Locus 2708

Sequence ID 3R_DroMel_CAF1
Location 7,278,278 – 7,278,397
Length 119
Max. P 0.770488
window4397 window4398

overview

Window 7

Location 7,278,278 – 7,278,397
Length 119
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 82.68
Mean single sequence MFE -41.97
Consensus MFE -27.26
Energy contribution -28.71
Covariance contribution 1.45
Combinations/Pair 1.03
Mean z-score -2.23
Structure conservation index 0.65
SVM decision value 0.53
SVM RNA-class probability 0.770488
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7278278 119 + 27905053
CCCAGAAUGGUUUCGUCCGCAUGUGAGGAUUGGC-GGGUACUUUUGGACCCCAAAACCACUACGCAUCACCUCGCAUGGCGAGCCAAUGUCAAAUGGCUGGAAAAACCUUUCGAUGCGCC
....(((.(((((..(((((((((((((....((-((((..((((((...))))))..))).)))....)))))))).)).(((((........)))))))).))))).)))........ ( -42.40)
>DroSim_CAF1 3534 111 + 1
CCUAGAAUGGUUUCGUCCGCAUGUGGGGAUUGGCUGGGGACUUUUGGACCCCU-AACCACUCCGCAUCCCCCCGCAUGGCGAGCCAAUGUCAAAUGGCUGGAAAAACCUUUC--------
....(((.(((((..(((((((((((((...((.((.(((....(((......-..))).))).)).)))))))))).)).(((((........)))))))).))))).)))-------- ( -41.00)
>DroYak_CAF1 4536 109 + 1
CCUAGAUUGGC-UCGUCCGCAUGUGAGGAUUGGG--GG---UAUUGGACCCCU-A---ACUCCGCAUAACC-CGCAUGGCGAGCCAAUGUCAAAUGGCUGGAAAAACCUUUCGAUGUGGC
.....((((((-(((((.((.((((.((((((((--((---(.....))))))-)---).))).))))...-.))..)))))))))))((((..(((..((.....))..)))...)))) ( -42.50)
>consensus
CCUAGAAUGGUUUCGUCCGCAUGUGAGGAUUGGC_GGG_ACUUUUGGACCCCU_AACCACUCCGCAUCACC_CGCAUGGCGAGCCAAUGUCAAAUGGCUGGAAAAACCUUUCGAUG_G_C
....(((.(((((..(((((((((((((....((..((.......((...)).......))..))....)))))))).)).(((((........)))))))).))))).)))........ (-27.26 = -28.71 +   1.45)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 7,278,278 – 7,278,397
Length 119
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 82.68
Mean single sequence MFE -41.43
Consensus MFE -27.81
Energy contribution -29.70
Covariance contribution 1.89
Combinations/Pair 1.06
Mean z-score -1.80
Structure conservation index 0.67
SVM decision value 0.07
SVM RNA-class probability 0.567450
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7278278 119 - 27905053
GGCGCAUCGAAAGGUUUUUCCAGCCAUUUGACAUUGGCUCGCCAUGCGAGGUGAUGCGUAGUGGUUUUGGGGUCCAAAAGUACCC-GCCAAUCCUCACAUGCGGACGAAACCAUUCUGGG
........(((.((((((((((((((........))))).((.(((.((((....(((..(((.((((((...)))))).))).)-))....)))).)))))))).)))))).))).... ( -41.30)
>DroSim_CAF1 3534 111 - 1
--------GAAAGGUUUUUCCAGCCAUUUGACAUUGGCUCGCCAUGCGGGGGGAUGCGGAGUGGUU-AGGGGUCCAAAAGUCCCCAGCCAAUCCCCACAUGCGGACGAAACCAUUCUAGG
--------(((.((((((((((((((........))))).((.(((.(((((.........(((((-.((((.(.....).))))))))).))))).)))))))).)))))).))).... ( -45.00)
>DroYak_CAF1 4536 109 - 1
GCCACAUCGAAAGGUUUUUCCAGCCAUUUGACAUUGGCUCGCCAUGCG-GGUUAUGCGGAGU---U-AGGGGUCCAAUA---CC--CCCAAUCCUCACAUGCGGACGA-GCCAAUCUAGG
.((...(((((.((((.....)))).))))).(((((((((((..(((-.....)))(((..---.-.(((((.....)---))--))...)))........)).)))-))))))...)) ( -38.00)
>consensus
G_C_CAUCGAAAGGUUUUUCCAGCCAUUUGACAUUGGCUCGCCAUGCG_GGUGAUGCGGAGUGGUU_AGGGGUCCAAAAGU_CCC_GCCAAUCCUCACAUGCGGACGAAACCAUUCUAGG
........(((.((((((((((((((........))))).((.(((.((((..........((((...(((...........))).))))..)))).)))))))).)))))).))).... (-27.81 = -29.70 +   1.89)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:42:49 2006