Locus 1110

Sequence ID 3R_DroMel_CAF1
Location 3,356,978 – 3,357,138
Length 160
Max. P 0.995964
window1815 window1816

overview

Window 5

Location 3,356,978 – 3,357,098
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.42
Mean single sequence MFE -47.21
Consensus MFE -41.04
Energy contribution -41.84
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -1.61
Structure conservation index 0.87
SVM decision value 1.11
SVM RNA-class probability 0.917365
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3356978 120 - 27905053
UGUCGGAGGGCAUCUGGCCAUCGGGCUGGAUGCCGUGCUCCAGGCAAUAGAGCUCCCAGCAGGCAUUUCCAAUCUGGACUCCGGCCUGGCCCACGUGGAUAGAGAUACAUUCGCGCAUAU
........((((((..(((....)))..))))))(((..((((((....(((...((((..((.....))...)))).)))..))))))..)))((((((........))))))...... ( -48.00)
>DroSec_CAF1 50409 120 - 1
UGUCGGAGGGCAUCUGUCCAUCGGGCUGGAUGCCGUGCUCCAGGCAAUAGAGCUCCCAACAGGCAUUUCCAAUCUGGACACCGGCCUGGCCCACGUGGAUAGAGAUACAUUCGCGCAUAU
(((((((.(...(((((((((.(((((((..(((.(((.....)))...).))..))).(((((...(((.....))).....)))))))))..)))))))))....).)))).)))... ( -45.60)
>DroSim_CAF1 44715 120 - 1
UGUCGGAGGGCAUCUGCCCAUCGGGCUGGAUGCCGUGCUCCAGGCAAUAGAGCUCCCAACAGGCGUUUCCAAUCUGGACACCGGCCUGGCCCACGUGGAUAGAGAUACAUUCGCGCAUAU
....(..((((....))))..)((((..(..((((((.((((((.....((((.((.....)).))))....)))))))).)))))..)))).(((((((........)))))))..... ( -46.10)
>DroEre_CAF1 43682 120 - 1
UGUCAGAGGGCAUCUGGCCAUCGGGCUGGAUGCCGUGCUCCAGGCAGUAGAGCUCCCAGCAGGCGUUUCCAAUCUGGACACCAGCCUGGCCCACGUGGAUAGAGAUACAUUCCCGCAUAU
........((((((..(((....)))..))))))(((..((((((......((.....)).((.(..(((.....)))).)).))))))..)))((((..............)))).... ( -46.94)
>DroYak_CAF1 64947 120 - 1
UGUCAGAAGGCAUCUGGCCAUCGGGCUGGAUGCCGUGCUCCAGGCAGUAGAGCUCCCAGCAGGCGUUUCCAAUCUGGACACCAGCCUGGCCCACGUGGAUGGAGAUACAUUCCCGCAUAU
........((((((..(((....)))..))))))(((..((((((......((.....)).((.(..(((.....)))).)).))))))..)))(((((((......)))..)))).... ( -49.40)
>consensus
UGUCGGAGGGCAUCUGGCCAUCGGGCUGGAUGCCGUGCUCCAGGCAAUAGAGCUCCCAGCAGGCGUUUCCAAUCUGGACACCGGCCUGGCCCACGUGGAUAGAGAUACAUUCGCGCAUAU
........(((((((((((....)))))))))))(((..((((((......(((.......)))...(((.....))).....))))))..)))((((((........))))))...... (-41.04 = -41.84 +   0.80)

alignment

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secondary structure

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dotplot

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Window 6

Location 3,357,018 – 3,357,138
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.08
Mean single sequence MFE -48.34
Consensus MFE -44.00
Energy contribution -43.84
Covariance contribution -0.16
Combinations/Pair 1.08
Mean z-score -1.99
Structure conservation index 0.91
SVM decision value 2.64
SVM RNA-class probability 0.995964
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3357018 120 + 27905053
AGUCCAGAUUGGAAAUGCCUGCUGGGAGCUCUAUUGCCUGGAGCACGGCAUCCAGCCCGAUGGCCAGAUGCCCUCCGACAAGACCGUAGGCGGAGGUGAUGACUCGUUUAACACCUUCUU
..(((.....)))...((((((.((..((((((.....))))))..((((((..(((....)))..))))))...........))))))))(((((((.(((.....))).))))))).. ( -47.10)
>DroSec_CAF1 50449 120 + 1
UGUCCAGAUUGGAAAUGCCUGUUGGGAGCUCUAUUGCCUGGAGCACGGCAUCCAGCCCGAUGGACAGAUGCCCUCCGACAAGACCGUGGGCGGAGGUGAUGACUCGUUCAACACCUUCUU
.(((((...(((.....(.(((((((.((((((.....))))))..((((((...((....))...)))))).))))))).).))))))))(((((((.(((.....))).))))))).. ( -45.80)
>DroSim_CAF1 44755 120 + 1
UGUCCAGAUUGGAAACGCCUGUUGGGAGCUCUAUUGCCUGGAGCACGGCAUCCAGCCCGAUGGGCAGAUGCCCUCCGACAAGACCGUGGGCGGAGGUGAUGACUCGUUCAACACCUUCUU
.(((((....(....)...(((((((.((((((.....))))))..((((((..((((...)))).)))))).)))))))......)))))(((((((.(((.....))).))))))).. ( -51.70)
>DroEre_CAF1 43722 120 + 1
UGUCCAGAUUGGAAACGCCUGCUGGGAGCUCUACUGCCUGGAGCACGGCAUCCAGCCCGAUGGCCAGAUGCCCUCUGACAAGACCGUGGGCGGAGGUGAUGACUCGUUCAACACCUUCUU
..(((.....)))...(((..(.((..((((((.....))))))..((((((..(((....)))..))))))...........)))..)))(((((((.(((.....))).))))))).. ( -48.30)
>DroYak_CAF1 64987 120 + 1
UGUCCAGAUUGGAAACGCCUGCUGGGAGCUCUACUGCCUGGAGCACGGCAUCCAGCCCGAUGGCCAGAUGCCUUCUGACAAGACCGUGGGCGGAGGUGAUGACUCGUUCAACACCUUCUU
..(((.....)))...(((..(.((..((((((.....))))))..((((((..(((....)))..)))))).(((....))))))..)))(((((((.(((.....))).))))))).. ( -48.80)
>consensus
UGUCCAGAUUGGAAACGCCUGCUGGGAGCUCUAUUGCCUGGAGCACGGCAUCCAGCCCGAUGGCCAGAUGCCCUCCGACAAGACCGUGGGCGGAGGUGAUGACUCGUUCAACACCUUCUU
..(((.....)))...((((((.((..((((((.....))))))..((((((..(((....)))..))))))...........))))))))(((((((.(((.....))).))))))).. (-44.00 = -43.84 +  -0.16)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:01:08 2006