Locus 4008

Sequence ID X_DroMel_CAF1
Location 10,609,628 – 10,609,726
Length 98
Max. P 0.606549
window6589 window6590

overview

Window 9

Location 10,609,628 – 10,609,726
Length 98
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 68.42
Mean single sequence MFE -32.00
Consensus MFE -11.00
Energy contribution -11.56
Covariance contribution 0.56
Combinations/Pair 1.25
Mean z-score -1.80
Structure conservation index 0.34
SVM decision value 0.15
SVM RNA-class probability 0.606549
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10609628 98 + 22224390
GAUAUUGCUUUGCAGCACUUG-----AUGGUGUGACCAGCUGUGUUUUGAUGACAGUGCUGCCCAUAAAAA-CGUUUGUG-GGCG-GCAAUUUUGAA-UGGCUAGCA-------------
.....((((..(((((((...-----.(((.....)))...)))))..........(((((((((((((..-..))))))-))))-)))........-..)).))))------------- ( -33.70)
>DroSec_CAF1 6770 99 + 1
GAUAUUGCUUUGCUGAACUUG-----AAAGUGUGACCAGCAAUGUUUCGAUGGCAGUGCUGCCCAUAAAAA-CGUUUGUG-GGCG-GCAAUUUUGAAUUGGCUAGCA-------------
.....((((..((..(..(..-----(((...((.((((((.((((.....)))).))))(((((((((..-..))))))-))))-))).)))..).)..)).))))------------- ( -33.10)
>DroEre_CAF1 6742 97 + 1
GAUAUAGCUUUGCAGCACUUG-----AUAGUGCGACCAGCCGUGUUUCGGUGGCAGUGCUGCCCAUAAUUAAAGCUUGUG-GGCG-CUAGUUUUGAA-UGG--AACA-------------
....((((...((((((((..-----..)))))(.(((.(((.....)))))))..))).((((((((.......)))))-))))-)))(((((...-.))--))).------------- ( -34.20)
>DroYak_CAF1 7331 97 + 1
GAU-UAGCUUUGCAGCACACG-----AUAGUGUGACCAGCCGUGUUUCGGUGACAGUGCUGCCCAUUAAUG-AGCUUUUG-GGCG-CCAGUUUUGAA-UGACAGACA-------------
...-.(((.((((..(((((.-----...)))))....((((.....))))).))).)))(((((......-......))-))).-...(((.....-.))).....------------- ( -24.30)
>DroAna_CAF1 9050 109 + 1
-------CUGUCCAGCACUUGGCCAAAAAGUGUGGCCAAUUUUGUUAAG--GCCAGUGCUGCCCAUCAAGU-GGAUGGUAAGGCGCGCAAUUCAAAA-UAGCUAGACUUGCUACUUAGUG
-------..(((.(((...((((((.......))))))((((((.....--((..(((((..(((((....-.)))))...)))))))....)))))-).))).)))............. ( -34.70)
>consensus
GAUAUAGCUUUGCAGCACUUG_____AUAGUGUGACCAGCCGUGUUUCGAUGACAGUGCUGCCCAUAAAAA_AGCUUGUG_GGCG_GCAAUUUUGAA_UGGCUAGCA_____________
..............(((((.........)))))....(((..((((.....))))..)))((((((((.......))))).))).................................... (-11.00 = -11.56 +   0.56)

alignment

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secondary structure

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dotplot

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Window 0

Location 10,609,628 – 10,609,726
Length 98
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 68.42
Mean single sequence MFE -25.88
Consensus MFE -8.09
Energy contribution -8.89
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -1.81
Structure conservation index 0.31
SVM decision value 0.08
SVM RNA-class probability 0.575549
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 10609628 98 - 22224390
-------------UGCUAGCCA-UUCAAAAUUGC-CGCC-CACAAACG-UUUUUAUGGGCAGCACUGUCAUCAAAACACAGCUGGUCACACCAU-----CAAGUGCUGCAAAGCAAUAUC
-------------((((..(((-(..(((.(((.-....-..)))...-)))..))))((((((((((.......))...(.(((.....))).-----).))))))))..))))..... ( -22.60)
>DroSec_CAF1 6770 99 - 1
-------------UGCUAGCCAAUUCAAAAUUGC-CGCC-CACAAACG-UUUUUAUGGGCAGCACUGCCAUCGAAACAUUGCUGGUCACACUUU-----CAAGUUCAGCAAAGCAAUAUC
-------------((((..............(((-.(((-((.(((..-..))).))))).)))..............(((((((....(((..-----..))))))))))))))..... ( -23.00)
>DroEre_CAF1 6742 97 - 1
-------------UGUU--CCA-UUCAAAACUAG-CGCC-CACAAGCUUUAAUUAUGGGCAGCACUGCCACCGAAACACGGCUGGUCGCACUAU-----CAAGUGCUGCAAAGCUAUAUC
-------------....--...-........(((-((((-((.((.......)).))))).(((..(((((((.....))).)))).(((((..-----..))))))))...)))).... ( -29.20)
>DroYak_CAF1 7331 97 - 1
-------------UGUCUGUCA-UUCAAAACUGG-CGCC-CAAAAGCU-CAUUAAUGGGCAGCACUGUCACCGAAACACGGCUGGUCACACUAU-----CGUGUGCUGCAAAGCUA-AUC
-------------.........-........(((-((((-((......-......))))).(((...((((((.....))).))).(((((...-----.))))).)))...))))-... ( -23.20)
>DroAna_CAF1 9050 109 - 1
CACUAAGUAGCAAGUCUAGCUA-UUUUGAAUUGCGCGCCUUACCAUCC-ACUUGAUGGGCAGCACUGGC--CUUAACAAAAUUGGCCACACUUUUUGGCCAAGUGCUGGACAG-------
..(.(((((((.......))))-))).)..............(((((.-....))))).((((((((((--(.....((((.((....)).)))).)))).))))))).....------- ( -31.40)
>consensus
_____________UGCUAGCCA_UUCAAAAUUGC_CGCC_CACAAACG_UAUUUAUGGGCAGCACUGCCACCGAAACACAGCUGGUCACACUAU_____CAAGUGCUGCAAAGCAAUAUC
..........................................................((((((((...................................))))))))........... ( -8.09 =  -8.89 +   0.80)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:14:08 2006