Locus 7820

Sequence ID 3L_DroMel_CAF1
Location 20,914,265 – 20,914,385
Length 120
Max. P 0.995678
window12728 window12729 window12730 window12731

overview

Window 8

Location 20,914,265 – 20,914,370
Length 105
Sequences 5
Columns 110
Reading direction forward
Mean pairwise identity 78.50
Mean single sequence MFE -22.78
Consensus MFE -10.08
Energy contribution -11.16
Covariance contribution 1.08
Combinations/Pair 1.08
Mean z-score -2.55
Structure conservation index 0.44
SVM decision value 1.66
SVM RNA-class probability 0.970668
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20914265 105 + 23771897
UUUAAUCAAAUUCACAUUAACAACAGCAAAGCCUGCAACUGCAACAGC---AA-GACUGCAACACCAACAGCGGCAAAUGCAGCAAUUU-UAGCGCAGCUGCAGCAAUGA
..............................((.((((.((((....((---(.-...)))..........((.((....)).)).....-....)))).))))))..... ( -21.90)
>DroSec_CAF1 170411 105 + 1
UUUAAUCAAAUUCACAUUAACAACAGCAAAGCCUGCAACUGCAACAGC---AA-GACUGCAACACCAACUGCGGCAAAUGCAGCAAUUU-UAGCGCAGCUGCAGCAAUGA
..............................((.((((.((((....((---(.-..(((((........)))))....))).((.....-..)))))).))))))..... ( -23.90)
>DroSim_CAF1 167378 105 + 1
UUUAAUCAAAUUCACAUUAACAACAGCACAGCCUGCAACUGCAACAGC---GA-GACUGCAACACCAACUGCGGCGAAUGCAGCAAUUU-UAGCGCAGCUGCAGCAAUGA
............................((..(((((.((((....((---(.-(.(((((........))))))...))).((.....-..)))))).)))))...)). ( -24.20)
>DroWil_CAF1 215663 88 + 1
UUUAAUCAAAUUCACAUUAACAACAGCA------GCAGCAGCCGCAGC---AA--------AAGCCAACU---GCAACUGCAACAAUUUCCAAUGCAGCUGCAAUAAC--
.........................(((------((.((((..((...---..--------..))...))---))...((((...........)))))))))......-- ( -18.10)
>DroYak_CAF1 173183 109 + 1
UUUAAUCAAAUUCACAUUAACAAUAGCAAAGGCUGCAGCCUGAACAACUGCAACACCAACUGCAGCAAAGACAGCAAAGGCAGCAAUUU-UAGCGCAGCUGCAGCAAAGA
...............................(((((((((((.....(((((........)))))......))).....((.((.....-..)))).))))))))..... ( -25.80)
>consensus
UUUAAUCAAAUUCACAUUAACAACAGCAAAGCCUGCAACUGCAACAGC___AA_GACUGCAACACCAACUGCGGCAAAUGCAGCAAUUU_UAGCGCAGCUGCAGCAAUGA
................................(((((.((((...............................((....)).((........)))))).)))))...... (-10.08 = -11.16 +   1.08)

alignment

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secondary structure

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dotplot

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Window 9

Location 20,914,265 – 20,914,370
Length 105
Sequences 5
Columns 110
Reading direction reverse
Mean pairwise identity 78.50
Mean single sequence MFE -31.40
Consensus MFE -17.84
Energy contribution -20.40
Covariance contribution 2.56
Combinations/Pair 1.28
Mean z-score -2.25
Structure conservation index 0.57
SVM decision value 1.30
SVM RNA-class probability 0.939868
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20914265 105 - 23771897
UCAUUGCUGCAGCUGCGCUA-AAAUUGCUGCAUUUGCCGCUGUUGGUGUUGCAGUC-UU---GCUGUUGCAGUUGCAGGCUUUGCUGUUGUUAAUGUGAAUUUGAUUAAA
(((...(((((((((((.((-..(..((((((..(((((....))))).)))))).-.)---..)).)))))))))))..((..(..........)..))..)))..... ( -31.40)
>DroSec_CAF1 170411 105 - 1
UCAUUGCUGCAGCUGCGCUA-AAAUUGCUGCAUUUGCCGCAGUUGGUGUUGCAGUC-UU---GCUGUUGCAGUUGCAGGCUUUGCUGUUGUUAAUGUGAAUUUGAUUAAA
(((...((((((((((((..-.((((((.((....)).))))))...)).((((..-..---.)))).))))))))))..((..(..........)..))..)))..... ( -32.00)
>DroSim_CAF1 167378 105 - 1
UCAUUGCUGCAGCUGCGCUA-AAAUUGCUGCAUUCGCCGCAGUUGGUGUUGCAGUC-UC---GCUGUUGCAGUUGCAGGCUGUGCUGUUGUUAAUGUGAAUUUGAUUAAA
((((.((.(((((.((((((-..(((((.((....)).))))))))))).((((((-((---((((...))).)).)))))))))))).))....))))........... ( -33.30)
>DroWil_CAF1 215663 88 - 1
--GUUAUUGCAGCUGCAUUGGAAAUUGUUGCAGUUGC---AGUUGGCUU--------UU---GCUGCGGCUGCUGC------UGCUGUUGUUAAUGUGAAUUUGAUUAAA
--.....((((((((((...........)))))))))---)((((((..--------..---((.(((((....))------))).)).))))))............... ( -28.40)
>DroYak_CAF1 173183 109 - 1
UCUUUGCUGCAGCUGCGCUA-AAAUUGCUGCCUUUGCUGUCUUUGCUGCAGUUGGUGUUGCAGUUGUUCAGGCUGCAGCCUUUGCUAUUGUUAAUGUGAAUUUGAUUAAA
.....(((((((((......-.((((((.(((...(((((.......))))).)))...)))))).....))))))))).((..(..........)..)).......... ( -31.90)
>consensus
UCAUUGCUGCAGCUGCGCUA_AAAUUGCUGCAUUUGCCGCAGUUGGUGUUGCAGUC_UU___GCUGUUGCAGUUGCAGGCUUUGCUGUUGUUAAUGUGAAUUUGAUUAAA
......((((((((((((....((((((.((....)).))))))...)).(((((.......))))).))))))))))................................ (-17.84 = -20.40 +   2.56)

alignment

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secondary structure

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dotplot

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Window 0

Location 20,914,295 – 20,914,385
Length 90
Sequences 4
Columns 91
Reading direction forward
Mean pairwise identity 79.56
Mean single sequence MFE -24.08
Consensus MFE -14.32
Energy contribution -15.70
Covariance contribution 1.38
Combinations/Pair 1.11
Mean z-score -2.48
Structure conservation index 0.60
SVM decision value 1.47
SVM RNA-class probability 0.956911
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20914295 90 + 23771897
GCCUGCAACUGCAACAGCAAGACUGCAACACCAACAGCGGCAAAUGCAGCAAUUU-UAGCGCAGCUGCAGCAAUGAAGGCAAGUCACAACU
((((.((..(((....(((....)))..........(((((...(((.((.....-..)))))))))).))).)).))))........... ( -24.50)
>DroSec_CAF1 170441 90 + 1
GCCUGCAACUGCAACAGCAAGACUGCAACACCAACUGCGGCAAAUGCAGCAAUUU-UAGCGCAGCUGCAGCAAUGAAGGCAAGUCACAACU
((((.((..(((..((((..(.(((((........))))))...(((.((.....-..)))))))))..))).)).))))........... ( -26.20)
>DroSim_CAF1 167408 90 + 1
GCCUGCAACUGCAACAGCGAGACUGCAACACCAACUGCGGCGAAUGCAGCAAUUU-UAGCGCAGCUGCAGCAAUGAAGGCAAGUCACAACU
((((.((..(((..((((..(.(((((........))))))...(((.((.....-..)))))))))..))).)).))))........... ( -26.20)
>DroWil_CAF1 215691 75 + 1
----GCAGCAGCCGCAGCAA-------AAGCCAACU---GCAACUGCAACAAUUUCCAAUGCAGCUGCAAUAAC--UGGCAACUCGCAACU
----((.(((((.(((((..-------..))....(---((....)))...........))).)))))......--.(....)..)).... ( -19.40)
>consensus
GCCUGCAACUGCAACAGCAAGACUGCAACACCAACUGCGGCAAAUGCAGCAAUUU_UAGCGCAGCUGCAGCAAUGAAGGCAAGUCACAACU
..(((((.((((....(((...(((((........)))))....))).((........)))))).)))))..................... (-14.32 = -15.70 +   1.38)

alignment

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secondary structure

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dotplot

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Window 1

Location 20,914,295 – 20,914,385
Length 90
Sequences 4
Columns 91
Reading direction reverse
Mean pairwise identity 79.56
Mean single sequence MFE -31.90
Consensus MFE -21.50
Energy contribution -22.75
Covariance contribution 1.25
Combinations/Pair 1.14
Mean z-score -2.75
Structure conservation index 0.67
SVM decision value 2.60
SVM RNA-class probability 0.995678
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20914295 90 - 23771897
AGUUGUGACUUGCCUUCAUUGCUGCAGCUGCGCUA-AAAUUGCUGCAUUUGCCGCUGUUGGUGUUGCAGUCUUGCUGUUGCAGUUGCAGGC
.....................(((((((((((.((-..(..((((((..(((((....))))).))))))..)..)).))))))))))).. ( -30.60)
>DroSec_CAF1 170441 90 - 1
AGUUGUGACUUGCCUUCAUUGCUGCAGCUGCGCUA-AAAUUGCUGCAUUUGCCGCAGUUGGUGUUGCAGUCUUGCUGUUGCAGUUGCAGGC
.....................((((((((((((..-.((((((.((....)).))))))...)).((((.....)))).)))))))))).. ( -31.20)
>DroSim_CAF1 167408 90 - 1
AGUUGUGACUUGCCUUCAUUGCUGCAGCUGCGCUA-AAAUUGCUGCAUUCGCCGCAGUUGGUGUUGCAGUCUCGCUGUUGCAGUUGCAGGC
...........((((.((..((((((((.(((...-.....((((((..(((((....))))).))))))..))).)))))))))).)))) ( -33.90)
>DroWil_CAF1 215691 75 - 1
AGUUGCGAGUUGCCA--GUUAUUGCAGCUGCAUUGGAAAUUGUUGCAGUUGC---AGUUGGCUU-------UUGCUGCGGCUGCUGC----
((((((.(((.((((--...((((((((((((...........)))))))))---)))))))..-------..))))))))).....---- ( -31.90)
>consensus
AGUUGUGACUUGCCUUCAUUGCUGCAGCUGCGCUA_AAAUUGCUGCAUUUGCCGCAGUUGGUGUUGCAGUCUUGCUGUUGCAGUUGCAGGC
.....................((((((((((......((((((.((....)).))))))((((.........))))...)))))))))).. (-21.50 = -22.75 +   1.25)

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 12:57:50 2006