Locus 5122

Sequence ID 3R_DroMel_CAF1
Location 13,484,666 – 13,484,843
Length 177
Max. P 0.970494
window8356 window8357 window8358

overview

Window 6

Location 13,484,666 – 13,484,767
Length 101
Sequences 5
Columns 101
Reading direction forward
Mean pairwise identity 89.50
Mean single sequence MFE -25.89
Consensus MFE -19.02
Energy contribution -19.94
Covariance contribution 0.92
Combinations/Pair 1.08
Mean z-score -2.61
Structure conservation index 0.73
SVM decision value 1.22
SVM RNA-class probability 0.931722
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13484666 101 + 27905053
UUGAUUUGUUUGGUCUUCAACUCAGCUCAACUCAACCCCAGCAGCAUCAACAAUAACACGUCUCCUUAUCGGAACCGGAAACGGUUCCCAAGAAAGAGGUC
((((((((((.((.......................)).))))).))))).......((.(((.(((...(((((((....))))))).)))..))).)). ( -24.00)
>DroSec_CAF1 34611 100 + 1
UUGAUUUGUUUGGUC-CCAACUCAGCUCAACUCAACCCCACCAGCAUCAACAAUAACACGUCUCCUUAUCGGAACCGGAAACGGUUCCCAAGAAAGAGGAC
((((.(((.(((...-.)))..))).)))).............................(((..(((.(((((((((....)))))))...)))))..))) ( -24.70)
>DroSim_CAF1 33479 101 + 1
UUGAGUUGUUUGGUCCCCAACUCAGCUCAACUCAACCCCAGCAGCAUCAACAAUAACACGUCUCCUUAUCGGAACCGGAAACGGCUCCCAAGAAAGAGGUC
((((((((.((((...))))..))))))))...........................((.(((.(((...(((.(((....))).))).)))..))).)). ( -25.40)
>DroEre_CAF1 31224 101 + 1
UUGAUUUGCUUGGUCCCCAACUCAACUCAACUCAACCCCCGCAGGAUCAACAAUAACACGUUCCCUUAUCGGAACCGGAAACGGUUCCCAAGAAAGAGGUC
((((.(((.((((...))))..))).))))(((.........(((...(((........))).)))....(((((((....))))))).......)))... ( -24.20)
>DroYak_CAF1 39278 90 + 1
UUGAUUUGUUUG-UCCCCAA----------CUCAACCCCCGCAGGAUCAACAAUAACACGACUCCUUAUCGGAACCGGAAACGGUUCCCAAGAAAGGGGUC
.....(((((.(-(((....----------.............)))).)))))......((((((((.(((((((((....)))))))...)))))))))) ( -31.13)
>consensus
UUGAUUUGUUUGGUCCCCAACUCAGCUCAACUCAACCCCAGCAGCAUCAACAAUAACACGUCUCCUUAUCGGAACCGGAAACGGUUCCCAAGAAAGAGGUC
((((((((((.((.......................)).))))).))))).............((((.(((((((((....)))))))...))..)))).. (-19.02 = -19.94 +   0.92)

alignment

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secondary structure

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dotplot

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Window 7

Location 13,484,703 – 13,484,806
Length 103
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 80.77
Mean single sequence MFE -37.51
Consensus MFE -22.92
Energy contribution -24.53
Covariance contribution 1.61
Combinations/Pair 1.10
Mean z-score -3.60
Structure conservation index 0.61
SVM decision value 1.66
SVM RNA-class probability 0.970494
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13484703 103 + 27905053
CCAGCAGCAUCAACAAUAACACGU-------------CUCCUUAUCGGAACCGGAAACGGUUCCCAA--GAAAGAGGUCCUAAAAGAGUCCUCA-AAGUCACGGUGGCGUGUGUGACAA
.............((...((((((-------------(.((.....(((((((....)))))))...--....((((.((.....).).)))).-.......)).))))))).)).... ( -36.60)
>DroPse_CAF1 45156 115 + 1
-CAGCAAGAACAACAAUAGCACGUUCACGUUCCUGUGCCCGUUAUCGGAACCGGAAACGGGUCCACACAGAACGA---AAGGAAAAAGUCCACAAAAGUCACGGUGGCGUGUGUGACAA
-......((((...........)))).(((((.((((((((((.(((....))).))))))....))))))))).---.........(((((((...(((.....))).)))).))).. ( -35.90)
>DroSec_CAF1 34647 103 + 1
CCACCAGCAUCAACAAUAACACGU-------------CUCCUUAUCGGAACCGGAAACGGUUCCCAA--GAAAGAGGACCUGAAAGAGUCCUCA-AAGUCACGGUGGCGUGUGUGACAA
.............((...((((((-------------(.((.....(((((((....)))))))...--....((((((.(....).)))))).-.......)).))))))).)).... ( -41.00)
>DroEre_CAF1 31261 103 + 1
CCCGCAGGAUCAACAAUAACACGU-------------UCCCUUAUCGGAACCGGAAACGGUUCCCAA--GAAAGAGGUCCUGAAAGAGUCCUCA-AAGUCACGGUGGCGUGUGUGACAA
.............((...((((((-------------..((.....(((((((....)))))))...--....((((.(.(....).).)))).-.......))..)))))).)).... ( -36.20)
>DroYak_CAF1 39304 103 + 1
CCCGCAGGAUCAACAAUAACACGA-------------CUCCUUAUCGGAACCGGAAACGGUUCCCAA--GAAAGGGGUCCUGAAGGAGUCCUCA-AAGUCACGGUGGCGUGUGUGACAA
...(.(((((.........((.((-------------((((((.(((((((((....)))))))...--)))))))))).)).....)))))).-..((((((........)))))).. ( -37.24)
>DroPer_CAF1 42256 115 + 1
-CAGCAAGAACAACAAUAACACGUUCACGUUCCUGUGCCCGUUAUCGGAACCGGAAACGGGUCCACACAGAACGA---AAGGAAAAAGUCCACAAAAGUCACGCUGGCGUGUGUGACAA
-......((((...........)))).(((((.((((((((((.(((....))).))))))....))))))))).---..(((.....)))......(((((((......))))))).. ( -38.10)
>consensus
CCAGCAGGAUCAACAAUAACACGU_____________CCCCUUAUCGGAACCGGAAACGGUUCCCAA__GAAAGAGGUCCUGAAAGAGUCCUCA_AAGUCACGGUGGCGUGUGUGACAA
.............((...((((((......................(((((((....))))))).........((((.(........).)))).............)))))).)).... (-22.92 = -24.53 +   1.61)

alignment

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secondary structure

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dotplot

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Window 8

Location 13,484,730 – 13,484,843
Length 113
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 79.57
Mean single sequence MFE -34.22
Consensus MFE -18.20
Energy contribution -18.37
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -2.32
Structure conservation index 0.53
SVM decision value 0.69
SVM RNA-class probability 0.822893
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13484730 113 + 27905053
CUUAUCG-GAACCGGAAACGGUUCCCAA--GAAAGAGGUCCUAAAAGAGUCCUCA-AAGUCACGGUGGCGUGUGUGACAAGUCCUUUCUAAUGAGCAGGAAGAAUGCACGUA---GACUG
......(-((((((....)))))))...--....((((.((.....).).)))).-......((((.((((((((......(((((((....))).))))...)))))))).---.)))) ( -39.70)
>DroPse_CAF1 45195 102 + 1
GUUAUCG-GAACCGGAAACGGGUCCACACAGAACGA---AAGGAAAAAGUCCACAAAAGUCACGGUGGCGUGUGUGACAAGUCCUUUCUAAUGAGCAGGAA--------------GAGGG
(((...(-((.(((....))).))).........((---(((((....(((((((...(((.....))).)))).)))...))))))).....))).....--------------..... ( -33.60)
>DroSec_CAF1 34674 113 + 1
CUUAUCG-GAACCGGAAACGGUUCCCAA--GAAAGAGGACCUGAAAGAGUCCUCA-AAGUCACGGUGGCGUGUGUGACAAGUCCUUUCUAAUGAGCAGGAAGAAUGCACGGA---GACUG
.((((((-((((((....)))))))...--....((((((.(....).)))))).-.......)))))(((((((......(((((((....))).))))...)))))))..---..... ( -41.10)
>DroSim_CAF1 33543 113 + 1
CUUAUCG-GAACCGGAAACGGCUCCCAA--GAAAGAGGUCCUGAAAGAGUCCUCA-AAGUCACGGUGGCGUGUGUGACAAGUCCUUUGUAAUGAGCAGGAAGAAUGCACGUA---GACUG
......(-((.(((....))).)))...--....((((.(.(....).).)))).-......((((.((((((((......((((..((.....))))))...)))))))).---.)))) ( -33.20)
>DroAna_CAF1 35744 94 + 1
CUUAUCGGGAACCGGAAACGG----------------------AAAAAGUCCACA-AAGUCACGGUGGCGUAUGUGACAAGUCCUUUCUAAUGAGCAGGAAGAAUGCACGUU---UACAA
......((((.(((....)))----------------------............-..((((((........))))))...))))....((((.(((.......))).))))---..... ( -22.00)
>DroPer_CAF1 42295 116 + 1
GUUAUCG-GAACCGGAAACGGGUCCACACAGAACGA---AAGGAAAAAGUCCACAAAAGUCACGCUGGCGUGUGUGACAAGUCCUUUCUAAUGAGCAGGAAGAAGGCGAGCAUAAGAGGG
((..(((-((.(((....))).))).........((---(((((....(((((((...(((.....))).)))).)))...))))))).............))..))............. ( -35.70)
>consensus
CUUAUCG_GAACCGGAAACGGGUCCCAA__GAAAGA___CCUGAAAAAGUCCACA_AAGUCACGGUGGCGUGUGUGACAAGUCCUUUCUAAUGAGCAGGAAGAAUGCACGUA___GACUG
...........(((....))).....................................((((((........))))))...(((((((....))).)))).................... (-18.20 = -18.37 +   0.17)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:46:51 2006