Locus 7516

Sequence ID 3L_DroMel_CAF1
Location 20,202,467 – 20,202,616
Length 149
Max. P 0.933205
window12224 window12225

overview

Window 4

Location 20,202,467 – 20,202,576
Length 109
Sequences 5
Columns 109
Reading direction reverse
Mean pairwise identity 89.28
Mean single sequence MFE -23.38
Consensus MFE -18.96
Energy contribution -18.64
Covariance contribution -0.32
Combinations/Pair 1.08
Mean z-score -1.95
Structure conservation index 0.81
SVM decision value 1.23
SVM RNA-class probability 0.933205
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20202467 109 - 23771897
GCUUUAUAAGCAUGCGGAUCUGUCAACAACGAUUGCACUUUCUUGCCAAAUUCGCAUGAAAUAUAGAGAAAUGCAUCAAAUGACUCAUUGUUUUUUUUUUUUUGGAAAC
.(((((((..(((((((((.((.(((.((.(......).)).))).)).)))))))))...))))))).((((..((....))..))))((((((........)))))) ( -21.40)
>DroSec_CAF1 16368 103 - 1
GCUUUAUAAGCAUGCGGAUCUGUCAACAACGAUUGCACUUUCUUGACAAAUUCGCAUGAAUUAUAGAGAUAUGCAUCAAAUGACUCAUUGUUU------UUUUGGAAAC
.((((((((.(((((((((.((((((.((.(......).)).)))))).)))))))))..)))))))).......(((((.(((.....))).------.))))).... ( -27.40)
>DroSim_CAF1 11325 102 - 1
GCUUUAUAAGCAUGCGGAUCUGUCAACAACGAUUGCACUUUCUUGACAAAUUCGCAUGAAUUAUAGAGAUAUGCAUCAAAUGACUCAUUGUUU-------UUUGGAAAC
.((((((((.(((((((((.((((((.((.(......).)).)))))).)))))))))..)))))))).......(((((.(((.....))).-------))))).... ( -28.40)
>DroEre_CAF1 11628 102 - 1
GCUUUAUAAGUAUGCGAAUCUGUCAAAAAUGAUUGUACUUUCUUGCCAAAUUCGCAUGAAUUAUAGAGAUAUGCCUUAAAUGAAUCAUUGUU-------UUUUAAAAGC
.((((((((.(((((((((.((.(((.((..........)).))).)).)))))))))..))))))))........................-------.......... ( -17.90)
>DroYak_CAF1 24970 103 - 1
GCUUUAUAAGCAUGCGGAUCUGUCAAAAACGAUUGUACUUUCUUGCCAAAUUCGCAUGAAUUAUAGAGAUAUGCAUUAAAAGAAUCUUUGUUG------UUUUAAAAAC
.((((((((.(((((((((.((.(((.((.(......).)).))).)).)))))))))..)))))))).......((((((.(((....))).------)))))).... ( -21.80)
>consensus
GCUUUAUAAGCAUGCGGAUCUGUCAACAACGAUUGCACUUUCUUGCCAAAUUCGCAUGAAUUAUAGAGAUAUGCAUCAAAUGACUCAUUGUUU______UUUUGGAAAC
.(((((((..(((((((((.((.(((.((.(......).)).))).)).)))))))))...)))))))......................................... (-18.96 = -18.64 +  -0.32)

alignment

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secondary structure

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dotplot

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Window 5

Location 20,202,496 – 20,202,616
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.73
Mean single sequence MFE -26.34
Consensus MFE -18.96
Energy contribution -18.64
Covariance contribution -0.32
Combinations/Pair 1.08
Mean z-score -2.06
Structure conservation index 0.72
SVM decision value 0.37
SVM RNA-class probability 0.710661
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20202496 120 - 23771897
CAAGUUCAUUUUGACAAAAGAUGCAUUUAUUAUUUAAUUGGCUUUAUAAGCAUGCGGAUCUGUCAACAACGAUUGCACUUUCUUGCCAAAUUCGCAUGAAAUAUAGAGAAAUGCAUCAAA
((((.....))))......(((((((((.(((......)))(((((((..(((((((((.((.(((.((.(......).)).))).)).)))))))))...))))))))))))))))... ( -28.50)
>DroSec_CAF1 16391 118 - 1
CAAGUUGACUUUGUCAUAAGAUACAUUUAUU--UUUAUAGGCUUUAUAAGCAUGCGGAUCUGUCAACAACGAUUGCACUUUCUUGACAAAUUCGCAUGAAUUAUAGAGAUAUGCAUCAAA
....((((...((((....))))........--..((((..((((((((.(((((((((.((((((.((.(......).)).)))))).)))))))))..)))))))).))))..)))). ( -27.80)
>DroSim_CAF1 11347 118 - 1
CAAGUUGACUUUGUCAUAAGAUACAUUUAUU--UUUAUAGGCUUUAUAAGCAUGCGGAUCUGUCAACAACGAUUGCACUUUCUUGACAAAUUCGCAUGAAUUAUAGAGAUAUGCAUCAAA
....((((...((((....))))........--..((((..((((((((.(((((((((.((((((.((.(......).)).)))))).)))))))))..)))))))).))))..)))). ( -27.80)
>DroEre_CAF1 11650 118 - 1
CAAGUUGACUUUGACAACAGAAACAUUUAUU--UUUACUGGCUUUAUAAGUAUGCGAAUCUGUCAAAAAUGAUUGUACUUUCUUGCCAAAUUCGCAUGAAUUAUAGAGAUAUGCCUUAAA
...((((.......)))).............--........((((((((.(((((((((.((.(((.((..........)).))).)).)))))))))..))))))))............ ( -20.20)
>DroYak_CAF1 24993 118 - 1
CAAGGUGACUUGGGCAACAAAAACAUUUAUU--UUUACUGGCUUUAUAAGCAUGCGGAUCUGUCAAAAACGAUUGUACUUUCUUGCCAAAUUCGCAUGAAUUAUAGAGAUAUGCAUUAAA
((((....)))).(((..(((((......))--))).....((((((((.(((((((((.((.(((.((.(......).)).))).)).)))))))))..))))))))...)))...... ( -27.40)
>consensus
CAAGUUGACUUUGACAAAAGAUACAUUUAUU__UUUAUUGGCUUUAUAAGCAUGCGGAUCUGUCAACAACGAUUGCACUUUCUUGCCAAAUUCGCAUGAAUUAUAGAGAUAUGCAUCAAA
.........................................(((((((..(((((((((.((.(((.((.(......).)).))).)).)))))))))...)))))))............ (-18.96 = -18.64 +  -0.32)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:49:16 2006