Locus 10249

Sequence ID 3R_DroMel_CAF1
Location 27,456,481 – 27,456,600
Length 119
Max. P 0.973215
window16332 window16333 window16334

overview

Window 2

Location 27,456,481 – 27,456,586
Length 105
Sequences 6
Columns 105
Reading direction forward
Mean pairwise identity 81.40
Mean single sequence MFE -36.23
Consensus MFE -23.97
Energy contribution -24.83
Covariance contribution 0.86
Combinations/Pair 1.09
Mean z-score -1.54
Structure conservation index 0.66
SVM decision value 0.11
SVM RNA-class probability 0.590328
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27456481 105 + 27905053
CGGUAGGGGUGGGGGAGGGGAGAGGAGGUGGGCACACGAGGCUGCCAAAUACGUGCGUGGCUGAGAUUUGUUUGGCUCUCAUCCGCGCACAUCCUGCGCUUUGCU
.(((((((.((.((((..........((..(.(......).)..))......((((((((.(((((.((....)).))))).)))))))).)))).))))))))) ( -42.40)
>DroPse_CAF1 16026 82 + 1
UGGCAGUGGC----------------AGUGG-------UAGAGGCGAACGACGUGCGUGGCUGAGAUUUGUUUGGCUCUCAUCCGCGCACUUCCUUAGCUUUGCU
.(((((.(((----------------.((.(-------(........)).))((((((((.(((((.((....)).))))).)))))))).......)))))))) ( -30.20)
>DroSec_CAF1 12443 89 + 1
CGGAAGGGGC----------------GGUGGGUACACGUGGCUGCCAAAUACGUGCGUGGCUGAGAUUUGUUUGGCUCUCAUCCGCGCACAUCCUGCGCUUCGCU
.....(((((----------------((..(.((....)).)..))......((((((((.(((((.((....)).))))).)))))))).......)))))... ( -35.50)
>DroSim_CAF1 12332 89 + 1
CGGAAGGGGC----------------GGUGGGUACACGAGGCUGCCAAAUACGUGCGUGGCUGAGAUUUGUUUGGCUCUCAUCCGCGCACAUCCUGCGCUUCGCU
(....).(((----------------.(((....)))(((((.((.......((((((((.(((((.((....)).))))).)))))))).....)))))))))) ( -34.40)
>DroEre_CAF1 12214 88 + 1
U-GGGUGGGG----------------GCUGGCUACACGAGGCUGCCAAAUACGUGCGUGGCUGAGAUUUGUUUGGCUCUCAUCCGCGCACAUCCUGCGCUUUGCU
.-(.(..(((----------------((.((((......)))))))......((((((((.(((((.((....)).))))).))))))))..))..).)...... ( -37.20)
>DroYak_CAF1 12350 87 + 1
--GAGUGGGG----------------GAUGGCUACACGAGGCUGCCAAAUACGUGCGUGGCUGAGAUUUGUUUGGCUCUCAUCCGCGCACAUCCUGCGCUUUGCU
--(((((.((----------------((((((..(.....)..)))......((((((((.(((((.((....)).))))).))))))))))))).))))).... ( -37.70)
>consensus
CGGAAGGGGC________________GGUGGGUACACGAGGCUGCCAAAUACGUGCGUGGCUGAGAUUUGUUUGGCUCUCAUCCGCGCACAUCCUGCGCUUUGCU
....................................((((((.((.......((((((((.(((((.((....)).))))).)))))))).....)))))))).. (-23.97 = -24.83 +   0.86)

alignment

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secondary structure

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dotplot

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Window 3

Location 27,456,481 – 27,456,586
Length 105
Sequences 6
Columns 105
Reading direction reverse
Mean pairwise identity 81.40
Mean single sequence MFE -27.78
Consensus MFE -22.28
Energy contribution -22.78
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.16
Structure conservation index 0.80
SVM decision value -0.02
SVM RNA-class probability 0.522486
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27456481 105 - 27905053
AGCAAAGCGCAGGAUGUGCGCGGAUGAGAGCCAAACAAAUCUCAGCCACGCACGUAUUUGGCAGCCUCGUGUGCCCACCUCCUCUCCCCUCCCCCACCCCUACCG
.((.....))((((((((((.((.(((((..........))))).)).)))))))....((((........)))).......................))).... ( -27.80)
>DroPse_CAF1 16026 82 - 1
AGCAAAGCUAAGGAAGUGCGCGGAUGAGAGCCAAACAAAUCUCAGCCACGCACGUCGUUCGCCUCUA-------CCACU----------------GCCACUGCCA
......((.((.((.(((((.((.(((((..........))))).)).))))).)).)).)).....-------.....----------------.......... ( -22.80)
>DroSec_CAF1 12443 89 - 1
AGCGAAGCGCAGGAUGUGCGCGGAUGAGAGCCAAACAAAUCUCAGCCACGCACGUAUUUGGCAGCCACGUGUACCCACC----------------GCCCCUUCCG
.(((..((.(((((((((((.((.(((((..........))))).)).))))))).))))))......(((....))))----------------))........ ( -29.00)
>DroSim_CAF1 12332 89 - 1
AGCGAAGCGCAGGAUGUGCGCGGAUGAGAGCCAAACAAAUCUCAGCCACGCACGUAUUUGGCAGCCUCGUGUACCCACC----------------GCCCCUUCCG
.((((.((((...(((((((.((.(((((..........))))).)).))))))).....)).)).)))).........----------------.......... ( -29.40)
>DroEre_CAF1 12214 88 - 1
AGCAAAGCGCAGGAUGUGCGCGGAUGAGAGCCAAACAAAUCUCAGCCACGCACGUAUUUGGCAGCCUCGUGUAGCCAGC----------------CCCCACCC-A
.((.....)).(((((((((.((.(((((..........))))).)).)))))))..(((((.((.....)).))))).----------------..))....-. ( -29.10)
>DroYak_CAF1 12350 87 - 1
AGCAAAGCGCAGGAUGUGCGCGGAUGAGAGCCAAACAAAUCUCAGCCACGCACGUAUUUGGCAGCCUCGUGUAGCCAUC----------------CCCCACUC--
.((.....)).(((((((((.((.(((((..........))))).)).)))))))...((((.((.....)).))))..----------------..))....-- ( -28.60)
>consensus
AGCAAAGCGCAGGAUGUGCGCGGAUGAGAGCCAAACAAAUCUCAGCCACGCACGUAUUUGGCAGCCUCGUGUACCCACC________________GCCCCUUCCG
......((.(((((((((((.((.(((((..........))))).)).))))))).))))))........................................... (-22.28 = -22.78 +   0.50)

alignment

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secondary structure

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dotplot

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Window 4

Location 27,456,506 – 27,456,600
Length 94
Sequences 6
Columns 94
Reading direction reverse
Mean pairwise identity 93.93
Mean single sequence MFE -29.55
Consensus MFE -26.85
Energy contribution -27.22
Covariance contribution 0.36
Combinations/Pair 1.04
Mean z-score -1.76
Structure conservation index 0.91
SVM decision value 1.71
SVM RNA-class probability 0.973215
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27456506 94 - 27905053
GAGAGCAAAAAGUUAGCAAAGCGCAGGAUGUGCGCGGAUGAGAGCCAAACAAAUCUCAGCCACGCACGUAUUUGGCAGCCUCGUGUGCCCACCU
(((.((.....(....)...((.(((((((((((.((.(((((..........))))).)).))))))).)))))).)))))(((....))).. ( -30.30)
>DroSec_CAF1 12453 93 - 1
GAGAGCAAAAAGUUAGCGAAGCGCAGGAUGUGCGCGGAUGAGAGCCAAACAAAUCUCAGCCACGCACGUAUUUGGCAGCCACGUGUACCCACC-
...............(((..((((...(((((((.((.(((((..........))))).)).))))))).....)).))..))).........- ( -26.80)
>DroSim_CAF1 12342 93 - 1
GAGAGCAAAAAGUUAGCGAAGCGCAGGAUGUGCGCGGAUGAGAGCCAAACAAAUCUCAGCCACGCACGUAUUUGGCAGCCUCGUGUACCCACC-
(((.((.....(....)...((.(((((((((((.((.(((((..........))))).)).))))))).)))))).)))))(((....))).- ( -30.30)
>DroEre_CAF1 12223 93 - 1
GAGAGCAAAAAGUUAGCAAAGCGCAGGAUGUGCGCGGAUGAGAGCCAAACAAAUCUCAGCCACGCACGUAUUUGGCAGCCUCGUGUAGCCAGC-
(((.((.....(....)...((.(((((((((((.((.(((((..........))))).)).))))))).)))))).)))))...........- ( -29.50)
>DroYak_CAF1 12358 93 - 1
GAGAGCAAAAAGUUAGCAAAGCGCAGGAUGUGCGCGGAUGAGAGCCAAACAAAUCUCAGCCACGCACGUAUUUGGCAGCCUCGUGUAGCCAUC-
(((.((.....(....)...((.(((((((((((.((.(((((..........))))).)).))))))).)))))).)))))...........- ( -29.50)
>DroAna_CAF1 13361 93 - 1
GCGAGCAAAAAGUUAGCAAAGCCCAGGAAGUGUGCGGAUGAGAGCAAAACAAAUCUCAGCCACGCACGUCUUUGGCAGCCUCGUGUACUAACU-
((((((.....(....)...(((.((((.(((((.((.(((((..........))))).)).))))).)))).))).).))))).........- ( -30.90)
>consensus
GAGAGCAAAAAGUUAGCAAAGCGCAGGAUGUGCGCGGAUGAGAGCCAAACAAAUCUCAGCCACGCACGUAUUUGGCAGCCUCGUGUACCCACC_
(((.((.....(....)...((.(((((((((((.((.(((((..........))))).)).))))))).)))))).)))))............ (-26.85 = -27.22 +   0.36)

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 13:52:36 2006