Locus 4298

Sequence ID 3R_DroMel_CAF1
Location 11,419,471 – 11,419,586
Length 115
Max. P 0.992066
window7002 window7003 window7004

overview

Window 2

Location 11,419,471 – 11,419,571
Length 100
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 86.02
Mean single sequence MFE -30.04
Consensus MFE -21.24
Energy contribution -21.36
Covariance contribution 0.12
Combinations/Pair 1.07
Mean z-score -1.79
Structure conservation index 0.71
SVM decision value 0.20
SVM RNA-class probability 0.630563
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11419471 100 - 27905053
---UUUUCGGCUGCCUGUAUUUGAACCAAGCACUUCAAAAGCAGCGUUAGAUUGCAUAAAAGCAAAUGCGGAAGUGGUAACUGCAACUGAAAGGGC-----------------GGUGGAA
---..(((.(((((((.((.(((.....(.((((((....(((((....).))))......((....)).)))))).).....))).))...))))-----------------))).))) ( -29.70)
>DroSec_CAF1 167031 100 - 1
---UUUUCGGCUGCCUGUAUUUGAACCAAGCACUUCAAAAGCAGCGUUAGAUUGCAUAAAAGCAAAUGCGGAAGUGGUAACUGCAGCUGAAAGGGC-----------------GGUGGGA
---(((((((((((((((.((((((........)))))).)))).((((..((((......))))..((....))..)))).)))))))))))...-----------------....... ( -30.70)
>DroSim_CAF1 159849 100 - 1
---UUUUCGGCUGCCUGUAUUUGAACCAAGCACUUCAAAAGCAGCGUUAGAUUGCAUAAAAGCAAAUGCGGAAGUGGUAACUGCAUCUGAAAGGGC-----------------GGUGGGA
---..(((.(((((((((.((((((........)))))).))....(((((((((......)))).(((((.........))))))))))..))))-----------------))).))) ( -28.80)
>DroEre_CAF1 155007 120 - 1
CUUUUUUCGGCUGGCUGUAUUUGAAGCAAGCACUUCAAAAGCAGCGUUAGAUUGCAUAAAAGCAAAUGCGGAAGUGGUAACUGCAACUGAGGGGGCGGGUGGGGUGGUUAAGCGGUGGGA
.....(((.(((.(((((.(((((((......))))))).)))))(((.(((..(......((....((....)).....((((..(....)..))))))...)..))).)))))).))) ( -35.30)
>DroYak_CAF1 159162 93 - 1
---GUUUCGACUGGCUGUAUUUGAAGCAAGCACUUCAAAAGCAGCGUUAGAUUGCAUAAAAGCAAAUGCGGAAGUGGUAACUGCAACUGAGGG------------------------GGA
---.(..(.....(((((.(((((((......))))))).))))).((((.((((......)))).(((((.........))))).)))))..------------------------).. ( -25.70)
>consensus
___UUUUCGGCUGCCUGUAUUUGAACCAAGCACUUCAAAAGCAGCGUUAGAUUGCAUAAAAGCAAAUGCGGAAGUGGUAACUGCAACUGAAAGGGC_________________GGUGGGA
....((((((.(((((((.((((((........)))))).)))).((((..((((......))))..((....))..)))).))).))))))............................ (-21.24 = -21.36 +   0.12)

alignment

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secondary structure

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dotplot

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Window 3

Location 11,419,494 – 11,419,586
Length 92
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 84.09
Mean single sequence MFE -26.74
Consensus MFE -18.96
Energy contribution -19.80
Covariance contribution 0.84
Combinations/Pair 1.05
Mean z-score -3.20
Structure conservation index 0.71
SVM decision value 2.30
SVM RNA-class probability 0.992066
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11419494 92 + 27905053
UUACCACUUCCGCAUUUGCUUUUAUGCAAUCUAACGCUGCUUUUGAAGUGCUUGGUUCAAAUACAGGCAGCCGAAAA----------------------------AAGCGGAAAUAAAAU
.......((((((..((((......))))......((((((((((((.(....).))))))....))))))......----------------------------..))))))....... ( -25.70)
>DroSec_CAF1 167054 92 + 1
UUACCACUUCCGCAUUUGCUUUUAUGCAAUCUAACGCUGCUUUUGAAGUGCUUGGUUCAAAUACAGGCAGCCGAAAA----------------------------AAGCGGAAAUAAAAU
.......((((((..((((......))))......((((((((((((.(....).))))))....))))))......----------------------------..))))))....... ( -25.70)
>DroSim_CAF1 159872 92 + 1
UUACCACUUCCGCAUUUGCUUUUAUGCAAUCUAACGCUGCUUUUGAAGUGCUUGGUUCAAAUACAGGCAGCCGAAAA----------------------------AAGCGGAAAUAAAAU
.......((((((..((((......))))......((((((((((((.(....).))))))....))))))......----------------------------..))))))....... ( -25.70)
>DroEre_CAF1 155047 120 + 1
UUACCACUUCCGCAUUUGCUUUUAUGCAAUCUAACGCUGCUUUUGAAGUGCUUGCUUCAAAUACAGCCAGCCGAAAAAAGCCAAAAAGGGCGAAAAAGGGGGAAAAAGCGGAAAUAAAAU
.......((((((..((((......))))(((..(((((..((((((((....))))))))..))))............(((......)))......)..)))....))))))....... ( -36.10)
>DroYak_CAF1 159178 100 + 1
UUACCACUUCCGCAUUUGCUUUUAUGCAAUCUAACGCUGCUUUUGAAGUGCUUGCUUCAAAUACAGCCAGUCGAAAC-------------CGAAAA-------AAAACCAAAAAAAAAGU
.......(((.((..((((......))))......((((..((((((((....))))))))..))))..)).)))..-------------......-------................. ( -20.50)
>consensus
UUACCACUUCCGCAUUUGCUUUUAUGCAAUCUAACGCUGCUUUUGAAGUGCUUGGUUCAAAUACAGGCAGCCGAAAA____________________________AAGCGGAAAUAAAAU
.......((((((..((((......))))......((((((((((((........))))))....))))))....................................))))))....... (-18.96 = -19.80 +   0.84)

alignment

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secondary structure

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dotplot

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Window 4

Location 11,419,494 – 11,419,586
Length 92
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 84.09
Mean single sequence MFE -27.46
Consensus MFE -23.44
Energy contribution -23.36
Covariance contribution -0.08
Combinations/Pair 1.10
Mean z-score -2.44
Structure conservation index 0.85
SVM decision value 2.11
SVM RNA-class probability 0.988272
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11419494 92 - 27905053
AUUUUAUUUCCGCUU----------------------------UUUUCGGCUGCCUGUAUUUGAACCAAGCACUUCAAAAGCAGCGUUAGAUUGCAUAAAAGCAAAUGCGGAAGUGGUAA
...((((((((((..----------------------------......(((((.....((((((........)))))).)))))......((((......))))..))))))))))... ( -25.70)
>DroSec_CAF1 167054 92 - 1
AUUUUAUUUCCGCUU----------------------------UUUUCGGCUGCCUGUAUUUGAACCAAGCACUUCAAAAGCAGCGUUAGAUUGCAUAAAAGCAAAUGCGGAAGUGGUAA
...((((((((((..----------------------------......(((((.....((((((........)))))).)))))......((((......))))..))))))))))... ( -25.70)
>DroSim_CAF1 159872 92 - 1
AUUUUAUUUCCGCUU----------------------------UUUUCGGCUGCCUGUAUUUGAACCAAGCACUUCAAAAGCAGCGUUAGAUUGCAUAAAAGCAAAUGCGGAAGUGGUAA
...((((((((((..----------------------------......(((((.....((((((........)))))).)))))......((((......))))..))))))))))... ( -25.70)
>DroEre_CAF1 155047 120 - 1
AUUUUAUUUCCGCUUUUUCCCCCUUUUUCGCCCUUUUUGGCUUUUUUCGGCUGGCUGUAUUUGAAGCAAGCACUUCAAAAGCAGCGUUAGAUUGCAUAAAAGCAAAUGCGGAAGUGGUAA
...((((((((((..............(((((......)))............(((((.(((((((......))))))).)))))....))((((......))))..))))))))))... ( -34.60)
>DroYak_CAF1 159178 100 - 1
ACUUUUUUUUUGGUUUU-------UUUUCG-------------GUUUCGACUGGCUGUAUUUGAAGCAAGCACUUCAAAAGCAGCGUUAGAUUGCAUAAAAGCAAAUGCGGAAGUGGUAA
((((((..((((.((((-------....((-------------((((.(((..(((((.(((((((......))))))).))))))))))))))...)))).))))...))))))..... ( -25.60)
>consensus
AUUUUAUUUCCGCUU____________________________UUUUCGGCUGCCUGUAUUUGAACCAAGCACUUCAAAAGCAGCGUUAGAUUGCAUAAAAGCAAAUGCGGAAGUGGUAA
...((((((((((................................((..((.(.((((.((((((........)))))).)))))))..))((((......))))..))))))))))... (-23.44 = -23.36 +  -0.08)

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 11:25:14 2006