Locus 4774

Sequence ID 3R_DroMel_CAF1
Location 12,506,932 – 12,507,052
Length 120
Max. P 0.984002
window7826 window7827 window7828

overview

Window 6

Location 12,506,932 – 12,507,025
Length 93
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 77.05
Mean single sequence MFE -24.39
Consensus MFE -14.53
Energy contribution -15.08
Covariance contribution 0.56
Combinations/Pair 1.16
Mean z-score -1.71
Structure conservation index 0.60
SVM decision value 0.61
SVM RNA-class probability 0.799873
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12506932 93 + 27905053
--UC-CAGCUGGCGACGCUUUGGUUUAU--------CCUUUAUCCUUAUGCUUUUUUGCACAUUAUUUGCUUUUGCAAUUCAAAGCGAUUAAGUGU-----CUCCA--------GUC---
--..-..(((((.(((((((......((--------(((((.......(((......)))......((((....))))...)))).))).))))))-----).)))--------)).--- ( -25.00)
>DroPse_CAF1 29233 102 + 1
---G-CCGCCGGCGACGCUUUGGUUUAU--------CCUUUAUCCUUAUGCCUUUUUGCACAUUAUUUGCUUUUGCAAUUCAAAGCGAUUAAGUGCGACAUCGCCGAGG---AGGAC---
---.-((..((((((.((...((..((.--------....))..))...))....((((((.(((.(((((((........))))))).)))))))))..)))))).))---.....--- ( -30.30)
>DroGri_CAF1 80857 103 + 1
GCUU-GUGCUGGCGACGCUAUGGUUUAUCCUUUUAUCCUUUAUCCUUAUGCUUUUUUGCACAUUAUUUGCUUUUGCAAUUCAAAGCGAUUAAGUGC-----GACGA--------CGC---
((..-..))..(((..((...((..((.............))..))...))....((((((.(((.(((((((........))))))).)))))))-----))...--------)))--- ( -19.72)
>DroMoj_CAF1 55301 101 + 1
------UGCUGGCGACGCCAUGGUUUAUCCUUUUAUCCUUUAUCCUUAUGCUUUUUUGCACAUUAUUUGCUUUUGCAAUUCAAAGCGAUUAAGUGA-----GACGA--------CGCGGC
------.((((.((.((.(..((.....)).....(((((.((((((.(((......)))......((((....))))....))).))).))).))-----).)).--------)))))) ( -18.90)
>DroAna_CAF1 26891 85 + 1
--GCCACAUUGGCGACGCUUUGGUUUAU--------CCUUUAUCCUUAUGCUUUUUUGCACAUUAUUUGCUUUUGCAAUUCAAAGCGAUUAAGUG-------------------------
--(((.....)))..((((((((.....--------............(((......)))......((((....)))).))))))))........------------------------- ( -20.70)
>DroPer_CAF1 30169 105 + 1
---G-CCGCCGGCGACGCUUUGGUUUAU--------CCUUUAUCCUUAUGCCUUUUUGCACAUUAUUUGCUUUUGCAAUUCAAAGCGAUUAAGUGCGACAUCGCCGAGGAGGAGGAC---
---(-(((.((....))...))))...(--------(((((.(((((..((..(.((((((.(((.(((((((........))))))).))))))))).)..)).))))))))))).--- ( -31.70)
>consensus
___C_CCGCUGGCGACGCUUUGGUUUAU________CCUUUAUCCUUAUGCUUUUUUGCACAUUAUUUGCUUUUGCAAUUCAAAGCGAUUAAGUGC_____CACCA________GAC___
......((((.....((((((((.........................(((......)))......((((....)))).))))))))....))))......................... (-14.53 = -15.08 +   0.56)

alignment

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secondary structure

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dotplot

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Window 7

Location 12,506,932 – 12,507,025
Length 93
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 77.05
Mean single sequence MFE -25.71
Consensus MFE -15.97
Energy contribution -16.17
Covariance contribution 0.20
Combinations/Pair 1.06
Mean z-score -2.54
Structure conservation index 0.62
SVM decision value 1.96
SVM RNA-class probability 0.984002
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12506932 93 - 27905053
---GAC--------UGGAG-----ACACUUAAUCGCUUUGAAUUGCAAAAGCAAAUAAUGUGCAAAAAAGCAUAAGGAUAAAGG--------AUAAACCAAAGCGUCGCCAGCUG-GA--
---..(--------(((.(-----((.(((.((((((((........)))))......(((((......)))))..)))...((--------.....)).))).))).))))...-..-- ( -23.90)
>DroPse_CAF1 29233 102 - 1
---GUCCU---CCUCGGCGAUGUCGCACUUAAUCGCUUUGAAUUGCAAAAGCAAAUAAUGUGCAAAAAGGCAUAAGGAUAAAGG--------AUAAACCAAAGCGUCGCCGGCGG-C---
---.....---((((((((((((........(((.(((((..((((....))))....(((((......)))))....))))))--------))........)))))))))).))-.--- ( -29.69)
>DroGri_CAF1 80857 103 - 1
---GCG--------UCGUC-----GCACUUAAUCGCUUUGAAUUGCAAAAGCAAAUAAUGUGCAAAAAAGCAUAAGGAUAAAGGAUAAAAGGAUAAACCAUAGCGUCGCCAGCAC-AAGC
---((.--------.((.(-----((.(((.((((((((........)))))......(((((......)))))..))).))).......((.....))...))).))...))..-.... ( -24.20)
>DroMoj_CAF1 55301 101 - 1
GCCGCG--------UCGUC-----UCACUUAAUCGCUUUGAAUUGCAAAAGCAAAUAAUGUGCAAAAAAGCAUAAGGAUAAAGGAUAAAAGGAUAAACCAUGGCGUCGCCAGCA------
((.(((--------.((((-----((.(((.((((((((........)))))......(((((......)))))..))).))))).....((.....))..)))).)))..)).------ ( -26.80)
>DroAna_CAF1 26891 85 - 1
-------------------------CACUUAAUCGCUUUGAAUUGCAAAAGCAAAUAAUGUGCAAAAAAGCAUAAGGAUAAAGG--------AUAAACCAAAGCGUCGCCAAUGUGGC--
-------------------------........(((((((..((((....))))....(((((......)))))..........--------......)))))))..(((.....)))-- ( -20.00)
>DroPer_CAF1 30169 105 - 1
---GUCCUCCUCCUCGGCGAUGUCGCACUUAAUCGCUUUGAAUUGCAAAAGCAAAUAAUGUGCAAAAAGGCAUAAGGAUAAAGG--------AUAAACCAAAGCGUCGCCGGCGG-C---
---........((((((((((((........(((.(((((..((((....))))....(((((......)))))....))))))--------))........)))))))))).))-.--- ( -29.69)
>consensus
___GCC________UGGCG_____GCACUUAAUCGCUUUGAAUUGCAAAAGCAAAUAAUGUGCAAAAAAGCAUAAGGAUAAAGG________AUAAACCAAAGCGUCGCCAGCGG_C___
.................................(((((((..((((....))))....(((((......)))))........................)))))))............... (-15.97 = -16.17 +   0.20)

alignment

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secondary structure

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dotplot

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Window 8

Location 12,506,961 – 12,507,052
Length 91
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 80.13
Mean single sequence MFE -23.20
Consensus MFE -12.35
Energy contribution -11.68
Covariance contribution -0.67
Combinations/Pair 1.12
Mean z-score -2.00
Structure conservation index 0.53
SVM decision value 0.07
SVM RNA-class probability 0.567078
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12506961 91 + 27905053
UAUCCUUAUGCUUUUUUGCACAUUAUUUGCUUUUGCAAUUCAAAGCGAUUAAGUGU-----CUCCA--------GUCUCGCAACUA------GCAACUCGCAUCUCGGAU
.((((..((((......((((.(((.(((((((........))))))).)))))))-----.....--------.....((.....------)).....))))...)))) ( -18.70)
>DroPse_CAF1 29261 101 + 1
UAUCCUUAUGCCUUUUUGCACAUUAUUUGCUUUUGCAAUUCAAAGCGAUUAAGUGCGACAUCGCCGAGG---AGGACUCGAGAGAG------UCGCCUCGAGACUCGACG
.........((..(.((((((.(((.(((((((........))))))).))))))))).)..))(((((---..(((((....)))------)).))))).......... ( -34.10)
>DroSim_CAF1 29361 91 + 1
UAUCCUUAUGCUUUUUUGCACAUUAUUUGCUUUUGCAAUUCAAAGCGAUUAAGUGU-----CUCCA--------GUCUCGCAACUA------GCAACUAGCAACUCGCAU
........((((...(((((((((..(((((((........)))))))...)))))-----....(--------((......))).------))))..))))........ ( -16.20)
>DroEre_CAF1 28827 97 + 1
UAUCCUUAUGCUUUUUUGCACAUUAUUUGCUUUUGCAAUUCAAAGCGAUUAAGUGU-----CUCCA--------GUCUCGCAACUCGCACUCGCAACUAGCAACUAGCAA
........((((...((((.......((((....))))......((((....((((-----....(--------((......))).)))))))).....))))..)))). ( -19.20)
>DroYak_CAF1 29077 91 + 1
UAUCCUUAUGCUUUUUUGCACAUUAUUUGCUUUUGCAAUUCAAAGCGAUUAAGUGU-----CUCCA--------GUCUCGCAACUC------GCAACUAGCAACUCGCAU
........((((...((((.......((((....))))......((((...(.((.-----...))--------.).)))).....------))))..))))........ ( -16.00)
>DroPer_CAF1 30197 104 + 1
UAUCCUUAUGCCUUUUUGCACAUUAUUUGCUUUUGCAAUUCAAAGCGAUUAAGUGCGACAUCGCCGAGGAGGAGGACUCGAGAGAG------UCGCCUCGAGACUCGACG
.........((..(.((((((.(((.(((((((........))))))).))))))))).)..))((((((((..(((((....)))------)).))))....))))... ( -35.00)
>consensus
UAUCCUUAUGCUUUUUUGCACAUUAUUUGCUUUUGCAAUUCAAAGCGAUUAAGUGU_____CUCCA________GUCUCGCAACUA______GCAACUAGCAACUCGCAU
.................((((.(((.(((((((........))))))).)))))))....................................((.....))......... (-12.35 = -11.68 +  -0.67)

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 11:38:31 2006