Locus 783

Sequence ID 3R_DroMel_CAF1
Location 2,696,085 – 2,696,274
Length 189
Max. P 0.879920
window1248 window1249 window1250 window1251

overview

Window 8

Location 2,696,085 – 2,696,182
Length 97
Sequences 6
Columns 100
Reading direction reverse
Mean pairwise identity 88.21
Mean single sequence MFE -34.72
Consensus MFE -28.81
Energy contribution -29.45
Covariance contribution 0.64
Combinations/Pair 1.15
Mean z-score -2.01
Structure conservation index 0.83
SVM decision value 0.41
SVM RNA-class probability 0.724171
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2696085 97 - 27905053
--GCCAUCCACUGAAUCCGAGGAUGCAUAUGCAUCCUCAUAUGUUUUUUCGGCGGCCUCUUUGACACGAAAAUCCGCGAUGGAUGCCGGUCCUCUUCGG-
--..((((((.((.....((((((((....))))))))....(..((((((.(((.....)))...))))))..).)).))))))((((......))))- ( -31.60)
>DroSec_CAF1 6050 97 - 1
--GCCAUCCGCUGAAUCCGAGGAUGCAUAUGCAUCCUCACAUGUUGUUUCGGCGGCCUCUUUGACACGAAAAUCCGCGGUGGAUGCCGGUCCUCUUCGG-
--..(((((((((.....((((((((....))))))))........(((((.(((.....)))...))))).....)))))))))((((......))))- ( -34.90)
>DroSim_CAF1 6063 96 - 1
--GCCAUCCGCUGAAUCCGAGGAUGCAUAUGCAUCCUCACAUGUUGUUUCGGCGGCCUCUUUGACACGAAAAUCCGCG-UGGAUGCCGGUCCUCUUCGG-
--.((..((((((((...((((((((....))))))))((.....)))))))))).......(((.((...((((...-.))))..)))))......))- ( -34.00)
>DroEre_CAF1 7008 96 - 1
--GCCAUCCGCUGAAUCCGAGGAUGCAUAUGCAUCCUCACAUGUU-UUUCGGCGGCCUCUUUGACAAGAAUAUCCGCGGUGGAUGCCGGUCCUCUUCGG-
--..((((((((......((((((((....)))))))).......-.....((((..((((....))))....))))))))))))((((......))))- ( -36.60)
>DroYak_CAF1 7209 96 - 1
--GCCAUCCGCUGAAUCCGAGGAUGCAUAUGCAUCCUCACAUGUU-UUUCGUCGGCCUCUUUGACACGAAAAUCUGCGGUGGAUGCUGGCCCUCUUCGG-
--(((((((((((.....((((((((....)))))))).((.(((-(((.(((((.....)))))..)))))).)))))))))...)))).........- ( -35.00)
>DroAna_CAF1 6944 93 - 1
GUGCCAUCCGCGGAUUCUGAGGAUGU------CUGCUCAUGUGUU-UUUCGGCGGUCUCUUUGACUCGAAAAUCCGCGGUGGAUGCCGCUCGUCGGCGGU
...(((.(((((((...((((.....------...)))).....(-(((((..((((.....))))))))))))))))))))..((((((....)))))) ( -36.20)
>consensus
__GCCAUCCGCUGAAUCCGAGGAUGCAUAUGCAUCCUCACAUGUU_UUUCGGCGGCCUCUUUGACACGAAAAUCCGCGGUGGAUGCCGGUCCUCUUCGG_
....((((((((......((((((((....)))))))).............((((..((........))....))))))))))))((((......)))). (-28.81 = -29.45 +   0.64)

alignment

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secondary structure

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Window 9

Location 2,696,111 – 2,696,210
Length 99
Sequences 6
Columns 106
Reading direction reverse
Mean pairwise identity 82.45
Mean single sequence MFE -32.45
Consensus MFE -22.64
Energy contribution -23.17
Covariance contribution 0.53
Combinations/Pair 1.18
Mean z-score -1.80
Structure conservation index 0.70
SVM decision value 0.25
SVM RNA-class probability 0.655299
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2696111 99 - 27905053
GCUCUCAAGAUGUGCUACGUCGAGCGGUGCCAUCCACUGA-----AUCCGAGGAUGCAUAUGCAUCCUCAUAUGUUU--UUUCGGCGGCCUCUUUGACACGAAAAU
....(((((..(.((..((((((((((((.....))))).-----....((((((((....))))))))........--.))))))))))..)))))......... ( -31.80)
>DroPse_CAF1 36088 103 - 1
CCACUCAAGAUGUGCUACGUCGAGCGGUGCAACGUUUUGUGUGUCGUCCGUGGAUGCCU---CCUCCUCACAUGGCGGUUUUUGGCGGUCUCUUUGACACAAAAUU
.....((((((((((..((.....))..)).))))))))(((((((.((((.((.(((.---((.........)).)))..)).))))......)))))))..... ( -31.60)
>DroSim_CAF1 6088 99 - 1
GUUCUCAAGAUGUGCUACGUCGAGCGGUGCCAUCCGCUGA-----AUCCGAGGAUGCAUAUGCAUCCUCACAUGUUG--UUUCGGCGGCCUCUUUGACACGAAAAU
((..(((((..(.((..((((((((((......))))...-----....((((((((....))))))))........--..)))))))))..))))).))...... ( -34.30)
>DroEre_CAF1 7034 98 - 1
CCUCUCAAGAUGUGCUACGUCGAGCGGUGCCAUCCGCUGA-----AUCCGAGGAUGCAUAUGCAUCCUCACAUGUU---UUUCGGCGGCCUCUUUGACAAGAAUAU
....(((((..(.((..((((((((((......))))...-----....((((((((....)))))))).......---..)))))))))..)))))......... ( -33.90)
>DroYak_CAF1 7235 98 - 1
CCUCUCAAGAUGUGCUACGUCGAGCGGUGCCAUCCGCUGA-----AUCCGAGGAUGCAUAUGCAUCCUCACAUGUU---UUUCGUCGGCCUCUUUGACACGAAAAU
....(((((..(.((((((((.(((((......)))))))-----....((((((((....)))))))).......---...))).))))..)))))......... ( -31.50)
>DroPer_CAF1 36103 103 - 1
CCACUCAAGAUGUGCUACGUCGAGCGGUGCAACGUUUUGUGUGUCGUCCGUGGAUGCCU---CCUCCUCACAUGGCGGUUUUUGGCGGUCUCUUUGACACAAAAUU
.....((((((((((..((.....))..)).))))))))(((((((.((((.((.(((.---((.........)).)))..)).))))......)))))))..... ( -31.60)
>consensus
CCUCUCAAGAUGUGCUACGUCGAGCGGUGCCAUCCGCUGA_____AUCCGAGGAUGCAUAUGCAUCCUCACAUGUUG__UUUCGGCGGCCUCUUUGACACGAAAAU
....(((((..(.((..((((((((((((.....)))))..........((((((((....))))))))...........))))))))))..)))))......... (-22.64 = -23.17 +   0.53)

alignment

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secondary structure

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dotplot

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Window 0

Location 2,696,182 – 2,696,274
Length 92
Sequences 5
Columns 92
Reading direction forward
Mean pairwise identity 93.70
Mean single sequence MFE -23.18
Consensus MFE -18.82
Energy contribution -19.62
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -1.48
Structure conservation index 0.81
SVM decision value 0.23
SVM RNA-class probability 0.645456
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2696182 92 + 27905053
ACCGCUCGACGUAGCACAUCUUGAGAGCUAUAGAACCACUACCACCGCCUCCGCAUCGGCGGUAUUUAGCUUUAGCUAUAUCACGCAUUAUU
...((..((..((((.(.....)((((((((((.....)))..((((((........))))))...))))))).))))..))..))...... ( -25.10)
>DroSec_CAF1 6147 92 + 1
ACCGCUCGACGUAGCACAUCUUGAGAACUAGAGAGCCACUACCACCGCCUCCGCAUCGGCGGUAUUUAGCUUUAGCUAUAUCACGCAUUAUA
...((..((..((((...((....)).....(((((.......((((((........)))))).....))))).))))..))..))...... ( -23.20)
>DroSim_CAF1 6159 92 + 1
ACCGCUCGACGUAGCACAUCUUGAGAACUAGAGAACCACUACCACCGCCUCCGCAUCGGCGAUAUUUAGCUUUAGCUAUAUCACGCUUUAUA
...((..((..((((...((((........))))...........((((........)))).............))))..))..))...... ( -17.50)
>DroEre_CAF1 7104 92 + 1
ACCGCUCGACGUAGCACAUCUUGAGAGGUAGAGAACCACCAGCACCGCCUCCGCAUCGGCGGAAUUUAGCUUUAGCUAUAUCACGCAUUAUA
(((.(((((.((.....)).))))).)))............((.(((((........)))))....((((....))))......))...... ( -23.10)
>DroYak_CAF1 7305 92 + 1
ACCGCUCGACGUAGCACAUCUUGAGAGGUAGAGUGCCACUACUACCGCCUCCGCAUCGGCGGUACUUAGCUUUAGCUAUAUCACGCAUUAUA
(((.(((((.((.....)).))))).)))..(((((......(((((((........)))))))..((((....))))......)))))... ( -27.00)
>consensus
ACCGCUCGACGUAGCACAUCUUGAGAGCUAGAGAACCACUACCACCGCCUCCGCAUCGGCGGUAUUUAGCUUUAGCUAUAUCACGCAUUAUA
...((..((..((((...((((........)))).........((((((........))))))...........))))..))..))...... (-18.82 = -19.62 +   0.80)

alignment

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secondary structure

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dotplot

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Window 1

Location 2,696,182 – 2,696,274
Length 92
Sequences 5
Columns 92
Reading direction reverse
Mean pairwise identity 93.70
Mean single sequence MFE -29.22
Consensus MFE -26.16
Energy contribution -26.00
Covariance contribution -0.16
Combinations/Pair 1.12
Mean z-score -1.40
Structure conservation index 0.90
SVM decision value 0.91
SVM RNA-class probability 0.879920
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2696182 92 - 27905053
AAUAAUGCGUGAUAUAGCUAAAGCUAAAUACCGCCGAUGCGGAGGCGGUGGUAGUGGUUCUAUAGCUCUCAAGAUGUGCUACGUCGAGCGGU
.....(((.(((...(((((.(((((..(((((((........)))))))....)))))...))))).))).((((.....))))..))).. ( -28.00)
>DroSec_CAF1 6147 92 - 1
UAUAAUGCGUGAUAUAGCUAAAGCUAAAUACCGCCGAUGCGGAGGCGGUGGUAGUGGCUCUCUAGUUCUCAAGAUGUGCUACGUCGAGCGGU
.....(((.((((.((((....))))..(((((((........)))))))...(((((.((((........))).).))))))))).))).. ( -29.90)
>DroSim_CAF1 6159 92 - 1
UAUAAAGCGUGAUAUAGCUAAAGCUAAAUAUCGCCGAUGCGGAGGCGGUGGUAGUGGUUCUCUAGUUCUCAAGAUGUGCUACGUCGAGCGGU
......((.((((.((((....))))..(((((((........)))))))...(((((.((((........))).).))))))))).))... ( -24.90)
>DroEre_CAF1 7104 92 - 1
UAUAAUGCGUGAUAUAGCUAAAGCUAAAUUCCGCCGAUGCGGAGGCGGUGCUGGUGGUUCUCUACCUCUCAAGAUGUGCUACGUCGAGCGGU
.....(((.(((..((((...(((......(((((........))))).)))(((((....)))))...........))))..))).))).. ( -28.80)
>DroYak_CAF1 7305 92 - 1
UAUAAUGCGUGAUAUAGCUAAAGCUAAGUACCGCCGAUGCGGAGGCGGUAGUAGUGGCACUCUACCUCUCAAGAUGUGCUACGUCGAGCGGU
.....(((.((((.((((....))))(.(((((((........))))))).).((((((((((........))).))))))))))).))).. ( -34.50)
>consensus
UAUAAUGCGUGAUAUAGCUAAAGCUAAAUACCGCCGAUGCGGAGGCGGUGGUAGUGGUUCUCUAGCUCUCAAGAUGUGCUACGUCGAGCGGU
......((.((((.((((....))))..(((((((........)))))))...(((((.((((........))).).))))))))).))... (-26.16 = -26.00 +  -0.16)

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 09:52:04 2006