Locus 6729

Sequence ID X_DroMel_CAF1
Location 16,751,334 – 16,751,481
Length 147
Max. P 0.876942
window10987 window10988 window10989

overview

Window 7

Location 16,751,334 – 16,751,441
Length 107
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 82.87
Mean single sequence MFE -21.30
Consensus MFE -15.64
Energy contribution -15.70
Covariance contribution 0.06
Combinations/Pair 1.04
Mean z-score -1.75
Structure conservation index 0.73
SVM decision value 0.44
SVM RNA-class probability 0.738730
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16751334 107 - 22224390
AAACGAUCGCAGA-----ACGAUAUCAACAGCAGAUA--------UAGCUGCCAUAAAGCAGCCGCAAAAAAAAAAAGAAUAAAAUUCAGAUAUUAUUAUCAGCAUUGUGUUUCGGUUUU
...(((.(((((.-----...(((((.......))))--------).(((((......))))).((...........((((...)))).((((....)))).)).)))))..)))..... ( -21.50)
>DroSec_CAF1 38518 101 - 1
AAACGAUCGCAGA-----ACGAUAUCAACAGCAGAUA--------UAGCUGCCAUAAAGCAGACGCAAAAAAAAAA------GAACUCAGAUAUUAUUAUCAUCAUUGUGUUUCGGUUUU
....((((((((.-----...(((((.......))))--------)..))))......(.((((((((........------(....).((((....))))....))))))))))))).. ( -18.30)
>DroEre_CAF1 30061 92 - 1
AAACGAUCGCAGC-----ACGAUAUCAACAGCAGAUA--------UAGCUGUCAUAAAGCAGCCGCAAA---------------AGUCAGAUAUUAUUAUCAGCAUUGUGUUUCGGUUUU
....(((((.(((-----(((((....(((((.....--------..)))))......((....((...---------------.))..((((....)))).)))))))))).))))).. ( -20.90)
>DroYak_CAF1 30078 105 - 1
AAACGAUCGCAGCACGGCACGAUAUCAACAGCAGAUAUACAUACAUAGCUGCCAUAAAGCAGCCGCAAA---------------ACUCAGAUAUUAUUAUCAGCAUUGUGUUUCGGUUUU
....(((((.((((((((...(((((.......))))).........(((((......))))).))...---------------.....((((....)))).....)))))).))))).. ( -24.50)
>consensus
AAACGAUCGCAGA_____ACGAUAUCAACAGCAGAUA________UAGCUGCCAUAAAGCAGCCGCAAA_______________ACUCAGAUAUUAUUAUCAGCAUUGUGUUUCGGUUUU
...(((.(((((.......((.((((.......))))..........(((((......)))))))........................((((....))))....)))))..)))..... (-15.64 = -15.70 +   0.06)

alignment

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secondary structure

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dotplot

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Window 8

Location 16,751,374 – 16,751,481
Length 107
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 84.74
Mean single sequence MFE -30.68
Consensus MFE -23.75
Energy contribution -24.25
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.73
Structure conservation index 0.77
SVM decision value 0.47
SVM RNA-class probability 0.748563
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16751374 107 + 22224390
UUCUUUUUUUUUUUGCGGCUGCUUUAUGGCAGCUA--------UAUCUGCUGUUGAUAUCGU-----UCUGCGAUCGUUUGCACAACAACUUCGUCUUGAAUGACAGCGUAGAAGACGGC
........(((((((((((((((....))))))).--------.....((((((......((-----(.(((((....))))).)))...(((.....))).)))))))))))))).... ( -31.40)
>DroSec_CAF1 38556 103 + 1
----UUUUUUUUUUGCGUCUGCUUUAUGGCAGCUA--------UAUCUGCUGUUGAUAUCGU-----UCUGCGAUCGUUUGCACAACAACUUCGUCUUGAAUGACAGCGUUGAAGACGGC
----............(.(((((....)))))).(--------((((.......))))).((-----(.(((((....))))).)))....(((((((.((((....)))).))))))). ( -26.40)
>DroEre_CAF1 30097 96 + 1
-----------UUUGCGGCUGCUUUAUGACAGCUA--------UAUCUGCUGUUGAUAUCGU-----GCUGCGAUCGUUUGCACAAUAACUUCGUCUUGAAUGACAGCGCAGAAGACGGC
-----------......((((((((..((((((..--------.....))))))......((-----(((((((....))))...........(((......)))))))).)))).)))) ( -28.10)
>DroYak_CAF1 30114 109 + 1
-----------UUUGCGGCUGCUUUAUGGCAGCUAUGUAUGUAUAUCUGCUGUUGAUAUCGUGCCGUGCUGCGAUCGUUUGCACAGCAACUUCGUCUUGAAUGACAGCGUAGAAGACGGC
-----------.(((((((((((....)))))))..(((((.(((((.......)))))))))).((((.((....))..)))).))))..(((((((..(((....)))..))))))). ( -36.80)
>consensus
___________UUUGCGGCUGCUUUAUGGCAGCUA________UAUCUGCUGUUGAUAUCGU_____GCUGCGAUCGUUUGCACAACAACUUCGUCUUGAAUGACAGCGUAGAAGACGGC
................(((((((....)))))))..............((((((.....(((.......(((((....)))))..........(((......))).))).....)))))) (-23.75 = -24.25 +   0.50)

alignment

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secondary structure

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dotplot

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Window 9

Location 16,751,374 – 16,751,481
Length 107
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 84.74
Mean single sequence MFE -27.10
Consensus MFE -18.92
Energy contribution -19.04
Covariance contribution 0.12
Combinations/Pair 1.08
Mean z-score -2.16
Structure conservation index 0.70
SVM decision value 0.90
SVM RNA-class probability 0.876942
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16751374 107 - 22224390
GCCGUCUUCUACGCUGUCAUUCAAGACGAAGUUGUUGUGCAAACGAUCGCAGA-----ACGAUAUCAACAGCAGAUA--------UAGCUGCCAUAAAGCAGCCGCAAAAAAAAAAAGAA
((..........((((((......)))((.((((((.(((........))).)-----))))).))...))).....--------..(((((......))))).)).............. ( -26.70)
>DroSec_CAF1 38556 103 - 1
GCCGUCUUCAACGCUGUCAUUCAAGACGAAGUUGUUGUGCAAACGAUCGCAGA-----ACGAUAUCAACAGCAGAUA--------UAGCUGCCAUAAAGCAGACGCAAAAAAAAAA----
((.((((.....((((((......)))((.((((((.(((........))).)-----))))).))...))).....--------..(((.......)))))))))..........---- ( -26.10)
>DroEre_CAF1 30097 96 - 1
GCCGUCUUCUGCGCUGUCAUUCAAGACGAAGUUAUUGUGCAAACGAUCGCAGC-----ACGAUAUCAACAGCAGAUA--------UAGCUGUCAUAAAGCAGCCGCAAA-----------
((.....(((((..((((......))))..(.((((((((...........))-----)))))).)....)))))..--------..(((((......))))).))...----------- ( -26.20)
>DroYak_CAF1 30114 109 - 1
GCCGUCUUCUACGCUGUCAUUCAAGACGAAGUUGCUGUGCAAACGAUCGCAGCACGGCACGAUAUCAACAGCAGAUAUACAUACAUAGCUGCCAUAAAGCAGCCGCAAA-----------
(((((.....((..((((......))))..)).((((((........))))))))))).(((((((.......))))).........(((((......)))))))....----------- ( -29.40)
>consensus
GCCGUCUUCUACGCUGUCAUUCAAGACGAAGUUGUUGUGCAAACGAUCGCAGA_____ACGAUAUCAACAGCAGAUA________UAGCUGCCAUAAAGCAGCCGCAAA___________
((((((((..............))))))...(((((((.......((((..........))))....))))))).............(((((......))))).)).............. (-18.92 = -19.04 +   0.12)

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 12:21:06 2006