Locus 346

Sequence ID 3L_DroMel_CAF1
Location 1,003,680 – 1,003,780
Length 100
Max. P 0.868894
window512 window513

overview

Window 2

Location 1,003,680 – 1,003,780
Length 100
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 77.28
Mean single sequence MFE -35.08
Consensus MFE -22.57
Energy contribution -23.51
Covariance contribution 0.95
Combinations/Pair 1.13
Mean z-score -1.69
Structure conservation index 0.64
SVM decision value 0.86
SVM RNA-class probability 0.868894
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1003680 100 + 23771897
-------AGUAUAUCAAGAUUGGGAAGAUGUGGCAGGUGCGCCAUAGCGACUGCCACUUCAGUCGGUCCGCCGAUCU-------CGGAAUCGCAGCCGAGCAAUUAUGACUGGG
-------......(((.(((((....((.(((((((...(((....))).))))))).)).(((((....)))))((-------(((........)))))))))).)))..... ( -36.50)
>DroSec_CAF1 21888 100 + 1
-------AGUAUCUCAAGAUUGGGAAGAUGUGGCAGGUGCGCCAUAGCGACUGCCACUUCAGCCGGUCCGCCGAUCU-------CGGAAUCGCAGCCGAGCAAUUAUGACUGGG
-------....(((((....))))).((.(((((((...(((....))).))))))).))..((((((.......((-------(((........))))).......)))))). ( -38.44)
>DroSim_CAF1 22091 100 + 1
-------AGUAUCUCAAGAUUGGGAAGAUGUGGCAGGUGCGCCAUAGCGACUGCCACUUCAGCCGGUCCGCCGAUCU-------CGGAAUCGCAGCCGAGCAAUUAUGACUGGG
-------....(((((....))))).((.(((((((...(((....))).))))))).))..((((((.......((-------(((........))))).......)))))). ( -38.44)
>DroEre_CAF1 23547 107 + 1
-------AACAUCCCAAGAUUGGGAAGCUGUGGCAGGUGCGCCAUAGCGACUGCCACUUCACCCGGUCCGCCGAUCUCGGAUCUCGGAAUCGCAGCCAAACAAUUAUGACUGGC
-------....(((((....))))).((.(((((((...(((....))).)))))))....((.((((((.......))))))..))....)).((((..((....))..)))) ( -38.10)
>DroYak_CAF1 22550 84 + 1
-------AACAUCCCAAGAUUGGGAAGAUGUGGCAGGUGCGCCAUAGCCACUGCCACUUCACCCGGUCCGCCGAUCG-----------------------CAAUUAUGACUGGG
-------....(((((....))))).((.(((((((..((......))..))))))).)).(((((((.((.....)-----------------------)......))))))) ( -33.80)
>DroAna_CAF1 27305 95 + 1
UUCGAAAGGCCUCAC-AAAUUCAGAAGAUGCGGCAGGUGCGCUAUAGCGACUGCCACUUGGUCCGAUCU-----------------GAACCG-AUCCUAGCAAUUAUGAUUGCG
.((....))......-...((((((.((((.(((((...(((....))).))))).)...)))...)))-----------------)))...-......(((((....))))). ( -25.20)
>consensus
_______AGCAUCUCAAGAUUGGGAAGAUGUGGCAGGUGCGCCAUAGCGACUGCCACUUCAGCCGGUCCGCCGAUCU_______CGGAAUCGCAGCCGAGCAAUUAUGACUGGG
...........(((((....))))).((.(((((((.(((......))).))))))).))..((((((.......................................)))))). (-22.57 = -23.51 +   0.95)

alignment

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secondary structure

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dotplot

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Window 3

Location 1,003,680 – 1,003,780
Length 100
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 77.28
Mean single sequence MFE -34.58
Consensus MFE -18.76
Energy contribution -19.52
Covariance contribution 0.75
Combinations/Pair 1.15
Mean z-score -1.62
Structure conservation index 0.54
SVM decision value -0.06
SVM RNA-class probability 0.505050
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1003680 100 - 23771897
CCCAGUCAUAAUUGCUCGGCUGCGAUUCCG-------AGAUCGGCGGACCGACUGAAGUGGCAGUCGCUAUGGCGCACCUGCCACAUCUUCCCAAUCUUGAUAUACU-------
....((((..((((.((((((((((((...-------.)))).)))).))))..((.(((((((.(((....)))...))))))).))....))))..)))).....------- ( -35.10)
>DroSec_CAF1 21888 100 - 1
CCCAGUCAUAAUUGCUCGGCUGCGAUUCCG-------AGAUCGGCGGACCGGCUGAAGUGGCAGUCGCUAUGGCGCACCUGCCACAUCUUCCCAAUCUUGAGAUACU-------
.....(((..((((...((((((((((...-------.)))).)))).))((..((.(((((((.(((....)))...))))))).))..))))))..)))......------- ( -33.70)
>DroSim_CAF1 22091 100 - 1
CCCAGUCAUAAUUGCUCGGCUGCGAUUCCG-------AGAUCGGCGGACCGGCUGAAGUGGCAGUCGCUAUGGCGCACCUGCCACAUCUUCCCAAUCUUGAGAUACU-------
.....(((..((((...((((((((((...-------.)))).)))).))((..((.(((((((.(((....)))...))))))).))..))))))..)))......------- ( -33.70)
>DroEre_CAF1 23547 107 - 1
GCCAGUCAUAAUUGUUUGGCUGCGAUUCCGAGAUCCGAGAUCGGCGGACCGGGUGAAGUGGCAGUCGCUAUGGCGCACCUGCCACAGCUUCCCAAUCUUGGGAUGUU-------
(((((.((....)).)))))....(((((((((((((.......))))..(((.(..(((((((.(((....)))...)))))))..)..)))..)))))))))...------- ( -43.20)
>DroYak_CAF1 22550 84 - 1
CCCAGUCAUAAUUG-----------------------CGAUCGGCGGACCGGGUGAAGUGGCAGUGGCUAUGGCGCACCUGCCACAUCUUCCCAAUCUUGGGAUGUU-------
(((((......(((-----------------------(.....))))...(((.((.(((((((((((....)).)).))))))).))..)))....))))).....------- ( -31.40)
>DroAna_CAF1 27305 95 - 1
CGCAAUCAUAAUUGCUAGGAU-CGGUUC-----------------AGAUCGGACCAAGUGGCAGUCGCUAUAGCGCACCUGCCGCAUCUUCUGAAUUU-GUGAGGCCUUUCGAA
.((..((((((...(.(((((-.(((((-----------------.....)))))..(((((((.(((....)))...))))))))))))..)...))-)))).))........ ( -30.40)
>consensus
CCCAGUCAUAAUUGCUCGGCUGCGAUUCCG_______AGAUCGGCGGACCGGCUGAAGUGGCAGUCGCUAUGGCGCACCUGCCACAUCUUCCCAAUCUUGAGAUACU_______
.....(((..((((..........................((((....)))).....(((((((..((......))..))))))).......))))..)))............. (-18.76 = -19.52 +   0.75)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:39:43 2006