Locus 4461

Sequence ID 2L_DroMel_CAF1
Location 12,805,072 – 12,805,262
Length 190
Max. P 0.999455
window7013 window7014 window7015 window7016 window7017

overview

Window 3

Location 12,805,072 – 12,805,192
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 95.83
Mean single sequence MFE -41.88
Consensus MFE -38.50
Energy contribution -38.50
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.85
Structure conservation index 0.92
SVM decision value 0.73
SVM RNA-class probability 0.834344
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12805072 120 + 22407834
GGAUGCGGAUGAUCGGAAGGGGGAUCGGGCUAAGGACGAUGGAGGAGCAGGUGGUCGAGCCAGUGGAACCUGGCAAUGGAAACUGGCAGCUGCUGGCAGCAGUUGGCAGUUGGCAGCUUG
....((...(((((........))))).)).................(((((.(((..(((((......)))))......(((((.(((((((.....))))))).)))))))).))))) ( -40.30)
>DroSec_CAF1 70831 120 + 1
GGAUGCGGAUGAUCGGGAGGGGGAUCGGACUAAGGACGAUGGAGGAGCAGGUGGUCGAGCCAGUGGAACCUGGCAAUGGAAACUGGCAGCUGCUGGCAGCAGUUGGCAGUUGGCAGCUUG
......(..(((((........)))))..).................(((((.(((..(((((......)))))......(((((.(((((((.....))))))).)))))))).))))) ( -40.60)
>DroEre_CAF1 74208 120 + 1
GGAUGUGGAUGAUCAGGAGGGGGAUCGGACUAAGGACGUCGGAGGAGCAGGUGGUCGAGCCAGUGGAACCUGGCAAUGGAAACUGGCAGCUGCUGGCAGCAGUUGGCAGUUGGCAGCUUG
.((((((..(((((........)))))..).....))))).......(((((.(((..(((((......)))))......(((((.(((((((.....))))))).)))))))).))))) ( -43.50)
>DroYak_CAF1 74080 119 + 1
-GAUGCGGAUGAUCAGUAGGGGGAUCGGAGCAAGGACGAUGGAGGAGCAGGUGGUCGAGCCAGUGGAACCUGGCAAUGGAAACUGGCAGCUGCUGGCAGCAGUUGGCAGUUGGCAGCUUG
-..(((...(((((........)))))..)))...............(((((.(((..(((((......)))))......(((((.(((((((.....))))))).)))))))).))))) ( -43.10)
>consensus
GGAUGCGGAUGAUCAGGAGGGGGAUCGGACUAAGGACGAUGGAGGAGCAGGUGGUCGAGCCAGUGGAACCUGGCAAUGGAAACUGGCAGCUGCUGGCAGCAGUUGGCAGUUGGCAGCUUG
.........(((((........)))))....................(((((.(((..(((((......)))))......(((((.(((((((.....))))))).)))))))).))))) (-38.50 = -38.50 +   0.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 12,805,072 – 12,805,192
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 95.83
Mean single sequence MFE -27.30
Consensus MFE -26.25
Energy contribution -26.25
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.45
Structure conservation index 0.96
SVM decision value 0.14
SVM RNA-class probability 0.602108
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12805072 120 - 22407834
CAAGCUGCCAACUGCCAACUGCUGCCAGCAGCUGCCAGUUUCCAUUGCCAGGUUCCACUGGCUCGACCACCUGCUCCUCCAUCGUCCUUAGCCCGAUCCCCCUUCCGAUCAUCCGCAUCC
...((((..(((((.((.((((.....)))).)).)))))......(((((......)))))..........................))))..((((........)))).......... ( -26.90)
>DroSec_CAF1 70831 120 - 1
CAAGCUGCCAACUGCCAACUGCUGCCAGCAGCUGCCAGUUUCCAUUGCCAGGUUCCACUGGCUCGACCACCUGCUCCUCCAUCGUCCUUAGUCCGAUCCCCCUCCCGAUCAUCCGCAUCC
...((.((.(((((.((.((((.....)))).)).)))))......(((((......)))))..........))....................((((........))))....)).... ( -26.80)
>DroEre_CAF1 74208 120 - 1
CAAGCUGCCAACUGCCAACUGCUGCCAGCAGCUGCCAGUUUCCAUUGCCAGGUUCCACUGGCUCGACCACCUGCUCCUCCGACGUCCUUAGUCCGAUCCCCCUCCUGAUCAUCCACAUCC
..(((((..(((((.((.((((.....)))).)).)))))..))..(((((......)))))..........))).....(((.......))).((((........)))).......... ( -28.20)
>DroYak_CAF1 74080 119 - 1
CAAGCUGCCAACUGCCAACUGCUGCCAGCAGCUGCCAGUUUCCAUUGCCAGGUUCCACUGGCUCGACCACCUGCUCCUCCAUCGUCCUUGCUCCGAUCCCCCUACUGAUCAUCCGCAUC-
..(((((..(((((.((.((((.....)))).)).)))))..))..(((((......)))))..........))).............(((...((((........))))....)))..- ( -27.30)
>consensus
CAAGCUGCCAACUGCCAACUGCUGCCAGCAGCUGCCAGUUUCCAUUGCCAGGUUCCACUGGCUCGACCACCUGCUCCUCCAUCGUCCUUAGUCCGAUCCCCCUCCCGAUCAUCCGCAUCC
..(((((..(((((.((.((((.....)))).)).)))))..))..(((((......)))))..........)))...................((((........)))).......... (-26.25 = -26.25 +   0.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 12,805,112 – 12,805,232
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.00
Mean single sequence MFE -52.22
Consensus MFE -43.02
Energy contribution -44.46
Covariance contribution 1.44
Combinations/Pair 1.16
Mean z-score -3.58
Structure conservation index 0.82
SVM decision value 3.62
SVM RNA-class probability 0.999455
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12805112 120 + 22407834
GGAGGAGCAGGUGGUCGAGCCAGUGGAACCUGGCAAUGGAAACUGGCAGCUGCUGGCAGCAGUUGGCAGUUGGCAGCUUGACGUCGACAUUGCUUGUCAUGUUUGUGACACACACUUCAG
((((((((((...((((((((((......)))))..((..(((((.(((((((..((....))..))))))).))).))..))))))).))))))(((((....))))).....)))).. ( -54.30)
>DroPse_CAF1 99042 104 + 1
-----AGCUGGCUAACAGGCUCCUGGAGCCUGGU--------CUGGCGGCUGUUGGC---AGUUGGCAGUUGCCGGCUUGACGUCGACAUUGCCUGUCAUGUUUGUGACACACACUUCAG
-----.((..(....(((((((...)))))))..--------)..))((((((((((---(((((((....)))))))....)))))))..)))((((((....)))))).......... ( -43.90)
>DroSec_CAF1 70871 120 + 1
GGAGGAGCAGGUGGUCGAGCCAGUGGAACCUGGCAAUGGAAACUGGCAGCUGCUGGCAGCAGUUGGCAGUUGGCAGCUUGACGUCGACAUUGCUUGUCAUGUUUGUGACACACACUUCAG
((((((((((...((((((((((......)))))..((..(((((.(((((((..((....))..))))))).))).))..))))))).))))))(((((....))))).....)))).. ( -54.30)
>DroEre_CAF1 74248 120 + 1
GGAGGAGCAGGUGGUCGAGCCAGUGGAACCUGGCAAUGGAAACUGGCAGCUGCUGGCAGCAGUUGGCAGUUGGCAGCUUGACGUCGACAUUGCUUGUCAUGUUUGUGACACACACUUCAG
((((((((((...((((((((((......)))))..((..(((((.(((((((..((....))..))))))).))).))..))))))).))))))(((((....))))).....)))).. ( -54.30)
>DroYak_CAF1 74119 120 + 1
GGAGGAGCAGGUGGUCGAGCCAGUGGAACCUGGCAAUGGAAACUGGCAGCUGCUGGCAGCAGUUGGCAGUUGGCAGCUUGACGUCGACAUUGCUUGUCAUGUUUGUGACACACACUUCAG
((((((((((...((((((((((......)))))..((..(((((.(((((((..((....))..))))))).))).))..))))))).))))))(((((....))))).....)))).. ( -54.30)
>consensus
GGAGGAGCAGGUGGUCGAGCCAGUGGAACCUGGCAAUGGAAACUGGCAGCUGCUGGCAGCAGUUGGCAGUUGGCAGCUUGACGUCGACAUUGCUUGUCAUGUUUGUGACACACACUUCAG
((((((((((...((((((((((......)))))........(((.(((((((..((....))..))))))).))).......))))).))))))(((((....))))).....)))).. (-43.02 = -44.46 +   1.44)

alignment

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secondary structure

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dotplot

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Window 6

Location 12,805,152 – 12,805,262
Length 110
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 87.63
Mean single sequence MFE -41.20
Consensus MFE -33.14
Energy contribution -34.50
Covariance contribution 1.36
Combinations/Pair 1.09
Mean z-score -2.14
Structure conservation index 0.80
SVM decision value 1.42
SVM RNA-class probability 0.952548
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12805152 110 + 22407834
AACUGGCAGCUGCUGGCAGCAGUUGGCAGUUGGCAGCUUGACGUCGACAUUGCUUGUCAUGUUUGUGACACACACUUCAGUCUUC---CGUCUU-------CAGUCAGUUGAGGUGCCAG
(((((.(((((((.....))))))).)))))((((.((..((...(((..((..((((((....))))))..))....((.(...---.).)).-------..))).))..)).)))).. ( -42.00)
>DroPse_CAF1 99071 103 + 1
--CUGGCGGCUGUUGGC---AGUUGGCAGUUGCCGGCUUGACGUCGACAUUGCCUGUCAUGUUUGUGACACACACUUCAGUCCUCGGCCGUCUU-------CAGUCAG-----GUGGCAG
--..((((((((..(((---....((((((.(.((((.....)))).)))))))((((((....)))))).........)))..))))))))..-------..(((..-----..))).. ( -38.50)
>DroSec_CAF1 70911 103 + 1
AACUGGCAGCUGCUGGCAGCAGUUGGCAGUUGGCAGCUUGACGUCGACAUUGCUUGUCAUGUUUGUGACACACACUUCAGUC----------UU-------CAGUCAGCUGAAGUGCCAG
(((((.(((((((.....))))))).)))))(((.((..(((((.((((.....))))))))).)).......(((((((.(----------(.-------.....)))))))))))).. ( -40.50)
>DroEre_CAF1 74288 110 + 1
AACUGGCAGCUGCUGGCAGCAGUUGGCAGUUGGCAGCUUGACGUCGACAUUGCUUGUCAUGUUUGUGACACACACUUCAGUCUUC---CGUCUU-------CAGUCAGUUGAGGUGCCAG
(((((.(((((((.....))))))).)))))((((.((..((...(((..((..((((((....))))))..))....((.(...---.).)).-------..))).))..)).)))).. ( -42.00)
>DroYak_CAF1 74159 117 + 1
AACUGGCAGCUGCUGGCAGCAGUUGGCAGUUGGCAGCUUGACGUCGACAUUGCUUGUCAUGUUUGUGACACACACUUCAGUCUUC---CGUCUUCAGUCUUCAGUCAGUUGAGGUGCCAG
(((((.(((((((.....))))))).)))))((((.((..((...(((......((((((....))))))...(((..((.(...---.).))..))).....))).))..)).)))).. ( -43.00)
>consensus
AACUGGCAGCUGCUGGCAGCAGUUGGCAGUUGGCAGCUUGACGUCGACAUUGCUUGUCAUGUUUGUGACACACACUUCAGUCUUC___CGUCUU_______CAGUCAGUUGAGGUGCCAG
.((((.(((((((.....))))))).))))(((((.((((((...(((......((((((....))))))...((....))......................))).)))))).))))). (-33.14 = -34.50 +   1.36)

alignment

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secondary structure

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dotplot

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Window 7

Location 12,805,152 – 12,805,262
Length 110
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 87.63
Mean single sequence MFE -34.22
Consensus MFE -25.16
Energy contribution -26.36
Covariance contribution 1.20
Combinations/Pair 1.00
Mean z-score -1.55
Structure conservation index 0.74
SVM decision value -0.04
SVM RNA-class probability 0.511763
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12805152 110 - 22407834
CUGGCACCUCAACUGACUG-------AAGACG---GAAGACUGAAGUGUGUGUCACAAACAUGACAAGCAAUGUCGACGUCAAGCUGCCAACUGCCAACUGCUGCCAGCAGCUGCCAGUU
(((((..............-------..((((---...(((.....(((.(((((......))))).)))..)))..)))).((((((.....((.....)).....))))))))))).. ( -36.20)
>DroPse_CAF1 99071 103 - 1
CUGCCAC-----CUGACUG-------AAGACGGCCGAGGACUGAAGUGUGUGUCACAAACAUGACAGGCAAUGUCGACGUCAAGCCGGCAACUGCCAACU---GCCAACAGCCGCCAG--
.((((..-----((.....-------.))..(((....((((((..(((.(((((......))))).)))...)))..)))..))))))).(((.(..((---(....)))..).)))-- ( -27.50)
>DroSec_CAF1 70911 103 - 1
CUGGCACUUCAGCUGACUG-------AA----------GACUGAAGUGUGUGUCACAAACAUGACAAGCAAUGUCGACGUCAAGCUGCCAACUGCCAACUGCUGCCAGCAGCUGCCAGUU
((((((...((((((((.(-------..----------(((.....(((.(((((......))))).)))..)))..)))).))))).............((((....)))))))))).. ( -35.00)
>DroEre_CAF1 74288 110 - 1
CUGGCACCUCAACUGACUG-------AAGACG---GAAGACUGAAGUGUGUGUCACAAACAUGACAAGCAAUGUCGACGUCAAGCUGCCAACUGCCAACUGCUGCCAGCAGCUGCCAGUU
(((((..............-------..((((---...(((.....(((.(((((......))))).)))..)))..)))).((((((.....((.....)).....))))))))))).. ( -36.20)
>DroYak_CAF1 74159 117 - 1
CUGGCACCUCAACUGACUGAAGACUGAAGACG---GAAGACUGAAGUGUGUGUCACAAACAUGACAAGCAAUGUCGACGUCAAGCUGCCAACUGCCAACUGCUGCCAGCAGCUGCCAGUU
(((((.......................((((---...(((.....(((.(((((......))))).)))..)))..)))).((((((.....((.....)).....))))))))))).. ( -36.20)
>consensus
CUGGCACCUCAACUGACUG_______AAGACG___GAAGACUGAAGUGUGUGUCACAAACAUGACAAGCAAUGUCGACGUCAAGCUGCCAACUGCCAACUGCUGCCAGCAGCUGCCAGUU
(((((.................................((((((..(((.(((((......))))).)))...)))..))).((((((.....((.....)).....))))))))))).. (-25.16 = -26.36 +   1.20)

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 11:18:20 2006