Locus 1942

Sequence ID 3L_DroMel_CAF1
Location 5,395,463 – 5,395,566
Length 103
Max. P 0.985384
window3033 window3034

overview

Window 3

Location 5,395,463 – 5,395,566
Length 103
Sequences 4
Columns 103
Reading direction forward
Mean pairwise identity 94.93
Mean single sequence MFE -26.45
Consensus MFE -23.15
Energy contribution -23.40
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.85
Structure conservation index 0.88
SVM decision value 0.58
SVM RNA-class probability 0.790108
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5395463 103 + 23771897
GACAUUGACCCUUUGCAUGUCCAAAGGGACAAAAGGGUGUUACUGUGUCACAGACGUAAUUAAUUGUAAAUAAUUGUGCAUGUGUCACUUGCAAUUUAUUUAU
((((((((((((((...(((((....))))).))))).))))..)))))................((((((((...((((.(.....).))))..)))))))) ( -28.10)
>DroSec_CAF1 44323 101 + 1
GACUUUGACCCUUUGCACGUCCG-AGGGACA-AAGGGUGUUACUGUGUCACAGACGUAAUUAAUUGUAAAUAAUUGUGCAUGUGUCACUUGCAAUUUAUUUAU
.......((((((((..(.....-..)..))-))))))((....(((.((((..((((((((........))))))))..)))).)))..))........... ( -24.60)
>DroSim_CAF1 44134 101 + 1
GACAUUGACCCUUUGCACGUCCG-AGGGACA-AAGGGUGUUACUGUGUCACAGACGUAAUUAAUUGUAAAUAAUUGUGCGUGUGUCACUUGCAAUUUAUUUAU
((((((((((((((....((((.-..)))).-))))).))))..)))))(((.(((((..((((((....))))))))))).))).................. ( -24.70)
>DroYak_CAF1 44115 101 + 1
GACAUUGACCCUUGGCACCUCCA-AGGGACA-AAGGGUGUUACUGUGUCACAGACGUAAUUAAUUGUAAAUAAUUGUGCAUGUGUCACUUGUAAUUUUUUUAU
.....((.(((((((.....)))-)))).))-(((((.(((((.(((.((((..((((((((........))))))))..)))).)))..))))).))))).. ( -28.40)
>consensus
GACAUUGACCCUUUGCACGUCCA_AGGGACA_AAGGGUGUUACUGUGUCACAGACGUAAUUAAUUGUAAAUAAUUGUGCAUGUGUCACUUGCAAUUUAUUUAU
.......((((((.....((((....))))..))))))......(((.((((..((((((((........))))))))..)))).)))............... (-23.15 = -23.40 +   0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 5,395,463 – 5,395,566
Length 103
Sequences 4
Columns 103
Reading direction reverse
Mean pairwise identity 94.93
Mean single sequence MFE -23.40
Consensus MFE -22.48
Energy contribution -22.35
Covariance contribution -0.13
Combinations/Pair 1.07
Mean z-score -2.40
Structure conservation index 0.96
SVM decision value 2.01
SVM RNA-class probability 0.985384
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5395463 103 - 23771897
AUAAAUAAAUUGCAAGUGACACAUGCACAAUUAUUUACAAUUAAUUACGUCUGUGACACAGUAACACCCUUUUGUCCCUUUGGACAUGCAAAGGGUCAAUGUC
........((((...(((.((((.((..(((((........)))))..)).)))).)))......((((((((((((....)))))...)))))))))))... ( -24.00)
>DroSec_CAF1 44323 101 - 1
AUAAAUAAAUUGCAAGUGACACAUGCACAAUUAUUUACAAUUAAUUACGUCUGUGACACAGUAACACCCUU-UGUCCCU-CGGACGUGCAAAGGGUCAAAGUC
................((((...((((((((((........)))))..(((((.((((.((.......)).-))))...-))))))))))....))))..... ( -22.60)
>DroSim_CAF1 44134 101 - 1
AUAAAUAAAUUGCAAGUGACACACGCACAAUUAUUUACAAUUAAUUACGUCUGUGACACAGUAACACCCUU-UGUCCCU-CGGACGUGCAAAGGGUCAAUGUC
........((((...(((.((((.((..(((((........)))))..)).)))).)))......((((((-((..(..-.....)..))))))))))))... ( -22.00)
>DroYak_CAF1 44115 101 - 1
AUAAAAAAAUUACAAGUGACACAUGCACAAUUAUUUACAAUUAAUUACGUCUGUGACACAGUAACACCCUU-UGUCCCU-UGGAGGUGCCAAGGGUCAAUGUC
.........((((..(((.((((.((..(((((........)))))..)).)))).))).))))......(-((.((((-(((.....))))))).))).... ( -25.00)
>consensus
AUAAAUAAAUUGCAAGUGACACAUGCACAAUUAUUUACAAUUAAUUACGUCUGUGACACAGUAACACCCUU_UGUCCCU_CGGACGUGCAAAGGGUCAAUGUC
.........((((..(((.((((.((..(((((........)))))..)).)))).))).)))).((((((.(((((....)))))....))))))....... (-22.48 = -22.35 +  -0.13)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:20:37 2006