Locus 859

Sequence ID 3L_DroMel_CAF1
Location 2,603,061 – 2,603,293
Length 232
Max. P 0.968154
window1319 window1320 window1321 window1322

overview

Window 9

Location 2,603,061 – 2,603,177
Length 116
Sequences 5
Columns 116
Reading direction forward
Mean pairwise identity 93.28
Mean single sequence MFE -41.18
Consensus MFE -37.64
Energy contribution -38.20
Covariance contribution 0.56
Combinations/Pair 1.11
Mean z-score -1.24
Structure conservation index 0.91
SVM decision value 0.53
SVM RNA-class probability 0.771861
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2603061 116 + 23771897
GCUUGGUUGCAUCCGCCGCCGUGGCUUUUGUUGCACUUAUCUGGCGUUGCCGUUACGCACAAGUGGCUAUGGCGAAAGGAUAUGCACUAGGCGAAAUCAAGGAUGCAUCUCGAGAG
.(((((.((((((((((((....))......((((..(((((....(((((((..(((....)))...)))))))..)))))))))...)))(....)..))))))).).)))).. ( -42.50)
>DroSec_CAF1 1392 108 + 1
GCUUGGCUACAUCCGCCGCCGUGGCUUUUGUUGCACUUAUCUGGCGCUGCCGUUACGCACAAGUGGCUAUGGCGCAAGGAUAUGCACUAGGCGAAAUCAAGGA--------AGGAG
((((((....((((..(((((((((((((((.((.......((((...))))....))))))).))))))))))...)))).....))))))...........--------..... ( -35.20)
>DroSim_CAF1 3821 116 + 1
GCUUGGCUGCAUCCGCCGCCGUGGCUUUUGUUGCACUUAUCUGGCGCUGCCGUUACGCACAAGUGGCUAUGGCGAAAGGAUAUGCACUAGGCGAAAUCAAGGAUGCAUCUCAAGAG
.(((((.((((((((((((((((((((((((.((.......((((...))))....))))))).)))))))))...((........)).)))(....)..))))))).).)))).. ( -42.30)
>DroEre_CAF1 1409 116 + 1
GCUUGGCUGCAUCCGCCGCCGUGGCUUUUGUUGCACUUAUCUGGCGCUGCCGUUACGCACAAGUGGCUAUGGCGAAAGGAUGUGCACUAGGCGAAAUCUAGGAUGCAUCUCAAGAA
.(((((.(((((((..(((((((((((((((.((.......((((...))))....))))))).))))))))))...((((.(((.....)))..)))).))))))).).)))).. ( -43.70)
>DroYak_CAF1 4377 116 + 1
GCUUGGCUGCAUCCGCCGCCGUGGCUUUUGUUGCACUUAUCUGGCGCUGCCGUUACGCACAAGUGGCUUUGGCGAAAGGAUAUGCACUCGGCGAAAUCAAGGAUGCAUCUCAAGAA
.(((((.(((((((..(((((.(((....))((((..(((((..(((((..(((((......)))))..)))))...)))))))))).))))).......))))))).).)))).. ( -42.20)
>consensus
GCUUGGCUGCAUCCGCCGCCGUGGCUUUUGUUGCACUUAUCUGGCGCUGCCGUUACGCACAAGUGGCUAUGGCGAAAGGAUAUGCACUAGGCGAAAUCAAGGAUGCAUCUCAAGAG
.(((((.((((((((((((....))......((((..(((((..(((((..(((((......)))))..)))))...)))))))))...)))(....)..))))))).).)))).. (-37.64 = -38.20 +   0.56) 

alignment

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secondary structure

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Window 0

Location 2,603,137 – 2,603,257
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 74.92
Mean single sequence MFE -27.72
Consensus MFE -13.48
Energy contribution -12.88
Covariance contribution -0.60
Combinations/Pair 1.33
Mean z-score -1.73
Structure conservation index 0.49
SVM decision value 0.02
SVM RNA-class probability 0.541493
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2603137 120 + 23771897
AGGAUAUGCACUAGGCGAAAUCAAGGAUGCAUCUCGAGAGUAUCAAGAACGUGCUCUAAAGGUAUGCAAGCACAUUUUUUGAAUGCAAAAGUCGAAUUGAAUAUGCACUGCAUACUUUUA
..((.(((((((..(......)..)).))))).)).(((((((.......)))))))(((((((((((.(((.(((((((((.(.....).)))))..)))).)))..))))))))))). ( -29.50)
>DroSec_CAF1 1468 112 + 1
AGGAUAUGCACUAGGCGAAAUCAAGGA--------AGGAGUAUCAAGAAGGUGCUCUAGAAGUGUGCAAGCACACUUUUUGAAUGCAAAAGUCUAAUUUAAUAUUCACUGCAUACUUUUA
.((((((....(((((...........--------.((((((((.....))))))))(((((((((....)))))))))...........))))).....)))))).............. ( -29.20)
>DroSim_CAF1 3897 119 + 1
AGGAUAUGCACUAGGCGAAAUCAAGGAUGCAUCUCAAGAGUAUCAAGAAGGUGCUCUAGAAGUGUGCAAGCACAUUUUUUGAAUGCAAAAGUCAAAUUUAAUAUUCACUGCAUACUU-UA
.((((((......((((....).....(((((.(((((((((((.....))))))))(((((((((....)))))))))))))))))...))).......))))))...........-.. ( -29.12)
>DroEre_CAF1 1485 95 + 1
AGGAUGUGCACUAGGCGAAAUCUAGGAUGCAUCUCAAGAAUAUAUCGAAGGUGCUCCAAGGGUAUGCAAGCACGCCUUUUGAA-------------------------UGCAAAGGUCCG
.((((.((((..(((((...(((.(((.((((((...((.....))..))))))))).)))((......)).)))))......-------------------------))))...)))). ( -28.90)
>DroYak_CAF1 4453 108 + 1
AGGAUAUGCACUCGGCGAAAUCAAGGAUGCAUCUCAAGAAUAUAUCGAAGGUGCUCUAAGGGUAUGCAAGCACAUUUUUUGACAGCUUA------------AAUUCACUGCAUACUUCUA
((((((((((....(((...((..(((.((((((...((.....))..)))))))))..))...)))((((.((.....))...)))).------------.......)))))).)))). ( -21.90)
>consensus
AGGAUAUGCACUAGGCGAAAUCAAGGAUGCAUCUCAAGAGUAUCAAGAAGGUGCUCUAAAGGUAUGCAAGCACAUUUUUUGAAUGCAAAAGUC_AAUU_AAUAUUCACUGCAUACUUCUA
....((((((..........................(((((((.......)))))))((((((.((....)).)))))).............................))))))...... (-13.48 = -12.88 +  -0.60) 

alignment

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secondary structure

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Window 1

Location 2,603,177 – 2,603,293
Length 116
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 77.27
Mean single sequence MFE -26.29
Consensus MFE -17.17
Energy contribution -18.43
Covariance contribution 1.25
Combinations/Pair 1.20
Mean z-score -2.18
Structure conservation index 0.65
SVM decision value 1.62
SVM RNA-class probability 0.968154
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2603177 116 + 23771897
UAUCAAGAACGUGCUCUAAAGGUAUGCAAGCACAUUUUUUGAAUGCAAAAGUCGAAUUGAAUAUGCACUGCAUACUUUUAGACACCUGGCAUUCUUAAUA-AAUUAUUUUUGA---AUGC
..........(((.((((((((((((((.(((.(((((((((.(.....).)))))..)))).)))..)))))))))))))))))...((((((..((..-......))..))---)))) ( -32.70)
>DroSec_CAF1 1500 119 + 1
UAUCAAGAAGGUGCUCUAGAAGUGUGCAAGCACACUUUUUGAAUGCAAAAGUCUAAUUUAAUAUUCACUGCAUACUUUUAGACACCUUGCAUUUUUAAUA-AAUAAUUUAGCAGCUAUGA
.......((((((.((((((((((((((((....)))..((((((..(((......)))..))))))..)))))))))))))))))))............-................... ( -28.60)
>DroSim_CAF1 3937 115 + 1
UAUCAAGAAGGUGCUCUAGAAGUGUGCAAGCACAUUUUUUGAAUGCAAAAGUCAAAUUUAAUAUUCACUGCAUACUU-UAGA---CUUGCAUUUUUAACA-AAUAAUUUGGCAGCUAUGA
........((.((((..(((((((((....))))))))).(((((((..((((........................-..))---)))))))))......-........)))).)).... ( -21.77)
>DroYak_CAF1 4493 108 + 1
UAUAUCGAAGGUGCUCUAAGGGUAUGCAAGCACAUUUUUUGACAGCUUA------------AAUUCACUGCAUACUUCUAAACACCUUGCAGUUUAAAUGAAAUAGUUUGGCAGUGAAGA
.......(((.((.((.((((((.((....)).)))))).)))).))).------------..((((((((..((((((((((........)))))...))...)))...)))))))).. ( -22.10)
>consensus
UAUCAAGAAGGUGCUCUAAAAGUAUGCAAGCACAUUUUUUGAAUGCAAAAGUC_AAUUUAAUAUUCACUGCAUACUUUUAGACACCUUGCAUUUUUAAUA_AAUAAUUUGGCAGCUAUGA
.......((((((.((((((((((((((........................................))))))))))))))))))))................................ (-17.17 = -18.43 +   1.25) 

alignment

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secondary structure

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dotplot

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Window 2

Location 2,603,177 – 2,603,293
Length 116
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 77.27
Mean single sequence MFE -25.57
Consensus MFE -14.39
Energy contribution -17.64
Covariance contribution 3.25
Combinations/Pair 1.08
Mean z-score -2.14
Structure conservation index 0.56
SVM decision value 0.77
SVM RNA-class probability 0.845283
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2603177 116 - 23771897
GCAU---UCAAAAAUAAUU-UAUUAAGAAUGCCAGGUGUCUAAAAGUAUGCAGUGCAUAUUCAAUUCGACUUUUGCAUUCAAAAAAUGUGCUUGCAUACCUUUAGAGCACGUUCUUGAUA
....---............-(((((((((((....((.((((((.((((((((.(((((((.........(((((....)))))))))))))))))))).)))))))).))))))))))) ( -32.00)
>DroSec_CAF1 1500 119 - 1
UCAUAGCUGCUAAAUUAUU-UAUUAAAAAUGCAAGGUGUCUAAAAGUAUGCAGUGAAUAUUAAAUUAGACUUUUGCAUUCAAAAAGUGUGCUUGCACACUUCUAGAGCACCUUCUUGAUA
(((.((.((((........-.......(((((((((.((((((.(((((.......)))))...)))))))))))))))....(((((((....)))))))....)))).))...))).. ( -29.30)
>DroSim_CAF1 3937 115 - 1
UCAUAGCUGCCAAAUUAUU-UGUUAAAAAUGCAAG---UCUA-AAGUAUGCAGUGAAUAUUAAAUUUGACUUUUGCAUUCAAAAAAUGUGCUUGCACACUUCUAGAGCACCUUCUUGAUA
(((.((.(((.......((-(((.......)))))---((((-((((.((((((.((........)).))....((((.........)))).)))).)))).))))))).))...))).. ( -19.50)
>DroYak_CAF1 4493 108 - 1
UCUUCACUGCCAAACUAUUUCAUUUAAACUGCAAGGUGUUUAGAAGUAUGCAGUGAAUU------------UAAGCUGUCAAAAAAUGUGCUUGCAUACCCUUAGAGCACCUUCGAUAUA
..((((((((.....((((((...(((((........))))))))))).))))))))..------------.....((((.......((((((...........))))))....)))).. ( -21.50)
>consensus
UCAUAGCUGCCAAAUUAUU_UAUUAAAAAUGCAAGGUGUCUAAAAGUAUGCAGUGAAUAUUAAAUU_GACUUUUGCAUUCAAAAAAUGUGCUUGCACACCUCUAGAGCACCUUCUUGAUA
................................(((((((((((((((((((((.....................((((.........))))))))))))))))))).))))))....... (-14.39 = -17.64 +   3.25) 

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:52:57 2006