Locus 3029

Sequence ID 2L_DroMel_CAF1
Location 8,627,945 – 8,628,089
Length 144
Max. P 0.994867
window4819 window4820

overview

Window 9

Location 8,627,945 – 8,628,049
Length 104
Sequences 5
Columns 116
Reading direction reverse
Mean pairwise identity 74.44
Mean single sequence MFE -26.02
Consensus MFE -7.66
Energy contribution -7.86
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.77
Structure conservation index 0.29
SVM decision value 0.31
SVM RNA-class probability 0.682230
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8627945 104 - 22407834
CAAAU--GCAGUCUGUCAAUAAUAAAGGCUUCCGGAAGGAAGUUACACAAUGCGGAGGUCUUCUGGACUCCUAAGUUUAUUAUG----------AGGAAAAAAUAUUCCAUUGUUA
.....--(((((...(((.((((((((((((((....))))))).........((((..(....)..))))....)))))))))----------)((((......))))))))).. ( -28.70)
>DroSec_CAF1 56160 95 - 1
CAAAUGUGCAGUCAGUCAAUAAUAAAGGCUUCCGGAAGGAAGAUAUGCAAGGCG-----------GACUCCUAAGAUUAUAAAG----------ACGAAAAAAUAUUCCAUUGUUA
..(((((....((.(((.(((((..((((((((....)))))...(((...)))-----------....)))...)))))...)----------))))....)))))......... ( -17.40)
>DroSim_CAF1 62515 95 - 1
CAAAUGUGCAGUCUGUCAAUAAUAAAGGCUUCCGGAAGGAAGAUAUGCAAGGCG-----------GACUCCUAAGAUUAUAAAG----------ACGAAAAAAUAUUCCAUUGUUA
.......(.((((((((....(((....(((((....))))).)))....))))-----------)))).)............(----------((((............))))). ( -20.50)
>DroEre_CAF1 57419 116 - 1
CAACGGCAAAGUCUGUCAAUAAUGAAGGCUUCCGGAAGAAAAAUAUGCAAGGCAGAGUUCUUCUGGACUCCUAAGAUGAUUAUGAACGGAGCAGACGAAAAAACGUGCGAUUGUUG
...((((((..(((((..(((((.((((..((((((((((.....(((...)))...))))))))))..)))....).)))))..)))))((..(((......)))))..)))))) ( -32.70)
>DroYak_CAF1 59078 114 - 1
CAACGGCA--GUCUGUCAAUAAUGAAGGCUUCCGGUAGGAAAAUAUGCAAGGCGGAGGUCUUCUGGACUCCUAAGAUGAUUAUGAACAGAUCAUGCGAAAAAACGUUCGUUUCUGG
....((.(--(((((........(((((((((((.(..(........)..).)))))))))))))))))))...............((((....(((((......))))).)))). ( -30.80)
>consensus
CAAAUGCGCAGUCUGUCAAUAAUAAAGGCUUCCGGAAGGAAGAUAUGCAAGGCGGAG_UCUUCUGGACUCCUAAGAUUAUUAUG__________ACGAAAAAAUAUUCCAUUGUUA
..........(((.(((.........)))((((....))))........................)))................................................ ( -7.66 =  -7.86 +   0.20)

alignment

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secondary structure

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dotplot

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Window 0

Location 8,627,975 – 8,628,089
Length 114
Sequences 5
Columns 116
Reading direction reverse
Mean pairwise identity 75.54
Mean single sequence MFE -32.06
Consensus MFE -12.88
Energy contribution -14.20
Covariance contribution 1.32
Combinations/Pair 1.11
Mean z-score -2.60
Structure conservation index 0.40
SVM decision value 2.52
SVM RNA-class probability 0.994867
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8627975 114 - 22407834
AAUGGCCAUAAAACGCCGGGACUAGCGCUCAGCAGAAAGGCAAAU--GCAGUCUGUCAAUAAUAAAGGCUUCCGGAAGGAAGUUACACAAUGCGGAGGUCUUCUGGACUCCUAAGU
...(((........)))((((((..(((...(((((...((....--))..)))))..........(((((((....))))))).......))).))(((.....))))))).... ( -33.80)
>DroSec_CAF1 56190 105 - 1
AAAGGCCAUAAAACGCCAGGACUAGCGCUCAGCAGAAAGGCAAAUGUGCAGUCAGUCAAUAAUAAAGGCUUCCGGAAGGAAGAUAUGCAAGGCG-----------GACUCCUAAGA
...(((........)))((((.(..((((..(((((...(((....)))..))...............(((((....)))))...)))..))))-----------.).)))).... ( -30.00)
>DroSim_CAF1 62545 105 - 1
AAAGGCCAUAAAACGGCAGGACUAGCGCUCAGCAGAAAGGCAAAUGUGCAGUCUGUCAAUAAUAAAGGCUUCCGGAAGGAAGAUAUGCAAGGCG-----------GACUCCUAAGA
....(((.......)))((((...((((...((......))....)))).(((((((....(((....(((((....))))).)))....))))-----------))))))).... ( -33.80)
>DroEre_CAF1 57459 116 - 1
AAAGGAUACAAAACGCCAGGACUAGAGCUCCGCAGAAAGGCAACGGCAAAGUCUGUCAAUAAUGAAGGCUUCCGGAAGAAAAAUAUGCAAGGCAGAGUUCUUCUGGACUCCUAAGA
..((((........(((.((((....).)))(((((...((....))....)))))..........))).((((((((((.....(((...)))...)))))))))).)))).... ( -33.90)
>DroYak_CAF1 59118 93 - 1
AAGG---------------------CGUUCCGUAGAAAGGCAACGGCA--GUCUGUCAAUAAUGAAGGCUUCCGGUAGGAAAAUAUGCAAGGCGGAGGUCUUCUGGACUCCUAAGA
.(((---------------------.((((.(((((...((....)).--.)))).)......(((((((((((.(..(........)..).))))))))))).)))).))).... ( -28.80)
>consensus
AAAGGCCAUAAAACGCCAGGACUAGCGCUCAGCAGAAAGGCAAAUGCGCAGUCUGUCAAUAAUAAAGGCUUCCGGAAGGAAGAUAUGCAAGGCGGAG_UCUUCUGGACUCCUAAGA
.........................((((..(((((.((((.........)))).))...........(((((....)))))...)))..))))...................... (-12.88 = -14.20 +   1.32)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:42:34 2006