Locus 3506

Sequence ID 3L_DroMel_CAF1
Location 10,288,003 – 10,288,095
Length 92
Max. P 0.795851
window5475 window5476

overview

Window 5

Location 10,288,003 – 10,288,095
Length 92
Sequences 4
Columns 103
Reading direction forward
Mean pairwise identity 73.43
Mean single sequence MFE -10.32
Consensus MFE -6.99
Energy contribution -7.42
Covariance contribution 0.44
Combinations/Pair 1.12
Mean z-score -1.56
Structure conservation index 0.68
SVM decision value 0.60
SVM RNA-class probability 0.795851
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10288003 92 + 23771897
GCCAUGACAAUGAACCAAACUGUCUUUUCCAGUUUUGAAAGUUCAUAAGUUUUU----UAAACUUUUUUACUUUU-------UUUAACUCCCAAAACUCCCAU
.....((((...........))))......((((..((((((....(((((...----..)))))....))))))-------...)))).............. ( -10.50)
>DroSec_CAF1 162975 87 + 1
GCCAUGACAAUGAACCAAACUGUCUUUUUCAAUUUUGUAAGUUCAUAAGUAUAUUAAUUAUACUUAUUUACUUUU-------UUUAACUCCCAA---------
.....((((...........))))..............((((..(((((((((.....)))))))))..))))..-------............--------- ( -11.70)
>DroSim_CAF1 169431 89 + 1
GCCAUGACAAUGAACCAAACUGUCUUUUCCAAUUUUUUAAGUUCAUAAGUAUUU----UAUACUUAUUUACUUU--------UUUAACUCCCAAAUC--CUUU
.....((((...........))))..............((((..((((((((..----.))))))))..)))).--------...............--.... (  -8.70)
>DroYak_CAF1 171205 83 + 1
GCCAUGACAAUGAACCAAAUUGUCUUUUCGAAUUUUUCAAGUUCAUAAGUUCAA----GUGACAUAUUUACUCUUAUAGUAGUUUAC----------------
.....((((((.......)))))).....(((((.....)))))(((((....(----((((.....))))))))))..........---------------- ( -10.40)
>consensus
GCCAUGACAAUGAACCAAACUGUCUUUUCCAAUUUUGUAAGUUCAUAAGUAUAU____UAUACUUAUUUACUUUU_______UUUAACUCCCAA_________
.....((((...........))))..............((((..((((((((.......))))))))..)))).............................. ( -6.99 =  -7.42 +   0.44)

alignment

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secondary structure

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dotplot

Postscript

Window 6

Location 10,288,003 – 10,288,095
Length 92
Sequences 4
Columns 103
Reading direction reverse
Mean pairwise identity 73.43
Mean single sequence MFE -14.52
Consensus MFE -10.75
Energy contribution -11.12
Covariance contribution 0.38
Combinations/Pair 1.17
Mean z-score -1.38
Structure conservation index 0.74
SVM decision value 0.48
SVM RNA-class probability 0.752138
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10288003 92 - 23771897
AUGGGAGUUUUGGGAGUUAAA-------AAAAGUAAAAAAGUUUA----AAAAACUUAUGAACUUUCAAAACUGGAAAAGACAGUUUGGUUCAUUGUCAUGGC
.....(((((((..((((...-------(.((((...........----....)))).).))))..)))))))......((((((.......))))))..... ( -18.36)
>DroSec_CAF1 162975 87 - 1
---------UUGGGAGUUAAA-------AAAAGUAAAUAAGUAUAAUUAAUAUACUUAUGAACUUACAAAAUUGAAAAAGACAGUUUGGUUCAUUGUCAUGGC
---------(((..((((...-------........(((((((((.....))))))))).))))..)))..........((((((.......))))))..... ( -15.30)
>DroSim_CAF1 169431 89 - 1
AAAG--GAUUUGGGAGUUAAA--------AAAGUAAAUAAGUAUA----AAAUACUUAUGAACUUAAAAAAUUGGAAAAGACAGUUUGGUUCAUUGUCAUGGC
....--(((...(((......--------.((((..((((((((.----..))))))))..))))...((((((.......))))))..)))...)))..... ( -14.00)
>DroYak_CAF1 171205 83 - 1
----------------GUAAACUACUAUAAGAGUAAAUAUGUCAC----UUGAACUUAUGAACUUGAAAAAUUCGAAAAGACAAUUUGGUUCAUUGUCAUGGC
----------------......((((.....)))).....((((.----.(((....(((((((........((.....))......)))))))..))))))) ( -10.44)
>consensus
_________UUGGGAGUUAAA_______AAAAGUAAAUAAGUAUA____AAAAACUUAUGAACUUAAAAAAUUGGAAAAGACAGUUUGGUUCAUUGUCAUGGC
..............................((((..((((((((.......))))))))..))))..............((((((.......))))))..... (-10.75 = -11.12 +   0.38)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:59:48 2006