Locus 3047

Sequence ID 3R_DroMel_CAF1
Location 8,090,787 – 8,090,964
Length 177
Max. P 0.999706
window4922 window4923 window4924 window4925 window4926

overview

Window 2

Location 8,090,787 – 8,090,884
Length 97
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 77.67
Mean single sequence MFE -31.56
Consensus MFE -22.42
Energy contribution -24.78
Covariance contribution 2.36
Combinations/Pair 1.10
Mean z-score -3.04
Structure conservation index 0.71
SVM decision value 3.30
SVM RNA-class probability 0.998950
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8090787 97 + 27905053
UGGCUUUUGUGCUAUUUGGAACGAGUUGUCAAAUAAAAGCGGCAGCCGGCGAAAUAGAAGAAGGAGCCAGGGA-----------------------AGCCUGCCGAAGGGGGCAGGAGGA
((((((((...((((((.(..((.((((((..........)))))))).).))))))....))))))))....-----------------------..((((((......)))))).... ( -35.80)
>DroSec_CAF1 42576 83 + 1
UGGCUUUUGUGCUAUUUGGAACGAGUUGUCAAAUAAAAGCGGCAGCCGGCGGAAUAGGAGAAGGAGCCAGGGA-----------------------AG--------------GAGGAGGA
((((((((.(.((((((.(..((.((((((..........)))))))).).)))))).)..))))))))....-----------------------..--------------........ ( -24.40)
>DroSim_CAF1 14581 83 + 1
UGGCUUUUGUGCUAUUUGGAACGAGUUGUCAAAUAAAAGCGGCAGCCGGCGGAAUAGGAGAAGGAGCCAGGGA-----------------------AG--------------GAGGAGGA
((((((((.(.((((((.(..((.((((((..........)))))))).).)))))).)..))))))))....-----------------------..--------------........ ( -24.40)
>DroEre_CAF1 17551 120 + 1
UGGCUUUUGUGCUAUUUGGAACGAGUUGUCAAAUAAAAGCGGCAGCCGGCGGAGAAGUAGAAGGAUCCAGGAACCAGUAACCAGUAACCAGGAGCCAUCCUGCCGAAGGCGGCAGGAGGA
(((((((((((((..((((..((.((((((..........))))))))..(((............))).....)))).....))))..)))))))))((((((((....))))))))... ( -41.70)
>DroYak_CAF1 10946 96 + 1
UGGCUUUUGUGCUAUUUGGAACGAGUUGUCAAAUAAAAGCGGCAGCCGGCGGA-AAGUAGAAGGAACCGGGGA-----------------------GUCCUGCCGAAGGCGGCAGGAGGA
.((.((((...((((((....((.((((((..........)))))))).....-))))))..)))))).....-----------------------.((((((((....))))))))... ( -31.50)
>consensus
UGGCUUUUGUGCUAUUUGGAACGAGUUGUCAAAUAAAAGCGGCAGCCGGCGGAAUAGGAGAAGGAGCCAGGGA_______________________AGCCUGCCGAAGG_GGCAGGAGGA
((((((((...((((((.(..((.((((((..........)))))))).).))))))....)))))))).............................((((((......)))))).... (-22.42 = -24.78 +   2.36)

alignment

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secondary structure

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dotplot

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Window 3

Location 8,090,787 – 8,090,884
Length 97
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 77.67
Mean single sequence MFE -21.34
Consensus MFE -13.22
Energy contribution -15.10
Covariance contribution 1.88
Combinations/Pair 1.05
Mean z-score -2.20
Structure conservation index 0.62
SVM decision value 1.52
SVM RNA-class probability 0.960960
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8090787 97 - 27905053
UCCUCCUGCCCCCUUCGGCAGGCU-----------------------UCCCUGGCUCCUUCUUCUAUUUCGCCGGCUGCCGCUUUUAUUUGACAACUCGUUCCAAAUAGCACAAAAGCCA
....((((((......))))))..-----------------------.....(((...............)))((((...(((...(((((...........)))))))).....)))). ( -22.16)
>DroSec_CAF1 42576 83 - 1
UCCUCCUC--------------CU-----------------------UCCCUGGCUCCUUCUCCUAUUCCGCCGGCUGCCGCUUUUAUUUGACAACUCGUUCCAAAUAGCACAAAAGCCA
........--------------..-----------------------.....(((...............)))((((...(((...(((((...........)))))))).....)))). ( -11.96)
>DroSim_CAF1 14581 83 - 1
UCCUCCUC--------------CU-----------------------UCCCUGGCUCCUUCUCCUAUUCCGCCGGCUGCCGCUUUUAUUUGACAACUCGUUCCAAAUAGCACAAAAGCCA
........--------------..-----------------------.....(((...............)))((((...(((...(((((...........)))))))).....)))). ( -11.96)
>DroEre_CAF1 17551 120 - 1
UCCUCCUGCCGCCUUCGGCAGGAUGGCUCCUGGUUACUGGUUACUGGUUCCUGGAUCCUUCUACUUCUCCGCCGGCUGCCGCUUUUAUUUGACAACUCGUUCCAAAUAGCACAAAAGCCA
...((((((((....))))))))(((((...(((..(((((....((....((((....)))).....)))))))..)))(((...(((((...........)))))))).....))))) ( -36.40)
>DroYak_CAF1 10946 96 - 1
UCCUCCUGCCGCCUUCGGCAGGAC-----------------------UCCCCGGUUCCUUCUACUU-UCCGCCGGCUGCCGCUUUUAUUUGACAACUCGUUCCAAAUAGCACAAAAGCCA
...((((((((....)))))))).-----------------------....(((............-.)))..((((...(((...(((((...........)))))))).....)))). ( -24.22)
>consensus
UCCUCCUGCC_CCUUCGGCAGGCU_______________________UCCCUGGCUCCUUCUACUAUUCCGCCGGCUGCCGCUUUUAUUUGACAACUCGUUCCAAAUAGCACAAAAGCCA
....((((((......))))))..............................(((...............)))((((...(((...(((((...........)))))))).....)))). (-13.22 = -15.10 +   1.88)

alignment

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secondary structure

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dotplot

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Window 4

Location 8,090,827 – 8,090,924
Length 97
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 77.29
Mean single sequence MFE -43.16
Consensus MFE -31.15
Energy contribution -33.03
Covariance contribution 1.88
Combinations/Pair 1.08
Mean z-score -4.44
Structure conservation index 0.72
SVM decision value 3.92
SVM RNA-class probability 0.999706
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8090827 97 + 27905053
GGCAGCCGGCGAAAUAGAAGAAGGAGCCAGGGA-----------------------AGCCUGCCGAAGGGGGCAGGAGGAGCUGGAUCGUUGACUUGGCUGGCUGGCUGCCAUCAAAAUG
((((((((((.(..(((...((.((.((((...-----------------------..((((((......)))))).....)))).)).))...)))..).))))))))))......... ( -43.70)
>DroSec_CAF1 42616 83 + 1
GGCAGCCGGCGGAAUAGGAGAAGGAGCCAGGGA-----------------------AG--------------GAGGAGGAGCUGGAUCGUUGACUUGGCUGGCUGGCUGCCAUCAAAAUG
((((((((((.(..((((..((.((.((((...-----------------------..--------------.........)))).)).))..))))..).))))))))))......... ( -33.24)
>DroSim_CAF1 14621 83 + 1
GGCAGCCGGCGGAAUAGGAGAAGGAGCCAGGGA-----------------------AG--------------GAGGAGGAGCUGGAUCGUUGACUUGGCUGGCUGGCUGCCAUCAAAAUG
((((((((((.(..((((..((.((.((((...-----------------------..--------------.........)))).)).))..))))..).))))))))))......... ( -33.24)
>DroEre_CAF1 17591 120 + 1
GGCAGCCGGCGGAGAAGUAGAAGGAUCCAGGAACCAGUAACCAGUAACCAGGAGCCAUCCUGCCGAAGGCGGCAGGAGGAGCAGGAUCGUUGACUUGGCUGGCUGGCUGCCAUCAAAAUG
((((((((((((..((((..((.(((((.((.........)).........(..((.((((((((....))))))))))..).))))).)).))))..)).))))))))))......... ( -56.30)
>DroYak_CAF1 10986 96 + 1
GGCAGCCGGCGGA-AAGUAGAAGGAACCGGGGA-----------------------GUCCUGCCGAAGGCGGCAGGAGGAGCUGGAUCGUUGACUUGGCUGGCUGGCUGCCAUCAAAAUG
((((((((((((.-((((..((.((.((((...-----------------------.((((((((....))))))))....)))).)).)).))))..)).))))))))))......... ( -49.30)
>consensus
GGCAGCCGGCGGAAUAGGAGAAGGAGCCAGGGA_______________________AGCCUGCCGAAGG_GGCAGGAGGAGCUGGAUCGUUGACUUGGCUGGCUGGCUGCCAUCAAAAUG
((((((((((.(.............((((((...........................((((((......))))))..((......)).....))))))).))))))))))......... (-31.15 = -33.03 +   1.88)

alignment

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secondary structure

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dotplot

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Window 5

Location 8,090,827 – 8,090,924
Length 97
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 77.29
Mean single sequence MFE -30.16
Consensus MFE -20.58
Energy contribution -22.38
Covariance contribution 1.80
Combinations/Pair 1.00
Mean z-score -2.67
Structure conservation index 0.68
SVM decision value 2.77
SVM RNA-class probability 0.996955
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8090827 97 - 27905053
CAUUUUGAUGGCAGCCAGCCAGCCAAGUCAACGAUCCAGCUCCUCCUGCCCCCUUCGGCAGGCU-----------------------UCCCUGGCUCCUUCUUCUAUUUCGCCGGCUGCC
.........(((((((.((.............((.((((.....((((((......))))))..-----------------------...)))).)).............)).))))))) ( -33.07)
>DroSec_CAF1 42616 83 - 1
CAUUUUGAUGGCAGCCAGCCAGCCAAGUCAACGAUCCAGCUCCUCCUC--------------CU-----------------------UCCCUGGCUCCUUCUCCUAUUCCGCCGGCUGCC
.........(((((((((((((..(((.....((......))......--------------))-----------------------)..)))))).................))))))) ( -19.92)
>DroSim_CAF1 14621 83 - 1
CAUUUUGAUGGCAGCCAGCCAGCCAAGUCAACGAUCCAGCUCCUCCUC--------------CU-----------------------UCCCUGGCUCCUUCUCCUAUUCCGCCGGCUGCC
.........(((((((((((((..(((.....((......))......--------------))-----------------------)..)))))).................))))))) ( -19.92)
>DroEre_CAF1 17591 120 - 1
CAUUUUGAUGGCAGCCAGCCAGCCAAGUCAACGAUCCUGCUCCUCCUGCCGCCUUCGGCAGGAUGGCUCCUGGUUACUGGUUACUGGUUCCUGGAUCCUUCUACUUCUCCGCCGGCUGCC
.........(((((((.((.....((((....(((((.(((..((((((((....)))))))).)))....((..((..(...)..)).)).))))).....))))....)).))))))) ( -44.50)
>DroYak_CAF1 10986 96 - 1
CAUUUUGAUGGCAGCCAGCCAGCCAAGUCAACGAUCCAGCUCCUCCUGCCGCCUUCGGCAGGAC-----------------------UCCCCGGUUCCUUCUACUU-UCCGCCGGCUGCC
.........(((((((.((.....((((....((.((.(....((((((((....)))))))).-----------------------...).)).)).....))))-...)).))))))) ( -33.40)
>consensus
CAUUUUGAUGGCAGCCAGCCAGCCAAGUCAACGAUCCAGCUCCUCCUGCC_CCUUCGGCAGGCU_______________________UCCCUGGCUCCUUCUACUAUUCCGCCGGCUGCC
.........(((((((.((.(((...(((...)))...)))...((((((......))))))................................................)).))))))) (-20.58 = -22.38 +   1.80)

alignment

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secondary structure

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dotplot

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Window 6

Location 8,090,860 – 8,090,964
Length 104
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 84.04
Mean single sequence MFE -42.20
Consensus MFE -35.53
Energy contribution -37.33
Covariance contribution 1.80
Combinations/Pair 1.00
Mean z-score -2.79
Structure conservation index 0.84
SVM decision value 2.65
SVM RNA-class probability 0.996041
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8090860 104 + 27905053
----------------AGCCUGCCGAAGGGGGCAGGAGGAGCUGGAUCGUUGACUUGGCUGGCUGGCUGCCAUCAAAAUGGCGUCUGGCCCGGCAAGGACUUUAAAAAGCUGCUCGGAAA
----------------...(((((......)))))(((.((((..........((((.(.(((..(.((((((....)))))).)..))).).))))..........)))).)))..... ( -44.25)
>DroSec_CAF1 42649 90 + 1
----------------AG--------------GAGGAGGAGCUGGAUCGUUGACUUGGCUGGCUGGCUGCCAUCAAAAUGGCGUCUGGCCCAGCAAGGACUUUAAAAAGCUGCUCGGAAA
----------------..--------------...(((.((((..........((((.(((((..(.((((((....)))))).)..).))))))))..........)))).)))..... ( -33.85)
>DroSim_CAF1 14654 90 + 1
----------------AG--------------GAGGAGGAGCUGGAUCGUUGACUUGGCUGGCUGGCUGCCAUCAAAAUGGCGUCUGGCCCGGCAAGGACUUUAAAAAGCUGCUCGGAAA
----------------..--------------...(((.((((..........((((.(.(((..(.((((((....)))))).)..))).).))))..........)))).)))..... ( -35.55)
>DroEre_CAF1 17631 120 + 1
CCAGUAACCAGGAGCCAUCCUGCCGAAGGCGGCAGGAGGAGCAGGAUCGUUGACUUGGCUGGCUGGCUGCCAUCAAAAUGGCGUCUGGCCCGGCAAGGACUUUAAAAAGCUGCUCGGAAA
((........))..((.((((((((....)))))))).((((((.........((((.(.(((..(.((((((....)))))).)..))).).))))..(((....)))))))))))... ( -51.20)
>DroYak_CAF1 11018 104 + 1
----------------GUCCUGCCGAAGGCGGCAGGAGGAGCUGGAUCGUUGACUUGGCUGGCUGGCUGCCAUCAAAAUGGCGUCUGGCCCGGCAAGGACUUUAAAAAGCUGCUCGGAAA
----------------...((((((....))))))(((.((((..........((((.(.(((..(.((((((....)))))).)..))).).))))..........)))).)))..... ( -46.15)
>consensus
________________AGCCUGCCGAAGG_GGCAGGAGGAGCUGGAUCGUUGACUUGGCUGGCUGGCUGCCAUCAAAAUGGCGUCUGGCCCGGCAAGGACUUUAAAAAGCUGCUCGGAAA
...................(((((......)))))(((.((((..........((((.(.(((..(.((((((....)))))).)..))).).))))..........)))).)))..... (-35.53 = -37.33 +   1.80)

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 10:51:25 2006