Locus 1259

Sequence ID 2R_DroMel_CAF1
Location 4,914,948 – 4,915,042
Length 94
Max. P 0.659285
window2182 window2183

overview

Window 2

Location 4,914,948 – 4,915,042
Length 94
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 78.41
Mean single sequence MFE -20.53
Consensus MFE -11.16
Energy contribution -11.63
Covariance contribution 0.47
Combinations/Pair 1.09
Mean z-score -1.86
Structure conservation index 0.54
SVM decision value 0.26
SVM RNA-class probability 0.659285
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4914948 94 + 20766785
GCUAACAAGCCACUUGCCGCCG--CGAAUAUUUAUGAAAUUGUCUGACAACCAGUCAAAAUAUCAUAAAUAAACAAACCAACUGGUC-UGGGCGA-----------------UU
(((....))).......((((.--....(((((((((.(((...((((.....)))).))).)))))))))..((.(((....))).-)))))).-----------------.. ( -24.30)
>DroPse_CAF1 1552 109 + 1
GCUAACAAGCCACUUGCCGCAAGAGAAAUGUUUAUGAAAUAGCCUGACAAGCAGUCAAAAUAUCAUAAAUAAACAAAACCACUGGGAAUGGCAGA-----UUCAAUAUUGAAUU
........((((.((.((....).....(((((((((..((...((((.....))))...)))))))))))............).)).)))).((-----((((....)))))) ( -20.30)
>DroEre_CAF1 2234 94 + 1
GCUAACAAGCCACUUGCCGCCG--CGAAUAUUUAUGAAAUUGUCUGACAUCCAGUCAAAAUAUCAUAAAUAAGCAAGCCAACUGCUC-UGGGCUA-----------------UU
.......((((..((((....)--))).(((((((((.(((...((((.....)))).))).)))))))))((((.......)))).-..)))).-----------------.. ( -21.50)
>DroYak_CAF1 4048 94 + 1
GCUAACAAGCCACUUGCCGCCG--CAAAUACUUAUGAAACUGUCUGACAUCCAGUCAAAAUAUCAUAAAUAAACAAACCAACUGCUC-UGGGCAA-----------------UU
(((....(((...((((....)--)))....((((((...((.(((.....))).)).....))))))...............))).-..)))..-----------------.. ( -14.40)
>DroAna_CAF1 1703 98 + 1
GCUAACAAGCCACUUGCCGCCG--CGAAUAUUUAUGGAAUUGUCAGACAUCCAGUCAAAAUAUCAUAAAUAAACAAGCU-AUUGGGC-UGGGAUAGCUGU------------CU
((((.(.((((..((((....)--))).(((((((((.(((....(((.....)))..))).)))))))))........-....)))-)..).))))...------------.. ( -22.40)
>DroPer_CAF1 723 109 + 1
GCUAACAAGCCACUUGCCGCAAGAGAAAUGUUUAUGAAAUAGCCUGACAAGCAGUCAAAAUAUCAUAAAUAAACAAAACCACUGGGAAUGGCAGA-----UUCAAUAUUGAAUU
........((((.((.((....).....(((((((((..((...((((.....))))...)))))))))))............).)).)))).((-----((((....)))))) ( -20.30)
>consensus
GCUAACAAGCCACUUGCCGCCG__CAAAUAUUUAUGAAAUUGUCUGACAACCAGUCAAAAUAUCAUAAAUAAACAAACCAACUGGGC_UGGGAGA_________________UU
((...((((...))))..))........(((((((((.(((...((((.....)))).))).)))))))))........................................... (-11.16 = -11.63 +   0.47)

alignment

Postscript

secondary structure

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dotplot

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Window 3

Location 4,914,948 – 4,915,042
Length 94
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 78.41
Mean single sequence MFE -25.13
Consensus MFE -14.73
Energy contribution -15.12
Covariance contribution 0.39
Combinations/Pair 1.19
Mean z-score -1.64
Structure conservation index 0.59
SVM decision value 0.21
SVM RNA-class probability 0.633963
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4914948 94 - 20766785
AA-----------------UCGCCCA-GACCAGUUGGUUUGUUUAUUUAUGAUAUUUUGACUGGUUGUCAGACAAUUUCAUAAAUAUUCG--CGGCGGCAAGUGGCUUGUUAGC
..-----------------.((((((-((((....))))))..(((((((((...((((((.....)))))).....)))))))))....--.))))(((((...))))).... ( -27.90)
>DroPse_CAF1 1552 109 - 1
AAUUCAAUAUUGAA-----UCUGCCAUUCCCAGUGGUUUUGUUUAUUUAUGAUAUUUUGACUGCUUGUCAGGCUAUUUCAUAAACAUUUCUCUUGCGGCAAGUGGCUUGUUAGC
.(((((....))))-----)..(((((((((((.((...(((((((....((((.((((((.....)))))).))))..)))))))...)).))).))..))))))........ ( -25.40)
>DroEre_CAF1 2234 94 - 1
AA-----------------UAGCCCA-GAGCAGUUGGCUUGCUUAUUUAUGAUAUUUUGACUGGAUGUCAGACAAUUUCAUAAAUAUUCG--CGGCGGCAAGUGGCUUGUUAGC
..-----------------..(((..-((((.....))))((.(((((((((...((((((.....)))))).....)))))))))...)--))))((((((...))))))... ( -25.60)
>DroYak_CAF1 4048 94 - 1
AA-----------------UUGCCCA-GAGCAGUUGGUUUGUUUAUUUAUGAUAUUUUGACUGGAUGUCAGACAGUUUCAUAAGUAUUUG--CGGCGGCAAGUGGCUUGUUAGC
..-----------------..(((((-((((((.....)))).(((((((((.((((((((.....))))))..)).)))))))))))))--.)))((((((...))))))... ( -23.90)
>DroAna_CAF1 1703 98 - 1
AG------------ACAGCUAUCCCA-GCCCAAU-AGCUUGUUUAUUUAUGAUAUUUUGACUGGAUGUCUGACAAUUCCAUAAAUAUUCG--CGGCGGCAAGUGGCUUGUUAGC
.(------------((((((((....-(((....-.(((((..((((((((..(((..(((.....)))....)))..))))))))..))--.))))))..))))).))))... ( -22.60)
>DroPer_CAF1 723 109 - 1
AAUUCAAUAUUGAA-----UCUGCCAUUCCCAGUGGUUUUGUUUAUUUAUGAUAUUUUGACUGCUUGUCAGGCUAUUUCAUAAACAUUUCUCUUGCGGCAAGUGGCUUGUUAGC
.(((((....))))-----)..(((((((((((.((...(((((((....((((.((((((.....)))))).))))..)))))))...)).))).))..))))))........ ( -25.40)
>consensus
AA_________________UCGCCCA_GACCAGUUGGUUUGUUUAUUUAUGAUAUUUUGACUGGAUGUCAGACAAUUUCAUAAAUAUUCG__CGGCGGCAAGUGGCUUGUUAGC
................................((((...((..(((((((((...((((((.....)))))).....)))))))))..))..))))((((((...))))))... (-14.73 = -15.12 +   0.39)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:00:18 2006