Locus 4675

Sequence ID 2L_DroMel_CAF1
Location 13,435,515 – 13,435,619
Length 104
Max. P 0.960078
window7389 window7390

overview

Window 9

Location 13,435,515 – 13,435,619
Length 104
Sequences 6
Columns 104
Reading direction forward
Mean pairwise identity 79.34
Mean single sequence MFE -28.26
Consensus MFE -20.46
Energy contribution -21.63
Covariance contribution 1.17
Combinations/Pair 1.25
Mean z-score -2.49
Structure conservation index 0.72
SVM decision value 1.51
SVM RNA-class probability 0.960078
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13435515 104 + 22407834
AAGCACAGAUAAAAAAAAUAAAAAAUAGAAAACCGUCUGCAGACCAAUUGGCUUGGCCUGAUAAGCGAGUUGGCUGAUUGGCAGGGACCCCAAACAGCUGUGAU
...(((((..........................(((..(((.((((((.(((((......))))).)))))))))...))).((....))......))))).. ( -30.50)
>DroSec_CAF1 42428 99 + 1
AAGCACAGAUAAAAA-----AAAAAUAGAAAACCGUCUGCAGACCAGUUGGCUUGGCCUGAUAAGCGAGUUGGCUGAUUGGCAGGGAUCCCAAACAGCUGUGAU
...(((((.......-----..............(((..(((.(((..(.(((((......))))).)..))))))...))).((....))......))))).. ( -27.70)
>DroSim_CAF1 43597 103 + 1
AAGCACAGAUAAAAAAUA-AAAAAAUAGAAAACCGUCUGCAGACCAAUUGGCUUGGCCUGAUAAGCGAGUUGGCUGAUUGGCAGGGACCCCAAACAGCUGUGAU
...(((((..........-...............(((..(((.((((((.(((((......))))).)))))))))...))).((....))......))))).. ( -30.50)
>DroEre_CAF1 46962 94 + 1
AACCACAGA-A---------AAAAAUAGAAAGCCGUCUGCAGGCCAAUUGGCUUGGCCUGAUAAGCGAGUUGGCUGAUUGGCGGGGACCCCAAACAGCUGUGAU
...(((...-.---------..........(((((..((((((((((.....)))))))).))..)).)))(((((.((((.(....).)))).)))))))).. ( -35.70)
>DroYak_CAF1 43302 95 + 1
AACCGCAGAUA---------AAAAAUAGAAAAUCGUCUGCAGUCCAAUUGGCUUGGCCUGAUAACACAGUUGGCUGAUUGGCAGGGACCCCAAACAGCUGUGAU
....((((((.---------..............))))))((.((((.....)))).)).....(((((((((((....))).((....))...)))))))).. ( -27.26)
>DroPer_CAF1 54992 82 + 1
G-------GUAAAA------AAAAAGAGAA---CAACUUCGGACCAAGCCAAUUGGCCUGUUA-UCACCUGGGCUGACUGGU-----GCCCAAACAGCUGUGAU
(-------((....------.....((.((---((.(....).....(((....))).)))).-))...(((((........-----)))))....)))..... ( -17.90)
>consensus
AAGCACAGAUAAAA______AAAAAUAGAAAACCGUCUGCAGACCAAUUGGCUUGGCCUGAUAAGCGAGUUGGCUGAUUGGCAGGGACCCCAAACAGCUGUGAU
...(((((..........................(((..(((.((((((.(((((......))))).)))))))))...))).((....))......))))).. (-20.46 = -21.63 +   1.17)

alignment

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secondary structure

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dotplot

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Window 0

Location 13,435,515 – 13,435,619
Length 104
Sequences 6
Columns 104
Reading direction reverse
Mean pairwise identity 79.34
Mean single sequence MFE -26.17
Consensus MFE -18.92
Energy contribution -20.00
Covariance contribution 1.08
Combinations/Pair 1.10
Mean z-score -1.97
Structure conservation index 0.72
SVM decision value 1.13
SVM RNA-class probability 0.919235
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13435515 104 - 22407834
AUCACAGCUGUUUGGGGUCCCUGCCAAUCAGCCAACUCGCUUAUCAGGCCAAGCCAAUUGGUCUGCAGACGGUUUUCUAUUUUUUAUUUUUUUUAUCUGUGCUU
..((((((((.((((........)))).)))).(((.((((...((((((((.....)))))))).)).))))).......................))))... ( -25.60)
>DroSec_CAF1 42428 99 - 1
AUCACAGCUGUUUGGGAUCCCUGCCAAUCAGCCAACUCGCUUAUCAGGCCAAGCCAACUGGUCUGCAGACGGUUUUCUAUUUUU-----UUUUUAUCUGUGCUU
..((((((((.((((........)))).)))).(((.((((...(((((((.......))))))).)).)))))..........-----........))))... ( -23.80)
>DroSim_CAF1 43597 103 - 1
AUCACAGCUGUUUGGGGUCCCUGCCAAUCAGCCAACUCGCUUAUCAGGCCAAGCCAAUUGGUCUGCAGACGGUUUUCUAUUUUUU-UAUUUUUUAUCUGUGCUU
..((((((((.((((........)))).)))).(((.((((...((((((((.....)))))))).)).)))))...........-...........))))... ( -25.60)
>DroEre_CAF1 46962 94 - 1
AUCACAGCUGUUUGGGGUCCCCGCCAAUCAGCCAACUCGCUUAUCAGGCCAAGCCAAUUGGCCUGCAGACGGCUUUCUAUUUUU---------U-UCUGUGGUU
((((((((((.((((((...)).)))).))))......(((..(((((((((.....)))))))).)...)))...........---------.-..)))))). ( -31.40)
>DroYak_CAF1 43302 95 - 1
AUCACAGCUGUUUGGGGUCCCUGCCAAUCAGCCAACUGUGUUAUCAGGCCAAGCCAAUUGGACUGCAGACGAUUUUCUAUUUUU---------UAUCUGCGGUU
..((((((((.((((........)))).))))....))))......(((...))).....(((((((((..(...........)---------..))))))))) ( -26.30)
>DroPer_CAF1 54992 82 - 1
AUCACAGCUGUUUGGGC-----ACCAGUCAGCCCAGGUGA-UAACAGGCCAAUUGGCUUGGUCCGAAGUUG---UUCUCUUUUU------UUUUAC-------C
...((((((..((((((-----....((((.(....))))-)..((((((....)))))))))))))))))---).........------......-------. ( -24.30)
>consensus
AUCACAGCUGUUUGGGGUCCCUGCCAAUCAGCCAACUCGCUUAUCAGGCCAAGCCAAUUGGUCUGCAGACGGUUUUCUAUUUUU______UUUUAUCUGUGCUU
..((((((((.((((........)))).))))............((((((((.....))))))))................................))))... (-18.92 = -20.00 +   1.08)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:24:18 2006