Locus 9452

Sequence ID 3R_DroMel_CAF1
Location 25,033,464 – 25,033,555
Length 91
Max. P 0.996296
window15134 window15135

overview

Window 4

Location 25,033,464 – 25,033,555
Length 91
Sequences 5
Columns 108
Reading direction forward
Mean pairwise identity 83.69
Mean single sequence MFE -23.20
Consensus MFE -19.04
Energy contribution -19.84
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -2.90
Structure conservation index 0.82
SVM decision value 2.68
SVM RNA-class probability 0.996296
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25033464 91 + 27905053
UCUCAAUGCGCUGCUCUGCUUAAAUCAUCAUCGUGGCCAAGACGCAGCCGAUCUUGGCCAUCCCACUGAUCGCACCAAUCCCAAUCUC----CC-------------A
......(((((......))....((((.....((((((((((((....)).)))))))))).....)))).)))..............----..-------------. ( -23.20)
>DroSec_CAF1 54384 91 + 1
UCUCAGUGCUCUGCUCCGCUUUAAUCAUCGUCGUGGCCAAGACGCAGCCGAUCUUGGCCAUCCCACUGAUCGCACCAAUCGCAAUCUC----CC-------------A
..(((((((........))..........(..((((((((((((....)).))))))))))..))))))..((.......))......----..-------------. ( -24.30)
>DroSim_CAF1 48743 91 + 1
UCUCAGUGCUCUGCUCCGCUUAAAUCAUCGUCGUGGCCAAGACGCAGCCGAUCUUGGCCAUCCCACUGAUCGCACCAAUCCCAAUCUC----CC-------------A
.....((((...((...))....((((..(..((((((((((((....)).))))))))))..)..)))).)))).............----..-------------. ( -23.90)
>DroEre_CAF1 56600 82 + 1
UCUCAGUGCGCUGCUCUGCUUAAAUCAU---CGCGGCCAAGACACAGCCGAUCUUGGCCAUCCCACCGAUCGCACCAAUCCCAAU-----------------------
.....((((((......)).........---...(((((((((......).))))))))............))))..........----------------------- ( -21.60)
>DroYak_CAF1 49705 105 + 1
UCUCAGUGCGCUGCUCUGCUUAAAUCAU---CGUGGCCAAGACACAACCGAUCUUGGCCAUCCCACCGAUCGCACCAAUCUCAAUCUCAAUACCAAUACCAAUAGCAA
.....((((((......)).........---.(((((((((((......).))))))))))..........))))................................. ( -23.00)
>consensus
UCUCAGUGCGCUGCUCUGCUUAAAUCAUC_UCGUGGCCAAGACGCAGCCGAUCUUGGCCAUCCCACUGAUCGCACCAAUCCCAAUCUC____CC_____________A
.....((((...((...))....((((.....(((((((((((......).)))))))))).....)))).))))................................. (-19.04 = -19.84 +   0.80)

alignment

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secondary structure

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dotplot

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Window 5

Location 25,033,464 – 25,033,555
Length 91
Sequences 5
Columns 108
Reading direction reverse
Mean pairwise identity 83.69
Mean single sequence MFE -30.12
Consensus MFE -28.14
Energy contribution -27.34
Covariance contribution -0.80
Combinations/Pair 1.17
Mean z-score -1.58
Structure conservation index 0.93
SVM decision value 0.51
SVM RNA-class probability 0.765512
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25033464 91 - 27905053
U-------------GG----GAGAUUGGGAUUGGUGCGAUCAGUGGGAUGGCCAAGAUCGGCUGCGUCUUGGCCACGAUGAUGAUUUAAGCAGAGCAGCGCAUUGAGA
.-------------..----..........(..(((((((((......(((((((((.((....)))))))))))......)))))...((......))))))..).. ( -29.20)
>DroSec_CAF1 54384 91 - 1
U-------------GG----GAGAUUGCGAUUGGUGCGAUCAGUGGGAUGGCCAAGAUCGGCUGCGUCUUGGCCACGACGAUGAUUAAAGCGGAGCAGAGCACUGAGA
.-------------..----..........(..(((((((((.((...(((((((((.((....)))))))))))...)).)))))...((...))...))))..).. ( -30.40)
>DroSim_CAF1 48743 91 - 1
U-------------GG----GAGAUUGGGAUUGGUGCGAUCAGUGGGAUGGCCAAGAUCGGCUGCGUCUUGGCCACGACGAUGAUUUAAGCGGAGCAGAGCACUGAGA
.-------------..----..........(..(((((((((.((...(((((((((.((....)))))))))))...)).)))))...((...))...))))..).. ( -29.80)
>DroEre_CAF1 56600 82 - 1
-----------------------AUUGGGAUUGGUGCGAUCGGUGGGAUGGCCAAGAUCGGCUGUGUCUUGGCCGCG---AUGAUUUAAGCAGAGCAGCGCACUGAGA
-----------------------.......(..(((((...........(((((((((.......)))))))))((.---.((.......))..))..)))))..).. ( -28.70)
>DroYak_CAF1 49705 105 - 1
UUGCUAUUGGUAUUGGUAUUGAGAUUGAGAUUGGUGCGAUCGGUGGGAUGGCCAAGAUCGGUUGUGUCUUGGCCACG---AUGAUUUAAGCAGAGCAGCGCACUGAGA
((((.((..((.(..((......))..).))..))))))((((((...((((((((((.......))))))))))..---.........((......)).)))))).. ( -32.50)
>consensus
U_____________GG____GAGAUUGGGAUUGGUGCGAUCAGUGGGAUGGCCAAGAUCGGCUGCGUCUUGGCCACGA_GAUGAUUUAAGCAGAGCAGCGCACUGAGA
..............................(..(((((((((......(((((((((.((....)))))))))))......)))))...((...))...))))..).. (-28.14 = -27.34 +  -0.80)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:34:56 2006