)))..)))--))))...))).)))))........-----. ( -21.90)
>consensus
______UUUGCCGGAGAAGAAAAGAAAACUUAAGAAAAGCAAAAUGUUCAGAAAGUUGUUGCAUUGUGUCAGAGUU_UGGACAAUGG__CACGAUGGCGGUGGAAAAAUUGAA_____A
......(((((((.............(((((..(((.(......).)))...)))))....((((((((((..(((...)))..)))..))))))).)))))))............... (-14.95 = -15.20 +   0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 4,978,931 – 4,979,031
Length 100
Sequences 3
Columns 100
Reading direction forward
Mean pairwise identity 84.75
Mean single sequence MFE -16.97
Consensus MFE -12.47
Energy contribution -12.47
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.16
Structure conservation index 0.73
SVM decision value 0.48
SVM RNA-class probability 0.754188
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4978931 100 + 22224390
AAAAUGUUCAGAAAGUUGUUGCAUUGUGUCAGAGUUUGGACAAUGGUGCACGAUGGCGGUGGAAAAAUUGAACCAAAAAAAAAAAAAAGAAAAGGAAGAG
.....((((((....(..(((((((((((((..((....))..))..))))))).))))..).....))))))........................... ( -17.60)
>DroSec_CAF1 44455 95 + 1
AAAAUGUUCAGAAAGUUGUUGCAUUGUGUCAGAGUUUGAACAAUGGUGCACGAUGGCGGUGGAAAAAUUGAA-----AAAAAAAACAAAAAUACGUAGAG
......(((((....(..((((((((((.((..(((.....)))..)))))))).))))..).....)))))-----....................... ( -15.00)
>DroEre_CAF1 49940 84 + 1
AAAAUGUUCAGAAAGUUGUUGCAUUGUGUCAGAGUUUGGACAAUGG--CACGAUGGCGGGGGAAAAAUUGAA-----AAAAAAACC---------AAGAG
......(((((....((.(((((((((((((..((....))..)))--)))))).)))).)).....)))))-----.........---------..... ( -18.30)
>consensus
AAAAUGUUCAGAAAGUUGUUGCAUUGUGUCAGAGUUUGGACAAUGGUGCACGAUGGCGGUGGAAAAAUUGAA_____AAAAAAAACAA_AA_A_GAAGAG
......(((((....(..(((((((((((((..((....))..)))..)))))).))))..).....)))))............................ (-12.47 = -12.47 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:19:07 2006