Locus 2831

Sequence ID 2L_DroMel_CAF1
Location 8,103,315 – 8,103,496
Length 181
Max. P 0.981078
window4499 window4500 window4501

overview

Window 9

Location 8,103,315 – 8,103,433
Length 118
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 67.85
Mean single sequence MFE -46.53
Consensus MFE -19.65
Energy contribution -23.91
Covariance contribution 4.27
Combinations/Pair 1.17
Mean z-score -1.58
Structure conservation index 0.42
SVM decision value -0.02
SVM RNA-class probability 0.521006
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8103315 118 + 22407834
AGAGCAGACCACCAUUUCAGCAGCCACCAGCACAAGGGCCAUGAUGGGUGGCGGUGGUGGCGUUGCUGGUGCGGGCUUUUCCGCGGGCGCCAGUGGCCCAAUGCUGGGUGCUGGCGGU
..........(((...((((((....((((((...(((((((....((((.(.((((.(((.((((....)))))))...)))).).)))).)))))))..)))))).)))))).))) ( -56.60)
>DroSec_CAF1 59310 118 + 1
AGAGCAGACCACCAUUUCAGCAGCCACCAGCACAAGGGCCAUGAUGGGUGGCGGUGGUGGUGUUGCUGGUUCGGGCUUUUCCGCGGGCGCCAGUGGCCCUAUGCUGGGUGCUGGCGGU
(((((......((...((((((((.((((.(((....(((((.....))))).))).))))))))))))...))))))).((((.((((((...(((.....))).)))))).)))). ( -54.00)
>DroSim_CAF1 60748 118 + 1
AGAGCAGACCACCAUUUCAGCAGCCACUAGCACAAGGGCCAUGAUGGGUGGCGGUGGUGGUNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
.......(((((((((......((((((..((.........))...)))))))))))))))......................................................... ( -20.20)
>DroEre_CAF1 59978 106 + 1
AGAGCAGACCACCAUUUCAGCAGCCACCAGCACAAGGGCCAUGAUGGGUGG------------UGCUGGUGCGGGCAUUUCUGCGGGCGCCAGUGGCCCAAUGCUGGGUGCUGGCGGC
...((.((........))..((((..((((((...(((((((......(((------------((((..((((((....))))))))))))))))))))..))))))..))))))... ( -46.80)
>DroYak_CAF1 60940 118 + 1
AGAGCACACCACCAUUUCAGCAGCCACCAGCACAAGGGCCAUGAUGGGUGGCGGUGGUGGCGCUGCUGCUGCGGGCAUUUCUGCGGGCGCGAGUGGCCAAAUGCUGGGUGCUGGCGGC
..(((((.(((.((((((((((((..(((.(((....(((((.....))))).))).))).)))))))(((((((....)))))))((....))....))))).))))))))...... ( -51.20)
>DroAna_CAF1 61695 100 + 1
GGAACAGACCACCAUAUCGGCAGCCACCAGCACAAUAGCCAUGUCUGGUCUGGGUGCUGGUGCUGCUGGUGGUGGCU---CCGU---------------GAUGAUGGGUGCUGUUAAC
..(((((.(((((((..(((((((.((((((((....((((....))))....)))))))))))))))))))))).(---((((---------------....)))))..)))))... ( -50.40)
>consensus
AGAGCAGACCACCAUUUCAGCAGCCACCAGCACAAGGGCCAUGAUGGGUGGCGGUGGUGGUG_UGCUGGUGCGGGCUUUUCCGCGGGCGCCAGUGGCCCAAUGCUGGGUGCUGGCGGC
...........((...(((((((((((((.(.(....(((......))).).).)))))))..))))))....)).....((((.(((((.................))))).)))). (-19.65 = -23.91 +   4.27)

alignment

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secondary structure

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dotplot

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Window 0

Location 8,103,315 – 8,103,433
Length 118
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 67.85
Mean single sequence MFE -42.38
Consensus MFE -17.01
Energy contribution -19.60
Covariance contribution 2.59
Combinations/Pair 1.10
Mean z-score -2.33
Structure conservation index 0.40
SVM decision value 1.88
SVM RNA-class probability 0.981078
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8103315 118 - 22407834
ACCGCCAGCACCCAGCAUUGGGCCACUGGCGCCCGCGGAAAAGCCCGCACCAGCAACGCCACCACCGCCACCCAUCAUGGCCCUUGUGCUGGUGGCUGCUGAAAUGGUGGUCUGCUCU
((((((((..(((......)))...)))))(((.((((......))))..(((((..(((((((.(((...((.....)).....))).))))))))))))....))))))....... ( -48.70)
>DroSec_CAF1 59310 118 - 1
ACCGCCAGCACCCAGCAUAGGGCCACUGGCGCCCGCGGAAAAGCCCGAACCAGCAACACCACCACCGCCACCCAUCAUGGCCCUUGUGCUGGUGGCUGCUGAAAUGGUGGUCUGCUCU
..((((((..(((......)))...))))))...(((((...(((.....(((((.(((((.(((.((((.......))))....))).)))))..)))))....)))..)))))... ( -47.50)
>DroSim_CAF1 60748 118 - 1
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNACCACCACCGCCACCCAUCAUGGCCCUUGUGCUAGUGGCUGCUGAAAUGGUGGUCUGCUCU
..................................................................((((((..((((((((((......)).))))).)))...))))))....... ( -17.90)
>DroEre_CAF1 59978 106 - 1
GCCGCCAGCACCCAGCAUUGGGCCACUGGCGCCCGCAGAAAUGCCCGCACCAGCA------------CCACCCAUCAUGGCCCUUGUGCUGGUGGCUGCUGAAAUGGUGGUCUGCUCU
(((((((((..(((((((.((((((((((.((..(((....)))..)).))))..------------..........))))))..)))))))..))........)))))))....... ( -47.50)
>DroYak_CAF1 60940 118 - 1
GCCGCCAGCACCCAGCAUUUGGCCACUCGCGCCCGCAGAAAUGCCCGCAGCAGCAGCGCCACCACCGCCACCCAUCAUGGCCCUUGUGCUGGUGGCUGCUGAAAUGGUGGUGUGCUCU
......((((((((.(((((........(((...(((....))).)))..(((((((((((.(((.((((.......))))....))).)))).)))))))))))).))).))))).. ( -49.60)
>DroAna_CAF1 61695 100 - 1
GUUAACAGCACCCAUCAUC---------------ACGG---AGCCACCACCAGCAGCACCAGCACCCAGACCAGACAUGGCUAUUGUGCUGGUGGCUGCCGAUAUGGUGGUCUGUUCC
...................---------------..((---(((.((((((((((((((((((((..((.(((....)))))...)))))))).))))).....)))))))..))))) ( -43.10)
>consensus
GCCGCCAGCACCCAGCAUUGGGCCACUGGCGCCCGCGGAAAAGCCCGCACCAGCA_CACCACCACCGCCACCCAUCAUGGCCCUUGUGCUGGUGGCUGCUGAAAUGGUGGUCUGCUCU
...((((((((........((((.......))))................................((((.......))))....))))))))(((..((.....))..)))...... (-17.01 = -19.60 +   2.59)

alignment

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secondary structure

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dotplot

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Window 1

Location 8,103,393 – 8,103,496
Length 103
Sequences 5
Columns 103
Reading direction forward
Mean pairwise identity 81.26
Mean single sequence MFE -47.42
Consensus MFE -34.56
Energy contribution -38.72
Covariance contribution 4.16
Combinations/Pair 1.11
Mean z-score -2.00
Structure conservation index 0.73
SVM decision value 0.96
SVM RNA-class probability 0.889278
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8103393 103 + 22407834
UUCCGCGGGCGCCAGUGGCCCAAUGCUGGGUGCUGGCGGUCACAUGCUGAUGGGUGGCCAGGGGCAUCAGGUGCAUCUGCAGCACCAGACGCUCUUGCCCGUC
....(((((((((((((.((((....)))))))))))((((((..........))))))((((((.((.(((((.......))))).)).)))))))))))). ( -54.40)
>DroSec_CAF1 59388 103 + 1
UUCCGCGGGCGCCAGUGGCCCUAUGCUGGGUGCUGGCGGUCACAUGCUGAUGGGUGGCCAGGGGCAUCAGGUGCAUCUGCAGCACCAGACGCUCUUGCCCGUC
....(((((((((((((.(((......))))))))))((((((..........))))))((((((.((.(((((.......))))).)).)))))))))))). ( -54.00)
>DroEre_CAF1 60044 103 + 1
UUCUGCGGGCGCCAGUGGCCCAAUGCUGGGUGCUGGCGGCCACAUGCUGAUGGGUGGCCAGGGGCAUCAGGUGCAUCUGCAGCACCAGACGCUCUUGCCCGUC
....(((((((((((((.((((....)))))))))))((((((..........))))))((((((.((.(((((.......))))).)).)))))))))))). ( -57.00)
>DroYak_CAF1 61018 103 + 1
UUCUGCGGGCGCGAGUGGCCAAAUGCUGGGUGCUGGCGGCCACAUGCUGAUGGGUGGCCAGGGGCAUCAGGUGCAUCUGCAGCACCAGACGCUCUUGCCCGUC
....((((((((.((((.(((.....))).)))).))((((((..........))))))((((((.((.(((((.......))))).)).)))))))))))). ( -51.60)
>DroAna_CAF1 61772 80 + 1
--CCGU---------------GAUGAUGGGUGCUGUUAACCACAUGAUGAUGGGUGGU------GGUCAGUUGCUUCAGCCCUCCCAGACGCUCUUGCCUAUC
--((((---------------.((.((((((.......))).))).)).))))..(((------((.(((..((.((..........)).))..))).))))) ( -20.10)
>consensus
UUCCGCGGGCGCCAGUGGCCCAAUGCUGGGUGCUGGCGGCCACAUGCUGAUGGGUGGCCAGGGGCAUCAGGUGCAUCUGCAGCACCAGACGCUCUUGCCCGUC
....(((((((((((((.(((......))))))))))((((((..........))))))((((((.((.(((((.......))))).)).)))))))))))). (-34.56 = -38.72 +   4.16)

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 10:37:22 2006