Locus 597

Sequence ID 3L_DroMel_CAF1
Location 1,713,751 – 1,713,887
Length 136
Max. P 0.978286
window908 window909 window910 window911

overview

Window 8

Location 1,713,751 – 1,713,848
Length 97
Sequences 4
Columns 97
Reading direction forward
Mean pairwise identity 87.37
Mean single sequence MFE -23.73
Consensus MFE -18.45
Energy contribution -19.52
Covariance contribution 1.06
Combinations/Pair 1.05
Mean z-score -2.86
Structure conservation index 0.78
SVM decision value 1.81
SVM RNA-class probability 0.978286
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1713751 97 + 23771897
AAGAAGUCGACGAAAGCGCAAAACUAAAGCCAAAGAAAGGCCAUUAAAUUGUGCGAAAGAGAAACCAGAACAGGUUUAACUGUUCUUGGUGUGCGCC
...............(((((...((...(((.......)))............(....)))..((((((((((......)))))).)))).))))). ( -25.20)
>DroSec_CAF1 13852 97 + 1
AAGAAGUCGACGAAAGCGCAAAACCAAAGCCAAAGAAAGGCCAUUAAAUUGUGCGAAAGAGAAACCAGAACAGGUUUAACUGUUCUUGGUGUGCGCC
...............(((((..(((((.(((.......)))............(....)........((((((......))))))))))).))))). ( -25.30)
>DroEre_CAF1 14372 82 + 1
--GAA---GACGAACGCGCGAAACCAAAGCCAAAUAAAGGCUACUAAAUUGUGCGAAAGAGAAACCAGAACAGGUUUAACUGUUCUU----------
--...---......(((((((......((((.......))))......)))))))...........(((((((......))))))).---------- ( -23.00)
>DroYak_CAF1 14024 93 + 1
AAGAA---GACGAAAGCGCAAAACCAAAGCAAAAGAAAGGCCAUUAAAUUGUGCGAAAGAGAAACCAAAACAGGUUUAACUGUUCUUGGUGUGCGC-
.....---.......(((((..((((((((.........((((......)).))...((..(((((......)))))..))))).))))).)))))- ( -21.40)
>consensus
AAGAA___GACGAAAGCGCAAAACCAAAGCCAAAGAAAGGCCAUUAAAUUGUGCGAAAGAGAAACCAGAACAGGUUUAACUGUUCUUGGUGUGCGC_
...............((((((.......(((.......))).......)))))).........((((((((((......)))))).))))....... (-18.45 = -19.52 +   1.06) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 1,713,751 – 1,713,848
Length 97
Sequences 4
Columns 97
Reading direction reverse
Mean pairwise identity 87.37
Mean single sequence MFE -23.32
Consensus MFE -17.34
Energy contribution -18.02
Covariance contribution 0.69
Combinations/Pair 1.14
Mean z-score -2.68
Structure conservation index 0.74
SVM decision value 1.42
SVM RNA-class probability 0.952075
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1713751 97 - 23771897
GGCGCACACCAAGAACAGUUAAACCUGUUCUGGUUUCUCUUUCGCACAAUUUAAUGGCCUUUCUUUGGCUUUAGUUUUGCGCUUUCGUCGACUUCUU
((((...((((.((((((......))))))))))........((((.((((....((((.......))))..)))).))))....))))........ ( -26.60)
>DroSec_CAF1 13852 97 - 1
GGCGCACACCAAGAACAGUUAAACCUGUUCUGGUUUCUCUUUCGCACAAUUUAAUGGCCUUUCUUUGGCUUUGGUUUUGCGCUUUCGUCGACUUCUU
((((...((((.((((((......))))))))))........((((.((((....((((.......))))..)))).))))....))))........ ( -26.50)
>DroEre_CAF1 14372 82 - 1
----------AAGAACAGUUAAACCUGUUCUGGUUUCUCUUUCGCACAAUUUAGUAGCCUUUAUUUGGCUUUGGUUUCGCGCGUUCGUC---UUC--
----------..((((((..(((((......)))))..))..(((..((((....((((.......))))..))))..))).))))...---...-- ( -18.50)
>DroYak_CAF1 14024 93 - 1
-GCGCACACCAAGAACAGUUAAACCUGUUUUGGUUUCUCUUUCGCACAAUUUAAUGGCCUUUCUUUUGCUUUGGUUUUGCGCUUUCGUC---UUCUU
-(((((.((((((((.((..(((((......)))))..)))))((.((......))))............)))))..))))).......---..... ( -21.70)
>consensus
_GCGCACACCAAGAACAGUUAAACCUGUUCUGGUUUCUCUUUCGCACAAUUUAAUGGCCUUUCUUUGGCUUUGGUUUUGCGCUUUCGUC___UUCUU
.......((((.((((((......))))))))))........((((.((((....((((.......))))..)))).))))................ (-17.34 = -18.02 +   0.69) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 1,713,788 – 1,713,887
Length 99
Sequences 5
Columns 99
Reading direction forward
Mean pairwise identity 82.13
Mean single sequence MFE -24.64
Consensus MFE -14.54
Energy contribution -17.18
Covariance contribution 2.64
Combinations/Pair 1.05
Mean z-score -2.19
Structure conservation index 0.59
SVM decision value 0.58
SVM RNA-class probability 0.787230
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1713788 99 + 23771897
AGGCCAUUAAAUUGUGCGAAAGAGAAACCAGAACAGGUUUAACUGUUCUUGGUGUGCGCCCGAUAAAAGCGCUAAUUGACACGCACACAAGUGCACUAC
((..((((....((((((........((((((((((......)))))).))))..((((.........)))).........))))))..))))..)).. ( -29.10)
>DroPse_CAF1 16686 89 + 1
AGGCA-------CGCAAGAAAGAGAAACCAGAACAGGUUUAACUGUUCUUGGAGUGCUC-GCUUAACAACGCUAAUUGACACGCACACAGGCACACA--
((((.-------(....)...(((...(((((((((......)))))).)))....)))-))))..................((......)).....-- ( -21.50)
>DroSec_CAF1 13889 99 + 1
AGGCCAUUAAAUUGUGCGAAAGAGAAACCAGAACAGGUUUAACUGUUCUUGGUGUGCGCCCAAUAAAAGCGCUAAUUGACACGCACACAAGUGCACUAC
((..((((....((((((........((((((((((......)))))).))))..((((.........)))).........))))))..))))..)).. ( -29.10)
>DroEre_CAF1 14404 82 + 1
AGGCUACUAAAUUGUGCGAAAGAGAAACCAGAACAGGUUUAACUGUUCUU--------------AAAAGCGCUAAUUGACACACACACAAGUGCAC---
..((.(((....(((((....).......(((((((......))))))).--------------.................))))....)))))..--- ( -16.30)
>DroYak_CAF1 14058 98 + 1
AGGCCAUUAAAUUGUGCGAAAGAGAAACCAAAACAGGUUUAACUGUUCUUGGUGUGCGC-CAAUAAAAGCGCUAAUUGACACGCACACAAGUGCACUAC
((..((((....((((((........((((((((((......))))).)))))..((((-........)))).........))))))..))))..)).. ( -27.20)
>consensus
AGGCCAUUAAAUUGUGCGAAAGAGAAACCAGAACAGGUUUAACUGUUCUUGGUGUGCGC_CAAUAAAAGCGCUAAUUGACACGCACACAAGUGCACUAC
.............(((((.........(.(((((((......))))))).)(((((((.......................)))))))...)))))... (-14.54 = -17.18 +   2.64) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 1,713,788 – 1,713,887
Length 99
Sequences 5
Columns 99
Reading direction reverse
Mean pairwise identity 82.13
Mean single sequence MFE -26.43
Consensus MFE -17.48
Energy contribution -17.28
Covariance contribution -0.20
Combinations/Pair 1.29
Mean z-score -1.95
Structure conservation index 0.66
SVM decision value 0.51
SVM RNA-class probability 0.764232
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1713788 99 - 23771897
GUAGUGCACUUGUGUGCGUGUCAAUUAGCGCUUUUAUCGGGCGCACACCAAGAACAGUUAAACCUGUUCUGGUUUCUCUUUCGCACAAUUUAAUGGCCU
..((.((.....((((((.........((((((.....))))))..((((.((((((......))))))))))........))))))........)))) ( -29.52)
>DroPse_CAF1 16686 89 - 1
--UGUGUGCCUGUGUGCGUGUCAAUUAGCGUUGUUAAGC-GAGCACUCCAAGAACAGUUAAACCUGUUCUGGUUUCUCUUUCUUGCG-------UGCCU
--.(..(((..((((.(((..((((....))))....))-).)))).(((.((((((......)))))))))............)))-------..).. ( -23.80)
>DroSec_CAF1 13889 99 - 1
GUAGUGCACUUGUGUGCGUGUCAAUUAGCGCUUUUAUUGGGCGCACACCAAGAACAGUUAAACCUGUUCUGGUUUCUCUUUCGCACAAUUUAAUGGCCU
..((.((.....((((((.........((((((.....))))))..((((.((((((......))))))))))........))))))........)))) ( -30.22)
>DroEre_CAF1 14404 82 - 1
---GUGCACUUGUGUGUGUGUCAAUUAGCGCUUUU--------------AAGAACAGUUAAACCUGUUCUGGUUUCUCUUUCGCACAAUUUAGUAGCCU
---..(((((..(((((((((......))))....--------------.(((((((......)))))))............)))))....))).)).. ( -19.30)
>DroYak_CAF1 14058 98 - 1
GUAGUGCACUUGUGUGCGUGUCAAUUAGCGCUUUUAUUG-GCGCACACCAAGAACAGUUAAACCUGUUUUGGUUUCUCUUUCGCACAAUUUAAUGGCCU
...((((.((((.(((.((((((((..........))))-)))).)))))))...((..(((((......)))))..))...))))............. ( -29.30)
>consensus
GUAGUGCACUUGUGUGCGUGUCAAUUAGCGCUUUUAUUG_GCGCACACCAAGAACAGUUAAACCUGUUCUGGUUUCUCUUUCGCACAAUUUAAUGGCCU
...((((........((((........))))................(((.((((((......)))))))))..........))))............. (-17.48 = -17.28 +  -0.20) 

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript


Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:46:14 2006