Locus 1873

Sequence ID X_DroMel_CAF1
Location 5,183,097 – 5,183,275
Length 178
Max. P 0.990351
window3041 window3042 window3043

overview

Window 1

Location 5,183,097 – 5,183,202
Length 105
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 73.36
Mean single sequence MFE -22.60
Consensus MFE -12.49
Energy contribution -13.92
Covariance contribution 1.44
Combinations/Pair 1.14
Mean z-score -1.74
Structure conservation index 0.55
SVM decision value 0.15
SVM RNA-class probability 0.608595
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5183097 105 + 22224390
CUUUUCUAUUAUACCACUUUGAUCCACUAUAUAUUUUAAUAUGUGCAAUAGAU---------------UUGCAUUUAAGGUUGAAUCUUAGGUCUAACUAUCCUAAGGUCAAUGUUAAGU
............................((((((....))))))((((.....---------------))))((((((.(((((.(((((((.........)))))))))))).)))))) ( -20.60)
>DroSec_CAF1 4398 113 + 1
-------AUUAUACCAUUUUGAUUCACAAUAUGUUUAAAUAUGUGUAAUAGAUUGUUAGCUUUUGCAUUUGCAUUUAAGGUUGAAUCUUAGGUCUAACUAUCCUAAGGUCAAUGUUAAGU
-------(((((((...(((((..((.....)).)))))...))))))).........((....))......((((((.(((((.(((((((.........)))))))))))).)))))) ( -22.50)
>DroEre_CAF1 4379 108 + 1
CUGUUCUAUUAUAUCAUUUUGAUCCAUAA--GAUUGAAGUAUGUG----------UAAGCUUUUCCAUUUGCACAUUAAGUUGAACCUUCGCUCUUACCAUCCUAAGGUCAAUGUUAAGU
..((((.(((.....((((..(((.....--)))..))))(((((----------((((........)))))))))..))).))))(((.((....(((.......)))....)).))). ( -18.60)
>DroYak_CAF1 4303 119 + 1
CUUAUCUAUUAUACCAUUGGGAGCUAUAA-ACAAUGCAAUAUGUGUAAUAGAUUGUAAGCUUUUCCAUUUGCAUAUAAAGUUGAACCUUAGGUCUAACCAUCCUAAGGUCAAUGUUAAGU
(((((((((((((((((((..........-.)))))......))))))))))(((((.((..........)).))))).(((((.(((((((.........))))))))))))..)))). ( -28.70)
>consensus
CUUUUCUAUUAUACCAUUUUGAUCCACAA_AUAUUGAAAUAUGUGUAAUAGAU__UAAGCUUUUCCAUUUGCAUAUAAAGUUGAACCUUAGGUCUAACCAUCCUAAGGUCAAUGUUAAGU
.......................................(((((((((....................)))))))))..(((((.(((((((.........))))))))))))....... (-12.49 = -13.92 +   1.44)

alignment

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secondary structure

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Window 2

Location 5,183,137 – 5,183,235
Length 98
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 78.02
Mean single sequence MFE -26.20
Consensus MFE -19.19
Energy contribution -20.00
Covariance contribution 0.81
Combinations/Pair 1.10
Mean z-score -2.32
Structure conservation index 0.73
SVM decision value 2.21
SVM RNA-class probability 0.990351
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5183137 98 + 22224390
AUGUGCAAUAGAU---------------UUGCAUUUAAGGUUGAAUCUUAGGUCUAACUAUCCUAAGGUCAAUGUUAAGUGCU------U-UCGGGCUGCUUUCUCACACUCUCGUUAAC
....(((...((.---------------..((((((((.(((((.(((((((.........)))))))))))).)))))))).------.-))....))).................... ( -26.90)
>DroSec_CAF1 4431 112 + 1
AUGUGUAAUAGAUUGUUAGCUUUUGCAUUUGCAUUUAAGGUUGAAUCUUAGGUCUAACUAUCCUAAGGUCAAUGUUAAGUGCU------C-UCG-GCUGCUUUCUCGCACUCUCGUUAAC
..((((...(((..((.((((.........((((((((.(((((.(((((((.........)))))))))))).)))))))).------.-..)-)))))..))).)))).......... ( -32.02)
>DroEre_CAF1 4417 103 + 1
AUGUG----------UAAGCUUUUCCAUUUGCACAUUAAGUUGAACCUUCGCUCUUACCAUCCUAAGGUCAAUGUUAAGUGCU------CCUCG-GCUGCUUUCUCAUACUCUCGUUAAC
.((((----------.((((....((....((((.(((((((((.((((...............))))))))).)))))))).------....)-)..))))...))))........... ( -18.46)
>DroYak_CAF1 4342 119 + 1
AUGUGUAAUAGAUUGUAAGCUUUUCCAUUUGCAUAUAAAGUUGAACCUUAGGUCUAACCAUCCUAAGGUCAAUGUUAAGUGCUUUCUCUGCUCG-UCUGCUUUCUCCUACUAUCGUUAAC
....(((..(((..(((..(..........((((.(((.(((((.(((((((.........)))))))))))).))).))))...........)-..)))..)))..))).......... ( -27.40)
>consensus
AUGUGUAAUAGAU__UAAGCUUUUCCAUUUGCAUAUAAAGUUGAACCUUAGGUCUAACCAUCCUAAGGUCAAUGUUAAGUGCU______C_UCG_GCUGCUUUCUCACACUCUCGUUAAC
..............................((((((((.(((((.(((((((.........)))))))))))).))))))))...................................... (-19.19 = -20.00 +   0.81)

alignment

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secondary structure

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dotplot

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Window 3

Location 5,183,162 – 5,183,275
Length 113
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 89.40
Mean single sequence MFE -31.59
Consensus MFE -23.31
Energy contribution -23.88
Covariance contribution 0.56
Combinations/Pair 1.06
Mean z-score -1.86
Structure conservation index 0.74
SVM decision value 0.37
SVM RNA-class probability 0.707909
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5183162 113 + 22224390
UUGAAUCUUAGGUCUAACUAUCCUAAGGUCAAUGUUAAGUGCU------U-UCGGGCUGCUUUCUCACACUCUCGUUAACUGAAAUGUGGCAGUAAAACUGACAAGUGCCGAGGCACUCU
((((.(((((((.........))))))))))).....((((((------(-.((((((((.....((((...(((.....)))..)))))))))...(((....))).)))))))))).. ( -31.50)
>DroSec_CAF1 4471 112 + 1
UUGAAUCUUAGGUCUAACUAUCCUAAGGUCAAUGUUAAGUGCU------C-UCG-GCUGCUUUCUCGCACUCUCGUUAACUGAAAUGUGGCAGUAAAACUGACAAGUGCCGAGGCACUCU
((((.(((((((.........))))))))))).....(((((.------(-(((-((.((((..(((((...(((.....)))..)))))(((.....)))..))))))))))))))).. ( -34.80)
>DroEre_CAF1 4447 113 + 1
UUGAACCUUCGCUCUUACCAUCCUAAGGUCAAUGUUAAGUGCU------CCUCG-GCUGCUUUCUCAUACUCUCGUUAACUGAAAUGCGGCCGUAAAACUGACAAGUGCCGAGGCACUCU
((((.((((...............))))))))(((((.((...------...((-(((((((((....((....)).....)))).)))))))....)))))))(((((....))))).. ( -29.86)
>DroYak_CAF1 4382 119 + 1
UUGAACCUUAGGUCUAACCAUCCUAAGGUCAAUGUUAAGUGCUUUCUCUGCUCG-UCUGCUUUCUCCUACUAUCGUUAACUGAAAUGUGGCAGUAAAACUGACAAGUGCCGGGGCACACU
((((.(((((((.........)))))))))))......(((((((...((((.(-((.(.(((((.((((..(((.....)))...)))).)).))).).))).))))..)))))))... ( -30.20)
>consensus
UUGAACCUUAGGUCUAACCAUCCUAAGGUCAAUGUUAAGUGCU______C_UCG_GCUGCUUUCUCACACUCUCGUUAACUGAAAUGUGGCAGUAAAACUGACAAGUGCCGAGGCACUCU
((((.(((((((.........)))))))))))(((((..((((............(((((((((....((....)).....)))).)))))))))....))))).((((....))))... (-23.31 = -23.88 +   0.56)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:20:43 2006