Locus 3158

Sequence ID 3R_DroMel_CAF1
Location 8,365,254 – 8,365,390
Length 136
Max. P 0.962049
window5114 window5115 window5116

overview

Window 4

Location 8,365,254 – 8,365,364
Length 110
Sequences 4
Columns 110
Reading direction forward
Mean pairwise identity 84.24
Mean single sequence MFE -30.45
Consensus MFE -24.45
Energy contribution -24.32
Covariance contribution -0.13
Combinations/Pair 1.25
Mean z-score -1.57
Structure conservation index 0.80
SVM decision value 0.23
SVM RNA-class probability 0.645266
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8365254 110 + 27905053
UUACUACUAUUAUAAAAUCGAAAAAUCAGGCUUAUGAAAGUGUGAGUCGGCCGAAAAAAGGCUUAUUCGCCCACACUGGCAUUGGUUGCCAUGGGGCAUUGUGCCUGUUG
..........................(((((............((((.((((.......)))).))))((((.((.(((((.....))))))))))).....)))))... ( -35.00)
>DroSec_CAF1 27453 110 + 1
UGACUACUAUUAUAAAAUGGGAAAAUUAGGCUUGUGAAAGUGUGAGUCGGCUGAAAAAAGGACUAUUCGCCCACACUGGCAAUGGUUGCCAUGGGGCAUUGUGCCUGUUG
.(((..(((((....))))).....(((.((((....)))).))))))(((.(((..........)))((((.((.(((((.....))))))))))).....)))..... ( -29.60)
>DroSim_CAF1 26137 100 + 1
UUACUACUAUUAUAAAAUCGAAAAAUUAGGCUU----------GAGUUGGCUGAAAAAAGGACUAUUUGCCCACACUGGCAUUGGUUGCCAUGGGGCAUUGUGCCUGUUG
..........................(((((..----------.((((..((......))))))...(((((.((.(((((.....))))))))))))....)))))... ( -25.40)
>DroYak_CAF1 27962 109 + 1
UUACAACUAUUAUAAUAACGG-AAAUUACGUUUGUGGAAGAGAGAGUCGGCUCAAAAAAGGCUUAUUCGUCCACACUGGCAUUGGUUGCCAUGGCACAUUGUGCCCGUUG
...((((.........((((.-......))))((((((.(((.(((((...........))))).))).)))))).(((((.....))))).(((((...))))).)))) ( -31.80)
>consensus
UUACUACUAUUAUAAAAUCGAAAAAUUAGGCUUGUGAAAGUGUGAGUCGGCUGAAAAAAGGACUAUUCGCCCACACUGGCAUUGGUUGCCAUGGGGCAUUGUGCCUGUUG
..........................(((((............((((.((((.......)))).))))((((.((.(((((.....))))))))))).....)))))... (-24.45 = -24.32 +  -0.13)

alignment

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secondary structure

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dotplot

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Window 5

Location 8,365,254 – 8,365,364
Length 110
Sequences 4
Columns 110
Reading direction reverse
Mean pairwise identity 84.24
Mean single sequence MFE -25.27
Consensus MFE -17.86
Energy contribution -17.55
Covariance contribution -0.31
Combinations/Pair 1.12
Mean z-score -1.65
Structure conservation index 0.71
SVM decision value 0.23
SVM RNA-class probability 0.642718
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8365254 110 - 27905053
CAACAGGCACAAUGCCCCAUGGCAACCAAUGCCAGUGUGGGCGAAUAAGCCUUUUUUCGGCCGACUCACACUUUCAUAAGCCUGAUUUUUCGAUUUUAUAAUAGUAGUAA
...(((((....((((....))))....(((..((((((((((.....(((.......))))).))))))))..)))..))))).......................... ( -30.70)
>DroSec_CAF1 27453 110 - 1
CAACAGGCACAAUGCCCCAUGGCAACCAUUGCCAGUGUGGGCGAAUAGUCCUUUUUUCAGCCGACUCACACUUUCACAAGCCUAAUUUUCCCAUUUUAUAAUAGUAGUCA
.....(((.....(((((((((((.....))))).)).))))(((..........))).)))((((.((..................................)))))). ( -24.08)
>DroSim_CAF1 26137 100 - 1
CAACAGGCACAAUGCCCCAUGGCAACCAAUGCCAGUGUGGGCAAAUAGUCCUUUUUUCAGCCAACUC----------AAGCCUAAUUUUUCGAUUUUAUAAUAGUAGUAA
....((((....((((((((((((.....))))).)).))))).......((......)).......----------..))))........................... ( -21.30)
>DroYak_CAF1 27962 109 - 1
CAACGGGCACAAUGUGCCAUGGCAACCAAUGCCAGUGUGGACGAAUAAGCCUUUUUUGAGCCGACUCUCUCUUCCACAAACGUAAUUU-CCGUUAUUAUAAUAGUUGUAA
((((.(((((...))))).(((((.....))))).((((((.((....(.(((....))).).......)).))))))((((......-.)))).........))))... ( -25.00)
>consensus
CAACAGGCACAAUGCCCCAUGGCAACCAAUGCCAGUGUGGGCGAAUAAGCCUUUUUUCAGCCGACUCACACUUUCACAAGCCUAAUUUUCCGAUUUUAUAAUAGUAGUAA
.....(((.....(((((((((((.....))))).)).))))(((........)))...)))................................................ (-17.86 = -17.55 +  -0.31)

alignment

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secondary structure

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dotplot

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Window 6

Location 8,365,294 – 8,365,390
Length 96
Sequences 5
Columns 101
Reading direction forward
Mean pairwise identity 74.10
Mean single sequence MFE -28.70
Consensus MFE -15.48
Energy contribution -16.96
Covariance contribution 1.48
Combinations/Pair 1.20
Mean z-score -2.11
Structure conservation index 0.54
SVM decision value 1.53
SVM RNA-class probability 0.962049
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8365294 96 + 27905053
UGUGAGUCGGCCGAAAAAAGGCUUAUUCGCCCACACUGGCAUUGGUUGCCAUGGGGCAUUGUGCCUGUUGUCAAUACAUUGGUACAAAGA-----GGAAAA
...((((.((((.......)))).))))((((.((.(((((.....))))))))))).(((((((...(((....)))..)))))))...-----...... ( -36.50)
>DroSec_CAF1 27493 96 + 1
UGUGAGUCGGCUGAAAAAAGGACUAUUCGCCCACACUGGCAAUGGUUGCCAUGGGGCAUUGUGCCUGUUGUCAAUACAUUGGUACAAAGG-----GUAAAA
....((((..((......))))))((((((((.((.(((((.....))))))))))).(((((((...(((....)))..))))))).))-----)).... ( -29.90)
>DroSim_CAF1 26170 93 + 1
---GAGUUGGCUGAAAAAAGGACUAUUUGCCCACACUGGCAUUGGUUGCCAUGGGGCAUUGUGCCUGUUGUCAAUACAUUGGUACAAAGG-----GUGAAA
---...((.(((...............(((((.((.(((((.....))))))))))))(((((((...(((....)))..)))))))..)-----)).)). ( -29.80)
>DroYak_CAF1 28001 96 + 1
AGAGAGUCGGCUCAAAAAAGGCUUAUUCGUCCACACUGGCAUUGGUUGCCAUGGCACAUUGUGCCCGUUGUCAUUACAUUGGUACAAAGA-----UGAAAA
...((((.((((.......)))).))))(((((...(((((.....)))))))).)).(((((((...(((....)))..)))))))...-----...... ( -25.90)
>DroAna_CAF1 28643 84 + 1
----------------AAUUGCUGAUUUGUCAGAACUGGUAUUGGUGCUUGGGGGCCAUUGUUC-UCCAGCCAAUACAUUGCUACAAAGACACAAAGAAAA
----------------..(((.((.(((((.((.....((((((((....((((((....))))-))..))))))))....)))))))..)))))...... ( -21.40)
>consensus
_G_GAGUCGGCUGAAAAAAGGCUUAUUCGCCCACACUGGCAUUGGUUGCCAUGGGGCAUUGUGCCUGUUGUCAAUACAUUGGUACAAAGA_____GGAAAA
............................((((.((.(((((.....))))))))))).(((((((...((......))..))))))).............. (-15.48 = -16.96 +   1.48)

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 10:54:28 2006