Locus 3271

Sequence ID 2L_DroMel_CAF1
Location 9,479,463 – 9,479,593
Length 130
Max. P 0.998402
window5194 window5195 window5196 window5197

overview

Window 4

Location 9,479,463 – 9,479,554
Length 91
Sequences 4
Columns 91
Reading direction forward
Mean pairwise identity 98.34
Mean single sequence MFE -36.00
Consensus MFE -33.92
Energy contribution -35.93
Covariance contribution 2.00
Combinations/Pair 1.00
Mean z-score -5.61
Structure conservation index 0.94
SVM decision value 0.19
SVM RNA-class probability 0.625567
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9479463 91 + 22407834
AUCAGUGUGUGGGUGUGGAAGGUCCUGUGCACUGGUUGACGCCAAAGAAAUUUGGCGUCAGUUUUAUGCGAAGAGCGGAGCAAAAAAAGAA
(((((((((..((..........))..)))))))))((((((((((....))))))))))((((..(((.....))))))).......... ( -36.20)
>DroSec_CAF1 40544 90 + 1
AUCAGUGUGUGGGUGUGGAAGGUCCUGUGCACUGGUUGACGCCAAAGAAAUUUGGCGUCAGUUUUAUGCGAAGAGCGGAGCAAA-AAAGAA
(((((((((..((..........))..)))))))))((((((((((....))))))))))((((..(((.....)))))))...-...... ( -36.20)
>DroEre_CAF1 41372 90 + 1
AUCAGUGUGUGGGUGUGGAAGGUCCUGUGCACUGGUUGACGCCAAAGAAAUUUGGCGUCAGUUUUAUGCGAGGAGCGGAGCAAA-AAAGAA
(((((((((..((..........))..)))))))))((((((((((....))))))))))((((..(((.....)))))))...-...... ( -36.20)
>DroYak_CAF1 41887 90 + 1
AUCAGUGUGUGGGUGUGGAAGGUCCUGUGCACUGGUUGACGCCAAAGAAAUUUGGCGUCAGUUUUAUGCGAAGUGCGGAGCAAA-AAAGAA
(((((((((..((..........))..)))))))))((((((((((....))))))))))((((..(((...)))..))))...-...... ( -35.40)
>consensus
AUCAGUGUGUGGGUGUGGAAGGUCCUGUGCACUGGUUGACGCCAAAGAAAUUUGGCGUCAGUUUUAUGCGAAGAGCGGAGCAAA_AAAGAA
(((((((((..((..........))..)))))))))((((((((((....))))))))))((((..(((.....))))))).......... (-33.92 = -35.93 +   2.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 9,479,463 – 9,479,554
Length 91
Sequences 4
Columns 91
Reading direction reverse
Mean pairwise identity 98.34
Mean single sequence MFE -22.07
Consensus MFE -21.52
Energy contribution -21.52
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -4.06
Structure conservation index 0.98
SVM decision value 1.30
SVM RNA-class probability 0.939378
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9479463 91 - 22407834
UUCUUUUUUUGCUCCGCUCUUCGCAUAAAACUGACGCCAAAUUUCUUUGGCGUCAACCAGUGCACAGGACCUUCCACACCCACACACUGAU
....((((.(((..........))).)))).((((((((((....))))))))))..(((((....((..........))....))))).. ( -22.10)
>DroSec_CAF1 40544 90 - 1
UUCUUU-UUUGCUCCGCUCUUCGCAUAAAACUGACGCCAAAUUUCUUUGGCGUCAACCAGUGCACAGGACCUUCCACACCCACACACUGAU
...(((-(.(((..........))).)))).((((((((((....))))))))))..(((((....((..........))....))))).. ( -22.00)
>DroEre_CAF1 41372 90 - 1
UUCUUU-UUUGCUCCGCUCCUCGCAUAAAACUGACGCCAAAUUUCUUUGGCGUCAACCAGUGCACAGGACCUUCCACACCCACACACUGAU
......-........(.((((.((((.....((((((((((....))))))))))....))))..)))).).................... ( -22.20)
>DroYak_CAF1 41887 90 - 1
UUCUUU-UUUGCUCCGCACUUCGCAUAAAACUGACGCCAAAUUUCUUUGGCGUCAACCAGUGCACAGGACCUUCCACACCCACACACUGAU
...(((-(.(((..........))).)))).((((((((((....))))))))))..(((((....((..........))....))))).. ( -22.00)
>consensus
UUCUUU_UUUGCUCCGCUCUUCGCAUAAAACUGACGCCAAAUUUCUUUGGCGUCAACCAGUGCACAGGACCUUCCACACCCACACACUGAU
...............((.....)).......((((((((((....))))))))))..(((((....((..........))....))))).. (-21.52 = -21.52 +   0.00)

alignment

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secondary structure

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dotplot

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Window 6

Location 9,479,483 – 9,479,593
Length 110
Sequences 5
Columns 116
Reading direction forward
Mean pairwise identity 80.46
Mean single sequence MFE -33.05
Consensus MFE -20.78
Energy contribution -23.22
Covariance contribution 2.44
Combinations/Pair 1.05
Mean z-score -2.82
Structure conservation index 0.63
SVM decision value 2.21
SVM RNA-class probability 0.990338
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9479483 110 + 22407834
G---GUCCUGUGCACUGGUUGACGCCAAAGAAAUUUGGCGUCAGUUUUAUGCGAAGAGCGGA--GCAAAAAAAGAAGGUGA-ACGCUGAGGUCGAAUUGGGUUAGAUCGCUGAGGA
.---.((((.((((..(..((((((((((....))))))))))..)...))))...((((((--((.......((.(((..-..)))....)).......)))...))))).)))) ( -33.54)
>DroSec_CAF1 40564 109 + 1
G---GUCCUGUGCACUGGUUGACGCCAAAGAAAUUUGGCGUCAGUUUUAUGCGAAGAGCGGA--GCAAA-AAAGAAGGUGA-ACGCUGAGGUCGGUUUGGGUUAGAUCGUUGAGGA
.---.((((((.((((...((((((((((....))))))))))((((..(((.....)))))--))...-......)))).-)).....((((...........))))....)))) ( -33.00)
>DroEre_CAF1 41392 98 + 1
G---GUCCUGUGCACUGGUUGACGCCAAAGAAAUUUGGCGUCAGUUUUAUGCGAGGAGCGGA--GCAAA-AAAGAAGGUGA-ACGG-----------CGGGUUAGAUCGGAAGGGA
.---..(((((.((((...((((((((((....))))))))))((((..(((.....)))))--))...-......)))).-...)-----------)))).....((....)).. ( -32.70)
>DroYak_CAF1 41907 98 + 1
G---GUCCUGUGCACUGGUUGACGCCAAAGAAAUUUGGCGUCAGUUUUAUGCGAAGUGCGGA--GCAAA-AAAGAAGGUGA-ACGG-----------UGGGUUAGAUCCGAAAGGA
.---.((((((.((((...((((((((((....))))))))))((((..(((...)))..))--))...-......)))).-))))-----------.))......(((....))) ( -34.30)
>DroAna_CAF1 59551 103 + 1
GUGAGCGCUGUGCCUUGCUUGACGCCAAAGAAAUUUGGCGUCAGUUUUAUGCGAAAACCAAAAGGCAAA-AAAGAAGGUAGCAUUC-----------UCGGUUA-UUCGGAACAGA
....(((((.((((((...((((((((((....))))))))))(((((.....)))))...))))))..-......))).)).(((-----------.(((...-.)))))).... ( -31.70)
>consensus
G___GUCCUGUGCACUGGUUGACGCCAAAGAAAUUUGGCGUCAGUUUUAUGCGAAGAGCGGA__GCAAA_AAAGAAGGUGA_ACGC___________UGGGUUAGAUCGGAAAGGA
....(..((.((((..(((((((((((((....)))))))))))))...)))).))..)......................................................... (-20.78 = -23.22 +   2.44)

alignment

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secondary structure

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dotplot

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Window 7

Location 9,479,483 – 9,479,593
Length 110
Sequences 5
Columns 116
Reading direction reverse
Mean pairwise identity 80.46
Mean single sequence MFE -25.36
Consensus MFE -18.26
Energy contribution -18.30
Covariance contribution 0.04
Combinations/Pair 1.07
Mean z-score -3.27
Structure conservation index 0.72
SVM decision value 3.09
SVM RNA-class probability 0.998402
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9479483 110 - 22407834
UCCUCAGCGAUCUAACCCAAUUCGACCUCAGCGU-UCACCUUCUUUUUUUGC--UCCGCUCUUCGCAUAAAACUGACGCCAAAUUUCUUUGGCGUCAACCAGUGCACAGGAC---C
((((.((((..............(....)((((.-..............)))--).))))....((((.....((((((((((....))))))))))....))))..)))).---. ( -26.16)
>DroSec_CAF1 40564 109 - 1
UCCUCAACGAUCUAACCCAAACCGACCUCAGCGU-UCACCUUCUUU-UUUGC--UCCGCUCUUCGCAUAAAACUGACGCCAAAUUUCUUUGGCGUCAACCAGUGCACAGGAC---C
((((...................((.(..((((.-...........-..)))--)..).))...((((.....((((((((((....))))))))))....))))..)))).---. ( -23.94)
>DroEre_CAF1 41392 98 - 1
UCCCUUCCGAUCUAACCCG-----------CCGU-UCACCUUCUUU-UUUGC--UCCGCUCCUCGCAUAAAACUGACGCCAAAUUUCUUUGGCGUCAACCAGUGCACAGGAC---C
.....(((..........(-----------(.(.-.((........-..)).--.).)).....((((.....((((((((((....))))))))))....))))...))).---. ( -22.20)
>DroYak_CAF1 41907 98 - 1
UCCUUUCGGAUCUAACCCA-----------CCGU-UCACCUUCUUU-UUUGC--UCCGCACUUCGCAUAAAACUGACGCCAAAUUUCUUUGGCGUCAACCAGUGCACAGGAC---C
((((...((.......)).-----------..((-.(((....(((-(.(((--..........))).)))).((((((((((....))))))))))....))).)))))).---. ( -24.30)
>DroAna_CAF1 59551 103 - 1
UCUGUUCCGAA-UAACCGA-----------GAAUGCUACCUUCUUU-UUUGCCUUUUGGUUUUCGCAUAAAACUGACGCCAAAUUUCUUUGGCGUCAAGCAAGGCACAGCGCUCAC
.((((.(((((-.((((((-----------((..((..........-...)).))))))))))).........((((((((((....)))))))))).....)).))))....... ( -30.22)
>consensus
UCCUUUCCGAUCUAACCCA___________GCGU_UCACCUUCUUU_UUUGC__UCCGCUCUUCGCAUAAAACUGACGCCAAAUUUCUUUGGCGUCAACCAGUGCACAGGAC___C
................................................................((((.....((((((((((....))))))))))....))))........... (-18.26 = -18.30 +   0.04)

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 10:48:32 2006