Locus 4239

Sequence ID 3R_DroMel_CAF1
Location 11,376,298 – 11,376,618
Length 320
Max. P 0.999410
window6872 window6873 window6874 window6875 window6876

overview

Window 2

Location 11,376,298 – 11,376,418
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.50
Mean single sequence MFE -43.56
Consensus MFE -36.44
Energy contribution -36.68
Covariance contribution 0.24
Combinations/Pair 1.16
Mean z-score -1.46
Structure conservation index 0.84
SVM decision value 0.49
SVM RNA-class probability 0.754870
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11376298 120 - 27905053
GGUUACGAAGCGGAGGAGAUUUUCUGCUCUGGAAUGGUGCGCCACUCGGAACAACCAGUGGGUGUAAUCGUGGCUCUUACUGCUGACCAAGCCCAAAGGGCAACAAAGCUUGUCAAGAUC
.(((((((..(((((.((.....)).)))))......(((((((((.((.....))))).)))))).)))))))((((((.(((......((((...)))).....)))..)).)))).. ( -39.40)
>DroSec_CAF1 123937 120 - 1
GGUUACGAAGCGGAGGAGAUCUUCUGCUCUGGAACGGUGCGCCACUCCGAACAACCAGUGGGUGUAAUCGUGGCUCUUACUGCUGACCAAGCUCAAAGGGCCACAAAACUGGUCAAGAUC
((((((((.(((((((....)))))))))((((..((....))..))))....(((....)))))))))(((((((((...(((.....)))...)))))))))................ ( -42.30)
>DroSim_CAF1 114941 120 - 1
GGUUACGAAGCGGAGGAGAUCUUCUGCUCUGGAAUGGUGCGCCACUCCGAACAGCCAGUGGGUGUAAUCGUGGCUCUUACUGCUGACCAAGCACAAAGGGCCACAAAACUGGUCAGGAUC
((((((((.(((((((....)))))))))((((.(((....))).))))....(((....)))))))))(((((((((..((((.....))))..)))))))))................ ( -46.20)
>DroEre_CAF1 111492 120 - 1
GGCUACGAAGCCGAGGAGAUCUUUUGCUCCGGAUUGGUGCGCCACUCGGAACAGCCAGUGGGUGUAAUCGUGGCUCUCACUGCUGACCAAGCGCAAAGGGCCACUAAGUUGGUCAAGAUU
((((....))))..((((........)))).(((..((((((((((.((.....))))).))))))...((((((((...((((.....))))...))))))))....)..)))...... ( -43.50)
>DroYak_CAF1 114034 120 - 1
GGCUACGAAGCCGAGGAGAUCUUCUGCUCGGGAUUGGUGCGCCACUCGGAGCAGCCAGUGGGUGUAAUCGUGGCUCUUACUGCUGACCAAGCCCAAAGGGCCACUAAGUUGGUCAAGAUU
((((((....(((((.((.....)).)))))((((.(..(.(((((.((.....))))))))..)))))(((((((((...(((.....)))...)))))))))...).)))))...... ( -46.40)
>consensus
GGUUACGAAGCGGAGGAGAUCUUCUGCUCUGGAAUGGUGCGCCACUCGGAACAGCCAGUGGGUGUAAUCGUGGCUCUUACUGCUGACCAAGCCCAAAGGGCCACAAAGCUGGUCAAGAUC
((((.((.((((((((....)))))))).))((...(..(.(((((.((.....))))))))..)..))(((((((((...(((.....)))...)))))))))..)))).......... (-36.44 = -36.68 +   0.24)

alignment

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secondary structure

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dotplot

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Window 3

Location 11,376,418 – 11,376,538
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.42
Mean single sequence MFE -37.92
Consensus MFE -33.27
Energy contribution -32.75
Covariance contribution -0.52
Combinations/Pair 1.17
Mean z-score -1.31
Structure conservation index 0.88
SVM decision value 0.42
SVM RNA-class probability 0.728566
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11376418 120 - 27905053
AAGGUGGGAGCCACCAUUGAUCAAAUCGAUGCUACGGAAGCUCUCCAACAUCCAGGAGUGGUGGCCUUUUACACUGCGAAGGACAUUCCCGGAACGAAUACUUUCUGUGAGCCCAGUUUU
(((.((((.((((((((((((...))))))(((.....))).((((........)))).))))))..(((((((((.(((.....))).)))...(((....))))))))))))).))). ( -33.10)
>DroSec_CAF1 124057 120 - 1
AAAGUGGGAGCCACCAUCGAUCAAAUCGAUGCUUCGGAAGCUCUUCAACAUCCUGGAGUGGUGGCCUUCUACACUGCGAAGGACAUUCCCGGAACGAAUACUUUCUGUGAGCCCAGUUUU
(((.((((...((((((((((...))))))).(((((((....)))....(((.((((((....(((((........))))).)))))).))).))))........)))..)))).))). ( -38.60)
>DroSim_CAF1 115061 120 - 1
AAAGUGGGAGCCACCAUCGAUCAAAUCGAUGCUUCGGAAGCUCUCCAACAUCCAGGAGUGGUGGCCUUCUACACUGCGAAGGACAUUCCCGGAACGAAUACUUUCUGUGAGCCCAGUUUU
(((.((((...((((((((((...))))))).((((((.....)))....(((.((((((....(((((........))))).)))))).)))..)))........)))..)))).))). ( -38.40)
>DroEre_CAF1 111612 120 - 1
AAGGUGGGAGCCACCGUCGAUCAAAUCGAUGCUUCGGCAGCUCUCCAAUAUCCAGGAGUGGUGGCCUUUUACACUGCAAAGGACAUUCCCGGCACGAAUACUUUCUGUGAGCCCAGUUUU
(((.((((.((((((((((((...))))))((....))....((((........)))).))))))..((((((.(((...((......)).))).(((....))))))))))))).))). ( -39.30)
>DroYak_CAF1 114154 120 - 1
AAGGUGGGAGCCACCAUCGACCAAAUCGAUGCCUCGGAAGCUCUACAACAUCCAGGCGUGGUGGCCUUUUACACUGCGAAGGACAUUCCCGGAACGAAUACUUUCUGUGAGCCCAGCUUU
(((.((((.(((((((((((.....)))))((((.(((.(........).)))))))..))))))..(((((((((.(((.....))).)))...(((....))))))))))))).))). ( -40.20)
>consensus
AAGGUGGGAGCCACCAUCGAUCAAAUCGAUGCUUCGGAAGCUCUCCAACAUCCAGGAGUGGUGGCCUUUUACACUGCGAAGGACAUUCCCGGAACGAAUACUUUCUGUGAGCCCAGUUUU
(((.((((...(((((((((.....))))))....(((((..........(((.((((((....(((((........))))).)))))).))).......))))).)))..)))).))). (-33.27 = -32.75 +  -0.52)

alignment

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secondary structure

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Window 4

Location 11,376,458 – 11,376,578
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.58
Mean single sequence MFE -43.16
Consensus MFE -39.00
Energy contribution -39.24
Covariance contribution 0.24
Combinations/Pair 1.14
Mean z-score -1.21
Structure conservation index 0.90
SVM decision value 0.35
SVM RNA-class probability 0.699519
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11376458 120 + 27905053
UUCGCAGUGUAAAAGGCCACCACUCCUGGAUGUUGGAGAGCUUCCGUAGCAUCGAUUUGAUCAAUGGUGGCUCCCACCUUUGUGGCGCCCACAAAGGCGCAGUAAACGGAGUUGGAAGUG
..(((.........((((((((((((........)))).(((.....)))..............)))))))).(((.((((((.(((((......))))).....)))))).)))..))) ( -42.60)
>DroSec_CAF1 124097 120 + 1
UUCGCAGUGUAGAAGGCCACCACUCCAGGAUGUUGAAGAGCUUCCGAAGCAUCGAUUUGAUCGAUGGUGGCUCCCACUUUCGUGGCGCCCACAAAGGCGCAGUAAACGGAGUUGGAAGUG
..(((.........(((((((......(((.(((....))).))).....((((((...))))))))))))).(((.((((((.(((((......))))).....)))))).)))..))) ( -41.80)
>DroSim_CAF1 115101 120 + 1
UUCGCAGUGUAGAAGGCCACCACUCCUGGAUGUUGGAGAGCUUCCGAAGCAUCGAUUUGAUCGAUGGUGGCUCCCACUUUCGUGGCACCCACGAAGGCGCAGUAAACGGAGUUGGAAGUG
((((.(.(((.(..(((((((.((((........)))).(((.....)))((((((...)))))))))))))..).(((((((((...))))))))).))).)...)))).......... ( -39.40)
>DroEre_CAF1 111652 120 + 1
UUUGCAGUGUAAAAGGCCACCACUCCUGGAUAUUGGAGAGCUGCCGAAGCAUCGAUUUGAUCGACGGUGGCUCCCACCUUUGUGGCGCCCACAAAGGCGCAGUAAACGGAGUUGGAAGUG
...((.........(((((((.((((........)))).(((.....))).(((((...))))).))))))).(((.((((((.(((((......))))).....)))))).)))..)). ( -43.70)
>DroYak_CAF1 114194 120 + 1
UUCGCAGUGUAAAAGGCCACCACGCCUGGAUGUUGUAGAGCUUCCGAGGCAUCGAUUUGGUCGAUGGUGGCUCCCACCUUUGUGGCGCCCACAAAGGCGCAGUAGACGGAGUUGGAAGUG
..(((.........(((((((..(((((((.(((....))).))).))))((((((...))))))))))))).(((.((((((.(((((......))))).....)))))).)))..))) ( -48.30)
>consensus
UUCGCAGUGUAAAAGGCCACCACUCCUGGAUGUUGGAGAGCUUCCGAAGCAUCGAUUUGAUCGAUGGUGGCUCCCACCUUUGUGGCGCCCACAAAGGCGCAGUAAACGGAGUUGGAAGUG
..(((.........(((((((.((((........)))).(((.....)))((((((...))))))))))))).(((.((((((.(((((......))))).....)))))).)))..))) (-39.00 = -39.24 +   0.24)

alignment

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secondary structure

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dotplot

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Window 5

Location 11,376,458 – 11,376,578
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.58
Mean single sequence MFE -42.34
Consensus MFE -38.54
Energy contribution -38.26
Covariance contribution -0.28
Combinations/Pair 1.11
Mean z-score -2.28
Structure conservation index 0.91
SVM decision value 3.58
SVM RNA-class probability 0.999410
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11376458 120 - 27905053
CACUUCCAACUCCGUUUACUGCGCCUUUGUGGGCGCCACAAAGGUGGGAGCCACCAUUGAUCAAAUCGAUGCUACGGAAGCUCUCCAACAUCCAGGAGUGGUGGCCUUUUACACUGCGAA
..(((((..(((((....)..(((((((((((...)))))))))))))))....(((((((...)))))))....)))))...(((........)))(..(((........)))..)... ( -40.50)
>DroSec_CAF1 124097 120 - 1
CACUUCCAACUCCGUUUACUGCGCCUUUGUGGGCGCCACGAAAGUGGGAGCCACCAUCGAUCAAAUCGAUGCUUCGGAAGCUCUUCAACAUCCUGGAGUGGUGGCCUUCUACACUGCGAA
..(((((..((((.......((((((....))))))(((....)))))))....(((((((...)))))))....)))))...((((......))))(..(((........)))..)... ( -42.70)
>DroSim_CAF1 115101 120 - 1
CACUUCCAACUCCGUUUACUGCGCCUUCGUGGGUGCCACGAAAGUGGGAGCCACCAUCGAUCAAAUCGAUGCUUCGGAAGCUCUCCAACAUCCAGGAGUGGUGGCCUUCUACACUGCGAA
..(((((..((((.......((((((....))))))(((....)))))))....(((((((...)))))))....)))))...(((........)))(..(((........)))..)... ( -42.40)
>DroEre_CAF1 111652 120 - 1
CACUUCCAACUCCGUUUACUGCGCCUUUGUGGGCGCCACAAAGGUGGGAGCCACCGUCGAUCAAAUCGAUGCUUCGGCAGCUCUCCAAUAUCCAGGAGUGGUGGCCUUUUACACUGCAAA
...................(((((((((((((...))))))))))(((.((((((((((((...))))))((....))....((((........)))).))))))))).......))).. ( -42.80)
>DroYak_CAF1 114194 120 - 1
CACUUCCAACUCCGUCUACUGCGCCUUUGUGGGCGCCACAAAGGUGGGAGCCACCAUCGACCAAAUCGAUGCCUCGGAAGCUCUACAACAUCCAGGCGUGGUGGCCUUUUACACUGCGAA
............(((......(((((((((((...)))))))))))((.(((((((((((.....)))))((((.(((.(........).)))))))..))))))))........))).. ( -43.30)
>consensus
CACUUCCAACUCCGUUUACUGCGCCUUUGUGGGCGCCACAAAGGUGGGAGCCACCAUCGAUCAAAUCGAUGCUUCGGAAGCUCUCCAACAUCCAGGAGUGGUGGCCUUUUACACUGCGAA
..(((((..((((.......((((((....))))))(((....)))))))....((((((.....))))))....))))).................(..(((........)))..)... (-38.54 = -38.26 +  -0.28)

alignment

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secondary structure

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dotplot

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Window 6

Location 11,376,498 – 11,376,618
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.67
Mean single sequence MFE -41.76
Consensus MFE -37.72
Energy contribution -38.12
Covariance contribution 0.40
Combinations/Pair 1.14
Mean z-score -1.22
Structure conservation index 0.90
SVM decision value 0.33
SVM RNA-class probability 0.693120
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11376498 120 - 27905053
AGUGCUCCGGAGAGGCCACAUAUAUGAACGAUGUGCUGACCACUUCCAACUCCGUUUACUGCGCCUUUGUGGGCGCCACAAAGGUGGGAGCCACCAUUGAUCAAAUCGAUGCUACGGAAG
.(((((((((((.((.(((((((.......))))).)).)).))))...............(((((((((((...))))))))))))))).)))(((((((...)))))))...(....) ( -39.70)
>DroSec_CAF1 124137 120 - 1
AGUGCUCCGGAGAGGCCACCUACAUGAACGAUGUGCUGACCACUUCCAACUCCGUUUACUGCGCCUUUGUGGGCGCCACGAAAGUGGGAGCCACCAUCGAUCAAAUCGAUGCUUCGGAAG
.....(((((((.(((..(((((.((((((..((...((.....))..))..))))))..((((((....)))))).......))))).)))..(((((((...)))))))))))))).. ( -44.20)
>DroSim_CAF1 115141 120 - 1
AGUGCUCCGGAGAGGCCACCUACAUGAACGAUGUGCUGACCACUUCCAACUCCGUUUACUGCGCCUUCGUGGGUGCCACGAAAGUGGGAGCCACCAUCGAUCAAAUCGAUGCUUCGGAAG
.....(((((((.((((((((((......((.(((.....))).))......(((.....))).....)))))))((((....))))..)))..(((((((...)))))))))))))).. ( -43.40)
>DroEre_CAF1 111692 120 - 1
AGUGCUCCGGCGAGGCCACCUACAUGAAUGAUGUGCUGACCACUUCCAACUCCGUUUACUGCGCCUUUGUGGGCGCCACAAAGGUGGGAGCCACCGUCGAUCAAAUCGAUGCUUCGGCAG
.((((((((((...))).......((((((..((...((.....))..))..))))))...(((((((((((...))))))))))))))).))).((((((...))))))((....)).. ( -40.60)
>DroYak_CAF1 114234 120 - 1
AGUGCUCCGGAGAGGCCACCUACAUGAACGAUGUGCUGACCACUUCCAACUCCGUCUACUGCGCCUUUGUGGGCGCCACAAAGGUGGGAGCCACCAUCGACCAAAUCGAUGCCUCGGAAG
.((((((((((((((...)))........((.(((.....))).))...))))........(((((((((((...))))))))))))))).)))((((((.....))))))......... ( -40.90)
>consensus
AGUGCUCCGGAGAGGCCACCUACAUGAACGAUGUGCUGACCACUUCCAACUCCGUUUACUGCGCCUUUGUGGGCGCCACAAAGGUGGGAGCCACCAUCGAUCAAAUCGAUGCUUCGGAAG
.....(((((((.(((..(((((.((((((..((...((.....))..))..))))))..((((((....)))))).......))))).)))..((((((.....))))))))))))).. (-37.72 = -38.12 +   0.40)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:23:08 2006