Locus 274

Sequence ID 2R_DroMel_CAF1
Location 1,673,529 – 1,673,626
Length 97
Max. P 0.913048
window581 window582

overview

Window 1

Location 1,673,529 – 1,673,626
Length 97
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 77.78
Mean single sequence MFE -31.92
Consensus MFE -28.04
Energy contribution -28.04
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -0.78
Structure conservation index 0.88
SVM decision value 0.07
SVM RNA-class probability 0.568090
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1673529 97 + 20766785
AUUCCAUGGGGCCCAUUAGCUCAGUUGGUUAGAGCGUCGUGCUAAUAACGCGAAGGUCGCGGGUUCGAUCCCCUCAUGGGCCAACGGUAAUUAUUUU-----------------------
...((....(((((((..((((.........))))((((.(((.....((((.....))))))).))))......)))))))...))..........----------------------- ( -28.90)
>DroPse_CAF1 90030 116 + 1
---GCAACAGGCCCAUUAGCUCAGCUGGUUAGAGCGUCGUGCUAAUAACGCGAAGGCCGCGGGUUCGAUCCCCCCAUGGGCCAGGAGUUACUUUUUGGUUUUUUU-UUCAGUGUAAUUUU
---......(((((((.......((.((((...((((..(....)..))))...))))))(((......)))...))))))).((((((((...((((.......-.)))).)))))))) ( -35.70)
>DroSec_CAF1 57474 97 + 1
AUUCAAUCGGGCCCAUUAGCUCAGUUGGUUAGAGCGUCGUGCUAAUAACGCGAAGGUCGCGGGUUCGAUCCCCUCAUGGGCCAUAGAUUAUUAUUUU-----------------------
....((((.(((((((..((((.........))))((((.(((.....((((.....))))))).))))......)))))))...))))........----------------------- ( -30.90)
>DroSim_CAF1 54441 97 + 1
AUUCCAUCGGGCCCAUUAGCUCAGUUGGUUAGAGCGUCGUGCUAAUAACGCGAAGGUCGCGGGUUCGAUCCCCUCAUGGGCCACAGAUUAUUAUUUU-----------------------
.....(((.(((((((..((((.........))))((((.(((.....((((.....))))))).))))......)))))))...))).........----------------------- ( -29.40)
>DroPer_CAF1 83937 117 + 1
---GCAACAGGCCCAUUAGCUCAGCUGGUUAGAGCGUCGUGCUAAUAACGCGAAGGCCGCGGGUUCGAUCCCCCCAUGGGCCAGGAGUUACUUUUUGGUUUUUUUAUUCAGUGCAAUUUU
---(((...(((((((.......((.((((...((((..(....)..))))...))))))(((......)))...))))))).((((..(((....)))..))))......)))...... ( -34.70)
>consensus
AUUCCAUCGGGCCCAUUAGCUCAGUUGGUUAGAGCGUCGUGCUAAUAACGCGAAGGUCGCGGGUUCGAUCCCCUCAUGGGCCAGAGGUUAUUAUUUU_______________________
.........(((((((..((((.........))))((((.(((.....((((.....))))))).))))......)))))))...................................... (-28.04 = -28.04 +  -0.00)

alignment

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secondary structure

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dotplot

Postscript

Window 2

Location 1,673,529 – 1,673,626
Length 97
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 77.78
Mean single sequence MFE -30.48
Consensus MFE -26.88
Energy contribution -26.40
Covariance contribution -0.48
Combinations/Pair 1.10
Mean z-score -1.46
Structure conservation index 0.88
SVM decision value 1.09
SVM RNA-class probability 0.913048
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1673529 97 - 20766785
-----------------------AAAAUAAUUACCGUUGGCCCAUGAGGGGAUCGAACCCGCGACCUUCGCGUUAUUAGCACGACGCUCUAACCAACUGAGCUAAUGGGCCCCAUGGAAU
-----------------------..........((((.(((((((..(((.......)))(((.....)))..............((((.........))))..)))))))..))))... ( -31.00)
>DroPse_CAF1 90030 116 - 1
AAAAUUACACUGAA-AAAAAAACCAAAAAGUAACUCCUGGCCCAUGGGGGGAUCGAACCCGCGGCCUUCGCGUUAUUAGCACGACGCUCUAACCAGCUGAGCUAAUGGGCCUGUUGC---
..............-..............(((((....((((((((.(((.......))).).....(((.((.....)).))).((((.........))))..))))))).)))))--- ( -31.30)
>DroSec_CAF1 57474 97 - 1
-----------------------AAAAUAAUAAUCUAUGGCCCAUGAGGGGAUCGAACCCGCGACCUUCGCGUUAUUAGCACGACGCUCUAACCAACUGAGCUAAUGGGCCCGAUUGAAU
-----------------------.......(((((...(((((((..(((.......)))(((.....)))..............((((.........))))..))))))).)))))... ( -29.60)
>DroSim_CAF1 54441 97 - 1
-----------------------AAAAUAAUAAUCUGUGGCCCAUGAGGGGAUCGAACCCGCGACCUUCGCGUUAUUAGCACGACGCUCUAACCAACUGAGCUAAUGGGCCCGAUGGAAU
-----------------------..........((((((((((((..(((.......)))(((.....)))..............((((.........))))..)))))))..))))).. ( -29.20)
>DroPer_CAF1 83937 117 - 1
AAAAUUGCACUGAAUAAAAAAACCAAAAAGUAACUCCUGGCCCAUGGGGGGAUCGAACCCGCGGCCUUCGCGUUAUUAGCACGACGCUCUAACCAGCUGAGCUAAUGGGCCUGUUGC---
.............................(((((....((((((((.(((.......))).).....(((.((.....)).))).((((.........))))..))))))).)))))--- ( -31.30)
>consensus
_______________________AAAAUAAUAACCCCUGGCCCAUGAGGGGAUCGAACCCGCGACCUUCGCGUUAUUAGCACGACGCUCUAACCAACUGAGCUAAUGGGCCCGAUGGAAU
......................................((((((((((((..(((......))))))))((.......)).....((((.........))))..)))))))......... (-26.88 = -26.40 +  -0.48)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:34:18 2006