Locus 2452

Sequence ID 3R_DroMel_CAF1
Location 6,780,357 – 6,780,494
Length 137
Max. P 0.969023
window4015 window4016

overview

Window 5

Location 6,780,357 – 6,780,461
Length 104
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 91.59
Mean single sequence MFE -32.75
Consensus MFE -28.04
Energy contribution -28.10
Covariance contribution 0.06
Combinations/Pair 1.08
Mean z-score -2.50
Structure conservation index 0.86
SVM decision value 1.64
SVM RNA-class probability 0.969023
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6780357 104 - 27905053
CUUGCAACACAGCGGGAAAUUGCACAAAAAUGAAUUGUGUUGUGGAGCAUUUAGUGCUGAAAUAUAAGUGACCUGCUGGGCGGGACAACUGAA------AAGGAGGGUCA----------
.((((....(((((((..((.((((((.......)))))).))..(((((...))))).............))))))).))))(((..((...------.))....))).---------- ( -28.70)
>DroSec_CAF1 44521 104 - 1
CUUGCAACACAGCGGGAAAUUGCACAAAAAUGAAUUGUGUUGUGCAGCAUUUAGUGCUGAAAUAUAAGUGACCUGCUGGGCGGGACAACUGAA------AAGGAGGGUCG----------
.((((....(((((((..((.((((((.......)))))).)).((((((...))))))............))))))).))))(((..((...------.))....))).---------- ( -31.50)
>DroSim_CAF1 48532 104 - 1
CUUGCAACACAGCGGGAAAUUGCACAAAAAUGAAUUGUGUUGUGCAGCAUUUAGUGCUGAAAUAUAAGUGACCUGCUGGGCGGGACAACUGAA------AAGGAGGGUCG----------
.((((....(((((((..((.((((((.......)))))).)).((((((...))))))............))))))).))))(((..((...------.))....))).---------- ( -31.50)
>DroEre_CAF1 29701 104 - 1
CUUGCAACACAGCGGGAAAUUGCACAAAAAUGAAUUGUGUUGUGCAGCAUUUAGUGCUGAAAUAUAAGUGACCCGCUGGGCGGGACAACUGAA------AAGGAGGGUCG----------
.((((....(((((((..((.((((((.......)))))).)).((((((...))))))............))))))).))))(((..((...------.))....))).---------- ( -33.70)
>DroYak_CAF1 42083 104 - 1
CUUGCAACACAGCGGGAAAUUGCACAAAAAUGAAUUGUGUUGUGCAGCAUUUAGUGCUGAAAUAUAAGUGACCUGCUGGGCGGGACAACUGAA------AAGGAGGGUCA----------
.((((....(((((((..((.((((((.......)))))).)).((((((...))))))............))))))).))))(((..((...------.))....))).---------- ( -31.50)
>DroAna_CAF1 1663 120 - 1
CUUGGCACACAGCGGGAAAUUGCACAAAAAUGAAUUGUGUUGUGCAGCAUUUAAUGCUGAAAUAUAAGUGUCCUGCUGGGCGGGACAGCUGACCAGUGCAAGGAUGCUCGAACUGGGUUA
.(..((...(((((..(((((((((((..(.....)...)))))))..))))..))))).........((((((((...))))))))))..)((((((((....)))....))))).... ( -39.60)
>consensus
CUUGCAACACAGCGGGAAAUUGCACAAAAAUGAAUUGUGUUGUGCAGCAUUUAGUGCUGAAAUAUAAGUGACCUGCUGGGCGGGACAACUGAA______AAGGAGGGUCG__________
(((((....(((((((..((.((((((.......)))))).)).((((((...))))))............))))))).))))).................................... (-28.04 = -28.10 +   0.06)

alignment

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secondary structure

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dotplot

Postscript

Window 6

Location 6,780,381 – 6,780,494
Length 113
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 93.72
Mean single sequence MFE -35.03
Consensus MFE -28.80
Energy contribution -29.08
Covariance contribution 0.28
Combinations/Pair 1.14
Mean z-score -1.83
Structure conservation index 0.82
SVM decision value -0.06
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6780381 113 - 27905053
UUGCACGUAUGCGGUGGUGUGGGUGA--GUGUCAGCUUGCAACACAGCGGGAAAUUGCACAAAAAUGAAUUGUGUUGUGGAGCAUUUAGUGCUGAAAUAUAAGUGACCUGCUGGG
(..(.((....)))..)(((..(..(--((....)))..).)))(((((((..((.((((((.......)))))).))..(((((...))))).............))))))).. ( -30.50)
>DroSec_CAF1 44545 113 - 1
UUGCACGUAUGCGCUGGUGUGGCUGA--GUGUCAGCUUGCAACACAGCGGGAAAUUGCACAAAAAUGAAUUGUGUUGUGCAGCAUUUAGUGCUGAAAUAUAAGUGACCUGCUGGG
..((((..((((((((.((((((((.--....)))).))))...)))).......(((((((..(.....)...)))))))))))...))))..............((....)). ( -35.50)
>DroSim_CAF1 48556 113 - 1
UUGCACGUAUGCGCUGGUGUGGGUGA--GUGUCAGCUUGCAACACAGCGGGAAAUUGCACAAAAAUGAAUUGUGUUGUGCAGCAUUUAGUGCUGAAAUAUAAGUGACCUGCUGGG
..((((..((((((((.(((..(..(--((....)))..).))))))).......(((((((..(.....)...)))))))))))...))))..............((....)). ( -35.20)
>DroEre_CAF1 29725 113 - 1
UUGCACGUAUGUGCUGGUGUGGGUGA--GUGUCAGCUUGCAACACAGCGGGAAAUUGCACAAAAAUGAAUUGUGUUGUGCAGCAUUUAGUGCUGAAAUAUAAGUGACCCGCUGGG
..((((....))))..((((..(..(--((....)))..).))))((((((..((.((((((.......)))))).)).((((((...))))))............))))))... ( -37.70)
>DroYak_CAF1 42107 115 - 1
UUGCACGUACGCGCUGGUGUGGGUGAGAGUGUCAGCUUGCAACACAGCGGGAAAUUGCACAAAAAUGAAUUGUGUUGUGCAGCAUUUAGUGCUGAAAUAUAAGUGACCUGCUGGG
((((((.(((((....))))).))..((((....))))))))..(((((((..((.((((((.......)))))).)).((((((...))))))............))))))).. ( -35.70)
>DroAna_CAF1 1703 109 - 1
UUGCGG----GCGGGUAUGUGGGUGA--GUGUCAGCUUGGCACACAGCGGGAAAUUGCACAAAAAUGAAUUGUGUUGUGCAGCAUUUAAUGCUGAAAUAUAAGUGUCCUGCUGGG
...(.(----(((((.(..(..(((.--(((((.....))))).(((((..(((((((((((..(.....)...)))))))..))))..)))))...)))..)..))))))).). ( -35.60)
>consensus
UUGCACGUAUGCGCUGGUGUGGGUGA__GUGUCAGCUUGCAACACAGCGGGAAAUUGCACAAAAAUGAAUUGUGUUGUGCAGCAUUUAGUGCUGAAAUAUAAGUGACCUGCUGGG
..((......))(((((..(........)..)))))........(((((((..((.((((((.......)))))).)).((((((...))))))............))))))).. (-28.80 = -29.08 +   0.28)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:36:40 2006