Locus 10227

Sequence ID 3R_DroMel_CAF1
Location 27,416,922 – 27,417,082
Length 160
Max. P 0.997473
window16293 window16294 window16295 window16296

overview

Window 3

Location 27,416,922 – 27,417,042
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.25
Mean single sequence MFE -46.16
Consensus MFE -38.10
Energy contribution -38.58
Covariance contribution 0.48
Combinations/Pair 1.06
Mean z-score -1.47
Structure conservation index 0.83
SVM decision value 0.42
SVM RNA-class probability 0.729106
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27416922 120 + 27905053
GCUUGGUGCUGUAAUAGGCACCUGAAAGUGCCCAAUCUGCCAGAGGGAGUACCCUUGCCGUACUCCCUCGUGACGGUCCUGGUGGACCGGAUCGACUUCACCAGUGUCUCACCCCAGGGC
((((((((((......))))))...))))((((.........((((((((((.......))))))))))((((((((((....))))))....(((.........)))))))....)))) ( -52.80)
>DroSec_CAF1 19020 120 + 1
GCUUGGUGCUGUAAUAGGCACCUCAAAGUGCCCAAUCUGCCGGAGGGAGUGCCCUUGCCAUACUCCAUCGUGACGGUCCUGGUGGACCGGAUCGACUUCACCAGUGUCUCACCCCAGGGC
((((((((((......))))))...))))((((........(((((((((((....))...))))).(((...((((((....))))))...)))))))....(((...)))....)))) ( -43.00)
>DroSim_CAF1 18843 120 + 1
GCUUGGUGCUGUAAUAGACACCUCAAAGUGCCCAAUCUGCCGGAGGGAGUGCCCUUGCCGUACUCCCUUGUGACGGUCCUGGUGGACCGGAUCGACUUCACCAGUGUCUCACCCCAGGGC
(((((((((((...))).))))...))))((((.........((((((((((.......))))))))))((((((((((....))))))....(((.........)))))))....)))) ( -45.70)
>DroEre_CAF1 19393 120 + 1
GCUUGGUGCUGUCAUAGGCACCUGGUAGUCCCCAAUCUGCCGGAGGGAGUACCUCUACCGUACUCCAUCGUGACGGUCCUGGUGGACCGAAUCGACUUCACCAGUGUCGCACCCCUAGGC
(((((((((.(.(((.((.....(((((........)))))(((((((((((.......))))))).(((...((((((....))))))...))))))).)).))).))))))...)))) ( -49.30)
>DroYak_CAF1 19260 120 + 1
GCUUGGUGCUGUCACAGGCACCUGAAAGUGCCCAAUCUGCCGGAGGGAGUCCCCUUACCGUACUCCAUCGUGACGGUCCUGGUGGACCGAAUUGACUUCACUAGUGUCUCACCCAAUGGC
(((.((((..(.(((.(((((......))))).........((((((((((........).))))).(((...((((((....))))))...)))))))....))).).))))....))) ( -40.00)
>consensus
GCUUGGUGCUGUAAUAGGCACCUGAAAGUGCCCAAUCUGCCGGAGGGAGUACCCUUGCCGUACUCCAUCGUGACGGUCCUGGUGGACCGGAUCGACUUCACCAGUGUCUCACCCCAGGGC
(((.((((((......))))))....))).........(((.((.(((((((.......))))))).))((((((((((....))))))....(((.........))))))).....))) (-38.10 = -38.58 +   0.48)

alignment

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secondary structure

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dotplot

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Window 4

Location 27,416,922 – 27,417,042
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.25
Mean single sequence MFE -47.62
Consensus MFE -37.94
Energy contribution -38.14
Covariance contribution 0.20
Combinations/Pair 1.12
Mean z-score -1.41
Structure conservation index 0.80
SVM decision value 0.05
SVM RNA-class probability 0.559477
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27416922 120 - 27905053
GCCCUGGGGUGAGACACUGGUGAAGUCGAUCCGGUCCACCAGGACCGUCACGAGGGAGUACGGCAAGGGUACUCCCUCUGGCAGAUUGGGCACUUUCAGGUGCCUAUUACAGCACCAAGC
(((....))).......(((((..(((((((.(((((....)))))((((.((((((((((.......)))))))))))))).)))))((((((....))))))....))..)))))... ( -56.20)
>DroSec_CAF1 19020 120 - 1
GCCCUGGGGUGAGACACUGGUGAAGUCGAUCCGGUCCACCAGGACCGUCACGAUGGAGUAUGGCAAGGGCACUCCCUCCGGCAGAUUGGGCACUUUGAGGUGCCUAUUACAGCACCAAGC
(((....))).......(((((..((((...((((((....))))))....((.(((((...((....))))))).))))))....((((((((....))))))))......)))))... ( -45.00)
>DroSim_CAF1 18843 120 - 1
GCCCUGGGGUGAGACACUGGUGAAGUCGAUCCGGUCCACCAGGACCGUCACAAGGGAGUACGGCAAGGGCACUCCCUCCGGCAGAUUGGGCACUUUGAGGUGUCUAUUACAGCACCAAGC
(((....))).......(((((..((((...((((((....)))))).....(((((((...((....))))))))).))))....((((((((....))))))))......)))))... ( -45.20)
>DroEre_CAF1 19393 120 - 1
GCCUAGGGGUGCGACACUGGUGAAGUCGAUUCGGUCCACCAGGACCGUCACGAUGGAGUACGGUAGAGGUACUCCCUCCGGCAGAUUGGGGACUACCAGGUGCCUAUGACAGCACCAAGC
.......(((((......((.(..((((...((((((....))))))...))))(((((((.......)))))))).))((((..((((......)))).)))).......))))).... ( -48.00)
>DroYak_CAF1 19260 120 - 1
GCCAUUGGGUGAGACACUAGUGAAGUCAAUUCGGUCCACCAGGACCGUCACGAUGGAGUACGGUAAGGGGACUCCCUCCGGCAGAUUGGGCACUUUCAGGUGCCUGUGACAGCACCAAGC
.......((((.(((.........))).....(((((....)))))(((((......((.(((..((((....))))))))).....(((((((....))))))))))))..)))).... ( -43.70)
>consensus
GCCCUGGGGUGAGACACUGGUGAAGUCGAUCCGGUCCACCAGGACCGUCACGAUGGAGUACGGCAAGGGCACUCCCUCCGGCAGAUUGGGCACUUUCAGGUGCCUAUUACAGCACCAAGC
(((....))).......(((((..((((...((((((....))))))....((.(((((.(.......).))))).))))))....((((((((....))))))))......)))))... (-37.94 = -38.14 +   0.20)

alignment

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secondary structure

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dotplot

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Window 5

Location 27,416,962 – 27,417,082
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.08
Mean single sequence MFE -52.24
Consensus MFE -44.94
Energy contribution -45.30
Covariance contribution 0.36
Combinations/Pair 1.11
Mean z-score -2.37
Structure conservation index 0.86
SVM decision value 2.87
SVM RNA-class probability 0.997473
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27416962 120 + 27905053
CAGAGGGAGUACCCUUGCCGUACUCCCUCGUGACGGUCCUGGUGGACCGGAUCGACUUCACCAGUGUCUCACCCCAGGGCACCCAAGACAUCCGUCUGUCUGGCCACGUGUCCUGGGUGG
..((((((((((.......))))))))))((((((((((....))))))....(((.........)))))))(((((((((((((.((((......)))))))....))))))))))... ( -60.00)
>DroSec_CAF1 19060 120 + 1
CGGAGGGAGUGCCCUUGCCAUACUCCAUCGUGACGGUCCUGGUGGACCGGAUCGACUUCACCAGUGUCUCACCCCAGGGCACCCAAGACAUCCGCCUGUCUGGCCAUGUGUCGUGGGUGG
.(((((((((((....))...))))).(((...((((((....))))))...)))))))............((....))((((((.(((((..(((.....)))...))))).)))))). ( -48.70)
>DroSim_CAF1 18883 120 + 1
CGGAGGGAGUGCCCUUGCCGUACUCCCUUGUGACGGUCCUGGUGGACCGGAUCGACUUCACCAGUGUCUCACCCCAGGGCACCCAAGACAUCCGCCUGUCUGGCCAUGUGUCCUGGGUGG
..((((((((((.......))))))))))((((((((((....))))))....(((.........)))))))(((((((((((((.((((......)))))))....))))))))))... ( -57.30)
>DroEre_CAF1 19433 120 + 1
CGGAGGGAGUACCUCUACCGUACUCCAUCGUGACGGUCCUGGUGGACCGAAUCGACUUCACCAGUGUCGCACCCCUAGGCACCCAGGACAUCCGCCUAUCCGGCCAUGUCUCCUGGGUGG
.((..(((((((.......)))))))...(((.(((..((((((((..........))))))))..)))))).))....(((((((((.((..(((.....)))...)).))))))))). ( -51.00)
>DroYak_CAF1 19300 120 + 1
CGGAGGGAGUCCCCUUACCGUACUCCAUCGUGACGGUCCUGGUGGACCGAAUUGACUUCACUAGUGUCUCACCCAAUGGCACCCAAGACAUCCGCCUAUCUGGCCACGUCUCCUGGGUGG
(((((((....))))..)))....((((.((((((((((....))))))....(((.........)))))))...))))((((((((((....(((.....)))...))))..)))))). ( -44.20)
>consensus
CGGAGGGAGUACCCUUGCCGUACUCCAUCGUGACGGUCCUGGUGGACCGGAUCGACUUCACCAGUGUCUCACCCCAGGGCACCCAAGACAUCCGCCUGUCUGGCCAUGUGUCCUGGGUGG
.(((((((((((.......))))))).(((...((((((....))))))...)))))))............((....))((((((.(((((..(((.....)))...))))).)))))). (-44.94 = -45.30 +   0.36)

alignment

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secondary structure

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dotplot

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Window 6

Location 27,416,962 – 27,417,082
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.08
Mean single sequence MFE -50.90
Consensus MFE -42.78
Energy contribution -43.82
Covariance contribution 1.04
Combinations/Pair 1.13
Mean z-score -1.44
Structure conservation index 0.84
SVM decision value 0.45
SVM RNA-class probability 0.740252
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27416962 120 - 27905053
CCACCCAGGACACGUGGCCAGACAGACGGAUGUCUUGGGUGCCCUGGGGUGAGACACUGGUGAAGUCGAUCCGGUCCACCAGGACCGUCACGAGGGAGUACGGCAAGGGUACUCCCUCUG
...((((((.(((....(((((((......)))).)))))).))))))(((((((.........)))....((((((....))))))))))((((((((((.......)))))))))).. ( -57.10)
>DroSec_CAF1 19060 120 - 1
CCACCCACGACACAUGGCCAGACAGGCGGAUGUCUUGGGUGCCCUGGGGUGAGACACUGGUGAAGUCGAUCCGGUCCACCAGGACCGUCACGAUGGAGUAUGGCAAGGGCACUCCCUCCG
.((((((.((((..(.(((.....))).).)))).))))))....((((...............((((...((((((....))))))...))))(((((...((....))))))))))). ( -44.70)
>DroSim_CAF1 18883 120 - 1
CCACCCAGGACACAUGGCCAGACAGGCGGAUGUCUUGGGUGCCCUGGGGUGAGACACUGGUGAAGUCGAUCCGGUCCACCAGGACCGUCACAAGGGAGUACGGCAAGGGCACUCCCUCCG
.(((((((((((..(.(((.....))).).)))))))))))((((...(((((((.........)))....((((((....)))))))))).))))....(((..((((....))))))) ( -53.00)
>DroEre_CAF1 19433 120 - 1
CCACCCAGGAGACAUGGCCGGAUAGGCGGAUGUCCUGGGUGCCUAGGGGUGCGACACUGGUGAAGUCGAUUCGGUCCACCAGGACCGUCACGAUGGAGUACGGUAGAGGUACUCCCUCCG
.(((((((((.(..(.(((.....))).).).)))))))))....((((...............((((...((((((....))))))...))))(((((((.......))))))))))). ( -52.60)
>DroYak_CAF1 19300 120 - 1
CCACCCAGGAGACGUGGCCAGAUAGGCGGAUGUCUUGGGUGCCAUUGGGUGAGACACUAGUGAAGUCAAUUCGGUCCACCAGGACCGUCACGAUGGAGUACGGUAAGGGGACUCCCUCCG
.(((((((((.(..(.(((.....))).).).)))))))))(((((..(((((((.........)))....((((((....)))))))))))))))....(((..((((....))))))) ( -47.10)
>consensus
CCACCCAGGACACAUGGCCAGACAGGCGGAUGUCUUGGGUGCCCUGGGGUGAGACACUGGUGAAGUCGAUCCGGUCCACCAGGACCGUCACGAUGGAGUACGGCAAGGGCACUCCCUCCG
.(((((((((((..(.(((.....))).).)))))))))))((((...(((((((.........)))....((((((....)))))))))).))))....(((..((((....))))))) (-42.78 = -43.82 +   1.04)

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 13:52:02 2006