Locus 4708

Sequence ID X_DroMel_CAF1
Location 12,248,889 – 12,249,018
Length 129
Max. P 0.999167
window7723 window7724 window7725 window7726

overview

Window 3

Location 12,248,889 – 12,248,992
Length 103
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 84.93
Mean single sequence MFE -31.86
Consensus MFE -26.74
Energy contribution -26.62
Covariance contribution -0.12
Combinations/Pair 1.08
Mean z-score -1.93
Structure conservation index 0.84
SVM decision value 1.04
SVM RNA-class probability 0.906000
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12248889 103 + 22224390
----CAGAGAGAGUAGUAGUUUGUCAAAAGUGCGACUACAAAAGCAC------UCGCUGCUUAUCGCACCAGACAGACUUUUCCGACGGUCGGAAAAGUCCAUGG-------GGGGAAAU
----......(((((((.(.....)...(((((..........))))------).))))))).((.(.(((....((((((((((.....))))))))))..)))-------.).))... ( -32.20)
>DroSec_CAF1 16944 102 + 1
----CAGAGAGAGUAGUAGUUUGUCAAAAGUGCGACUACAAAAGCAC------UCCCUGCUUAUCGCACCAGACAGACUUUUCCGACGGUCGGAAAAGUCCAUGG-------G-GGAAAU
----..((.(((.......))).))....((((..........))))------(((((((.....)))(((....((((((((((.....))))))))))..)))-------)-)))... ( -31.70)
>DroSim_CAF1 6729 102 + 1
----CAGAGAGAGUAGUAGUUUGUCAAAAGUGCGACUACAAAAGCAC------UCGCUGCUUAUCGCACCAGACAGACUUUUCCGACGGUCGGAAAAGUCCAUGG-------G-GGAAAU
----......(((((((.(.....)...(((((..........))))------).))))))).((.(.(((....((((((((((.....))))))))))..)))-------)-.))... ( -32.10)
>DroEre_CAF1 12047 101 + 1
----AAGAGAGAGUUGUAGUUUGUCAAAAGUGCGACUACAAAAGUGCGACUGCUCGCUGCUUAUCGCACCAGACAGACAUUUCCGACGGUCGGAAAAGUCGGCGG---------------
----.......(((((((.(((....))).)))))))......((((((..((.....))...))))))......(((.((((((.....)))))).))).....--------------- ( -31.90)
>DroYak_CAF1 5307 111 + 1
CACACAGAGAGAG---UAGUUUGUCAAAAGUGCGACUACAAAAGCAC-----UCCGCUGCUUAUCGCACCAGACAGACUUUUCCGACGGUCGGAAAAGUCCGCAGUCCAUAGG-GAAAAU
............(---(....((((....((((((.......(((..-----...))).....))))))..))))((((((((((.....)))))))))).))..(((....)-)).... ( -31.40)
>consensus
____CAGAGAGAGUAGUAGUUUGUCAAAAGUGCGACUACAAAAGCAC______UCGCUGCUUAUCGCACCAGACAGACUUUUCCGACGGUCGGAAAAGUCCAUGG_______G_GGAAAU
.....................((((....((((((......(((((...........))))).))))))..))))((((((((((.....)))))))))).................... (-26.74 = -26.62 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 4

Location 12,248,889 – 12,248,992
Length 103
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 84.93
Mean single sequence MFE -34.96
Consensus MFE -31.12
Energy contribution -31.72
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -3.02
Structure conservation index 0.89
SVM decision value 3.41
SVM RNA-class probability 0.999167
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12248889 103 - 22224390
AUUUCCCC-------CCAUGGACUUUUCCGACCGUCGGAAAAGUCUGUCUGGUGCGAUAAGCAGCGA------GUGCUUUUGUAGUCGCACUUUUGACAAACUACUACUCUCUCUG----
........-------....(((((((((((.....)))))))))))(((.(((((((((((((....------.))))).....))))))))...)))..................---- ( -34.90)
>DroSec_CAF1 16944 102 - 1
AUUUCC-C-------CCAUGGACUUUUCCGACCGUCGGAAAAGUCUGUCUGGUGCGAUAAGCAGGGA------GUGCUUUUGUAGUCGCACUUUUGACAAACUACUACUCUCUCUG----
......-.-------....(((((((((((.....)))))))))))(((.(((((((((((((....------.))))).....))))))))...)))..................---- ( -34.90)
>DroSim_CAF1 6729 102 - 1
AUUUCC-C-------CCAUGGACUUUUCCGACCGUCGGAAAAGUCUGUCUGGUGCGAUAAGCAGCGA------GUGCUUUUGUAGUCGCACUUUUGACAAACUACUACUCUCUCUG----
......-.-------....(((((((((((.....)))))))))))(((.(((((((((((((....------.))))).....))))))))...)))..................---- ( -34.90)
>DroEre_CAF1 12047 101 - 1
---------------CCGCCGACUUUUCCGACCGUCGGAAAUGUCUGUCUGGUGCGAUAAGCAGCGAGCAGUCGCACUUUUGUAGUCGCACUUUUGACAAACUACAACUCUCUCUU----
---------------.....(((.((((((.....)))))).)))((((.((((((((.....((((....))))((....)).))))))))...)))).................---- ( -32.20)
>DroYak_CAF1 5307 111 - 1
AUUUUC-CCUAUGGACUGCGGACUUUUCCGACCGUCGGAAAAGUCUGUCUGGUGCGAUAAGCAGCGGA-----GUGCUUUUGUAGUCGCACUUUUGACAAACUA---CUCUCUCUGUGUG
......-......(((((((((((((((((.....))))))))))).((((.(((.....))).))))-----........))))))((((....((.......---.)).....)))). ( -37.90)
>consensus
AUUUCC_C_______CCAUGGACUUUUCCGACCGUCGGAAAAGUCUGUCUGGUGCGAUAAGCAGCGA______GUGCUUUUGUAGUCGCACUUUUGACAAACUACUACUCUCUCUG____
....................((((((((((.....))))))))))((((.(((((((((((((...........))))).....))))))))...))))..................... (-31.12 = -31.72 +   0.60)

alignment

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secondary structure

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dotplot

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Window 5

Location 12,248,925 – 12,249,018
Length 93
Sequences 4
Columns 115
Reading direction forward
Mean pairwise identity 79.48
Mean single sequence MFE -30.89
Consensus MFE -19.45
Energy contribution -19.51
Covariance contribution 0.06
Combinations/Pair 1.05
Mean z-score -2.25
Structure conservation index 0.63
SVM decision value 1.27
SVM RNA-class probability 0.938817
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12248925 93 + 22224390
AAAGCAC-UCGCUGCUUAUCGCACCAGACAGACUUUUCCGACGGUCGGAAAAGUCCAUGG-------GGGGAAAUGGGUGAUGGGGGG--------------AAAAGCUAUUAUG
..(((..-...((.((((((((.(((..((((((((((((.....))))))))))..)).-------.......))))))))))).))--------------....)))...... ( -32.00)
>DroSec_CAF1 16980 90 + 1
AAAGCAC-UCCCUGCUUAUCGCACCAGACAGACUUUUCCGACGGUCGGAAAAGUCCAUGG-------G-GGAAAUGGGGGA--AGGGG--------------AAAGGAUAUUAUG
.......-(((((.(((((..(.(((....((((((((((.....))))))))))..)))-------.-.)..)))))...--.))))--------------)............ ( -29.40)
>DroSim_CAF1 6765 90 + 1
AAAGCAC-UCGCUGCUUAUCGCACCAGACAGACUUUUCCGACGGUCGGAAAAGUCCAUGG-------G-GGAAAUGGGGGA--GGGGG--------------AAAAGCUAUUAUG
..(((.(-((.((.(((.((.(.(((....((((((((((.....))))))))))..)))-------)-.))....))).)--).)))--------------....)))...... ( -30.50)
>DroYak_CAF1 5344 110 + 1
AAAGCACUCCGCUGCUUAUCGCACCAGACAGACUUUUCCGACGGUCGGAAAAGUCCGCAGUCCAUAGG-GAAAAUGGGAAAAAGGGGAAAAAGGGGGUAGGGAAA----AUUAUG
.......(((.((((((......((.....((((((((((.....))))))))))(.((.(((....)-))...)).)......))........)))))))))..----...... ( -31.64)
>consensus
AAAGCAC_UCGCUGCUUAUCGCACCAGACAGACUUUUCCGACGGUCGGAAAAGUCCAUGG_______G_GGAAAUGGGGGA__GGGGG______________AAAAGCUAUUAUG
.(((((......)))))......((.....((((((((((.....))))))))))(((...............)))........))............................. (-19.45 = -19.51 +   0.06)

alignment

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secondary structure

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dotplot

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Window 6

Location 12,248,925 – 12,249,018
Length 93
Sequences 4
Columns 115
Reading direction reverse
Mean pairwise identity 79.48
Mean single sequence MFE -27.25
Consensus MFE -22.40
Energy contribution -21.90
Covariance contribution -0.50
Combinations/Pair 1.18
Mean z-score -2.64
Structure conservation index 0.82
SVM decision value 2.79
SVM RNA-class probability 0.997071
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12248925 93 - 22224390
CAUAAUAGCUUUU--------------CCCCCCAUCACCCAUUUCCCC-------CCAUGGACUUUUCCGACCGUCGGAAAAGUCUGUCUGGUGCGAUAAGCAGCGA-GUGCUUU
......(((..((--------------(....................-------..(((((((((((((.....)))))))))))))..(.(((.....))).)))-).))).. ( -24.70)
>DroSec_CAF1 16980 90 - 1
CAUAAUAUCCUUU--------------CCCCU--UCCCCCAUUUCC-C-------CCAUGGACUUUUCCGACCGUCGGAAAAGUCUGUCUGGUGCGAUAAGCAGGGA-GUGCUUU
.............--------------.....--.....(((((((-(-------(.(((((((((((((.....)))))))))))))..))(((.....)))))))-))).... ( -28.30)
>DroSim_CAF1 6765 90 - 1
CAUAAUAGCUUUU--------------CCCCC--UCCCCCAUUUCC-C-------CCAUGGACUUUUCCGACCGUCGGAAAAGUCUGUCUGGUGCGAUAAGCAGCGA-GUGCUUU
......(((..((--------------(....--............-.-------..(((((((((((((.....)))))))))))))..(.(((.....))).)))-).))).. ( -24.70)
>DroYak_CAF1 5344 110 - 1
CAUAAU----UUUCCCUACCCCCUUUUUCCCCUUUUUCCCAUUUUC-CCUAUGGACUGCGGACUUUUCCGACCGUCGGAAAAGUCUGUCUGGUGCGAUAAGCAGCGGAGUGCUUU
......----............................((((....-...))))((((((((((((((((.....)))))))))))))(((.(((.....))).))))))..... ( -31.30)
>consensus
CAUAAUAGCUUUU______________CCCCC__UCCCCCAUUUCC_C_______CCAUGGACUUUUCCGACCGUCGGAAAAGUCUGUCUGGUGCGAUAAGCAGCGA_GUGCUUU
.......................................(((.((............(((((((((((((.....)))))))))))))..(.(((.....))).))).))).... (-22.40 = -21.90 +  -0.50)

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 11:31:31 2006