Locus 1188

Sequence ID X_DroMel_CAF1
Location 3,540,210 – 3,540,362
Length 152
Max. P 0.931179
window1907 window1908

overview

Window 7

Location 3,540,210 – 3,540,322
Length 112
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 75.04
Mean single sequence MFE -23.90
Consensus MFE -11.12
Energy contribution -10.40
Covariance contribution -0.72
Combinations/Pair 1.35
Mean z-score -1.81
Structure conservation index 0.47
SVM decision value 0.22
SVM RNA-class probability 0.641124
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3540210 112 - 22224390
UUCUAUGUGGGAAUAACUCUUUAUCUAUAUUUGUGUGUAUG--------UAUGCAUGUAUACAAGUUUAUUAAAGGUUAUCGCCUGCAAUCGAGCAUUUGGCUACACCUUGCUAUUAUAA
.....((..((.(((((.(((((.....(((((((((((((--------....)))))))))))))....))))))))))..))..))....((((...((.....)).))))....... ( -30.40)
>DroSec_CAF1 48306 111 - 1
UUCUAUGG-GCAAGAACUCUUUAUCUAUAUUUGUGUGUAUG--------UAUGCAUGUACACAAGUUUAUUAAGGGUUAUCGCCUGCGAUCGACCAUUUGACUACUCCUUCCUUUUAUAA
......((-((...(((((((.......(((((((((((((--------....))))))))))))).....)))))))...))))................................... ( -25.60)
>DroSim_CAF1 49858 111 - 1
UUCUAUGU-GAAAGAACUCUUUAUCUAUAUUUGUGUGUAUG--------UAUGCAUGUACACAAGUUUAUUAAGGGUUAUCGCCUGCGAUCGACCAUUUGACUACACCUUCCUUCUAUAA
...((((.-(((.(((.........((.(((((((((((((--------....))))))))))))).))(((((((((((((....)))).)))).))))).......))).))))))). ( -24.20)
>DroEre_CAF1 52443 87 - 1
----------------------GUCUAUAUAUGCAUAUG----------UAC-UAUGUACACGAGUUUAUUGGAGGUUAUCGCCUGCGAUCGACCAUUUGGCUACCCCUAACCACUAUAA
----------------------((.(((((((((....)----------)).-)))))).))(.(((.((((.((((....)))).)))).))))...(((.((....)).)))...... ( -16.20)
>DroYak_CAF1 48212 119 - 1
UUCUAUGU-AAAAUUACUCUAUAUCUAUAUAUGUAUGUGUGUAAAAAUGUACAUAUGUGCACAAAUUUAUUAGAGGUUAUCGCCUGCGAUCGACCAUUUGGCUACACUUUCCUAUUAUUA
.....(((-(.......((((..........((((((((((((......)))))))))))).........))))((((((((....)))).)))).......)))).............. ( -23.11)
>consensus
UUCUAUGU_GAAAGAACUCUUUAUCUAUAUUUGUGUGUAUG________UAUGCAUGUACACAAGUUUAUUAAAGGUUAUCGCCUGCGAUCGACCAUUUGGCUACACCUUCCUAUUAUAA
..................................(((((((........)))))))(((..(((((........((((((((....)))).)))))))))..)))............... (-11.12 = -10.40 +  -0.72)

alignment

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secondary structure

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dotplot

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Window 8

Location 3,540,250 – 3,540,362
Length 112
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 77.63
Mean single sequence MFE -27.04
Consensus MFE -13.62
Energy contribution -13.75
Covariance contribution 0.12
Combinations/Pair 1.23
Mean z-score -2.65
Structure conservation index 0.50
SVM decision value 1.21
SVM RNA-class probability 0.931179
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3540250 112 - 22224390
AAUGACGAUUAGUUUACUUUCCAUAGGUGUCUGGUUCGUCUUCUAUGUGGGAAUAACUCUUUAUCUAUAUUUGUGUGUAUG--------UAUGCAUGUAUACAAGUUUAUUAAAGGUUAU
...(((((((((..(((((.....))))).)))).)))))((((....))))(((((.(((((.....(((((((((((((--------....)))))))))))))....)))))))))) ( -28.30)
>DroSec_CAF1 48346 102 - 1
---------UAGUUUACAUUCCAUAGGUGUCUGGUUCGUGUUCUAUGG-GCAAGAACUCUUUAUCUAUAUUUGUGUGUAUG--------UAUGCAUGUACACAAGUUUAUUAAGGGUUAU
---------..........((((((((((...(((((.((((.....)-))).)))))...)))))))(((((((((((((--------....))))))))))))).......))).... ( -28.10)
>DroSim_CAF1 49898 102 - 1
---------UAGUUUACAUUCCUUAGGUGUCUGGUUCGUGUUCUAUGU-GAAAGAACUCUUUAUCUAUAUUUGUGUGUAUG--------UAUGCAUGUACACAAGUUUAUUAAGGGUUAU
---------..........((((((((((...(((((...(((.....-))).)))))...))))((.(((((((((((((--------....))))))))))))).)).)))))).... ( -26.00)
>DroYak_CAF1 48252 119 - 1
AAUGUCUAUAAGCUUGCAUACCAUAGGUGUCUGUAAUGUGUUCUAUGU-AAAAUUACUCUAUAUCUAUAUAUGUAUGUGUGUAAAAAUGUACAUAUGUGCACAAAUUUAUUAGAGGUUAU
(((.((((((((.(((......((((((((..(((((...........-...)))))...))))))))...((((((((((((......))))))))))))))).)))).)))).))).. ( -25.74)
>consensus
_________UAGUUUACAUUCCAUAGGUGUCUGGUUCGUGUUCUAUGU_GAAAGAACUCUUUAUCUAUAUUUGUGUGUAUG________UAUGCAUGUACACAAGUUUAUUAAAGGUUAU
.....................((((((...(......)...)))))).......(((.(((((.....((((((((..(((............)))..))))))))....)))))))).. (-13.62 = -13.75 +   0.12)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:03:26 2006