Locus 1002

Sequence ID 2R_DroMel_CAF1
Location 4,205,923 – 4,206,163
Length 240
Max. P 0.994388
window1772 window1773 window1774

overview

Window 2

Location 4,205,923 – 4,206,043
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.00
Mean single sequence MFE -44.74
Consensus MFE -40.86
Energy contribution -41.02
Covariance contribution 0.16
Combinations/Pair 1.15
Mean z-score -1.84
Structure conservation index 0.91
SVM decision value 2.47
SVM RNA-class probability 0.994388
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4205923 120 + 20766785
AAGCUUCGCCUGACACUCUUCUCGCUCCACCAGUGGCAGGUUGAUCCGCUUGAGCACAUGCUCCAACUUGUCGCUGCCCGCCUCCUUGGUGCCCCAACCAGUGGCGUAACAGGUGACCGA
.....(((((((..................(((((((((((((........((((....)))))))))))))))))..((((...(((((......))))).))))...))))))).... ( -44.70)
>DroSec_CAF1 17731 120 + 1
AAGCUUCGCCUGACACUCUUCCCGCUCCACCAGUGGCAGGUUGAUCCGCUUGAGCACAUGCUCCAGCUUGUCGCUGCCCGCCUCCUUGGUGCCCCAACCAGUGGCGUAACAGGUGACCGA
.....(((((((..................(((((((((((((........((((....)))))))))))))))))..((((...(((((......))))).))))...))))))).... ( -44.70)
>DroSim_CAF1 43885 120 + 1
AAGCUUCGCCUGACACUCUUCCCGCUCCACCAGUGGCAGGUUGAUCCGCUUGAGCACAUGCUCCAGCUUGUCGCUGCCCGCCUCCUUGGUGCCCCAGCCAGUGGCGUAACAGGUGGACGA
..(.((((((((..................(((((((((((((........((((....)))))))))))))))))..((((...(((((......))))).))))...))))))))).. ( -44.90)
>DroEre_CAF1 19911 120 + 1
CAGCUUCGCCUGGCACUCUUCCCGCUCCACCAGCGGCAGGUUAAUCCGCUUGAGUACGUGCUCCAGCUGGUCGCUGUCCGCCUGCUUGCUGCCCCAACCAGUGGCGUAACAGGUGGACGA
.(((...(((.((....(((.(((((.....))))).))).....))(((.((((....)))).))).))).)))(((((((((.((((.(((.(.....).)))))))))))))))).. ( -47.40)
>DroYak_CAF1 20006 120 + 1
CAGCUUCGCCUGACACUCUUCCCGCUCCACCAGUGGCAGGUUAAUCCGCUUGAGCACAUGCUCCAGCUUGUCGCUGCCCGCCUCCUUGGAGCCCCAACCAGUGGCGUAACAGGUGACCGA
.....(((((((..................((((((((((.....))(((.((((....)))).))).))))))))..((((.(.((((....))))...).))))...))))))).... ( -42.00)
>consensus
AAGCUUCGCCUGACACUCUUCCCGCUCCACCAGUGGCAGGUUGAUCCGCUUGAGCACAUGCUCCAGCUUGUCGCUGCCCGCCUCCUUGGUGCCCCAACCAGUGGCGUAACAGGUGACCGA
.....(((((((..................(((((((((((((........((((....)))))))))))))))))..((((...(((((......))))).))))...))))))).... (-40.86 = -41.02 +   0.16) 

alignment

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secondary structure

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dotplot

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Window 3

Location 4,205,963 – 4,206,083
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.17
Mean single sequence MFE -50.34
Consensus MFE -39.32
Energy contribution -40.20
Covariance contribution 0.88
Combinations/Pair 1.12
Mean z-score -1.69
Structure conservation index 0.78
SVM decision value 0.40
SVM RNA-class probability 0.722405
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4205963 120 + 20766785
UUGAUCCGCUUGAGCACAUGCUCCAACUUGUCGCUGCCCGCCUCCUUGGUGCCCCAACCAGUGGCGUAACAGGUGACCGAUAGCAGCUGGUUGGUCAACUCCGGAGAUUCCGGAGGCGGC
.....((((((((((....)).((((((....(((((.((((...(((((......))))).))))...(.(....).)...))))).))))))))))((((((.....)))))))))). ( -48.30)
>DroSec_CAF1 17771 120 + 1
UUGAUCCGCUUGAGCACAUGCUCCAGCUUGUCGCUGCCCGCCUCCUUGGUGCCCCAACCAGUGGCGUAACAGGUGACCGAGAGCAGCUGGUUGGUCAAUUCCGGAGAUUCUGAAGGCGGC
..(((..(((.((((....)))).)))..)))((((((((((.....))))..(((((((((.((....(.(....).)...)).))))))))).......(((.....)))..)))))) ( -47.30)
>DroSim_CAF1 43925 120 + 1
UUGAUCCGCUUGAGCACAUGCUCCAGCUUGUCGCUGCCCGCCUCCUUGGUGCCCCAGCCAGUGGCGUAACAGGUGGACGAGAGCAGCUGGUUGGUCAAUUCCGGAGAUUCUGGAGGCGGC
..(((..(((.((((....)))).)))..)))((((((((((.....))))..(((((((((.((......(.....)....)).))))))))).....(((((.....))))))))))) ( -49.80)
>DroEre_CAF1 19951 120 + 1
UUAAUCCGCUUGAGUACGUGCUCCAGCUGGUCGCUGUCCGCCUGCUUGCUGCCCCAACCAGUGGCGUAACAGGUGGACGAGAGCAGCUGGUUGACCAAUUCCGGAGAUUCCGGAGGCGGC
.....(((((((.((.((....(((((((.((..((((((((((.((((.(((.(.....).))))))))))))))))).)).))))))).)))))))((((((.....)))))))))). ( -58.90)
>DroYak_CAF1 20046 120 + 1
UUAAUCCGCUUGAGCACAUGCUCCAGCUUGUCGCUGCCCGCCUCCUUGGAGCCCCAACCAGUGGCGUAACAGGUGACCGAGAGCAGCCGCUUGACCAACUCCGGAGAUUCCGGAGGCGGC
.....(((((..(((...(((((..(...((((((...((((.(.((((....))))...).)))).....)))))))..)))))...)))..)....((((((.....)))))))))). ( -47.40)
>consensus
UUGAUCCGCUUGAGCACAUGCUCCAGCUUGUCGCUGCCCGCCUCCUUGGUGCCCCAACCAGUGGCGUAACAGGUGACCGAGAGCAGCUGGUUGGUCAAUUCCGGAGAUUCCGGAGGCGGC
.......(((.((((....)))).))).....((((((((((.....))))..(((((((((.((......(.....)....)).))))))))).....(((((.....))))))))))) (-39.32 = -40.20 +   0.88) 

alignment

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secondary structure

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dotplot

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Window 4

Location 4,206,043 – 4,206,163
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.83
Mean single sequence MFE -45.86
Consensus MFE -38.46
Energy contribution -38.42
Covariance contribution -0.04
Combinations/Pair 1.15
Mean z-score -1.53
Structure conservation index 0.84
SVM decision value 0.64
SVM RNA-class probability 0.809914
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4206043 120 + 20766785
UAGCAGCUGGUUGGUCAACUCCGGAGAUUCCGGAGGCGGCAAGCACAGCGGCUGGAUAUGUGGAGCGAGACGGAUGGGCUCGUCCAGGAGCAAUAGUGCUAUGUCGUUGUACAACGAGUU
((((.(((((((.(((..((((((.....))))))..))).))).)))).))))....((((.(((((.(.(((((....)))))...((((....)))).).))))).))))....... ( -48.70)
>DroSec_CAF1 17851 120 + 1
GAGCAGCUGGUUGGUCAAUUCCGGAGAUUCUGAAGGCGGCAAGCACAGCGGCUGAAUGUGAGGAGCCAGUCGGAUGGGCUCGUCCAGGAGCAACAAUGCUAUGUCGUUGUACAACGAGUU
....((((.((((........(((.....)))..(((((((((((..(..(((...((.((.(((((.........))))).))))..)))..)..)))).)))))))...)))).)))) ( -39.50)
>DroSim_CAF1 44005 120 + 1
GAGCAGCUGGUUGGUCAAUUCCGGAGAUUCUGGAGGCGGCAAGCACAGUGGCUGGAUGUGAGGAGCCAGUCGGAUGGGCUCGUCGAGGAGCAACAGUGCUAUGUCGUUGUACAACGAGUA
.....(((.((((..((.((((((.....))))))(((((((((((.((.(((.....(((.(((((.........))))).)))...))).)).))))).))))))))..)))).))). ( -46.70)
>DroEre_CAF1 20031 120 + 1
GAGCAGCUGGUUGACCAAUUCCGGAGAUUCCGGAGGCGGCAGGCACAGAGGCUGGAUGUGCGGAGCCAGGCGGAUGGGCUCGUCCAGGAGCAACAGUGCUAUGUCGUUGUACAGCGAGUA
.....(((.((((((....(((((.....)))))((((((((((((.(..((((((((.((....((....))....)).)))))...)))..).))))).))))))))).)))).))). ( -46.20)
>DroYak_CAF1 20126 120 + 1
GAGCAGCCGCUUGACCAACUCCGGAGAUUCCGGAGGCGGCAGGCACAGAGGCUGGAUGUGCGGAGCCAGACGGAUGGGUUCGUCCAGGAGCAACAGUGCUAUGUCGUUGUACAACGAGUC
...((((((((((.((..((((((.....))))))..))))))).....)))))..((..((((.(((......))).))))..))..((((....))))...(((((....)))))... ( -48.20)
>consensus
GAGCAGCUGGUUGGUCAAUUCCGGAGAUUCCGGAGGCGGCAAGCACAGAGGCUGGAUGUGAGGAGCCAGACGGAUGGGCUCGUCCAGGAGCAACAGUGCUAUGUCGUUGUACAACGAGUA
.....(((.((((..((.((((((.....))))))(((((((((((...((((..........))))..........((((......))))....))))).))))))))..)))).))). (-38.46 = -38.42 +  -0.04) 

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 09:53:48 2006