Locus 9081

Sequence ID 3R_DroMel_CAF1
Location 24,250,837 – 24,250,952
Length 115
Max. P 0.999626
window14537 window14538 window14539 window14540

overview

Window 7

Location 24,250,837 – 24,250,929
Length 92
Sequences 5
Columns 92
Reading direction forward
Mean pairwise identity 89.87
Mean single sequence MFE -33.68
Consensus MFE -29.52
Energy contribution -29.92
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.59
Structure conservation index 0.88
SVM decision value 1.02
SVM RNA-class probability 0.901796
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24250837 92 + 27905053
AGUUCGUCCUAGUCCUGCACCCGGAGUCCUGAGCCUGGCCUGAAGCACUUUUAGGCGCUCUUAGCGCGCCCAAACUUCGAGUGGCCAGGCUG
.........(((..((.(....).))..)))((((((((((((((....(((.(((((.......))))).))))))))...))))))))). ( -34.80)
>DroSec_CAF1 73765 90 + 1
AGUUCGUCCUAGUCCUGAACCUG--GUCCUGAGCCUGGCCUGAAGCACUUUUAGGCGCUCUUAGCGCGCCCAAACUUCGAGUGGCCAGGCUG
.....(..((((........)))--)..)..((((((((((((((....(((.(((((.......))))).))))))))...))))))))). ( -34.40)
>DroSim_CAF1 78307 92 + 1
AGUUCGUCCUAGUCCUGAACCCGGAGUCCUGAGCCUGGCCUGAAGCACUUUUAGGCGCUCUUAGCGCGCCCAAACUUCGAGUGGCCAGGCUG
((..(.(((..((.....))..))))..)).((((((((((((((....(((.(((((.......))))).))))))))...))))))))). ( -33.90)
>DroEre_CAF1 79023 92 + 1
AGUUCGCCCUAGUCCUGAACACGGGGUCCUGAGCCUGGCCUGAAGCACUUUUAGGCGCCCUUAGCGCGCCCAAAGUUCGAGUGGCCAGGCUG
.....(((((.((.......)))))))....(((((((((....(.(((((..(((((.......))))).))))).)....))))))))). ( -37.40)
>DroYak_CAF1 77265 78 + 1
AGUUCACCCUAGUCC--------------UGAGCCUGGCCUGAAGCACUUUUAGGCGCUCUUAGCGCGCCCAAACUUCGAGUAGCCAGGCUG
...............--------------..((((((((((((((....(((.(((((.......))))).))))))).))..)))))))). ( -27.90)
>consensus
AGUUCGUCCUAGUCCUGAACCCGG_GUCCUGAGCCUGGCCUGAAGCACUUUUAGGCGCUCUUAGCGCGCCCAAACUUCGAGUGGCCAGGCUG
...............................((((((((((((((....(((.(((((.......))))).))))))))...))))))))). (-29.52 = -29.92 +   0.40)

alignment

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secondary structure

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Window 8

Location 24,250,837 – 24,250,929
Length 92
Sequences 5
Columns 92
Reading direction reverse
Mean pairwise identity 89.87
Mean single sequence MFE -38.50
Consensus MFE -34.24
Energy contribution -34.28
Covariance contribution 0.04
Combinations/Pair 1.05
Mean z-score -2.71
Structure conservation index 0.89
SVM decision value 3.80
SVM RNA-class probability 0.999626
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24250837 92 - 27905053
CAGCCUGGCCACUCGAAGUUUGGGCGCGCUAAGAGCGCCUAAAAGUGCUUCAGGCCAGGCUCAGGACUCCGGGUGCAGGACUAGGACGAACU
.(((((((((....(((((((((((((.......))))))))....))))).))))))))).((..((((.(((.....))).))).)..)) ( -40.40)
>DroSec_CAF1 73765 90 - 1
CAGCCUGGCCACUCGAAGUUUGGGCGCGCUAAGAGCGCCUAAAAGUGCUUCAGGCCAGGCUCAGGAC--CAGGUUCAGGACUAGGACGAACU
.(((((((((....(((((((((((((.......))))))))....))))).))))))))).....(--(.((((...)))).))....... ( -38.90)
>DroSim_CAF1 78307 92 - 1
CAGCCUGGCCACUCGAAGUUUGGGCGCGCUAAGAGCGCCUAAAAGUGCUUCAGGCCAGGCUCAGGACUCCGGGUUCAGGACUAGGACGAACU
.(((((((((....(((((((((((((.......))))))))....))))).))))))))).((..((((.((((...)))).))).)..)) ( -40.40)
>DroEre_CAF1 79023 92 - 1
CAGCCUGGCCACUCGAACUUUGGGCGCGCUAAGGGCGCCUAAAAGUGCUUCAGGCCAGGCUCAGGACCCCGUGUUCAGGACUAGGGCGAACU
.(((((((((......(((((((((((.(...).)))))).)))))......))))))))).((..((((..(((...)))..))).)..)) ( -39.00)
>DroYak_CAF1 77265 78 - 1
CAGCCUGGCUACUCGAAGUUUGGGCGCGCUAAGAGCGCCUAAAAGUGCUUCAGGCCAGGCUCA--------------GGACUAGGGUGAACU
.(((((((((....(((((((((((((.......))))))))....))))).)))))))))..--------------............... ( -33.80)
>consensus
CAGCCUGGCCACUCGAAGUUUGGGCGCGCUAAGAGCGCCUAAAAGUGCUUCAGGCCAGGCUCAGGAC_CCGGGUUCAGGACUAGGACGAACU
.(((((((((....(((((((((((((.......))))))))....))))).)))))))))............................... (-34.24 = -34.28 +   0.04)

alignment

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secondary structure

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Window 9

Location 24,250,860 – 24,250,952
Length 92
Sequences 6
Columns 94
Reading direction forward
Mean pairwise identity 82.51
Mean single sequence MFE -32.52
Consensus MFE -25.71
Energy contribution -26.68
Covariance contribution 0.97
Combinations/Pair 1.18
Mean z-score -1.77
Structure conservation index 0.79
SVM decision value 0.47
SVM RNA-class probability 0.749817
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24250860 92 + 27905053
GAGUCCUGAGCCUGGCCUGAAGCACUUUUAGGCGCUCUUAGCGCGCCCAAACUUCGAGUGGCCAGGCUGAAACGGCUAAA--ACGGCUGAAUGG
......(.((((((((((((((....(((.(((((.......))))).))))))))...))))))))).)..(((((...--..)))))..... ( -36.80)
>DroSec_CAF1 73788 90 + 1
--GUCCUGAGCCUGGCCUGAAGCACUUUUAGGCGCUCUUAGCGCGCCCAAACUUCGAGUGGCCAGGCUGAAACAUUUAAA--ACGGCUGAAUGG
--....(.((((((((((((((....(((.(((((.......))))).))))))))...))))))))).)..((((((..--.....)))))). ( -34.30)
>DroSim_CAF1 78330 92 + 1
GAGUCCUGAGCCUGGCCUGAAGCACUUUUAGGCGCUCUUAGCGCGCCCAAACUUCGAGUGGCCAGGCUGAAACAGCUAAA--ACGGCUGAAUGG
......(.((((((((((((((....(((.(((((.......))))).))))))))...))))))))).)..(((((...--..)))))..... ( -37.50)
>DroEre_CAF1 79046 92 + 1
GGGUCCUGAGCCUGGCCUGAAGCACUUUUAGGCGCCCUUAGCGCGCCCAAAGUUCGAGUGGCCAGGCUGAAACGGCUAAA--ACGGCUGAAUGG
......(.(((((((((....(.(((((..(((((.......))))).))))).)....))))))))).)..(((((...--..)))))..... ( -37.80)
>DroYak_CAF1 77280 86 + 1
------UGAGCCUGGCCUGAAGCACUUUUAGGCGCUCUUAGCGCGCCCAAACUUCGAGUAGCCAGGCUGAAACAGCUAAA--ACGACUGAAUGG
------(.((((((((((((((....(((.(((((.......))))).))))))).))..)))))))).)..((((....--..).)))..... ( -29.40)
>DroAna_CAF1 70954 78 + 1
--GUCCUGAUCCCGGCCUGAAGCGAUUUUAUCC---------GCACACAAACUUCGAGUGCCCAGAAUGAACUGGAUGGAUGGCGGCUG-----
--..........(((((....((.....(((((---------((((.(.......).))))((((......))))..))))))))))))----- ( -19.30)
>consensus
__GUCCUGAGCCUGGCCUGAAGCACUUUUAGGCGCUCUUAGCGCGCCCAAACUUCGAGUGGCCAGGCUGAAACAGCUAAA__ACGGCUGAAUGG
......(.((((((((((((((....(((.(((((.......))))).))))))))...))))))))).)..(((((.......)))))..... (-25.71 = -26.68 +   0.97)

alignment

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secondary structure

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Window 0

Location 24,250,860 – 24,250,952
Length 92
Sequences 6
Columns 94
Reading direction reverse
Mean pairwise identity 82.51
Mean single sequence MFE -34.47
Consensus MFE -30.17
Energy contribution -29.90
Covariance contribution -0.27
Combinations/Pair 1.27
Mean z-score -2.55
Structure conservation index 0.88
SVM decision value 1.49
SVM RNA-class probability 0.958741
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24250860 92 - 27905053
CCAUUCAGCCGU--UUUAGCCGUUUCAGCCUGGCCACUCGAAGUUUGGGCGCGCUAAGAGCGCCUAAAAGUGCUUCAGGCCAGGCUCAGGACUC
............--.......((((.(((((((((....(((((((((((((.......))))))))....))))).)))))))))..)))).. ( -37.60)
>DroSec_CAF1 73788 90 - 1
CCAUUCAGCCGU--UUUAAAUGUUUCAGCCUGGCCACUCGAAGUUUGGGCGCGCUAAGAGCGCCUAAAAGUGCUUCAGGCCAGGCUCAGGAC--
............--.......((((.(((((((((....(((((((((((((.......))))))))....))))).)))))))))..))))-- ( -36.10)
>DroSim_CAF1 78330 92 - 1
CCAUUCAGCCGU--UUUAGCUGUUUCAGCCUGGCCACUCGAAGUUUGGGCGCGCUAAGAGCGCCUAAAAGUGCUUCAGGCCAGGCUCAGGACUC
((...((((...--....))))....(((((((((....(((((((((((((.......))))))))....))))).)))))))))..)).... ( -40.80)
>DroEre_CAF1 79046 92 - 1
CCAUUCAGCCGU--UUUAGCCGUUUCAGCCUGGCCACUCGAACUUUGGGCGCGCUAAGGGCGCCUAAAAGUGCUUCAGGCCAGGCUCAGGACCC
((....(((.((--....)).)))..(((((((((......(((((((((((.(...).)))))).)))))......)))))))))..)).... ( -36.30)
>DroYak_CAF1 77280 86 - 1
CCAUUCAGUCGU--UUUAGCUGUUUCAGCCUGGCUACUCGAAGUUUGGGCGCGCUAAGAGCGCCUAAAAGUGCUUCAGGCCAGGCUCA------
.....((((...--....))))....(((((((((....(((((((((((((.......))))))))....))))).)))))))))..------ ( -35.50)
>DroAna_CAF1 70954 78 - 1
-----CAGCCGCCAUCCAUCCAGUUCAUUCUGGGCACUCGAAGUUUGUGUGC---------GGAUAAAAUCGCUUCAGGCCGGGAUCAGGAC--
-----...((.((((((..((((......))))((((.(((...))).))))---------))))......((.....))..))....))..-- ( -20.50)
>consensus
CCAUUCAGCCGU__UUUAGCCGUUUCAGCCUGGCCACUCGAAGUUUGGGCGCGCUAAGAGCGCCUAAAAGUGCUUCAGGCCAGGCUCAGGAC__
..........................(((((((((....(((((((((((((.......))))))))....))))).)))))))))........ (-30.17 = -29.90 +  -0.27)

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 13:26:13 2006