Locus 1260

Sequence ID 2R_DroMel_CAF1
Location 4,924,188 – 4,924,357
Length 169
Max. P 0.993777
window2184 window2185 window2186

overview

Window 4

Location 4,924,188 – 4,924,291
Length 103
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 73.03
Mean single sequence MFE -25.08
Consensus MFE -7.42
Energy contribution -11.02
Covariance contribution 3.60
Combinations/Pair 1.00
Mean z-score -2.31
Structure conservation index 0.30
SVM decision value 2.06
SVM RNA-class probability 0.986985
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4924188 103 + 20766785
-----------------GGAAUUGUUUUCACGUUUUCGAGCUUUUCCAAAUUCAUAUAUCCUAAAGUCGUAAGAAAUAUUUGUUUGGAAAAGCUGUCCAAAUGCAAGCAAUUCGCACUAU
-----------------.(((((((((.((((....))(((((((((((((..((((.((.((......)).)).))))..))))))))))))).......)).)))))))))....... ( -29.00)
>DroSec_CAF1 13034 103 + 1
-----------------AGUAUUGUUUAUAAUUUUUAGAACUUUUCCAAAUGCAUAUAUCCUCAAGUCGUAGGAAAUAUUUGUUUGGAAAAGCUGUCCAAAUGCAACAAUUCCGCACUAU
-----------------.((((((((....((((.(((..((((((((((((.((((.(((((.....).)))).)))).)))))))))))))))...))))..))))))...))..... ( -21.80)
>DroSim_CAF1 13200 103 + 1
-----------------AGUAUUGUUUAUAAGUUUUAGAGCUUUUCCAAAUGCAUAUAUCCUCAAGUCGUAGGAAAUAUUUGUUUGGAAAAGCUAUCCAAAUGCAACAAUUCCGCACUAU
-----------------.((((((((.....((((...((((((((((((((.((((.(((((.....).)))).)))).))))))))))))))....))))..))))))...))..... ( -27.00)
>DroEre_CAF1 11262 113 + 1
UGCUAUAAUCUGAAUUUGGUGCUGCUCUUAAGGUAUAGAGCUUUUUCAUAUGCAUAUAUGCCAAAGUCGUAAAAAAUAUGUGUUUU------CUGCCCAAGUGCAGCAACU-CGCACUAA
(((......(((.((((((.((.(((((........)))))..........((((((((................))))))))...------..)))))))).))).....-.))).... ( -24.79)
>DroYak_CAF1 13258 113 + 1
GGCUAGAAUCUAAAUUUGGCAUUGUUUUCAAGUUAUAGAGCUUUUUCACAUGCAUAUAUCCUCAAGUCGUAAGAAAUAUUUGUUUU------CUGCCCAAGUGCAGCAAUU-CGCACUAU
(((.((((..(((((...((((.((....(((((....)))))....)))))).............((....))...)))))..))------)))))..(((((.......-.))))).. ( -22.80)
>consensus
_________________GGUAUUGUUUUUAAGUUUUAGAGCUUUUCCAAAUGCAUAUAUCCUCAAGUCGUAAGAAAUAUUUGUUUGGAAAAGCUGUCCAAAUGCAACAAUU_CGCACUAU
......................................(((((((((((((..((((.((............)).))))..))))))))))))).......(((.........))).... ( -7.42 = -11.02 +   3.60)

alignment

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secondary structure

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dotplot

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Window 5

Location 4,924,188 – 4,924,291
Length 103
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 73.03
Mean single sequence MFE -25.22
Consensus MFE -13.66
Energy contribution -16.58
Covariance contribution 2.92
Combinations/Pair 1.19
Mean z-score -2.37
Structure conservation index 0.54
SVM decision value 2.42
SVM RNA-class probability 0.993777
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4924188 103 - 20766785
AUAGUGCGAAUUGCUUGCAUUUGGACAGCUUUUCCAAACAAAUAUUUCUUACGACUUUAGGAUAUAUGAAUUUGGAAAAGCUCGAAAACGUGAAAACAAUUCC-----------------
..(((((((.....))))))).(((.((((((((((((...((((.(((((......))))).))))...)))))))))))).......((....))...)))----------------- ( -28.40)
>DroSec_CAF1 13034 103 - 1
AUAGUGCGGAAUUGUUGCAUUUGGACAGCUUUUCCAAACAAAUAUUUCCUACGACUUGAGGAUAUAUGCAUUUGGAAAAGUUCUAAAAAUUAUAAACAAUACU-----------------
.......((.((((((...((((((..(((((((((((...((((.((((........)))).))))...))))))))))))))))).......)))))).))----------------- ( -26.10)
>DroSim_CAF1 13200 103 - 1
AUAGUGCGGAAUUGUUGCAUUUGGAUAGCUUUUCCAAACAAAUAUUUCCUACGACUUGAGGAUAUAUGCAUUUGGAAAAGCUCUAAAACUUAUAAACAAUACU-----------------
.......((.((((((...((((((..(((((((((((...((((.((((........)))).))))...))))))))))))))))).......)))))).))----------------- ( -27.50)
>DroEre_CAF1 11262 113 - 1
UUAGUGCG-AGUUGCUGCACUUGGGCAG------AAAACACAUAUUUUUUACGACUUUGGCAUAUAUGCAUAUGAAAAAGCUCUAUACCUUAAGAGCAGCACCAAAUUCAGAUUAUAGCA
.......(-(((((((((.((((((.((------((((......))))))..((((((..(((((....)))))..)))).)).....)))))).))))))....))))........... ( -23.80)
>DroYak_CAF1 13258 113 - 1
AUAGUGCG-AAUUGCUGCACUUGGGCAG------AAAACAAAUAUUUCUUACGACUUGAGGAUAUAUGCAUGUGAAAAAGCUCUAUAACUUGAAAACAAUGCCAAAUUUAGAUUCUAGCC
..((((((-......))))))..(((((------((.....((((((((((.....)))))).))))((((((....(((........)))....)).))))..........)))).))) ( -20.30)
>consensus
AUAGUGCG_AAUUGUUGCAUUUGGACAGCUUUUCCAAACAAAUAUUUCUUACGACUUGAGGAUAUAUGCAUUUGGAAAAGCUCUAAAACUUAAAAACAAUACC_________________
..(((((((.....))))))).....((((((((((((...((((.((((........)))).))))...))))))))))))...................................... (-13.66 = -16.58 +   2.92)

alignment

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secondary structure

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dotplot

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Window 6

Location 4,924,251 – 4,924,357
Length 106
Sequences 5
Columns 107
Reading direction reverse
Mean pairwise identity 85.16
Mean single sequence MFE -27.26
Consensus MFE -16.90
Energy contribution -16.74
Covariance contribution -0.16
Combinations/Pair 1.23
Mean z-score -2.05
Structure conservation index 0.62
SVM decision value 0.06
SVM RNA-class probability 0.564494
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4924251 106 - 20766785
CACAAAAUUUCUGAGUGCUUACGGCGUAUAAUU-UUGCACACUUUUUUGGGCAAUUUGCAAAUGUUUAUAGUGCGAAUUGCUUGCAUUUGGACAGCUUUUCCAAACA
.........((..(((((.....(((.......-.)))..........((((((((((((...........)))))))))))))))))..))............... ( -25.50)
>DroSec_CAF1 13097 105 - 1
CACAG-AUUUCUGAGUGCUUUCGGCGUAUAAUU-UUGCCCACUUUUUUGGGCAAUUUGCAAAUGUUUAUAGUGCGGAAUUGUUGCAUUUGGACAGCUUUUCCAAACA
..(((-....))).(..((.(..((((...(..-(((((((......)))))))..)....))))..).))..)((((..((((........))))..))))..... ( -29.80)
>DroSim_CAF1 13263 105 - 1
CACAG-AUUUCUGAGUGCUUUCGGCGUAUAAUU-UUGCACACUUUUUUGGGCAAUUUGCAAAUGUUUAUAGUGCGGAAUUGUUGCAUUUGGAUAGCUUUUCCAAACA
..(((-....)))..........(((.((((((-((((((.((.....))((.....))...........))))))))))))))).((((((.......)))))).. ( -25.30)
>DroEre_CAF1 11342 99 - 1
CAUAC-AAUGCUGAGUGCUUUCGGCGUAAAAUUUUUGCUCAUUCUUUUGGGCAAUUUGUAAAUGUUUUUAGUGCG-AGUUGCUGCACUUGGGCAG------AAAACA
..(((-(((((((((....)))))))).......(((((((......)))))))..))))..(((((((.((.((-(((......))))).)).)------)))))) ( -31.10)
>DroYak_CAF1 13338 98 - 1
CAGAG-AAUUCUGAGUGCUUUCGGCGUUUAAUU-UUGCACACUUUUUUGGGCAAUUUGUAAAUGUUUAUAGUGCG-AAUUGCUGCACUUGGGCAG------AAAACA
.....-...((..(((((.....(((.......-.)))...........(((((((((((...........))))-))))))))))))..))...------...... ( -24.60)
>consensus
CACAG_AUUUCUGAGUGCUUUCGGCGUAUAAUU_UUGCACACUUUUUUGGGCAAUUUGCAAAUGUUUAUAGUGCG_AAUUGUUGCAUUUGGACAGCUUUUCCAAACA
.........((..(((((....((((.........))).).........(((((((((((...........)))).))))))))))))..))............... (-16.90 = -16.74 +  -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 10:00:20 2006