Locus 4260

Sequence ID 2L_DroMel_CAF1
Location 12,176,305 – 12,176,435
Length 130
Max. P 0.835163
window6724 window6725

overview

Window 4

Location 12,176,305 – 12,176,419
Length 114
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 71.86
Mean single sequence MFE -24.88
Consensus MFE -3.58
Energy contribution -4.66
Covariance contribution 1.08
Combinations/Pair 1.14
Mean z-score -1.83
Structure conservation index 0.14
SVM decision value 0.73
SVM RNA-class probability 0.835163
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12176305 114 - 22407834
CAAAAUUAAAGUGGUAAACAAAUUAGCAAGCCACUGUGAACUAAUUUUAGAUAGAGCCUGUGACUCAUUUAGAAGUAAACAAUGUUGUGUAUCUA---ACAAUUUUUACAGCGUUAU
.........((((((..............))))))((..(((...(((((((.(((.......)))))))))))))..))(((((((((......---........))))))))).. ( -19.68)
>DroSec_CAF1 2954 105 - 1
GAAAAUUAAAGUGCUAAGCUAAUUAGCAAGCCAGUUUAAGCUGAUUUUAGAUCGAGUCUGUGACUCAU-UAGAAGUAAACAAUGUUGUUUAUCUC---ACAA------CAGCGUA--
..(((((....((((((.....))))))....)))))..((((..........(((((...)))))..-..((..((((((....))))))..))---....------))))...-- ( -25.10)
>DroSim_CAF1 3073 113 - 1
GAAAAUUUCAGUGCUAAGCAAAUUAGCAAGCCAGUUUGAACUAAUUUUAGAUAGAGCAUGUGACUCAU-UGGAAGUAAACAAUGUUGUUUAUCUC---ACAAUUUUUACAGCGUUAU
...........((((((.....)))))).(((.(((((((.....))))))).).)).(((((...((-((((..((((((....))))))..))---.))))..)))))....... ( -22.00)
>DroEre_CAF1 3160 100 - 1
GUAC----------------AAUUAGGAAGCCCUGGUGAAUUAAUUUUAGAGUGAGUCUGUGACUCAU-UCAAAGAAAACAAAGUGGAGUAUUUUUCCGCGCUUUUUACAGGGGCAU
....----------------.........(((((.(((((....((((.(((((((((...)))))))-)).)))).......((((((.....))))))....))))).))))).. ( -33.80)
>DroYak_CAF1 3300 116 - 1
GUAUAUUAAAUUGCUAAACAAAUUAGUAAGCCAGUGUGAACUAAUUUUAGAAUGAGUCUGUGACUCAU-UAAAAGUAAACAAAGUUGUAGAUUUUUCCGCACUUUUAUCAGUGGUAA
..........(((((((.....)))))))((((.((.......(((((..((((((((...)))))))-).)))))....(((((.(..((....))..))))))...)).)))).. ( -23.80)
>consensus
GAAAAUUAAAGUGCUAAACAAAUUAGCAAGCCAGUGUGAACUAAUUUUAGAUAGAGUCUGUGACUCAU_UAGAAGUAAACAAUGUUGUGUAUCUC___ACAAUUUUUACAGCGUUAU
...................(((((((...((....))...)))))))......(((((...)))))................................................... ( -3.58 =  -4.66 +   1.08)

alignment

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secondary structure

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dotplot

Postscript

Window 5

Location 12,176,341 – 12,176,435
Length 94
Sequences 5
Columns 94
Reading direction reverse
Mean pairwise identity 73.88
Mean single sequence MFE -15.69
Consensus MFE -3.58
Energy contribution -4.66
Covariance contribution 1.08
Combinations/Pair 1.14
Mean z-score -1.61
Structure conservation index 0.23
SVM decision value 0.07
SVM RNA-class probability 0.571102
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12176341 94 - 22407834
AGAAAAUAAAAUUCAUCAAAAUUAAAGUGGUAAACAAAUUAGCAAGCCACUGUGAACUAAUUUUAGAUAGAGCCUGUGACUCAUUUAGAAGUAA
...........(((((.........((((((..............)))))))))))....((((((((.(((.......))))))))))).... ( -12.84)
>DroSec_CAF1 2982 93 - 1
AGAAAAUAAACUUAAUGAAAAUUAAAGUGCUAAGCUAAUUAGCAAGCCAGUUUAAGCUGAUUUUAGAUCGAGUCUGUGACUCAU-UAGAAGUAA
...........(((((....)))))..((((((.....))))))...((((....))))(((((.(((.(((((...)))))))-).))))).. ( -18.00)
>DroSim_CAF1 3109 93 - 1
AGAAAAUAAACUUAAUGAAAAUUUCAGUGCUAAGCAAAUUAGCAAGCCAGUUUGAACUAAUUUUAGAUAGAGCAUGUGACUCAU-UGGAAGUAA
.........(((((((((.........((((((.....)))))).(((.(((((((.....))))))).).)).......))))-))..))).. ( -14.90)
>DroEre_CAF1 3199 71 - 1
A------AAUUUAAGUGUAC----------------AAUUAGGAAGCCCUGGUGAAUUAAUUUUAGAGUGAGUCUGUGACUCAU-UCAAAGAAA
.------.............----------------.((((((....)))))).......((((.(((((((((...)))))))-)).)))).. ( -16.90)
>DroYak_CAF1 3339 93 - 1
AGAAAACAAAUUCAAUGUAUAUUAAAUUGCUAAACAAAUUAGUAAGCCAGUGUGAACUAAUUUUAGAAUGAGUCUGUGACUCAU-UAAAAGUAA
.(((......)))....((((((...(((((((.....)))))))...)))))).....(((((..((((((((...)))))))-).))))).. ( -15.80)
>consensus
AGAAAAUAAACUUAAUGAAAAUUAAAGUGCUAAACAAAUUAGCAAGCCAGUGUGAACUAAUUUUAGAUAGAGUCUGUGACUCAU_UAGAAGUAA
...................................(((((((...((....))...)))))))......(((((...)))))............ ( -3.58 =  -4.66 +   1.08)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:13:40 2006