Locus 5637

Sequence ID 3R_DroMel_CAF1
Location 14,829,239 – 14,829,382
Length 143
Max. P 0.969263
window9193 window9194

overview

Window 3

Location 14,829,239 – 14,829,342
Length 103
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 83.52
Mean single sequence MFE -29.83
Consensus MFE -24.55
Energy contribution -25.83
Covariance contribution 1.28
Combinations/Pair 1.03
Mean z-score -2.65
Structure conservation index 0.82
SVM decision value 1.64
SVM RNA-class probability 0.969263
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14829239 103 + 27905053
CAG------------CCUAAAAAAAAAUAACGAGCUU-----AAUUAAAACAGCGCGAAGCUGUCAUCGAUAGUUUCGUGAGUUGUAACUUAAAAUGAAUGAAUCAUCGCAAGUCGACAC
...------------...............(((.(((-----.......((((((((((((((((...)))))))))))..)))))........((((.....))))...)))))).... ( -21.00)
>DroSec_CAF1 7379 112 + 1
CAGGCCUUACGACGGCCUGAAAAAA---AGCGAACUU-----AAUUAAAACUGCGCGAAGCUGUCAUCGAUAGUUUUGUGAGUUGUAACUAAAAAUGAAUGAAUCAUCGCAAGUCGACGC
((((((.......))))))......---.((((..((-----(.(((.((((.((((((((((((...)))))))))))))))).))).)))...(((.....))))))).......... ( -33.50)
>DroSim_CAF1 7540 116 + 1
CAGGCCUUUCGGCGGCCUGAAA-AA---AGCGAACUUACCAUAAUUAAAACUGCGCGAAGCUGUCAUCGAUAGUUUCGUGAGUUGUAACUAAAAAUGAAUGAAUCAUCGCAAGUCGACAC
((((((.......))))))...-..---.((((...........(((.((((.((((((((((((...)))))))))))))))).))).......(((.....))))))).......... ( -35.00)
>consensus
CAGGCCUU_CG_CGGCCUGAAAAAA___AGCGAACUU_____AAUUAAAACUGCGCGAAGCUGUCAUCGAUAGUUUCGUGAGUUGUAACUAAAAAUGAAUGAAUCAUCGCAAGUCGACAC
((((((.......))))))..........((((...........(((.((((.((((((((((((...)))))))))))))))).))).......(((.....))))))).......... (-24.55 = -25.83 +   1.28)

alignment

Postscript

secondary structure

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dotplot

Postscript

Window 4

Location 14,829,264 – 14,829,382
Length 118
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 89.80
Mean single sequence MFE -27.53
Consensus MFE -23.22
Energy contribution -23.33
Covariance contribution 0.11
Combinations/Pair 1.03
Mean z-score -1.81
Structure conservation index 0.84
SVM decision value 0.04
SVM RNA-class probability 0.551332
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14829264 118 + 27905053
--AAUUAAAACAGCGCGAAGCUGUCAUCGAUAGUUUCGUGAGUUGUAACUUAAAAUGAAUGAAUCAUCGCAAGUCGACACAAUGUUGCUUUAGUGCUAUUCAUUUCCUUAGAAACUGCGU
--.......((((((((((((((((...)))))))))))..)))))..........((((((((...((((((.((((.....)))))))..)))..))))))))............... ( -28.00)
>DroSec_CAF1 7413 113 + 1
--AAUUAAAACUGCGCGAAGCUGUCAUCGAUAGUUUUGUGAGUUGUAACUAAAAAUGAAUGAAUCAUCGCAAGUCGACGCUAUGUUGUUUUAGUGCUAAACAAUUCCUUAGAAAU-----
--........(((.(((((((((((...)))))))))))(((((((.(((((((....(((..((..(....)..))..).))....))))))).....)))))))..)))....----- ( -25.00)
>DroSim_CAF1 7576 115 + 1
AUAAUUAAAACUGCGCGAAGCUGUCAUCGAUAGUUUCGUGAGUUGUAACUAAAAAUGAAUGAAUCAUCGCAAGUCGACACUAUGUUGUUUUAGUGCUGAACAAUUCCUUAGAAAU-----
....(((.((((.((((((((((((...)))))))))))))))).)))((((....((((...(((.((((((.((((.....)))).))).))).)))...)))).))))....----- ( -29.60)
>consensus
__AAUUAAAACUGCGCGAAGCUGUCAUCGAUAGUUUCGUGAGUUGUAACUAAAAAUGAAUGAAUCAUCGCAAGUCGACACUAUGUUGUUUUAGUGCUAAACAAUUCCUUAGAAAU_____
...((((((((..((((((((((((...)))))))))))).((((..(((....((((.....))))....)))))))........)))))))).......................... (-23.22 = -23.33 +   0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:00:08 2006