Locus 9990

Sequence ID 3R_DroMel_CAF1
Location 26,762,608 – 26,762,725
Length 117
Max. P 0.801173
window15922 window15923

overview

Window 2

Location 26,762,608 – 26,762,725
Length 117
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 80.00
Mean single sequence MFE -40.32
Consensus MFE -27.36
Energy contribution -28.12
Covariance contribution 0.76
Combinations/Pair 1.39
Mean z-score -1.19
Structure conservation index 0.68
SVM decision value -0.04
SVM RNA-class probability 0.514491
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26762608 117 + 27905053
UACUGGACCGCCUUCUGAUGGCGAUUGGCCAUGAAGUAGGCGCAGCCUAUCCAAAUACAAGUGAUCAGGACUACGCUGGAGAUGAUCAGCACUUUGGUGGGUAUGGAUUCCAGUGAA
(((((((((((((.((.(((((.....)))))..)).))))...(((((.(((((.....(((........)))(((((......)))))..))))))))))..))..))))))).. ( -42.00)
>DroSec_CAF1 66468 117 + 1
UACUGGACCGCCUUCUGAUGGUGAUUGGCCAUGAAGUAGGCGCAGCCAAUCCAAGUACAAGUGAUCAGGACUACGCUGGAGAUGAUCAGCACAUUUGUGGGGAUGGAUUCCAGUGAA
(((((((.(((((.((.(((((.....)))))..)).)))))...(((.(((...((((((((....(.....)(((((......))))).)))))))).))))))..))))))).. ( -42.20)
>DroSim_CAF1 70050 117 + 1
UACUGGACCGCCUUCUGAUGGCGAUUGGCCAUGAAGUAGGCGCAGCCAAUCCAAGUACAAGUGAUCAGGACUACGCUGGAGAUGAUCAGCACAUUGGUGGGGAUGGAUUCCAGUGAA
(((((((.(((((.((.(((((.....)))))..)).)))))...(((.(((...(((.((((....(.....)(((((......))))).)))).))).))))))..))))))).. ( -40.30)
>DroEre_CAF1 67689 117 + 1
UGCUGGACCGCCUUCUGAUGCCGAUUGGCCAUGAAGUAGGCGCAGCCUGUCCAAGUGAGAGUGAUCAGGACCACGCUGGCGAAGAUCAGCACUUUGGUGGGGAUGGAUUCCAGUGUG
.((((((.(((((.((.(((((....)).)))..)).)))))((.((..((.(((((....(((((....((.....))....))))).))))).))..))..))...))))))... ( -39.00)
>DroYak_CAF1 69059 117 + 1
UACUGGACCGCCUUCUGGUGGCGAUUGGCCAUGAAGAAGGCGCAGCCUACCCAAGUGACCGUGAUCACGACGACGCUGCAGAGGAUCAGCACCUUGGUGGGUACGGAUUCCAGCGUA
..((((((((((((((.(((((.....)))))..)))))))...(((((((...((((......))))......((((........)))).....)))))))..))..))))).... ( -47.20)
>DroPer_CAF1 76294 116 + 1
UACUGCAGUGCCUUCUGGUGCCUGCUGGUUAUGAAGUAGGUGCAGCCCAGCCAGACGGUGGACAAUACGAUAGCUCCGAUAAUUAUCAGAACGUUGCGGGGUAUUUCUUCGAU-GAA
..((((...(((....)))(((((((........))))))))))).(((.((....)))))......(((..((((((.((((.........))))))))))......)))..-... ( -31.20)
>consensus
UACUGGACCGCCUUCUGAUGGCGAUUGGCCAUGAAGUAGGCGCAGCCUAUCCAAGUACAAGUGAUCAGGACUACGCUGGAGAUGAUCAGCACAUUGGUGGGGAUGGAUUCCAGUGAA
(((((((.(((((.((.(((((.....)))))..)).)))))...((((((.........(((........)))(((((......))))).....)))))).......))))))).. (-27.36 = -28.12 +   0.76)

alignment

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secondary structure

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dotplot

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Window 3

Location 26,762,608 – 26,762,725
Length 117
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 80.00
Mean single sequence MFE -38.22
Consensus MFE -21.41
Energy contribution -24.17
Covariance contribution 2.75
Combinations/Pair 1.24
Mean z-score -2.22
Structure conservation index 0.56
SVM decision value 0.62
SVM RNA-class probability 0.801173
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26762608 117 - 27905053
UUCACUGGAAUCCAUACCCACCAAAGUGCUGAUCAUCUCCAGCGUAGUCCUGAUCACUUGUAUUUGGAUAGGCUGCGCCUACUUCAUGGCCAAUCGCCAUCAGAAGGCGGUCCAGUA
...((((((..((..............((((........))))((((.((((.(((........))).))))))))((((.((..(((((.....))))).)).)))))))))))). ( -38.50)
>DroSec_CAF1 66468 117 - 1
UUCACUGGAAUCCAUCCCCACAAAUGUGCUGAUCAUCUCCAGCGUAGUCCUGAUCACUUGUACUUGGAUUGGCUGCGCCUACUUCAUGGCCAAUCACCAUCAGAAGGCGGUCCAGUA
...((((((..((..............((((........))))((((((..((((.(........)))))))))))((((.((..((((.......)))).)).)))))))))))). ( -33.90)
>DroSim_CAF1 70050 117 - 1
UUCACUGGAAUCCAUCCCCACCAAUGUGCUGAUCAUCUCCAGCGUAGUCCUGAUCACUUGUACUUGGAUUGGCUGCGCCUACUUCAUGGCCAAUCGCCAUCAGAAGGCGGUCCAGUA
...((((((..((..............((((........))))((((((..((((.(........)))))))))))((((.((..(((((.....))))).)).)))))))))))). ( -37.40)
>DroEre_CAF1 67689 117 - 1
CACACUGGAAUCCAUCCCCACCAAAGUGCUGAUCUUCGCCAGCGUGGUCCUGAUCACUCUCACUUGGACAGGCUGCGCCUACUUCAUGGCCAAUCGGCAUCAGAAGGCGGUCCAGCA
(((.((((.....(((..(((....)))..))).....)))).)))(((((((......)))...))))..((((.(((..((((...(((....)))....))))..))).)))). ( -38.70)
>DroYak_CAF1 69059 117 - 1
UACGCUGGAAUCCGUACCCACCAAGGUGCUGAUCCUCUGCAGCGUCGUCGUGAUCACGGUCACUUGGGUAGGCUGCGCCUUCUUCAUGGCCAAUCGCCACCAGAAGGCGGUCCAGUA
...((((((..((.((((((....(..((((........))))..)...(((((....))))).))))))))...((((((((...((((.....))))..)))))))).)))))). ( -50.50)
>DroPer_CAF1 76294 116 - 1
UUC-AUCGAAGAAAUACCCCGCAACGUUCUGAUAAUUAUCGGAGCUAUCGUAUUGUCCACCGUCUGGCUGGGCUGCACCUACUUCAUAACCAGCAGGCACCAGAAGGCACUGCAGUA
...-...((((..............((((((((....))))))))....(((..(((((((....)).)))))))).....)))).......((((((........)).)))).... ( -30.30)
>consensus
UUCACUGGAAUCCAUACCCACCAAAGUGCUGAUCAUCUCCAGCGUAGUCCUGAUCACUUGCACUUGGAUAGGCUGCGCCUACUUCAUGGCCAAUCGCCAUCAGAAGGCGGUCCAGUA
...((((((..((..............((((........))))((((.((((.(((........))).))))))))((((.((..(((((.....))))).)).)))))))))))). (-21.41 = -24.17 +   2.75)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:46:30 2006