Locus 2782

Sequence ID 2R_DroMel_CAF1
Location 9,722,313 – 9,722,454
Length 141
Max. P 0.769984
window4602 window4603 window4604

overview

Window 2

Location 9,722,313 – 9,722,415
Length 102
Sequences 5
Columns 102
Reading direction forward
Mean pairwise identity 86.42
Mean single sequence MFE -34.40
Consensus MFE -25.32
Energy contribution -26.40
Covariance contribution 1.08
Combinations/Pair 1.08
Mean z-score -1.87
Structure conservation index 0.74
SVM decision value 0.44
SVM RNA-class probability 0.737015
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9722313 102 + 20766785
AGCGGUGCGGCAAGGUAAUAAAAGCCAUUUUGGUUUUCGGCCACAGUCAAAGCCGGCUCGGCUCGACUGGCGAGGCUGAAUCUGGAUAAAGUGGCGGAGUAG
.((..(((.((..(((.......)))..((..(..(((((((.(((((..(((((...))))).)))))....))))))).)..))....)).)))..)).. ( -36.20)
>DroSec_CAF1 40064 102 + 1
AGCGGUGCGGCAAGGUAAUAAAAGCCAUUUUGGUUUUCGGCCACAGUCAAAGCCGGCUCGGUUCGACUGGCGAGGCUGAGGCUGGAUGAAGUGGCGGAGUAG
.((......))............((((((((....(((((((.(((((...(((((.(((...))))))))..))))).))))))).))))))))....... ( -39.70)
>DroSim_CAF1 31340 102 + 1
AGCGGAGCGGCAAGGUAAUAAAAGCCAUUUUGGUUUUCGGCCACAGUCAAAGCCGGCUCGGCUCGACUGGCGAGGCUGAGGCUGGAUGAAGUGGCGGAGUAG
.((......))............((((((((....(((((((.(((((...(((((.(((...))))))))..))))).))))))).))))))))....... ( -39.70)
>DroEre_CAF1 32963 91 + 1
AGCGGUGCGGCAAGGUAAUAAAAGCCAUUUUGGUUUUCGGCCACAGUCGAAGCCAGCUC----------GCGAGGCUGGG-AAGGAUGAUGUGGCGGAGUAG
.((..(((.(((.(((....((((((.....))))))..))).((..(....(((((.(----------....)))))).-..)..)).))).)))..)).. ( -29.60)
>DroYak_CAF1 38870 91 + 1
AGCGGUGUGGCAAGGUAAUAAAAGCCAUUUUGGUUUUCGGCCACAGUCGAAGUCAGUUU----------GCGAGGCUGGA-AAGGAUGAGGUGGCGGAGUAG
..(((.(((((............))))).)))...(((.(((((.(((....((((((.----------....)))))).-...)))...))))).)))... ( -26.80)
>consensus
AGCGGUGCGGCAAGGUAAUAAAAGCCAUUUUGGUUUUCGGCCACAGUCAAAGCCGGCUCGG_UCGACUGGCGAGGCUGAG_CUGGAUGAAGUGGCGGAGUAG
.((..(((.((..(((....((((((.....))))))..))).(((((...(((((..........)))))..)))))............)).)))..)).. (-25.32 = -26.40 +   1.08)

alignment

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secondary structure

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dotplot

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Window 3

Location 9,722,345 – 9,722,454
Length 109
Sequences 4
Columns 109
Reading direction forward
Mean pairwise identity 86.88
Mean single sequence MFE -41.38
Consensus MFE -29.80
Energy contribution -30.18
Covariance contribution 0.38
Combinations/Pair 1.04
Mean z-score -1.71
Structure conservation index 0.72
SVM decision value 0.31
SVM RNA-class probability 0.683285
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9722345 109 + 20766785
GUUUUCGGCCACAGUCAAAGCCGGCUCGGCUCGACUGGCGAGGCUGAAUCUGGAUAAAGUGGCGGAGUAGGAGGUGGCUGGUGGGACCUGGAGGUGGGUGUGGCCACAG
......(((((((.((...((((((.((.(((.(((..((..(((..((....))..)))..)).)))..))).))))))))...(((....))))).))))))).... ( -40.80)
>DroSec_CAF1 40096 107 + 1
GUUUUCGGCCACAGUCAAAGCCGGCUCGGUUCGACUGGCGAGGCUGAGGCUGGAUGAAGUGGCGGAGUAGGAGGUGGCUGGUGGGACCUGGAGGUGGGUGUGGCC--AG
...(((.(((((..(((...(((((((((((((.....))).))))).))))).))).))))).)))..........(((((.(.((((......)))).).)))--)) ( -43.60)
>DroSim_CAF1 31372 107 + 1
GUUUUCGGCCACAGUCAAAGCCGGCUCGGCUCGACUGGCGAGGCUGAGGCUGGAUGAAGUGGCGGAGUAGGAGGUGGCUGGUGGGACCUGGAGGUGGGUGUGGCC--AG
...(((.(((((..(((...(((((((((((((.....))).))))).))))).))).))))).)))..........(((((.(.((((......)))).).)))--)) ( -46.00)
>DroEre_CAF1 32995 92 + 1
GUUUUCGGCCACAGUCGAAGCCAGCUC----------GCGAGGCUGGG-AAGGAUGAUGUGGCGGAGUAGGAGG---CUGGG-GGGCCUGGAGGUGGGUGUGGCC--AG
...(((.(((((((((....(((((.(----------....)))))).-...)))..)))))).))).....((---((...-(.((((......)))).)))))--.. ( -35.10)
>consensus
GUUUUCGGCCACAGUCAAAGCCGGCUCGGCUCGACUGGCGAGGCUGAGGCUGGAUGAAGUGGCGGAGUAGGAGGUGGCUGGUGGGACCUGGAGGUGGGUGUGGCC__AG
...(((.(((((.(((..((((.(((.(......).)))..)))).......)))...))))).)))............(((.(.((((......)))).).))).... (-29.80 = -30.18 +   0.38)

alignment

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secondary structure

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dotplot

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Window 4

Location 9,722,345 – 9,722,454
Length 109
Sequences 4
Columns 109
Reading direction reverse
Mean pairwise identity 86.88
Mean single sequence MFE -27.61
Consensus MFE -19.51
Energy contribution -19.57
Covariance contribution 0.06
Combinations/Pair 1.00
Mean z-score -1.95
Structure conservation index 0.71
SVM decision value 0.53
SVM RNA-class probability 0.769984
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9722345 109 - 20766785
CUGUGGCCACACCCACCUCCAGGUCCCACCAGCCACCUCCUACUCCGCCACUUUAUCCAGAUUCAGCCUCGCCAGUCGAGCCGAGCCGGCUUUGACUGUGGCCGAAAAC
..(((((.......(((....))).......))))).........................(((.(((....(((((((((((...)))).))))))).))).)))... ( -30.64)
>DroSec_CAF1 40096 107 - 1
CU--GGCCACACCCACCUCCAGGUCCCACCAGCCACCUCCUACUCCGCCACUUCAUCCAGCCUCAGCCUCGCCAGUCGAACCGAGCCGGCUUUGACUGUGGCCGAAAAC
.(--(((.......(((....))).......))))........((.(((((.(((...((((...((.(((..........))))).)))).)))..))))).)).... ( -26.14)
>DroSim_CAF1 31372 107 - 1
CU--GGCCACACCCACCUCCAGGUCCCACCAGCCACCUCCUACUCCGCCACUUCAUCCAGCCUCAGCCUCGCCAGUCGAGCCGAGCCGGCUUUGACUGUGGCCGAAAAC
.(--(((.......(((....))).......))))........((.(((((........((....))......((((((((((...)))).))))))))))).)).... ( -28.34)
>DroEre_CAF1 32995 92 - 1
CU--GGCCACACCCACCUCCAGGCCC-CCCAG---CCUCCUACUCCGCCACAUCAUCCUU-CCCAGCCUCGC----------GAGCUGGCUUCGACUGUGGCCGAAAAC
.(--(((((((..(......((((..-....)---)))......................-.((((((....----------).)))))....)..))))))))..... ( -25.30)
>consensus
CU__GGCCACACCCACCUCCAGGUCCCACCAGCCACCUCCUACUCCGCCACUUCAUCCAGCCUCAGCCUCGCCAGUCGAGCCGAGCCGGCUUUGACUGUGGCCGAAAAC
....(((((((..(.......((.....))..................................((((..((..(......)..)).))))..)..)))))))...... (-19.51 = -19.57 +   0.06)

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 10:39:19 2006