Locus 316

Sequence ID 3L_DroMel_CAF1
Location 925,713 – 925,803
Length 90
Max. P 0.989975
window473 window474

overview

Window 3

Location 925,713 – 925,803
Length 90
Sequences 5
Columns 99
Reading direction forward
Mean pairwise identity 80.02
Mean single sequence MFE -28.76
Consensus MFE -11.22
Energy contribution -13.54
Covariance contribution 2.32
Combinations/Pair 1.24
Mean z-score -3.15
Structure conservation index 0.39
SVM decision value 2.19
SVM RNA-class probability 0.989975
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 925713 90 + 23771897
AA----AGAGAAAAAUUAGCUGCCCAUAAUGUGAUUUCGAUUGC---GGCAAGGUUGGAGCGAA-ACU-UCAACUGCGCUGCACUUAAUGGAGCAGCAG
..----............(((((((((....((....))..(((---(((..((((((((....-.))-))))))..))))))....)))).))))).. ( -32.20)
>DroSim_CAF1 52696 89 + 1
AA----AGAGAAAAAUUAGCUGGCCAUAAUGCGAUUUCGAUUGC---GGCAAGG-UGGAGCGCA-ACU-UCAGCUGCGCUGCACUUAAUGGAGCAGCUG
..----..........((((((.((((..((((((....)))))---)...(((-((.((((((-.(.-...).)))))).))))).))))..)))))) ( -33.00)
>DroEre_CAF1 63164 90 + 1
AA----AGAAAAAAAUUAGCUGCCCAUAAUGCGAUUUCGAUUGC---GGCAAGGUUGGAGCGAA-ACU-UUAACUGAGCUGCACUUAAUGGGGCAGCUG
..----..........(((((((((......((....))..(((---(((..((((((((....-.))-))))))..)))))).......))))))))) ( -34.90)
>DroYak_CAF1 62350 94 + 1
AAAGAGAGAGAAAAAUUAGCUGCCCAUAAUGCGAUUUCGAUUGC---GGCAAGGUUCGAGCGAA-ACU-UUAACUGCGCUGCACUUAAUGGAGCAGCUG
................(((((((((((....((....))..(((---(((..((((.(((....-.))-).))))..))))))....)))).))))))) ( -29.60)
>DroAna_CAF1 65820 88 + 1
AA----AAAAAAA--GAAACUG----AAAUGCAAUUUCAAUUGCCAGGAUAUGGU-UAACCGAAAACUUUUAUUUCCCCAGCACUUAAUGGAGCGGCAG
..----.......--((((.((----.....)).))))...((((.((....((.-...))((((.......)))).)).((.((....)).)))))). ( -14.10)
>consensus
AA____AGAGAAAAAUUAGCUGCCCAUAAUGCGAUUUCGAUUGC___GGCAAGGUUGGAGCGAA_ACU_UUAACUGCGCUGCACUUAAUGGAGCAGCUG
..................(((((((((...(((((....)))))...(((..((((((((......)).))))))..))).......)))).))))).. (-11.22 = -13.54 +   2.32) 

alignment

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secondary structure

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dotplot

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Window 4

Location 925,713 – 925,803
Length 90
Sequences 5
Columns 99
Reading direction reverse
Mean pairwise identity 80.02
Mean single sequence MFE -23.91
Consensus MFE -10.68
Energy contribution -13.16
Covariance contribution 2.48
Combinations/Pair 1.09
Mean z-score -2.40
Structure conservation index 0.45
SVM decision value 0.88
SVM RNA-class probability 0.873690
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 925713 90 - 23771897
CUGCUGCUCCAUUAAGUGCAGCGCAGUUGA-AGU-UUCGCUCCAACCUUGCC---GCAAUCGAAAUCACAUUAUGGGCAGCUAAUUUUUCUCU----UU
..(((((.((((....(((.(((..((((.-((.-....)).))))..))).---)))..............)))))))))............----.. ( -23.57)
>DroSim_CAF1 52696 89 - 1
CAGCUGCUCCAUUAAGUGCAGCGCAGCUGA-AGU-UGCGCUCCA-CCUUGCC---GCAAUCGAAAUCGCAUUAUGGCCAGCUAAUUUUUCUCU----UU
.(((((.........(((.((((((((...-.))-)))))).))-)...(((---(.(((((....)).))).)))))))))...........----.. ( -29.80)
>DroEre_CAF1 63164 90 - 1
CAGCUGCCCCAUUAAGUGCAGCUCAGUUAA-AGU-UUCGCUCCAACCUUGCC---GCAAUCGAAAUCGCAUUAUGGGCAGCUAAUUUUUUUCU----UU
.((((((((.......(((.((...(((..-((.-....))..)))...)).---)))..((....))......))))))))...........----.. ( -23.00)
>DroYak_CAF1 62350 94 - 1
CAGCUGCUCCAUUAAGUGCAGCGCAGUUAA-AGU-UUCGCUCGAACCUUGCC---GCAAUCGAAAUCGCAUUAUGGGCAGCUAAUUUUUCUCUCUCUUU
.((((((.((((..(((((.((((((((..-((.-....))..)))..)).)---))....(....))))))))))))))))................. ( -25.80)
>DroAna_CAF1 65820 88 - 1
CUGCCGCUCCAUUAAGUGCUGGGGAAAUAAAAGUUUUCGGUUA-ACCAUAUCCUGGCAAUUGAAAUUGCAUUU----CAGUUUC--UUUUUUU----UU
................(((..((((((.......))))((...-.))....))..)))...(((((((.....----)))))))--.......----.. ( -17.40)
>consensus
CAGCUGCUCCAUUAAGUGCAGCGCAGUUAA_AGU_UUCGCUCCAACCUUGCC___GCAAUCGAAAUCGCAUUAUGGGCAGCUAAUUUUUCUCU____UU
..(((((.((((..(((((((((..............))))......((((....))))........)))))))))))))).................. (-10.68 = -13.16 +   2.48) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript


Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:39:05 2006