Locus 8164

Sequence ID 3R_DroMel_CAF1
Location 21,958,441 – 21,958,607
Length 166
Max. P 0.878378
window13126 window13127 window13128

overview

Window 6

Location 21,958,441 – 21,958,538
Length 97
Sequences 4
Columns 97
Reading direction reverse
Mean pairwise identity 90.55
Mean single sequence MFE -26.42
Consensus MFE -25.48
Energy contribution -25.98
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.37
Structure conservation index 0.96
SVM decision value 0.39
SVM RNA-class probability 0.718946
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21958441 97 - 27905053
AUUUGUCGCCGACUUAUUAGCGCAGAGGUGCGAACGCUCAAGUAGGUGAAUUAAAGUGCUUCCGCUGUUUACGGUUUGCGAUCUUUGAAUUAAUAUU
....(((((.((((...(((((..((((..(...((((......)))).......)..))))))))).....)))).)))))............... ( -23.40)
>DroSec_CAF1 64193 97 - 1
AUUUGUCGCCGACUUAUUAGCGCGGAGGUGCGAACGCUCAAGUAGGUGAAUUAAAGUGCUUCCGCUGUUUACGGUUUGCGAUCUUUAAAUUAAUAUU
....(((((.((((....((((((((((..(...((((......)))).......)..))))))).)))...)))).)))))............... ( -28.70)
>DroSim_CAF1 73621 87 - 1
AUUUGUCGCCGACUUAUUAGCGCGGAGGUGCGAACGCUCAAGUAGGUGAAUUAAAGUGCUUCCGCUGUUUACGGUUUGCGAUCU----------AUU
....(((((.((((....((((((((((..(...((((......)))).......)..))))))).)))...)))).)))))..----------... ( -28.70)
>DroEre_CAF1 66428 97 - 1
AUUUGUCGCCGACUUUUUAGCGCGGAGGUGCGAAAGAUCAAGUAGGUGAAUUGAAGUGCUUCCGCUGUUUACGGUUUUCGAUCUUUGAUUUAAUAUA
....((((..((((....((((((((((..(...((.(((......))).))...)..))))))).)))...))))..))))............... ( -24.90)
>consensus
AUUUGUCGCCGACUUAUUAGCGCGGAGGUGCGAACGCUCAAGUAGGUGAAUUAAAGUGCUUCCGCUGUUUACGGUUUGCGAUCUUUGAAUUAAUAUU
....(((((.((((....((((((((((..(......(((......)))......)..))))))).)))...)))).)))))............... (-25.48 = -25.98 +   0.50)

alignment

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secondary structure

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dotplot

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Window 7

Location 21,958,498 – 21,958,607
Length 109
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 78.37
Mean single sequence MFE -32.12
Consensus MFE -20.13
Energy contribution -20.55
Covariance contribution 0.42
Combinations/Pair 1.35
Mean z-score -1.72
Structure conservation index 0.63
SVM decision value 0.65
SVM RNA-class probability 0.811108
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21958498 109 + 27905053
UGAGCGUUCGCACCUCUGCGCUAAUAAGUCGGCGACAAAUCGCUGAUCAUCGACUUGUCCAGCAUGAUUAGGCUUACGAUCU-----UUCGAUCAGCGUGGCGCUAAUCAACAU
..(((((((((.(((....(((.((((((((..((((......)).))..))))))))..)))......))).....((((.-----...)))).))).))))))......... ( -31.40)
>DroVir_CAF1 79272 102 + 1
UAUUUGUUCGCAAGCAAUUGCUAAUGGGAUGGUACCAAAUUUUUGAUUAACGCAUG-CUUGCCUUCGAUGGGAUUGCGAGCA-----U------AAACUGGUGCUAAUUCAGUU
.........((((....))))...((((.((((((((((((...)))).....(((-(((((..((.....))..)))))))-----)------....)))))))).))))... ( -28.20)
>DroSec_CAF1 64250 109 + 1
UGAGCGUUCGCACCUCCGCGCUAAUAAGUCGGCGACAAAUCGCUGAUCAUCGACUUGUCCAGCAUGAUUAGGCUUACGAUCU-----UUCGAUCAGCGUGGUGCUAAUCAACAU
.........(((((..((((((.((((((((..((((......)).))..))))))))..)))..............((((.-----...)))).))).))))).......... ( -32.90)
>DroSim_CAF1 73668 109 + 1
UGAGCGUUCGCACCUCCGCGCUAAUAAGUCGGCGACAAAUCGCUGAUCAUCGACUUGUCCAGCACGAUUAGGCUUACGAUCU-----UUUGAUCAGCGUGGUGCUAAUCAACAU
.........(((((..((((((.((((((((..((((......)).))..))))))))..)))..............((((.-----...)))).))).))))).......... ( -33.50)
>DroEre_CAF1 66485 114 + 1
UGAUCUUUCGCACCUCCGCGCUAAAAAGUCGGCGACAAAUCGCUGAUCAUCGACUUGUCCAGUUUGAUUAGGUUUGCGAUCAUCAUCUGCGAUCAGCGUGGUGCUAAUCAACAU
.........(((((...(((((.....((((((((....)))))))).........((((((..(((((........)))))....))).))).)))))))))).......... ( -31.60)
>DroYak_CAF1 66043 109 + 1
UGAUCUUUCGCACCAACGCGCUAAUAAGUCGGCGACAAAUCGCUGAUCAUCGACUUGUCCAGCAUGAUUAGGCUUACGAUCU-----UUCGAUCAGCGUGGUGCUAAUCAACAU
.........((((((.((((((.((((((((..((((......)).))..))))))))..)))..............((((.-----...)))).))))))))).......... ( -35.10)
>consensus
UGAGCGUUCGCACCUCCGCGCUAAUAAGUCGGCGACAAAUCGCUGAUCAUCGACUUGUCCAGCAUGAUUAGGCUUACGAUCU_____UUCGAUCAGCGUGGUGCUAAUCAACAU
.........(((((...(((((.....(((((((......)))))))....((.((((..(((........))).)))))).............)))))))))).......... (-20.13 = -20.55 +   0.42)

alignment

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secondary structure

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dotplot

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Window 8

Location 21,958,498 – 21,958,607
Length 109
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 78.37
Mean single sequence MFE -33.67
Consensus MFE -20.92
Energy contribution -22.52
Covariance contribution 1.59
Combinations/Pair 1.32
Mean z-score -1.92
Structure conservation index 0.62
SVM decision value 0.90
SVM RNA-class probability 0.878378
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21958498 109 - 27905053
AUGUUGAUUAGCGCCACGCUGAUCGAA-----AGAUCGUAAGCCUAAUCAUGCUGGACAAGUCGAUGAUCAGCGAUUUGUCGCCGACUUAUUAGCGCAGAGGUGCGAACGCUCA
....(((((((.((...((.((((...-----.))))))..)))))))))(((..(((((((((........)))))))))((..(....)..)))))(((((....)).))). ( -36.20)
>DroVir_CAF1 79272 102 - 1
AACUGAAUUAGCACCAGUUU------A-----UGCUCGCAAUCCCAUCGAAGGCAAG-CAUGCGUUAAUCAAAAAUUUGGUACCAUCCCAUUAGCAAUUGCUUGCGAACAAAUA
(((((.........))))).------.-----((.((((....((......)).(((-((...((((((........((....))....))))))...))))))))).)).... ( -16.40)
>DroSec_CAF1 64250 109 - 1
AUGUUGAUUAGCACCACGCUGAUCGAA-----AGAUCGUAAGCCUAAUCAUGCUGGACAAGUCGAUGAUCAGCGAUUUGUCGCCGACUUAUUAGCGCGGAGGUGCGAACGCUCA
..........(((((.(((.((((...-----.))))....((.((((....(.((((((((((........))))))))).).)....)))))))))..)))))......... ( -36.20)
>DroSim_CAF1 73668 109 - 1
AUGUUGAUUAGCACCACGCUGAUCAAA-----AGAUCGUAAGCCUAAUCGUGCUGGACAAGUCGAUGAUCAGCGAUUUGUCGCCGACUUAUUAGCGCGGAGGUGCGAACGCUCA
...(((((((((.....))))))))).-----.((.(((..((((..(((((((((..((((((.......((((....)))))))))).)))))))))))))....))).)). ( -39.01)
>DroEre_CAF1 66485 114 - 1
AUGUUGAUUAGCACCACGCUGAUCGCAGAUGAUGAUCGCAAACCUAAUCAAACUGGACAAGUCGAUGAUCAGCGAUUUGUCGCCGACUUUUUAGCGCGGAGGUGCGAAAGAUCA
....(((((.(((((.((((((((((.(((....))))).......(((..(((.....))).))))))))))).((((.(((..(....)..))))))))))))....))))) ( -34.90)
>DroYak_CAF1 66043 109 - 1
AUGUUGAUUAGCACCACGCUGAUCGAA-----AGAUCGUAAGCCUAAUCAUGCUGGACAAGUCGAUGAUCAGCGAUUUGUCGCCGACUUAUUAGCGCGUUGGUGCGAAAGAUCA
....(((((.(((((((((.((((...-----.))))....((.((((....(.((((((((((........))))))))).).)....))))))))).))))))....))))) ( -39.30)
>consensus
AUGUUGAUUAGCACCACGCUGAUCGAA_____AGAUCGUAAGCCUAAUCAUGCUGGACAAGUCGAUGAUCAGCGAUUUGUCGCCGACUUAUUAGCGCGGAGGUGCGAACGAUCA
...(((((((((.....))))))))).........((((..((((.....((((((...(((((.(((.(((....)))))).)))))..))))))...))))))))....... (-20.92 = -22.52 +   1.59)

alignment

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secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:04:03 2006