Locus 3694

Sequence ID 3L_DroMel_CAF1
Location 10,760,692 – 10,760,838
Length 146
Max. P 0.690983
window5767 window5768 window5769

overview

Window 7

Location 10,760,692 – 10,760,804
Length 112
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 85.73
Mean single sequence MFE -38.04
Consensus MFE -26.39
Energy contribution -27.64
Covariance contribution 1.25
Combinations/Pair 1.00
Mean z-score -1.79
Structure conservation index 0.69
SVM decision value 0.15
SVM RNA-class probability 0.605567
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10760692 112 + 23771897
GGGGU-CGGCAACGCCAAAGUGUGAAGCGGUAACCGCUUUAAAGCGACUCGGGUCCACCCAAGUCGGCACCA-----CUACUCAGCUUAACCCAGCUGAACCGAGAUCGGGCCAAGAC--
..((.-((....))))...((.((((((((...))))))))..))((((.(((....))).))))(((....-----....((((((......)))))).(((....)))))).....-- ( -43.70)
>DroSec_CAF1 94420 110 + 1
AGGGU-CCGCAGCGCCAAAGUGUGAAGCGGUAACCGCUUUAAAGCGACUCGGGUCCACCCAAGACGGCUCCA-----CU---CAGCUUAACCCAGCUGAACCGAGAUCG-GCCAAGACAG
.((..-(((.(((((.......((((((((...))))))))..))).)))))..))........((((((..-----.(---(((((......))))))...))).)))-.......... ( -38.30)
>DroSim_CAF1 97249 101 + 1
AGGGU-CCGCAGCGCCAAAGUGUGAAGCGGUAACCGCUUUAAAGCGACUCAGGUCCACCCAAGUCGGCUCCA-----CU---CA----------GCUGAACCGAGAUCGGGCCAAGACUG
..(((-(((((((.....((((((((((((...)))))))).(((((((..((....))..)))).))).))-----))---..----------)))).........))))))....... ( -34.90)
>DroEre_CAF1 99157 110 + 1
CGGACCCAACAAUGCAAAAGUGUGAAGCGGUAACCGCUUUAAAGCGACUCAGGUCCACCCAAGUCGGCUCCA-----CU---CAGCUUAACCCAGCUGAACCGAGAUCGGGCCAAGAG--
.((.(((...............((((((((...))))))))...(((((..((....))..))))).(((..-----.(---(((((......))))))...)))...))))).....-- ( -36.30)
>DroYak_CAF1 110197 115 + 1
GGGGU-CCACAAUGCAAAAGUGUGAAGCGGUAACCGCUUUAAAGCGACUCAGGUCCACCCAAGUCGGCUCCACCACACU---CAGCUUAACCCAGGUGAACCGAGAUCGGGCCAAGACU-
..(((-((.....((...((((((((((((...))))))...(((((((..((....))..)))).)))....))))))---..))........((....))......)))))......- ( -37.00)
>consensus
AGGGU_CCGCAACGCCAAAGUGUGAAGCGGUAACCGCUUUAAAGCGACUCAGGUCCACCCAAGUCGGCUCCA_____CU___CAGCUUAACCCAGCUGAACCGAGAUCGGGCCAAGAC__
.((((..............((.((((((((...))))))))..))(((....))).)))).....(((..............(((((......)))))..(((....))))))....... (-26.39 = -27.64 +   1.25)

alignment

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secondary structure

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dotplot

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Window 8

Location 10,760,692 – 10,760,804
Length 112
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 85.73
Mean single sequence MFE -44.24
Consensus MFE -29.00
Energy contribution -30.16
Covariance contribution 1.16
Combinations/Pair 1.13
Mean z-score -1.80
Structure conservation index 0.66
SVM decision value -0.05
SVM RNA-class probability 0.510279
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10760692 112 - 23771897
--GUCUUGGCCCGAUCUCGGUUCAGCUGGGUUAAGCUGAGUAG-----UGGUGCCGACUUGGGUGGACCCGAGUCGCUUUAAAGCGGUUACCGCUUCACACUUUGGCGUUGCCG-ACCCC
--((((((..(((....)))..)))...(((...((..(((((-----(((((((((((((((....))))))))(((....))))).)))))))....)).)..))...))))-))... ( -46.60)
>DroSec_CAF1 94420 110 - 1
CUGUCUUGGC-CGAUCUCGGUUCAGCUGGGUUAAGCUG---AG-----UGGAGCCGUCUUGGGUGGACCCGAGUCGCUUUAAAGCGGUUACCGCUUCACACUUUGGCGCUGCGG-ACCCU
..(.((..((-((....))))..))).(((((.(((.(---((-----((((((.(.((((((....)))))).)))))..((((((...))))))..)))))....)))...)-)))). ( -43.20)
>DroSim_CAF1 97249 101 - 1
CAGUCUUGGCCCGAUCUCGGUUCAGC----------UG---AG-----UGGAGCCGACUUGGGUGGACCUGAGUCGCUUUAAAGCGGUUACCGCUUCACACUUUGGCGCUGCGG-ACCCU
..((((((..(((....)))..))((----------..---((-----((((((.((((..((....))..))))))))..((((((...))))))..))).)..)).....))-))... ( -39.40)
>DroEre_CAF1 99157 110 - 1
--CUCUUGGCCCGAUCUCGGUUCAGCUGGGUUAAGCUG---AG-----UGGAGCCGACUUGGGUGGACCUGAGUCGCUUUAAAGCGGUUACCGCUUCACACUUUUGCAUUGUUGGGUCCG
--.....(((((((((((((.....)))))....((.(---((-----((((((.((((..((....))..))))))))..((((((...))))))..)))))..))...)))))))).. ( -44.80)
>DroYak_CAF1 110197 115 - 1
-AGUCUUGGCCCGAUCUCGGUUCACCUGGGUUAAGCUG---AGUGUGGUGGAGCCGACUUGGGUGGACCUGAGUCGCUUUAAAGCGGUUACCGCUUCACACUUUUGCAUUGUGG-ACCCC
-.....((..(((....)))..))...(((((..((.(---((((((((((((((((((..((....))..))))(((....))))))).))))..)))))))..))......)-)))). ( -47.20)
>consensus
__GUCUUGGCCCGAUCUCGGUUCAGCUGGGUUAAGCUG___AG_____UGGAGCCGACUUGGGUGGACCUGAGUCGCUUUAAAGCGGUUACCGCUUCACACUUUGGCGUUGCGG_ACCCC
......((..(((....)))..))...((((...((............((((((.((((((((....))))))))))))))((((((...))))))..............))...)))). (-29.00 = -30.16 +   1.16)

alignment

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secondary structure

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dotplot

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Window 9

Location 10,760,731 – 10,760,838
Length 107
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 83.75
Mean single sequence MFE -35.56
Consensus MFE -23.30
Energy contribution -24.11
Covariance contribution 0.81
Combinations/Pair 1.05
Mean z-score -1.96
Structure conservation index 0.66
SVM decision value 0.33
SVM RNA-class probability 0.690983
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10760731 107 - 23771897
GCAAAUAAUC------AUAAUUAUAUGACAGACAGACAAA--GUCUUGGCCCGAUCUCGGUUCAGCUGGGUUAAGCUGAGUAG-----UGGUGCCGACUUGGGUGGACCCGAGUCGCUUU
((......((------(((....))))).((((.......--)))).((((((..(((((((.(((...))).)))))))...-----))).)))((((((((....))))))))))... ( -37.80)
>DroSec_CAF1 94459 105 - 1
GCAAAUAAUC------AUAAUUAUAUGACAGACAGACAGACUGUCUUGGC-CGAUCUCGGUUCAGCUGGGUUAAGCUG---AG-----UGGAGCCGUCUUGGGUGGACCCGAGUCGCUUU
........((------(((....)))))(((((((.....))))).))((-((....))))((((((......)))))---).-----.(((((.(.((((((....)))))).)))))) ( -35.70)
>DroSim_CAF1 97288 96 - 1
GCAAAUAAUC------AUAAUUAUAUGACAGACAGACAGACAGUCUUGGCCCGAUCUCGGUUCAGC----------UG---AG-----UGGAGCCGACUUGGGUGGACCUGAGUCGCUUU
((......((------(((....))))).....((((.....)))).((((((..(((((.....)----------))---))-----))).)))((((..((....))..))))))... ( -31.30)
>DroEre_CAF1 99197 100 - 1
GCAAAUAAUC------AUAAUUAUAUGACAGCCAGU------CUCUUGGCCCGAUCUCGGUUCAGCUGGGUUAAGCUG---AG-----UGGAGCCGACUUGGGUGGACCUGAGUCGCUUU
........((------(((....)))))..(((((.------...)))))(((....)))(((((((......)))))---))-----.(((((.((((..((....))..))))))))) ( -34.50)
>DroYak_CAF1 110236 112 - 1
GCAAAUAAUCAUAAUCAUAAUUAUAUGACAGGCGGC-----AGUCUUGGCCCGAUCUCGGUUCACCUGGGUUAAGCUG---AGUGUGGUGGAGCCGACUUGGGUGGACCUGAGUCGCUUU
.........(((..(((((....)))))((.((..(-----((.(((((((((....)((....)).)))))))))))---.)).)))))((((.((((..((....))..)))))))). ( -38.50)
>consensus
GCAAAUAAUC______AUAAUUAUAUGACAGACAGACA_A__GUCUUGGCCCGAUCUCGGUUCAGCUGGGUUAAGCUG___AG_____UGGAGCCGACUUGGGUGGACCUGAGUCGCUUU
((.............................................((((((.........(((((......)))))..........))).)))((((((((....))))))))))... (-23.30 = -24.11 +   0.81)

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 11:04:28 2006