Locus 489

Sequence ID 2R_DroMel_CAF1
Location 2,702,605 – 2,702,795
Length 190
Max. P 0.996419
window928 window929 window930 window931 window932

overview

Window 8

Location 2,702,605 – 2,702,705
Length 100
Sequences 5
Columns 100
Reading direction forward
Mean pairwise identity 90.70
Mean single sequence MFE -24.12
Consensus MFE -18.86
Energy contribution -19.26
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -3.40
Structure conservation index 0.78
SVM decision value 2.69
SVM RNA-class probability 0.996419
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2702605 100 + 20766785
UCGAUGGCGUCACUUACACAUGUCGAACAACCGCCAUCAAUAAAUACUAACGGUGCCUCGCGGCAUCAACUCCACAUCCACAUCCAAAGUGCAACACUCC
..(((((((((((........)).)).....))))))).............((((((....))))))...........(((.......)))......... ( -21.60)
>DroSec_CAF1 17493 100 + 1
UCGAUGGCGUCACUUACACAUGUCGAACAACCGCCAUCAAUAAAUACUAACGGUGCCUUGCGGCAUCAACUCCGCAUCCACAUCCAAAGUGCAAAACUCC
..(((((((((((........)).)).....))))))).............((((((....))))))......((((...........))))........ ( -23.50)
>DroSim_CAF1 14898 100 + 1
UCGAUGGCGUCACUUACACAUGUCGAACAACCGCCAUCAAUAAAUACUAACGGUGCCUUGCGGCAUCAACUCCACAUCCACAUCCAAAGCGCAACACUCC
..(((((((((((........)).)).....))))))).............((((((....))))))................................. ( -21.00)
>DroEre_CAF1 14936 89 + 1
UCGCUGGCGUCACUUACACAUGUCGAACAACCGCCAUCAAUAAAUACUAACGGUGCCUCGCGGCAUC-----------CACAUCCAAAGUGCGCCACUCC
....(((((.(((((....(((.((......)).)))..............((((((....))))))-----------........)))))))))).... ( -23.90)
>DroYak_CAF1 14614 100 + 1
UCGAUGGCGUCACUUACACAUGUCGAACAACCGCCAUCAAUAAAUACUAACGGCGCCUCGCGGCAUCAACUCCACAUCGACAUCCAAAGUGCGCCACUAU
....(((((.(((((....(((((((......(((................)))(((....)))............)))))))...)))))))))).... ( -30.59)
>consensus
UCGAUGGCGUCACUUACACAUGUCGAACAACCGCCAUCAAUAAAUACUAACGGUGCCUCGCGGCAUCAACUCCACAUCCACAUCCAAAGUGCAACACUCC
..(((((((((((........)).)).....))))))).............((((((....))))))................................. (-18.86 = -19.26 +   0.40) 

alignment

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secondary structure

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dotplot

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Window 9

Location 2,702,605 – 2,702,705
Length 100
Sequences 5
Columns 100
Reading direction reverse
Mean pairwise identity 90.70
Mean single sequence MFE -33.34
Consensus MFE -25.12
Energy contribution -25.40
Covariance contribution 0.28
Combinations/Pair 1.07
Mean z-score -2.04
Structure conservation index 0.75
SVM decision value 0.70
SVM RNA-class probability 0.826416
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2702605 100 - 20766785
GGAGUGUUGCACUUUGGAUGUGGAUGUGGAGUUGAUGCCGCGAGGCACCGUUAGUAUUUAUUGAUGGCGGUUGUUCGACAUGUGUAAGUGACGCCAUCGA
((((((...)))))).((((...((((.(((....((((....))))((((((((....))))))))......))).))))((((.....)))))))).. ( -28.30)
>DroSec_CAF1 17493 100 - 1
GGAGUUUUGCACUUUGGAUGUGGAUGCGGAGUUGAUGCCGCAAGGCACCGUUAGUAUUUAUUGAUGGCGGUUGUUCGACAUGUGUAAGUGACGCCAUCGA
((.(((((((((((((.((....)).))))(((((((((....))))((((((((....)))))))).......)))))..))))))..))).))..... ( -30.70)
>DroSim_CAF1 14898 100 - 1
GGAGUGUUGCGCUUUGGAUGUGGAUGUGGAGUUGAUGCCGCAAGGCACCGUUAGUAUUUAUUGAUGGCGGUUGUUCGACAUGUGUAAGUGACGCCAUCGA
.(.((((..(....((.((((.((...........((((....))))((((((((....)))))))).......)).)))).))...)..)))))..... ( -29.10)
>DroEre_CAF1 14936 89 - 1
GGAGUGGCGCACUUUGGAUGUG-----------GAUGCCGCGAGGCACCGUUAGUAUUUAUUGAUGGCGGUUGUUCGACAUGUGUAAGUGACGCCAGCGA
....((((((((((((.((((.-----------((((((....))))((((((((....)))))))).......)).)))).)).))))).))))).... ( -35.10)
>DroYak_CAF1 14614 100 - 1
AUAGUGGCGCACUUUGGAUGUCGAUGUGGAGUUGAUGCCGCGAGGCGCCGUUAGUAUUUAUUGAUGGCGGUUGUUCGACAUGUGUAAGUGACGCCAUCGA
...(((((((((((((.((((((((((((........)))))((.((((((((((....)))))))))).))..))))))).)).))))).))))))... ( -43.50)
>consensus
GGAGUGUUGCACUUUGGAUGUGGAUGUGGAGUUGAUGCCGCGAGGCACCGUUAGUAUUUAUUGAUGGCGGUUGUUCGACAUGUGUAAGUGACGCCAUCGA
...(((...(((((((.((((.((...........((((....))))((((((((....)))))))).......)).)))).)).))))).)))...... (-25.12 = -25.40 +   0.28) 

alignment

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secondary structure

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dotplot

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Window 0

Location 2,702,626 – 2,702,730
Length 104
Sequences 5
Columns 106
Reading direction reverse
Mean pairwise identity 90.47
Mean single sequence MFE -37.10
Consensus MFE -30.82
Energy contribution -32.90
Covariance contribution 2.08
Combinations/Pair 1.06
Mean z-score -2.25
Structure conservation index 0.83
SVM decision value 2.14
SVM RNA-class probability 0.988977
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2702626 104 - 20766785
--AGAUCCAAGAUGCCAUAUGCCAGAUGGAGUGUUGCACUUUGGAUGUGGAUGUGGAGUUGAUGCCGCGAGGCACCGUUAGUAUUUAUUGAUGGCGGUUGUUCGAC
--...((((.....((((((.(((....(((((...))))))))))))))...))))(((((((((....))))((((((((....)))))))).......))))) ( -34.50)
>DroSec_CAF1 17514 106 - 1
CCAGAUCCAAGUUGCCAUAUGCCAGAUGGAGUUUUGCACUUUGGAUGUGGAUGCGGAGUUGAUGCCGCAAGGCACCGUUAGUAUUUAUUGAUGGCGGUUGUUCGAC
(((.(((((((.(((......((....))......))).))))))).))).......(((((((((....))))((((((((....)))))))).......))))) ( -37.10)
>DroSim_CAF1 14919 106 - 1
CCAGAUCCAAGAUGCCAUAUGCCAGAUGGAGUGUUGCGCUUUGGAUGUGGAUGUGGAGUUGAUGCCGCAAGGCACCGUUAGUAUUUAUUGAUGGCGGUUGUUCGAC
(((.(((((((.(((.((((.((....)).)))).))).))))))).))).......(((((((((....))))((((((((....)))))))).......))))) ( -39.60)
>DroEre_CAF1 14957 95 - 1
CCAGAUCCAAGAUGCCAUAUGCCAGAUGGAGUGGCGCACUUUGGAUGUG-----------GAUGCCGCGAGGCACCGUUAGUAUUUAUUGAUGGCGGUUGUUCGAC
(((.(((((((.((((((...((....)).))))))...))))))).))-----------).((((....))))((((((((....))))))))(((....))).. ( -37.10)
>DroYak_CAF1 14635 106 - 1
CCAGAUCCAAGAUGCCAUAUGCCAGAUAUAGUGGCGCACUUUGGAUGUCGAUGUGGAGUUGAUGCCGCGAGGCGCCGUUAGUAUUUAUUGAUGGCGGUUGUUCGAC
....(((((((.(((.....((((.......))))))).)))))))((((((((((........)))))((.((((((((((....)))))))))).))..))))) ( -37.20)
>consensus
CCAGAUCCAAGAUGCCAUAUGCCAGAUGGAGUGUUGCACUUUGGAUGUGGAUGUGGAGUUGAUGCCGCGAGGCACCGUUAGUAUUUAUUGAUGGCGGUUGUUCGAC
(((.(((((((.(((.((((.((....)).)))).))).))))))).))).......(((((((((....))))((((((((....)))))))).......))))) (-30.82 = -32.90 +   2.08) 

alignment

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secondary structure

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dotplot

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Window 1

Location 2,702,666 – 2,702,758
Length 92
Sequences 5
Columns 106
Reading direction forward
Mean pairwise identity 84.77
Mean single sequence MFE -26.10
Consensus MFE -20.17
Energy contribution -20.24
Covariance contribution 0.07
Combinations/Pair 1.14
Mean z-score -2.09
Structure conservation index 0.77
SVM decision value 1.04
SVM RNA-class probability 0.904944
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2702666 92 + 20766785
GGCAUCAACUCCACAUCCACAUCCAAAGUGCAACACUCCAUCUGGCAUAUGGCAUCUUGGAUCU--------------GGGAUUUACAGCCUUCCAUCUUCUGCCG
((((.............((.((((((..(((......((....))......)))..)))))).)--------------)(((..........)))......)))). ( -23.10)
>DroSec_CAF1 17554 99 + 1
GGCAUCAACUCCGCAUCCACAUCCAAAGUGCAAAACUCCAUCUGGCAUAUGGCAACUUGGAUCUGGGA-------UCUGGGAUCUACAGCCUUCCAUCUUCUGCCU
((((.......((.((((..((((((..(((......((....))......)))..))))))...)))-------).))(((..........)))......)))). ( -25.60)
>DroSim_CAF1 14959 99 + 1
GGCAUCAACUCCACAUCCACAUCCAAAGCGCAACACUCCAUCUGGCAUAUGGCAUCUUGGAUCUGGGA-------UCUGGGAUCUACAGCCUUCCAUCUUCUGCCU
((((.......((.((((..((((((...((......((....))......))...))))))...)))-------).))(((..........)))......)))). ( -22.90)
>DroEre_CAF1 14997 88 + 1
GGCAUC-----------CACAUCCAAAGUGCGCCACUCCAUCUGGCAUAUGGCAUCUUGGAUCUGGGA-------UCUGGGAUCUACAGCCUUCCAUCUUCUGCCU
((((((-----------((.((((((..(((((((.......)))).....)))..)))))).)))).-------..(((((.........))))).....)))). ( -27.90)
>DroYak_CAF1 14675 106 + 1
GGCAUCAACUCCACAUCGACAUCCAAAGUGCGCCACUAUAUCUGGCAUAUGGCAUCUUGGAUCUGGGAUCUUGGAUCUGGGAUCCACAGCUUUCCAUCUUCUGCCU
((((................((((((..(((((((.......)))).....)))..))))))((((((((((......))))))).)))............)))). ( -31.00)
>consensus
GGCAUCAACUCCACAUCCACAUCCAAAGUGCAACACUCCAUCUGGCAUAUGGCAUCUUGGAUCUGGGA_______UCUGGGAUCUACAGCCUUCCAUCUUCUGCCU
((((.......................((((.............))))..(((....(((((((.((((.....)))).)))))))..)))..........)))). (-20.17 = -20.24 +   0.07) 

alignment

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secondary structure

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dotplot

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Window 2

Location 2,702,705 – 2,702,795
Length 90
Sequences 5
Columns 104
Reading direction forward
Mean pairwise identity 91.18
Mean single sequence MFE -30.44
Consensus MFE -29.77
Energy contribution -29.64
Covariance contribution -0.13
Combinations/Pair 1.11
Mean z-score -1.21
Structure conservation index 0.98
SVM decision value 0.60
SVM RNA-class probability 0.797102
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2702705 90 + 20766785
AUCUGGCAUAUGGCAUCUUGGAUCU--------------GGGAUUUACAGCCUUCCAUCUUCUGCCGUGGACCAAACGCCGGAAGUCUUUGUUUGGGCAUUCGC
.((((((.(((((((...((((.((--------------(.......)))...)))).....)))))))(......))))))).((((......))))...... ( -26.40)
>DroSec_CAF1 17593 97 + 1
AUCUGGCAUAUGGCAACUUGGAUCUGGGA-------UCUGGGAUCUACAGCCUUCCAUCUUCUGCCUUGGACCAACCGCCGGAAGUCUUUGUUUGGGCAUUCGC
.((((((....((((...((((.((((((-------((...))))).)))...)))).....))))..((.....)))))))).((((......))))...... ( -29.80)
>DroSim_CAF1 14998 97 + 1
AUCUGGCAUAUGGCAUCUUGGAUCUGGGA-------UCUGGGAUCUACAGCCUUCCAUCUUCUGCCUUGGACCAACCGCCGGAAGUCUUUGUUUGGGCAUUCGU
.((((((....((((...((((.((((((-------((...))))).)))...)))).....))))..((.....)))))))).((((......))))...... ( -29.80)
>DroEre_CAF1 15025 97 + 1
AUCUGGCAUAUGGCAUCUUGGAUCUGGGA-------UCUGGGAUCUACAGCCUUCCAUCUUCUGCCUUGGACCAACCGCCGGAAGUCUUUGUUUGGGCAUUCGC
.((((((....((((...((((.((((((-------((...))))).)))...)))).....))))..((.....)))))))).((((......))))...... ( -29.80)
>DroYak_CAF1 14714 104 + 1
AUCUGGCAUAUGGCAUCUUGGAUCUGGGAUCUUGGAUCUGGGAUCCACAGCUUUCCAUCUUCUGCCUUGGACCAACCGCCGGAAGUCUUUGUUUGGGCAUUUGC
.((((((....((((...((((.((((((((((......))))))).)))...)))).....))))..((.....)))))))).((((......))))...... ( -36.40)
>consensus
AUCUGGCAUAUGGCAUCUUGGAUCUGGGA_______UCUGGGAUCUACAGCCUUCCAUCUUCUGCCUUGGACCAACCGCCGGAAGUCUUUGUUUGGGCAUUCGC
.((((((....(((....(((((((.((((.....)))).)))))))..))).((((..........))))......)))))).((((......))))...... (-29.77 = -29.64 +  -0.13) 

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 09:39:59 2006