Locus 3155

Sequence ID 2L_DroMel_CAF1
Location 9,026,895 – 9,027,028
Length 133
Max. P 0.903634
window5016 window5017 window5018

overview

Window 6

Location 9,026,895 – 9,027,005
Length 110
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 79.05
Mean single sequence MFE -23.30
Consensus MFE -16.07
Energy contribution -16.10
Covariance contribution 0.03
Combinations/Pair 1.04
Mean z-score -1.89
Structure conservation index 0.69
SVM decision value 1.03
SVM RNA-class probability 0.903634
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9026895 110 + 22407834
AGGUUUUCCACCC--ACUGUCAGCAGCACAUC-AGAUGUCUCCUUGUCAUUUUAAAGCCAUUUGAUGUAUGACAAAUCAAAUUUGACAAACUGCCAACAGUUGUUUUGCAUCU
.((....))....--(((((..((((....((-((((......(((((((.(((((....)))))...))))))).....))))))....))))..)))))............ ( -24.50)
>DroVir_CAF1 45264 100 + 1
---CACUGCCAUUUGGCUG---GCAGCCCUCGU-------UUCUUGUCAUUUUAAAGCCAUUUGAUGUAUGACAAAUCAAAUUUGACAAACUGCCAACAGUUGUUUUGCAUCU
---.((((((....)))((---((((.......-------...(((((((.(((((....)))))...))))))).(((....)))....))))))..)))............ ( -21.50)
>DroPse_CAF1 24528 105 + 1
AUAUACUCCAUCCUGGCUGUCAGCAG-ACAUC-------UUCCUUGUCAUUUUAAAGCCAUUUGAUGUAUGACAAAUCAAAUUUGACAAACUGCCAGCAGUUGUUUUGCAUCU
.............(((((.......(-(((..-------.....)))).......)))))...((((((.(((...(((....)))..(((((....)))))))).)))))). ( -23.84)
>DroWil_CAF1 44048 106 + 1
-ACUUUU---CCU-ACUUGUCAGCUACAUGGC--GACAGCUCCUUGUCAUUUUAAAGCCAUUUGAUGUAUGACAAAUCAAAUUUGACAAACUGCCAGCAGUUGUUUUGCAUCU
-......---...-...((((.(((....)))--))))((...(((((((.(((((....)))))...))))))).........(((((.(((....))))))))..)).... ( -21.90)
>DroMoj_CAF1 39397 110 + 1
---AAAAGUCAUUUGGGUGAAAGCAGCUCCCGUUGCCUGCUUCUUGUCAUUUUAAAGCCAUUUGAUGUAUGACAAAUCAAAUUUGACAAACUGCCAACAGUUGUUUUGCAUCU
---....((((..(...((((((((((.......).)))))).(((((((.(((((....)))))...))))))).))).)..)))).(((((....)))))........... ( -24.20)
>DroPer_CAF1 24475 105 + 1
AUAUACUCCAUCCUGGCUGUCAGCAG-ACAUC-------UUCCUUGUCAUUUUAAAGCCAUUUGAUGUAUGACAAAUCAAAUUUGACAAACUGCCAGCAGUUGUUUUGCAUCU
.............(((((.......(-(((..-------.....)))).......)))))...((((((.(((...(((....)))..(((((....)))))))).)))))). ( -23.84)
>consensus
___UACUCCAACCUGGCUGUCAGCAGCACAUC_______CUCCUUGUCAUUUUAAAGCCAUUUGAUGUAUGACAAAUCAAAUUUGACAAACUGCCAACAGUUGUUUUGCAUCU
......................((((.................(((((((.(((((....)))))...))))))).........(((((.(((....)))))))))))).... (-16.07 = -16.10 +   0.03)

alignment

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secondary structure

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Window 7

Location 9,026,895 – 9,027,005
Length 110
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 79.05
Mean single sequence MFE -26.05
Consensus MFE -15.30
Energy contribution -15.82
Covariance contribution 0.53
Combinations/Pair 1.04
Mean z-score -1.67
Structure conservation index 0.59
SVM decision value 0.18
SVM RNA-class probability 0.621661
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9026895 110 - 22407834
AGAUGCAAAACAACUGUUGGCAGUUUGUCAAAUUUGAUUUGUCAUACAUCAAAUGGCUUUAAAAUGACAAGGAGACAUCU-GAUGUGCUGCUGACAGU--GGGUGGAAAACCU
............(((((..(((((((((((..(((((...(((((.......))))).))))).))))))(....)....-.....)))))..)))))--((((.....)))) ( -32.90)
>DroVir_CAF1 45264 100 - 1
AGAUGCAAAACAACUGUUGGCAGUUUGUCAAAUUUGAUUUGUCAUACAUCAAAUGGCUUUAAAAUGACAAGAA-------ACGAGGGCUGC---CAGCCAAAUGGCAGUG---
...(((..(((....))).))).(((((((..(((((...(((((.......))))).))))).)))))))..-------......(((((---((......))))))).--- ( -25.50)
>DroPse_CAF1 24528 105 - 1
AGAUGCAAAACAACUGCUGGCAGUUUGUCAAAUUUGAUUUGUCAUACAUCAAAUGGCUUUAAAAUGACAAGGAA-------GAUGU-CUGCUGACAGCCAGGAUGGAGUAUAU
..((((....((..(.(((((..(((((((..(((((...(((((.......))))).))))).)))))))...-------..(((-(....))))))))).)))..)))).. ( -25.30)
>DroWil_CAF1 44048 106 - 1
AGAUGCAAAACAACUGCUGGCAGUUUGUCAAAUUUGAUUUGUCAUACAUCAAAUGGCUUUAAAAUGACAAGGAGCUGUC--GCCAUGUAGCUGACAAGU-AGG---AAAAGU-
.............((((((((..(((((((..(((((...(((((.......))))).))))).)))))))..)))(((--((......)).))).)))-)).---......- ( -24.20)
>DroMoj_CAF1 39397 110 - 1
AGAUGCAAAACAACUGUUGGCAGUUUGUCAAAUUUGAUUUGUCAUACAUCAAAUGGCUUUAAAAUGACAAGAAGCAGGCAACGGGAGCUGCUUUCACCCAAAUGACUUUU---
.((.(((...(..((((((((..(((((((..(((((...(((((.......))))).))))).)))))))..))...))))))..).)))..))...............--- ( -23.10)
>DroPer_CAF1 24475 105 - 1
AGAUGCAAAACAACUGCUGGCAGUUUGUCAAAUUUGAUUUGUCAUACAUCAAAUGGCUUUAAAAUGACAAGGAA-------GAUGU-CUGCUGACAGCCAGGAUGGAGUAUAU
..((((....((..(.(((((..(((((((..(((((...(((((.......))))).))))).)))))))...-------..(((-(....))))))))).)))..)))).. ( -25.30)
>consensus
AGAUGCAAAACAACUGCUGGCAGUUUGUCAAAUUUGAUUUGUCAUACAUCAAAUGGCUUUAAAAUGACAAGGAG_______GAUGUGCUGCUGACAGCCAAGAUGGAGUA___
.............(((..((((((((((((..(((((...(((((.......))))).))))).)))))))................)))))..)))................ (-15.30 = -15.82 +   0.53)

alignment

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secondary structure

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dotplot

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Window 8

Location 9,026,932 – 9,027,028
Length 96
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 84.22
Mean single sequence MFE -19.93
Consensus MFE -14.21
Energy contribution -14.10
Covariance contribution -0.11
Combinations/Pair 1.08
Mean z-score -1.91
Structure conservation index 0.71
SVM decision value -0.01
SVM RNA-class probability 0.526303
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9026932 96 + 22407834
UCCUUGUCAUUUUAAAGCCAUUUGAUGUAUGACAAAUCAAAUUUGACAAACUG-------CCAACAGUUGUUUUGCAUCUUUGCAACAUUUUUCACAGCA------GCC-----------
...(((((((.(((((....)))))...)))))))...............(((-------(........((.(((((....))))).))........)))------)..----------- ( -17.29)
>DroVir_CAF1 45291 96 + 1
UUCUUGUCAUUUUAAAGCCAUUUGAUGUAUGACAAAUCAAAUUUGACAAACUG-------CCAACAGUUGUUUUGCAUCUUUGCAACAUUUUUCAACGCC------UUC-----------
...(((((((.(((((....)))))...))))))).......((((..(((((-------....)))))...(((((....)))))......))))....------...----------- ( -16.80)
>DroPse_CAF1 24560 100 + 1
UCCUUGUCAUUUUAAAGCCAUUUGAUGUAUGACAAAUCAAAUUUGACAAACUG-------CCAGCAGUUGUUUUGCAUCUUUGCAACAUUUUUCACAGAGGACCCUG-------------
((((((((((.(((((....)))))...)))))))......((((...(((((-------....)))))...(((((....))))).........))))))).....------------- ( -21.00)
>DroGri_CAF1 32188 103 + 1
UUCAUGUCAUUUUAAAGUCAUUUGAUGUAUGACAAAUCAAAUUUGACAAACUGCCAACUGCCAACAGUUGUUUUGCAUCUUUGCAACAUUUUUCAACUCC------UCC-----------
....((((((.(((((....)))))...))))))........((((.(((.((.((((((....))))))..(((((....)))))))))).))))....------...----------- ( -18.80)
>DroWil_CAF1 44081 107 + 1
UCCUUGUCAUUUUAAAGCCAUUUGAUGUAUGACAAAUCAAAUUUGACAAACUG-------CCAGCAGUUGUUUUGCAUCUUUGUAGCAUUUUUCAAAACA------GAGCGCAGAGUCGA
...(((((((.(((((....)))))...))))))).......(((((.(((((-------....)))))..(((((..((((((.............)))------))).)))))))))) ( -24.72)
>DroPer_CAF1 24507 102 + 1
UCCUUGUCAUUUUAAAGCCAUUUGAUGUAUGACAAAUCAAAUUUGACAAACUG-------CCAGCAGUUGUUUUGCAUCUUUGCAACAUUUUUCACAGAGGACCCUGCC-----------
((((((((((.(((((....)))))...)))))))......((((...(((((-------....)))))...(((((....))))).........))))))).......----------- ( -21.00)
>consensus
UCCUUGUCAUUUUAAAGCCAUUUGAUGUAUGACAAAUCAAAUUUGACAAACUG_______CCAACAGUUGUUUUGCAUCUUUGCAACAUUUUUCAAAGCA______GCC___________
...(((((((.(((((....)))))...))))))).........(((((.(((...........))))))))(((((....))))).................................. (-14.21 = -14.10 +  -0.11)

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 10:45:42 2006