Locus 2349

Sequence ID 2L_DroMel_CAF1
Location 6,367,085 – 6,367,244
Length 159
Max. P 0.991980
window3788 window3789 window3790

overview

Window 8

Location 6,367,085 – 6,367,205
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 80.45
Mean single sequence MFE -32.27
Consensus MFE -21.41
Energy contribution -22.09
Covariance contribution 0.67
Combinations/Pair 1.14
Mean z-score -2.25
Structure conservation index 0.66
SVM decision value 1.12
SVM RNA-class probability 0.918021
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6367085 120 - 22407834
CCGCUUCGGUACAGGAAAUCAACAUUUACCUUUAUUUCCGUUCCGGUUCAGUUACAGUUACAGUGAACCGGUUAACCUUCGGCUACAGAUUCCGGUUCUAAAUGUUUACCGUGCCAAAAU
.......(((((.((((.((...................(((((((((((.(.........).))))))))..)))(....).....))))))(((.(.....)...))))))))..... ( -27.30)
>DroSec_CAF1 11959 118 - 1
CCGCUUCGGUGCAGGAAAUCAACAUUUACGUUUAUUUCCGUUCCGGUUCACUUACAGGU--AGUGAACCGGUUAACCUUCGGCUACAGAUUCCGGUUCUAAAUGUGUACCGUGCCAUAAU
..((..(((((((((((((.(((......))).))))))(((((((((((((.......--))))))))))..)))..((((.........)))).........))))))).))...... ( -38.60)
>DroEre_CAF1 11841 116 - 1
CUGAUUCGGUAAAG-GAACUAACGCGUAUGUUUAUUUCCGUACCGGUUCGUUUACAAGU--ACUGAACCGGUUAAU-UUCGUUUACCGAUUUCGGUUCUAAGUUUCUUUCCUGCCAAAAU
((((.((((((((.-(((.((((..(((((........)))))((((((((........--)).))))))))))..-))).))))))))..))))......................... ( -30.90)
>consensus
CCGCUUCGGUACAGGAAAUCAACAUUUACGUUUAUUUCCGUUCCGGUUCACUUACAGGU__AGUGAACCGGUUAACCUUCGGCUACAGAUUCCGGUUCUAAAUGUCUACCGUGCCAAAAU
.......(((((.((((((.(((......))).))))))...((((((((.............)))))))).......................................)))))..... (-21.41 = -22.09 +   0.67)

alignment

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secondary structure

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dotplot

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Window 9

Location 6,367,125 – 6,367,244
Length 119
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 73.31
Mean single sequence MFE -32.03
Consensus MFE -17.94
Energy contribution -18.62
Covariance contribution 0.68
Combinations/Pair 1.20
Mean z-score -2.35
Structure conservation index 0.56
SVM decision value 2.08
SVM RNA-class probability 0.987434
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6367125 119 + 22407834
GAAGGUUAACCGGUUCACUGUAACUGUAACUGAACCGGAACGGAAAUAAAGGUAAAUGUUGAUUUCCUGUACCGAAGCGGUAGAACUGGUUAAGGGUUUAAACCUAAUUGAUUUCAUUU-
((((.((((((((((((((((....((......))(((.((((((((.((.(....).)).)))))).)).)))..))))).)))))))))))((((....))))......))))....- ( -32.70)
>DroSec_CAF1 11999 116 + 1
GAAGGUUAACCGGUUCACU--ACCUGUAAGUGAACCGGAACGGAAAUAAACGUAAAUGUUGAUUUCCUGCACCGAAGCGGUUAAGCUUGC-GAGGUUUCACGCCUAAUUGAUUUAAUUU-
..((((...((((((((((--.......))))))))))...((((((.((((....)))).)))))).((..((((((......)))).)-)..)).....))))..............- ( -35.50)
>DroEre_CAF1 11881 113 + 1
GAA-AUUAACCGGUUCAGU--ACUUGUAAACGAACCGGUACGGAAAUAAACAUACGCGUUAGUUC-CUUUACCGAAUCAGUAAACCGG---ACCGGUUCGAACCCAUUUAUUUACAUUUU
...-.......(((((.((--........))((((((((..((((...(((......)))..)))-)....(((...........)))---)))))))))))))................ ( -27.90)
>consensus
GAAGGUUAACCGGUUCACU__ACCUGUAAAUGAACCGGAACGGAAAUAAACGUAAAUGUUGAUUUCCUGUACCGAAGCGGUAAAACUGG__AAGGGUUCAAACCUAAUUGAUUUCAUUU_
.........((((((((.............))))))))...((((((.(((......))).))))))...........(((.(((((......)))))...)))................ (-17.94 = -18.62 +   0.68)

alignment

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secondary structure

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dotplot

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Window 0

Location 6,367,125 – 6,367,244
Length 119
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 73.31
Mean single sequence MFE -30.17
Consensus MFE -17.28
Energy contribution -17.95
Covariance contribution 0.67
Combinations/Pair 1.14
Mean z-score -2.34
Structure conservation index 0.57
SVM decision value 2.30
SVM RNA-class probability 0.991980
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6367125 119 - 22407834
-AAAUGAAAUCAAUUAGGUUUAAACCCUUAACCAGUUCUACCGCUUCGGUACAGGAAAUCAACAUUUACCUUUAUUUCCGUUCCGGUUCAGUUACAGUUACAGUGAACCGGUUAACCUUC
-..............(((((..................(((((...)))))..((((((.((........)).))))))...((((((((.(.........).))))))))..))))).. ( -22.40)
>DroSec_CAF1 11999 116 - 1
-AAAUUAAAUCAAUUAGGCGUGAAACCUC-GCAAGCUUAACCGCUUCGGUGCAGGAAAUCAACAUUUACGUUUAUUUCCGUUCCGGUUCACUUACAGGU--AGUGAACCGGUUAACCUUC
-............((((((((((....))-))..)))))).(((....)))..((((((.(((......))).))))))(((((((((((((.......--))))))))))..))).... ( -35.50)
>DroEre_CAF1 11881 113 - 1
AAAAUGUAAAUAAAUGGGUUCGAACCGGU---CCGGUUUACUGAUUCGGUAAAG-GAACUAACGCGUAUGUUUAUUUCCGUACCGGUUCGUUUACAAGU--ACUGAACCGGUUAAU-UUC
.......((((.(((.(((((((((((((---.((((((((((...))))))).-((((..........))))....))).))))))))((........--)).))))).))).))-)). ( -32.60)
>consensus
_AAAUGAAAUCAAUUAGGUUUGAACCCUU__CCAGCUUUACCGCUUCGGUACAGGAAAUCAACAUUUACGUUUAUUUCCGUUCCGGUUCACUUACAGGU__AGUGAACCGGUUAACCUUC
......................................(((((...)))))..((((((.(((......))).))))))...((((((((.............))))))))......... (-17.28 = -17.95 +   0.67)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:25:57 2006