Locus 780

Sequence ID 3R_DroMel_CAF1
Location 2,689,283 – 2,689,469
Length 186
Max. P 0.874734
window1243 window1244 window1245

overview

Window 3

Location 2,689,283 – 2,689,394
Length 111
Sequences 5
Columns 111
Reading direction forward
Mean pairwise identity 86.76
Mean single sequence MFE -33.28
Consensus MFE -27.30
Energy contribution -27.72
Covariance contribution 0.42
Combinations/Pair 1.15
Mean z-score -1.45
Structure conservation index 0.82
SVM decision value 0.01
SVM RNA-class probability 0.540746
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2689283 111 + 27905053
UACUAGUCAUUUUGGAAGUGCGUUUGUUGGUUUUUAGGCAAAUACCGGGCACAGGAGUGAGUUUGGGAAUCGGGAGUUGCGCACUUGCUUGGCCACGAGGGCAAACAAAAA
.........(((((.((((((((((.(((((((((((((..((.((.......)).))..))))))))))))).))..))))))))..(((.((....)).))).))))). ( -32.20)
>DroSec_CAF1 48543 111 + 1
AACUAGUCAGUUUGGAAGUGCGUUUGUUGGUUUUUAGGCAAAUAACGGGCACAGGAGUGAGUUUGGGAAUCGGGAGUUGCGCACUUGCUUGCCCACGAGGGCAAACAAAAA
.........(((((.((((((((((.(((((((((((((..((..(.......)..))..))))))))))))).))..)))))))).)..((((....))))))))..... ( -33.60)
>DroSim_CAF1 41755 111 + 1
AACUAGUCAGUUUGGAAGUGCGUUUGUUGGUUUUUAGGCAAAUAACGGGCACAGGAGUGAGUUUGGGAAUCGGGAGUUGCGCACUUGCUUGGCCACGAGGGCAAACAAAAA
.........(((((.((((((((((.(((((((((((((..((..(.......)..))..))))))))))))).))..)))))))).((((....))))..)))))..... ( -30.60)
>DroEre_CAF1 42843 91 + 1
UACUAGUCAUGUUGGAAGUGCGCCUCCUGGUUUUUAGGCAAAUACCAGGCACGGGAGUGAGUUUGGGACUCGGGAGUUGCGCACUUGCUUG--------------------
.............(.((((((((((((((..((((((((..((.((.......)).))..))))))))..))))))..)))))))).)...-------------------- ( -32.10)
>DroYak_CAF1 49511 111 + 1
UACUAGUCAUUUGGGAAGUGCGUCUGUUGGUUUUUAGGCAAAUACCGGGCACAGGAGUGAGUUUGGAAACCGGGAGUUGCGCACUUGCUUGGCCACGAGGGCAAACAAAAA
.........(((((.((((((((((.(((((((((((((..((.((.......)).))..))))))))))))).))..)))))))).)(((.((....)).))).)))).. ( -37.90)
>consensus
UACUAGUCAUUUUGGAAGUGCGUUUGUUGGUUUUUAGGCAAAUACCGGGCACAGGAGUGAGUUUGGGAAUCGGGAGUUGCGCACUUGCUUGGCCACGAGGGCAAACAAAAA
.............(.((((((((((.(((((((((((((..((.((.......)).))..))))))))))))).))..)))))))).)(((.((....)).)))....... (-27.30 = -27.72 +   0.42) 

alignment

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secondary structure

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Window 4

Location 2,689,323 – 2,689,434
Length 111
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 87.61
Mean single sequence MFE -43.54
Consensus MFE -37.56
Energy contribution -38.28
Covariance contribution 0.72
Combinations/Pair 1.06
Mean z-score -1.70
Structure conservation index 0.86
SVM decision value 0.89
SVM RNA-class probability 0.874734
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2689323 111 - 27905053
GGAUCAGGAAUACGCGUGGCCGAGGGUCGCGUGUUUGCGCUUUUUGUUUGCCCUCGUGGCCAAGCAAGUGCGCAACUCCCGAUUCC-----CAA----ACUCACUCCUGUGCCCGGUAUU
(((((.(((..((((((((((...))))))))))((((((..((((((((.((....)).)))))))).)))))).))).))))).-----...----((((((....)))...)))... ( -43.20)
>DroSec_CAF1 48583 111 - 1
GGACCAGGACUACGCGUGGCCGAGGGUCGCGUGUUUGCGCUUUUUGUUUGCCCUCGUGGGCAAGCAAGUGCGCAACUCCCGAUUCC-----CAA----ACUCACUCCUGUGCCCGUUAUU
((..(((((..((((((((((...))))))))))((((((..(((((((((((....))))))))))).))))))...........-----...----......)))))..))....... ( -49.90)
>DroSim_CAF1 41795 111 - 1
GGACCAGGACUACGCGUGGCCGAGGGUCGCGUGUUUGCGCUUUUUGUUUGCCCUCGUGGCCAAGCAAGUGCGCAACUCCCGAUUCC-----CAA----ACUCACUCCUGUGCCCGUUAUU
((..(((((..((((((((((...))))))))))((((((..((((((((.((....)).)))))))).))))))...........-----...----......)))))..))....... ( -42.80)
>DroYak_CAF1 49551 111 - 1
GGACCAGGACUACGCGUGGCCGAGGGUCGCGUGUUUGCGCUUUUUGUUUGCCCUCGUGGCCAAGCAAGUGCGCAACUCCCGGUUUC-----CAA----ACUCACUCCUGUGCCCGGUAUU
(((((.(((..((((((((((...))))))))))((((((..((((((((.((....)).)))))))).)))))).))).))..))-----)..----((((((....)))...)))... ( -43.20)
>DroAna_CAF1 35062 114 - 1
GGAUGGCGAUUGCGCGUG--CGAGGGUCGCGUGUUUGCGCUUUUUGUUUGCCCUCGUGGCC-AGCAAGUGCGCAACUCCCGCUCCCGCUCCUCAGCUCACUCACU---CCUCCCGGCAUG
(((.((.((.((.((..(--.(((((..(((.(.((((((..((((((.(((.....))).-)))))).))))))..).)))..)).))))...)).)).))...---)))))....... ( -38.60)
>consensus
GGACCAGGACUACGCGUGGCCGAGGGUCGCGUGUUUGCGCUUUUUGUUUGCCCUCGUGGCCAAGCAAGUGCGCAACUCCCGAUUCC_____CAA____ACUCACUCCUGUGCCCGGUAUU
((..(((((..((((((((((...))))))))))((((((..((((((((.((....)).)))))))).)))))).............................)))))..))....... (-37.56 = -38.28 +   0.72) 

alignment

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secondary structure

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dotplot

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Window 5

Location 2,689,354 – 2,689,469
Length 115
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.05
Mean single sequence MFE -46.87
Consensus MFE -38.50
Energy contribution -38.58
Covariance contribution 0.08
Combinations/Pair 1.08
Mean z-score -1.28
Structure conservation index 0.82
SVM decision value -0.08
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2689354 115 - 27905053
G--GGCGGCC---AAAGGAUAACAUUACGUCCGAUCCCUGGGAUCAGGAAUACGCGUGGCCGAGGGUCGCGUGUUUGCGCUUUUUGUUUGCCCUCGUGGCCAAGCAAGUGCGCAACUCCC
(--((((...---..............)))))(((((...))))).(((..((((((((((...))))))))))((((((..((((((((.((....)).)))))))).)))))).))). ( -47.93)
>DroSec_CAF1 48614 115 - 1
G--GGCGGCC---AAAGGAUAACAUUACGUCCGAUCCCUGGGACCAGGACUACGCGUGGCCGAGGGUCGCGUGUUUGCGCUUUUUGUUUGCCCUCGUGGGCAAGCAAGUGCGCAACUCCC
(--((.(((.---...((((........))))((.((((.((.(((.(......).))))).))))))))....((((((..(((((((((((....))))))))))).))))))).))) ( -53.30)
>DroSim_CAF1 41826 115 - 1
G--GGCGGCC---AAAGGAUAACAUUACGUCCGAUCCCUGGGACCAGGACUACGCGUGGCCGAGGGUCGCGUGUUUGCGCUUUUUGUUUGCCCUCGUGGCCAAGCAAGUGCGCAACUCCC
(--((.(((.---...((((........))))((.((((.((.(((.(......).))))).))))))))....((((((..((((((((.((....)).)))))))).))))))).))) ( -46.20)
>DroYak_CAF1 49582 113 - 1
G---GCGGCC---AAAGGAUAACAUUACGUCCGAUC-CUGGGACCAGGACUACGCGUGGCCGAGGGUCGCGUGUUUGCGCUUUUUGUUUGCCCUCGUGGCCAAGCAAGUGCGCAACUCCC
.---..((((---..(((((.((.....))...)))-)).)).)).(((..((((((((((...))))))))))((((((..((((((((.((....)).)))))))).)))))).))). ( -45.10)
>DroAna_CAF1 35099 117 - 1
GUCGUCCGCCCAAAAAGGAUAACAUUGCGUCCGAUCCCGAGGAUGGCGAUUGCGCGUG--CGAGGGUCGCGUGUUUGCGCUUUUUGUUUGCCCUCGUGGCC-AGCAAGUGCGCAACUCCC
(((((((.........((((........))))........)))))))((((((((.((--(...(((((((.((..(((.....)))..))...)))))))-.)))...)))))).)).. ( -41.83)
>consensus
G__GGCGGCC___AAAGGAUAACAUUACGUCCGAUCCCUGGGACCAGGACUACGCGUGGCCGAGGGUCGCGUGUUUGCGCUUUUUGUUUGCCCUCGUGGCCAAGCAAGUGCGCAACUCCC
......((((......((((........))))........)).)).(((..((((((((((...))))))))))((((((..((((((((.((....)).)))))))).)))))).))). (-38.50 = -38.58 +   0.08) 

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:51:58 2006