Locus 4592

Sequence ID 3R_DroMel_CAF1
Location 12,083,775 – 12,083,935
Length 160
Max. P 0.999647
window7543 window7544

overview

Window 3

Location 12,083,775 – 12,083,895
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.17
Mean single sequence MFE -46.86
Consensus MFE -43.26
Energy contribution -43.74
Covariance contribution 0.48
Combinations/Pair 1.05
Mean z-score -2.64
Structure conservation index 0.92
SVM decision value 3.83
SVM RNA-class probability 0.999647
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12083775 120 - 27905053
GCUUCAGCGUAUUGCAAAUGAGCACCGAGCGGUACAGCGACUGCUCAGAAACCUGCCGGAAACGGGAGAGUUUGAACAUGGACAGAUUGCGUAUCUUCAGGCGCGUGUCCUUGUAGCAAC
((....))...((((...........(((((((......)))))))..((((((.(((....))).)).))))..(((.(((((...(((((........)))))))))).))).)))). ( -42.50)
>DroSec_CAF1 20472 120 - 1
GCUUCAGCGUAUUGCAAAUGAGCACCGAGCGGUACAGCGACUGCUCGGAAACCUGCCGGAAACGGGAGAGUUUGAACAUGGACAGAUUGCGUAUCUUCAGGCGCGUGUCCUUGUAGCAAC
((....))...((((.........(((((((((......)))))))))((((((.(((....))).)).))))..(((.(((((...(((((........)))))))))).))).)))). ( -47.80)
>DroSim_CAF1 20660 120 - 1
GCUUCAGCGUAUUGCAAAUGAGCACCGAGCGGUACAGCGACUGCUCGGAAACCUGCCGGAAACGGGAGAGCUUGAACAUGGACAGAUUGCGUAUCUUCAGGCGCGUGUCCUUGUAGCAAC
((....))...((((....((((.(((((((((......)))))))))....((.(((....))).)).))))..(((.(((((...(((((........)))))))))).))).)))). ( -50.00)
>DroEre_CAF1 22566 120 - 1
GUUUCAGCGUGUUGCAAAUGAGCACCGAGCGGUACAGCGACUGCUCGGAAACCUGCCGGAAACGGGAGAGUUUGAACAUGGACAGAUUGCGUAUCUUCAGGCGCGUGUCCUUAUAGCAAC
......(((((((.(((((.....(((((((((......)))))))))....((.(((....))).)).))))))))))(((((...(((((........)))))))))).....))... ( -47.30)
>DroYak_CAF1 22951 120 - 1
GCUUCAGCGUGUUACAAAUGAGCACCGAGCGGUAUAGCGACUGCUCGGAAACCUGCCGGAAACGGGACAGUUUGAACAUGGACAGAUUGCGUAUCUUCAGGCGCGUGUCCUUGUAGCAAC
(((.(((.(((((.(((((...(.(((((((((......))))))))).......(((....))))...))))))))))(((((...(((((........))))))))))))).)))... ( -46.70)
>consensus
GCUUCAGCGUAUUGCAAAUGAGCACCGAGCGGUACAGCGACUGCUCGGAAACCUGCCGGAAACGGGAGAGUUUGAACAUGGACAGAUUGCGUAUCUUCAGGCGCGUGUCCUUGUAGCAAC
((....))...((((....((((.(((((((((......)))))))))....((.(((....))).)).))))..(((.(((((...(((((........)))))))))).))).)))). (-43.26 = -43.74 +   0.48)

alignment

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secondary structure

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dotplot

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Window 4

Location 12,083,815 – 12,083,935
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.33
Mean single sequence MFE -45.22
Consensus MFE -42.94
Energy contribution -43.54
Covariance contribution 0.60
Combinations/Pair 1.06
Mean z-score -1.97
Structure conservation index 0.95
SVM decision value 3.06
SVM RNA-class probability 0.998299
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12083815 120 - 27905053
UGCAGCUCCUUGGCCUCUGCUUCGAUCUCCCGAUCAAUGCGCUUCAGCGUAUUGCAAAUGAGCACCGAGCGGUACAGCGACUGCUCAGAAACCUGCCGGAAACGGGAGAGUUUGAACAUG
....((((....((.........((((....))))(((((((....)))))))))....))))...(((((((......)))))))..((((((.(((....))).)).))))....... ( -43.30)
>DroSec_CAF1 20512 120 - 1
UGCAGCUCCUUGGCCUCUGCUUCGAUCUCACGAUCAAUGCGCUUCAGCGUAUUGCAAAUGAGCACCGAGCGGUACAGCGACUGCUCGGAAACCUGCCGGAAACGGGAGAGUUUGAACAUG
....((((....((.........((((....))))(((((((....)))))))))....)))).(((((((((......)))))))))((((((.(((....))).)).))))....... ( -48.60)
>DroSim_CAF1 20700 120 - 1
UGCAGCUCCUUGGCCUCUGCUUCGAUCUCACGAUCUAUGCGCUUCAGCGUAUUGCAAAUGAGCACCGAGCGGUACAGCGACUGCUCGGAAACCUGCCGGAAACGGGAGAGCUUGAACAUG
.((.((((....((.........((((....)))).((((((....)))))).))....)))).(((((((((......)))))))))....((.(((....))).)).))......... ( -45.30)
>DroEre_CAF1 22606 120 - 1
UGCAGCUCCUUGGCCUCUGCUUCGAUCUCCCGAUCAAUGCGUUUCAGCGUGUUGCAAAUGAGCACCGAGCGGUACAGCGACUGCUCGGAAACCUGCCGGAAACGGGAGAGUUUGAACAUG
....((((....((.........((((....))))(((((((....)))))))))....)))).(((((((((......)))))))))((((((.(((....))).)).))))....... ( -45.60)
>DroYak_CAF1 22991 120 - 1
UGCAGCUCCUUGGCCUCGGCUUCGAUCUCCCGAUCAAUGCGCUUCAGCGUGUUACAAAUGAGCACCGAGCGGUAUAGCGACUGCUCGGAAACCUGCCGGAAACGGGACAGUUUGAACAUG
....((((.(((((....))...((((....))))(((((((....))))))).)))..)))).(((((((((......)))))))))((((.(.(((....))).)..))))....... ( -43.30)
>consensus
UGCAGCUCCUUGGCCUCUGCUUCGAUCUCCCGAUCAAUGCGCUUCAGCGUAUUGCAAAUGAGCACCGAGCGGUACAGCGACUGCUCGGAAACCUGCCGGAAACGGGAGAGUUUGAACAUG
....((((....((.........((((....))))(((((((....)))))))))....)))).(((((((((......)))))))))((((((.(((....))).)).))))....... (-42.94 = -43.54 +   0.60)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:33:56 2006