Locus 1139

Sequence ID 2L_DroMel_CAF1
Location 3,106,685 – 3,106,782
Length 97
Max. P 0.771305
window1851 window1852

overview

Window 1

Location 3,106,685 – 3,106,782
Length 97
Sequences 5
Columns 97
Reading direction forward
Mean pairwise identity 91.23
Mean single sequence MFE -24.86
Consensus MFE -18.48
Energy contribution -18.72
Covariance contribution 0.24
Combinations/Pair 1.04
Mean z-score -2.05
Structure conservation index 0.74
SVM decision value 0.53
SVM RNA-class probability 0.771305
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3106685 97 + 22407834
GACAUUACGGAUAUAGAACAUUAGUGAGAUUCCUCUGUGUGUGCAAACAGUUGGUUACGCCUACUGACCAUUUUUCCCACUGAUGAUUUCCGUAAUA
...((((((((....((.((((((((.((.....((((........)))).((((((.......))))))....)).)))))))).)))))))))). ( -26.80)
>DroSec_CAF1 31847 93 + 1
GGCACUACGGAUAUAGAACAUUAGUGAGAUUCCUCUGUG--UGGAAACUGUUUGUUACGCCUACUGACCAUUC--UCCACUAAUGAUUUCCGUAAUA
.....((((((....((.(((((((((((....((.(((--.((.(((.....)))...))))).))....))--).)))))))).))))))))... ( -23.50)
>DroSim_CAF1 32070 88 + 1
-----UACGGAUAUAGAACAUUAGUGAGAUUCCUCUGUG--UGGAAACUGUUUGUUACGCCUACUGACCAUUU--CCCACUGAUGAUUUCCGUAAUA
-----((((((....((.(((((((((((....)))...--.(((((..(((.((.......)).)))..)))--)))))))))).))))))))... ( -22.00)
>DroEre_CAF1 32310 93 + 1
GACACUACGGAUAUAGAACAUUAGUGAGAUUCCUCUGUG--UGGAAACGGUUGGUUACGCCUACUGACCAUUU--CCCACUGAUGAUUUCCGUAAUA
.....((((((....((.(((((((((((....)))...--.(((((.(((..((.......))..))).)))--)))))))))).))))))))... ( -29.40)
>DroYak_CAF1 32823 93 + 1
GGCACUACGGAUAUAGAACAUUAGUGAGAUUCCUCUGUG--GGGAAACAGUUCGUUACGCCUACUGACCAUUU--CCCACCGAUGAUUUCCGUAAUA
.....((((((....((.((((...(((....))).(((--(((((.((((..(.....)..))))....)))--))))).)))).))))))))... ( -22.60)
>consensus
GACACUACGGAUAUAGAACAUUAGUGAGAUUCCUCUGUG__UGGAAACAGUUGGUUACGCCUACUGACCAUUU__CCCACUGAUGAUUUCCGUAAUA
.....((((((....((.((((((((...((((.........))))...((..((.......))..)).........)))))))).))))))))... (-18.48 = -18.72 +   0.24) 

alignment

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secondary structure

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dotplot

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Window 2

Location 3,106,685 – 3,106,782
Length 97
Sequences 5
Columns 97
Reading direction reverse
Mean pairwise identity 91.23
Mean single sequence MFE -25.72
Consensus MFE -17.76
Energy contribution -18.48
Covariance contribution 0.72
Combinations/Pair 1.08
Mean z-score -2.25
Structure conservation index 0.69
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3106685 97 - 22407834
UAUUACGGAAAUCAUCAGUGGGAAAAAUGGUCAGUAGGCGUAACCAACUGUUUGCACACACAGAGGAAUCUCACUAAUGUUCUAUAUCCGUAAUGUC
(((((((((...(((.(((((((....((((..(....)...)))).((((........)))).....))))))).))).......))))))))).. ( -25.50)
>DroSec_CAF1 31847 93 - 1
UAUUACGGAAAUCAUUAGUGGA--GAAUGGUCAGUAGGCGUAACAAACAGUUUCCA--CACAGAGGAAUCUCACUAAUGUUCUAUAUCCGUAGUGCC
(((((((((...((((((((.(--((...(((....)))............((((.--......))))))))))))))).......))))))))).. ( -25.10)
>DroSim_CAF1 32070 88 - 1
UAUUACGGAAAUCAUCAGUGGG--AAAUGGUCAGUAGGCGUAACAAACAGUUUCCA--CACAGAGGAAUCUCACUAAUGUUCUAUAUCCGUA-----
...((((((...(((.((((((--(....(((....)))............((((.--......))))))))))).))).......))))))----- ( -20.80)
>DroEre_CAF1 32310 93 - 1
UAUUACGGAAAUCAUCAGUGGG--AAAUGGUCAGUAGGCGUAACCAACCGUUUCCA--CACAGAGGAAUCUCACUAAUGUUCUAUAUCCGUAGUGUC
(((((((((........(((((--(((((((..((.......))..))))))))).--))).(((....)))..............))))))))).. ( -29.50)
>DroYak_CAF1 32823 93 - 1
UAUUACGGAAAUCAUCGGUGGG--AAAUGGUCAGUAGGCGUAACGAACUGUUUCCC--CACAGAGGAAUCUCACUAAUGUUCUAUAUCCGUAGUGCC
(((((((((...(((..(((((--(((((((..((.......))..))))))))))--....(((....)))))..))).......))))))))).. ( -27.70)
>consensus
UAUUACGGAAAUCAUCAGUGGG__AAAUGGUCAGUAGGCGUAACAAACAGUUUCCA__CACAGAGGAAUCUCACUAAUGUUCUAUAUCCGUAGUGCC
(((((((((...(((.((((((.......(((....)))............((((.........)))).)))))).))).......))))))))).. (-17.76 = -18.48 +   0.72) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript


Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:54:39 2006