Locus 9331

Sequence ID 3R_DroMel_CAF1
Location 24,796,552 – 24,796,684
Length 132
Max. P 0.985194
window14930 window14931 window14932

overview

Window 0

Location 24,796,552 – 24,796,653
Length 101
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 76.43
Mean single sequence MFE -28.45
Consensus MFE -12.40
Energy contribution -12.57
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -2.00
Structure conservation index 0.44
SVM decision value 0.03
SVM RNA-class probability 0.549960
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24796552 101 - 27905053
GGCAAACGCGAUUGCAGCAAAUCAGAAAAUACUCGC--ACAAGUGCGAAUGUGAAUAUUGAUGCCACGGC-----GUA--GGU-------AUGUUUGACUUA---UAAUAUAUGUAUAGA
(((....((.......))..(((((...(((.((((--(....))))).))).....)))))))).....-----(((--.((-------(((((.......---.))))))).)))... ( -23.10)
>DroPse_CAF1 6884 111 - 1
GGCUGACGCGAUUGCAGCAAAUCAGAAAAUACUCGC--ACAAGUGCGAAUGUGAAUAUUGAUGCCAUGGC-----GUAUAAGUAUUAGGAGUGUAUGAGUGUUGCUUGUGUGUCU--UCU
((..((((((...((((((..(((....((((((((--(....))).......((((((.((((....))-----))...))))))..)))))).))).))))))...)))))).--.)) ( -35.80)
>DroWil_CAF1 5861 96 - 1
GGCUG-CGCGAUUGCAGCAAAUCAGAAAAUACUCGCUCACAAGUGCGAAUGUGAAUAUUGAUGGCAAACC-----AAA--AGA-------AUGUUUC---UA---U-AUACAUAU--AUC
.((((-((....))))))..............((((........))))(((((.((((.((.((((....-----...--...-------.))))))---.)---)-)).)))))--... ( -19.10)
>DroYak_CAF1 7736 98 - 1
GGCAAACGCGAUUGCAGCAAAUCAGAAAAUACUCGC--ACAAGUGCGAAUGUGAAUAUUGAUGCCACGGC-----GUA--GGU-------AUGUAUGGCUU----UAAUAUAUAU--UAU
......(((((((......)))).........((((--(....)))))..))).(((((((.((((..((-----((.--...-------)))).)))).)----))))))....--... ( -23.60)
>DroAna_CAF1 5587 104 - 1
GGCAGACGCGAUUGCAGCAAAUCAGAAAAUACUCGC--ACAAGUGCGAAUGUGAAUAUUGAUGCCGUGGCAUCGCAUA--AGU-------CUGUAUGUGCGA---UUAUGUACAU--AAA
.(((((((((((.((.((..(((((...(((.((((--(....))))).))).....)))))...)).)))))))...--.))-------))))((((((..---....))))))--... ( -33.30)
>DroPer_CAF1 7036 111 - 1
GGCUGACGCGAUUGCAGCAAAUCAGAAAAUACUCGC--ACAAGUGCGAAUGUGAAUAUUGAUGCCAUGGC-----GUAUAAGUAUUAGGAGUGUAUGAGUGUUGCUUGUGUGUCU--UCU
((..((((((...((((((..(((....((((((((--(....))).......((((((.((((....))-----))...))))))..)))))).))).))))))...)))))).--.)) ( -35.80)
>consensus
GGCAGACGCGAUUGCAGCAAAUCAGAAAAUACUCGC__ACAAGUGCGAAUGUGAAUAUUGAUGCCAUGGC_____GUA__AGU_______AUGUAUGAGUGA___UUAUAUAUAU__AAU
(((....((.......))..(((((...(((.((((........)))).))).....))))))))....................................................... (-12.40 = -12.57 +   0.17)

alignment

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secondary structure

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Window 1

Location 24,796,582 – 24,796,684
Length 102
Sequences 6
Columns 107
Reading direction forward
Mean pairwise identity 96.14
Mean single sequence MFE -26.27
Consensus MFE -24.35
Energy contribution -24.55
Covariance contribution 0.20
Combinations/Pair 1.04
Mean z-score -1.67
Structure conservation index 0.93
SVM decision value 2.00
SVM RNA-class probability 0.985194
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24796582 102 + 27905053
UAC-----GCCGUGGCAUCAAUAUUCACAUUCGCACUUGUGCGAGUAUUUUCUGAUUUGCUGCAAUCGCGUUUGCCAACAACGAACUUGGCUAACAACAACAGCUGC
...-----((.(..(((...........(((((((....)))))))...........)))..)......(((.(((((........))))).))).......))... ( -25.65)
>DroSec_CAF1 12852 102 + 1
UAC-----GCCGUGGCAUCAAUAUUCACAUUCGCACUUGUGCGAGUAUUUUCUGAUUUGCUGCAAUCGCGUUUGCCAACAACGAACUUGGCUAACAACAACAGCUGC
...-----((.(..(((...........(((((((....)))))))...........)))..)......(((.(((((........))))).))).......))... ( -25.65)
>DroSim_CAF1 12899 102 + 1
UAC-----GCCGUGGCAUCAAUAUUCACAUUCGCACUUGUGCGAGUAUUUUCUGAUUUGCUGCAAUCGCGUUUGCCAACAACGAACUUGGCUAACAACAACAGCUGC
...-----((.(..(((...........(((((((....)))))))...........)))..)......(((.(((((........))))).))).......))... ( -25.65)
>DroEre_CAF1 7528 102 + 1
UAC-----GCCGUGGCAUCAAUAUUCACAUUCGCACUUGUGCGAGUAUUCUCUGAUUUGCUGCAAUCGCGUUUGCCAACAACGAACUUGGCUAACAACAACAGCUGC
...-----((.(..(((...........(((((((....)))))))...........)))..)......(((.(((((........))))).))).......))... ( -25.65)
>DroYak_CAF1 7763 102 + 1
UAC-----GCCGUGGCAUCAAUAUUCACAUUCGCACUUGUGCGAGUAUUUUCUGAUUUGCUGCAAUCGCGUUUGCCAACAACGAACUUGGCUAACAACAACAGCUGC
...-----((.(..(((...........(((((((....)))))))...........)))..)......(((.(((((........))))).))).......))... ( -25.65)
>DroAna_CAF1 5615 107 + 1
UAUGCGAUGCCACGGCAUCAAUAUUCACAUUCGCACUUGUGCGAGUAUUUUCUGAUUUGCUGCAAUCGCGUCUGCCAACAACAAACUUGGCUAACAACAACAGCUUC
...(((((....(((((...........(((((((....)))))))...........)))))..)))))((..(((((........)))))..))............ ( -29.35)
>consensus
UAC_____GCCGUGGCAUCAAUAUUCACAUUCGCACUUGUGCGAGUAUUUUCUGAUUUGCUGCAAUCGCGUUUGCCAACAACGAACUUGGCUAACAACAACAGCUGC
........((.((((((...........(((((((....)))))))...........))))))......(((.(((((........))))).))).......))... (-24.35 = -24.55 +   0.20)

alignment

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secondary structure

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dotplot

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Window 2

Location 24,796,582 – 24,796,684
Length 102
Sequences 6
Columns 107
Reading direction reverse
Mean pairwise identity 96.14
Mean single sequence MFE -30.45
Consensus MFE -28.48
Energy contribution -28.48
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.49
Structure conservation index 0.94
SVM decision value 1.72
SVM RNA-class probability 0.973782
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24796582 102 - 27905053
GCAGCUGUUGUUGUUAGCCAAGUUCGUUGUUGGCAAACGCGAUUGCAGCAAAUCAGAAAAUACUCGCACAAGUGCGAAUGUGAAUAUUGAUGCCACGGC-----GUA
...(((((.(((((..(((((........)))))....))))).)))))..(((((...(((.(((((....))))).))).....)))))((....))-----... ( -29.90)
>DroSec_CAF1 12852 102 - 1
GCAGCUGUUGUUGUUAGCCAAGUUCGUUGUUGGCAAACGCGAUUGCAGCAAAUCAGAAAAUACUCGCACAAGUGCGAAUGUGAAUAUUGAUGCCACGGC-----GUA
...(((((.(((((..(((((........)))))....))))).)))))..(((((...(((.(((((....))))).))).....)))))((....))-----... ( -29.90)
>DroSim_CAF1 12899 102 - 1
GCAGCUGUUGUUGUUAGCCAAGUUCGUUGUUGGCAAACGCGAUUGCAGCAAAUCAGAAAAUACUCGCACAAGUGCGAAUGUGAAUAUUGAUGCCACGGC-----GUA
...(((((.(((((..(((((........)))))....))))).)))))..(((((...(((.(((((....))))).))).....)))))((....))-----... ( -29.90)
>DroEre_CAF1 7528 102 - 1
GCAGCUGUUGUUGUUAGCCAAGUUCGUUGUUGGCAAACGCGAUUGCAGCAAAUCAGAGAAUACUCGCACAAGUGCGAAUGUGAAUAUUGAUGCCACGGC-----GUA
...(((((.(((((..(((((........)))))....))))).)))))..(((((...(((.(((((....))))).))).....)))))((....))-----... ( -29.90)
>DroYak_CAF1 7763 102 - 1
GCAGCUGUUGUUGUUAGCCAAGUUCGUUGUUGGCAAACGCGAUUGCAGCAAAUCAGAAAAUACUCGCACAAGUGCGAAUGUGAAUAUUGAUGCCACGGC-----GUA
...(((((.(((((..(((((........)))))....))))).)))))..(((((...(((.(((((....))))).))).....)))))((....))-----... ( -29.90)
>DroAna_CAF1 5615 107 - 1
GAAGCUGUUGUUGUUAGCCAAGUUUGUUGUUGGCAGACGCGAUUGCAGCAAAUCAGAAAAUACUCGCACAAGUGCGAAUGUGAAUAUUGAUGCCGUGGCAUCGCAUA
...((.(((((.(((.(((((........))))).)))))))).)).((..........(((.(((((....))))).))).......(((((....)))))))... ( -33.20)
>consensus
GCAGCUGUUGUUGUUAGCCAAGUUCGUUGUUGGCAAACGCGAUUGCAGCAAAUCAGAAAAUACUCGCACAAGUGCGAAUGUGAAUAUUGAUGCCACGGC_____GUA
...(((((.(((((..(((((........)))))....))))).)))))..(((((...(((.(((((....))))).))).....)))))((....))........ (-28.48 = -28.48 +  -0.00)

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 13:31:58 2006