Locus 4919

Sequence ID X_DroMel_CAF1
Location 12,805,577 – 12,805,707
Length 130
Max. P 0.999766
window8023 window8024

overview

Window 3

Location 12,805,577 – 12,805,687
Length 110
Sequences 4
Columns 117
Reading direction reverse
Mean pairwise identity 84.38
Mean single sequence MFE -36.60
Consensus MFE -25.08
Energy contribution -27.20
Covariance contribution 2.12
Combinations/Pair 1.06
Mean z-score -1.86
Structure conservation index 0.69
SVM decision value 0.46
SVM RNA-class probability 0.746333
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12805577 110 - 22224390
-------UCCUUGAGAUCCAUAAGGUCCUUGUGAUCCAUAAGGUCCUUGGGAUCCAUAGGCUCCACGAGAUCCAACGUUCGGUUGGUAAGGAUUAAUCGCAUAGGGAUUGUAGUUUU
-------.(((((.(((((.(((((.(((((((...))))))).)))))))))))).)))....((..(((((...((.((((((((....)))))))).))..)))))...))... ( -37.10)
>DroSec_CAF1 3590 110 - 1
-------UCCUUGAGAUCCAUAAGGUCCUUGUGAUUCAUAAGGUCCUUGGGAUCCAUGGGCUCCUCGAGAUCCAACGUUCGGUUGGUAAGGAUUAAUCGCAUAGGGAUUGUAGUUUU
-------(((.((.(((((.(((((.(((((((...))))))).)))))))))))).)))........(((((...((.((((((((....)))))))).))..)))))........ ( -37.00)
>DroEre_CAF1 11401 108 - 1
UC---------UGAGAUCCGUAAGGUCCUUGAGACCCGUAAGGUCCUUGGGAUCCAUAGGCUCUUCCAGUUUCGAUGCUCGGUUGGUAAGGAUUAAUCGCAUAGGGAUUGUAGUUUU
..---------((.(((((.(((((.(((((.......))))).)))))))))))).(((((....((((..(.((((..(((((((....))))))))))).)..)))).))))). ( -32.50)
>DroYak_CAF1 13509 117 - 1
CUUGAGAUCCUUGAGAUCCAUAAGGUCCUUGAGAGCCGUAAGGUCCUUGGGCGCCAUAGGGUCCACGAGCUUGGAUGUUCGGUUGGUAGGGAUUAAUCGCAUAGGGAUUGUAGUUCU
((...((((((((.(((((.((.(((.((..((..((....))..))..)).))).)))))))...((((......))))(((((((....)))))))...))))))))..)).... ( -39.80)
>consensus
_______UCCUUGAGAUCCAUAAGGUCCUUGAGAUCCAUAAGGUCCUUGGGAUCCAUAGGCUCCACGAGAUCCAACGUUCGGUUGGUAAGGAUUAAUCGCAUAGGGAUUGUAGUUUU
........(((((.(((((.(((((.(((((((...))))))).)))))))))))).)))........(((((......((((((((....)))))))).....)))))........ (-25.08 = -27.20 +   2.12)

alignment

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secondary structure

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dotplot

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Window 4

Location 12,805,614 – 12,805,707
Length 93
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 71.01
Mean single sequence MFE -42.28
Consensus MFE -22.99
Energy contribution -25.05
Covariance contribution 2.06
Combinations/Pair 1.09
Mean z-score -3.05
Structure conservation index 0.54
SVM decision value 4.03
SVM RNA-class probability 0.999766
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12805614 93 - 22224390
GGAGAUUGCGGCCCAUAGGG---------------------------UCCUUGAGAUCCAUAAGGUCCUUGUGAUCCAUAAGGUCCUUGGGAUCCAUAGGCUCCACGAGAUCCAACGUUC
(((..(((.(((((...)))---------------------------.(((((.(((((.(((((.(((((((...))))))).)))))))))))).)))..)).)))..)))....... ( -36.30)
>DroSec_CAF1 3627 93 - 1
GGAGAUUGCGGCCCAUAAGG---------------------------UCCUUGAGAUCCAUAAGGUCCUUGUGAUUCAUAAGGUCCUUGGGAUCCAUGGGCUCCUCGAGAUCCAACGUUC
(((..(((.((.......((---------------------------(((.((.(((((.(((((.(((((((...))))))).)))))))))))).))))))).)))..)))....... ( -38.51)
>DroEre_CAF1 11438 111 - 1
GGAGAUUGCGGCCUAUAUGAACCGUAGGCUUCAGGGGAACUC---------UGAGAUCCGUAAGGUCCUUGAGACCCGUAAGGUCCUUGGGAUCCAUAGGCUCUUCCAGUUUCGAUGCUC
.(((((((.(((((((.......)))))))...(((((.((.---------((.(((((.(((((.(((((.......))))).)))))))))))).))..))))))))))))....... ( -39.40)
>DroYak_CAF1 13546 120 - 1
GGAGAUUGUGGCCCAUAUGGACCGUAGGCUCCAGGAGAUCCUUGAGAUCCUUGAGAUCCAUAAGGUCCUUGAGAGCCGUAAGGUCCUUGGGCGCCAUAGGGUCCACGAGCUUGGAUGUUC
(((..(((((((((....(((((...(((((((((.((.(((((.((((.....))))..))))))))))).)))))....)))))...)).)))))))..)))..((((......)))) ( -54.90)
>consensus
GGAGAUUGCGGCCCAUAUGG___________________________UCCUUGAGAUCCAUAAGGUCCUUGAGAUCCAUAAGGUCCUUGGGAUCCAUAGGCUCCACGAGAUCCAACGUUC
(((..(((.(((((((.................((....))...........(.(((((.(((((.(((((((...))))))).))))))))))))))))))...)))..)))....... (-22.99 = -25.05 +   2.06)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:36:04 2006