Locus 3628

Sequence ID 2L_DroMel_CAF1
Location 10,581,509 – 10,581,663
Length 154
Max. P 0.882524
window5723 window5724

overview

Window 3

Location 10,581,509 – 10,581,629
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 78.76
Mean single sequence MFE -27.43
Consensus MFE -15.73
Energy contribution -16.48
Covariance contribution 0.75
Combinations/Pair 1.19
Mean z-score -2.17
Structure conservation index 0.57
SVM decision value 0.92
SVM RNA-class probability 0.882524
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10581509 120 - 22407834
UCAAAUUAAAAAGUCCAAAACGACCACCAAGAAAUUGGUGAAAUCAUCUCCGAAAGCUCAACUUCCAAAAGCUGCGGCACAGAAUCAAAUUUUUAGUUGCCAAUUCGAGGUGUUUGGUCA
............(.(((((.....((((((....))))))....((((((.(((((((...........))))..(((((((((......)))).).))))..)))))))))))))).). ( -31.00)
>DroSec_CAF1 69021 117 - 1
UCAAAUUAAAAAGUCCAAAACGACCACCAAGAAAUUGGUGAAAUCAGCUCCGAAAAGU---GUUCCAAAUGCUGCGGCAGAUAAUCAAAUUUUUUGUUGCCAAUUUGAAGUGUUUGGUCA
............(.(((((((...((((((....))))))((((..((..((((((((---........(((....))).........))))))))..))..))))...)).))))).). ( -27.53)
>DroSim_CAF1 69001 117 - 1
UCAAAUUAAAAAGUCCAAAACGACCACCAAGAAAUUGGUGAAAUCAGCUCCGAAAAGU---GUUCCAAAUGCUGCGGCAGAUGAUCAAAUUUUUUGUUGCCAAUUUGAAGUUUUUGGUCA
............(.(((((((...((((((....))))))((((..((..((((((((---....((..(((....)))..)).....))))))))..))..))))...).)))))).). ( -28.40)
>DroEre_CAF1 69989 117 - 1
UCAAAUUAAAAAGUCAAAGACGACCACCAAGAAAUUGGUGAAAUCACCUCCAAAAAGU---GCACCAAAAUCCGCGGCAGAGAAUCAAAUUUUUAGCUGCCAAUUCGAAGUGUUCGGUCA
............(((...)))(((((((((....)))))(((..(((.((........---((..........))(((((..((........))..))))).....)).)))))))))). ( -28.10)
>DroYak_CAF1 71808 117 - 1
UCAAAUUAAAAAGUCAAAAACGACCACCAAGAAAUUGGUGAAGUCAUCUCCAAAAAGU---CCACCAAAAGCUGCGGCAGAGAAUCAAAUUUUUAGUUGCCAAUUCGAAGUGUUUGGUCA
.....................(((((((((....))))))..))).............---..((((((.(((..(((((..((........))..))))).......))).)))))).. ( -24.90)
>DroAna_CAF1 73079 102 - 1
CCAAAUUGAUAAGUCGAAGGUGACAGCCCCGCGUCUGGUCAAAUCGGUU--AAUAAGC-------------CCAAGGCAG---AUCAAAUAUUCACCUGCCAGUUUGAGAUUUUUGGCAA
((((((((((.((.((..(((....)))...)).)).)))))(((((((--....)))-------------)...(((((---.............))))).......))).)))))... ( -24.62)
>consensus
UCAAAUUAAAAAGUCCAAAACGACCACCAAGAAAUUGGUGAAAUCAGCUCCAAAAAGU___GUUCCAAAAGCUGCGGCAGAGAAUCAAAUUUUUAGUUGCCAAUUCGAAGUGUUUGGUCA
.....................(((((((((....)))))....................................(((((..((........))..)))))..............)))). (-15.73 = -16.48 +   0.75)

alignment

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secondary structure

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dotplot

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Window 4

Location 10,581,549 – 10,581,663
Length 114
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 78.29
Mean single sequence MFE -21.42
Consensus MFE -12.98
Energy contribution -13.90
Covariance contribution 0.92
Combinations/Pair 1.12
Mean z-score -1.73
Structure conservation index 0.61
SVM decision value 0.54
SVM RNA-class probability 0.773700
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10581549 114 - 22407834
GGAAAGUAUAAG---AAAUUUCUUUAAAAAUGAGCAGUCAAAUUAAAAAGUCCAAAACGACCACCAAGAAAUUGGUGAAAUCAUCUCCGAAAGCUCAACUUCCAAAAGCUGCGGCAC
((((.((..(((---(....))))......(((((..((..........(((......)))((((((....))))))...........))..)))))))))))....((....)).. ( -26.30)
>DroSec_CAF1 69061 111 - 1
GGAAAGUAUAAC---AAAUUUCUUUAAAAAUGAGCAGUCAAAUUAAAAAGUCCAAAACGACCACCAAGAAAUUGGUGAAAUCAGCUCCGAAAAGU---GUUCCAAAUGCUGCGGCAG
(((.......((---(..((((.........((((..............(((......)))((((((....))))))......)))).))))..)---)))))...(((....))). ( -21.41)
>DroSim_CAF1 69041 111 - 1
GGAAAGUAUAAC---AAAUUUGUUUAAAAAUGAGCAGUCAAAUUAAAAAGUCCAAAACGACCACCAAGAAAUUGGUGAAAUCAGCUCCGAAAAGU---GUUCCAAAUGCUGCGGCAG
((((.....(((---(....)))).......((((..............(((......)))((((((....))))))......))))........---.))))...(((....))). ( -22.80)
>DroEre_CAF1 70029 111 - 1
AGAAAGUAUAGC---AAAUUUGUUUGAAAAUGAGCAGUCAAAUUAAAAAGUCAAAGACGACCACCAAGAAAUUGGUGAAAUCACCUCCAAAAAGU---GCACCAAAAUCCGCGGCAG
.....((...((---.((((((.(((........))).)))))).....(((......)))((((((....))))))..................---............)).)).. ( -18.50)
>DroYak_CAF1 71848 111 - 1
GGAAAUUAUAAC---AAAUUUGUUUAAAAAUGAGCAGUCAAAUUAAAAAGUCAAAAACGACCACCAAGAAAUUGGUGAAGUCAUCUCCAAAAAGU---CCACCAAAAGCUGCGGCAG
(((.........---....(((((((....))))))).....................(((((((((....))))))..)))...))).....((---(((.(....).)).))).. ( -20.50)
>DroAna_CAF1 73116 102 - 1
ACACAGCAUAACUUUUAAUAAUUUUCAAAAUGAUGAGCCAAAUUGAUAAGUCGAAGGUGACAGCCCCGCGUCUGGUCAAAUCGGUU--AAUAAGC-------------CCAAGGCAG
....................................(((...(((((.((.((..(((....)))...)).)).)))))...((((--....)))-------------)...))).. ( -19.00)
>consensus
GGAAAGUAUAAC___AAAUUUGUUUAAAAAUGAGCAGUCAAAUUAAAAAGUCCAAAACGACCACCAAGAAAUUGGUGAAAUCAGCUCCAAAAAGU___GUUCCAAAAGCUGCGGCAG
..............................((.(((((...........(((......)))((((((....))))))..............................)))))..)). (-12.98 = -13.90 +   0.92)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:57:12 2006