Locus 5003

Sequence ID 2R_DroMel_CAF1
Location 16,300,575 – 16,300,713
Length 138
Max. P 0.764892
window8009 window8010

overview

Window 9

Location 16,300,575 – 16,300,687
Length 112
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 79.23
Mean single sequence MFE -42.57
Consensus MFE -28.72
Energy contribution -29.83
Covariance contribution 1.11
Combinations/Pair 1.18
Mean z-score -1.54
Structure conservation index 0.67
SVM decision value 0.51
SVM RNA-class probability 0.764892
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16300575 112 - 20766785
CCUCCGAGUUCUGCUCAAGAUUCUCCUCCAGGGGAAUGGCCAUUGCCAUGGCUCCGAAGAGCGCCAGGCACAGGAAGAGUACCAGUUUGGUGCUCAUGGUGAA-GAGGGUGUU
((((.(((.....)))...(((((((....))))))).(((((((((.((((.(......).))))))))......(((((((.....))))))))))))...-))))..... ( -44.40)
>DroSec_CAF1 3371 112 - 1
CCUCCGAGUUCUGCCCUAGAUUCUCCUCUAGGGGAUUGGACAUAGCCAUGGCUCCGAAGAGCGCCAGGCACAGGAAGAGUACCAGUUUGGUGCUCAUGGUGAA-GAGGGUGUU
((((....((((((((((((......)))))))...........(((.((((.(......).))))))).))))).(((((((.....)))))))........-))))..... ( -43.10)
>DroSim_CAF1 3418 112 - 1
CCUCCGUGUUCUGCCCAAGAUUCUCCUCUAGGGGAUUGGCCAUGGCCAUGGCUCCGAAGAGCGCCAGGCACAGGAAGAGUACCAGUUUGGUGCUCAUGGUGAA-GAGGGUGUU
............((((....(((.((....((((..((((....))))...))))...(((((((((((...((.......)).)))))))))))..)).)))-..))))... ( -42.60)
>DroEre_CAF1 2710 100 - 1
CC------------UGAAGAUUCUCCCUCAUGGGAACAGCCAUUGCCAUGGCUCCGCAGAGCGCCACGCACAGGAAGAGUACCAGUUUGGUGCUCAUGAUGGA-GAGGGUGUU
..------------........(.(((((.((....))(((((....)))))((((((((((((((.((...((.......)).)).)))))))).)).))))-))))).).. ( -36.20)
>DroYak_CAF1 3399 112 - 1
ACACCGCGUUCUGUUCGAUAUUCUCCUCCAGGGGAAGGGCCAUGGCCAUGGCUCCGCAGAGCGCCAGGCACAGGAAGAGUACCAGUUUGGUGCUCAUGGUGGA-GUGGGUGUU
((((((((((((((......((((((....))))))(((((((....))))).)))))))))))....(((.....(((((((.....)))))))...)))..-...))))). ( -51.30)
>DroAna_CAF1 4157 111 - 1
GCUCGGCAGUUGGAUCGACGGUAUCCACAUCAGGACGGGCCGUGGCUAGGGCUCCGAAGAGUGCCAGGCAUAGGCAGAGAACCAAUUUGGUGCUCAUGGCAGAAUAGG--GCU
((((((.((((..(.(.(((((.(((......)))...))))).).)..))))))......(((((.((....)).(((.(((.....))).))).))))).....))--)). ( -37.80)
>consensus
CCUCCGAGUUCUGCUCAAGAUUCUCCUCCAGGGGAAUGGCCAUGGCCAUGGCUCCGAAGAGCGCCAGGCACAGGAAGAGUACCAGUUUGGUGCUCAUGGUGAA_GAGGGUGUU
((((...................((((....))))...(((((.(((.((((.(......).))))))).......(((((((.....))))))))))))....))))..... (-28.72 = -29.83 +   1.11)

alignment

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secondary structure

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dotplot

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Window 0

Location 16,300,614 – 16,300,713
Length 99
Sequences 6
Columns 105
Reading direction reverse
Mean pairwise identity 77.82
Mean single sequence MFE -36.00
Consensus MFE -24.35
Energy contribution -24.97
Covariance contribution 0.61
Combinations/Pair 1.12
Mean z-score -1.39
Structure conservation index 0.68
SVM decision value 0.51
SVM RNA-class probability 0.762517
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16300614 99 - 20766785
GCUAUUCAACU------CCUGGCUGUUCUCCACCUCCGAGUUCUGCUCAAGAUUCUCCUCCAGGGGAAUGGCCAUUGCCAUGGCUCCGAAGAGCGCCAGGCACAG
...........------((((((.(((((.(......(((.....)))...(((((((....)))))))((((((....))))))..).)))))))))))..... ( -34.20)
>DroSec_CAF1 3410 99 - 1
GCUGUUCAGCU------CCUGGCUGUUCUCCACCUCCGAGUUCUGCCCUAGAUUCUCCUCUAGGGGAUUGGACAUAGCCAUGGCUCCGAAGAGCGCCAGGCACAG
(((....))).------((((((.(((((.(...(((((....(.(((((((......))))))).))))))...(((....)))..).)))))))))))..... ( -36.40)
>DroSim_CAF1 3457 99 - 1
GCUGUUCAGCU------CCUGGCUGUUCUCCACCUCCGUGUUCUGCCCAAGAUUCUCCUCUAGGGGAUUGGCCAUGGCCAUGGCUCCGAAGAGCGCCAGGCACAG
(((....))).------((((((.(((((.(....(((((..(((.((((...(((((....))))))))).)).)..)))))....).)))))))))))..... ( -37.00)
>DroEre_CAF1 2749 87 - 1
GCUGGUUAGCU------CCUGGCUGUCCUCCACC------------UGAAGAUUCUCCCUCAUGGGAACAGCCAUUGCCAUGGCUCCGCAGAGCGCCACGCACAG
((((((..(((------(.(((((((..(((.(.------------(((.(......).))).)))))))))))..((....))......)))))))).)).... ( -29.40)
>DroYak_CAF1 3438 99 - 1
GCUGUUCAGCU------CCUGGCUGUUCUCCAACACCGCGUUCUGUUCGAUAUUCUCCUCCAGGGGAAGGGCCAUGGCCAUGGCUCCGCAGAGCGCCAGGCACAG
(((....))).------((((((((((....))))....(((((((......((((((....))))))(((((((....))))).)))))))))))))))..... ( -40.30)
>DroAna_CAF1 4195 105 - 1
GCUGUUCAGCUCCUGCUCCUGGCUGUUCUCCAGCUCGGCAGUUGGAUCGACGGUAUCCACAUCAGGACGGGCCGUGGCUAGGGCUCCGAAGAGUGCCAGGCAUAG
(((.....((((..((.(((((((....(((((((....)))))))...(((((.(((......)))...))))))))))))))......))))....))).... ( -38.70)
>consensus
GCUGUUCAGCU______CCUGGCUGUUCUCCACCUCCGAGUUCUGCUCAAGAUUCUCCUCCAGGGGAAUGGCCAUGGCCAUGGCUCCGAAGAGCGCCAGGCACAG
(((....))).......((((((.(((((.(........................((((....))))..((((((....))))))..).)))))))))))..... (-24.35 = -24.97 +   0.61)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:34:14 2006