Locus 4893

Sequence ID 2L_DroMel_CAF1
Location 13,973,786 – 13,973,941
Length 155
Max. P 0.992449
window7756 window7757 window7758 window7759

overview

Window 6

Location 13,973,786 – 13,973,901
Length 115
Sequences 3
Columns 115
Reading direction forward
Mean pairwise identity 84.05
Mean single sequence MFE -27.80
Consensus MFE -21.40
Energy contribution -21.40
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.66
Structure conservation index 0.77
SVM decision value 1.35
SVM RNA-class probability 0.944672
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13973786 115 + 22407834
UUAUCUAUUGGAUUGAUUAACCACACAGAAACUCUGUAUGGGAAUAGAUACAUAUAUGACAAGUACUGAAAAAGGAAACGCUGAUACGACUGGUUGGUAUCAGCGUUUUCUUUUC
.((((((((...........(((.((((.....)))).))).))))))))...................((((((((((((((((((.(.....).)))))))))))))))))). ( -35.80)
>DroSec_CAF1 61170 96 + 1
-----------AAUGAUUUAGCACUCAGAAACUCUGUAUGGGAAUAGGU----AUAUGAC----ACUGAAAAAGGAAACGCUGAUACGACUGGAUGGUAUCAGCAUUUUCUUUUC
-----------.....(((((...(((...((.((((......))))))----...))).----.)))))((((((((.((((((((.(.....).)))))))).)))))))).. ( -23.80)
>DroSim_CAF1 64947 96 + 1
-----------AAUGAUUUAGCACUCAGAAACUCUGUAUGGGAAUAGGU----AUAUGAC----ACUGAAAAAGGAAACGCUGAUACGACUGGAUGGUAUCAGCAUUUUCUUUUC
-----------.....(((((...(((...((.((((......))))))----...))).----.)))))((((((((.((((((((.(.....).)))))))).)))))))).. ( -23.80)
>consensus
___________AAUGAUUUAGCACUCAGAAACUCUGUAUGGGAAUAGGU____AUAUGAC____ACUGAAAAAGGAAACGCUGAUACGACUGGAUGGUAUCAGCAUUUUCUUUUC
.....................((..(((.....)))..)).............................(((((((((.((((((((.(.....).)))))))).))))))))). (-21.40 = -21.40 +   0.00)

alignment

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secondary structure

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dotplot

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Window 7

Location 13,973,786 – 13,973,901
Length 115
Sequences 3
Columns 115
Reading direction reverse
Mean pairwise identity 84.05
Mean single sequence MFE -26.43
Consensus MFE -23.22
Energy contribution -23.00
Covariance contribution -0.22
Combinations/Pair 1.04
Mean z-score -3.40
Structure conservation index 0.88
SVM decision value 2.33
SVM RNA-class probability 0.992449
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13973786 115 - 22407834
GAAAAGAAAACGCUGAUACCAACCAGUCGUAUCAGCGUUUCCUUUUUCAGUACUUGUCAUAUAUGUAUCUAUUCCCAUACAGAGUUUCUGUGUGGUUAAUCAAUCCAAUAGAUAA
((((((.((((((((((((.........)))))))))))).))))))..................((((((((.((((((((.....))))))))...........)))))))). ( -35.10)
>DroSec_CAF1 61170 96 - 1
GAAAAGAAAAUGCUGAUACCAUCCAGUCGUAUCAGCGUUUCCUUUUUCAGU----GUCAUAU----ACCUAUUCCCAUACAGAGUUUCUGAGUGCUAAAUCAUU-----------
((((((.((((((((((((.........)))))))))))).))))))....----.......----.........(((.(((.....))).)))..........----------- ( -22.10)
>DroSim_CAF1 64947 96 - 1
GAAAAGAAAAUGCUGAUACCAUCCAGUCGUAUCAGCGUUUCCUUUUUCAGU----GUCAUAU----ACCUAUUCCCAUACAGAGUUUCUGAGUGCUAAAUCAUU-----------
((((((.((((((((((((.........)))))))))))).))))))....----.......----.........(((.(((.....))).)))..........----------- ( -22.10)
>consensus
GAAAAGAAAAUGCUGAUACCAUCCAGUCGUAUCAGCGUUUCCUUUUUCAGU____GUCAUAU____ACCUAUUCCCAUACAGAGUUUCUGAGUGCUAAAUCAUU___________
((((((.((((((((((((.........)))))))))))).))))))............................(((.(((.....))).)))..................... (-23.22 = -23.00 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 8

Location 13,973,826 – 13,973,941
Length 115
Sequences 3
Columns 115
Reading direction forward
Mean pairwise identity 91.10
Mean single sequence MFE -37.13
Consensus MFE -28.70
Energy contribution -29.03
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -5.46
Structure conservation index 0.77
SVM decision value 0.62
SVM RNA-class probability 0.803290
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13973826 115 + 22407834
GGAAUAGAUACAUAUAUGACAAGUACUGAAAAAGGAAACGCUGAUACGACUGGUUGGUAUCAGCGUUUUCUUUUCCAGUACUCGUAAAGUAUUCGUAUAAAUCUUCUUAACUAUU
((((.(.((((..((((.((.(((((((.((((((((((((((((((.(.....).)))))))))))))))))).))))))).))...))))..))))...).))))........ ( -42.60)
>DroSec_CAF1 61199 107 + 1
GGAAUAGGU----AUAUGAC----ACUGAAAAAGGAAACGCUGAUACGACUGGAUGGUAUCAGCAUUUUCUUUUCCAGUAGUCGUAAAGUAUUCGUAAAAAUCUUCUUAACCAUA
.(((((..(----.((((((----((((.(((((((((.((((((((.(.....).)))))))).))))))))).)))).)))))))..)))))..................... ( -34.40)
>DroSim_CAF1 64976 107 + 1
GGAAUAGGU----AUAUGAC----ACUGAAAAAGGAAACGCUGAUACGACUGGAUGGUAUCAGCAUUUUCUUUUCCAGUAGUCGUAAAGUAUUCGUAAAAAUCUUCUUAACCAUA
.(((((..(----.((((((----((((.(((((((((.((((((((.(.....).)))))))).))))))))).)))).)))))))..)))))..................... ( -34.40)
>consensus
GGAAUAGGU____AUAUGAC____ACUGAAAAAGGAAACGCUGAUACGACUGGAUGGUAUCAGCAUUUUCUUUUCCAGUAGUCGUAAAGUAUUCGUAAAAAUCUUCUUAACCAUA
.(((((..(.....((((((....((((.(((((((((.((((((((.(.....).)))))))).))))))))).)))).)))))))..)))))..................... (-28.70 = -29.03 +   0.33)

alignment

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secondary structure

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dotplot

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Window 9

Location 13,973,826 – 13,973,941
Length 115
Sequences 3
Columns 115
Reading direction reverse
Mean pairwise identity 91.10
Mean single sequence MFE -37.03
Consensus MFE -31.21
Energy contribution -31.10
Covariance contribution -0.11
Combinations/Pair 1.05
Mean z-score -6.19
Structure conservation index 0.84
SVM decision value 0.70
SVM RNA-class probability 0.827889
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13973826 115 - 22407834
AAUAGUUAAGAAGAUUUAUACGAAUACUUUACGAGUACUGGAAAAGAAAACGCUGAUACCAACCAGUCGUAUCAGCGUUUCCUUUUUCAGUACUUGUCAUAUAUGUAUCUAUUCC
............(((..(((((.(((....((((((((((((((((.((((((((((((.........)))))))))))).))))))))))))))))..))).)))))..))).. ( -41.90)
>DroSec_CAF1 61199 107 - 1
UAUGGUUAAGAAGAUUUUUACGAAUACUUUACGACUACUGGAAAAGAAAAUGCUGAUACCAUCCAGUCGUAUCAGCGUUUCCUUUUUCAGU----GUCAUAU----ACCUAUUCC
...(((...((((((((....)))).))))..(((.((((((((((.((((((((((((.........)))))))))))).))))))))))----)))....----)))...... ( -34.60)
>DroSim_CAF1 64976 107 - 1
UAUGGUUAAGAAGAUUUUUACGAAUACUUUACGACUACUGGAAAAGAAAAUGCUGAUACCAUCCAGUCGUAUCAGCGUUUCCUUUUUCAGU----GUCAUAU----ACCUAUUCC
...(((...((((((((....)))).))))..(((.((((((((((.((((((((((((.........)))))))))))).))))))))))----)))....----)))...... ( -34.60)
>consensus
UAUGGUUAAGAAGAUUUUUACGAAUACUUUACGACUACUGGAAAAGAAAAUGCUGAUACCAUCCAGUCGUAUCAGCGUUUCCUUUUUCAGU____GUCAUAU____ACCUAUUCC
.((((....((((((((....)))).))))..(((.((((((((((.((((((((((((.........)))))))))))).))))))))))....)))..........))))... (-31.21 = -31.10 +  -0.11)

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 11:30:19 2006