Locus 3938

Sequence ID 2R_DroMel_CAF1
Location 12,995,115 – 12,995,249
Length 134
Max. P 0.580250
window6357 window6358

overview

Window 7

Location 12,995,115 – 12,995,209
Length 94
Sequences 6
Columns 98
Reading direction forward
Mean pairwise identity 73.45
Mean single sequence MFE -15.06
Consensus MFE -6.71
Energy contribution -7.18
Covariance contribution 0.47
Combinations/Pair 1.27
Mean z-score -1.79
Structure conservation index 0.45
SVM decision value 0.09
SVM RNA-class probability 0.580250
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12995115 94 + 20766785
UCGCCAGAUGCUAUUGUAACUAUUAUUUUAUUGUUUUCCGCA-UUCUCUUACUAUAUUUCAUCAAUAU---ACCUUUCAAUAGUCUCUGGGCAACCAU
..((((((.(((((((...............(((.....)))-.........((((((.....)))))---).....))))))).))).)))...... ( -15.60)
>DroVir_CAF1 18183 88 + 1
CAGCCGGAUGCUAUUGUAAGUGCCAAU-CAG--C--UCGUAAAUA-UAUUCCCAUAAUAACUACUU-U---GCUUUUUUGCAGUCACUUGGAAACCAC
.....((...(((..((.(.(((.((.-.((--(--..(((..((-(.........)))..)))..-.---)))..)).))).).)).)))...)).. ( -11.30)
>DroSec_CAF1 10484 93 + 1
UCACCAGAUGCUAUUGUAACUAUUAAU-UGUUGUUAUCCGCA-UCCUUUUAUUAAGUUUAAUCAACAU---ACAUUUCAAUAGUCUCUGGGCAACCAU
...(((((.(((((((...........-((((((((..(...-............)..))).))))).---......))))))).)))))........ ( -18.93)
>DroSim_CAF1 9561 93 + 1
UCACCAGAUGCUAUUGUAACUAUCAAU-UGUUGUUAUCCGCA-UCCUUUUAUUAUAUUUAAUCAACAU---ACACUUCAAUAGUCUCUGGGCAACCAU
...(((((.(((((((...........-((((((((......-...............))).))))).---......))))))).)))))........ ( -17.27)
>DroEre_CAF1 9594 93 + 1
UCGCCAGAUGCUAUUGUAACUAUUAAU-UGAUGUUAUCCGCA-UUCGCUCACUAUAUUUUAUGAACCU---GCAUUUGAAUAGUCCCUGGGCAACCAU
....(((((((....(((((.(((...-.))))))))..((.-...))....................---))))))).........(((....))). ( -15.50)
>DroYak_CAF1 9739 95 + 1
UCGCCAGAUGCUAUUGUAACUAUUAAC-U-AUCAUAACCGCA-UCAUCUUACCAUAUUUCAUUAAUAUAUAACAUUUGAAUAGUCCCUGGGCAACCAU
..(((.(((((..((((..........-.-...))))..)))-))........(((((.....))))).....................)))...... ( -11.74)
>consensus
UCGCCAGAUGCUAUUGUAACUAUUAAU_UGUUGUUAUCCGCA_UCCUCUUACUAUAUUUAAUCAACAU___ACAUUUCAAUAGUCUCUGGGCAACCAU
...((((..(((((((.............................................................)))))))..))))........ ( -6.71 =  -7.18 +   0.47)

alignment

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secondary structure

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dotplot

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Window 8

Location 12,995,150 – 12,995,249
Length 99
Sequences 6
Columns 103
Reading direction forward
Mean pairwise identity 78.94
Mean single sequence MFE -22.00
Consensus MFE -14.04
Energy contribution -13.52
Covariance contribution -0.53
Combinations/Pair 1.27
Mean z-score -1.36
Structure conservation index 0.64
SVM decision value 0.07
SVM RNA-class probability 0.569841
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12995150 99 + 20766785
UUCCGCA-UUCUCUUACUAUAUUUCAUCAAUAU---ACCUUUCAAUAGUCUCUGGGCAACCAUGAGUUUGAUCAGAAUGUUGAGGGUUUGGUGCCCUUCCUAA
.((.(((-((((.....((((((.....)))))---)....((((....((((((....))).))).))))..))))))).))((((.....))))....... ( -24.80)
>DroVir_CAF1 18214 97 + 1
-UCGUAAAUA-UAUUCCCAUAAUAACUACUU-U---GCUUUUUUGCAGUCACUUGGAAACCACGAGUUUGAUAAGAACGUUAAGGGUCUGAUACCAUUCCUCA
-.......((-(...(((.((((........-(---((......)))((((((((.......)))))..)))......)))).)))....))).......... ( -13.20)
>DroSec_CAF1 10518 99 + 1
AUCCGCA-UCCUUUUAUUAAGUUUAAUCAACAU---ACAUUUCAAUAGUCUCUGGGCAACCAUGAGUUUGACCAGAAUGUUGAGGGUUUGGUGCCCUUCCUCA
.......-..................(((((((---.(...((((....((((((....))).))).))))...).)))))))((((.....))))....... ( -23.60)
>DroSim_CAF1 9595 99 + 1
AUCCGCA-UCCUUUUAUUAUAUUUAAUCAACAU---ACACUUCAAUAGUCUCUGGGCAACCAUGAGUUUGACCAGAAUGUUGAGGGUUUGGUGCCCUUCCUCA
.......-..................(((((((---.(...((((....((((((....))).))).))))...).)))))))((((.....))))....... ( -23.60)
>DroEre_CAF1 9628 99 + 1
AUCCGCA-UUCGCUCACUAUAUUUUAUGAACCU---GCAUUUGAAUAGUCCCUGGGCAACCAUGAGUUCGACCAGAAUGUUGAGGGUUUGGUGCCCUUCCUCA
.((.(((-((((((((((((.((..(((.....---.)))..)))))))...(((....))).)))).......)))))).))((((.....))))....... ( -23.51)
>DroYak_CAF1 9772 102 + 1
AACCGCA-UCAUCUUACCAUAUUUCAUUAAUAUAUAACAUUUGAAUAGUCCCUGGGCAACCAUGAGUUCGACCAGAAUGUUGAGGGUUUGGUGCCCUUCCUCA
....(((-(((....((((((((.....))))).((((((((.....(..(((((....))).).)..).....))))))))..))).))))))......... ( -23.30)
>consensus
AUCCGCA_UCCUCUUACUAUAUUUAAUCAACAU___ACAUUUCAAUAGUCUCUGGGCAACCAUGAGUUUGACCAGAAUGUUGAGGGUUUGGUGCCCUUCCUCA
.....................................................(((((.(((.(..((((((......))))))..).))))))))....... (-14.04 = -13.52 +  -0.53)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:07:47 2006