Locus 3809

Sequence ID 3R_DroMel_CAF1
Location 10,341,143 – 10,341,346
Length 203
Max. P 0.997230
window6105 window6106 window6107

overview

Window 5

Location 10,341,143 – 10,341,239
Length 96
Sequences 5
Columns 97
Reading direction reverse
Mean pairwise identity 93.36
Mean single sequence MFE -20.52
Consensus MFE -16.44
Energy contribution -16.56
Covariance contribution 0.12
Combinations/Pair 1.09
Mean z-score -1.42
Structure conservation index 0.80
SVM decision value 0.00
SVM RNA-class probability 0.534191
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10341143 96 - 27905053
AACUCACAUUA-AAAAUCUUGUUGUGCUCCACCUGCAUCUACUACAGGAUUUGGUACUCGAUUUCGUUUGGUUUGAAUGUUUUUGUUUGUGAAACUA
...(((((...-.(((((((((.((((.......)))).....)))))))))......(((...(((((.....)))))...)))..)))))..... ( -18.20)
>DroSec_CAF1 3464 96 - 1
AACUCACAUAA-AAAAUCUUGUUGUGCUCCACCUGUAUCUAUUACAGGAUUUAGUACUCGAUUUCGUUUGGUUUGAAUGUUUUUGUUUGUGAAACUU
...(((((..(-(((((.(((..(((((...((((((.....))))))....))))).))).((((.......)))).))))))...)))))..... ( -20.30)
>DroSim_CAF1 3472 96 - 1
AACUCACAUAA-AAAAUCUUGUUGUGCUCAACCUGUAUCUAUUACAGGAUUUGGUACUCGAUUUCGUUUGGUUUGAAUGUUUUUGUUUGUCAAACUA
...........-.(((((.....(((((.((((((((.....)))))).)).)))))..)))))....((((((((.............)))))))) ( -18.92)
>DroEre_CAF1 4013 96 - 1
AACUCACAAAA-AACAUCUUGUUGUGCUCCACCUGUACCCAUUGCAGGAUUUGGUACUCGAUUUCGUUUGGCUUGAAUGUUUUUGUUGGUGAAACUA
...((((.(((-((((((..((((((((...((((((.....))))))....))))).((....))...)))..).))))))))....))))..... ( -22.90)
>DroYak_CAF1 3512 97 - 1
AACUCACAAAAAAAAAUCUUGUUGUGCUCCACCUGUAUCCAUUACAGGAUUUGGUACUCGAUUUCGUUUGGUUUGAAUGUUUUUGUUUGUGAAACUA
...(((((((.((((((.(((..(((((...((((((.....))))))....))))).))).((((.......)))).)))))).)))))))..... ( -22.30)
>consensus
AACUCACAUAA_AAAAUCUUGUUGUGCUCCACCUGUAUCUAUUACAGGAUUUGGUACUCGAUUUCGUUUGGUUUGAAUGUUUUUGUUUGUGAAACUA
...((((................(((((...((((((.....))))))....))))).(((...(((((.....)))))...)))...))))..... (-16.44 = -16.56 +   0.12)

alignment

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secondary structure

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dotplot

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Window 6

Location 10,341,239 – 10,341,346
Length 107
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 90.06
Mean single sequence MFE -46.05
Consensus MFE -35.16
Energy contribution -35.55
Covariance contribution 0.39
Combinations/Pair 1.03
Mean z-score -4.72
Structure conservation index 0.76
SVM decision value 2.13
SVM RNA-class probability 0.988609
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10341239 107 + 27905053
--UUCAAA-----ACUCCAAAAUCCAAUUAGAACUCGGUCAUCCCCCCUCCG---CACUUGUGGUCAGUCUCACUGCCCGU---GGUGCUGGAGGGAGUCGCCAUAUUCUAAUUGGACGG
--......-----.........(((((((((((...(((.((...(((((((---((((...((.(((.....)))))...---))))).)))))).)).)))...)))))))))))... ( -41.30)
>DroSec_CAF1 3560 107 + 1
--UUCCAA-----ACUCCAAAAUCCAAUUAGAACUCGGUCAUCCCCCCUCCG---CACUUGUGGUCAGUCUCACUGACCGU---UGUGCUGGAGGGAGUCGCCAUAUUCUAAUUGGACGG
--......-----.........(((((((((((...(((.((...(((((((---(((...(((((((.....))))))).---.)))).)))))).)).)))...)))))))))))... ( -45.30)
>DroSim_CAF1 3568 107 + 1
--UUCCAA-----ACUCCAAAAUCCAAUUAGAACUCGGUCAUCCCCCCUCCG---CACUUGUGGUCAGUCUCACUGCCCGU---GGUGCUGGAGGGAGUCGCCAUAUUCUAAUUGGACGG
--......-----.........(((((((((((...(((.((...(((((((---((((...((.(((.....)))))...---))))).)))))).)).)))...)))))))))))... ( -41.30)
>DroEre_CAF1 4109 107 + 1
--UUGCAA-----ACUCCAAAAUCCAAUUAGAACUCGGUCAUCCCCCCUCCG---CACUUGUGGUCAGUUUCACUGCCCGU---GGUGCUGGAGGGAGUCGCCAUAUUCUAAUUGGACGG
--......-----.........(((((((((((...(((.((...(((((((---((((...((.(((.....)))))...---))))).)))))).)).)))...)))))))))))... ( -41.30)
>DroYak_CAF1 3609 107 + 1
--UUCGAA-----ACUCCAAAAUCCAAUUAGAAGUCGGUCAUCCCCCCUCCG---CACUUGUGGUCAGUUUCACUGCCCGU---GGUGCUGGAGGGAGUCGCCAUAUUCUAAUUGGACGG
--......-----.........(((((((((((...(((.((...(((((((---((((...((.(((.....)))))...---))))).)))))).)).)))...)))))))))))... ( -42.40)
>DroAna_CAF1 3042 120 + 1
UACUCCCAAAUCGACGGCGAAAUCCAAUUAGAACUCGGUCAGCCCCCCUCCGGCACUCUUCGGGUCAGUCUCACUGCCCGGGGUCGUGCUGGAGGGAGUUGCCAUGUUCUAAUUGGACGG
.....((...(((....)))..((((((((((((..((.((((..(((((((((((.(((((((.(((.....))))))))))..))))))))))).))))))..)))))))))))).)) ( -64.70)
>consensus
__UUCCAA_____ACUCCAAAAUCCAAUUAGAACUCGGUCAUCCCCCCUCCG___CACUUGUGGUCAGUCUCACUGCCCGU___GGUGCUGGAGGGAGUCGCCAUAUUCUAAUUGGACGG
......................(((((((((((...(((....(.(((((((...((((.((((.(((.....))).))))...)))).))))))).)..)))...)))))))))))... (-35.16 = -35.55 +   0.39)

alignment

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secondary structure

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dotplot

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Window 7

Location 10,341,239 – 10,341,346
Length 107
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 90.06
Mean single sequence MFE -51.55
Consensus MFE -41.06
Energy contribution -41.15
Covariance contribution 0.09
Combinations/Pair 1.06
Mean z-score -5.26
Structure conservation index 0.80
SVM decision value 2.82
SVM RNA-class probability 0.997230
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10341239 107 - 27905053
CCGUCCAAUUAGAAUAUGGCGACUCCCUCCAGCACC---ACGGGCAGUGAGACUGACCACAAGUG---CGGAGGGGGGAUGACCGAGUUCUAAUUGGAUUUUGGAGU-----UUUGAA--
(((((((((((((((.(((((.((((((((.((((.---...(((((.....))).))....)))---)))))))))..)).))).)))))))))))))...))...-----......-- ( -49.60)
>DroSec_CAF1 3560 107 - 1
CCGUCCAAUUAGAAUAUGGCGACUCCCUCCAGCACA---ACGGUCAGUGAGACUGACCACAAGUG---CGGAGGGGGGAUGACCGAGUUCUAAUUGGAUUUUGGAGU-----UUGGAA--
(((((((((((((((.(((((.((((((((.((((.---..((((((.....))))))....)))---)))))))))..)).))).)))))))))))))...))...-----......-- ( -53.10)
>DroSim_CAF1 3568 107 - 1
CCGUCCAAUUAGAAUAUGGCGACUCCCUCCAGCACC---ACGGGCAGUGAGACUGACCACAAGUG---CGGAGGGGGGAUGACCGAGUUCUAAUUGGAUUUUGGAGU-----UUGGAA--
(((((((((((((((.(((((.((((((((.((((.---...(((((.....))).))....)))---)))))))))..)).))).)))))))))))))...))...-----......-- ( -49.60)
>DroEre_CAF1 4109 107 - 1
CCGUCCAAUUAGAAUAUGGCGACUCCCUCCAGCACC---ACGGGCAGUGAAACUGACCACAAGUG---CGGAGGGGGGAUGACCGAGUUCUAAUUGGAUUUUGGAGU-----UUGCAA--
(((((((((((((((.(((((.((((((((.((((.---...(((((.....))).))....)))---)))))))))..)).))).)))))))))))))...))...-----......-- ( -49.60)
>DroYak_CAF1 3609 107 - 1
CCGUCCAAUUAGAAUAUGGCGACUCCCUCCAGCACC---ACGGGCAGUGAAACUGACCACAAGUG---CGGAGGGGGGAUGACCGACUUCUAAUUGGAUUUUGGAGU-----UUCGAA--
((((((((((((((..(((((.((((((((.((((.---...(((((.....))).))....)))---)))))))))..)).)))..))))))))))))...))...-----......-- ( -46.80)
>DroAna_CAF1 3042 120 - 1
CCGUCCAAUUAGAACAUGGCAACUCCCUCCAGCACGACCCCGGGCAGUGAGACUGACCCGAAGAGUGCCGGAGGGGGGCUGACCGAGUUCUAAUUGGAUUUCGCCGUCGAUUUGGGAGUA
..(((((((((((((.(((((.((((((((.((((.....(((((((.....))).))))....)))).))))))))..)).))).)))))))))))))(((.(((......)))))).. ( -60.60)
>consensus
CCGUCCAAUUAGAAUAUGGCGACUCCCUCCAGCACC___ACGGGCAGUGAGACUGACCACAAGUG___CGGAGGGGGGAUGACCGAGUUCUAAUUGGAUUUUGGAGU_____UUGGAA__
..(((((((((((((.(((((.((((((((..(((......((.(((.....))).))....)))....))))))))..)).))).)))))))))))))..................... (-41.06 = -41.15 +   0.09)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:10:38 2006