Locus 5649

Sequence ID 3R_DroMel_CAF1
Location 14,833,512 – 14,833,790
Length 278
Max. P 0.973833
window9222 window9223 window9224

overview

Window 2

Location 14,833,512 – 14,833,630
Length 118
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 93.85
Mean single sequence MFE -35.80
Consensus MFE -35.89
Energy contribution -35.23
Covariance contribution -0.66
Combinations/Pair 1.09
Mean z-score -1.84
Structure conservation index 1.00
SVM decision value 1.14
SVM RNA-class probability 0.921885
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14833512 118 + 27905053
CCUUCAUGUCCACAAACUGGUCACCAGUGCCGAGAGAAUAAAAUAUGCAUGUUGCAGGAGCACC--AGCUUCGUGGCAUGUGGCCGGGUUAUUAAAGUUAAUUACAAUUCUUCCUGGCAU
.....(((.(((....((((((((..((((((.............(((.....)))(((((...--.))))).))))))))))))))((.((((....)))).)).........)))))) ( -33.10)
>DroSec_CAF1 11699 118 + 1
CCUUCCUGUCCACAAACUGGCCACCACUGCCGAGAGAAAUAAAUAUGCAUGUUGCAGGAGCACC--AGCUCCGUGGCAUGUGGCCGGGUUAUUAAAGUUAAUUACAAUUCUUCCUGGCAU
......((.(((....((((((((...(((((.............(((.....)))(((((...--.))))).))))).))))))))((.((((....)))).)).........))))). ( -36.50)
>DroSim_CAF1 11849 120 + 1
CCUUCCUGUCCACAAACUGGCCACCACUGCCAAGAGAAUUAAAUAUGCAUGUUGCAGGAGCUCCGUGGCUCCGUGGCAUGUGGCCGGGUUAUUAAAGUUAAUUACAAUUCUUCCUGGCAU
......((.(((....((((((((...(((((.............(((.....)))((((((....)))))).))))).))))))))((.((((....)))).)).........))))). ( -37.80)
>consensus
CCUUCCUGUCCACAAACUGGCCACCACUGCCGAGAGAAUUAAAUAUGCAUGUUGCAGGAGCACC__AGCUCCGUGGCAUGUGGCCGGGUUAUUAAAGUUAAUUACAAUUCUUCCUGGCAU
......((.(((....((((((((...(((((.............(((.....)))(((((......))))).))))).))))))))((.((((....)))).)).........))))). (-35.89 = -35.23 +  -0.66)

alignment

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secondary structure

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dotplot

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Window 3

Location 14,833,552 – 14,833,670
Length 118
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 93.24
Mean single sequence MFE -30.06
Consensus MFE -29.71
Energy contribution -29.49
Covariance contribution -0.22
Combinations/Pair 1.05
Mean z-score -2.25
Structure conservation index 0.99
SVM decision value 1.72
SVM RNA-class probability 0.973833
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14833552 118 + 27905053
AAAUAUGCAUGUUGCAGGAGCACC--AGCUUCGUGGCAUGUGGCCGGGUUAUUAAAGUUAAUUACAAUUCUUCCUGGCAUUCAUUUUUUCUCGUAAUGAUAAUUCUGAUUUUUUUUCACC
......((((((..(.(((((...--.))))))..)))))).((((((........((.....)).......))))))..(((((.........)))))..................... ( -28.46)
>DroSec_CAF1 11739 115 + 1
AAAUAUGCAUGUUGCAGGAGCACC--AGCUCCGUGGCAUGUGGCCGGGUUAUUAAAGUUAAUUACAAUUCUUCCUGGCAUUCAUUUUUUCACGAAACGAUAAUUCUGAUUUUUUUUU---
......((((((..(.(((((...--.))))))..)))))).((((((........((.....)).......))))))..........(((.(((.......)))))).........--- ( -30.96)
>DroSim_CAF1 11889 117 + 1
AAAUAUGCAUGUUGCAGGAGCUCCGUGGCUCCGUGGCAUGUGGCCGGGUUAUUAAAGUUAAUUACAAUUCUUCCUGGCAUUCAUUUUUUCUCGUAACGAUAAUUCUGAUUUUUUUUU---
......((((((..(.((((((....)))))))..)))))).((((((........((.....)).......)))))).......................................--- ( -30.76)
>consensus
AAAUAUGCAUGUUGCAGGAGCACC__AGCUCCGUGGCAUGUGGCCGGGUUAUUAAAGUUAAUUACAAUUCUUCCUGGCAUUCAUUUUUUCUCGUAACGAUAAUUCUGAUUUUUUUUU___
......((((((..(.(((((......))))))..)))))).((((((........((.....)).......)))))).......................................... (-29.71 = -29.49 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 4

Location 14,833,670 – 14,833,790
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 94.93
Mean single sequence MFE -25.19
Consensus MFE -22.32
Energy contribution -22.43
Covariance contribution 0.11
Combinations/Pair 1.04
Mean z-score -1.84
Structure conservation index 0.89
SVM decision value 0.10
SVM RNA-class probability 0.581334
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14833670 120 - 27905053
GCCUCCGAUUUUGCAGUCUGUAAACAAAGGAAGCAAAAACAAGGCGAUGCCGCAAAUAAAUCAACGCGAAAAUUAAUAGAGUGGAAAAAUCGGCACAGAGCAAGGACACAGCACUUAACU
((((((((((((.((.(((((.....................(((...)))((............))........))))).))..))))))))...)).))................... ( -21.70)
>DroSec_CAF1 11854 115 - 1
GCCUCUGAUUUUGCAGUCUGUAAACAAAGGAAGCAAAAACAAGGCGAUGCCGCAAAUAAAUCAACACGAAAAUUAAUAGAGUGGAAAAAUCGCCACAGAGCAAGGACACAGCAUU-----
((.((((.((((((..(((........)))..))))))....((((((.((((...........................))))....)))))).))))))..............----- ( -28.23)
>DroSim_CAF1 12006 115 - 1
GCCUCCGAUUUUGCAGUCUGUAAACAAAGGAAGCAAAAACAAGGCGAUGCCGCAAAUAAAUCAACGCGAAAAUUAAUAGAGUGGAAAAAUCGCCACAGAGCAAGGACACAGCAUU-----
((.((((.((((((..(((........)))..)))))).)..((((((.((((...........................))))....)))))).........)))....))...----- ( -25.63)
>consensus
GCCUCCGAUUUUGCAGUCUGUAAACAAAGGAAGCAAAAACAAGGCGAUGCCGCAAAUAAAUCAACGCGAAAAUUAAUAGAGUGGAAAAAUCGCCACAGAGCAAGGACACAGCAUU_____
((.((((.((((((..(((........)))..)))))).)..((((((.((((...........................))))....)))))).........)))....))........ (-22.32 = -22.43 +   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 12:00:36 2006