Locus 5434

Sequence ID 2L_DroMel_CAF1
Location 15,477,154 – 15,477,284
Length 130
Max. P 0.875653
window8628 window8629

overview

Window 8

Location 15,477,154 – 15,477,245
Length 91
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 74.17
Mean single sequence MFE -26.40
Consensus MFE -16.94
Energy contribution -18.22
Covariance contribution 1.28
Combinations/Pair 1.14
Mean z-score -1.51
Structure conservation index 0.64
SVM decision value 0.89
SVM RNA-class probability 0.875653
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15477154 91 + 22407834
CCCUGGCGGGUCUGAAA----------AUCUAAACGGACCCCAAAAACCAUCCCAGCAGC---------AAGCUCUAUUGUCGCAAGUCCUGCACUUGUGGCAGCUGCCU
....((((((((((...----------.......))))))).............(((((.---------...))....((((((((((.....)))))))))))))))). ( -29.80)
>DroSec_CAF1 215100 91 + 1
CCGUGGCGGGUCUGAAA----------AUCUAGACGGACCCCAAAAACCAUCCCAGCAGC---------AAGCUCUAUUGUCGCAAGUCCUGCACUUGUGGCAGCUGCCU
..((((.(((((((...----------.......)))))))......))))....(((((---------.........((((((((((.....))))))))))))))).. ( -29.80)
>DroSim_CAF1 222354 79 + 1
CCCUGGCGGGUCUGAAA----------AUCUAGACGGACCCCAAAA------------GC---------AAGCUCUAUUGUCGCAAGUCCUGCACUUGUGGCAGCUGCCU
....((((((((((...----------.......))))))).....------------..---------.((((.....(((((((((.....)))))))))))))))). ( -28.70)
>DroEre_CAF1 225828 79 + 1
CCCUGGAGGAUCUAAAA----------AUCUAGACAGACCCC------------AACAGC---------AAGCUCUAUUGUCGCAAGUCCUGCACUUGUGGCAGCUGCCU
...(((.((.((((...----------...))))....))))------------)...((---------(.(((.....(((((((((.....))))))))))))))).. ( -21.00)
>DroYak_CAF1 224256 91 + 1
CUCCGGCGGGUCUGAAA----------AUCUAGACAGAGCCCCAAAUCCAUCGGAGCAGC---------AAGCUCUUUUGUCGCAAGUCCUGCACUUGUGGCAGCUGCCU
....((((((((((...----------...)))))(((((......(((...))).....---------..))))).(((((((((((.....)))))))))))))))). ( -32.32)
>DroAna_CAF1 231144 103 + 1
-------AGAUCCAAAAAAAGACUUUGAUCCAGACAGGACCCCAAAACGAGAAAAGAAGAGGAGAAGUUGUGCUCUAUUGUCACCAGUCCUGCACUUGUGGCAGCUGCCU
-------.((((.(((.......)))))))..(.((((((......((((..........((((........)))).)))).....)))))))......(((....))). ( -16.80)
>consensus
CCCUGGCGGGUCUGAAA__________AUCUAGACAGACCCCAAAAACCAUC__AGCAGC_________AAGCUCUAUUGUCGCAAGUCCUGCACUUGUGGCAGCUGCCU
....((((((((((................)))))..........................................(((((((((((.....)))))))))))))))). (-16.94 = -18.22 +   1.28)

alignment

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secondary structure

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dotplot

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Window 9

Location 15,477,184 – 15,477,284
Length 100
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 75.02
Mean single sequence MFE -21.35
Consensus MFE -13.31
Energy contribution -13.33
Covariance contribution 0.03
Combinations/Pair 1.08
Mean z-score -1.27
Structure conservation index 0.62
SVM decision value 0.12
SVM RNA-class probability 0.592358
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15477184 100 + 22407834
CCAAAAACCAUCCCAGCAGC---------AAGCUCUAUUGUCGCAAGUCCUGCACUUGUGGCAGCUGCCUUGACUUCCAGUUCGAUUCCCCCUUGG-CUUCCCUUCUUCU
((((...........(((((---------.........((((((((((.....))))))))))))))).((((........)))).......))))-............. ( -20.90)
>DroSec_CAF1 215130 100 + 1
CCAAAAACCAUCCCAGCAGC---------AAGCUCUAUUGUCGCAAGUCCUGCACUUGUGGCAGCUGCCUUGACCUUCAGUUCGAUUCCCCCUUGG-CUUCCCUUCUUCU
((((...........(((((---------.........((((((((((.....))))))))))))))).((((.(....).)))).......))))-............. ( -21.30)
>DroSim_CAF1 222384 88 + 1
CCAAAA------------GC---------AAGCUCUAUUGUCGCAAGUCCUGCACUUGUGGCAGCUGCCUUGACUUCCAGUUCGAUCCCCCCUUGG-CUUCCCUUCUUCU
....((------------((---------(((..(..(((((((((((.....)))))))))))..).)))).))).......((..((.....))-..))......... ( -18.10)
>DroEre_CAF1 225858 76 + 1
CC------------AACAGC---------AAGCUCUAUUGUCGCAAGUCCUGCACUUGUGGCAGCUGCCUUGACUUCCAGUUCGAUUCCCC-------------UUUUCU
..------------...(((---------(((..(..(((((((((((.....)))))))))))..).)))).))................-------------...... ( -16.00)
>DroYak_CAF1 224286 99 + 1
CCCAAAUCCAUCGGAGCAGC---------AAGCUCUUUUGUCGCAAGUCCUGCACUUGUGGCAGCUGCCUUGACUUCCAGUUCGAUUCCCCC-UGG-AUUCCCUUUUCCU
....((((((..((((((((---------.........((((((((((.....))))))))))))))).((((........)))).)))...-)))-))).......... ( -26.70)
>DroAna_CAF1 231177 102 + 1
CCCAAAACGAGAAAAGAAGAGGAGAAGUUGUGCUCUAUUGUCACCAGUCCUGCACUUGUGGCAGCUGCCUUGACUCCGUCCUGGAUUCCCCCUCAGGAUU--------CU
.........((((.......((((.....((((...((((....))))...))))....(((....)))....)))).((((((........))))))))--------)) ( -25.10)
>consensus
CCAAAAACCAUC__AGCAGC_________AAGCUCUAUUGUCGCAAGUCCUGCACUUGUGGCAGCUGCCUUGACUUCCAGUUCGAUUCCCCCUUGG_CUUCCCUUCUUCU
...............................((....(((((((((((.....)))))))))))..)).......................................... (-13.31 = -13.33 +   0.03)

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 11:44:06 2006