Locus 4776

Sequence ID 3R_DroMel_CAF1
Location 12,510,926 – 12,511,059
Length 133
Max. P 0.991570
window7832 window7833 window7834

overview

Window 2

Location 12,510,926 – 12,511,024
Length 98
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 83.10
Mean single sequence MFE -31.72
Consensus MFE -25.92
Energy contribution -25.68
Covariance contribution -0.24
Combinations/Pair 1.07
Mean z-score -2.65
Structure conservation index 0.82
SVM decision value 2.27
SVM RNA-class probability 0.991440
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12510926 98 - 27905053
--------------GGCCAAGUGCGUGCGGAAAUAUGAAUUUUCAUAAUUUUCGCACAGUCUGCGGUUGGCAAAAAA---AAAAAGGUCGACUUCUGGACG-----GUCAUAAAACAGCU
--------------((((......((((((((((((((....)))).)))))))))).(((((.(((((((......---......))))))).).)))))-----)))........... ( -32.80)
>DroSec_CAF1 53 95 - 1
--------------GGCCAAGUGCGUGCGGAAAUAUGAAUUUUCAUAAUUUUCGCACAGUCUGCGGUUGGCAAAA------AAAAGGUCGACUUCUGGACG-----GUCAUAAAACAGCU
--------------((((......((((((((((((((....)))).)))))))))).(((((.(((((((....------.....))))))).).)))))-----)))........... ( -33.10)
>DroSim_CAF1 122 95 - 1
--------------GGCCAAGUGCGUGCGGAAAUAUGAAUUUUCAUAAUUUUCGCACAGUCUGCGGUUGGCAAAA------AAAAGGUCGACUUCUGGACG-----GUCAUAAAACAGCU
--------------((((......((((((((((((((....)))).)))))))))).(((((.(((((((....------.....))))))).).)))))-----)))........... ( -33.10)
>DroAna_CAF1 1652 113 - 1
CUCGCC--GCCGGCGACCAAGUGCGUGCGGAAAUAUGAAUUUUCAUAAUUUUCGCACAGUUUGCGGUUGGCAAAAAAAGAAAAAAGGUCGACUUCUGAACU-----GCCAUAAAACAGCU
.(((((--...)))))......((((((((((((((((....)))).)))))))))).((((.....(((((.....((((...........))))....)-----))))..)))).)). ( -33.00)
>DroPer_CAF1 1984 109 - 1
AUUCCCAGGCCG--GCCCAAGUGCGUGCCGAAAUAUGAAUUUUCAUAAUUUUUGCACAGUUUGCGGUUUGCAAA---------AAGGUCGACUUCUGAGCGAGAGUGUCAUAAAACAGCU
.......(((.(--(((....((((.(((....(((((....)))))......(((.....)))))).))))..---------..))))(((((((.....)))).)))........))) ( -26.60)
>consensus
______________GGCCAAGUGCGUGCGGAAAUAUGAAUUUUCAUAAUUUUCGCACAGUCUGCGGUUGGCAAAA______AAAAGGUCGACUUCUGGACG_____GUCAUAAAACAGCU
......................((((((((((((((((....)))).)))))))))).(((((.(((((((...............))))))).).)))).................)). (-25.92 = -25.68 +  -0.24)

alignment

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secondary structure

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Window 3

Location 12,510,961 – 12,511,059
Length 98
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 77.47
Mean single sequence MFE -28.54
Consensus MFE -15.74
Energy contribution -15.74
Covariance contribution 0.00
Combinations/Pair 1.26
Mean z-score -1.89
Structure conservation index 0.55
SVM decision value 0.45
SVM RNA-class probability 0.740141
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12510961 98 + 27905053
---UUUUUUGCCAACCGCAGACUGUGCGAAAAUUAUGAAAAUUCAUAUUUCCGCACGCACUUGGCC--------------GGGUAAUUUUCCG-UACCU-GCUGUUAUAGAA---UGACA
---......(((((..((.....(((((.((((.((((....)))))))).)))))))..)))))(--------------(((((........-)))))-)..(((((...)---)))). ( -24.30)
>DroSec_CAF1 87 96 + 1
-----UUUUGCCAACCGCAGACUGUGCGAAAAUUAUGAAAAUUCAUAUUUCCGCACGCACUUGGCC--------------GGGAAAUUUUCCA-UACCU-GCUGUUAUAGAA---UGACA
-----(((((..(((.((((...(((((.((((.((((....)))))))).)))))..........--------------((((....)))).-...))-)).))).)))))---..... ( -22.00)
>DroSim_CAF1 156 96 + 1
-----UUUUGCCAACCGCAGACUGUGCGAAAAUUAUGAAAAUUCAUAUUUCCGCACGCACUUGGCC--------------GGGAAAUUUUCCA-UACCU-GCUGUUAUAAAA---UGACA
-----(((((..(((.((((...(((((.((((.((((....)))))))).)))))..........--------------((((....)))).-...))-)).))).)))))---..... ( -21.90)
>DroAna_CAF1 1687 116 + 1
UCUUUUUUUGCCAACCGCAAACUGUGCGAAAAUUAUGAAAAUUCAUAUUUCCGCACGCACUUGGUCGCCGGC--GGCGAGGGGGAAUUUUCCG-UACCU-GCCGUCGGAAAACUGUCGCA
......(((((.....)))))..(((((.((((.((((....)))))))).)))))((...((((..(((((--(((.(((.(((....))).-..)))-))))))))...))))..)). ( -40.70)
>DroPer_CAF1 2021 106 + 1
------UUUGCAAACCGCAAACUGUGCAAAAAUUAUGAAAAUUCAUAUUUCGGCACGCACUUGGGC--CGGCCUGGGAAUUGGAAAAUCUCCGUUACCUUGCCGCAGU---C---CGGUG
------(((((.....)))))..((((..((((.((((....))))))))..)))).((((.((((--((((..(((...((((.....))))...))).))))..))---)---))))) ( -33.80)
>consensus
_____UUUUGCCAACCGCAGACUGUGCGAAAAUUAUGAAAAUUCAUAUUUCCGCACGCACUUGGCC______________GGGAAAUUUUCCG_UACCU_GCUGUUAUAAAA___UGACA
.........(((((..((.....(((((.((((.((((....)))))))).)))))))..)))))................(((.....)))...........((((........)))). (-15.74 = -15.74 +   0.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 12,510,961 – 12,511,059
Length 98
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 77.47
Mean single sequence MFE -32.17
Consensus MFE -21.64
Energy contribution -22.44
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -2.44
Structure conservation index 0.67
SVM decision value 2.28
SVM RNA-class probability 0.991570
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12510961 98 - 27905053
UGUCA---UUCUAUAACAGC-AGGUA-CGGAAAAUUACCC--------------GGCCAAGUGCGUGCGGAAAUAUGAAUUUUCAUAAUUUUCGCACAGUCUGCGGUUGGCAAAAAA---
(((((---..(.......((-((((.-(((........))--------------))))...)))((((((((((((((....)))).)))))))))).......)..))))).....--- ( -29.70)
>DroSec_CAF1 87 96 - 1
UGUCA---UUCUAUAACAGC-AGGUA-UGGAAAAUUUCCC--------------GGCCAAGUGCGUGCGGAAAUAUGAAUUUUCAUAAUUUUCGCACAGUCUGCGGUUGGCAAAA-----
.....---(((((((.(...-.).))-)))))........--------------.(((((.(((((((((((((((((....)))).)))))))))).....))).)))))....----- ( -30.40)
>DroSim_CAF1 156 96 - 1
UGUCA---UUUUAUAACAGC-AGGUA-UGGAAAAUUUCCC--------------GGCCAAGUGCGUGCGGAAAUAUGAAUUUUCAUAAUUUUCGCACAGUCUGCGGUUGGCAAAA-----
(((((---.......((.((-((((.-.(((.....))).--------------.)))...)))((((((((((((((....)))).)))))))))).)).......)))))...----- ( -27.94)
>DroAna_CAF1 1687 116 - 1
UGCGACAGUUUUCCGACGGC-AGGUA-CGGAAAAUUCCCCCUCGCC--GCCGGCGACCAAGUGCGUGCGGAAAUAUGAAUUUUCAUAAUUUUCGCACAGUUUGCGGUUGGCAAAAAAAGA
(((.........(((.((((-(((..-.(((....))).))).)))--).)))(((((....((((((((((((((((....)))).)))))))))).))....))))))))........ ( -41.30)
>DroPer_CAF1 2021 106 - 1
CACCG---G---ACUGCGGCAAGGUAACGGAGAUUUUCCAAUUCCCAGGCCG--GCCCAAGUGCGUGCCGAAAUAUGAAUUUUCAUAAUUUUUGCACAGUUUGCGGUUUGCAAA------
...((---(---((((((((..(((...((..(((....)))..))..))).--))).......((((.(((((((((....)))).))))).)))).....))))))))....------ ( -31.50)
>consensus
UGUCA___UUCUAUAACAGC_AGGUA_CGGAAAAUUUCCC______________GGCCAAGUGCGUGCGGAAAUAUGAAUUUUCAUAAUUUUCGCACAGUCUGCGGUUGGCAAAA_____
............................((.......))................(((((.(((((((((((((((((....)))).)))))))))).....))).)))))......... (-21.64 = -22.44 +   0.80)

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 11:38:36 2006