Locus 2700

Sequence ID 2R_DroMel_CAF1
Location 9,510,576 – 9,510,798
Length 222
Max. P 0.999484
window4456 window4457 window4458

overview

Window 6

Location 9,510,576 – 9,510,696
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 97.31
Mean single sequence MFE -42.88
Consensus MFE -38.90
Energy contribution -39.10
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.46
Structure conservation index 0.91
SVM decision value 0.82
SVM RNA-class probability 0.860245
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9510576 120 + 20766785
CGCUGCAUUGUAGCAGGCGCUCAGCUGCAUUCACCGCACGAUUGUGUGCAGUGGCCGCAUGUUGCAAGUUGUUGCACCAGCAACACUCAAGCGAAUCUUUCGCGAAAGCCCGAGACGCAG
((((...((((((((.(((..((.((((((.((.........)).))))))))..))).))))))))..((((((....))))))....))))..((((..((....))..))))..... ( -42.50)
>DroSec_CAF1 7600 118 + 1
CGCUGCAUUGUAGCAGGCGCUCAGCUGCAUUCACCGCACGAUUG--UGCAGUGGCCGCAUGUUGCAAGUUGUUGCACCAGCAACACUCAAGCGAAUCUUUCGCGAAAGCCCGAGACGCAG
((((...((((((((.(((..((.((((((((.......))..)--)))))))..))).))))))))..((((((....))))))....))))..((((..((....))..))))..... ( -41.90)
>DroSim_CAF1 7623 118 + 1
CGCUGCAUUGUAGCAGGCGCUCAGCUGCAUUCACCGCACGAUUG--UGCAGUGGCCGCAUGUUGCAAGUUGUUGCACCAGCAACACUCAAGCGAAUCUUUCGCGAAAGCCCGAGACGCAG
((((...((((((((.(((..((.((((((((.......))..)--)))))))..))).))))))))..((((((....))))))....))))..((((..((....))..))))..... ( -41.90)
>DroEre_CAF1 7726 118 + 1
CGCUGCAUUGUAGCAGGCGCUCAGCUGCAUUAACCGCACGAUUG--UGCAGUGGUCGCAUGUUGCAAGUUGUUGCACCAGCAACACUCCAGCGAAUCUUUCGCGAAAGCCCGAGACGCAG
(((((..((((((((.(((..((.((((((.............)--)))))))..))).))))))))..((((((....))))))...)))))..((((..((....))..))))..... ( -44.02)
>DroYak_CAF1 7632 118 + 1
CGCUGCAUUGUAGCAGGCGCUCAGCUGCAUUCACCGCACGAUUG--UGCAGUGGUCGCAUGUGGCAAGUUGUUGCACCAGCAACACUCCAGCGAAUCUUUCGCGAAAGCACGAGACGCAG
.(((((...)))))..((((((.(((((..((((.((((....)--))).))))..)))..(((..(((.(((((....))))))))))))).........((....))..))).))).. ( -44.10)
>consensus
CGCUGCAUUGUAGCAGGCGCUCAGCUGCAUUCACCGCACGAUUG__UGCAGUGGCCGCAUGUUGCAAGUUGUUGCACCAGCAACACUCAAGCGAAUCUUUCGCGAAAGCCCGAGACGCAG
((((...((((((((.(((..((.(((((.....(....)......)))))))..))).))))))))..((((((....))))))....))))..((((..((....))..))))..... (-38.90 = -39.10 +   0.20)

alignment

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secondary structure

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dotplot

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Window 7

Location 9,510,576 – 9,510,696
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.31
Mean single sequence MFE -49.92
Consensus MFE -45.28
Energy contribution -45.88
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -2.75
Structure conservation index 0.91
SVM decision value 3.64
SVM RNA-class probability 0.999484
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9510576 120 - 20766785
CUGCGUCUCGGGCUUUCGCGAAAGAUUCGCUUGAGUGUUGCUGGUGCAACAACUUGCAACAUGCGGCCACUGCACACAAUCGUGCGGUGAAUGCAGCUGAGCGCCUGCUACAAUGCAGCG
..(((.(((((((((..((((.....))))..))))(((((.(((......))).))))).((((..((((((((......))))))))..)))).))))))))((((......)))).. ( -51.80)
>DroSec_CAF1 7600 118 - 1
CUGCGUCUCGGGCUUUCGCGAAAGAUUCGCUUGAGUGUUGCUGGUGCAACAACUUGCAACAUGCGGCCACUGCA--CAAUCGUGCGGUGAAUGCAGCUGAGCGCCUGCUACAAUGCAGCG
..(((.(((((((((..((((.....))))..))))(((((.(((......))).))))).((((..(((((((--(....))))))))..)))).))))))))((((......)))).. ( -51.60)
>DroSim_CAF1 7623 118 - 1
CUGCGUCUCGGGCUUUCGCGAAAGAUUCGCUUGAGUGUUGCUGGUGCAACAACUUGCAACAUGCGGCCACUGCA--CAAUCGUGCGGUGAAUGCAGCUGAGCGCCUGCUACAAUGCAGCG
..(((.(((((((((..((((.....))))..))))(((((.(((......))).))))).((((..(((((((--(....))))))))..)))).))))))))((((......)))).. ( -51.60)
>DroEre_CAF1 7726 118 - 1
CUGCGUCUCGGGCUUUCGCGAAAGAUUCGCUGGAGUGUUGCUGGUGCAACAACUUGCAACAUGCGACCACUGCA--CAAUCGUGCGGUUAAUGCAGCUGAGCGCCUGCUACAAUGCAGCG
..(((.(((((((((..((((.....))))..))))(((((.(((......))).))))).((((...((((((--(....)))))))...)))).))))))))((((......)))).. ( -47.60)
>DroYak_CAF1 7632 118 - 1
CUGCGUCUCGUGCUUUCGCGAAAGAUUCGCUGGAGUGUUGCUGGUGCAACAACUUGCCACAUGCGACCACUGCA--CAAUCGUGCGGUGAAUGCAGCUGAGCGCCUGCUACAAUGCAGCG
..(((.((((.((....((((.....))))(((..((((((....)))))).....)))..((((..(((((((--(....))))))))..)))))))))))))((((......)))).. ( -47.00)
>consensus
CUGCGUCUCGGGCUUUCGCGAAAGAUUCGCUUGAGUGUUGCUGGUGCAACAACUUGCAACAUGCGGCCACUGCA__CAAUCGUGCGGUGAAUGCAGCUGAGCGCCUGCUACAAUGCAGCG
..(((.(((((((((..((((.....))))..))))(((((.(((......))).))))).((((..(((((((........)))))))..)))).))))))))((((......)))).. (-45.28 = -45.88 +   0.60)

alignment

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secondary structure

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dotplot

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Window 8

Location 9,510,696 – 9,510,798
Length 102
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 86.98
Mean single sequence MFE -39.48
Consensus MFE -31.18
Energy contribution -30.94
Covariance contribution -0.24
Combinations/Pair 1.10
Mean z-score -2.70
Structure conservation index 0.79
SVM decision value 2.17
SVM RNA-class probability 0.989566
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9510696 102 - 20766785
AAACAGGCGAUAAGGAAGAAAGCAUAGGCGGCCAAUGCGAAUGGGGGAAAAUGGCUGGAAAACCGGUGCAGAAAUGCCAGUCGC------------------CGUCGCCAUCGUCUGUGC
..(((((((((..(........)...((((((....((((.(((.(.....(((((((....))))).))....).))).))))------------------.))))))))))))))).. ( -37.50)
>DroSec_CAF1 7718 102 - 1
AAACAGGCGAUAAGGAAGAAAGCAUAGGCGGCCAAUGCGAAUGGGGGAAAAUGGCUGGAAAACCGGUGCAGAAAUGCCAGUUGC------------------CGUCGCCAUCGUCUGUGC
..(((((((((..(........)...((((((....((((.(((.(.....(((((((....))))).))....).))).))))------------------.))))))))))))))).. ( -35.40)
>DroSim_CAF1 7741 102 - 1
AAACAGGCGAUAAGGAAGAAAGCAUAGGCGGCCAAUGCGAAUGGGGGAAAAUGGCUGGAAAACCGGUGCAGAAAUGCCAGUUGC------------------CGUCGCCAUCGUCUGUGC
..(((((((((..(........)...((((((....((((.(((.(.....(((((((....))))).))....).))).))))------------------.))))))))))))))).. ( -35.40)
>DroEre_CAF1 7844 120 - 1
AAACAGGCGAUAAGGAAGAAAGCAUAGGCGGCCAAUGCGAAUGGGGGAAAAUGCCUGGAAAACCGGUGCAGAAAUGCCAGUCGCCCUCGCCCUCGCCGUCGCCGUCGCCGUUGUCUGUGU
..(((((((((..((..((..((...((((((....((((..(((.((...((.((((....)))).(((....))))).)).)))))))....))))))))..)).))))))))))).. ( -44.90)
>DroYak_CAF1 7750 117 - 1
AAACAGGCGAUAAGGAAGAAAGCAUAGGCGGCCAACGCGAAUGGGGGAAAAUAGCUGGAAAACCGGUGCAGAAAUGCCAGUCGCCGACG---GCGAGGGGGACGUCGCAGUCGUCUGUGU
..(((((((((...............((((((.....................(((((....)))))(((....)))..))))))....---((((.(....).)))).))))))))).. ( -44.20)
>consensus
AAACAGGCGAUAAGGAAGAAAGCAUAGGCGGCCAAUGCGAAUGGGGGAAAAUGGCUGGAAAACCGGUGCAGAAAUGCCAGUCGC__________________CGUCGCCAUCGUCUGUGC
..(((((((((..(........)...((((((....((((.(((.(.......(((((....))))).......).))).))))...................))))))))))))))).. (-31.18 = -30.94 +  -0.24)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:36:56 2006