Locus 9999

Sequence ID 3R_DroMel_CAF1
Location 26,773,080 – 26,773,235
Length 155
Max. P 0.999846
window15938 window15939 window15940

overview

Window 8

Location 26,773,080 – 26,773,195
Length 115
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 84.10
Mean single sequence MFE -27.70
Consensus MFE -23.27
Energy contribution -22.91
Covariance contribution -0.36
Combinations/Pair 1.12
Mean z-score -2.12
Structure conservation index 0.84
SVM decision value 1.40
SVM RNA-class probability 0.950501
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26773080 115 + 27905053
-----CCUAGUUCUAUUUAUUCCAUAUUUGCAGAGGCAUUGAUAACCGAAUCAGAAAAGCUUUGAGCAAGUGGCCAAAUAUGCAAAGCUUAACUGAUUUGGAAUGCAGCUUAAUCCACAU
-----..........................((..(((((.....(((((((((..(((((((..(((.((......)).))))))))))..))))))))))))))..)).......... ( -26.40)
>DroSec_CAF1 76497 115 + 1
-----CCUAGCUCUUUUUAUUCCAUAUUUGCCGAGGCAUUAAUAACCGAAUCAGAAAAGCUUUGAGAAAUUGGCCAAAUAUGCAAAGCUUAACUGAUUUGGAAUGCAGCUUAAUCCACAU
-----...((((................(((....))).......(((((((((..((((((((....(((.....)))...))))))))..))))))))).....)))).......... ( -27.80)
>DroSim_CAF1 80250 115 + 1
-----CCUAGCUCUUUUUAUUCCAUAUUUGCCGAGGCAUUGAUAACCGAAUCAGAAAAGCUUUGAGAAAUUGGCCAAAUAUGCAAAGCUUAACUGAUUUGGAAUGCAGCUUAAUCCACAU
-----...((((............(((((((....)))..)))).(((((((((..((((((((....(((.....)))...))))))))..))))))))).....)))).......... ( -28.00)
>DroEre_CAF1 78010 120 + 1
CUGUCCCCAACUCCCUUUAUUCCAUAUUAGCCGAGGCAUUGAUAACCAAAUCAGAAAAGCUUUGAGCAUGUGGCCAAAUAUGCAAAGCUUAACUGAUUGGGAAUGCAGUUUAAUCCGCUU
((((.(((................(((((((....))..)))))....((((((..(((((((..((((((......)))))))))))))..)))))))))...))))............ ( -29.30)
>DroYak_CAF1 79564 94 + 1
--------AA------------------UGCCGAGGCAUUGAUAACCGAAUCGGAAAAGCUUUGAGCAAGUGGCCAAAUAUGCAGAGCUUAACUGAUUUGGAAUGCAGUUUAAUCCGCUU
--------((------------------(((....))))).....(((((((((..(((((((..(((.((......)).))))))))))..)))))))))...((.(......).)).. ( -27.00)
>consensus
_____CCUAGCUCUUUUUAUUCCAUAUUUGCCGAGGCAUUGAUAACCGAAUCAGAAAAGCUUUGAGCAAGUGGCCAAAUAUGCAAAGCUUAACUGAUUUGGAAUGCAGCUUAAUCCACAU
.............................((....(((((.....(((((((((..((((((((..................))))))))..)))))))))))))).))........... (-23.27 = -22.91 +  -0.36)

alignment

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secondary structure

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Window 9

Location 26,773,115 – 26,773,235
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.25
Mean single sequence MFE -35.28
Consensus MFE -32.05
Energy contribution -31.29
Covariance contribution -0.76
Combinations/Pair 1.14
Mean z-score -2.63
Structure conservation index 0.91
SVM decision value 4.24
SVM RNA-class probability 0.999846
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26773115 120 + 27905053
GAUAACCGAAUCAGAAAAGCUUUGAGCAAGUGGCCAAAUAUGCAAAGCUUAACUGAUUUGGAAUGCAGCUUAAUCCACAUGAUACGAGCUCGUUGAGCUGAUGUUUCUCGAAUGCAGGAA
.....(((((((((..(((((((..(((.((......)).))))))))))..)))))))))..((((((((.(((.....)))..))))(((..((((....))))..))).)))).... ( -34.90)
>DroSec_CAF1 76532 120 + 1
AAUAACCGAAUCAGAAAAGCUUUGAGAAAUUGGCCAAAUAUGCAAAGCUUAACUGAUUUGGAAUGCAGCUUAAUCCACAUGAUACGGGCUCGUUGAGCUGAUGUUUCUCGAAUGCAGUAA
.....(((((((((..((((((((....(((.....)))...))))))))..)))))))))..((((((((.(((.....)))..))))(((..((((....))))..))).)))).... ( -33.80)
>DroSim_CAF1 80285 120 + 1
GAUAACCGAAUCAGAAAAGCUUUGAGAAAUUGGCCAAAUAUGCAAAGCUUAACUGAUUUGGAAUGCAGCUUAAUCCACAUGAUACGGGCUCGUUGAGCUGAUGUUCCUCGAAUGCAGGAA
.....(((((((((..((((((((....(((.....)))...))))))))..)))))))))..((((((((.(((.....)))..))))(((..((((....))))..))).)))).... ( -35.50)
>DroEre_CAF1 78050 120 + 1
GAUAACCAAAUCAGAAAAGCUUUGAGCAUGUGGCCAAAUAUGCAAAGCUUAACUGAUUGGGAAUGCAGUUUAAUCCGCUUGAUACGAGCUCGAUGAGCUGAUGUUUCUCGAAUGCAGGAA
.....((.((((((..(((((((..((((((......)))))))))))))..))))))(((((..(((((((.((.(((((...)))))..)))))))))....))))).......)).. ( -37.80)
>DroYak_CAF1 79578 120 + 1
GAUAACCGAAUCGGAAAAGCUUUGAGCAAGUGGCCAAAUAUGCAGAGCUUAACUGAUUUGGAAUGCAGUUUAAUCCGCUUGAUACGAGCUCGAUGAGCUGAUGUUUCCCGAAUGCAGAAA
.....(((((((((..(((((((..(((.((......)).))))))))))..)))))))))..((((.........(((((...)))))(((..((((....))))..))).)))).... ( -34.40)
>consensus
GAUAACCGAAUCAGAAAAGCUUUGAGCAAGUGGCCAAAUAUGCAAAGCUUAACUGAUUUGGAAUGCAGCUUAAUCCACAUGAUACGAGCUCGUUGAGCUGAUGUUUCUCGAAUGCAGGAA
.....(((((((((..((((((((..................))))))))..)))))))))..((((((((.(((.....)))..))))(((..((((....))))..))).)))).... (-32.05 = -31.29 +  -0.76)

alignment

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secondary structure

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dotplot

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Window 0

Location 26,773,115 – 26,773,235
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.25
Mean single sequence MFE -27.68
Consensus MFE -23.29
Energy contribution -23.69
Covariance contribution 0.40
Combinations/Pair 1.06
Mean z-score -1.32
Structure conservation index 0.84
SVM decision value 0.17
SVM RNA-class probability 0.619024
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26773115 120 - 27905053
UUCCUGCAUUCGAGAAACAUCAGCUCAACGAGCUCGUAUCAUGUGGAUUAAGCUGCAUUCCAAAUCAGUUAAGCUUUGCAUAUUUGGCCACUUGCUCAAAGCUUUUCUGAUUCGGUUAUC
.(((.((((.(((((....)).((((...)))))))....)))))))............((.((((((..((((((((.......(((.....)))))))))))..)))))).))..... ( -28.41)
>DroSec_CAF1 76532 120 - 1
UUACUGCAUUCGAGAAACAUCAGCUCAACGAGCCCGUAUCAUGUGGAUUAAGCUGCAUUCCAAAUCAGUUAAGCUUUGCAUAUUUGGCCAAUUUCUCAAAGCUUUUCUGAUUCGGUUAUU
...(..(((..((......)).((((...)))).......)))..).............((.((((((..((((((((.....((....)).....))))))))..)))))).))..... ( -25.40)
>DroSim_CAF1 80285 120 - 1
UUCCUGCAUUCGAGGAACAUCAGCUCAACGAGCCCGUAUCAUGUGGAUUAAGCUGCAUUCCAAAUCAGUUAAGCUUUGCAUAUUUGGCCAAUUUCUCAAAGCUUUUCUGAUUCGGUUAUC
(((((.......))))).....((((...)))).......(((..(......)..))).((.((((((..((((((((.....((....)).....))))))))..)))))).))..... ( -27.70)
>DroEre_CAF1 78050 120 - 1
UUCCUGCAUUCGAGAAACAUCAGCUCAUCGAGCUCGUAUCAAGCGGAUUAAACUGCAUUCCCAAUCAGUUAAGCUUUGCAUAUUUGGCCACAUGCUCAAAGCUUUUCUGAUUUGGUUAUC
.............((.((...(((((...))))).)).))..((((......))))...((.((((((..((((((((.......(((.....)))))))))))..)))))).))..... ( -29.41)
>DroYak_CAF1 79578 120 - 1
UUUCUGCAUUCGGGAAACAUCAGCUCAUCGAGCUCGUAUCAAGCGGAUUAAACUGCAUUCCAAAUCAGUUAAGCUCUGCAUAUUUGGCCACUUGCUCAAAGCUUUUCCGAUUCGGUUAUC
...(((...(((((((.....((((....((((..((.....((((......))))...(((((((((.......)))...))))))..))..))))..)))))))))))..)))..... ( -27.50)
>consensus
UUCCUGCAUUCGAGAAACAUCAGCUCAACGAGCUCGUAUCAUGUGGAUUAAGCUGCAUUCCAAAUCAGUUAAGCUUUGCAUAUUUGGCCACUUGCUCAAAGCUUUUCUGAUUCGGUUAUC
....(((....((......)).((((...))))..)))....((((......))))...((.((((((..((((((((.......(((.....)))))))))))..)))))).))..... (-23.29 = -23.69 +   0.40)

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 13:46:45 2006