Locus 7837

Sequence ID 3R_DroMel_CAF1
Location 20,989,367 – 20,989,502
Length 135
Max. P 0.997242
window12631 window12632 window12633

overview

Window 1

Location 20,989,367 – 20,989,476
Length 109
Sequences 5
Columns 116
Reading direction reverse
Mean pairwise identity 74.60
Mean single sequence MFE -39.02
Consensus MFE -22.42
Energy contribution -25.22
Covariance contribution 2.80
Combinations/Pair 1.24
Mean z-score -2.57
Structure conservation index 0.57
SVM decision value 2.82
SVM RNA-class probability 0.997242
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20989367 109 - 27905053
AUGUGUA----UGUG--UGUGUACACAAACACA-ACUGUGCGUCGGCUGUAGAGUCGAGGCGAUUCGAGUCCUGGCGUGGUCGUCAGAUGGCUAGGAUGCAGUCUUGAUACAUGAG
.(((((.----((((--(....))))).)))))-(((((((.((((((....)))))).)).......((((((((...(((....))).)))))))))))))............. ( -40.60)
>DroSec_CAF1 29954 113 - 1
AUAUAUGUGUGUGUG--UGUGUGCACACAUACA-ACUGUGCGUCGGCUGUGGAGUCGAAGCGAUUCGAGUCCUGGCGUGGUCGUCAGAUGGCUAGGAUGCAGUCUUGAUACAUGAG
...((((((((((((--((....))))))))).-....(((((((((((((((.(((((....))))).)))(((((....))))).))))))..))))))........))))).. ( -44.70)
>DroSim_CAF1 25382 115 - 1
AUGUGUGUGUGUGUGUUUGUGUGCACACAUACA-ACUGUGCGUCGGCUGUGGAGUCGAGGCGAUUCGAGUCCUGGCGUGGCCGUCAGAUGGCUAGGAUGCAGUCUUGAUACAUGAG
((((((((((((((((......)))))))))).-....((((((.((((.(((.(((((....))))).))))))).(((((((...))))))).))))))......))))))... ( -48.50)
>DroWil_CAF1 40408 96 - 1
AUGUAUGCAUGAAUG--UUUGUACAUAUAUACAUACAGAAAGUCGACUGCUU---------------GCUCUUGGCCUGG---GCAGGUGGCUAGAAUGCAGUCUUGAUACAUGAG
.((((((.(((.(((--(....)))).))).)))))).......((((((..---------------.((..(.((((..---..)))).)..))...))))))............ ( -26.60)
>DroYak_CAF1 31457 93 - 1
AU----------------------ACACAUUCA-ACUGUGCGUCGGCUGUGGAGUCGAGGCGAUUCGAGUCCUGGCCUGGUCGUCAGAUGGCUAGGAUGCAGUCUUGAUACAUGAG
..----------------------...((((((-(((((((.((((((....)))))).)).......(((((((((..(((....)))))))))))))))))..)))...))).. ( -34.70)
>consensus
AUGUAUG__UGUGUG__UGUGUACACACAUACA_ACUGUGCGUCGGCUGUGGAGUCGAGGCGAUUCGAGUCCUGGCGUGGUCGUCAGAUGGCUAGGAUGCAGUCUUGAUACAUGAG
.((((((.(((((........))))).))))))....(((.(((((((((.((((((...))))))..((((((((..............))))))))))))))..))).)))... (-22.42 = -25.22 +   2.80)

alignment

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secondary structure

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dotplot

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Window 2

Location 20,989,406 – 20,989,502
Length 96
Sequences 3
Columns 102
Reading direction forward
Mean pairwise identity 90.79
Mean single sequence MFE -33.30
Consensus MFE -28.14
Energy contribution -29.70
Covariance contribution 1.56
Combinations/Pair 1.06
Mean z-score -1.87
Structure conservation index 0.85
SVM decision value 0.06
SVM RNA-class probability 0.566176
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20989406 96 + 27905053
CGCCAGGACUCGAAUCGCCUCGACUCUACAGCCGACGCACAGUUGUGUUUGUGUACACA--CACA----UACACAUAGGUGCGUGUGUCCGUUCGUGUUCGC
.....((((.((((((((..((.((....)).))((((((...(((((.(((((....)--))))----.)))))...)))))))))...))))).)))).. ( -32.90)
>DroSec_CAF1 29993 100 + 1
CGCCAGGACUCGAAUCGCUUCGACUCCACAGCCGACGCACAGUUGUAUGUGUGCACACA--CACACACACAUAUAUAGGUGCGUGUGUCCGUUCGUGUUCGC
.....((((.((((((((..((.((....)).))((((((...((((((((((......--....))))))))))...)))))))))...))))).)))).. ( -33.00)
>DroSim_CAF1 25421 102 + 1
CGCCAGGACUCGAAUCGCCUCGACUCCACAGCCGACGCACAGUUGUAUGUGUGCACACAAACACACACACACACAUAGGUGCGUGUGUCCGUUCGUGUUCGC
.....(((.((((......)))).)))(((..((((.....))))..)))(((.((((.(((..((((((.(((....))).))))))..))).)))).))) ( -34.00)
>consensus
CGCCAGGACUCGAAUCGCCUCGACUCCACAGCCGACGCACAGUUGUAUGUGUGCACACA__CACACACACACACAUAGGUGCGUGUGUCCGUUCGUGUUCGC
.....((((.((((((((..((.((....)).))((((((...((((((((((............))))))))))...)))))))))...))))).)))).. (-28.14 = -29.70 +   1.56)

alignment

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secondary structure

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dotplot

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Window 3

Location 20,989,406 – 20,989,502
Length 96
Sequences 3
Columns 102
Reading direction reverse
Mean pairwise identity 90.79
Mean single sequence MFE -42.37
Consensus MFE -32.88
Energy contribution -34.33
Covariance contribution 1.45
Combinations/Pair 1.12
Mean z-score -3.14
Structure conservation index 0.78
SVM decision value 0.85
SVM RNA-class probability 0.866060
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20989406 96 - 27905053
GCGAACACGAACGGACACACGCACCUAUGUGUA----UGUG--UGUGUACACAAACACAACUGUGCGUCGGCUGUAGAGUCGAGGCGAUUCGAGUCCUGGCG
((.(((.((((((((((((..(((....)))..----))))--)((((......))))..))))((.((((((....)))))).))...))).))..).)). ( -33.40)
>DroSec_CAF1 29993 100 - 1
GCGAACACGAACGGACACACGCACCUAUAUAUGUGUGUGUG--UGUGUGCACACAUACAACUGUGCGUCGGCUGUGGAGUCGAAGCGAUUCGAGUCCUGGCG
.......((((((.((((((((((........)))))))))--).)))(((((........))))).)))((((.(((.(((((....))))).))))))). ( -42.20)
>DroSim_CAF1 25421 102 - 1
GCGAACACGAACGGACACACGCACCUAUGUGUGUGUGUGUGUUUGUGUGCACACAUACAACUGUGCGUCGGCUGUGGAGUCGAGGCGAUUCGAGUCCUGGCG
.((((((((((((.((((((((((....)))))))))).)))))))))(((((........))))).)))((((.(((.(((((....))))).))))))). ( -51.50)
>consensus
GCGAACACGAACGGACACACGCACCUAUGUGUGUGUGUGUG__UGUGUGCACACAUACAACUGUGCGUCGGCUGUGGAGUCGAGGCGAUUCGAGUCCUGGCG
((........((((...(((((((...((((((((((((........))))))))))))...)))))).).))))(((.(((((....))))).)))..)). (-32.88 = -34.33 +   1.45)

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 12:56:02 2006