Locus 5321

Sequence ID X_DroMel_CAF1
Location 13,907,149 – 13,907,355
Length 206
Max. P 0.988265
window8613 window8614 window8615

overview

Window 3

Location 13,907,149 – 13,907,251
Length 102
Sequences 3
Columns 112
Reading direction forward
Mean pairwise identity 89.60
Mean single sequence MFE -28.33
Consensus MFE -21.93
Energy contribution -22.27
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -3.48
Structure conservation index 0.77
SVM decision value 1.12
SVM RNA-class probability 0.917709
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13907149 102 + 22224390
CAACGCAGCAGCAGCAGCAACAUCAACUGCU---------GCAACUGCAACUGCAAUGCGGACAUCGAUGUGCGUGCUUGACCAAAAAGCAAAAAUAAAUAUAAA-AAGAAG
..(((((((((..((((((........))))---------))..))))..((((...)))).........)))))((((.......))))...............-...... ( -29.30)
>DroSec_CAF1 7565 103 + 1
CAACGCAGCAGCAUCAGCAACAUCAACUGCU---------GCAACUGCAAUUCCAAUGCGGACAUCGAUGUGCGUGCUUGACCGAAAAGCAAAAAUAAAUGCAAAAAAUAAG
....((((((.((((.(((.((.....)).)---------))..(((((.......))))).....))))))).(((((.......)))))........))).......... ( -24.90)
>DroSim_CAF1 29356 112 + 1
CAACGCAGCAGCAUCAGCAACAUCAACUGCUGCAACUGCUGCAACUGCAAUUGCAAUGCGGACAUCGAUGUGCGUGCUUGACCGAAAAGCAAAAAUAAAUACAAAAAAUAAG
....(((((((...(((((........)))))...)))))))...(((....)))..(((.(((....))).)))((((.......))))...................... ( -30.80)
>consensus
CAACGCAGCAGCAUCAGCAACAUCAACUGCU_________GCAACUGCAAUUGCAAUGCGGACAUCGAUGUGCGUGCUUGACCGAAAAGCAAAAAUAAAUACAAAAAAUAAG
..((((....((....)).(((((...(((.((....)).))).(((((.......))))).....)))))))))((((.......))))...................... (-21.93 = -22.27 +   0.33)

alignment

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secondary structure

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dotplot

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Window 4

Location 13,907,251 – 13,907,355
Length 104
Sequences 5
Columns 108
Reading direction forward
Mean pairwise identity 91.50
Mean single sequence MFE -21.94
Consensus MFE -17.36
Energy contribution -17.56
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -2.66
Structure conservation index 0.79
SVM decision value 2.11
SVM RNA-class probability 0.988265
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13907251 104 + 22224390
CAAUAC---AAAAAAGAAAAAAUCCCCACUCUGCUCAAUUCCGCAGCUCGCUUUAAUUGAAAGAUGUCA-AUUUGCAAACGCACAAAGUGCGUUGCGCAACAGCAACA
......---......................((((......((((((.((((((((((((......)))-)))(((....))).)))))).))))))....))))... ( -22.20)
>DroSec_CAF1 7668 99 + 1
CAACAC---AAA------AAAAUCCCCACUCUGCUCAAUUCCGCAGCUCGCUUUAAUUGAAAGAUGUCAAAUUUGCAAACACACAAAGUGCGUUGCGCAACAGCAACA
......---...------.............((((......((((((.((((((..((((......))))...((......)).)))))).))))))....))))... ( -17.40)
>DroSim_CAF1 29468 98 + 1
CAACAC---AAA------AAAAUGCCCACUCCGCUCAAUUCCGCAGCUCGCUUUAAUUGAAAGAUGUCA-AUUUGCAAACGCACAAAGUGCGUUGCGCAACAGCAACA
......---...------..............(((......((((((.((((((((((((......)))-)))(((....))).)))))).))))))....))).... ( -21.70)
>DroEre_CAF1 3338 101 + 1
AAAUACAACAAA------AAAAUAUCCACUCUGCUCAAUUCCGCAGCGCGCUAUAAUUGAAAGAUGUCA-AUUUGCAAACGCACAAAGUGCGUUGCGCAACGGCAACA
............------.............((((......(((((((((((..((((((......)))-)))(((....)))...)))))))))))....))))... ( -26.20)
>DroYak_CAF1 17716 99 + 1
AAAUACG--AAA------AAAAUGCCCACUCUGCUCAAUUCCGCAGCUCGCUUUAAUUGAAAGAUGUCA-AUUUGCAAACGCACAAAGUGCGUUGCGCAACAGCAACA
.......--...------.............((((......((((((.((((((((((((......)))-)))(((....))).)))))).))))))....))))... ( -22.20)
>consensus
CAAUAC___AAA______AAAAUCCCCACUCUGCUCAAUUCCGCAGCUCGCUUUAAUUGAAAGAUGUCA_AUUUGCAAACGCACAAAGUGCGUUGCGCAACAGCAACA
................................((((((((..((.....))...))))))............((((.(((((((...)))))))..))))..)).... (-17.36 = -17.56 +   0.20)

alignment

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secondary structure

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dotplot

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Window 5

Location 13,907,251 – 13,907,355
Length 104
Sequences 5
Columns 108
Reading direction reverse
Mean pairwise identity 91.50
Mean single sequence MFE -26.92
Consensus MFE -24.94
Energy contribution -24.62
Covariance contribution -0.32
Combinations/Pair 1.07
Mean z-score -1.15
Structure conservation index 0.93
SVM decision value 0.13
SVM RNA-class probability 0.596484
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13907251 104 - 22224390
UGUUGCUGUUGCGCAACGCACUUUGUGCGUUUGCAAAU-UGACAUCUUUCAAUUAAAGCGAGCUGCGGAAUUGAGCAGAGUGGGGAUUUUUUCUUUUUU---GUAUUG
.(((((......)))))((((...))))((((((.(((-(((......))))))...))))))(((((((..(((.(((((....))))))))..))))---)))... ( -27.00)
>DroSec_CAF1 7668 99 - 1
UGUUGCUGUUGCGCAACGCACUUUGUGUGUUUGCAAAUUUGACAUCUUUCAAUUAAAGCGAGCUGCGGAAUUGAGCAGAGUGGGGAUUUU------UUU---GUGUUG
.(((((......))))).(((((((((((((.........)))))...((((((...((.....))..))))))))))))))........------...---...... ( -23.80)
>DroSim_CAF1 29468 98 - 1
UGUUGCUGUUGCGCAACGCACUUUGUGCGUUUGCAAAU-UGACAUCUUUCAAUUAAAGCGAGCUGCGGAAUUGAGCGGAGUGGGCAUUUU------UUU---GUGUUG
.(((((......))))).((((((((((((((((.(((-(((......))))))...)))))).))........))))))))(((((...------...---))))). ( -27.20)
>DroEre_CAF1 3338 101 - 1
UGUUGCCGUUGCGCAACGCACUUUGUGCGUUUGCAAAU-UGACAUCUUUCAAUUAUAGCGCGCUGCGGAAUUGAGCAGAGUGGAUAUUUU------UUUGUUGUAUUU
.....((((.(((((((((((...))))))).((.(((-(((......))))))...)))))).)))).....(((((((.........)------))))))...... ( -29.30)
>DroYak_CAF1 17716 99 - 1
UGUUGCUGUUGCGCAACGCACUUUGUGCGUUUGCAAAU-UGACAUCUUUCAAUUAAAGCGAGCUGCGGAAUUGAGCAGAGUGGGCAUUUU------UUU--CGUAUUU
.(((((......)))))((((...))))((((((.(((-(((......))))))...))))))(((((((..((((.......)).))..------)))--))))... ( -27.30)
>consensus
UGUUGCUGUUGCGCAACGCACUUUGUGCGUUUGCAAAU_UGACAUCUUUCAAUUAAAGCGAGCUGCGGAAUUGAGCAGAGUGGGCAUUUU______UUU___GUAUUG
(((((...(((((.(((((((...))))))))))))...)))))((((((((((...((.....))..))))))).)))............................. (-24.94 = -24.62 +  -0.32)

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 11:44:52 2006