Locus 970

Sequence ID 3L_DroMel_CAF1
Location 2,886,663 – 2,886,801
Length 138
Max. P 0.956233
window1490 window1491 window1492

overview

Window 0

Location 2,886,663 – 2,886,761
Length 98
Sequences 5
Columns 104
Reading direction reverse
Mean pairwise identity 93.58
Mean single sequence MFE -22.84
Consensus MFE -22.70
Energy contribution -22.74
Covariance contribution 0.04
Combinations/Pair 1.05
Mean z-score -0.99
Structure conservation index 0.99
SVM decision value 0.03
SVM RNA-class probability 0.547076
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2886663 98 - 23771897
CCGCACCUUGAGUGCAAAUAUGGCCAGAUACAAGAUACUCAUGUCACUUCUCCAUGCAACUCACACAGAUACUCGCAGUCACCUGCGGCCGUGUGCUA------
..((((.....))))..((((((((........((((....)))).............................((((....))))))))))))....------ ( -24.40)
>DroSec_CAF1 131180 98 - 1
CCGCACCUUGAGUGCAAAUAUGGCCAGAUACAAGAUACUCAUGUCACUUCUCCAUGCAACUCACACAGAUACUUGCAGUCACCUGCGGCCGUGUCCUA------
..((((.....))))..((((((((........((((....)))).............................((((....))))))))))))....------ ( -23.50)
>DroSim_CAF1 121787 98 - 1
CCGCACCUUGAGUGCAAAUAUGGCCAGAUACAAGAUACUCAUGUCACUUCUCCAUGCAACUCACACAGAUACUCGCAGUCACCUGCGGCCGUGUGCUA------
..((((.....))))..((((((((........((((....)))).............................((((....))))))))))))....------ ( -24.40)
>DroEre_CAF1 138202 97 - 1
CCGCACCUUGAGUGCAAAUAUUGCCAGAUACAAGAUACUCAUGUCACUUCUCCAUGCAACUCACACAGAUACUCGCAGUCACCUGCGGCCGUGU-----UGU--
..((((.....)))).(((((.(((........((((....)))).............................((((....))))))).))))-----)..-- ( -19.50)
>DroYak_CAF1 139100 104 - 1
CCGCACCUUGAGUGCAAAUAUGGCCAGAUACAAGAUACUCAUGUCACUUCACCAUGCAACUCACACAGAUACUCGUAGUCACCUGCGGCCGUGUGCUACUGUGU
..((((.....))))..((((((((........((((....)))).............................((((....)))))))))))).......... ( -22.40)
>consensus
CCGCACCUUGAGUGCAAAUAUGGCCAGAUACAAGAUACUCAUGUCACUUCUCCAUGCAACUCACACAGAUACUCGCAGUCACCUGCGGCCGUGUGCUA______
..((((.....))))..((((((((........((((....)))).............................((((....)))))))))))).......... (-22.70 = -22.74 +   0.04) 

alignment

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secondary structure

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dotplot

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Window 1

Location 2,886,697 – 2,886,801
Length 104
Sequences 5
Columns 104
Reading direction forward
Mean pairwise identity 93.03
Mean single sequence MFE -32.58
Consensus MFE -26.80
Energy contribution -26.80
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.76
Structure conservation index 0.82
SVM decision value 1.04
SVM RNA-class probability 0.905810
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2886697 104 + 23771897
GUGAGUUGCAUGGAGAAGUGACAUGAGUAUCUUGUAUCUGGCCAUAUUUGCACUCAAGGUGCGGCACCACGGAUGCAGAUACAAGAGUAUACUGGAUGCUUCCU
....((..(........)..))...(((((((((((((((.((......((((.....))))(....)..))...)))))))))))...))))(((....))). ( -31.00)
>DroSec_CAF1 131214 104 + 1
GUGAGUUGCAUGGAGAAGUGACAUGAGUAUCUUGUAUCUGGCCAUAUUUGCACUCAAGGUGCGGCACCACGGAUGCAGAUACAGGAGGAUACUGGAUGCUUCCU
....((..(........)..))..((((((((.((((((..((.((((((((..(..((((...))))..)..))))))))..)).)))))).))))))))... ( -36.50)
>DroSim_CAF1 121821 104 + 1
GUGAGUUGCAUGGAGAAGUGACAUGAGUAUCUUGUAUCUGGCCAUAUUUGCACUCAAGGUGCGGCACCACGGAUGCAGAUACAAGAGGAAACUGGAUGCUUCCU
....((..(........)..))..((((((((((((((((.((......((((.....))))(....)..))...))))))))).((....)).)))))))... ( -31.80)
>DroEre_CAF1 138235 94 + 1
GUGAGUUGCAUGGAGAAGUGACAUGAGUAUCUUGUAUCUGGCAAUAUUUGCACUCAAGGUGCGGCACCACGGAUGCAGAUACAG----------GAUGCUUCCU
....((..(........)..))..((((((((((((((((.((......((((.....))))(....).....)))))))))))----------)))))))... ( -32.70)
>DroYak_CAF1 139140 97 + 1
GUGAGUUGCAUGGUGAAGUGACAUGAGUAUCUUGUAUCUGGCCAUAUUUGCACUCAAGGUGCGGCACCACGGAUGCAGAUACAGGAG-------GAUGCUUCCU
....((..(........)..))....((((((.((((((((((......((((.....)))))))....)))))))))))))(((((-------(...)))))) ( -30.90)
>consensus
GUGAGUUGCAUGGAGAAGUGACAUGAGUAUCUUGUAUCUGGCCAUAUUUGCACUCAAGGUGCGGCACCACGGAUGCAGAUACAGGAG_A_ACUGGAUGCUUCCU
(..(((..((((.........)))).((((((.(((((((.......((((((.....)))))).....)))))))))))))...............)))..). (-26.80 = -26.80 +   0.00) 

alignment

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secondary structure

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dotplot

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Window 2

Location 2,886,697 – 2,886,801
Length 104
Sequences 5
Columns 104
Reading direction reverse
Mean pairwise identity 93.03
Mean single sequence MFE -26.02
Consensus MFE -22.20
Energy contribution -22.40
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.76
Structure conservation index 0.85
SVM decision value 1.46
SVM RNA-class probability 0.956233
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2886697 104 - 23771897
AGGAAGCAUCCAGUAUACUCUUGUAUCUGCAUCCGUGGUGCCGCACCUUGAGUGCAAAUAUGGCCAGAUACAAGAUACUCAUGUCACUUCUCCAUGCAACUCAC
.((((((((..((((...(((((((((((...(((((.....((((.....))))...))))).))))))))))))))).)))...)))))............. ( -28.10)
>DroSec_CAF1 131214 104 - 1
AGGAAGCAUCCAGUAUCCUCCUGUAUCUGCAUCCGUGGUGCCGCACCUUGAGUGCAAAUAUGGCCAGAUACAAGAUACUCAUGUCACUUCUCCAUGCAACUCAC
.((((((((..((((((....((((((((...(((((.....((((.....))))...))))).)))))))).)))))).)))...)))))............. ( -26.40)
>DroSim_CAF1 121821 104 - 1
AGGAAGCAUCCAGUUUCCUCUUGUAUCUGCAUCCGUGGUGCCGCACCUUGAGUGCAAAUAUGGCCAGAUACAAGAUACUCAUGUCACUUCUCCAUGCAACUCAC
.((((((.....))))))(((((((((((...(((((.....((((.....))))...))))).)))))))))))....((((.........))))........ ( -30.90)
>DroEre_CAF1 138235 94 - 1
AGGAAGCAUC----------CUGUAUCUGCAUCCGUGGUGCCGCACCUUGAGUGCAAAUAUUGCCAGAUACAAGAUACUCAUGUCACUUCUCCAUGCAACUCAC
.....((((.----------.(((((((((((.....)))).((((.....))))..........))))))).((((....))))........))))....... ( -21.40)
>DroYak_CAF1 139140 97 - 1
AGGAAGCAUC-------CUCCUGUAUCUGCAUCCGUGGUGCCGCACCUUGAGUGCAAAUAUGGCCAGAUACAAGAUACUCAUGUCACUUCACCAUGCAACUCAC
.....((((.-------....((((((((...(((((.....((((.....))))...))))).)))))))).((((....))))........))))....... ( -23.30)
>consensus
AGGAAGCAUCCAGU_U_CUCCUGUAUCUGCAUCCGUGGUGCCGCACCUUGAGUGCAAAUAUGGCCAGAUACAAGAUACUCAUGUCACUUCUCCAUGCAACUCAC
.....((((............((((((((...(((((.....((((.....))))...))))).)))))))).((((....))))........))))....... (-22.20 = -22.40 +   0.20) 

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:55:40 2006