Locus 5958

Sequence ID 2L_DroMel_CAF1
Location 16,778,991 – 16,779,191
Length 200
Max. P 0.998990
window9467 window9468 window9469

overview

Window 7

Location 16,778,991 – 16,779,111
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 94.61
Mean single sequence MFE -42.42
Consensus MFE -39.52
Energy contribution -40.05
Covariance contribution 0.53
Combinations/Pair 1.11
Mean z-score -2.26
Structure conservation index 0.93
SVM decision value 3.32
SVM RNA-class probability 0.998990
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16778991 120 + 22407834
AUCAACCACUUGAACAAGGUUAAGGCCAAGCUCGAGCAGACCCUCGAUGAACUGGAGGAUUCGCUGGAGCGCGAGAAGAAGGUGCGCGGCGAUGUUGAGAAGUCCAAGCGCAAGGUUGAG
.((((((.((((.....(((....)))..((((.(((..(.((((.(.....).)))).)..))).)))).)))).......(((((...(((........)))...))))).)))))). ( -43.60)
>DroVir_CAF1 9113 120 + 1
AUUAACCACUUGAACAAGGUUAAGGCCAAGCUCGAGCAGACUCUCGAUGAGCUCGAGGAUUCGCUGGAGCGCGAGAAGAAGGUGCGCGGCGAUGUUGAGAAGUCUAAGCGCAAGGUUGAG
.((((((.((((.....(((....)))..((((.(((..(..(((((.....)))))..)..))).)))).)))).......(((((...(((........)))...))))).)))))). ( -43.90)
>DroGri_CAF1 9311 120 + 1
AUCAAUCACUUGAACAAGGUGAAGGCCAAGCUCGAGCAGACUCUCGAUGAGCUCGAGGAUUCGCUGGAGCGCGAGAAGAAGGUGCGCGGCGAUGUUGAGAAGGGCAAGCGCAAGGUUGAG
.((((((.(((....)))(((...(((...(((.((((...((((((.....))))))..((((((..((((.........)))).)))))))))))))...)))...)))..)))))). ( -42.90)
>DroSec_CAF1 8598 120 + 1
AUCAACCACUUGAACAAGGUUAAGGCCAAGCUCGAGCAGACCCUCGAUGAACUGGAGGAUUCGCUGGAGCGCGAGAAGAAGGUGCGCGGCGAUGUUGAGAAGUCCAAGCGCAAGGUUGAG
.((((((.((((.....(((....)))..((((.(((..(.((((.(.....).)))).)..))).)))).)))).......(((((...(((........)))...))))).)))))). ( -43.60)
>DroWil_CAF1 8712 120 + 1
AUUAACCACUUGAACAAGGUUAAGGCCAAGCUCGAACAGACCCUCGAUGAACUCGAGGACUCUCUGGAGCGUGAGAAGAAGGUGCGCGGUGAUGUUGAGAAGUCCAAGCGCAAGGUUGAG
.((((((.(((..((..(((....)))..((((...((((.((((((.....))))))....))))))))))...)))....(((((...(((........)))...))))).)))))). ( -37.30)
>DroAna_CAF1 8823 120 + 1
AUCAACCACUUGAACAAGGUUAAGGCCAAGCUCGAGCAGACCCUCGACGAGCUCGAGGAUUCUCUGGAGCGUGAGAAGAAGGUGCGCGGUGAUGUUGAGAAGUCCAAGCGCAAGGUUGAG
.((((((.(((..((..(((....)))..((((.((.(((.((((((.....))))))..))))).))))))...)))....(((((...(((........)))...))))).)))))). ( -43.20)
>consensus
AUCAACCACUUGAACAAGGUUAAGGCCAAGCUCGAGCAGACCCUCGAUGAACUCGAGGAUUCGCUGGAGCGCGAGAAGAAGGUGCGCGGCGAUGUUGAGAAGUCCAAGCGCAAGGUUGAG
.((((((.((((.....(((....)))..((((.(((.((.((((((.....)))))).)).))).)))).)))).......(((((...(((........)))...))))).)))))). (-39.52 = -40.05 +   0.53)

alignment

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secondary structure

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dotplot

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Window 8

Location 16,778,991 – 16,779,111
Length 120
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 94.61
Mean single sequence MFE -35.44
Consensus MFE -30.79
Energy contribution -33.18
Covariance contribution 2.39
Combinations/Pair 1.06
Mean z-score -2.05
Structure conservation index 0.87
SVM decision value 1.38
SVM RNA-class probability 0.947945
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16778991 120 - 22407834
CUCAACCUUGCGCUUGGACUUCUCAACAUCGCCGCGCACCUUCUUCUCGCGCUCCAGCGAAUCCUCCAGUUCAUCGAGGGUCUGCUCGAGCUUGGCCUUAACCUUGUUCAAGUGGUUGAU
.((((((....((((((((...........((((((...........)))((((.((((.((((((.........)))))).)))).))))..))).........)))))))))))))). ( -40.25)
>DroVir_CAF1 9113 120 - 1
CUCAACCUUGCGCUUAGACUUCUCAACAUCGCCGCGCACCUUCUUCUCGCGCUCCAGCGAAUCCUCGAGCUCAUCGAGAGUCUGCUCGAGCUUGGCCUUAACCUUGUUCAAGUGGUUAAU
...((((........(((((........((((.((((...........))))....))))...(((((.....))))))))))(((.((((..((......))..)))).)))))))... ( -32.70)
>DroGri_CAF1 9311 120 - 1
CUCAACCUUGCGCUUGCCCUUCUCAACAUCGCCGCGCACCUUCUUCUCGCGCUCCAGCGAAUCCUCGAGCUCAUCGAGAGUCUGCUCGAGCUUGGCCUUCACCUUGUUCAAGUGAUUGAU
.((((...(((((..((.............)).)))))........((((((((.((((.(..(((((.....)))))..).)))).))))(((..(........)..))))))))))). ( -32.12)
>DroSec_CAF1 8598 120 - 1
CUCAACCUUGCGCUUGGACUUCUCAACAUCGCCGCGCACCUUCUUCUCGCGCUCCAGCGAAUCCUCCAGUUCAUCGAGGGUCUGCUCGAGCUUGGCCUUAACCUUGUUCAAGUGGUUGAU
.((((((....((((((((...........((((((...........)))((((.((((.((((((.........)))))).)))).))))..))).........)))))))))))))). ( -40.25)
>DroWil_CAF1 8712 120 - 1
CUCAACCUUGCGCUUGGACUUCUCAACAUCACCGCGCACCUUCUUCUCACGCUCCAGAGAGUCCUCGAGUUCAUCGAGGGUCUGUUCGAGCUUGGCCUUAACCUUGUUCAAGUGGUUAAU
..........(((((((((...............................((((.(.(((.(((((((.....)))))))))).)..))))..((......))..)))))))))...... ( -31.10)
>DroAna_CAF1 8823 120 - 1
CUCAACCUUGCGCUUGGACUUCUCAACAUCACCGCGCACCUUCUUCUCACGCUCCAGAGAAUCCUCGAGCUCGUCGAGGGUCUGCUCGAGCUUGGCCUUAACCUUGUUCAAGUGGUUGAU
.((((((....((((((((...............................((((.(((((.(((((((.....)))))))))).)).))))..((......))..)))))))))))))). ( -36.20)
>consensus
CUCAACCUUGCGCUUGGACUUCUCAACAUCGCCGCGCACCUUCUUCUCGCGCUCCAGCGAAUCCUCGAGCUCAUCGAGGGUCUGCUCGAGCUUGGCCUUAACCUUGUUCAAGUGGUUGAU
.((((((....((((((((...........((((((...........)))((((.((((.((((((((.....)))))))).)))).))))..))).........)))))))))))))). (-30.79 = -33.18 +   2.39)

alignment

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secondary structure

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dotplot

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Window 9

Location 16,779,071 – 16,779,191
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 93.33
Mean single sequence MFE -45.70
Consensus MFE -40.24
Energy contribution -41.18
Covariance contribution 0.95
Combinations/Pair 1.25
Mean z-score -1.91
Structure conservation index 0.88
SVM decision value 1.34
SVM RNA-class probability 0.944298
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16779071 120 + 22407834
GGUGCGCGGCGAUGUUGAGAAGUCCAAGCGCAAGGUUGAGGGCGACCUCAAGCUCACCCAGGAGGCUGUUGCCGAUCUGGAGCGCAACAAGAAGGAGCUCGAGCAGACCAUCCAGCGCAA
..(((((.(.(((((((((...(((..((((.((.((((((....)))))).))...(((((.(((....)))..))))).))))........))).)))))......))))).))))). ( -47.00)
>DroVir_CAF1 9193 120 + 1
GGUGCGCGGCGAUGUUGAGAAGUCUAAGCGCAAGGUUGAGGGUGACCUCAAGCUGACCCAGGAGGCUGUUUCCGAUCUGGAGCGCAACAAGAAGGAGUUGGAGCAGACCAUCCAGCGUAA
(((((((...(((........)))...)))).((.((((((....)))))).)).)))..((((((((((.(((((((....(.......)..))).))))))))).)).)))....... ( -42.80)
>DroGri_CAF1 9391 120 + 1
GGUGCGCGGCGAUGUUGAGAAGGGCAAGCGCAAGGUUGAGGGUGACCUCAAGCUGACCCAGGAGGCUGUUGCCGAUCUGGAGCGCAACAAGAAGGAGCUGGAGCAGACCAUUCAGCGCAA
..((((((((..((((......)))).((((.((.((((((....)))))).))...(((((.(((....)))..))))).))))...........)))((......)).....))))). ( -48.00)
>DroSec_CAF1 8678 120 + 1
GGUGCGCGGCGAUGUUGAGAAGUCCAAGCGCAAGGUUGAGGGCGACCUCAAGCUCACCCAGGAGGCUGUUGCCGAUCUGGAGCGCAACAAGAAGGAGCUCGAGCAGACCAUCCAGCGCAA
..(((((.(.(((((((((...(((..((((.((.((((((....)))))).))...(((((.(((....)))..))))).))))........))).)))))......))))).))))). ( -47.00)
>DroWil_CAF1 8792 120 + 1
GGUGCGCGGUGAUGUUGAGAAGUCCAAGCGCAAGGUUGAGGGUGACCUUAAGUUGACUCAGGAGGCUGUCGCUGAUCUUGAGCGCAACAAGAAGGAGUUGGAACAGACCAUCCAACGCAA
..(((((...(((........)))...)))))...((((((....))))))((((.((((((((((....)))..)))))))..))))........((((((........)))))).... ( -41.00)
>DroAna_CAF1 8903 120 + 1
GGUGCGCGGUGAUGUUGAGAAGUCCAAGCGCAAGGUUGAGGGAGACCUCAAGCUCACCCAGGAGGCUGUUGCCGAUCUGGAGCGCAACAAGAAGGAAUUGGAGCAGACCAUCCAGCGCAA
..(((((.(.(((((((.....(((((((((.((.((((((....)))))).))...(((((.(((....)))..))))).))))..(.....)...))))).)))..))))).))))). ( -48.40)
>consensus
GGUGCGCGGCGAUGUUGAGAAGUCCAAGCGCAAGGUUGAGGGUGACCUCAAGCUCACCCAGGAGGCUGUUGCCGAUCUGGAGCGCAACAAGAAGGAGCUGGAGCAGACCAUCCAGCGCAA
..(((((.(.((((.............((((.((.((((((....)))))).))...(((((.(((....)))..))))).))))...........((....))....))))).))))). (-40.24 = -41.18 +   0.95)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:57:32 2006