Locus 4444

Sequence ID 3L_DroMel_CAF1
Location 12,948,618 – 12,948,763
Length 145
Max. P 0.951114
window6906 window6907 window6908

overview

Window 6

Location 12,948,618 – 12,948,738
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 98.50
Mean single sequence MFE -31.14
Consensus MFE -28.32
Energy contribution -28.16
Covariance contribution -0.16
Combinations/Pair 1.03
Mean z-score -1.77
Structure conservation index 0.91
SVM decision value 1.41
SVM RNA-class probability 0.951114
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12948618 120 + 23771897
GGGCCACUUUAUUGUUACCAGUUUGUUGCAUAGGUAGGCAAUAAUUUACAGAAAUUAUACAUGACCACUUAAGUUGUCAUUAACGUUAACGACCACCAAACCGAAAGGGAGCGGUCGAAA
..(((((((...(((.((......)).))).)))).))).(((((((....)))))))..(((((.((....)).))))).........(((((.(....((....))..).)))))... ( -29.30)
>DroSec_CAF1 65746 120 + 1
GGGCCACUUUAUUGUUACCAGUUUGUUGCAUAGGUGGGCAAUAAUUUACAGAAAUUAUACAUGACCACUUAAGUUGUCAUUAACGUUAACGACCACCAAACCGAAAGGGAGCGGUCGAAA
.(.((((((...(((.((......)).))).)))))).).(((((((....)))))))..(((((.((....)).))))).........(((((.(....((....))..).)))))... ( -31.80)
>DroSim_CAF1 70545 120 + 1
GGGCCACUUUAUUGUUACCAGUUUGUUGCAUAGGUAGGCAAUAAUUUACAGAAAUUAUACAUGACCACUUAAGUUGUCAUUAACGUUAACGACCACCAAACCGAAAGGGAGCGGUCGAAA
..(((((((...(((.((......)).))).)))).))).(((((((....)))))))..(((((.((....)).))))).........(((((.(....((....))..).)))))... ( -29.30)
>DroEre_CAF1 71877 120 + 1
GGGCCACUUUAUUGUUACCAGUUUGUUGCAUAGGUAGGCAAUAAUUUACAGAAAUUAUACAUGACCACUUAAGUUGUCGUUAACGUUAACGACCGCCAAACCAAAAGGGAGCGGUCGAAA
..(((((((...(((.((......)).))).)))).))).(((((((....)))))))..(((((.((....)).))))).........(((((((....((....))..)))))))... ( -30.60)
>DroYak_CAF1 69623 120 + 1
GGGCCACUUUAUUGUUACCAGUUUGUUGCAUAGGUAGGCAAUAAUUUACAGAAAUUAUACAUGACCACUUAAGUUGUCAUUAACGUUAACGACCGCCAAACCGAAAGGGAGCGGUCGAAA
..(((((((...(((.((......)).))).)))).))).(((((((....)))))))..(((((.((....)).))))).........(((((((....((....))..)))))))... ( -34.70)
>consensus
GGGCCACUUUAUUGUUACCAGUUUGUUGCAUAGGUAGGCAAUAAUUUACAGAAAUUAUACAUGACCACUUAAGUUGUCAUUAACGUUAACGACCACCAAACCGAAAGGGAGCGGUCGAAA
..(((((((...(((.((......)).))).)))).))).(((((((....)))))))..(((((.((....)).))))).........(((((.(....((....))..).)))))... (-28.32 = -28.16 +  -0.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 12,948,658 – 12,948,763
Length 105
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.23
Mean single sequence MFE -32.86
Consensus MFE -22.07
Energy contribution -21.75
Covariance contribution -0.32
Combinations/Pair 1.08
Mean z-score -2.84
Structure conservation index 0.67
SVM decision value 0.30
SVM RNA-class probability 0.677386
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12948658 105 + 23771897
AUAAUUUACAGAAAUUAUACAUGACCACUUAAGUUGUCAUUAACGUUAACGACCACCAAACCGAAAGGGAGCGGUCGAAAUGUGUGUCGGGCCAUUAUG------------GCCUCG---
(((((((....)))))))....((((((....((((....)))).....(((((.(....((....))..).)))))....))).)))(((((.....)------------))))..--- ( -31.10)
>DroSec_CAF1 65786 105 + 1
AUAAUUUACAGAAAUUAUACAUGACCACUUAAGUUGUCAUUAACGUUAACGACCACCAAACCGAAAGGGAGCGGUCGAAAUGUGUGUCGGGCCAUUAUG------------GCCUCG---
(((((((....)))))))....((((((....((((....)))).....(((((.(....((....))..).)))))....))).)))(((((.....)------------))))..--- ( -31.10)
>DroSim_CAF1 70585 105 + 1
AUAAUUUACAGAAAUUAUACAUGACCACUUAAGUUGUCAUUAACGUUAACGACCACCAAACCGAAAGGGAGCGGUCGAAAUGUGUGUCGGGCCAUUAUG------------GCCUCG---
(((((((....)))))))....((((((....((((....)))).....(((((.(....((....))..).)))))....))).)))(((((.....)------------))))..--- ( -31.10)
>DroEre_CAF1 71917 117 + 1
AUAAUUUACAGAAAUUAUACAUGACCACUUAAGUUGUCGUUAACGUUAACGACCGCCAAACCAAAAGGGAGCGGUCGAAAUGUAUGUCGGGGCAUUAUGAAAUGUUUAAGAGCCCCG---
...............((((((((((.((....)).)))...........(((((((....((....))..)))))))..))))))).((((((.(((.........)))..))))))--- ( -34.40)
>DroYak_CAF1 69663 120 + 1
AUAAUUUACAGAAAUUAUACAUGACCACUUAAGUUGUCAUUAACGUUAACGACCGCCAAACCGAAAGGGAGCGGUCGAAAUGUGUGUCGGGGCAUUAUGAAAUGUUUAAGAGCCUCGCAG
(((((((....)))))))..(((((.((....)).)))))..(((((..(((((((....((....))..))))))).))))).((.((((((.(((.........)))..)))))))). ( -36.60)
>consensus
AUAAUUUACAGAAAUUAUACAUGACCACUUAAGUUGUCAUUAACGUUAACGACCACCAAACCGAAAGGGAGCGGUCGAAAUGUGUGUCGGGCCAUUAUG____________GCCUCG___
...............((((((((((.((....)).)))...........(((((.(....((....))..).)))))..))))))).((((......................))))... (-22.07 = -21.75 +  -0.32)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 12,948,658 – 12,948,763
Length 105
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 90.23
Mean single sequence MFE -29.23
Consensus MFE -21.42
Energy contribution -21.02
Covariance contribution -0.40
Combinations/Pair 1.07
Mean z-score -1.88
Structure conservation index 0.73
SVM decision value 0.27
SVM RNA-class probability 0.663405
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12948658 105 - 23771897
---CGAGGC------------CAUAAUGGCCCGACACACAUUUCGACCGCUCCCUUUCGGUUUGGUGGUCGUUAACGUUAAUGACAACUUAAGUGGUCAUGUAUAAUUUCUGUAAAUUAU
---.(.(((------------(.....)))))(((.(((....((((((((.((....))...))))))))((((.(((......)))))))))))))....(((((((....))))))) ( -28.30)
>DroSec_CAF1 65786 105 - 1
---CGAGGC------------CAUAAUGGCCCGACACACAUUUCGACCGCUCCCUUUCGGUUUGGUGGUCGUUAACGUUAAUGACAACUUAAGUGGUCAUGUAUAAUUUCUGUAAAUUAU
---.(.(((------------(.....)))))(((.(((....((((((((.((....))...))))))))((((.(((......)))))))))))))....(((((((....))))))) ( -28.30)
>DroSim_CAF1 70585 105 - 1
---CGAGGC------------CAUAAUGGCCCGACACACAUUUCGACCGCUCCCUUUCGGUUUGGUGGUCGUUAACGUUAAUGACAACUUAAGUGGUCAUGUAUAAUUUCUGUAAAUUAU
---.(.(((------------(.....)))))(((.(((....((((((((.((....))...))))))))((((.(((......)))))))))))))....(((((((....))))))) ( -28.30)
>DroEre_CAF1 71917 117 - 1
---CGGGGCUCUUAAACAUUUCAUAAUGCCCCGACAUACAUUUCGACCGCUCCCUUUUGGUUUGGCGGUCGUUAACGUUAACGACAACUUAAGUGGUCAUGUAUAAUUUCUGUAAAUUAU
---((((((..................))))))..((((((...(((((((.((....))...((..(((((((....)))))))..))..)))))))))))))................ ( -34.77)
>DroYak_CAF1 69663 120 - 1
CUGCGAGGCUCUUAAACAUUUCAUAAUGCCCCGACACACAUUUCGACCGCUCCCUUUCGGUUUGGCGGUCGUUAACGUUAAUGACAACUUAAGUGGUCAUGUAUAAUUUCUGUAAAUUAU
.((((.(((..................))).)(((.(((....((((((((.((....))...))))))))((((.(((......))))))))))))).............)))...... ( -26.47)
>consensus
___CGAGGC____________CAUAAUGGCCCGACACACAUUUCGACCGCUCCCUUUCGGUUUGGUGGUCGUUAACGUUAAUGACAACUUAAGUGGUCAUGUAUAAUUUCUGUAAAUUAU
................................(((.(((....((((((((.((....))...))))))))((((.(((......)))))))))))))....(((((((....))))))) (-21.42 = -21.02 +  -0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:23:04 2006