Locus 1724

Sequence ID 2R_DroMel_CAF1
Location 6,489,616 – 6,489,750
Length 134
Max. P 0.994695
window2880 window2881 window2882 window2883

overview

Window 0

Location 6,489,616 – 6,489,715
Length 99
Sequences 4
Columns 107
Reading direction forward
Mean pairwise identity 84.50
Mean single sequence MFE -27.15
Consensus MFE -21.70
Energy contribution -20.95
Covariance contribution -0.75
Combinations/Pair 1.13
Mean z-score -2.61
Structure conservation index 0.80
SVM decision value 1.97
SVM RNA-class probability 0.984330
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6489616 99 + 20766785
UAAAAAAGUUUUAUGUUAUUUUUAUGGUGAUGACAAUUGCGUUG------AAGUUCGCUUGUGUUGGUGCACACACAUACGCG--UGUGUGUGUGUGUGUGAGAGAG
..............((((((.....))))))((((...(((...------.....)))...))))....(((((((((((((.--...)))))))))))))...... ( -28.30)
>DroSec_CAF1 57350 92 + 1
UAAAAAAGUUUUAUGUUAUUUUUAUGGUGAUGACAAUUGCGUUG------AAGUUCGCUUGUGUUGGUGCACACAUAUACUA---CUCGUGUGUGUGU------GAG
..............((((((.....))))))((((...(((...------.....)))...))))....(((((((((((..---...))))))))))------).. ( -22.80)
>DroSim_CAF1 44870 93 + 1
UAAAAAAGUUUUAUGUUAUUUUUAUGGUGAUGACAAUUGCGUUG------AAGUUCGCUUGUGUUGGUGCACACACAUACUCG--UUUGUGUGUGUGU------GAG
..............((((((.....))))))((((...(((...------.....)))...))))....(((((((((((...--...))))))))))------).. ( -25.50)
>DroYak_CAF1 60682 101 + 1
UAAAAAAGUUUUAUGUUAUUUUUAUGGUGAUGACAAUUGCGUUUGCGUUCGCGUUCGCUUGUGUUGGUGGGCACACACACGUAUAUGUGUGUGUGUGC------GGG
..............((((((.....))))))((((...(((..(((....)))..)))...)))).....(((((((((((......)))))))))))------... ( -32.00)
>consensus
UAAAAAAGUUUUAUGUUAUUUUUAUGGUGAUGACAAUUGCGUUG______AAGUUCGCUUGUGUUGGUGCACACACAUACGCG__UGUGUGUGUGUGU______GAG
.......((....(((((((........)))))))...))...............((((......)))).((((((((((........))))))))))......... (-21.70 = -20.95 +  -0.75)

alignment

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secondary structure

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Window 1

Location 6,489,616 – 6,489,715
Length 99
Sequences 4
Columns 107
Reading direction reverse
Mean pairwise identity 84.50
Mean single sequence MFE -16.20
Consensus MFE -11.19
Energy contribution -11.07
Covariance contribution -0.12
Combinations/Pair 1.08
Mean z-score -3.20
Structure conservation index 0.69
SVM decision value 2.07
SVM RNA-class probability 0.987085
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6489616 99 - 20766785
CUCUCUCACACACACACACACA--CGCGUAUGUGUGUGCACCAACACAAGCGAACUU------CAACGCAAUUGUCAUCACCAUAAAAAUAACAUAAAACUUUUUUA
........((((((((.((...--...)).))))))))...........(((.....------...)))...................................... ( -15.70)
>DroSec_CAF1 57350 92 - 1
CUC------ACACACACACGAG---UAGUAUAUGUGUGCACCAACACAAGCGAACUU------CAACGCAAUUGUCAUCACCAUAAAAAUAACAUAAAACUUUUUUA
...------..........(((---(..(((.(((((......))))).(((.....------...)))........................)))..))))..... ( -10.70)
>DroSim_CAF1 44870 93 - 1
CUC------ACACACACACAAA--CGAGUAUGUGUGUGCACCAACACAAGCGAACUU------CAACGCAAUUGUCAUCACCAUAAAAAUAACAUAAAACUUUUUUA
..(------(((((((.((...--...)).))))))))...........(((.....------...)))...................................... ( -15.30)
>DroYak_CAF1 60682 101 - 1
CCC------GCACACACACACAUAUACGUGUGUGUGCCCACCAACACAAGCGAACGCGAACGCAAACGCAAUUGUCAUCACCAUAAAAAUAACAUAAAACUUUUUUA
...------((((((((((........))))))))))............(((...((....))...)))...................................... ( -23.10)
>consensus
CUC______ACACACACACAAA__CGAGUAUGUGUGUGCACCAACACAAGCGAACUU______CAACGCAAUUGUCAUCACCAUAAAAAUAACAUAAAACUUUUUUA
.........(((((((.((........)).)))))))............(((..............)))...................................... (-11.19 = -11.07 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 2

Location 6,489,655 – 6,489,750
Length 95
Sequences 4
Columns 103
Reading direction forward
Mean pairwise identity 83.33
Mean single sequence MFE -30.15
Consensus MFE -25.05
Energy contribution -24.93
Covariance contribution -0.12
Combinations/Pair 1.22
Mean z-score -2.81
Structure conservation index 0.83
SVM decision value 2.50
SVM RNA-class probability 0.994695
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6489655 95 + 20766785
CGUUG------AAGUUCGCUUGUGUUGGUGCACACACAUACGCG--UGUGUGUGUGUGUGUGAGAGAGUAUUAUUGUUGCUUACUCAACAUGCAUUUAUGCCC
.....------(((....)))((((..((((((((((((((((.--...)))))))))))((((.(((((.......))))).))))...)))))..)))).. ( -32.30)
>DroSec_CAF1 57389 88 + 1
CGUUG------AAGUUCGCUUGUGUUGGUGCACACAUAUACUA---CUCGUGUGUGUGU------GAGUAUUAUUGUUGCUUACUCAACAUGCAUUUAUGCCC
.((((------(.((..((......((((((.(((((((((..---.....))))))))------).)))))).....))..)))))))..(((....))).. ( -26.40)
>DroSim_CAF1 44909 89 + 1
CGUUG------AAGUUCGCUUGUGUUGGUGCACACACAUACUCG--UUUGUGUGUGUGU------GAGUAUUAUUGUUGCUUACUCAACAUGCAUUUAUGCCC
.((((------(.((..((......((((((.(((((((((...--.....))))))))------).)))))).....))..)))))))..(((....))).. ( -28.60)
>DroYak_CAF1 60721 97 + 1
CGUUUGCGUUCGCGUUCGCUUGUGUUGGUGGGCACACACACGUAUAUGUGUGUGUGUGC------GGGUGUUAUUGUUGCUUACUCAACAUGCAUUUAUGCCC
.....(((..((((((((((......)))))))(((((((((......)))))))))))------)..)))...(((((......))))).(((....))).. ( -33.30)
>consensus
CGUUG______AAGUUCGCUUGUGUUGGUGCACACACAUACGCG__UGUGUGUGUGUGU______GAGUAUUAUUGUUGCUUACUCAACAUGCAUUUAUGCCC
.................((..((((((((((((((((((((......))))))))))))......(((((.......))))))).)))))))).......... (-25.05 = -24.93 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 3

Location 6,489,655 – 6,489,750
Length 95
Sequences 4
Columns 103
Reading direction reverse
Mean pairwise identity 83.33
Mean single sequence MFE -22.77
Consensus MFE -16.75
Energy contribution -16.62
Covariance contribution -0.12
Combinations/Pair 1.05
Mean z-score -2.63
Structure conservation index 0.74
SVM decision value 1.91
SVM RNA-class probability 0.982337
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6489655 95 - 20766785
GGGCAUAAAUGCAUGUUGAGUAAGCAACAAUAAUACUCUCUCACACACACACACACA--CGCGUAUGUGUGUGCACCAACACAAGCGAACUU------CAACG
(((((....))).(((((......)))))..............((((((((.((...--...)).))))))))..))...............------..... ( -20.00)
>DroSec_CAF1 57389 88 - 1
GGGCAUAAAUGCAUGUUGAGUAAGCAACAAUAAUACUC------ACACACACACGAG---UAGUAUAUGUGUGCACCAACACAAGCGAACUU------CAACG
..(((....)))..(((((((..((....(((.(((((------..........)))---)).))).(((((......))))).))..)).)------)))). ( -20.80)
>DroSim_CAF1 44909 89 - 1
GGGCAUAAAUGCAUGUUGAGUAAGCAACAAUAAUACUC------ACACACACACAAA--CGAGUAUGUGUGUGCACCAACACAAGCGAACUU------CAACG
..(((....)))..(((((((..((............(------(((((((.((...--...)).))))))))...........))..)).)------)))). ( -21.80)
>DroYak_CAF1 60721 97 - 1
GGGCAUAAAUGCAUGUUGAGUAAGCAACAAUAACACCC------GCACACACACACAUAUACGUGUGUGUGCCCACCAACACAAGCGAACGCGAACGCAAACG
(((((....))).(((((......))))).......))------((((((((((........))))))))))............(((........)))..... ( -28.50)
>consensus
GGGCAUAAAUGCAUGUUGAGUAAGCAACAAUAAUACUC______ACACACACACAAA__CGAGUAUGUGUGUGCACCAACACAAGCGAACUU______CAACG
(((((....))).(((((......)))))...............(((((((.((........)).)))))))...)).......................... (-16.75 = -16.62 +  -0.12)

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 10:11:45 2006