Locus 7640

Sequence ID 3L_DroMel_CAF1
Location 20,554,006 – 20,554,134
Length 128
Max. P 0.995672
window12410 window12411 window12412

overview

Window 0

Location 20,554,006 – 20,554,098
Length 92
Sequences 3
Columns 92
Reading direction reverse
Mean pairwise identity 92.75
Mean single sequence MFE -20.36
Consensus MFE -19.18
Energy contribution -18.96
Covariance contribution -0.22
Combinations/Pair 1.06
Mean z-score -2.64
Structure conservation index 0.94
SVM decision value 1.75
SVM RNA-class probability 0.975526
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20554006 92 - 23771897
GCAGCCAGGAGUGCCCUCACACAAAGGUGUGGUCACUCCAUAAAAACUCGCAUUCAAAACACAGAAGGCGUAAAAACAGCACCAAAUAAAGU
((.(((.((((((.((.(((......))).)).)))))).............(((........))))))((....)).))............ ( -24.70)
>DroSec_CAF1 95868 92 - 1
GCAGCCAGGAGUGCCCUCACACAAAGGUGUGGUCACUCUAUAAAAAAUCGCAUUAAAAACACAGAAAGCGUAAAAAUAGCACCAAAUAAAGU
((.....((((((.((.(((......))).)).)))))).........(((................)))........))............ ( -18.29)
>DroEre_CAF1 98438 91 - 1
GCAGCCAGGAGUGCCCUCACACAAAGGUGUGGUCACUCUAUAAA-AAUCGCAUCAAAAAUACAGAAAGCGUAAAAACAGCUCAAAAUAAAGU
(.(((..((((((.((.(((......))).)).)))))).....-...(((................)))........)))).......... ( -18.09)
>consensus
GCAGCCAGGAGUGCCCUCACACAAAGGUGUGGUCACUCUAUAAAAAAUCGCAUUAAAAACACAGAAAGCGUAAAAACAGCACCAAAUAAAGU
((.....((((((.((.(((......))).)).)))))).........(((................)))........))............ (-19.18 = -18.96 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 1

Location 20,554,042 – 20,554,134
Length 92
Sequences 4
Columns 92
Reading direction forward
Mean pairwise identity 95.11
Mean single sequence MFE -26.30
Consensus MFE -24.52
Energy contribution -24.78
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.51
Structure conservation index 0.93
SVM decision value 0.26
SVM RNA-class probability 0.657935
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20554042 92 + 23771897
UGAAUGCGAGUUUUUAUGGAGUGACCACACCUUUGUGUGAGGGCACUCCUGGCUGCGCACGCGCACUUGCCGUAAAUUUCUUUAUUUCCGCU
.....(((.........((((((.((((((....))))).)..)))))).(((((((....))))...))).................))). ( -29.40)
>DroSec_CAF1 95904 92 + 1
UUAAUGCGAUUUUUUAUAGAGUGACCACACCUUUGUGUGAGGGCACUCCUGGCUGCGCACGCGCACUUGCCGUAAAUUUCUUUCUUUCCGCU
.....(((..........(((((.((((((....))))).)..)))))..(((((((....))))...))).................))). ( -25.90)
>DroSim_CAF1 97395 92 + 1
UUAAUGCGAUUUUUUAUAGAGGGACCACACCUUUGUGUGAGGGCACUCCUGGCUGCGCACGCGCACUUGCCGUAAAUUUCUUUAUUUCCGCU
.....(((.......((((((..(.(((((....)))))..((((.....((.((((....)))))))))).....)..))))))...))). ( -24.00)
>DroEre_CAF1 98474 90 + 1
UUGAUGCGAUU-UUUAUAGAGUGACCACACCUUUGUGUGAGGGCACUCCUGGCUGCGCACGCGCACUUGCCGCAAAUUUCU-UAUUUCCGCU
.....(((...-......(((((.((((((....))))).)..)))))..(((((((....))))...)))..........-......))). ( -25.90)
>consensus
UUAAUGCGAUUUUUUAUAGAGUGACCACACCUUUGUGUGAGGGCACUCCUGGCUGCGCACGCGCACUUGCCGUAAAUUUCUUUAUUUCCGCU
.....(((..........(((((.((((((....))))).)..)))))..(((((((....))))...))).................))). (-24.52 = -24.78 +   0.25)

alignment

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secondary structure

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dotplot

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Window 2

Location 20,554,042 – 20,554,134
Length 92
Sequences 4
Columns 92
Reading direction reverse
Mean pairwise identity 95.11
Mean single sequence MFE -29.55
Consensus MFE -29.26
Energy contribution -29.32
Covariance contribution 0.06
Combinations/Pair 1.05
Mean z-score -2.88
Structure conservation index 0.99
SVM decision value 2.60
SVM RNA-class probability 0.995672
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20554042 92 - 23771897
AGCGGAAAUAAAGAAAUUUACGGCAAGUGCGCGUGCGCAGCCAGGAGUGCCCUCACACAAAGGUGUGGUCACUCCAUAAAAACUCGCAUUCA
.((((...((((....)))).(((...((((....))))))).((((((.((.(((......))).)).))))))........))))..... ( -32.70)
>DroSec_CAF1 95904 92 - 1
AGCGGAAAGAAAGAAAUUUACGGCAAGUGCGCGUGCGCAGCCAGGAGUGCCCUCACACAAAGGUGUGGUCACUCUAUAAAAAAUCGCAUUAA
.((((................(((...((((....))))))).((((((.((.(((......))).)).))))))........))))..... ( -29.80)
>DroSim_CAF1 97395 92 - 1
AGCGGAAAUAAAGAAAUUUACGGCAAGUGCGCGUGCGCAGCCAGGAGUGCCCUCACACAAAGGUGUGGUCCCUCUAUAAAAAAUCGCAUUAA
.((((...((((....)))).(((...((((....))))))).((((.(..(.(((((....))))))..)))))........))))..... ( -25.90)
>DroEre_CAF1 98474 90 - 1
AGCGGAAAUA-AGAAAUUUGCGGCAAGUGCGCGUGCGCAGCCAGGAGUGCCCUCACACAAAGGUGUGGUCACUCUAUAAA-AAUCGCAUCAA
.((((.....-..........(((...((((....))))))).((((((.((.(((......))).)).)))))).....-..))))..... ( -29.80)
>consensus
AGCGGAAAUAAAGAAAUUUACGGCAAGUGCGCGUGCGCAGCCAGGAGUGCCCUCACACAAAGGUGUGGUCACUCUAUAAAAAAUCGCAUUAA
.((((................(((...((((....))))))).((((((.((.(((......))).)).))))))........))))..... (-29.26 = -29.32 +   0.06)

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 12:52:25 2006