Locus 737

Sequence ID 2L_DroMel_CAF1
Location 2,125,322 – 2,125,512
Length 190
Max. P 0.971883
window1215 window1216 window1217 window1218

overview

Window 5

Location 2,125,322 – 2,125,432
Length 110
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 85.16
Mean single sequence MFE -28.55
Consensus MFE -19.46
Energy contribution -20.52
Covariance contribution 1.06
Combinations/Pair 1.03
Mean z-score -1.79
Structure conservation index 0.68
SVM decision value 0.33
SVM RNA-class probability 0.691193
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2125322 110 - 22407834
GCCAGAAUAAAUUACAUGAAAUUUAUUUUGGCUGCUAUUGCUUCGAAUGAAAAUGAUGUGGAAACUGGCCGCACUGU----UGCAAUAUGUUUUUUCCAA------GUAUAGGAUGUUGC
(((((((((((((......))))))))))))).(((((((((((....)))(((..(((((.......)))))..))----))))))).))....(((..------.....)))...... ( -27.40)
>DroSec_CAF1 125583 114 - 1
GCCAGAAUAAAUUGCAUAAAAUUUAUUUUGGCUGCUAUUGCUUCGAAUGAAAAUGAUGUGCAAACUGGCCGCACUGUUGGUUGCAAUACGUUUUUUCCAA------GUAUAGGAUGUUGC
(((((((((((((......)))))))))))))..((((.((((.((..(((((((...(((((.(..((......))..))))))...))))))))).))------))))))........ ( -34.70)
>DroEre_CAF1 128410 115 - 1
GCCAGAAUAAAUUACAUAACAUUUAUUUUGGCUGCUAUUGCUUUGGAUGAAAAUGAUGUGGAAACUAGCCGCACUA-----UGCAAUAUGUUUUUUCCAUUUCCAAGUAAAGGAUGCACC
((((((((((((........))))))))))))(((((((((..(((((....))..(((((.......))))))))-----.)))))).............(((.......))).))).. ( -27.50)
>DroYak_CAF1 130755 115 - 1
GCCAGCAUAAAUUGCAUAACAUUUAUUUUAGCUGCUAUUGCUUUGGAUGAAAAUGAUGUGGAAACUAGCCGCACUA-----UGCAAUAUGUUUUUUUCAAGUAUAGGGAUAGGAUGUUGC
..((((((..((((((((.((((((....(((.......))).)))))).......(((((.......))))).))-----)))))).(((((((.........)))))))..)))))). ( -24.60)
>consensus
GCCAGAAUAAAUUACAUAAAAUUUAUUUUGGCUGCUAUUGCUUCGAAUGAAAAUGAUGUGGAAACUAGCCGCACUA_____UGCAAUAUGUUUUUUCCAA______GUAUAGGAUGUUGC
(((((((((((((......))))))))))))).((((((((.....((....))..(((((.......))))).........)))))).))....(((.............)))...... (-19.46 = -20.52 +   1.06)

alignment

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secondary structure

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Window 6

Location 2,125,355 – 2,125,472
Length 117
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 90.42
Mean single sequence MFE -28.35
Consensus MFE -24.83
Energy contribution -25.20
Covariance contribution 0.37
Combinations/Pair 1.11
Mean z-score -2.21
Structure conservation index 0.88
SVM decision value 1.56
SVM RNA-class probability 0.964173
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2125355 117 - 22407834
GCCGCAAAAAUUUACAUAUUCAAGUAAAAAGUUUGCAGAAGCCAGAAUAAAUUACAUGAAAUUUAUUUUGGCUGCUAUUGCUUCGAAUGAAAAUGAUGUGGAAACUGGCCGCACUGU---
((.(((((..(((((........)))))...)))))((.((((((((((((((......)))))))))))))).))...))...............(((((.......)))))....--- ( -30.20)
>DroSec_CAF1 125617 120 - 1
GCCGCAAAAAUUUACAUAUUCAAGUAAAAAGUUUGCAGAAGCCAGAAUAAAUUGCAUAAAAUUUAUUUUGGCUGCUAUUGCUUCGAAUGAAAAUGAUGUGCAAACUGGCCGCACUGUUGG
((.((.....(((((........))))).((((((((.(((((((((((((((......))))))))))))))((....))...............).)))))))).)).))........ ( -35.00)
>DroEre_CAF1 128449 116 - 1
GCCACAAGAAUUUGCAUAUUCAAGUAAAAAGUUUGCAGAAGCCAGAAUAAAUUACAUAACAUUUAUUUUGGCUGCUAUUGCUUUGGAUGAAAAUGAUGUGGAAACUAGCCGCACUA----
.(((((...((((...(((((((((((...(....)((.(((((((((((((........))))))))))))).)).)))).))))))).))))..)))))...............---- ( -28.40)
>DroYak_CAF1 130794 116 - 1
GCCAUAGAAAUUUACAUAUUCGAGUAAAAAGUUUGCAGAAGCCAGCAUAAAUUGCAUAACAUUUAUUUUAGCUGCUAUUGCUUUGGAUGAAAAUGAUGUGGAAACUAGCCGCACUA----
.(((......(((((........)))))......((((.(((.(((((((((........))))))....)))))).))))..)))..........(((((.......)))))...---- ( -19.80)
>consensus
GCCACAAAAAUUUACAUAUUCAAGUAAAAAGUUUGCAGAAGCCAGAAUAAAUUACAUAAAAUUUAUUUUGGCUGCUAUUGCUUCGAAUGAAAAUGAUGUGGAAACUAGCCGCACUA____
.(((((...((((...(((((((((((...(....)((.((((((((((((((......)))))))))))))).)).)))))).))))).))))..)))))................... (-24.83 = -25.20 +   0.37)

alignment

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secondary structure

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Window 7

Location 2,125,392 – 2,125,512
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 93.33
Mean single sequence MFE -25.15
Consensus MFE -22.04
Energy contribution -21.98
Covariance contribution -0.06
Combinations/Pair 1.18
Mean z-score -2.51
Structure conservation index 0.88
SVM decision value 1.68
SVM RNA-class probability 0.971883
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2125392 120 + 22407834
CAAUAGCAGCCAAAAUAAAUUUCAUGUAAUUUAUUCUGGCUUCUGCAAACUUUUUACUUGAAUAUGUAAAUUUUUGCGGCAAACAAUGUGUAGAAAUUUGUAUAAAUUAAAAAUGCAAAC
....((.(((((.((((((((......)))))))).))))).))(((...((((((.((...((((((((((((((((.((.....)))))))))))))))))))).))))))))).... ( -26.10)
>DroSec_CAF1 125657 120 + 1
CAAUAGCAGCCAAAAUAAAUUUUAUGCAAUUUAUUCUGGCUUCUGCAAACUUUUUACUUGAAUAUGUAAAUUUUUGCGGCAAACAAUUUGCAGGAAUUUGUAUAAAUUAAAAAUGCAAAC
....((.(((((.((((((((......)))))))).))))).))(((...((((((.((...(((((((((((((((((........))))))))))))))))))).))))))))).... ( -26.60)
>DroEre_CAF1 128485 120 + 1
CAAUAGCAGCCAAAAUAAAUGUUAUGUAAUUUAUUCUGGCUUCUGCAAACUUUUUACUUGAAUAUGCAAAUUCUUGUGGCAAACAAUGUGCAGAAAUUUGUAUAAAUUAAAAAUGCAAAC
.....(((((((.(((((((........))))))).))))(((((((...(((((((..((((......))))..)))).))).....)))))))..................))).... ( -26.60)
>DroYak_CAF1 130830 120 + 1
CAAUAGCAGCUAAAAUAAAUGUUAUGCAAUUUAUGCUGGCUUCUGCAAACUUUUUACUCGAAUAUGUAAAUUUCUAUGGCAAACAAUGUGCAGAAAUUUGUAUAAAUUAAAAAUGGAAAC
..((((((...........))))))..(((((((((..(.(((((((.....(((((........)))))......((.....))...))))))).)..)))))))))............ ( -21.30)
>consensus
CAAUAGCAGCCAAAAUAAAUGUUAUGCAAUUUAUUCUGGCUUCUGCAAACUUUUUACUUGAAUAUGUAAAUUUUUGCGGCAAACAAUGUGCAGAAAUUUGUAUAAAUUAAAAAUGCAAAC
...(((.(((((.(((((((........))))))).))))).))).................((((((((((((((((.((.....))))))))))))))))))................ (-22.04 = -21.98 +  -0.06)

alignment

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secondary structure

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dotplot

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Window 8

Location 2,125,392 – 2,125,512
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 93.33
Mean single sequence MFE -25.32
Consensus MFE -20.69
Energy contribution -21.62
Covariance contribution 0.94
Combinations/Pair 1.12
Mean z-score -2.34
Structure conservation index 0.82
SVM decision value 0.94
SVM RNA-class probability 0.885956
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2125392 120 - 22407834
GUUUGCAUUUUUAAUUUAUACAAAUUUCUACACAUUGUUUGCCGCAAAAAUUUACAUAUUCAAGUAAAAAGUUUGCAGAAGCCAGAAUAAAUUACAUGAAAUUUAUUUUGGCUGCUAUUG
....((..............(((((...........)))))..(((((..(((((........)))))...)))))...((((((((((((((......))))))))))))))))..... ( -25.10)
>DroSec_CAF1 125657 120 - 1
GUUUGCAUUUUUAAUUUAUACAAAUUCCUGCAAAUUGUUUGCCGCAAAAAUUUACAUAUUCAAGUAAAAAGUUUGCAGAAGCCAGAAUAAAUUGCAUAAAAUUUAUUUUGGCUGCUAUUG
....((.....................(((((((((.(((((.....................))))).))))))))).((((((((((((((......))))))))))))))))..... ( -30.30)
>DroEre_CAF1 128485 120 - 1
GUUUGCAUUUUUAAUUUAUACAAAUUUCUGCACAUUGUUUGCCACAAGAAUUUGCAUAUUCAAGUAAAAAGUUUGCAGAAGCCAGAAUAAAUUACAUAACAUUUAUUUUGGCUGCUAUUG
....(((..................(((((((.(((.(((((.....((((......))))..))))).))).)))))))((((((((((((........)))))))))))))))..... ( -28.60)
>DroYak_CAF1 130830 120 - 1
GUUUCCAUUUUUAAUUUAUACAAAUUUCUGCACAUUGUUUGCCAUAGAAAUUUACAUAUUCGAGUAAAAAGUUUGCAGAAGCCAGCAUAAAUUGCAUAACAUUUAUUUUAGCUGCUAUUG
..........................((((((.(((.(((((....(((.........)))..))))).))).))))))(((.(((((((((........))))))....)))))).... ( -17.30)
>consensus
GUUUGCAUUUUUAAUUUAUACAAAUUUCUGCACAUUGUUUGCCACAAAAAUUUACAUAUUCAAGUAAAAAGUUUGCAGAAGCCAGAAUAAAUUACAUAAAAUUUAUUUUGGCUGCUAUUG
....(((..................(((((((..((((.....))))...(((((........))))).....)))))))(((((((((((((......))))))))))))))))..... (-20.69 = -21.62 +   0.94)

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 09:44:26 2006