Locus 2350

Sequence ID 3L_DroMel_CAF1
Location 6,598,705 – 6,598,806
Length 101
Max. P 0.999021
window3623 window3624

overview

Window 3

Location 6,598,705 – 6,598,806
Length 101
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 80.61
Mean single sequence MFE -41.12
Consensus MFE -22.85
Energy contribution -26.01
Covariance contribution 3.16
Combinations/Pair 1.07
Mean z-score -3.94
Structure conservation index 0.56
SVM decision value 3.25
SVM RNA-class probability 0.998846
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6598705 101 + 23771897
AUGCGGAAAAGGAGCAGUGGCAUGAGCA------GAAAUUGUCACUUACACUGCACUUGCAGCUGGGAUUUGGCCAAAAUGUGCUGCUCCUGCUCC------UGCUUCUGUUG
..((((((.((((((((..(((...(((------......((((....((((((....)))).)).....)))).....)))..)))..)))))))------)..)))))).. ( -38.80)
>DroSec_CAF1 61675 101 + 1
AUGCGAAAGAGGAGCAGUGGCAGGAGCA------GAAAUUGUCACUUACACUGCACUUGCAGCUGGGAUUUGGCCAAAAUGUGCUACUCCUGCUCC------UGCUCCUGUUG
......((.((((((((..(((((((.(------(..(((((((....((((((....)))).)).....))))...)))...)).)))))))..)------))))))).)). ( -42.70)
>DroSim_CAF1 61843 107 + 1
AUGCGAAAGAGGAGCAGUGGCAGGAGCA------GAAAUUGUCACUUACACUGCACUUGCAGCUGGGAUUUGGCCAAAAUGUGCUGCUCCUGCUCCUGUUCCUGCUCCUUUUG
......(((((((((((..(((((((((------(.....(.(((...((((((....)))).))((......)).....)))).....))))))))))..))))))))))). ( -49.50)
>DroEre_CAF1 61972 90 + 1
AUGGAAAA-AAAAGC--------------------AAAUUGUCACUUACACUGCACUUGCAGCUGGGAUUUGGCCAAAAC--CCAGCUCCAGCUCCAGCUCCAGCUCCUGUUG
.((((...-....((--------------------(...(((.....))).)))..(((.(((((((.(((....))).)--)))))).))).))))....((((....)))) ( -22.40)
>DroYak_CAF1 63576 113 + 1
AUAGGAAAAAGGAGCAGCAGCAGGAGCAGCAGUAGAAAUUGUCACUUACACUGCACUUGCAGCUGGGAUUUGGCCAAAAUGUGCUGCUCCUGCUCCUGCUUCAGCUCCUGUUU
((((((....(((((((.(((((((((((((.((......((((....((((((....)))).)).....)))).....))))))))))))))).)))))))...)))))).. ( -52.20)
>consensus
AUGCGAAAAAGGAGCAGUGGCAGGAGCA______GAAAUUGUCACUUACACUGCACUUGCAGCUGGGAUUUGGCCAAAAUGUGCUGCUCCUGCUCC_G_U_CUGCUCCUGUUG
.........((((((((.((((((((((............((((....((((((....)))).)).....))))..........)))))))))).)......))))))).... (-22.85 = -26.01 +   3.16)

alignment

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secondary structure

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dotplot

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Window 4

Location 6,598,705 – 6,598,806
Length 101
Sequences 5
Columns 113
Reading direction reverse
Mean pairwise identity 80.61
Mean single sequence MFE -40.86
Consensus MFE -22.46
Energy contribution -24.86
Covariance contribution 2.40
Combinations/Pair 1.12
Mean z-score -4.15
Structure conservation index 0.55
SVM decision value 3.33
SVM RNA-class probability 0.999021
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6598705 101 - 23771897
CAACAGAAGCA------GGAGCAGGAGCAGCACAUUUUGGCCAAAUCCCAGCUGCAAGUGCAGUGUAAGUGACAAUUUC------UGCUCAUGCCACUGCUCCUUUUCCGCAU
........((.------((((.((((((((.......((((.........(((((....)))))....((((((.....------)).)))))))))))))))).)))))).. ( -34.51)
>DroSec_CAF1 61675 101 - 1
CAACAGGAGCA------GGAGCAGGAGUAGCACAUUUUGGCCAAAUCCCAGCUGCAAGUGCAGUGUAAGUGACAAUUUC------UGCUCCUGCCACUGCUCCUCUUUCGCAU
....(((((((------(..(((((((((((((....(((.......)))(((((....)))))....))).......)------)))))))))..))))))))......... ( -43.61)
>DroSim_CAF1 61843 107 - 1
CAAAAGGAGCAGGAACAGGAGCAGGAGCAGCACAUUUUGGCCAAAUCCCAGCUGCAAGUGCAGUGUAAGUGACAAUUUC------UGCUCCUGCCACUGCUCCUCUUUCGCAU
....((((((((...((((((((((((..((((....(((.......)))(((((....)))))....))).)..))))------))))))))...))))))))......... ( -46.40)
>DroEre_CAF1 61972 90 - 1
CAACAGGAGCUGGAGCUGGAGCUGGAGCUGG--GUUUUGGCCAAAUCCCAGCUGCAAGUGCAGUGUAAGUGACAAUUU--------------------GCUUUU-UUUUCCAU
.....((((..(((((((..((((.((((((--(.(((....))).))))))).).))).))))((((((....))))--------------------)).)))-..)))).. ( -29.90)
>DroYak_CAF1 63576 113 - 1
AAACAGGAGCUGAAGCAGGAGCAGGAGCAGCACAUUUUGGCCAAAUCCCAGCUGCAAGUGCAGUGUAAGUGACAAUUUCUACUGCUGCUCCUGCUGCUGCUCCUUUUUCCUAU
....(((((..(.(((((.(((((((((((((....(((..((.......(((((....))))).....)).))).......))))))))))))).))))).)...))))).. ( -49.90)
>consensus
CAACAGGAGCAG_A_C_GGAGCAGGAGCAGCACAUUUUGGCCAAAUCCCAGCUGCAAGUGCAGUGUAAGUGACAAUUUC______UGCUCCUGCCACUGCUCCUCUUUCGCAU
....(((((((......(..(((((((((........(((.......)))(((((....))))).....................)))))))))..))))))))......... (-22.46 = -24.86 +   2.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:30:08 2006