Locus 908

Sequence ID 2R_DroMel_CAF1
Location 4,053,425 – 4,053,585
Length 160
Max. P 0.999018
window1595 window1596 window1597

overview

Window 5

Location 4,053,425 – 4,053,545
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.03
Mean single sequence MFE -32.96
Consensus MFE -23.99
Energy contribution -25.47
Covariance contribution 1.48
Combinations/Pair 1.03
Mean z-score -1.74
Structure conservation index 0.73
SVM decision value 0.13
SVM RNA-class probability 0.597814
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4053425 120 + 20766785
UGAAUGGAUUGCCUAUUGGUUCUGUGUUUGGAUUGGUUUUGCUGCACGUUGACUGGCAUGUAAAACAUGCCAAGAAAUCCAAAUAAAAUCCUUUUUGGAGCAGACAAGCCAUUGGUUCAG
......((..(((...((((((((((((((((((((((..((.....)).))))((((((.....))))))....)))))))))....(((.....))))))))...))))..))))).. ( -36.80)
>DroSec_CAF1 36093 119 + 1
UGAAUGGAUUGCCUAUUGGUUCUGUGUUUG-UUUGGUUUUGCUGCACGUUAACUGGCAUGUAAAACAUGCCAAGAAAUCCAAAUAAAACCCUUUUCGGAGCAGACAAGCCAUUGGUUUAG
..........(((...(((((((((.((((-(((((((((((.....))....(((((((.....))))))).)))).)))))))))..((.....)).)))))...))))..))).... ( -31.40)
>DroSim_CAF1 42218 120 + 1
UGAAUGGAUUGCCUAUUGGUUCUGUGUUUGGAUUGGUUUUGCUGCACGUUGACUGGCAUGUAAAACAUGCCAAGAAAUCCAAAUAAAACCCUUUUCGGAGCAGACAAGCCAUUGGUUUAG
..........(((...((((((((((((((((((((((..((.....)).))))((((((.....))))))....))))))))).....((.....)).)))))...))))..))).... ( -34.10)
>DroEre_CAF1 36053 114 + 1
UGAAUGGAUUGCCUAUUGGUUCUGUGCUUGGAUUGGAUUGGU------UUGACUGGCAUGUAAAACAGGCCAAGAAAUCCAAAUAAAAUCCUUUUUGGAGCAGACAAGCCAUUGGUUGGG
..........(((...(((((((((..(((((((...(((((------(((((......))....))))))))..)))))))......(((.....))))))))...))))..))).... ( -31.70)
>DroYak_CAF1 39544 109 + 1
UGAAUGGAUUGCCUAUUGGUUCUGUGCUUGGA-----UUGGU------UUGACUAGCAUGUAAAACAUGCCAAGAAAUUCAAAUAAAACCCUUUUGGGAGCAGACAAGCCAUUGGUGGAG
........(..((...(((((((((.((..((-----..(((------((.....(((((.....)))))...(.....).....)))))..))..)).)))))...))))..))..).. ( -30.80)
>consensus
UGAAUGGAUUGCCUAUUGGUUCUGUGUUUGGAUUGGUUUUGCUGCACGUUGACUGGCAUGUAAAACAUGCCAAGAAAUCCAAAUAAAACCCUUUUCGGAGCAGACAAGCCAUUGGUUGAG
..........(((...((((((((((((((((((...................(((((((.....)))))))...))))))))).....((.....)).)))))...))))..))).... (-23.99 = -25.47 +   1.48)

alignment

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secondary structure

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dotplot

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Window 6

Location 4,053,425 – 4,053,545
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.03
Mean single sequence MFE -29.14
Consensus MFE -24.74
Energy contribution -25.06
Covariance contribution 0.32
Combinations/Pair 1.12
Mean z-score -2.87
Structure conservation index 0.85
SVM decision value 3.33
SVM RNA-class probability 0.999018
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4053425 120 - 20766785
CUGAACCAAUGGCUUGUCUGCUCCAAAAAGGAUUUUAUUUGGAUUUCUUGGCAUGUUUUACAUGCCAGUCAACGUGCAGCAAAACCAAUCCAAACACAGAACCAAUAGGCAAUCCAUUCA
.......(((((.(((((((.(((.....))).....((((((((..((((((((.....)))))))).....((........)).))))))))...........))))))).))))).. ( -31.30)
>DroSec_CAF1 36093 119 - 1
CUAAACCAAUGGCUUGUCUGCUCCGAAAAGGGUUUUAUUUGGAUUUCUUGGCAUGUUUUACAUGCCAGUUAACGUGCAGCAAAACCAAA-CAAACACAGAACCAAUAGGCAAUCCAUUCA
.......(((((.(((((((..((.....))((((..(((((......(((((((.....)))))))((......)).......)))))-.))))..........))))))).))))).. ( -29.90)
>DroSim_CAF1 42218 120 - 1
CUAAACCAAUGGCUUGUCUGCUCCGAAAAGGGUUUUAUUUGGAUUUCUUGGCAUGUUUUACAUGCCAGUCAACGUGCAGCAAAACCAAUCCAAACACAGAACCAAUAGGCAAUCCAUUCA
.......(((((.(((((((((......))((((((.((((((((..((((((((.....)))))))).....((........)).))))))))...))))))..))))))).))))).. ( -33.50)
>DroEre_CAF1 36053 114 - 1
CCCAACCAAUGGCUUGUCUGCUCCAAAAAGGAUUUUAUUUGGAUUUCUUGGCCUGUUUUACAUGCCAGUCAA------ACCAAUCCAAUCCAAGCACAGAACCAAUAGGCAAUCCAUUCA
.......(((((.(((((((.........(((((....((((.((..(((((.((.....)).)))))..))------.))))...)))))..(........)..))))))).))))).. ( -25.50)
>DroYak_CAF1 39544 109 - 1
CUCCACCAAUGGCUUGUCUGCUCCCAAAAGGGUUUUAUUUGAAUUUCUUGGCAUGUUUUACAUGCUAGUCAA------ACCAA-----UCCAAGCACAGAACCAAUAGGCAAUCCAUUCA
.......(((((.(((((((..(((....))).....(((((.....((((((((.....))))))))))))------)....-----.................))))))).))))).. ( -25.50)
>consensus
CUAAACCAAUGGCUUGUCUGCUCCAAAAAGGGUUUUAUUUGGAUUUCUUGGCAUGUUUUACAUGCCAGUCAACGUGCAGCAAAACCAAUCCAAACACAGAACCAAUAGGCAAUCCAUUCA
.......(((((.(((((((.(((.....))).....((((((((...(((((((.....)))))))((.........))......))))))))...........))))))).))))).. (-24.74 = -25.06 +   0.32)

alignment

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secondary structure

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dotplot

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Window 7

Location 4,053,465 – 4,053,585
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 90.45
Mean single sequence MFE -28.79
Consensus MFE -24.42
Energy contribution -24.10
Covariance contribution -0.32
Combinations/Pair 1.12
Mean z-score -1.54
Structure conservation index 0.85
SVM decision value 0.73
SVM RNA-class probability 0.835987
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4053465 120 - 20766785
AAUUGAUAAAUGAAUUUCUAUACUGGCCGUCGCAUUCUUCCUGAACCAAUGGCUUGUCUGCUCCAAAAAGGAUUUUAUUUGGAUUUCUUGGCAUGUUUUACAUGCCAGUCAACGUGCAGC
.....................((.((((((.(..(((.....))).).)))))).))((((((((((..........))))))....((((((((.....)))))))).......)))). ( -27.60)
>DroSec_CAF1 36132 120 - 1
AAUUGAUAAAUGAAUUUCUGUACUGGCAGCCGCAUUCUUCCUAAACCAAUGGCUUGUCUGCUCCGAAAAGGGUUUUAUUUGGAUUUCUUGGCAUGUUUUACAUGCCAGUUAACGUGCAGC
.................((((((.((((((((.................)))).))))...((((((..........))))))....((((((((.....)))))))).....)))))). ( -28.13)
>DroSim_CAF1 42258 120 - 1
AAUUGAUAAAUGAAUUUCUGUACUGGCAGCCGCAUUCUUCCUAAACCAAUGGCUUGUCUGCUCCGAAAAGGGUUUUAUUUGGAUUUCUUGGCAUGUUUUACAUGCCAGUCAACGUGCAGC
.................((((((((((...........(((.(((((...(((......)))........))))).....))).....(((((((.....)))))))))))..)))))). ( -28.80)
>DroEre_CAF1 36093 114 - 1
AAUUGAUAAAUGAAUUCCUGUACUGGCAGCAGCAUUCUUUCCCAACCAAUGGCUUGUCUGCUCCAAAAAGGAUUUUAUUUGGAUUUCUUGGCCUGUUUUACAUGCCAGUCAA------AC
..((((((((((((.((((....(((.(((((((..((............))..)).))))))))...)))).)))))))........((((.((.....)).)))))))))------.. ( -30.80)
>DroYak_CAF1 39579 114 - 1
AAUUGAUAAAUGAAUUUCUGUACUGGCAGCAGCAUUCUUCCUCCACCAAUGGCUUGUCUGCUCCCAAAAGGGUUUUAUUUGAAUUUCUUGGCAUGUUUUACAUGCUAGUCAA------AC
..((((((((((((.((((....(((.(((((((..((............))..)).))))).)))..)))).)))))))........(((((((.....))))))))))))------.. ( -28.60)
>consensus
AAUUGAUAAAUGAAUUUCUGUACUGGCAGCCGCAUUCUUCCUAAACCAAUGGCUUGUCUGCUCCAAAAAGGGUUUUAUUUGGAUUUCUUGGCAUGUUUUACAUGCCAGUCAACGUGCAGC
..((((((((((((.((((.....(((((..(((..((............))..))))))))......)))).)))))))........(((((((.....))))))))))))........ (-24.42 = -24.10 +  -0.32)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:50:57 2006