Locus 8295

Sequence ID 3L_DroMel_CAF1
Location 21,742,762 – 21,742,910
Length 148
Max. P 0.948739
window13572 window13573 window13574

overview

Window 2

Location 21,742,762 – 21,742,870
Length 108
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.15
Mean single sequence MFE -38.99
Consensus MFE -31.26
Energy contribution -31.06
Covariance contribution -0.20
Combinations/Pair 1.06
Mean z-score -2.07
Structure conservation index 0.80
SVM decision value 1.38
SVM RNA-class probability 0.948739
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21742762 108 - 23771897
CGACGGCUUUCGAAGGAGAUUUCAGCAAUCACGUGGCGCACAUAGUGCCGAAAAACUUCGCGAUCGGUCGGAUAUAAUGC------G------AUUGCGAGAGCGAGAGAACAGCGAAAG
......((((((..(....((((.((.......((((((.....))))))......((((((((((.............)------)------)))))))).))))))...)..)))))) ( -31.72)
>DroSec_CAF1 24648 108 - 1
CGACGGCUUUCGAAGGAGAUUUCAGCAAUCACGUGGCGCACAUAGUGCCGAAAAACUUCGCGAUCGGUCGGAUAUAAUGC------G------AUUGCGAGAGCGAGAGAGCAGCGAAAG
((...((((((((((....)))).((.......((((((.....))))))......((((((((((.............)------)------)))))))).))..))))))..)).... ( -35.12)
>DroSim_CAF1 29534 108 - 1
CGACGGCUUUCGAAGGAGAUUUCAGCAAUCACGUGGCGCACAUAGUGCCGAAAAACUUCGCGAUCGGUCGGAUAUAAUGC------G------AUUGCGAGAGCGAGAGAGCAGCGAAAG
((...((((((((((....)))).((.......((((((.....))))))......((((((((((.............)------)------)))))))).))..))))))..)).... ( -35.12)
>DroEre_CAF1 11007 114 - 1
CGACGGCUUUCGAAGGAGACUUCAGCAAUCACGUGGCGCACAUAGUGCCGAAGAACUUCGCGAUCGGUCGGAUAUAAUGCGGCUGCG------AUUGCGAGAGCGAGAGAGCAGCGAAAG
((...((((((((((....)))).((..((...((((((.....))))))..))..((((((((((((((.((...)).))))..))------)))))))).))..))))))..)).... ( -46.60)
>DroYak_CAF1 82843 120 - 1
CGACGGCUUUCGAAGGAAACUUCAGUAAUCACGUGGCGCACAUAGUGCCGAAGAACUUCGCGAUCGGUCGGAUAUUAUGCGCUUGCGAUUCCGAUUGCGAGAGCGAGAGAGCAGCGAAAG
((...((((((((((....))))........((((((((.....))))).......((((((((((((((.(...........).)))..))))))))))).))).))))))..)).... ( -46.40)
>consensus
CGACGGCUUUCGAAGGAGAUUUCAGCAAUCACGUGGCGCACAUAGUGCCGAAAAACUUCGCGAUCGGUCGGAUAUAAUGC______G______AUUGCGAGAGCGAGAGAGCAGCGAAAG
((...((((((((((....)))).(((....((((((((.....)))))(((....))))))(((.....)))....)))..............((((....))))))))))..)).... (-31.26 = -31.06 +  -0.20)

alignment

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secondary structure

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dotplot

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Window 3

Location 21,742,790 – 21,742,910
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 97.33
Mean single sequence MFE -34.64
Consensus MFE -34.34
Energy contribution -34.46
Covariance contribution 0.12
Combinations/Pair 1.03
Mean z-score -1.20
Structure conservation index 0.99
SVM decision value 0.58
SVM RNA-class probability 0.789681
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21742790 120 + 23771897
GCAUUAUAUCCGACCGAUCGCGAAGUUUUUCGGCACUAUGUGCGCCACGUGAUUGCUGAAAUCUCCUUCGAAAGCCGUCGCUAUAUCAUCAGCGAUAAUUCGGAUUUAAGGUGUCAUGUG
(((((..((((((...(((((((((..((((((((.((((((...))))))..))))))))....))))...(((....))).........)))))...))))))....)))))...... ( -35.90)
>DroSec_CAF1 24676 120 + 1
GCAUUAUAUCCGACCGAUCGCGAAGUUUUUCGGCACUAUGUGCGCCACGUGAUUGCUGAAAUCUCCUUCGAAAGCCGUCGCUAUAUCAUCAGCGAUAAUUCGGAUUUAAGGUGUCAUGUG
(((((..((((((...(((((((((..((((((((.((((((...))))))..))))))))....))))...(((....))).........)))))...))))))....)))))...... ( -35.90)
>DroSim_CAF1 29562 120 + 1
GCAUUAUAUCCGACCGAUCGCGAAGUUUUUCGGCACUAUGUGCGCCACGUGAUUGCUGAAAUCUCCUUCGAAAGCCGUCGCUAUAUCAUCAGCGAUAAUUCGGAUUUAAGGUGUCAUGUG
(((((..((((((...(((((((((..((((((((.((((((...))))))..))))))))....))))...(((....))).........)))))...))))))....)))))...... ( -35.90)
>DroEre_CAF1 11041 120 + 1
GCAUUAUAUCCGACCGAUCGCGAAGUUCUUCGGCACUAUGUGCGCCACGUGAUUGCUGAAGUCUCCUUCGAAAGCCGUCGCUAUAUCAUCAGCAAUAAUUCGGAUUUAAGGUGUCAUGUG
(((((..(((((((.(....(((((..((((((((.((((((...))))))..))))))))....)))))....).)))(((........)))........))))....)))))...... ( -33.50)
>DroYak_CAF1 82883 120 + 1
GCAUAAUAUCCGACCGAUCGCGAAGUUCUUCGGCACUAUGUGCGCCACGUGAUUACUGAAGUUUCCUUCGAAAGCCGUCGCUAUAUCAUCAGCGAUAAUUCGGAUUUAAAGUGUCAUGUG
(((((...(((((....))).))(((.(....).))).)))))..((((((((.(((......(((..(....)..((((((........)))))).....))).....))))))))))) ( -32.00)
>consensus
GCAUUAUAUCCGACCGAUCGCGAAGUUUUUCGGCACUAUGUGCGCCACGUGAUUGCUGAAAUCUCCUUCGAAAGCCGUCGCUAUAUCAUCAGCGAUAAUUCGGAUUUAAGGUGUCAUGUG
(((((..((((((...(((((((((..((((((((.((((((...))))))..))))))))....))))...(((....))).........)))))...))))))....)))))...... (-34.34 = -34.46 +   0.12)

alignment

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secondary structure

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dotplot

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Window 4

Location 21,742,790 – 21,742,910
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.33
Mean single sequence MFE -34.04
Consensus MFE -32.74
Energy contribution -31.94
Covariance contribution -0.80
Combinations/Pair 1.10
Mean z-score -1.33
Structure conservation index 0.96
SVM decision value 0.87
SVM RNA-class probability 0.871158
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21742790 120 - 23771897
CACAUGACACCUUAAAUCCGAAUUAUCGCUGAUGAUAUAGCGACGGCUUUCGAAGGAGAUUUCAGCAAUCACGUGGCGCACAUAGUGCCGAAAAACUUCGCGAUCGGUCGGAUAUAAUGC
...........(((.((((((...(((((....((...(((....))).))((((..((((.....))))...((((((.....)))))).....)))))))))...)))))).)))... ( -32.90)
>DroSec_CAF1 24676 120 - 1
CACAUGACACCUUAAAUCCGAAUUAUCGCUGAUGAUAUAGCGACGGCUUUCGAAGGAGAUUUCAGCAAUCACGUGGCGCACAUAGUGCCGAAAAACUUCGCGAUCGGUCGGAUAUAAUGC
...........(((.((((((...(((((....((...(((....))).))((((..((((.....))))...((((((.....)))))).....)))))))))...)))))).)))... ( -32.90)
>DroSim_CAF1 29562 120 - 1
CACAUGACACCUUAAAUCCGAAUUAUCGCUGAUGAUAUAGCGACGGCUUUCGAAGGAGAUUUCAGCAAUCACGUGGCGCACAUAGUGCCGAAAAACUUCGCGAUCGGUCGGAUAUAAUGC
...........(((.((((((...(((((....((...(((....))).))((((..((((.....))))...((((((.....)))))).....)))))))))...)))))).)))... ( -32.90)
>DroEre_CAF1 11041 120 - 1
CACAUGACACCUUAAAUCCGAAUUAUUGCUGAUGAUAUAGCGACGGCUUUCGAAGGAGACUUCAGCAAUCACGUGGCGCACAUAGUGCCGAAGAACUUCGCGAUCGGUCGGAUAUAAUGC
...........(((.((((((...((((((...((...(((....))).))((((....))))))))))..((((((((.....)))))(((....)))))).....)))))).)))... ( -35.10)
>DroYak_CAF1 82883 120 - 1
CACAUGACACUUUAAAUCCGAAUUAUCGCUGAUGAUAUAGCGACGGCUUUCGAAGGAAACUUCAGUAAUCACGUGGCGCACAUAGUGCCGAAGAACUUCGCGAUCGGUCGGAUAUUAUGC
...............((((((...(((((((((((...(((....))).))((((....))))....))))...(((((.....)))))(((....))))))))...))))))....... ( -36.40)
>consensus
CACAUGACACCUUAAAUCCGAAUUAUCGCUGAUGAUAUAGCGACGGCUUUCGAAGGAGAUUUCAGCAAUCACGUGGCGCACAUAGUGCCGAAAAACUUCGCGAUCGGUCGGAUAUAAUGC
...............((((((...(((((....((...(((....))).))((((....((((.((......))(((((.....)))))))))..)))))))))...))))))....... (-32.74 = -31.94 +  -0.80)

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 13:11:49 2006