Locus 20

Sequence ID 2R_DroMel_CAF1
Location 1,151,938 – 1,152,089
Length 151
Max. P 0.999971
window37 window38 window39 window40

overview

Window 7

Location 1,151,938 – 1,152,050
Length 112
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 70.85
Mean single sequence MFE -22.80
Consensus MFE -11.73
Energy contribution -12.40
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -1.98
Structure conservation index 0.51
SVM decision value 0.65
SVM RNA-class probability 0.811520
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1151938 112 + 20766785
UACAUUAGUCCACCGCAACUACAAGUACACCGCAUAC----ACUCACAGUAUUUCGUAGACUCGCGUCACAAAGCAUCAA----AAAAUGAUGCGGUGUUUGUUUACUCGUUUCCUUUGC
..............((((..((.((((....(((.((----(((...........((.(((....)))))...((((((.----....))))))))))).))).)))).)).....)))) ( -21.90)
>DroSec_CAF1 2345 94 + 1
-----AAGUACACCGC--------AUAC-------------ACUCACAGUAUUUUGUAGACUUGCGUCACAAAGCACCGCAUCAUUUUUGAUGCGGUGUUUAUUCGCUCUUUUCAUUUGU
-----((((..((...--------((((-------------.......))))...))..))))(((.....(((((((((((((....)))))))))))))...)))............. ( -27.70)
>DroSim_CAF1 2992 107 + 1
-----AAGUACACCGC--------GUACACCGCAUACACUCACUCACAGUAUUUUGUAGACUUGCGUCACAAAGCACCACAUCAAAAAUGAAUCGGUGUUUAUUCGCUCUUUUCAUUUGU
-----.........((--------(.((((((................((.((((((.(((....))))))))).))....(((....)))..)))))).....)))............. ( -18.80)
>consensus
_____AAGUACACCGC________GUACACCGCAUAC____ACUCACAGUAUUUUGUAGACUUGCGUCACAAAGCACCACAUCAAAAAUGAUGCGGUGUUUAUUCGCUCUUUUCAUUUGU
..........((((((.........................((.....)).((((((.(((....)))))))))..................))))))...................... (-11.73 = -12.40 +   0.67)

alignment

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secondary structure

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dotplot

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Window 8

Location 1,151,938 – 1,152,050
Length 112
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 70.85
Mean single sequence MFE -32.47
Consensus MFE -18.72
Energy contribution -20.50
Covariance contribution 1.78
Combinations/Pair 1.05
Mean z-score -3.12
Structure conservation index 0.58
SVM decision value 5.05
SVM RNA-class probability 0.999971
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1151938 112 - 20766785
GCAAAGGAAACGAGUAAACAAACACCGCAUCAUUUU----UUGAUGCUUUGUGACGCGAGUCUACGAAAUACUGUGAGU----GUAUGCGGUGUACUUGUAGUUGCGGUGGACUAAUGUA
((((.....((((((......((((((((((((((.----..(.((.((((((((....))).))))).)))...))))----).)))))))))))))))..)))).............. ( -34.90)
>DroSec_CAF1 2345 94 - 1
ACAAAUGAAAAGAGCGAAUAAACACCGCAUCAAAAAUGAUGCGGUGCUUUGUGACGCAAGUCUACAAAAUACUGUGAGU-------------GUAU--------GCGGUGUACUU-----
......................((((((((((....)))))))))).((((((((....))).)))))(((((((....-------------....--------)))))))....----- ( -31.90)
>DroSim_CAF1 2992 107 - 1
ACAAAUGAAAAGAGCGAAUAAACACCGAUUCAUUUUUGAUGUGGUGCUUUGUGACGCAAGUCUACAAAAUACUGUGAGUGAGUGUAUGCGGUGUAC--------GCGGUGUACUU-----
.....................(((((.((((((((.....(..(((.((((((((....))).))))).)))..)))))))))....(((.....)--------)))))))....----- ( -30.60)
>consensus
ACAAAUGAAAAGAGCGAAUAAACACCGCAUCAUUUUUGAUGUGGUGCUUUGUGACGCAAGUCUACAAAAUACUGUGAGU____GUAUGCGGUGUAC________GCGGUGUACUU_____
......................((((((...................((((((((....))).)))))(((((((............)))))))..........)))))).......... (-18.72 = -20.50 +   1.78)

alignment

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secondary structure

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dotplot

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Window 9

Location 1,151,975 – 1,152,089
Length 114
Sequences 3
Columns 119
Reading direction forward
Mean pairwise identity 79.66
Mean single sequence MFE -31.56
Consensus MFE -18.26
Energy contribution -19.60
Covariance contribution 1.34
Combinations/Pair 1.10
Mean z-score -2.82
Structure conservation index 0.58
SVM decision value 1.40
SVM RNA-class probability 0.950434
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1151975 114 + 20766785
-ACUCACAGUAUUUCGUAGACUCGCGUCACAAAGCAUCAA----AAAAUGAUGCGGUGUUUGUUUACUCGUUUCCUUUGCGCACUCCUCCUAUGCGGUGCCAAAUAUGUGCAGGUACUU
-.((((((.......((((((......(((...((((((.----....)))))).)))...))))))........((((.(((((.(......).)))))))))..)))).))...... ( -30.00)
>DroSec_CAF1 2360 111 + 1
-ACUCACAGUAUUUUGUAGACUUGCGUCACAAAGCACCGCAUCAUUUUUGAUGCGGUGUUUAUUCGCUCUUUUCAUUUGUGCACUCCUUCUAUGCGGUGCGAUAUAUGAGCA-------
-.............(((.(((....))))))(((((((((((((....)))))))))))))....((((..........((((((.(......).))))))......)))).------- ( -37.29)
>DroSim_CAF1 3019 112 + 1
CACUCACAGUAUUUUGUAGACUUGCGUCACAAAGCACCACAUCAAAAAUGAAUCGGUGUUUAUUCGCUCUUUUCAUUUGUGCACUUCCUCUAUGCGGUGCUAUAUAUGAGCA-------
..((((.......((((.(((....)))))))((((((.......(((((((..((((......))))...)))))))..(((.........))))))))).....))))..------- ( -27.40)
>consensus
_ACUCACAGUAUUUUGUAGACUUGCGUCACAAAGCACCACAUCAAAAAUGAUGCGGUGUUUAUUCGCUCUUUUCAUUUGUGCACUCCUUCUAUGCGGUGCCAUAUAUGAGCA_______
..((((......(((((.(((....))))))))(((((.......((((((...((((......))))....))))))..(((.........))))))))......))))......... (-18.26 = -19.60 +   1.34)

alignment

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secondary structure

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dotplot

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Window 0

Location 1,151,975 – 1,152,089
Length 114
Sequences 3
Columns 119
Reading direction reverse
Mean pairwise identity 79.66
Mean single sequence MFE -35.07
Consensus MFE -24.71
Energy contribution -25.60
Covariance contribution 0.89
Combinations/Pair 1.07
Mean z-score -3.39
Structure conservation index 0.70
SVM decision value 3.25
SVM RNA-class probability 0.998843
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1151975 114 - 20766785
AAGUACCUGCACAUAUUUGGCACCGCAUAGGAGGAGUGCGCAAAGGAAACGAGUAAACAAACACCGCAUCAUUUU----UUGAUGCUUUGUGACGCGAGUCUACGAAAUACUGUGAGU-
......((.(((...((((((((..(......)..)))).))))(....).((((..........((((((....----.))))))((((((((....))).))))).))))))))).- ( -29.70)
>DroSec_CAF1 2360 111 - 1
-------UGCUCAUAUAUCGCACCGCAUAGAAGGAGUGCACAAAUGAAAAGAGCGAAUAAACACCGCAUCAAAAAUGAUGCGGUGCUUUGUGACGCAAGUCUACAAAAUACUGUGAGU-
-------.(((((((..((((...((((.......)))).....(....)..)))).....((((((((((....)))))))))).((((((((....))).)))))....)))))))- ( -39.60)
>DroSim_CAF1 3019 112 - 1
-------UGCUCAUAUAUAGCACCGCAUAGAGGAAGUGCACAAAUGAAAAGAGCGAAUAAACACCGAUUCAUUUUUGAUGUGGUGCUUUGUGACGCAAGUCUACAAAAUACUGUGAGUG
-------.((((((((((.(((((((((...((((((((.............))((((........)))))))))).)))))))))((((((((....))).)))))))).))))))). ( -35.92)
>consensus
_______UGCUCAUAUAUAGCACCGCAUAGAAGGAGUGCACAAAUGAAAAGAGCGAAUAAACACCGCAUCAUUUUUGAUGUGGUGCUUUGUGACGCAAGUCUACAAAAUACUGUGAGU_
........(((((((....(((((((((.......))))...........(((((.........))).))...........)))))((((((((....))).)))))....))))))). (-24.71 = -25.60 +   0.89)

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 09:23:41 2006