Locus 6135

Sequence ID 3R_DroMel_CAF1
Location 16,070,842 – 16,070,977
Length 135
Max. P 0.888344
window10002 window10003 window10004

overview

Window 2

Location 16,070,842 – 16,070,959
Length 117
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 82.82
Mean single sequence MFE -26.36
Consensus MFE -13.84
Energy contribution -17.12
Covariance contribution 3.28
Combinations/Pair 1.15
Mean z-score -2.78
Structure conservation index 0.53
SVM decision value 0.95
SVM RNA-class probability 0.888344
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16070842 117 + 27905053
GAGGAUAAAACUAAAAGUGCAUUAAUGCUUAAUUUAAUGAACGGUUUUUACACUCAAUCGAAUUAUUGCAGAGCAGGAAAUUUGAUGCAGAAACGCAACAAGUUAAUUGCAUUUUUA
(((...((((((....((.((((((........)))))).))))))))....))).................((((..((((((.(((......))).))))))..))))....... ( -23.30)
>DroSec_CAF1 31391 117 + 1
GAGGAUAAAACUAAAAGUGCAUUAAUGCUUAAUUUAAUGAACGGUUUUUACACUCAAUCGAAUUAUUGUAGAGCAGGAAAUUUGUUGCAGAAAUGCAACAAGUCAAUUCGAUUUCAA
(((...((((((....((.((((((........)))))).))))))))....)))(((((((((.(((.....)))...((((((((((....)))))))))).))))))))).... ( -31.30)
>DroSim_CAF1 37536 117 + 1
GAGGAUAAAACUAAAAGUGCAUUAAUGCUUAAUUUAAUGAACGGUUUUUACACUCAAUCGAAUUAUUGCAGAGCAGGAAAUUUGUUGCAGAAAUGCAACAAGUCAAUUCGAUUUCAA
(((...((((((....((.((((((........)))))).))))))))....)))(((((((((.((((...))))...((((((((((....)))))))))).))))))))).... ( -32.40)
>DroEre_CAF1 7025 117 + 1
GAGAAUAAAAUGAAAAGUGGAUUAAUGCUUAAUUUAAUGAACUUUUUUUACUCUCAAUCGAAUUAUUGUAGAACAGAAAGUUUGUUGCAGAAGUGCAACAAGUCAAUUCGAUUUUAA
((((.(((...(((((((..(((((........)))))..)))))))))).))))(((((((((.(((.....)))...((((((((((....))))))))).)))))))))).... ( -28.80)
>DroYak_CAF1 48983 101 + 1
--------AAUAUAA--------AAUGCUUAAUUAAUUGAACGGUUCUAACACUCAAUCGAAUUAUUCUAACACAGGAAGUUUGUUGCAGAAACGCAAUAACGCAAUUCGAUGUUAA
--------.......--------........................(((((.....(((((((.((((......))))(((((((((......))))))).)))))))))))))). ( -16.00)
>consensus
GAGGAUAAAACUAAAAGUGCAUUAAUGCUUAAUUUAAUGAACGGUUUUUACACUCAAUCGAAUUAUUGUAGAGCAGGAAAUUUGUUGCAGAAAUGCAACAAGUCAAUUCGAUUUUAA
(((...((((((....((.((((((........)))))).))))))))....)))(((((((((.((((...))))...(((((((((......))))))))).))))))))).... (-13.84 = -17.12 +   3.28)

alignment

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secondary structure

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dotplot

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Window 3

Location 16,070,842 – 16,070,959
Length 117
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 82.82
Mean single sequence MFE -21.92
Consensus MFE -12.06
Energy contribution -12.86
Covariance contribution 0.80
Combinations/Pair 1.10
Mean z-score -2.08
Structure conservation index 0.55
SVM decision value 0.04
SVM RNA-class probability 0.555897
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16070842 117 - 27905053
UAAAAAUGCAAUUAACUUGUUGCGUUUCUGCAUCAAAUUUCCUGCUCUGCAAUAAUUCGAUUGAGUGUAAAAACCGUUCAUUAAAUUAAGCAUUAAUGCACUUUUAGUUUUAUCCUC
...(((((((((......)))))))))....(((.((((...(((...)))..)))).))).(((..(((((...((.((((((........)))))).))......)))))..))) ( -17.30)
>DroSec_CAF1 31391 117 - 1
UUGAAAUCGAAUUGACUUGUUGCAUUUCUGCAACAAAUUUCCUGCUCUACAAUAAUUCGAUUGAGUGUAAAAACCGUUCAUUAAAUUAAGCAUUAAUGCACUUUUAGUUUUAUCCUC
....((((((((((..((((((((....))))))))......((.....)).))))))))))(((..(((((...((.((((((........)))))).))......)))))..))) ( -24.00)
>DroSim_CAF1 37536 117 - 1
UUGAAAUCGAAUUGACUUGUUGCAUUUCUGCAACAAAUUUCCUGCUCUGCAAUAAUUCGAUUGAGUGUAAAAACCGUUCAUUAAAUUAAGCAUUAAUGCACUUUUAGUUUUAUCCUC
....((((((((((..((((((((....))))))))......(((...))).))))))))))(((..(((((...((.((((((........)))))).))......)))))..))) ( -26.20)
>DroEre_CAF1 7025 117 - 1
UUAAAAUCGAAUUGACUUGUUGCACUUCUGCAACAAACUUUCUGUUCUACAAUAAUUCGAUUGAGAGUAAAAAAAGUUCAUUAAAUUAAGCAUUAAUCCACUUUUCAUUUUAUUCUC
....((((((((((..((((((((....))))))))......((.....)).))))))))))(((((((((((((((..(((((........)))))..)))))...)))))))))) ( -28.00)
>DroYak_CAF1 48983 101 - 1
UUAACAUCGAAUUGCGUUAUUGCGUUUCUGCAACAAACUUCCUGUGUUAGAAUAAUUCGAUUGAGUGUUAGAACCGUUCAAUUAAUUAAGCAUU--------UUAUAUU--------
.....((((((((((((....))))(((((..(((.......)))..))))).)))))))).(((((((...................))))))--------)......-------- ( -14.11)
>consensus
UUAAAAUCGAAUUGACUUGUUGCAUUUCUGCAACAAAUUUCCUGCUCUACAAUAAUUCGAUUGAGUGUAAAAACCGUUCAUUAAAUUAAGCAUUAAUGCACUUUUAGUUUUAUCCUC
....((((((((((..((((((((....))))))))......((.....)).))))))))))....................................................... (-12.06 = -12.86 +   0.80)

alignment

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secondary structure

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Window 4

Location 16,070,879 – 16,070,977
Length 98
Sequences 5
Columns 98
Reading direction reverse
Mean pairwise identity 85.51
Mean single sequence MFE -19.08
Consensus MFE -14.62
Energy contribution -15.62
Covariance contribution 1.00
Combinations/Pair 1.08
Mean z-score -1.77
Structure conservation index 0.77
SVM decision value 0.43
SVM RNA-class probability 0.734137
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16070879 98 - 27905053
ACAAAUAUUUUAUAAGCAUAAAAAUGCAAUUAACUUGUUGCGUUUCUGCAUCAAAUUUCCUGCUCUGCAAUAAUUCGAUUGAGUGUAAAAACCGUUCA
.......(((((((.(((...(((((((((......))))))))).)))(((.((((...(((...)))..)))).)))....)))))))........ ( -16.00)
>DroSec_CAF1 31428 98 - 1
ACAAAUAAUUUAUAGGCAUUGAAAUCGAAUUGACUUGUUGCAUUUCUGCAACAAAUUUCCUGCUCUACAAUAAUUCGAUUGAGUGUAAAAACCGUUCA
...............(((((..((((((((((..((((((((....))))))))......((.....)).)))))))))).)))))............ ( -20.80)
>DroSim_CAF1 37573 98 - 1
ACAAAUAAUUUAUAAGCAUUGAAAUCGAAUUGACUUGUUGCAUUUCUGCAACAAAUUUCCUGCUCUGCAAUAAUUCGAUUGAGUGUAAAAACCGUUCA
...............(((((..((((((((((..((((((((....))))))))......(((...))).)))))))))).)))))............ ( -22.90)
>DroEre_CAF1 7062 98 - 1
AAAUAUUUUGUACAAGCAUUAAAAUCGAAUUGACUUGUUGCACUUCUGCAACAAACUUUCUGUUCUACAAUAAUUCGAUUGAGAGUAAAAAAAGUUCA
...((((((((....)).....((((((((((..((((((((....))))))))......((.....)).)))))))))).))))))........... ( -18.00)
>DroYak_CAF1 49004 98 - 1
ACAUAUUUUUUACAAGCAUUAACAUCGAAUUGCGUUAUUGCGUUUCUGCAACAAACUUCCUGUGUUAGAAUAAUUCGAUUGAGUGUUAGAACCGUUCA
..............((((((...((((((((((((....))))(((((..(((.......)))..))))).))))))))..))))))........... ( -17.70)
>consensus
ACAAAUAUUUUAUAAGCAUUAAAAUCGAAUUGACUUGUUGCAUUUCUGCAACAAAUUUCCUGCUCUACAAUAAUUCGAUUGAGUGUAAAAACCGUUCA
...............((((...((((((((((..((((((((....))))))))......((.....)).))))))))))..))))............ (-14.62 = -15.62 +   1.00)

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 12:13:36 2006