Locus 1676

Sequence ID 3R_DroMel_CAF1
Location 4,805,896 – 4,806,050
Length 154
Max. P 0.998551
window2765 window2766 window2767

overview

Window 5

Location 4,805,896 – 4,806,010
Length 114
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 75.72
Mean single sequence MFE -18.35
Consensus MFE -13.60
Energy contribution -14.00
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.63
Structure conservation index 0.74
SVM decision value 1.20
SVM RNA-class probability 0.929217
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4805896 114 + 27905053
GGACAAACAAUUUU-UUUUCCCGCUUCUUUAAAAUUGAGUAGCUA----UGUACAGAAAUAAAACAAAUUAAACUGAUCUUGACUUCCAGAGAUCAGGAAGUCAUCAGAAAGUUCCAUC
((((..........-.......(((.(((.......))).)))..----........................((((...((((((((........))))))))))))...)))).... ( -22.60)
>DroSec_CAF1 41213 94 + 1
GGACAAACAAUUUUCUCUUUCCGCUUAUUUAAA-------------------------AUAAAACAUAUUAAACUGAUCUUGACAUCCAGAGACCAGGAAGUCAUCAGAAAGUUCCAUC
((((............................(-------------------------(((.....))))...((((...((((.(((........))).))))))))...)))).... ( -12.80)
>DroSim_CAF1 37427 94 + 1
GGACAAUCAAUCUACUCUUUCCGCUUAUUUAAA-------------------------AUAAAACAAAUUAAACUGAGCUUGACAUCCAGAGAUCAGGAAGUCAUCAGAAAGUUCCAUC
(((.............(((((.((((((((((.-------------------------..........))))).))))).((((.(((........))).))))...))))).)))... ( -16.04)
>DroEre_CAF1 42207 112 + 1
-GACAGUAAACUUGAUAUUUCCGCUUAUUU--AAUUAAAUAACUA----UAUAAAGGAAUAAAACAAAUUAAACUGACCUUGACUUCCCCAGAUCAGGAAGUCAUCAGAAAGUUCCAUC
-.......(((((.....((((..((((.(--(.((....)).))----.)))).))))..............((((...((((((((........)))))))))))).)))))..... ( -19.40)
>DroYak_CAF1 43349 119 + 1
AGACAGUAAACUUUAUAUUUCCGCUUAGGUAAAAUUAAAUAACUACAUAUAUUAAGGAAUAAAACAUAUUGAACUGACAUUGACUUCCAGAGAUCAGGAAGUCAUCAGAAAGUUCCAUC
........((((((....((((...((.(((............)))...))....))))..............((((...((((((((........))))))))))))))))))..... ( -20.90)
>consensus
GGACAAUCAAUUUUAUAUUUCCGCUUAUUUAAAAUU_A_UA_CUA____U_U__AG_AAUAAAACAAAUUAAACUGACCUUGACUUCCAGAGAUCAGGAAGUCAUCAGAAAGUUCCAUC
.........................................................................((((...((((((((........))))))))))))........... (-13.60 = -14.00 +   0.40)

alignment

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secondary structure

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dotplot

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Window 6

Location 4,805,935 – 4,806,050
Length 115
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 85.07
Mean single sequence MFE -20.34
Consensus MFE -19.54
Energy contribution -19.78
Covariance contribution 0.24
Combinations/Pair 1.04
Mean z-score -2.55
Structure conservation index 0.96
SVM decision value 3.14
SVM RNA-class probability 0.998551
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4805935 115 + 27905053
AGCUA----UGUACAGAAAUAAAACAAAUUAAACUGAUCUUGACUUCCAGAGAUCAGGAAGUCAUCAGAAAGUUCCAUCGAAAUAUUGAUUAGGAAAGGCUACAGCAAAAUAAAUACAA
((((.----........................((((...((((((((........))))))))))))....(((((((((....)))))..)))).)))).................. ( -23.70)
>DroSec_CAF1 41246 101 + 1
------------------AUAAAACAUAUUAAACUGAUCUUGACAUCCAGAGACCAGGAAGUCAUCAGAAAGUUCCAUCGAAAUAUUGAUUAGGAAAGGCAACAGCAAAAUAAAUACAA
------------------...............((((...((((.(((........))).))))))))....(((((((((....)))))..)))).(....)................ ( -17.10)
>DroSim_CAF1 37460 101 + 1
------------------AUAAAACAAAUUAAACUGAGCUUGACAUCCAGAGAUCAGGAAGUCAUCAGAAAGUUCCAUCGAAAUAUUGAUUAGGAAAGGCAACAGCAAAAUAAAUACAA
------------------...............((((...((((.(((........))).))))))))....(((((((((....)))))..)))).(....)................ ( -17.10)
>DroEre_CAF1 42244 115 + 1
AACUA----UAUAAAGGAAUAAAACAAAUUAAACUGACCUUGACUUCCCCAGAUCAGGAAGUCAUCAGAAAGUUCCAUCAAAAUAUUGAUUAGGAAAGGCUACAGCUAAAUAAGCACAA
.....----........................((((...((((((((........))))))))))))....(((((((((....)))))..))))........(((.....))).... ( -22.10)
>DroYak_CAF1 43389 119 + 1
AACUACAUAUAUUAAGGAAUAAAACAUAUUGAACUGACAUUGACUUCCAGAGAUCAGGAAGUCAUCAGAAAGUUCCAUCGAAAUAUUGAUUAGGAAAGGCUACAGCAAAAUAAAUACAA
..(((..........(((((....(.....)..((((...((((((((........))))))))))))...)))))(((((....)))))))).....((....))............. ( -21.70)
>consensus
A_CUA____U_U__AG_AAUAAAACAAAUUAAACUGACCUUGACUUCCAGAGAUCAGGAAGUCAUCAGAAAGUUCCAUCGAAAUAUUGAUUAGGAAAGGCUACAGCAAAAUAAAUACAA
.................................((((...((((((((........))))))))))))....(((((((((....)))))..))))..((....))............. (-19.54 = -19.78 +   0.24)

alignment

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secondary structure

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dotplot

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Window 7

Location 4,805,935 – 4,806,050
Length 115
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 85.07
Mean single sequence MFE -21.24
Consensus MFE -17.52
Energy contribution -17.60
Covariance contribution 0.08
Combinations/Pair 1.08
Mean z-score -1.57
Structure conservation index 0.82
SVM decision value 0.20
SVM RNA-class probability 0.632402
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4805935 115 - 27905053
UUGUAUUUAUUUUGCUGUAGCCUUUCCUAAUCAAUAUUUCGAUGGAACUUUCUGAUGACUUCCUGAUCUCUGGAAGUCAAGAUCAGUUUAAUUUGUUUUAUUUCUGUACA----UAGCU
.............(((((.....((((..(((........)))))))....((((((((((((........))))))))...)))).......................)----)))). ( -22.80)
>DroSec_CAF1 41246 101 - 1
UUGUAUUUAUUUUGCUGUUGCCUUUCCUAAUCAAUAUUUCGAUGGAACUUUCUGAUGACUUCCUGGUCUCUGGAUGUCAAGAUCAGUUUAAUAUGUUUUAU------------------
.......((((..((((......((((..(((........)))))))...(((..((((.(((........))).))))))).))))..))))........------------------ ( -16.90)
>DroSim_CAF1 37460 101 - 1
UUGUAUUUAUUUUGCUGUUGCCUUUCCUAAUCAAUAUUUCGAUGGAACUUUCUGAUGACUUCCUGAUCUCUGGAUGUCAAGCUCAGUUUAAUUUGUUUUAU------------------
....((..(((..((((..((..((((..(((........)))))))........((((.(((........))).)))).)).))))..)))..)).....------------------ ( -17.50)
>DroEre_CAF1 42244 115 - 1
UUGUGCUUAUUUAGCUGUAGCCUUUCCUAAUCAAUAUUUUGAUGGAACUUUCUGAUGACUUCCUGAUCUGGGGAAGUCAAGGUCAGUUUAAUUUGUUUUAUUCCUUUAUA----UAGUU
....((..(((.(((((..((((((((..(((((....)))))))))........(((((((((......)))))))))))))))))).)))..))..............----..... ( -27.90)
>DroYak_CAF1 43389 119 - 1
UUGUAUUUAUUUUGCUGUAGCCUUUCCUAAUCAAUAUUUCGAUGGAACUUUCUGAUGACUUCCUGAUCUCUGGAAGUCAAUGUCAGUUCAAUAUGUUUUAUUCCUUAAUAUAUGUAGUU
.............((....)).....(((....(((((..((((((((...((((((((((((........))))))))...))))........))))))))....)))))...))).. ( -21.10)
>consensus
UUGUAUUUAUUUUGCUGUAGCCUUUCCUAAUCAAUAUUUCGAUGGAACUUUCUGAUGACUUCCUGAUCUCUGGAAGUCAAGAUCAGUUUAAUUUGUUUUAUU_CU__A_A____UAG_U
....((..(((..((((......((((..(((........)))))))........((((((((........))))))))....))))..)))..))....................... (-17.52 = -17.60 +   0.08)

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 10:16:38 2006