Locus 1035

Sequence ID 3R_DroMel_CAF1
Location 3,229,433 – 3,229,555
Length 122
Max. P 0.979558
window1674 window1675 window1676

overview

Window 4

Location 3,229,433 – 3,229,531
Length 98
Sequences 5
Columns 100
Reading direction forward
Mean pairwise identity 97.77
Mean single sequence MFE -21.26
Consensus MFE -20.50
Energy contribution -20.50
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.13
Structure conservation index 0.96
SVM decision value 0.06
SVM RNA-class probability 0.564848
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3229433 98 + 27905053
--GGACUUCUCCCGCCUGCACUAUAUAGUUGUUGUCUGGCAGCUUUUCACAAAUCGAUUAAAUUUAAUUUGUUUUCCUUGCCGGCUUUCCGCUGCCAGUC
--(((....))).((..(((((....)).))).))((((((((.....((((((..(......)..))))))..........((....)))))))))).. ( -21.00)
>DroSec_CAF1 54006 98 + 1
--GGACUUCUCCCGCCUGCACUAUAUAGUUGUUGUCUGGCAGCUUUUCACAAAUCGAUUAAAUUUAAUUUGUUUUCCUUGCCGGCUUUCCGCUGCCAGUC
--(((....))).((..(((((....)).))).))((((((((.....((((((..(......)..))))))..........((....)))))))))).. ( -21.00)
>DroSim_CAF1 55426 98 + 1
--GGACUUCUCCCGCCUGCACUAUAUAGUUGUUGUCUGGCAGCUUUUCACAAAUCGAUUAAAUUUAAUUUGUUUUCCUUGCCGGCUUUCCGCUGCCAGUC
--(((....))).((..(((((....)).))).))((((((((.....((((((..(......)..))))))..........((....)))))))))).. ( -21.00)
>DroEre_CAF1 48409 100 + 1
CCGGACUUCGCCCGCCUGCACUACAUAGUUGUUGUCUGGCAGCUUUUCACAAAUCGAUUAAAUUUAAUUUGUUUUCCUUGCCGGCUUUCCGCUGCCAGUC
.(((.......))).....((.(((....))).))((((((((.....((((((..(......)..))))))..........((....)))))))))).. ( -22.40)
>DroYak_CAF1 39875 98 + 1
--GGACUUCGCCUGCCUGCACUAUAUAGUUGUUGUCUGGCAGCUUUUCACAAAUCGAUUAAAUUUAAUUUGUUUUCCUUGCCGGCUUUCCGCUGCCAGUC
--.((((.....((....))......)))).....((((((((.....((((((..(......)..))))))..........((....)))))))))).. ( -20.90)
>consensus
__GGACUUCUCCCGCCUGCACUAUAUAGUUGUUGUCUGGCAGCUUUUCACAAAUCGAUUAAAUUUAAUUUGUUUUCCUUGCCGGCUUUCCGCUGCCAGUC
..((......)).((..(((((....)).))).))((((((((.....((((((..(......)..))))))..........((....)))))))))).. (-20.50 = -20.50 +   0.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 3,229,433 – 3,229,531
Length 98
Sequences 5
Columns 100
Reading direction reverse
Mean pairwise identity 97.77
Mean single sequence MFE -23.98
Consensus MFE -22.86
Energy contribution -22.86
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.46
Structure conservation index 0.95
SVM decision value 1.17
SVM RNA-class probability 0.925766
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3229433 98 - 27905053
GACUGGCAGCGGAAAGCCGGCAAGGAAAACAAAUUAAAUUUAAUCGAUUUGUGAAAAGCUGCCAGACAACAACUAUAUAGUGCAGGCGGGAGAAGUCC--
..((((((((......((.....))...((((((..(......)..)))))).....))))))))...................(((.......))).-- ( -23.00)
>DroSec_CAF1 54006 98 - 1
GACUGGCAGCGGAAAGCCGGCAAGGAAAACAAAUUAAAUUUAAUCGAUUUGUGAAAAGCUGCCAGACAACAACUAUAUAGUGCAGGCGGGAGAAGUCC--
..((((((((......((.....))...((((((..(......)..)))))).....))))))))...................(((.......))).-- ( -23.00)
>DroSim_CAF1 55426 98 - 1
GACUGGCAGCGGAAAGCCGGCAAGGAAAACAAAUUAAAUUUAAUCGAUUUGUGAAAAGCUGCCAGACAACAACUAUAUAGUGCAGGCGGGAGAAGUCC--
..((((((((......((.....))...((((((..(......)..)))))).....))))))))...................(((.......))).-- ( -23.00)
>DroEre_CAF1 48409 100 - 1
GACUGGCAGCGGAAAGCCGGCAAGGAAAACAAAUUAAAUUUAAUCGAUUUGUGAAAAGCUGCCAGACAACAACUAUGUAGUGCAGGCGGGCGAAGUCCGG
..((((((((......((.....))...((((((..(......)..)))))).....))))))))((.(((....))).)).....(((((...))))). ( -27.90)
>DroYak_CAF1 39875 98 - 1
GACUGGCAGCGGAAAGCCGGCAAGGAAAACAAAUUAAAUUUAAUCGAUUUGUGAAAAGCUGCCAGACAACAACUAUAUAGUGCAGGCAGGCGAAGUCC--
..((((((((......((.....))...((((((..(......)..)))))).....))))))))...............(((......)))......-- ( -23.00)
>consensus
GACUGGCAGCGGAAAGCCGGCAAGGAAAACAAAUUAAAUUUAAUCGAUUUGUGAAAAGCUGCCAGACAACAACUAUAUAGUGCAGGCGGGAGAAGUCC__
..((((((((......((.....))...((((((..(......)..)))))).....))))))))...................(((.......)))... (-22.86 = -22.86 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 6

Location 3,229,460 – 3,229,555
Length 95
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 73.81
Mean single sequence MFE -23.10
Consensus MFE -11.37
Energy contribution -12.03
Covariance contribution 0.67
Combinations/Pair 1.06
Mean z-score -2.36
Structure conservation index 0.49
SVM decision value 1.84
SVM RNA-class probability 0.979558
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3229460 95 + 27905053
-------UGUUGUCUGGCAGCUUUUCACAAAUCGAUUAAAUUUAAUUUGUUUUCCUUGCCGGCUUUCC--GCUGCCAGUCAUUCUUGUCCCAGCGUUUC---------UUUC-------U
-------...((.((((((((.....((((((..(......)..))))))..........((....))--)))))))).))..................---------....-------. ( -22.00)
>DroVir_CAF1 61718 111 + 1
CGGUCUGCGCUGGCUGGCAGCUUUUCACAAAUCGAUUAAAUUUAAUUUGUUUUCUUUGCCGGCUUUUCGUUCUGCCCAUCAUCGUCAUGGCGAUUUUUCAACC--UAUUUUC-------U
.(((..(((..(((((((((......((((((..(......)..)))))).....)))))))))...)))...)))....(((((....))))).........--.......-------. ( -28.20)
>DroGri_CAF1 52567 118 + 1
CCGUCUGUGCUGGCUGGCAGCUUUUCACAAAUCGAUUAAAUUUAAUUUGUUUUCUUUGCCGUCUUGUCGUGCUGCCCGUCAUCAACAUCGCGAUUUUUCUACU--UAUUUUUCUGGUGCU
.(((.(((..((((.((((((.....((((((..(......)..)))))).........((......)).)))))).))))...)))..)))...........--............... ( -23.90)
>DroSim_CAF1 55453 95 + 1
-------UGUUGUCUGGCAGCUUUUCACAAAUCGAUUAAAUUUAAUUUGUUUUCCUUGCCGGCUUUCC--GCUGCCAGUCAUUCUCGUCCCAGCCUUUC---------UUUC-------U
-------...((.((((((((.....((((((..(......)..))))))..........((....))--)))))))).))..................---------....-------. ( -22.00)
>DroYak_CAF1 39902 95 + 1
-------UGUUGUCUGGCAGCUUUUCACAAAUCGAUUAAAUUUAAUUUGUUUUCCUUGCCGGCUUUCC--GCUGCCAGUCAUUCCCGUCCUAGCCCUUC---------AUUC-------C
-------...((.((((((((.....((((((..(......)..))))))..........((....))--)))))))).))..................---------....-------. ( -22.00)
>DroMoj_CAF1 68806 104 + 1
CACU---GGCUGGCUGGCAGCUUUUCCCAAAUCGAUUAAAUUUAAUUUGUUUUCUUUACCGGCAUUUCAUGCUGCGUGUCA------UCGCGAUUUUUCCAGCGGUAUUUUC-------U
.(((---(.((((...(((((......(((((..(......)..)))))...........((....))..)))))(((...------.))).......))))))))......-------. ( -20.50)
>consensus
_______UGCUGGCUGGCAGCUUUUCACAAAUCGAUUAAAUUUAAUUUGUUUUCCUUGCCGGCUUUCC__GCUGCCAGUCAUUCUCGUCCCAACUUUUC_________UUUC_______U
..........((.(.((((((.....((((((..(......)..))))))..........((....))..)))))).).))....................................... (-11.37 = -12.03 +   0.67)

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 09:58:55 2006