Locus 4514

Sequence ID 3L_DroMel_CAF1
Location 13,008,498 – 13,008,642
Length 144
Max. P 0.939520
window7051 window7052 window7053 window7054

overview

Window 1

Location 13,008,498 – 13,008,618
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 95.83
Mean single sequence MFE -37.50
Consensus MFE -35.62
Energy contribution -35.88
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -2.07
Structure conservation index 0.95
SVM decision value 1.30
SVM RNA-class probability 0.939520
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13008498 120 + 23771897
UAUAGCUGGGCCAUGGUCAGGGUCGUCGGUUCAACGACAGGCCAUAAAACACGUUACAACUCUUACGGAACUUCAGUUCAGUAAGACUAGUUGUAUUUCCAGCAUGAGACAGCACUUCCC
....((((((..((((((...(((((.......))))).)))))).........((((((((((((.((((....)))).))))))...))))))..))))))................. ( -38.20)
>DroSec_CAF1 15452 120 + 1
UAUAGCUGGGCCAUGGUCAGGGUCGUCGGUUCAACGACAGGCCAUAAAACACGUUACAACUCUUACGGAACUUCAGUUCAGUAAGACUAGUUGUAUUUUCAGCAUGAGACAGCACUUCCC
....((((..(((((.....((((((((......)))).))))...........((((((((((((.((((....)))).))))))...)))))).......)))).).))))....... ( -37.80)
>DroSim_CAF1 19603 120 + 1
UAUAGCUGGGCCAUGGUCAGGGUCGUCGGUUCAACGACAGGCCAUAAAACACGUUACAACUCUUACGGAACUUCAGUUCAGUAAGACUAGUUGUAUUUUCAGCAUGAGACAGCACUUCCC
....((((..(((((.....((((((((......)))).))))...........((((((((((((.((((....)))).))))))...)))))).......)))).).))))....... ( -37.80)
>DroYak_CAF1 17221 120 + 1
UGUAGCUGGGCCAUGGUCAGGGUCGUCGGUUCAACGACAGGCCAUAAAACACGUUACAACUCUUACGGAACCCCAGUUCAGUAAGACUAGUUGUACUUUGUGCAUGAGGCAGAACUUCUC
.........(((((((((...(((((.......))))).))))))....((((.((((((((((((.((((....)))).))))))...))))))...)))).....))).......... ( -36.20)
>consensus
UAUAGCUGGGCCAUGGUCAGGGUCGUCGGUUCAACGACAGGCCAUAAAACACGUUACAACUCUUACGGAACUUCAGUUCAGUAAGACUAGUUGUAUUUUCAGCAUGAGACAGCACUUCCC
....((((...((((.....((((((((......)))).))))...........((((((((((((.((((....)))).))))))...)))))).......))))...))))....... (-35.62 = -35.88 +   0.25)

alignment

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secondary structure

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dotplot

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Window 2

Location 13,008,498 – 13,008,618
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 95.83
Mean single sequence MFE -37.20
Consensus MFE -33.24
Energy contribution -33.42
Covariance contribution 0.19
Combinations/Pair 1.08
Mean z-score -1.61
Structure conservation index 0.89
SVM decision value 0.14
SVM RNA-class probability 0.601438
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13008498 120 - 23771897
GGGAAGUGCUGUCUCAUGCUGGAAAUACAACUAGUCUUACUGAACUGAAGUUCCGUAAGAGUUGUAACGUGUUUUAUGGCCUGUCGUUGAACCGACGACCCUGACCAUGGCCCAGCUAUA
((((.......))))..(((((...((((((...((((((.((((....)))).)))))))))))).......((((((.(.(((((((...)))))))...).)))))).))))).... ( -38.70)
>DroSec_CAF1 15452 120 - 1
GGGAAGUGCUGUCUCAUGCUGAAAAUACAACUAGUCUUACUGAACUGAAGUUCCGUAAGAGUUGUAACGUGUUUUAUGGCCUGUCGUUGAACCGACGACCCUGACCAUGGCCCAGCUAUA
(((..(((..(((....(((((((((((.((.(.((((((.((((....)))).)))))).).))...))))))).))))..(((((((...)))))))...))))))..)))....... ( -36.50)
>DroSim_CAF1 19603 120 - 1
GGGAAGUGCUGUCUCAUGCUGAAAAUACAACUAGUCUUACUGAACUGAAGUUCCGUAAGAGUUGUAACGUGUUUUAUGGCCUGUCGUUGAACCGACGACCCUGACCAUGGCCCAGCUAUA
(((..(((..(((....(((((((((((.((.(.((((((.((((....)))).)))))).).))...))))))).))))..(((((((...)))))))...))))))..)))....... ( -36.50)
>DroYak_CAF1 17221 120 - 1
GAGAAGUUCUGCCUCAUGCACAAAGUACAACUAGUCUUACUGAACUGGGGUUCCGUAAGAGUUGUAACGUGUUUUAUGGCCUGUCGUUGAACCGACGACCCUGACCAUGGCCCAGCUACA
..(.((((..(((....((((....((((((...((((((.((((....)))).))))))))))))..))))...((((.(.(((((((...)))))))...).)))))))..)))).). ( -37.10)
>consensus
GGGAAGUGCUGUCUCAUGCUGAAAAUACAACUAGUCUUACUGAACUGAAGUUCCGUAAGAGUUGUAACGUGUUUUAUGGCCUGUCGUUGAACCGACGACCCUGACCAUGGCCCAGCUAUA
((((.......))))..(((((((((((.((.(.((((((.((((....)))).)))))).).))...)))))))..((((.(((((((...))))))).........)))))))).... (-33.24 = -33.42 +   0.19)

alignment

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secondary structure

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dotplot

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Window 3

Location 13,008,538 – 13,008,642
Length 104
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 85.71
Mean single sequence MFE -22.52
Consensus MFE -16.33
Energy contribution -16.33
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.50
Structure conservation index 0.72
SVM decision value 0.08
SVM RNA-class probability 0.576077
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13008538 104 + 23771897
GCCAUAAAACACGUUACAACUCUUACGGAACUUCAGUUCAGUAAGACUAGUUGUAUUUCCAGCAUGAGACAGCACUUCCCUCCUUC---CGCGGAUUACCCGUUAUC-------------
((............((((((((((((.((((....)))).))))))...))))))((((......))))..)).............---.((((.....))))....------------- ( -20.90)
>DroSec_CAF1 15492 104 + 1
GCCAUAAAACACGUUACAACUCUUACGGAACUUCAGUUCAGUAAGACUAGUUGUAUUUUCAGCAUGAGACAGCACUUCCCUCCUUC---CGCCGAUUACCCGUUAUC-------------
.......(((....((((((((((((.((((....)))).))))))...))))))...((.((..(((..............))).---.)).))......)))...------------- ( -18.04)
>DroSim_CAF1 19643 103 + 1
GCCAUAAAACACGUUACAACUCUUACGGAACUUCAGUUCAGUAAGACUAGUUGUAUUUUCAGCAUGAGACAGCACUUCCCUCC-UC---CGCCGAUUACCCGUUAUC-------------
.......(((....((((((((((((.((((....)))).))))))...))))))...((.((..(((..............)-))---.)).))......)))...------------- ( -19.04)
>DroYak_CAF1 17261 120 + 1
GCCAUAAAACACGUUACAACUCUUACGGAACCCCAGUUCAGUAAGACUAGUUGUACUUUGUGCAUGAGGCAGAACUUCUCUCCUCCUAACUUCUCUUACCCGUUAUCAGCACGGGCCUAA
(((...........((((((((((((.((((....)))).))))))...))))))...(((((..((((.(((.....))))))).((((...........))))...)))))))).... ( -32.10)
>consensus
GCCAUAAAACACGUUACAACUCUUACGGAACUUCAGUUCAGUAAGACUAGUUGUAUUUUCAGCAUGAGACAGCACUUCCCUCCUUC___CGCCGAUUACCCGUUAUC_____________
.......(((....((((((((((((.((((....)))).))))))...))))))..........(((...........)))...................)))................ (-16.33 = -16.33 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 13,008,538 – 13,008,642
Length 104
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 85.71
Mean single sequence MFE -31.98
Consensus MFE -21.69
Energy contribution -23.12
Covariance contribution 1.44
Combinations/Pair 1.06
Mean z-score -1.77
Structure conservation index 0.68
SVM decision value 0.27
SVM RNA-class probability 0.661424
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13008538 104 - 23771897
-------------GAUAACGGGUAAUCCGCG---GAAGGAGGGAAGUGCUGUCUCAUGCUGGAAAUACAACUAGUCUUACUGAACUGAAGUUCCGUAAGAGUUGUAACGUGUUUUAUGGC
-------------...((((.((..((((((---...(((.((.....)).)))..))).)))..((((((...((((((.((((....)))).)))))))))))))).))))....... ( -28.90)
>DroSec_CAF1 15492 104 - 1
-------------GAUAACGGGUAAUCGGCG---GAAGGAGGGAAGUGCUGUCUCAUGCUGAAAAUACAACUAGUCUUACUGAACUGAAGUUCCGUAAGAGUUGUAACGUGUUUUAUGGC
-------------...((((.((..((((((---...(((.((.....)).)))..))))))...((((((...((((((.((((....)))).)))))))))))))).))))....... ( -30.50)
>DroSim_CAF1 19643 103 - 1
-------------GAUAACGGGUAAUCGGCG---GA-GGAGGGAAGUGCUGUCUCAUGCUGAAAAUACAACUAGUCUUACUGAACUGAAGUUCCGUAAGAGUUGUAACGUGUUUUAUGGC
-------------...((((.((..((((((---..-(((.((.....)).)))..))))))...((((((...((((((.((((....)))).)))))))))))))).))))....... ( -32.00)
>DroYak_CAF1 17261 120 - 1
UUAGGCCCGUGCUGAUAACGGGUAAGAGAAGUUAGGAGGAGAGAAGUUCUGCCUCAUGCACAAAGUACAACUAGUCUUACUGAACUGGGGUUCCGUAAGAGUUGUAACGUGUUUUAUGGC
....((((((.......)))))).......((...((((((((...)))).))))..))(((...((((((...((((((.((((....)))).))))))))))))...)))........ ( -36.50)
>consensus
_____________GAUAACGGGUAAUCGGCG___GAAGGAGGGAAGUGCUGUCUCAUGCUGAAAAUACAACUAGUCUUACUGAACUGAAGUUCCGUAAGAGUUGUAACGUGUUUUAUGGC
................((((.((..((((((......(((.((.....)).)))..))))))...((((((...((((((.((((....)))).)))))))))))))).))))....... (-21.69 = -23.12 +   1.44)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:25:28 2006