Locus 3873

Sequence ID 2R_DroMel_CAF1
Location 12,817,667 – 12,817,764
Length 97
Max. P 0.975268
window6254 window6255

overview

Window 4

Location 12,817,667 – 12,817,764
Length 97
Sequences 5
Columns 108
Reading direction forward
Mean pairwise identity 81.63
Mean single sequence MFE -27.02
Consensus MFE -19.16
Energy contribution -19.76
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -2.16
Structure conservation index 0.71
SVM decision value 1.13
SVM RNA-class probability 0.919166
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12817667 97 + 20766785
GCAGACAACAGACAACAGACU-ACAGACAGCCAG-------ACAUUUGGCCAUAUCUCGCCUUCCUGCUCUUGACCACAAGUGCAG---CAGCUAGCCAUGGCUGUCA
.....................-...((((((((.-------......(((........)))...((((.((((....)))).))))---..........)))))))). ( -27.90)
>DroSec_CAF1 161630 91 + 1
GCAGACAGC------AAGACU-ACAGACAGCCAG-------ACAUUUGGCCAUAUCUCGCCUUCCUGCUCUUGACCACAAGUGCAG---CAGCUAGCCAAGGCUGUCA
((.....))------......-...(((((((..-------......(((........)))...((((.((((....)))).))))---...........))))))). ( -28.10)
>DroSim_CAF1 166882 98 + 1
GCAGACAGC------CAGACU-ACAGACAGCCAGACUACAGACAUUUGGCCAUAUCUCGCCUUCCUGCUCUUGACCACAAGUGCAG---CAGCUAGCCAAUGCUGUCA
...((((((------..(.((-(......((((((.........))))))........((....((((.((((....)))).))))---..))))).)...)))))). ( -26.10)
>DroEre_CAF1 164372 98 + 1
ACAGACAACAGCCAACAGACUGGCAGACUGGCAG-------ACAUUUGGCCAUAUCUCGCCUUCCUGCUCUUGACCACAAGUGCAG---CAGCUAGCCAAAGCUGUCA
...((((.(.((((......)))).(.(((((..-------......(((........)))...((((.((((....)))).))))---..))))).)...).)))). ( -30.40)
>DroYak_CAF1 169225 79 + 1
AC----------------------GGACUGCCAG-------ACAUUUGGCCAUAUCUCGCCUUCCUGCUCUUGACCACAAGUGCAGCAGCAGCUAGCCAAAGCUGUCA
..----------------------((....)).(-------(((((((((..((.((.((....((((.((((....)))).))))..)))).))))))))..)))). ( -22.60)
>consensus
GCAGACAAC______CAGACU_ACAGACAGCCAG_______ACAUUUGGCCAUAUCUCGCCUUCCUGCUCUUGACCACAAGUGCAG___CAGCUAGCCAAAGCUGUCA
.........................((((((................(((........)))...((((.((((....)))).))))...............)))))). (-19.16 = -19.76 +   0.60)

alignment

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secondary structure

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dotplot

Postscript

Window 5

Location 12,817,667 – 12,817,764
Length 97
Sequences 5
Columns 108
Reading direction reverse
Mean pairwise identity 81.63
Mean single sequence MFE -36.30
Consensus MFE -24.99
Energy contribution -25.83
Covariance contribution 0.84
Combinations/Pair 1.04
Mean z-score -2.56
Structure conservation index 0.69
SVM decision value 1.75
SVM RNA-class probability 0.975268
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12817667 97 - 20766785
UGACAGCCAUGGCUAGCUG---CUGCACUUGUGGUCAAGAGCAGGAAGGCGAGAUAUGGCCAAAUGU-------CUGGCUGUCUGU-AGUCUGUUGUCUGUUGUCUGC
.((((((.(..((..((((---((((.((((....)))).)))(((.(((.((((((......))))-------)).))).)))))-)))..))..)..))))))... ( -37.30)
>DroSec_CAF1 161630 91 - 1
UGACAGCCUUGGCUAGCUG---CUGCACUUGUGGUCAAGAGCAGGAAGGCGAGAUAUGGCCAAAUGU-------CUGGCUGUCUGU-AGUCUU------GCUGUCUGC
.((((((...(((((....---((((.((((....)))).))))((.(((.((((((......))))-------)).))).))..)-))))..------))))))... ( -37.20)
>DroSim_CAF1 166882 98 - 1
UGACAGCAUUGGCUAGCUG---CUGCACUUGUGGUCAAGAGCAGGAAGGCGAGAUAUGGCCAAAUGUCUGUAGUCUGGCUGUCUGU-AGUCUG------GCUGUCUGC
.((((((...((((((((.---((((.((((....)))).))))...))).((((..(((((.((.......)).))))))))).)-))))..------))))))... ( -37.70)
>DroEre_CAF1 164372 98 - 1
UGACAGCUUUGGCUAGCUG---CUGCACUUGUGGUCAAGAGCAGGAAGGCGAGAUAUGGCCAAAUGU-------CUGCCAGUCUGCCAGUCUGUUGGCUGUUGUCUGU
.((((((...(((((((.(---(((..((((....)))).(((((..(((.((((((......))))-------)))))..)))))))))..)))))))))))))... ( -40.60)
>DroYak_CAF1 169225 79 - 1
UGACAGCUUUGGCUAGCUGCUGCUGCACUUGUGGUCAAGAGCAGGAAGGCGAGAUAUGGCCAAAUGU-------CUGGCAGUCC----------------------GU
...(((((......)))))....(((.((((....)))).)))(((..((.((((((......))))-------)).))..)))----------------------.. ( -28.70)
>consensus
UGACAGCCUUGGCUAGCUG___CUGCACUUGUGGUCAAGAGCAGGAAGGCGAGAUAUGGCCAAAUGU_______CUGGCUGUCUGU_AGUCUG______GCUGUCUGC
.(((((((((((((((((....((((.((((....)))).))))...)))......))))))).............)))))))......................... (-24.99 = -25.83 +   0.84)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:06:08 2006