Locus 7486

Sequence ID 3L_DroMel_CAF1
Location 20,090,017 – 20,090,183
Length 166
Max. P 0.957382
window12169 window12170 window12171

overview

Window 9

Location 20,090,017 – 20,090,108
Length 91
Sequences 4
Columns 98
Reading direction forward
Mean pairwise identity 81.03
Mean single sequence MFE -32.52
Consensus MFE -20.23
Energy contribution -23.47
Covariance contribution 3.25
Combinations/Pair 1.10
Mean z-score -2.16
Structure conservation index 0.62
SVM decision value 0.81
SVM RNA-class probability 0.857334
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20090017 91 + 23771897
CUCUUUGAUGGCCCCUCCGAAGUGUGAAGAUUGCAUCUGGAGGCCGCGUGGGAAUGGGAUGUAGGUGAUUCUGCAUCCCAUCUG-------CCCACAA
......(.(((((..((((..(((..(...)..))).))))))))))(((((.((((((((((((....))))))))))))...-------))))).. ( -41.60)
>DroSec_CAF1 4524 72 + 1
CUCUUUGAUGGCC-CUCCGAAGUGUGAAGAUUGCAUCUGGAGGUCGCGUGGAAAUGGGA---------UUCUGCAA----------------CCACAA
....(((.(((.(-(((((..(((..(...)..))).))))))....(..(((......---------)))..)..----------------)))))) ( -18.20)
>DroSim_CAF1 4581 90 + 1
CUCUUUGAUGGCC-CUCCGAAGUGUGAAGAUUGCAUCUGGAGGUCGCGUGGAAAUGGGAUGUAGUUGAUUCUGCAUCCCAUCCG-------CCCACAA
....(((.(((.(-(((((..(((..(...)..))).))))))....(((((..((((((((((......))))))))))))))-------))))))) ( -36.30)
>DroEre_CAF1 4507 96 + 1
CUCUUUGAUGGCC-CUCCGAAGUGUGAAGAUUGCAUCUGGAGG-CGCGUGGGCAUGGGUUGUUGCUGAUUCUGUAACCCAUCCGCAUCCAGCCCACAA
..........(((-(((((..(((..(...)..))).))))))-.))((((((.(((((.(((((.......)))))........))))))))))).. ( -34.00)
>consensus
CUCUUUGAUGGCC_CUCCGAAGUGUGAAGAUUGCAUCUGGAGGUCGCGUGGAAAUGGGAUGUAG_UGAUUCUGCAACCCAUCCG_______CCCACAA
......(.(((((..((((..(((..(...)..))).))))))))))(((((.(((((((((((......)))))))))))..........))))).. (-20.23 = -23.47 +   3.25)

alignment

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secondary structure

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dotplot

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Window 0

Location 20,090,056 – 20,090,148
Length 92
Sequences 5
Columns 114
Reading direction forward
Mean pairwise identity 69.28
Mean single sequence MFE -22.30
Consensus MFE -5.63
Energy contribution -9.43
Covariance contribution 3.80
Combinations/Pair 1.12
Mean z-score -1.75
Structure conservation index 0.25
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20090056 92 + 23771897
GAGGCCGCGUGGGAAUGGGAUGUAGG------UGAUUCUGCAUCCCAU---------CUG-------CCCACAAAAACUACUGCAAAUAAAAAACCAAACAUCAAGGAAUAUUC
........(((((.((((((((((((------....))))))))))))---------...-------))))).......................................... ( -28.60)
>DroSec_CAF1 4562 73 + 1
GAGGUCGCGUGGAAAUGGGA---------------UUCUGCAA-------------------------CCACAAAAACUACUGCAAAUAAA-AACCAAACAUCAAGGAAUAUUC
..((((.(((....))).))---------------...((((.-------------------------.............))))......-..)).................. (  -7.84)
>DroSim_CAF1 4619 91 + 1
GAGGUCGCGUGGAAAUGGGAUGUAGU------UGAUUCUGCAUCCCAU---------CCG-------CCCACAAAAACUACUGCAAAUAAA-AACCAAACAUCAAGGAAUAUUC
...((.(.(((((..((((((((((.------.....)))))))))))---------)))-------)).))...................-...................... ( -24.10)
>DroEre_CAF1 4545 96 + 1
GAGG-CGCGUGGGCAUGGGUUGUUGC------UGAUUCUGUAACCCAU---------CCGCAUCCAGCCCACAAAAACUACUGCGAAUAAA--AGCAAACAUCAAGAAAUAUUC
((..-...((((((.(((((.(((((------.......)))))....---------....))))))))))).........(((.......--.)))....))........... ( -22.10)
>DroAna_CAF1 4450 108 + 1
GGGGGCG--AGGG-ACAGGACGUACUCACCCAGGACCCUUUAUCCCCUGAGCCCUCCCCCCAGCCUGCCCACAGAAACUACUG-AAAUAAA--AGCAAACAUCAAGAAAUAUUU
(((((.(--((((-.((((..((....))...(((.......)))))))..)))))))))).((.......(((......)))-.......--.)).................. ( -28.86)
>consensus
GAGGUCGCGUGGGAAUGGGAUGUAGU______UGAUUCUGCAUCCCAU_________CCG_______CCCACAAAAACUACUGCAAAUAAA_AACCAAACAUCAAGGAAUAUUC
........(((((.(((((((((((............)))))))))))...................))))).......................................... ( -5.63 =  -9.43 +   3.80)

alignment

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secondary structure

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dotplot

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Window 1

Location 20,090,090 – 20,090,183
Length 93
Sequences 4
Columns 112
Reading direction forward
Mean pairwise identity 76.47
Mean single sequence MFE -24.50
Consensus MFE -11.85
Energy contribution -11.98
Covariance contribution 0.12
Combinations/Pair 1.20
Mean z-score -2.77
Structure conservation index 0.48
SVM decision value 1.48
SVM RNA-class probability 0.957382
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20090090 93 + 23771897
CAUCCCAU---------CUG-------CCCACAAAAACUACUGCAAAUAAAAAACCAAACAUCAAGGAAUAUUCUUCGUGUUUGUGUUGGU---CGGAAACGAGGCGGAAUU
.......(---------(((-------((.......................((((((((((.(((((...))))).))))))).)))..(---((....)))))))))... ( -25.30)
>DroSec_CAF1 4587 83 + 1
CAA-------------------------CCACAAAAACUACUGCAAAUAAA-AACCAAACAUCAAGGAAUAUUCUCCGUGUUUGUGUUGGU---CGGAAACGAGGCGGAAUU
...-------------------------............((((.......-((((((((((...(((......)))))))))).)))..(---((....))).)))).... ( -20.50)
>DroSim_CAF1 4653 92 + 1
CAUCCCAU---------CCG-------CCCACAAAAACUACUGCAAAUAAA-AACCAAACAUCAAGGAAUAUUCUCCGUGUUGGUGUUGGU---CGGAAACGAGGCGGAAUU
.......(---------(((-------((......................-..((((.(((((((((......)))...))))))))))(---((....)))))))))... ( -27.80)
>DroAna_CAF1 4487 109 + 1
UAUCCCCUGAGCCCUCCCCCCAGCCUGCCCACAGAAACUACUG-AAAUAAA--AGCAAACAUCAAGAAAUAUUUUCCGUAUUUAUGUUGGCGGCGGGCAACCAGCCGGAAUU
..(((...((....))......(((((((..(((......)))-.......--.((.(((((....((((((.....))))))))))).)))))))))........)))... ( -24.40)
>consensus
CAUCCCAU_________CCG_______CCCACAAAAACUACUGCAAAUAAA_AACCAAACAUCAAGGAAUAUUCUCCGUGUUUGUGUUGGU___CGGAAACGAGGCGGAAUU
........................................((((.........(((((.(((....((((((.....))))))))))))))...((....))..)))).... (-11.85 = -11.98 +   0.12)

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 12:48:24 2006