Locus 3829

Sequence ID 3L_DroMel_CAF1
Location 11,059,019 – 11,059,113
Length 94
Max. P 0.958826
window5963 window5964

overview

Window 3

Location 11,059,019 – 11,059,113
Length 94
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 78.06
Mean single sequence MFE -23.72
Consensus MFE -13.13
Energy contribution -15.22
Covariance contribution 2.08
Combinations/Pair 1.09
Mean z-score -2.51
Structure conservation index 0.55
SVM decision value 1.49
SVM RNA-class probability 0.958826
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11059019 94 + 23771897
AAUAAGCUGCACUUUAUUGUCGUCAUUAAAGUGAAGAGCAAUUUAAA-------------GUAAAAGAAGUCGGAAAGCGGU---GUGAUUGCAAAAACAUCACGCAGCG-
.....(((((((((((((((..((((....))))...))))..))))-------------))...............(.(((---((..........))))).)))))).- ( -22.60)
>DroSec_CAF1 3003 94 + 1
AAUAAGCUGCACUUUAUUGUCGUCAUUAAAGUGAAGAGCAAUUCAAA-------------GUAAAAGAAGCCGCAAAGCGGU---GUGAUUGCAAAAACAUCACGCAGCG-
.....(((((((((((((((..((((....))))...)))))..)))-------------)).......(((((...)))))---(((((.(......))))))))))).- ( -27.50)
>DroSim_CAF1 2947 94 + 1
AAUAAGCUGCACUUUAUUGUCGUCAUUAAAGUGAAGAGCAAUUCAAA-------------GUAAAAGAAGCCGGAAAGCGGU---GUGAUUGCAAAAACAUCACGCAGCG-
.....(((((((((((((((..((((....))))...)))))..)))-------------)).......((((.....))))---(((((.(......))))))))))).- ( -25.60)
>DroEre_CAF1 2904 74 + 1
AACAAGCUGCACUUUAUCGUCAU--------------------CAAA-------------GUAAAAGAAGCCGGGAAGCGGU---GUGAUUGCAAUAACAUCACGCAGCG-
.....((((((((((........--------------------.)))-------------)).......((((.....))))---(((((.(......))))))))))).- ( -18.40)
>DroYak_CAF1 2784 94 + 1
AAUAAGCUGCACUUUAUUGUCGUCAUUAAAGUGAAAAGCAAUUCAAA-------------GUAAAAGAAGCCGGGAAGCGGU---GUGAUUGCAAAAACAUCACGCAGCG-
.....(((((((((((((((..((((....))))...)))))..)))-------------)).......((((.....))))---(((((.(......))))))))))).- ( -25.60)
>DroAna_CAF1 2788 108 + 1
AAUAAGCUGCACUUUAUUGUCGGCAUUAAAAUGAAGAAGAACCUGAACCGAGCCAAGAAUGGAAAAAAAA---UAAAGUGUUGCAGUGAUUGCGAAAAGAGCACGCAGGGC
.....((.((((((((((.(((((((....))).((......))...)))).(((....)))......))---)))))))).)).(((..(((.......))))))..... ( -22.60)
>consensus
AAUAAGCUGCACUUUAUUGUCGUCAUUAAAGUGAAGAGCAAUUCAAA_____________GUAAAAGAAGCCGGAAAGCGGU___GUGAUUGCAAAAACAUCACGCAGCG_
.....(((((((((((.((....)).)))))).....................................((((.....))))...(((((.........)))))))))).. (-13.13 = -15.22 +   2.08)

alignment

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secondary structure

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dotplot

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Window 4

Location 11,059,019 – 11,059,113
Length 94
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 78.06
Mean single sequence MFE -21.14
Consensus MFE -11.29
Energy contribution -13.02
Covariance contribution 1.72
Combinations/Pair 1.05
Mean z-score -2.13
Structure conservation index 0.53
SVM decision value 0.77
SVM RNA-class probability 0.846676
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11059019 94 - 23771897
-CGCUGCGUGAUGUUUUUGCAAUCAC---ACCGCUUUCCGACUUCUUUUAC-------------UUUAAAUUGCUCUUCACUUUAAUGACGACAAUAAAGUGCAGCUUAUU
-.((((((((((((....)).)))))---....................((-------------((((..(((.((.(((......))).))))))))))))))))..... ( -21.30)
>DroSec_CAF1 3003 94 - 1
-CGCUGCGUGAUGUUUUUGCAAUCAC---ACCGCUUUGCGGCUUCUUUUAC-------------UUUGAAUUGCUCUUCACUUUAAUGACGACAAUAAAGUGCAGCUUAUU
-.((((((((((((....)).)))))---.((((...))))........((-------------(((..((((.((.(((......))).))))))))))))))))..... ( -25.00)
>DroSim_CAF1 2947 94 - 1
-CGCUGCGUGAUGUUUUUGCAAUCAC---ACCGCUUUCCGGCUUCUUUUAC-------------UUUGAAUUGCUCUUCACUUUAAUGACGACAAUAAAGUGCAGCUUAUU
-.((((((((((((....)).)))))---.(((.....)))........((-------------(((..((((.((.(((......))).))))))))))))))))..... ( -22.40)
>DroEre_CAF1 2904 74 - 1
-CGCUGCGUGAUGUUAUUGCAAUCAC---ACCGCUUCCCGGCUUCUUUUAC-------------UUUG--------------------AUGACGAUAAAGUGCAGCUUGUU
-.((((((((((((....)).)))))---.(((.....)))........((-------------((((--------------------.......)))))))))))..... ( -18.10)
>DroYak_CAF1 2784 94 - 1
-CGCUGCGUGAUGUUUUUGCAAUCAC---ACCGCUUCCCGGCUUCUUUUAC-------------UUUGAAUUGCUUUUCACUUUAAUGACGACAAUAAAGUGCAGCUUAUU
-.((((((((((((....)).)))))---.(((.....)))..........-------------...(((......)))((((((.((....)).)))))))))))..... ( -20.80)
>DroAna_CAF1 2788 108 - 1
GCCCUGCGUGCUCUUUUCGCAAUCACUGCAACACUUUA---UUUUUUUUCCAUUCUUGGCUCGGUUCAGGUUCUUCUUCAUUUUAAUGCCGACAAUAAAGUGCAGCUUAUU
....((((.........))))......((..(((((((---((......(((....))).(((((......................))))).)))))))))..))..... ( -19.25)
>consensus
_CGCUGCGUGAUGUUUUUGCAAUCAC___ACCGCUUUCCGGCUUCUUUUAC_____________UUUGAAUUGCUCUUCACUUUAAUGACGACAAUAAAGUGCAGCUUAUU
..((((((((((((....)).))))).....................................................((((((.((....)).)))))))))))..... (-11.29 = -13.02 +   1.72)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:07:42 2006