Locus 3493

Sequence ID 3L_DroMel_CAF1
Location 10,260,564 – 10,260,655
Length 91
Max. P 0.550895
window5454 window5455

overview

Window 4

Location 10,260,564 – 10,260,655
Length 91
Sequences 6
Columns 96
Reading direction forward
Mean pairwise identity 83.49
Mean single sequence MFE -15.85
Consensus MFE -12.50
Energy contribution -12.50
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.50
Structure conservation index 0.79
SVM decision value 0.03
SVM RNA-class probability 0.550895
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10260564 91 + 23771897
GCACCAACAACGACAGCUAAUACACAAUUUGCAUAUAUUUAUCCAUCAAAUUGAUGGAUGCUACUGCACACACAGAGCCAUA-----AGGAUCGGG
...((........................((((......((((((((.....))))))))....))))......((.((...-----.)).)))). ( -17.40)
>DroVir_CAF1 168865 80 + 1
----CAACAAGGACAGCUAAUACACAAUUUGCAUAUAUUUAUCCAUCAAAUUGAUGGAUGCUACUGCACAC--UGAGCCAGG--------AUGA--
----......((.(((........................(((((((.....)))))))((....))...)--))..))...--------....-- ( -14.60)
>DroGri_CAF1 149719 80 + 1
----CAACAAGGACUGCUAAUACACAAUUUGCAUAUAUUUAUCCAUCAAAUUGAUGGAUGCUACUGCACAC--UGAGCCACG--------UUGA--
----((((..((.((((.(((.....))).))........(((((((.....)))))))((....))....--..))))..)--------))).-- ( -16.70)
>DroSec_CAF1 135909 89 + 1
GCACCAACAACGACAGCUAAUACACAAUUUGCAUAUAUUUAUCCAUCAAAUUGAUGGAUGCUACUGCAC--ACAGAGCCAAA-----AGGAUCGGG
...((........................((((......((((((((.....))))))))....)))).--...((.((...-----.)).)))). ( -17.40)
>DroWil_CAF1 222711 92 + 1
----CAACAAGGACAGCUAAUACACAAUUUGCAUAUAUUUAUCCAUCAAAUUGAUGGAUGCUACUGCACACACACAGACACACACAGACAACCGAA
----......((...((.(((.....))).)).......((((((((.....))))))))...(((........)))..............))... ( -14.00)
>DroMoj_CAF1 191155 80 + 1
----CAACAAGGACAGCUAAUACACAAUUUGCAUAUAUUUAUCCAUCAAAUUGAUGGAUGCUACUGCACAC--UGAGCCAGG--------ACCA--
----......((.................((((......((((((((.....))))))))....))))..(--((...))).--------.)).-- ( -15.00)
>consensus
____CAACAAGGACAGCUAAUACACAAUUUGCAUAUAUUUAUCCAUCAAAUUGAUGGAUGCUACUGCACAC__AGAGCCACA________AUCA__
.............................((((......((((((((.....))))))))....))))............................ (-12.50 = -12.50 +   0.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 10,260,564 – 10,260,655
Length 91
Sequences 6
Columns 96
Reading direction reverse
Mean pairwise identity 83.49
Mean single sequence MFE -22.57
Consensus MFE -15.68
Energy contribution -16.18
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.78
Structure conservation index 0.69
SVM decision value 0.01
SVM RNA-class probability 0.536949
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10260564 91 - 23771897
CCCGAUCCU-----UAUGGCUCUGUGUGUGCAGUAGCAUCCAUCAAUUUGAUGGAUAAAUAUAUGCAAAUUGUGUAUUAGCUGUCGUUGUUGGUGC
.(((((...-----.(((((.((((....)))).((((((((((.....))))))).(((((((.......))))))).)))))))).)))))... ( -24.90)
>DroVir_CAF1 168865 80 - 1
--UCAU--------CCUGGCUCA--GUGUGCAGUAGCAUCCAUCAAUUUGAUGGAUAAAUAUAUGCAAAUUGUGUAUUAGCUGUCCUUGUUG----
--....--------...((((.(--(((..((((.(((((((((.....))))))........)))..))))..))))))))..........---- ( -20.20)
>DroGri_CAF1 149719 80 - 1
--UCAA--------CGUGGCUCA--GUGUGCAGUAGCAUCCAUCAAUUUGAUGGAUAAAUAUAUGCAAAUUGUGUAUUAGCAGUCCUUGUUG----
--.(((--------((.((((((--(((..((((.(((((((((.....))))))........)))..))))..)))).).))))..)))))---- ( -22.30)
>DroSec_CAF1 135909 89 - 1
CCCGAUCCU-----UUUGGCUCUGU--GUGCAGUAGCAUCCAUCAAUUUGAUGGAUAAAUAUAUGCAAAUUGUGUAUUAGCUGUCGUUGUUGGUGC
.(((((...-----..(((((..((--(..((((.(((((((((.....))))))........)))..))))..))).))))).....)))))... ( -23.70)
>DroWil_CAF1 222711 92 - 1
UUCGGUUGUCUGUGUGUGUCUGUGUGUGUGCAGUAGCAUCCAUCAAUUUGAUGGAUAAAUAUAUGCAAAUUGUGUAUUAGCUGUCCUUGUUG----
...((..((..(((..((..(((((((((((....))(((((((.....)))))))..)))))))))...))..)))..))...))......---- ( -22.60)
>DroMoj_CAF1 191155 80 - 1
--UGGU--------CCUGGCUCA--GUGUGCAGUAGCAUCCAUCAAUUUGAUGGAUAAAUAUAUGCAAAUUGUGUAUUAGCUGUCCUUGUUG----
--.((.--------(..((((.(--(((..((((.(((((((((.....))))))........)))..))))..))))))))).))......---- ( -21.70)
>consensus
__CGAU________CCUGGCUCA__GUGUGCAGUAGCAUCCAUCAAUUUGAUGGAUAAAUAUAUGCAAAUUGUGUAUUAGCUGUCCUUGUUG____
.................(((.....(((..((((.(((((((((.....))))))........)))..))))..))).....)))........... (-15.68 = -16.18 +   0.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:59:29 2006