Locus 4158

Sequence ID 3L_DroMel_CAF1
Location 12,145,983 – 12,146,104
Length 121
Max. P 0.981219
window6454 window6455 window6456

overview

Window 4

Location 12,145,983 – 12,146,084
Length 101
Sequences 4
Columns 101
Reading direction forward
Mean pairwise identity 87.44
Mean single sequence MFE -34.30
Consensus MFE -28.25
Energy contribution -29.25
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.63
Structure conservation index 0.82
SVM decision value 1.88
SVM RNA-class probability 0.981219
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12145983 101 + 23771897
CAGUUCUGUUCUGUUCGUUGCAGUUUGGUUUUUAUCCUGCGGCAAUGGAAGCCGCGGGAUGAUUGCGCGGAUACAAUUAUCCAGCCACUCGGGUGAAAUGG
..(((((((.((((.....))))....((..((((((((((((.......))))))))))))..))))))).))..((((((........))))))..... ( -36.60)
>DroSec_CAF1 23287 90 + 1
CAGUUCUGUUCUGU----------UUGGUUUUUAUCCUGCGGCAAUGGAAGCCGCGGGAUGAUUGCGCGGAUACAAUUAUCCAGGCACUUGGCUGAAAUG-
(((((..(((((..----------...((..((((((((((((.......))))))))))))..))..(((((....)))))))).))..))))).....- ( -35.40)
>DroSim_CAF1 23560 90 + 1
CAGUUCUGUUCUGU----------UUCGGUUUUAUCCUGCGGCAAUGGAAGCCGCGGGAUGAUUGCGCGGAUACAAUUAUCCAGCCACUUGGCUGAAAUG-
...........(((----------((((((.((((((((((((.......))))))))))))..)).)))).)))......(((((....))))).....- ( -35.50)
>DroYak_CAF1 23305 94 + 1
CAGUUCUGUUC-----GUUGCUGUUUGGUUUUUAGCCUGCGGCAAUUGAAGCCGCGGGAUGAUUGCGCGGAUACAAUUAUCCAGCCACUUGG-UGAAAUG-
...........-----.(..(((..(((((.(((.((((((((.......)))))))).)))......(((((....))))))))))..)))-..)....- ( -29.70)
>consensus
CAGUUCUGUUCUGU__________UUGGUUUUUAUCCUGCGGCAAUGGAAGCCGCGGGAUGAUUGCGCGGAUACAAUUAUCCAGCCACUUGGCUGAAAUG_
(((((..((..................((..((((((((((((.......))))))))))))..))..(((((....)))))....))..)))))...... (-28.25 = -29.25 +   1.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 12,145,983 – 12,146,084
Length 101
Sequences 4
Columns 101
Reading direction reverse
Mean pairwise identity 87.44
Mean single sequence MFE -25.80
Consensus MFE -22.25
Energy contribution -22.50
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -2.10
Structure conservation index 0.86
SVM decision value 1.35
SVM RNA-class probability 0.944719
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12145983 101 - 23771897
CCAUUUCACCCGAGUGGCUGGAUAAUUGUAUCCGCGCAAUCAUCCCGCGGCUUCCAUUGCCGCAGGAUAAAAACCAAACUGCAACGAACAGAACAGAACUG
.((.(((....((...((((((((....)))))).))..))((((.(((((.......))))).))))..........(((.......)))....))).)) ( -26.90)
>DroSec_CAF1 23287 90 - 1
-CAUUUCAGCCAAGUGCCUGGAUAAUUGUAUCCGCGCAAUCAUCCCGCGGCUUCCAUUGCCGCAGGAUAAAAACCAA----------ACAGAACAGAACUG
-((.(((......((((..(((((....)))))))))....((((.(((((.......))))).)))).........----------........))).)) ( -25.70)
>DroSim_CAF1 23560 90 - 1
-CAUUUCAGCCAAGUGGCUGGAUAAUUGUAUCCGCGCAAUCAUCCCGCGGCUUCCAUUGCCGCAGGAUAAAACCGAA----------ACAGAACAGAACUG
-...(((((((....)))))))..(((((......))))).((((.(((((.......))))).)))).........----------.............. ( -27.10)
>DroYak_CAF1 23305 94 - 1
-CAUUUCA-CCAAGUGGCUGGAUAAUUGUAUCCGCGCAAUCAUCCCGCGGCUUCAAUUGCCGCAGGCUAAAAACCAAACAGCAAC-----GAACAGAACUG
-((.(((.-....((.(((((((.(((((......))))).)))(((((((.......))))).))............)))).))-----.....))).)) ( -23.50)
>consensus
_CAUUUCAGCCAAGUGGCUGGAUAAUUGUAUCCGCGCAAUCAUCCCGCGGCUUCCAUUGCCGCAGGAUAAAAACCAA__________ACAGAACAGAACUG
.((.(((......(((.(.(((((....)))))))))....((((.(((((.......))))).))))...........................))).)) (-22.25 = -22.50 +   0.25)

alignment

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secondary structure

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dotplot

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Window 6

Location 12,146,014 – 12,146,104
Length 90
Sequences 6
Columns 97
Reading direction forward
Mean pairwise identity 86.11
Mean single sequence MFE -33.05
Consensus MFE -23.40
Energy contribution -24.90
Covariance contribution 1.50
Combinations/Pair 1.00
Mean z-score -2.85
Structure conservation index 0.71
SVM decision value 0.04
SVM RNA-class probability 0.552387
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12146014 90 + 23771897
UUAUCCUGCGGCAAU------GGAAGCCGCGGGAUGAUUGCGCGGAUACAAUUAUCCAGCCACUCGGGUGAAAUGGGCGGGAAAACGCUA-CAACGG
((((((((((((...------....))))))))))))..((..(((((....))))).))(((....))).....((((......)))).-...... ( -34.50)
>DroSec_CAF1 23308 90 + 1
UUAUCCUGCGGCAAU------GGAAGCCGCGGGAUGAUUGCGCGGAUACAAUUAUCCAGGCACUUGGCUGAAAUG-GCGGGAAAGCGCUAACAACGG
((((((((((((...------....))))))))))))..(((((((((....))))).....((((.(......)-.))))...))))......... ( -37.50)
>DroSim_CAF1 23581 90 + 1
UUAUCCUGCGGCAAU------GGAAGCCGCGGGAUGAUUGCGCGGAUACAAUUAUCCAGCCACUUGGCUGAAAUG-GCGGGAAAACGCUAACAACGG
((((((((((((...------....))))))))))))......(((((....)))))((((....))))....((-(((......)))))....... ( -37.50)
>DroEre_CAF1 20520 89 + 1
UUAUCCUGCGGCAAU------GAAAGCCGCGGGAUGAUUGCGCGGAUACAAUUAUCCAGCCACUUGG-UAAAAUG-GCGGCAAAACGCUAACAACGG
((((((((((((...------....))))))))))))((((..(((((....))))).((((.((..-..)).))-)).)))).............. ( -35.30)
>DroYak_CAF1 23331 89 + 1
UUAGCCUGCGGCAAU------UGAAGCCGCGGGAUGAUUGCGCGGAUACAAUUAUCCAGCCACUUGG-UGAAAUG-GCGGGAAAACGCUAACAACUA
....((((((((...------....)))))))).....((.(((((((....))))).))))..(((-(....((-(((......)))))...)))) ( -30.60)
>DroAna_CAF1 21478 86 + 1
---UCCUGCCGCAAUUUUUGCAGAAGCCGCGGGAUGAUUGCUCGGAAACAAUUACCCGGCCACUUGC-U-------GCUGGAAAUCGCUAACAACGC
---.......((.(((((((((((((..(((((.((((((........))))))))).))..))).)-)-------)).)))))).))......... ( -22.90)
>consensus
UUAUCCUGCGGCAAU______GGAAGCCGCGGGAUGAUUGCGCGGAUACAAUUAUCCAGCCACUUGG_UGAAAUG_GCGGGAAAACGCUAACAACGG
((((((((((((.............))))))))))))..((..(((((....))))).))................(((......)))......... (-23.40 = -24.90 +   1.50)

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 11:15:45 2006