Locus 2108

Sequence ID 3L_DroMel_CAF1
Location 5,771,289 – 5,771,449
Length 160
Max. P 0.941762
window3279 window3280 window3281 window3282

overview

Window 9

Location 5,771,289 – 5,771,409
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 93.33
Mean single sequence MFE -33.06
Consensus MFE -28.60
Energy contribution -29.60
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.01
Structure conservation index 0.87
SVM decision value 0.25
SVM RNA-class probability 0.651814
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5771289 120 + 23771897
AAACUUAAAAGGCAUGUGCUAAUAAAAGGAAAUUUAUUAAUUAGUUACCGCCUUCAUAGGCUCUCAAACUUCCUCGGCACAGUUUGAGAGCCGCUGACGAGCCCCCAUUUCGGUUGACGG
........(((((....((((((................))))))....)))))....((((((((((((.(....)...)))))))))))).(((.(.((((........))))).))) ( -31.29)
>DroSec_CAF1 13888 120 + 1
AAACUUAAAAGGUAUGAGUUAAUAAAGGGAAAUUUAUUAAUUAGUUCCCGUCUUCAUAGGCUCUCAAACCUCCUCGACACAGUUUGAGAGCCGCUGACGAGCCCCCAUUUUGGUUGACGG
..........((....((((((((((......))))))))))....))((((.(((..(((((((((((............)))))))))))..)))..((((........)))))))). ( -34.60)
>DroSim_CAF1 13751 120 + 1
AAACUUAAAAGGUAUGAGUUAAUAAAGGGAAAUUUAUUAAUUAGUUCCCGUCUUUAUUGGCUCUCAAACCUCCUCGACACAGUUUGAGAGCCGCUGACGAGCCCCCAUUUUGCUUGACGG
..........((....((((((((((......))))))))))....))((((.(((.((((((((((((............)))))))))))).))).((((.........)))))))). ( -33.30)
>consensus
AAACUUAAAAGGUAUGAGUUAAUAAAGGGAAAUUUAUUAAUUAGUUCCCGUCUUCAUAGGCUCUCAAACCUCCUCGACACAGUUUGAGAGCCGCUGACGAGCCCCCAUUUUGGUUGACGG
................((((((((((......)))))))))).....(((((......(((((((((((............)))))))))))(((....))).............))))) (-28.60 = -29.60 +   1.00)

alignment

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secondary structure

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dotplot

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Window 0

Location 5,771,289 – 5,771,409
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 93.33
Mean single sequence MFE -34.67
Consensus MFE -34.11
Energy contribution -33.23
Covariance contribution -0.88
Combinations/Pair 1.14
Mean z-score -2.03
Structure conservation index 0.98
SVM decision value 1.32
SVM RNA-class probability 0.941762
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5771289 120 - 23771897
CCGUCAACCGAAAUGGGGGCUCGUCAGCGGCUCUCAAACUGUGCCGAGGAAGUUUGAGAGCCUAUGAAGGCGGUAACUAAUUAAUAAAUUUCCUUUUAUUAGCACAUGCCUUUUAAGUUU
(((((..((......))......(((..((((((((((((...(....).))))))))))))..))).))))).((((...(((((((......)))))))((....))......)))). ( -36.20)
>DroSec_CAF1 13888 120 - 1
CCGUCAACCAAAAUGGGGGCUCGUCAGCGGCUCUCAAACUGUGUCGAGGAGGUUUGAGAGCCUAUGAAGACGGGAACUAAUUAAUAAAUUUCCCUUUAUUAACUCAUACCUUUUAAGUUU
(((((..((.....)).......(((..((((((((((((..........))))))))))))..))).))))).......((((((((......)))))))).................. ( -34.10)
>DroSim_CAF1 13751 120 - 1
CCGUCAAGCAAAAUGGGGGCUCGUCAGCGGCUCUCAAACUGUGUCGAGGAGGUUUGAGAGCCAAUAAAGACGGGAACUAAUUAAUAAAUUUCCCUUUAUUAACUCAUACCUUUUAAGUUU
(((((..((...((((....))))..))((((((((((((..........))))))))))))......))))).......((((((((......)))))))).................. ( -33.70)
>consensus
CCGUCAACCAAAAUGGGGGCUCGUCAGCGGCUCUCAAACUGUGUCGAGGAGGUUUGAGAGCCUAUGAAGACGGGAACUAAUUAAUAAAUUUCCCUUUAUUAACUCAUACCUUUUAAGUUU
(((((.............(((....)))((((((((((((...(....).))))))))))))......))))).......((((((((......)))))))).................. (-34.11 = -33.23 +  -0.88)

alignment

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secondary structure

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dotplot

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Window 1

Location 5,771,329 – 5,771,449
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 90.91
Mean single sequence MFE -34.13
Consensus MFE -30.17
Energy contribution -30.50
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.07
Structure conservation index 0.88
SVM decision value 0.59
SVM RNA-class probability 0.792873
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5771329 120 + 23771897
UUAGUUACCGCCUUCAUAGGCUCUCAAACUUCCUCGGCACAGUUUGAGAGCCGCUGACGAGCCCCCAUUUCGGUUGACGGCGCUUAAAAGCUCCCAAAGCUUCGCAUCGAGAAAACACCC
...(((...(((.(((..((((((((((((.(....)...))))))))))))..))).).)).....(((((((.(.(((.((((...........)))).))))))))))).))).... ( -35.60)
>DroSec_CAF1 13928 112 + 1
UUAGUUCCCGUCUUCAUAGGCUCUCAAACCUCCUCGACACAGUUUGAGAGCCGCUGACGAGCCCCCAUUUUGGUUGACGGCGCUUAAAAGCUCCCAAAGCUUCGCAUCGAGA--------
.......(((((.(((..(((((((((((............)))))))))))..)))..((((........))))))))).((....(((((.....))))).)).......-------- ( -33.40)
>DroSim_CAF1 13791 112 + 1
UUAGUUCCCGUCUUUAUUGGCUCUCAAACCUCCUCGACACAGUUUGAGAGCCGCUGACGAGCCCCCAUUUUGCUUGACGGCGCUUAAAAGCUCCCAAAGCUUCGCAUCGAGA--------
..........((((....(((((((((((............)))))))))))((((.(((((.........))))).))))((....(((((.....))))).))...))))-------- ( -33.40)
>consensus
UUAGUUCCCGUCUUCAUAGGCUCUCAAACCUCCUCGACACAGUUUGAGAGCCGCUGACGAGCCCCCAUUUUGGUUGACGGCGCUUAAAAGCUCCCAAAGCUUCGCAUCGAGA________
.......(((((......(((((((((((............)))))))))))(((....))).............))))).((....(((((.....))))).))............... (-30.17 = -30.50 +   0.33)

alignment

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secondary structure

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dotplot

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Window 2

Location 5,771,329 – 5,771,449
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 90.91
Mean single sequence MFE -41.57
Consensus MFE -39.47
Energy contribution -39.37
Covariance contribution -0.11
Combinations/Pair 1.06
Mean z-score -2.01
Structure conservation index 0.95
SVM decision value 1.13
SVM RNA-class probability 0.920057
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5771329 120 - 23771897
GGGUGUUUUCUCGAUGCGAAGCUUUGGGAGCUUUUAAGCGCCGUCAACCGAAAUGGGGGCUCGUCAGCGGCUCUCAAACUGUGCCGAGGAAGUUUGAGAGCCUAUGAAGGCGGUAACUAA
.(((....((((((.((...)).))))))(((((((.(.(((.(((.......))).))).)......((((((((((((...(....).))))))))))))..)))))))....))).. ( -42.90)
>DroSec_CAF1 13928 112 - 1
--------UCUCGAUGCGAAGCUUUGGGAGCUUUUAAGCGCCGUCAACCAAAAUGGGGGCUCGUCAGCGGCUCUCAAACUGUGUCGAGGAGGUUUGAGAGCCUAUGAAGACGGGAACUAA
--------(((((..(((((((((...)))))))...))(((.(((.......))).)))((.(((..((((((((((((..........))))))))))))..))).)))))))..... ( -41.10)
>DroSim_CAF1 13791 112 - 1
--------UCUCGAUGCGAAGCUUUGGGAGCUUUUAAGCGCCGUCAAGCAAAAUGGGGGCUCGUCAGCGGCUCUCAAACUGUGUCGAGGAGGUUUGAGAGCCAAUAAAGACGGGAACUAA
--------(((((..(((((((((...)))))))...(.(((.(((.......))).))).)....))((((((((((((..........))))))))))))........)))))..... ( -40.70)
>consensus
________UCUCGAUGCGAAGCUUUGGGAGCUUUUAAGCGCCGUCAACCAAAAUGGGGGCUCGUCAGCGGCUCUCAAACUGUGUCGAGGAGGUUUGAGAGCCUAUGAAGACGGGAACUAA
........(((((..(((((((((...)))))))...(.(((.(((.......))).))).)....))((((((((((((...(....).))))))))))))........)))))..... (-39.47 = -39.37 +  -0.11)

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 10:24:35 2006