Locus 2332

Sequence ID 3L_DroMel_CAF1
Location 6,546,894 – 6,547,001
Length 107
Max. P 0.966278
window3603 window3604

overview

Window 3

Location 6,546,894 – 6,547,001
Length 107
Sequences 5
Columns 107
Reading direction forward
Mean pairwise identity 91.40
Mean single sequence MFE -36.00
Consensus MFE -30.96
Energy contribution -31.64
Covariance contribution 0.68
Combinations/Pair 1.10
Mean z-score -1.80
Structure conservation index 0.86
SVM decision value 1.59
SVM RNA-class probability 0.966278
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6546894 107 + 23771897
AGCGUCUGCCACGGAUUGGCAGAUUGAUUGCGGAAUAGCUGCUGUAGUUUGCUUGGUACUGGGAAUUCUGCGUAGUACUUUUGAGUUAUUGCCGCAGCAUCGCAUGC
.((((((((((.....))))))))....(((((....(((((.(((((..(((((((((((.(.......).)))))))...)))).))))).))))).))))).)) ( -40.10)
>DroSec_CAF1 9425 107 + 1
AGCGUCUGCCACGGAUUGGCAGAUUGAUUGCGGAAUUGCUGCUGUAGUUUGCUGGGUACUGGGAAUUCUGCGUAGUACUUUUGAGUUAUUGCCGCAGCUUCGCUUGC
.((((((((((.....)))))))).....(((((...(((((.(((((..(((((((((((.(.......).))))))))...))).))))).))))))))))..)) ( -39.70)
>DroSim_CAF1 9526 107 + 1
AGCGUCUGCCACGGAUUGGCAGAUUGAUUGCGGAAUAGCUGCUGUAGUUUGCUGGGUACUGGGAAUUCUGCGUAGUACUUUUGAGUUAUUGCCGCAGCAUCGCAUGC
.((((((((((.....))))))))....(((((....(((((.(((((..(((((((((((.(.......).))))))))...))).))))).))))).))))).)) ( -39.30)
>DroEre_CAF1 9528 104 + 1
AGCGUCUGCCACGGAUUGGUAGAUUGAUUGCGGAAAAGCUGCAUUAGUUUGGUCUGUACUGGGAAUUCUACGUAGUACUUUUCAGUUAUUGCUACAGCAUCGCA---
.((((((((((.....)))))))).((((((((.....)))))...(((((((....((((..((..((....))...))..))))....)))).)))))))).--- ( -27.70)
>DroYak_CAF1 9692 107 + 1
AGCGUCUGCCACGGAUUGGCAGAUUGAUUGCGGAAUAGCUGUUGUACUUCGGUCGGUACUGGGAAUUCUGCGUAGAACUUUUGAGUUAUUGCUGCAGCAUCGCAUGC
.((((((((((.....))))))).((.(((((((((((((...(((((......)))))(..((.((((....)))).))..)))))))).)))))))).))).... ( -33.20)
>consensus
AGCGUCUGCCACGGAUUGGCAGAUUGAUUGCGGAAUAGCUGCUGUAGUUUGCUCGGUACUGGGAAUUCUGCGUAGUACUUUUGAGUUAUUGCCGCAGCAUCGCAUGC
...((((((((.....)))))))).....((((....(((((.(((((...(..(((((((.(.......).)))))))...)....))))).))))).)))).... (-30.96 = -31.64 +   0.68)

alignment

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secondary structure

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dotplot

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Window 4

Location 6,546,894 – 6,547,001
Length 107
Sequences 5
Columns 107
Reading direction reverse
Mean pairwise identity 91.40
Mean single sequence MFE -25.51
Consensus MFE -20.70
Energy contribution -20.94
Covariance contribution 0.24
Combinations/Pair 1.09
Mean z-score -1.50
Structure conservation index 0.81
SVM decision value 0.36
SVM RNA-class probability 0.704869
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6546894 107 - 23771897
GCAUGCGAUGCUGCGGCAAUAACUCAAAAGUACUACGCAGAAUUCCCAGUACCAAGCAAACUACAGCAGCUAUUCCGCAAUCAAUCUGCCAAUCCGUGGCAGACGCU
....(((....(((((.((((.((.....(((((.............)))))...((........)))).))))))))).....(((((((.....)))))))))). ( -27.72)
>DroSec_CAF1 9425 107 - 1
GCAAGCGAAGCUGCGGCAAUAACUCAAAAGUACUACGCAGAAUUCCCAGUACCCAGCAAACUACAGCAGCAAUUCCGCAAUCAAUCUGCCAAUCCGUGGCAGACGCU
...((((....(((((.(((.........(((((.............)))))...((........))....)))))))).....(((((((.....))))))))))) ( -26.72)
>DroSim_CAF1 9526 107 - 1
GCAUGCGAUGCUGCGGCAAUAACUCAAAAGUACUACGCAGAAUUCCCAGUACCCAGCAAACUACAGCAGCUAUUCCGCAAUCAAUCUGCCAAUCCGUGGCAGACGCU
....(((....(((((.((((.((.....(((((.............)))))...((........)))).))))))))).....(((((((.....)))))))))). ( -27.72)
>DroEre_CAF1 9528 104 - 1
---UGCGAUGCUGUAGCAAUAACUGAAAAGUACUACGUAGAAUUCCCAGUACAGACCAAACUAAUGCAGCUUUUCCGCAAUCAAUCUACCAAUCCGUGGCAGACGCU
---.(((.((((((((.....(((....))).))))(((((.......(((.((......))..))).((......))......)))))........))))..))). ( -18.60)
>DroYak_CAF1 9692 107 - 1
GCAUGCGAUGCUGCAGCAAUAACUCAAAAGUUCUACGCAGAAUUCCCAGUACCGACCGAAGUACAACAGCUAUUCCGCAAUCAAUCUGCCAAUCCGUGGCAGACGCU
((.((((..((((...............((((((....))))))....((((........))))..)))).....)))).....(((((((.....))))))).)). ( -26.80)
>consensus
GCAUGCGAUGCUGCGGCAAUAACUCAAAAGUACUACGCAGAAUUCCCAGUACCCAGCAAACUACAGCAGCUAUUCCGCAAUCAAUCUGCCAAUCCGUGGCAGACGCU
....(((..(((((((......)).....(((((.............))))).............)))))..............(((((((.....)))))))))). (-20.70 = -20.94 +   0.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:29:48 2006