Locus 8238

Sequence ID 3L_DroMel_CAF1
Location 21,643,746 – 21,643,844
Length 98
Max. P 0.774178
window13471 window13472

overview

Window 1

Location 21,643,746 – 21,643,844
Length 98
Sequences 6
Columns 101
Reading direction forward
Mean pairwise identity 82.01
Mean single sequence MFE -37.17
Consensus MFE -27.28
Energy contribution -28.03
Covariance contribution 0.75
Combinations/Pair 1.21
Mean z-score -1.91
Structure conservation index 0.73
SVM decision value 0.54
SVM RNA-class probability 0.774178
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21643746 98 + 23771897
CCUUCGCGACGGGGCUGCGCUUUAAUCACGUGCGUGCAAUGCGCACAUGAUGAUGCGCCCCAAUC---GUCCCCCGUUUCGCGCCCUCAGUAUGGCCCGAU
.....((((..(((..((((....((((.((((((.....)))))).))))...)))))))..))---))........(((.(((........))).))). ( -36.50)
>DroSec_CAF1 20422 101 + 1
CCAUCGCGCCGGGGCUGCGCUUUAAUCACGUGCGUGCAAUGCGCACAUGAUGAUGCGCCCCAAUCCGAGUCCCCCGGCUCGCGCCCUCAGUAUGGCCCGAU
..((((.((((((((.((((....((((.((((((.....)))))).))))...)))).......((((((....)))))).)))))......))).)))) ( -43.50)
>DroSim_CAF1 20689 101 + 1
CCAUCGCGACGGGGCUGCGCUUUAAUCACGUGCGUGCAAUGCGCACAUGAUGAUGCGCCCCAAUCCGAGUCCCCCGGCUCGCGCCCUCAGUAUGGCCCGAU
((((.((...(((((.((((....((((.((((((.....)))))).))))...)))).......((((((....)))))).)))))..))))))...... ( -41.20)
>DroEre_CAF1 19105 98 + 1
UCUUCGCGGCGGGGCUGCGCUUUAAUCACGUGCGUGCAAUGCGCAUAUGAUGAUGCGCCCCAAUCCGAAUCCCCCUGCUUGAGCCUUCAGUAUGGCUC---
.....((((.((((..((((....((((..(((((.....)))))..))))...))))............))))))))..(((((........)))))--- ( -38.14)
>DroYak_CAF1 28581 87 + 1
CGUUCGCGGCGGGGCUGCGCUUUAAUCACGUGCGUGCAAUGCGCACAUGACGAUGCGCCCCAAUCCGAAUCCCCCUGUGCGAGCCCU--------------
.(((((((.(((((..((((.....(((.((((((.....)))))).)))....))))..(.....).....))))))))))))...-------------- ( -34.20)
>DroPer_CAF1 8025 86 + 1
GUCUCGCGACGGGGCUACGCUUUAAUCACGUGCGUGCAAUGCGCACAUGAUGAUGCGCCCCAAUCCGUAUCCCCCA-UGCAUGCUCU--------------
.....(((..(((((...((....((((.((((((.....)))))).))))...))))))).....((((.....)-))).)))...-------------- ( -29.50)
>consensus
CCUUCGCGACGGGGCUGCGCUUUAAUCACGUGCGUGCAAUGCGCACAUGAUGAUGCGCCCCAAUCCGAAUCCCCCGGCUCGCGCCCUCAGUAUGGCCC___
.....((...(((((...((....((((.((((((.....)))))).))))...)))))))....(((((......))))).))................. (-27.28 = -28.03 +   0.75)

alignment

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secondary structure

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dotplot

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Window 2

Location 21,643,746 – 21,643,844
Length 98
Sequences 6
Columns 101
Reading direction reverse
Mean pairwise identity 82.01
Mean single sequence MFE -39.12
Consensus MFE -27.60
Energy contribution -28.02
Covariance contribution 0.42
Combinations/Pair 1.21
Mean z-score -1.36
Structure conservation index 0.71
SVM decision value -0.01
SVM RNA-class probability 0.530270
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21643746 98 - 23771897
AUCGGGCCAUACUGAGGGCGCGAAACGGGGGAC---GAUUGGGGCGCAUCAUCAUGUGCGCAUUGCACGCACGUGAUUAAAGCGCAGCCCCGUCGCGAAGG
.((((......))))...(((((..(((((..(---......)((((...((((((((((.......))))))))))....))))..)))))))))).... ( -40.50)
>DroSec_CAF1 20422 101 - 1
AUCGGGCCAUACUGAGGGCGCGAGCCGGGGGACUCGGAUUGGGGCGCAUCAUCAUGUGCGCAUUGCACGCACGUGAUUAAAGCGCAGCCCCGGCGCGAUGG
((((.(((........(((....)))((((..(((.....)))((((...((((((((((.......))))))))))....))))..))))))).)))).. ( -50.30)
>DroSim_CAF1 20689 101 - 1
AUCGGGCCAUACUGAGGGCGCGAGCCGGGGGACUCGGAUUGGGGCGCAUCAUCAUGUGCGCAUUGCACGCACGUGAUUAAAGCGCAGCCCCGUCGCGAUGG
(((((((.........(((....)))((((..(((.....)))((((...((((((((((.......))))))))))....))))..))))))).)))).. ( -44.50)
>DroEre_CAF1 19105 98 - 1
---GAGCCAUACUGAAGGCUCAAGCAGGGGGAUUCGGAUUGGGGCGCAUCAUCAUAUGCGCAUUGCACGCACGUGAUUAAAGCGCAGCCCCGCCGCGAAGA
---(((((........)))))..((.(((((..((......))((((...((((..((((.......))))..))))....))))..)))).).))..... ( -34.10)
>DroYak_CAF1 28581 87 - 1
--------------AGGGCUCGCACAGGGGGAUUCGGAUUGGGGCGCAUCGUCAUGUGCGCAUUGCACGCACGUGAUUAAAGCGCAGCCCCGCCGCGAACG
--------------...(.((((...((((...((......))((((...((((((((((.......))))))))))....))))..))))...)))).). ( -34.40)
>DroPer_CAF1 8025 86 - 1
--------------AGAGCAUGCA-UGGGGGAUACGGAUUGGGGCGCAUCAUCAUGUGCGCAUUGCACGCACGUGAUUAAAGCGUAGCCCCGUCGCGAGAC
--------------......((((-(((((..(((((((........)))((((((((((.......)))))))))).....)))).)))))).))).... ( -30.90)
>consensus
___GGGCCAUACUGAGGGCGCGAACCGGGGGACUCGGAUUGGGGCGCAUCAUCAUGUGCGCAUUGCACGCACGUGAUUAAAGCGCAGCCCCGUCGCGAAGG
....................((...(((((..(((.....)))((((...((((((((((.......))))))))))....))))..)))))...)).... (-27.60 = -28.02 +   0.42)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:10:11 2006