Locus 6430

Sequence ID 3R_DroMel_CAF1
Location 16,848,717 – 16,848,857
Length 140
Max. P 0.867159
window10476 window10477 window10478

overview

Window 6

Location 16,848,717 – 16,848,817
Length 100
Sequences 3
Columns 106
Reading direction forward
Mean pairwise identity 79.48
Mean single sequence MFE -21.94
Consensus MFE -12.11
Energy contribution -12.67
Covariance contribution 0.56
Combinations/Pair 1.08
Mean z-score -2.26
Structure conservation index 0.55
SVM decision value 0.08
SVM RNA-class probability 0.573988
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16848717 100 + 27905053
AUUCUUUUUCGUUUCUG------AUUCUAAUUCUAAUUCUGAUUCAGAAUGUAGAGCUCGUAACUGAGAAUUGAGAAUUAAGAACUGAGUACUGAGUACUGAGAAC
.....((((((((..((------(((((..(((((((((((...)))))).)))))((((....)))).....)))))))..)))..(((((...)))))))))). ( -23.40)
>DroSec_CAF1 1607 93 + 1
AUUCUUUUUCCUUUCUGAUUCUGAUUCUAAUUCUAAUUCUGAUUCAGAAUGUAGAGCUCAUAACUGAGAAUUGACAGUUAAGAACUGAGUACU-------------
.............(((((((((((.((.............)).))))))).))))(((((((((((........)))))).....)))))...------------- ( -19.62)
>DroEre_CAF1 1883 93 + 1
AUUCUUUUUCUUUUCUGAU------UCUGAUUCUAAUUCUGAUUCAGAAUUGAGAGCUCAUAACUGAGAUUUGAGAAUUAAGAACUUAGAACUGAG-------AAC
.....(((((..(((((((------((((((((((((((((...))))))).(((.((((....)))).))).)))))).)))).))))))..)))-------)). ( -22.80)
>consensus
AUUCUUUUUCCUUUCUGAU____AUUCUAAUUCUAAUUCUGAUUCAGAAUGUAGAGCUCAUAACUGAGAAUUGAGAAUUAAGAACUGAGUACUGAG_______AAC
.(((((....(((((...............(((((((((((...)))))).)))))((((....))))....)))))..)))))...................... (-12.11 = -12.67 +   0.56)

alignment

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secondary structure

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dotplot

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Window 7

Location 16,848,738 – 16,848,857
Length 119
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 79.21
Mean single sequence MFE -26.62
Consensus MFE -14.42
Energy contribution -15.30
Covariance contribution 0.88
Combinations/Pair 1.19
Mean z-score -2.17
Structure conservation index 0.54
SVM decision value 0.85
SVM RNA-class probability 0.867159
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16848738 119 + 27905053
UAAUUCUAAUUCUGAUUCAGAAUGUAGAGCUCGUAACUGAGAAUUGAGAAUUAAGAACUGAGUACUGAGUACUGAGAACUGAGAACUGAGAACUUAACACUGAGUACUGAGAGCUGAGU
(((((((.((((((...)))))).(((..((((....))))..))))))))))...(((.(((.((.((((((.((...((((.........))))...)).)))))).)).))).))) ( -29.70)
>DroSec_CAF1 1634 105 + 1
UAAUUCUAAUUCUGAUUCAGAAUGUAGAGCUCAUAACUGAGAAUUGACAGUUAAGAACUGAGUACU--------------GAGAACUGAGAACUUAGCACUGAGUACUGAGAGCUGAGU
....((((((((((...)))))).))))((((.((((((........))))))((..((.((((((--------------.((..((((....))))..)).)))))).))..)))))) ( -31.10)
>DroSim_CAF1 1612 91 + 1
UAAUUCUAAUUCUGAUUCAGAAUGUAGAGCUCAUAACUGAGAAUUGAGCGUUAAGAA----------------------------CUGAGAACUUAGCACUGAGUACUGAGAGCUGAGU
....((((((((((...)))))).))))(((((...((.((.(((.((.((((((..----------------------------.......)))))).)).))).)).))...))))) ( -23.00)
>DroEre_CAF1 1904 112 + 1
UGAUUCUAAUUCUGAUUCAGAAUUGAGAGCUCAUAACUGAGAUUUGAGAAUUAAGAACUUAGAACUGAG-------AACUGGGAACUGAGAACUGAGCACUGAGCACUGAGCGCUGGGU
...((((((((((.((((((...(((....)))...)))))...).)))))).))))(((((..((.(.-------...).))..))))).(((.(((.((.(....).)).))).))) ( -25.30)
>DroYak_CAF1 1645 96 + 1
CGAUUCUAAUUCUGAUUCAGAAUCGAGAGCUCAUAACUGAGAAUUGAGAAUUAAGAACUU--------------------GAGAAUUGAGAACUGAGUACUGAGUACUGAGAGCUG---
(((((((..(((((((((....((((...((((....))))..))))))))).))))...--------------------.)))))))((..((.(((((...))))).))..)).--- ( -24.00)
>consensus
UAAUUCUAAUUCUGAUUCAGAAUGUAGAGCUCAUAACUGAGAAUUGAGAAUUAAGAACUGAG_ACU______________GAGAACUGAGAACUUAGCACUGAGUACUGAGAGCUGAGU
(((((((.((((((...))))))......((((....)))).....)))))))......................................(((((((.((.(....).)).))))))) (-14.42 = -15.30 +   0.88)

alignment

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secondary structure

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dotplot

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Window 8

Location 16,848,738 – 16,848,857
Length 119
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 79.21
Mean single sequence MFE -20.48
Consensus MFE -11.90
Energy contribution -11.78
Covariance contribution -0.12
Combinations/Pair 1.15
Mean z-score -1.97
Structure conservation index 0.58
SVM decision value 0.56
SVM RNA-class probability 0.780854
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16848738 119 - 27905053
ACUCAGCUCUCAGUACUCAGUGUUAAGUUCUCAGUUCUCAGUUCUCAGUACUCAGUACUCAGUUCUUAAUUCUCAAUUCUCAGUUACGAGCUCUACAUUCUGAAUCAGAAUUAGAAUUA
.....((((.....(((.((.((((((..((.(((.((.(((.......))).)).))).))..))))))........)).)))...))))((((.((((((...)))))))))).... ( -22.50)
>DroSec_CAF1 1634 105 - 1
ACUCAGCUCUCAGUACUCAGUGCUAAGUUCUCAGUUCUC--------------AGUACUCAGUUCUUAACUGUCAAUUCUCAGUUAUGAGCUCUACAUUCUGAAUCAGAAUUAGAAUUA
.....((((..((.(((.((((((.((.........)).--------------)))))).))).))((((((........)))))).))))((((.((((((...)))))))))).... ( -25.80)
>DroSim_CAF1 1612 91 - 1
ACUCAGCUCUCAGUACUCAGUGCUAAGUUCUCAG----------------------------UUCUUAACGCUCAAUUCUCAGUUAUGAGCUCUACAUUCUGAAUCAGAAUUAGAAUUA
(((.((..((.(((((...))))).))..)).))----------------------------).......(((((...........)))))((((.((((((...)))))))))).... ( -17.90)
>DroEre_CAF1 1904 112 - 1
ACCCAGCGCUCAGUGCUCAGUGCUCAGUUCUCAGUUCCCAGUU-------CUCAGUUCUAAGUUCUUAAUUCUCAAAUCUCAGUUAUGAGCUCUCAAUUCUGAAUCAGAAUUAGAAUCA
....((((((........))))))..(((((.(((((...(((-------(..((((...(((((.(((((..........))))).)))))...))))..))))..)))))))))).. ( -19.70)
>DroYak_CAF1 1645 96 - 1
---CAGCUCUCAGUACUCAGUACUCAGUUCUCAAUUCUC--------------------AAGUUCUUAAUUCUCAAUUCUCAGUUAUGAGCUCUCGAUUCUGAAUCAGAAUUAGAAUCG
---.((..((.(((((...))))).))..))........--------------------.(((((.(((((..........))))).)))))..(((((((((.......))))))))) ( -16.50)
>consensus
ACUCAGCUCUCAGUACUCAGUGCUAAGUUCUCAGUUCUC______________AGU_CUAAGUUCUUAAUUCUCAAUUCUCAGUUAUGAGCUCUACAUUCUGAAUCAGAAUUAGAAUUA
....((..((.(((((...))))).))..))..............................((((.((((............)))).))))((((.((((((...)))))))))).... (-11.90 = -11.78 +  -0.12)

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 12:21:18 2006