Locus 9

Sequence ID 2L_DroMel_CAF1
Location 37,799 – 37,952
Length 153
Max. P 0.812564
window13 window14

overview

Window 3

Location 37,799 – 37,891
Length 92
Sequences 6
Columns 98
Reading direction reverse
Mean pairwise identity 80.92
Mean single sequence MFE -24.47
Consensus MFE -16.36
Energy contribution -17.17
Covariance contribution 0.81
Combinations/Pair 1.10
Mean z-score -1.99
Structure conservation index 0.67
SVM decision value 0.65
SVM RNA-class probability 0.812564
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 37799 92 - 22407834
AGCUACGACCUAUUUCACAUACAUCACUGAAGUGGCCGGGACAAAACUACCGCGCCAUUGACGCACCCCCUCUUCCACAGGUUUCUCAGCA------A
.(((..(((((...(((..........)))(((((((((..........))).))))))...................)))))....))).------. ( -18.90)
>DroSec_CAF1 15762 92 - 1
AGCUGCGACCUAUUUCACAUACAUCACUGAAGUGGCCGGUACAAAACUACCGCGCCAUUGACUCACCCCCCCUCCCGCAGGUUUCUCAGCA------A
.((((.(((((...(((..........)))(((((((((((......))))).))))))...................)))))...)))).------. ( -24.40)
>DroSim_CAF1 17342 92 - 1
AGCUGCGACCUAUUUCACAUACAUCACUGAAGUGGCCGGUACAAAACUACCGCGCCAUUGACUCACCCCCCCUCCCGCAGGUUUCUCAGCA------A
.((((.(((((...(((..........)))(((((((((((......))))).))))))...................)))))...)))).------. ( -24.40)
>DroEre_CAF1 15891 92 - 1
AGCUGCGACCUAUUUCACAUACAUCAAUAAAGUGGCCGGGCCAAAACUACCGUGCCAUUGACGCACACCCUUCCGCGCAGGUUCCUCAGCA------A
.((((.(((((...................(((((((((..........))).))))))(.(((..........)))))))))...)))).------. ( -25.40)
>DroYak_CAF1 14593 92 - 1
AGUUGCGACCCAUUCCUCAUACAUCAUUGAAGUGGCCGGGCCAAAACUACCGCGCCAUUGACGCACCCCCUUCCCCACCGAUUUCUCAGCA------A
...((((.........(((........)))(((((((((..........))).))))))..))))..........................------. ( -17.90)
>DroAna_CAF1 14802 98 - 1
AGCUGCGACCUGUGGGGCAGCGCUCCUCCAAGUGGCCGGGGCAGAACUACCGUGCCAUUGACGCUCCUCCGCCACCCCAGAAUUUUCAGCAGCAACAG
.(((((.....((((((.((((.((.....(((((((((..........))).)))))))))))).)))))).......((....)).)))))..... ( -35.80)
>consensus
AGCUGCGACCUAUUUCACAUACAUCACUGAAGUGGCCGGGACAAAACUACCGCGCCAUUGACGCACCCCCUCCCCCGCAGGUUUCUCAGCA______A
.((((.(((((..........((....)).(((((((((..........))).))))))...................)))))...))))........ (-16.36 = -17.17 +   0.81)

alignment

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secondary structure

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dotplot

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Window 4

Location 37,851 – 37,952
Length 101
Sequences 6
Columns 107
Reading direction forward
Mean pairwise identity 83.82
Mean single sequence MFE -31.99
Consensus MFE -22.62
Energy contribution -23.15
Covariance contribution 0.53
Combinations/Pair 1.30
Mean z-score -1.81
Structure conservation index 0.71
SVM decision value -0.00
SVM RNA-class probability 0.532239
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 37851 101 + 22407834
CCCGGCCACUUCAGUGAUGUAUGUGAAAUAGGUCGUAGCUGGCGUGGUCGUCUCUUCGACUCACCCGUGGCCACAUCAUCC------UCGUCUUCAUAUCCUUCCAU
...((((((......(((.(((.....))).)))......((.(((((((......)))).))))))))))).........------.................... ( -28.70)
>DroPse_CAF1 16555 106 + 1
CCCGUCCACUUGGUAGAAGUGUGCGUCACGGGGCGAAGUUGACGUGGGCGUCUUUUUGAUUCCCCUGUUGCCGCAUCCUCUGGGCUGUCGUCCCCGUCCCCGU-CAU
..((..(((((.....)))))..))..(((((((((....((((.(((.(((.....))).))).))))(((.((.....)))))..))).))))))......-... ( -36.40)
>DroSec_CAF1 15814 101 + 1
ACCGGCCACUUCAGUGAUGUAUGUGAAAUAGGUCGCAGCUGGCGUGGUCGUCUCUUCGACUCACCCGUGGCCACAUCAUCC------UCGUCUUCAUUUCCAUCCAU
...((((((....(((((.(((.....))).)))))....((.(((((((......)))).))))))))))).........------.................... ( -32.80)
>DroSim_CAF1 17394 101 + 1
ACCGGCCACUUCAGUGAUGUAUGUGAAAUAGGUCGCAGCUGGCGUGGUCGUCUCUUCGACUCACCCGUGGCCACAUCAUCC------UCGUCUUCAUAUCCAUCCAU
...((((((....(((((.(((.....))).)))))....((.(((((((......)))).))))))))))).........------.................... ( -32.80)
>DroEre_CAF1 15943 101 + 1
CCCGGCCACUUUAUUGAUGUAUGUGAAAUAGGUCGCAGCUGGCGUGGUCGUCUCUUCGACUCACCCGUGGCCACAUCAUCC------UCGUCUCCAUAUCCUUCCAU
...((((((......(((.(((.....))).)))......((.(((((((......)))).))))))))))).........------.................... ( -28.70)
>DroYak_CAF1 14645 101 + 1
CCCGGCCACUUCAAUGAUGUAUGAGGAAUGGGUCGCAACUGGCGUGGUCGUCUCUUCGACUCACCCGUGGCCACAUCAUCC------UCGUCUCCAUGUCCUUCCAU
...((........(((..(.((((((((((((((((....((.(((((((......)))).))))))))))).)))..)))------)))))..)))......)).. ( -32.54)
>consensus
CCCGGCCACUUCAGUGAUGUAUGUGAAAUAGGUCGCAGCUGGCGUGGUCGUCUCUUCGACUCACCCGUGGCCACAUCAUCC______UCGUCUCCAUAUCCUUCCAU
...((((((....(((((.(((.....))).)))))....((.(((((((......)))).)))))))))))................................... (-22.62 = -23.15 +   0.53)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:23:09 2006