Locus 2343

Sequence ID 2L_DroMel_CAF1
Location 6,351,602 – 6,351,766
Length 164
Max. P 0.998099
window3777 window3778 window3779

overview

Window 7

Location 6,351,602 – 6,351,704
Length 102
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 76.12
Mean single sequence MFE -33.01
Consensus MFE -20.61
Energy contribution -20.87
Covariance contribution 0.25
Combinations/Pair 1.24
Mean z-score -1.45
Structure conservation index 0.62
SVM decision value 0.43
SVM RNA-class probability 0.733926
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6351602 102 - 22407834
U-GACGGGCGGUGUUCCAGCAGCGAAGCACCGCCUGUUGUCAAUCCGAACUAUC-AGCCGAAUCGAAUCUCAA--------UCUCUCCAUAGAGCACCU---AUGACGUGGUC---GA
.-(((((((((((((.(......).))))))))))))).......(((.((((.-....((........))..--------......(((((.....))---)))..))))))---). ( -29.80)
>DroSec_CAF1 3345 102 - 1
U-GACGGGCGGUGUUCCAGCAGCGGAGCACCGCCUGUUGUCAAACCGAACUAUC-AACCGAAUCGAAUCUCAA--------UCUCUCAAUAGAGCACCU---AUGACGUGGUC---GA
.-(((((((((((((((......)))))))))))))))..............((-.((((..(((........--------.((((....)))).....---.)))..)))).---)) ( -35.36)
>DroSim_CAF1 2036 102 - 1
U-GACGGGCGGUGUUCCAGCAGCGGAGCACCGCCUGUUGUCAAACCGAACUAUC-AACCGAAUCGAAUCUCAA--------UCUCUCAAUAGAGCACCU---AUGACGUGGCC---GA
.-(((((((((((((((......)))))))))))))))((((...(((....((-....)).)))........--------.((((....)))).....---.))))......---.. ( -34.70)
>DroEre_CAF1 2047 87 - 1
U-GACGGGUGUUGUUCCAGCAGCGAAGCACCGCCUG-------------CUAUC-AAGC--AUCGAAUCUCAA--------UCUCUGCACAGAGCACCU---GUGACGUGGUC---GA
.-.(((((((((.....(((((((......)).)))-------------))...-..((--(..((.......--------))..)))....)))))))---))(((...)))---.. ( -24.30)
>DroYak_CAF1 2333 103 - 1
U-GACGGGCGGUGUUCCAGCAGUGAAGCACCGCCUGUUGUUUAACUCAACUAUC-AAGC--AACGAAUCUCAA--------UCUUUCAAUAGAGCACCUACUAUGACGUGGUG---GA
.-(((((((((((((.((....)).)))))))))))))...........(((((-(..(--(...........--------(((......)))..........))...)))))---). ( -29.60)
>DroAna_CAF1 2272 107 - 1
UGGAAAGGCGGUGUUCCAGCGCUGGAGCACCGCCUGUC-------CGA-CUGCCGCGGCUACUCGCAUAUCAACAAUCAAGCCCCUCGAGAGAGUUCCA---AUGACGUGGGCCCCGA
.(((.(((((((((((((....))))))))))))).))-------)..-...((((((((...................)))).(((....))).....---.....))))....... ( -44.31)
>consensus
U_GACGGGCGGUGUUCCAGCAGCGAAGCACCGCCUGUUGUCAAACCGAACUAUC_AACCGAAUCGAAUCUCAA________UCUCUCAAUAGAGCACCU___AUGACGUGGUC___GA
..(((((((((((((.(......).)))))))))))))............................................((((....)))).(((...........)))...... (-20.61 = -20.87 +   0.25)

alignment

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secondary structure

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dotplot

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Window 8

Location 6,351,633 – 6,351,744
Length 111
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 71.94
Mean single sequence MFE -35.27
Consensus MFE -19.44
Energy contribution -19.72
Covariance contribution 0.28
Combinations/Pair 1.21
Mean z-score -2.91
Structure conservation index 0.55
SVM decision value 3.01
SVM RNA-class probability 0.998099
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6351633 111 - 22407834
UUGAUAACACCCGGAGCAAAUACCACGUCUGUUGACCCACU-GACGGGCGGUGUUCCAGCAGCGAAGCACCGCCUGUUGUCAAUCCGAACUAUC-AGCCGAAUCGAAUCUCAA-----
((((((.....((((...........(((....))).....-(((((((((((((.(......).))))))))))))).....))))...))))-))................----- ( -31.90)
>DroSec_CAF1 3376 89 - 1
UUGAUAACAACCG----------------------CCCACU-GACGGGCGGUGUUCCAGCAGCGGAGCACCGCCUGUUGUCAAACCGAACUAUC-AACCGAAUCGAAUCUCAA-----
(((((((((...(----------------------(((...-...))))((((((((......))))))))...)))))))))...........-..................----- ( -31.70)
>DroSim_CAF1 2067 111 - 1
UUGAUAACACCGGGAGCAAAUACCCGGUCUGUUGACCCACU-GACGGGCGGUGUUCCAGCAGCGGAGCACCGCCUGUUGUCAAACCGAACUAUC-AACCGAAUCGAAUCUCAA-----
((((((..((((((........))))))...(((((.....-(((((((((((((((......)))))))))))))))))))).......))))-))................----- ( -45.70)
>DroEre_CAF1 2078 96 - 1
UUGAUAACACCCGGAGCAAAUACCAGGUGUGUUGACCCACU-GACGGGUGUUGUUCCAGCAGCGAAGCACCGCCUG-------------CUAUC-AAGC--AUCGAAUCUCAA-----
((((((......(((((((.((((.((((.(....).))))-....))))))))))).((((((......)).)))-------------)))))-))..--............----- ( -29.30)
>DroYak_CAF1 2367 109 - 1
UUGAUAACACCGAGAACAAAUACGAGGUCUGUUGACCCACU-GACGGGCGGUGUUCCAGCAGUGAAGCACCGCCUGUUGUUUAACUCAACUAUC-AAGC--AACGAAUCUCAA-----
((((((.....(((.........(.((((....)))))...-(((((((((((((.((....)).)))))))))))))......)))...))))-))..--............----- ( -34.20)
>DroAna_CAF1 2309 102 - 1
UUGAUAAUACGAAAAACAAAUAUUAG--------CCCCCCUGGAAAGGCGGUGUUCCAGCGCUGGAGCACCGCCUGUC-------CGA-CUGCCGCGGCUACUCGCAUAUCAACAAUC
((((((....................--------......((((.(((((((((((((....))))))))))))).))-------)).-.....((((....)))).))))))..... ( -38.80)
>consensus
UUGAUAACACCCGGAGCAAAUACCAGGUCUGUUGACCCACU_GACGGGCGGUGUUCCAGCAGCGAAGCACCGCCUGUUGUCAAACCGAACUAUC_AACCGAAUCGAAUCUCAA_____
..........................................(((((((((((((.(......).)))))))))))))........................................ (-19.44 = -19.72 +   0.28)

alignment

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secondary structure

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dotplot

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Window 9

Location 6,351,667 – 6,351,766
Length 99
Sequences 6
Columns 100
Reading direction reverse
Mean pairwise identity 72.81
Mean single sequence MFE -34.36
Consensus MFE -18.97
Energy contribution -19.25
Covariance contribution 0.28
Combinations/Pair 1.21
Mean z-score -2.42
Structure conservation index 0.55
SVM decision value 2.32
SVM RNA-class probability 0.992229
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6351667 99 - 22407834
GAUACGGAUGCCUCAAGCAGAGUUGAUAACACCCGGAGCAAAUACCACGUCUGUUGACCCACU-GACGGGCGGUGUUCCAGCAGCGAAGCACCGCCUGUU
...(((((((.(((.....)))............((........)).))))))).........-(((((((((((((.(......).))))))))))))) ( -30.60)
>DroSec_CAF1 3410 77 - 1
GAUACGGAUGCCUCAAGCAGAGUUGAUAACAACCG----------------------CCCACU-GACGGGCGGUGUUCCAGCAGCGGAGCACCGCCUGUU
.....((.(((.....)))(.((((....))))).----------------------.))...-(((((((((((((((......))))))))))))))) ( -34.00)
>DroSim_CAF1 2101 99 - 1
GAUACGGAUGCCUCAAGCAGAGUUGAUAACACCGGGAGCAAAUACCCGGUCUGUUGACCCACU-GACGGGCGGUGUUCCAGCAGCGGAGCACCGCCUGUU
.....((.(((.....)))..((..(((..((((((........)))))).)))..))))...-(((((((((((((((......))))))))))))))) ( -46.70)
>DroEre_CAF1 2099 97 - 1
GAUGCGGACACCUCAAGCAGAGUUGAUAACACCCGGAGCAAAUACCAGGUGUGUUGACCCACU-GACGGGUGUUGUUCCAGCAGCGAAGCACCGCCUG--
...((((((((((....(((.((..(((.((((.((........)).)))))))..))...))-)..)))))).......((......)).))))...-- ( -31.00)
>DroYak_CAF1 2399 99 - 1
AAUCCGGAUACCUCCAGCACAGUUGAUAACACCGAGAACAAAUACGAGGUCUGUUGACCCACU-GACGGGCGGUGUUCCAGCAGUGAAGCACCGCCUGUU
..(((((.......((((...))))......))).))........(.((((....)))))...-(((((((((((((.((....)).))))))))))))) ( -32.32)
>DroAna_CAF1 2341 76 - 1
ACU----------------AGGUUGAUAAUACGAAAAACAAAUAUUAG--------CCCCCCUGGAAAGGCGGUGUUCCAGCGCUGGAGCACCGCCUGUC
...----------------.((((((((..............))))))--------))......((.(((((((((((((....))))))))))))).)) ( -31.54)
>consensus
GAUACGGAUGCCUCAAGCAGAGUUGAUAACACCCGGAGCAAAUACCAGGUCUGUUGACCCACU_GACGGGCGGUGUUCCAGCAGCGAAGCACCGCCUGUU
................................................................(((((((((((((.(......).))))))))))))) (-18.97 = -19.25 +   0.28)

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 10:25:47 2006