Locus 2124

Sequence ID 2L_DroMel_CAF1
Location 5,730,392 – 5,730,527
Length 135
Max. P 0.992114
window3431 window3432

overview

Window 1

Location 5,730,392 – 5,730,497
Length 105
Sequences 5
Columns 112
Reading direction forward
Mean pairwise identity 90.31
Mean single sequence MFE -27.52
Consensus MFE -20.98
Energy contribution -20.10
Covariance contribution -0.88
Combinations/Pair 1.19
Mean z-score -1.77
Structure conservation index 0.76
SVM decision value 0.42
SVM RNA-class probability 0.727325
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5730392 105 + 22407834
CGCUUCUCGAGCGCUGCUUUUGUGCACAGUGAGCCAGGAAA---CUAUGCAAUCAGUCAAAAC-AAAAAUAG-CACUCGAACUGAAUUACUCCCCAGAGUUUUCAGUGUG--
(((...(((((.((((.((((((....(.(((((.((....---))..))..))).)....))-)))).)))-).)))))((((((..((((....)))).)))))))))-- ( -33.30)
>DroSec_CAF1 6323 107 + 1
CGCUCCUCGAGCACUGCCUUUGUGCACAGUGAGCCAGGAAA---CUAUGCAAUCAGUCAAAACCAAAAAUACCCACUCGAACUGAAUUACUCCCCAGAGUUUUCAGUGGG--
.((((((.(.((((.......)))).))).)))).((....---)).........................((((((......(((..((((....)))).)))))))))-- ( -26.00)
>DroSim_CAF1 2097 105 + 1
CGCUCCUCGAGCACUGCCUUUGUGCACAGUGAGCCAGGAAA---CUAUGCAAUCAGUCAAAAC-AAAAAUAC-CACUCGAACUGAAUUACUCCCCAGAGUUUUCAGUGUG--
(((...((((((((((..........))))).((.((....---))..)).............-........-..)))))((((((..((((....)))).)))))))))-- ( -24.70)
>DroEre_CAF1 2968 107 + 1
CGCUUCUCGAGCACUGCUGUUGUGCACAGUGAGCCAGGAAA---CUAUACUAUCAGUCCAAAC-AAACAUAC-CACUCUAACUGAAUUGCUGCGCACAGUUUUCAGUGUGGC
..........((((((...((((((.(((..(...((....---))......(((((......-........-.......))))).)..))).))))))....))))))... ( -27.70)
>DroYak_CAF1 2554 110 + 1
CGCUUCUCGAGCACUGCCUUUGUGCACAGUGAGCCAGGAAACAACUAUCCUAUCAGUCCAAAC-AAAAAUAC-CACUCUAACUGAAUUACUCCCCAGAGUUUUCAGUGUGGC
.((((((.(.((((.......)))).))).)))).((((........))))............-.......(-(((....((((((..((((....)))).)))))))))). ( -25.90)
>consensus
CGCUUCUCGAGCACUGCCUUUGUGCACAGUGAGCCAGGAAA___CUAUGCAAUCAGUCAAAAC_AAAAAUAC_CACUCGAACUGAAUUACUCCCCAGAGUUUUCAGUGUG__
.((((((.(.((((.......)))).))).))))..............................................((((((..((((....)))).))))))..... (-20.98 = -20.10 +  -0.88)

alignment

Postscript

secondary structure

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dotplot

Postscript

Window 2

Location 5,730,431 – 5,730,527
Length 96
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 74.84
Mean single sequence MFE -18.02
Consensus MFE -10.10
Energy contribution -9.62
Covariance contribution -0.48
Combinations/Pair 1.20
Mean z-score -2.39
Structure conservation index 0.56
SVM decision value 2.31
SVM RNA-class probability 0.992114
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5730431 96 + 22407834
AA---CUAUGCAAUCAGUCAAAAC-AAAAAUAG-CACUCGAACUGAAUUACUCCCCAGAGUUUUCAGUGUG----UAUA-AUUGCAGGGUAUUCACGCAU-------AAAAAC
..---.(((((.....((....))-........-.((((..((((((..((((....)))).)))))).((----((..-..))))))))......))))-------)..... ( -19.20)
>DroSec_CAF1 6362 98 + 1
AA---CUAUGCAAUCAGUCAAAACCAAAAAUACCCACUCGAACUGAAUUACUCCCCAGAGUUUUCAGUGGG----UACA-AUUGCACGGUAUUCACGCAU-------AAAAAC
.(---(..((((((..((....))......((((((((......(((..((((....)))).)))))))))----))..-))))))..))..........-------...... ( -20.90)
>DroSim_CAF1 2136 97 + 1
AA---CUAUGCAAUCAGUCAAAAC-AAAAAUAC-CACUCGAACUGAAUUACUCCCCAGAGUUUUCAGUGUG----UACAAAUUCCAGAGUAUUCACGCAU-------AAAAAC
..---.(((((.....((....))-........-.((((..((((((..((((....)))).))))))(..----..)........))))......))))-------)..... ( -16.50)
>DroEre_CAF1 3007 92 + 1
AA---CUAUACUAUCAGUCCAAAC-AAACAUAC-CACUCUAACUGAAUUGCUGCGCACAGUUUUCAGUGUGGCUAUC----------------CACACACCAUUUAAGAAAGU
..---....(((.((.........-........-.........((((..((((....)))).))))((((((....)----------------))))).........)).))) ( -16.00)
>DroYak_CAF1 2593 110 + 1
AACAACUAUCCUAUCAGUCCAAAC-AAAAAUAC-CACUCUAACUGAAUUACUCCCCAGAGUUUUCAGUGUGGCUCUACU-AUUGUACGGAACUUACUCACCAUUGAAAAAAGU
.............(((((......-.......(-(((....((((((..((((....)))).))))))))))((.(((.-...))).))............)))))....... ( -17.50)
>consensus
AA___CUAUGCAAUCAGUCAAAAC_AAAAAUAC_CACUCGAACUGAAUUACUCCCCAGAGUUUUCAGUGUG____UACA_AUUGCACGGUAUUCACGCAU_______AAAAAC
.........................................((((((..((((....)))).))))))............................................. (-10.10 =  -9.62 +  -0.48)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:20:13 2006