Locus 6862

Sequence ID 3L_DroMel_CAF1
Location 18,434,025 – 18,434,137
Length 112
Max. P 0.825787
window11129 window11130

overview

Window 9

Location 18,434,025 – 18,434,115
Length 90
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 79.38
Mean single sequence MFE -27.92
Consensus MFE -20.67
Energy contribution -21.70
Covariance contribution 1.03
Combinations/Pair 1.17
Mean z-score -1.17
Structure conservation index 0.74
SVM decision value 0.24
SVM RNA-class probability 0.648023
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18434025 90 - 23771897
----AAGACAGCCUGAUGGG--GCCUCUCAUCGGGAA-AGUUAAAGCCUGCUCGAGGCAGAUUUAUUGCAUUUUAAUGCGGGCUCUGGAUUGC---------------ACUC
----((..((((((((((((--....)))))))))..-......(((((((.....((((.....))))........))))))))))..))..---------------.... ( -28.62)
>DroSec_CAF1 76339 90 - 1
----AAGACAGCCUGAUGGG--GCCUCUCAUCAGGAA-AGUUAAAGCCUACUCGAGGCAGACUUAUUGCAUUUUAAUGCGGGCUCUGGAUUAC---------------ACUC
----((..((((((((((((--....))))))))).(-((((...((((.....)))).))))).((((((....))))))...)))..))..---------------.... ( -26.70)
>DroSim_CAF1 70851 90 - 1
----AAGACAGCCUGAUGGG--GCCUCUCAUCAGGAA-AGUUAAAGCCUGCUCGAGGCAGAUUUAUUGCAUUUUAAUGCGGGCUCUGGAUUGC---------------ACUC
----((..((((((((((((--....)))))))))..-......(((((((.....((((.....))))........))))))))))..))..---------------.... ( -29.32)
>DroEre_CAF1 76103 88 - 1
----AAGACAGCCUGAUG-G--GCCUCUCAUCAGG-A-AGUUUAAGCCUGCUCGAGGCAGAUUUAUUGCAUUUAAAUGCGGGCUCUGGAUUGC---------------GCCC
----.((((..(((((((-(--(...)))))))))-.-.))))..((((.....)))).........((((....))))((((.(......).---------------)))) ( -30.90)
>DroYak_CAF1 77839 94 - 1
GGAAAAGACAGCCUGAUGCG--GCCUCUCAUCAGCAA-AGUUAAAGCCUGCUGGAGGCAGAUUUAUUGCAUUUUAAUGCGGGCUCUGGAUUGC---------------ACUC
.((..(((..(((......)--)).)))..)).((((-..(((.((((((((((((((((.....)))).)))))..))))))).))).))))---------------.... ( -25.40)
>DroAna_CAF1 63644 102 - 1
----AAGACAGGAUGAUGAGCAACCACUCACCAGGAAAACUUAAAGCCUG------GCCCGUGAAUGGCGUUUUUAUGCGGGCUUCGAGCUGCCACAGGCAACUGCGAACUC
----....((((.((.((((......)))).)).............))))------((((((...............))))))((((((.((((...)))).)).))))... ( -26.60)
>consensus
____AAGACAGCCUGAUGGG__GCCUCUCAUCAGGAA_AGUUAAAGCCUGCUCGAGGCAGAUUUAUUGCAUUUUAAUGCGGGCUCUGGAUUGC_______________ACUC
........((((((((((((......))))))))).........(((((((.....((((.....))))........))))))))))......................... (-20.67 = -21.70 +   1.03)

alignment

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secondary structure

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dotplot

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Window 0

Location 18,434,043 – 18,434,137
Length 94
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 77.37
Mean single sequence MFE -30.57
Consensus MFE -17.57
Energy contribution -18.65
Covariance contribution 1.08
Combinations/Pair 1.18
Mean z-score -1.86
Structure conservation index 0.57
SVM decision value 0.70
SVM RNA-class probability 0.825787
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18434043 94 - 23771897
-------------AACUGAGAACUCG-AGCCCGGAA--------AAGACAGCCUGAUGGG--GCCUCUCAUCGGGAA-AGUUAAAGCCUGCUCGAGGCAGAUUUAUUGCAUUUUAAUGC
-------------..(((....((((-(((..((..--------..(((..(((((((((--....)))))))))..-.)))....)).))))))).))).......((((....)))) ( -33.90)
>DroSec_CAF1 76357 94 - 1
-------------AACUGGGAACUGG-AGCCCGGAA--------AAGACAGCCUGAUGGG--GCCUCUCAUCAGGAA-AGUUAAAGCCUACUCGAGGCAGACUUAUUGCAUUUUAAUGC
-------------..(((((......-..)))))..--------.......(((((((((--....))))))))).(-((((...((((.....)))).)))))...((((....)))) ( -29.70)
>DroSim_CAF1 70869 94 - 1
-------------AACUGGGAACUCG-AGCCCGGAA--------AAGACAGCCUGAUGGG--GCCUCUCAUCAGGAA-AGUUAAAGCCUGCUCGAGGCAGAUUUAUUGCAUUUUAAUGC
-------------..(((....((((-(((..((..--------..(((..(((((((((--....)))))))))..-.)))....)).))))))).))).......((((....)))) ( -33.50)
>DroEre_CAF1 76121 96 - 1
UGG---------CAACUGGGAGCUCC-UGCCCGGAA--------AAGACAGCCUGAUG-G--GCCUCUCAUCAGG-A-AGUUUAAGCCUGCUCGAGGCAGAUUUAUUGCAUUUAAAUGC
..(---------((((((((......-..)))))..--------.((((..(((((((-(--(...)))))))))-.-.))))..((((.....)))).......)))).......... ( -31.80)
>DroYak_CAF1 77857 115 - 1
UCAGGAACUCGGCAACUGGGUACUUU-AGUCCGGAAAAGAGGAAAAGACAGCCUGAUGCG--GCCUCUCAUCAGCAA-AGUUAAAGCCUGCUGGAGGCAGAUUUAUUGCAUUUUAAUGC
(((((.(((((....).)))).((((-..(((........)))))))....)))))....--(((((....(((((.-.((....)).)))))))))).........((((....)))) ( -29.60)
>DroAna_CAF1 63677 90 - 1
---------------CUGGGAACUCGAAGUCCUGAA--------AAGACAGGAUGAUGAGCAACCACUCACCAGGAAAACUUAAAGCCUG------GCCCGUGAAUGGCGUUUUUAUGC
---------------..(((..((((..((((((..--------....))))))..))))..........(((((...........))))------)))).......((((....)))) ( -24.90)
>consensus
_____________AACUGGGAACUCG_AGCCCGGAA________AAGACAGCCUGAUGGG__GCCUCUCAUCAGGAA_AGUUAAAGCCUGCUCGAGGCAGAUUUAUUGCAUUUUAAUGC
...............(((((.........))))).................(((((((((......)))))))))..........((((.....)))).........((((....)))) (-17.57 = -18.65 +   1.08)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:31:36 2006