Locus 6450

Sequence ID 3L_DroMel_CAF1
Location 17,227,456 – 17,227,608
Length 152
Max. P 0.998945
window10360 window10361 window10362

overview

Window 0

Location 17,227,456 – 17,227,568
Length 112
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.97
Mean single sequence MFE -32.94
Consensus MFE -29.10
Energy contribution -28.94
Covariance contribution -0.16
Combinations/Pair 1.04
Mean z-score -1.75
Structure conservation index 0.88
SVM decision value 1.77
SVM RNA-class probability 0.976273
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17227456 112 + 23771897
AC--AAGGCCCAAUGCUGGCUGUU------GCUGUUGGCGACAGCACUUGGCUUCGACUACCCUGGUAGCCAUUAAAGCCAAUUGCCCACAAAAUCAUGCCCGAUAUCAUAAUUGCUCUU
..--..(((.........((((((------((.....))))))))..(((((((..(((((....))))...)..)))))))..)))......(((......)))............... ( -30.40)
>DroSec_CAF1 110879 112 + 1
AC--AAGGCCCAAUGCUGGCUGUU------GCUGUUGGCGACAGCACUUGGCUUCGACUACCCUGGUAGCCAUUAAAGCCAAUUGCCCACAAAAUCAUGCCCGAUAUCAUAAUUGCUCUU
..--..(((.........((((((------((.....))))))))..(((((((..(((((....))))...)..)))))))..)))......(((......)))............... ( -30.40)
>DroSim_CAF1 104600 112 + 1
AC--AAGGCCCAAUGCUGGCUGUU------GCUGUUGGCGACAGCACUUGGCUUCGACUACCCUGGUAGCCAUUAAAGCCAAUUGCCCACAAAAUCAUGCCCGAUAUCAUAAUUGCUCUU
..--..(((.........((((((------((.....))))))))..(((((((..(((((....))))...)..)))))))..)))......(((......)))............... ( -30.40)
>DroEre_CAF1 114743 110 + 1
----AAGGCCUGAUGCUGGCUGUU------GCUGUUGGCGACAGCACUUGGCUUCGACUACCCUGGUAGCCAUUAAAGCCAAUUGCCCACAAAAUCAUGCCCGAUAUCAUAAUUGCUCUU
----..(((.((((..((((((((------((.....))))))))..(((((((..(((((....))))...)..))))))).......))..)))).)))................... ( -36.30)
>DroYak_CAF1 117581 120 + 1
ACAGAAGGCUCGAUGCUGGCUGUUGCUGUUGCUGUUGGCGACAGCACUUGGCUUCGACUGCCCUGGUAGCCAUUAAAGCCAAUUGCCCACAAAAUCAUGCCCGAUAUCAUAAUUGCUCUU
......(((..(((...(((...(((((((((.....))))))))).(((((((..(((((....))))...)..)))))))..)))......)))..)))................... ( -37.20)
>consensus
AC__AAGGCCCAAUGCUGGCUGUU______GCUGUUGGCGACAGCACUUGGCUUCGACUACCCUGGUAGCCAUUAAAGCCAAUUGCCCACAAAAUCAUGCCCGAUAUCAUAAUUGCUCUU
......(((....(((..((.((.......)).))..)))...(((.(((((((..(((((....))))...)..))))))).)))............)))................... (-29.10 = -28.94 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 1

Location 17,227,456 – 17,227,568
Length 112
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.97
Mean single sequence MFE -39.26
Consensus MFE -35.20
Energy contribution -35.00
Covariance contribution -0.20
Combinations/Pair 1.06
Mean z-score -2.30
Structure conservation index 0.90
SVM decision value 3.29
SVM RNA-class probability 0.998945
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17227456 112 - 23771897
AAGAGCAAUUAUGAUAUCGGGCAUGAUUUUGUGGGCAAUUGGCUUUAAUGGCUACCAGGGUAGUCGAAGCCAAGUGCUGUCGCCAACAGC------AACAGCCAGCAUUGGGCCUU--GU
(((.(((((((((........))))))).(((.(((..((((((((...((((((....)))))))))))))).((((((.....)))))------)...))).)))....)))))--.. ( -38.90)
>DroSec_CAF1 110879 112 - 1
AAGAGCAAUUAUGAUAUCGGGCAUGAUUUUGUGGGCAAUUGGCUUUAAUGGCUACCAGGGUAGUCGAAGCCAAGUGCUGUCGCCAACAGC------AACAGCCAGCAUUGGGCCUU--GU
(((.(((((((((........))))))).(((.(((..((((((((...((((((....)))))))))))))).((((((.....)))))------)...))).)))....)))))--.. ( -38.90)
>DroSim_CAF1 104600 112 - 1
AAGAGCAAUUAUGAUAUCGGGCAUGAUUUUGUGGGCAAUUGGCUUUAAUGGCUACCAGGGUAGUCGAAGCCAAGUGCUGUCGCCAACAGC------AACAGCCAGCAUUGGGCCUU--GU
(((.(((((((((........))))))).(((.(((..((((((((...((((((....)))))))))))))).((((((.....)))))------)...))).)))....)))))--.. ( -38.90)
>DroEre_CAF1 114743 110 - 1
AAGAGCAAUUAUGAUAUCGGGCAUGAUUUUGUGGGCAAUUGGCUUUAAUGGCUACCAGGGUAGUCGAAGCCAAGUGCUGUCGCCAACAGC------AACAGCCAGCAUCAGGCCUU----
..................((((.(((...(((.(((..((((((((...((((((....)))))))))))))).((((((.....)))))------)...))).)))))).)))).---- ( -40.20)
>DroYak_CAF1 117581 120 - 1
AAGAGCAAUUAUGAUAUCGGGCAUGAUUUUGUGGGCAAUUGGCUUUAAUGGCUACCAGGGCAGUCGAAGCCAAGUGCUGUCGCCAACAGCAACAGCAACAGCCAGCAUCGAGCCUUCUGU
..................((((.(((...(((.(((..(((((((..((.(((.....))).))..))))))).((((((.((.....)).))))))...))).)))))).))))..... ( -39.40)
>consensus
AAGAGCAAUUAUGAUAUCGGGCAUGAUUUUGUGGGCAAUUGGCUUUAAUGGCUACCAGGGUAGUCGAAGCCAAGUGCUGUCGCCAACAGC______AACAGCCAGCAUUGGGCCUU__GU
..................((((.(((...(((.(((..((((((((...((((((....))))))))))))))..(((((.....)))))..........))).)))))).))))..... (-35.20 = -35.00 +  -0.20)

alignment

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secondary structure

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dotplot

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Window 2

Location 17,227,488 – 17,227,608
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.33
Mean single sequence MFE -39.00
Consensus MFE -35.48
Energy contribution -35.60
Covariance contribution 0.12
Combinations/Pair 1.08
Mean z-score -1.33
Structure conservation index 0.91
SVM decision value 0.42
SVM RNA-class probability 0.728136
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17227488 120 - 23771897
CUCCCGCACAGCUGCCGGAUUACAGGGUAUGGAAACCACGAAGAGCAAUUAUGAUAUCGGGCAUGAUUUUGUGGGCAAUUGGCUUUAAUGGCUACCAGGGUAGUCGAAGCCAAGUGCUGU
...(((((...(((((.(((..((.(((......))).....((....)).))..))).)))).)....)))))(((.((((((((...((((((....)))))))))))))).)))... ( -39.70)
>DroSec_CAF1 110911 120 - 1
CUCCCGCACAGCUGCCGGAUUACAGGGUAUGGAAACCACGAAGAGCAAUUAUGAUAUCGGGCAUGAUUUUGUGGGCAAUUGGCUUUAAUGGCUACCAGGGUAGUCGAAGCCAAGUGCUGU
...(((((...(((((.(((..((.(((......))).....((....)).))..))).)))).)....)))))(((.((((((((...((((((....)))))))))))))).)))... ( -39.70)
>DroSim_CAF1 104632 120 - 1
CUCCCGCACAGCUGCCGGAUUACAGGGUAUGGAAACCACGAAGAGCAAUUAUGAUAUCGGGCAUGAUUUUGUGGGCAAUUGGCUUUAAUGGCUACCAGGGUAGUCGAAGCCAAGUGCUGU
...(((((...(((((.(((..((.(((......))).....((....)).))..))).)))).)....)))))(((.((((((((...((((((....)))))))))))))).)))... ( -39.70)
>DroEre_CAF1 114773 120 - 1
CUCGCGGACAGCUGCCGGAUUACAGGGUAUGGAAACCACGAAGAGCAAUUAUGAUAUCGGGCAUGAUUUUGUGGGCAAUUGGCUUUAAUGGCUACCAGGGUAGUCGAAGCCAAGUGCUGU
..((((((...(((((.(((..((.(((......))).....((....)).))..))).)))).)..))))))((((.((((((((...((((((....)))))))))))))).)))).. ( -39.20)
>DroYak_CAF1 117621 120 - 1
CGCCUGCACAGCUGUUGGAUUACAGGGUAUGCAAACCACGAAGAGCAAUUAUGAUAUCGGGCAUGAUUUUGUGGGCAAUUGGCUUUAAUGGCUACCAGGGCAGUCGAAGCCAAGUGCUGU
.((.(((....((((......)))).))).))...(((((((.....((((((........)))))))))))))(((.(((((((..((.(((.....))).))..))))))).)))... ( -36.70)
>consensus
CUCCCGCACAGCUGCCGGAUUACAGGGUAUGGAAACCACGAAGAGCAAUUAUGAUAUCGGGCAUGAUUUUGUGGGCAAUUGGCUUUAAUGGCUACCAGGGUAGUCGAAGCCAAGUGCUGU
...(((((...(((((.(((..((.(((......))).....((....)).))..))).)))).)....)))))(((.((((((((...((((((....)))))))))))))).)))... (-35.48 = -35.60 +   0.12)

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 12:19:16 2006