Locus 5334

Sequence ID 3R_DroMel_CAF1
Location 13,981,809 – 13,981,940
Length 131
Max. P 0.967107
window8695 window8696 window8697

overview

Window 5

Location 13,981,809 – 13,981,911
Length 102
Sequences 3
Columns 102
Reading direction forward
Mean pairwise identity 78.03
Mean single sequence MFE -20.87
Consensus MFE -12.24
Energy contribution -12.14
Covariance contribution -0.11
Combinations/Pair 1.12
Mean z-score -1.91
Structure conservation index 0.59
SVM decision value 0.24
SVM RNA-class probability 0.646620
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13981809 102 + 27905053
CAUAUAGUGUAAACAUAAUAAUCAACGGGCAUUAUAUGCCGAUAUUUGCCGAUAUAUAUAUAUUACAUACAUAUGCAUGUGGCGAUCAGCAGAAUGCGCUUU
..(((.(((....))).)))......(.(((((...(((.((...(((((.((((.(((((.........))))).))))))))))).))).))))).)... ( -21.10)
>DroEre_CAF1 243506 101 + 1
CAUAUAGUGUAAACAUAAUAAUCAACGGGCAUUAUAUGCCUACAUAUACCUAUGUAUAUACAU-ACGAGUAUAUGUAUGUGGCGAUCAGCAGAAUGCGCUUU
.....((((((..((((.........((((((...))))))((((((((((((((....))))-).).)))))))).))))((.....))....)))))).. ( -26.70)
>DroYak_CAF1 264907 81 + 1
CAUAUAGUGUAAACAUAAUAAUCAACGUACAUUAUAUGCCGA--UAUACCU-------------AC------AACUAUGUGGCGAUCAGCAGAAUGCGCUUU
..(((.(((....))).)))......(..((((...(((.((--(....((-------------((------(....)))))..))).))).))))..)... ( -14.80)
>consensus
CAUAUAGUGUAAACAUAAUAAUCAACGGGCAUUAUAUGCCGA_AUAUACCUAU_UAUAUA_AU_AC____AUAUGUAUGUGGCGAUCAGCAGAAUGCGCUUU
((((((((((..................))))))))))....................................((((...((.....))...))))..... (-12.24 = -12.14 +  -0.11)

alignment

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secondary structure

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Window 6

Location 13,981,838 – 13,981,940
Length 102
Sequences 3
Columns 102
Reading direction forward
Mean pairwise identity 79.34
Mean single sequence MFE -29.37
Consensus MFE -21.28
Energy contribution -23.23
Covariance contribution 1.95
Combinations/Pair 1.13
Mean z-score -1.82
Structure conservation index 0.72
SVM decision value 0.84
SVM RNA-class probability 0.863859
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13981838 102 + 27905053
CAUUAUAUGCCGAUAUUUGCCGAUAUAUAUAUAUUACAUACAUAUGCAUGUGGCGAUCAGCAGAAUGCGCUUUUGCAAAAUGGCCGGCGGUCAGCGCGGCCC
((((...(((.((...(((((.((((.(((((.........))))).))))))))))).))).)))).((....)).....(((((((.....)).))))). ( -28.30)
>DroEre_CAF1 243535 101 + 1
CAUUAUAUGCCUACAUAUACCUAUGUAUAUACAU-ACGAGUAUAUGUAUGUGGCGAUCAGCAGAAUGCGCUUUUGCAAAAUGGCCGGCGGUCAGCGCGGCCC
.......(((((((((((((((((((....))))-).).)))))))))...))))....((((((.....)))))).....(((((((.....)).))))). ( -34.60)
>DroYak_CAF1 264936 81 + 1
CAUUAUAUGCCGA--UAUACCU-------------AC------AACUAUGUGGCGAUCAGCAGAAUGCGCUUUUGCAAAAUGGCCGGCGGUCAGCGCGGCCC
((((...(((.((--(....((-------------((------(....)))))..))).))).)))).((....)).....(((((((.....)).))))). ( -25.20)
>consensus
CAUUAUAUGCCGA_AUAUACCUAU_UAUAUA_AU_AC____AUAUGUAUGUGGCGAUCAGCAGAAUGCGCUUUUGCAAAAUGGCCGGCGGUCAGCGCGGCCC
.......((((...((((((....((((((((.....))))))))))))))))))....((((((.....)))))).....(((((((.....)).))))). (-21.28 = -23.23 +   1.95)

alignment

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secondary structure

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dotplot

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Window 7

Location 13,981,838 – 13,981,940
Length 102
Sequences 3
Columns 102
Reading direction reverse
Mean pairwise identity 79.34
Mean single sequence MFE -30.47
Consensus MFE -21.79
Energy contribution -22.80
Covariance contribution 1.01
Combinations/Pair 1.15
Mean z-score -2.21
Structure conservation index 0.72
SVM decision value 1.61
SVM RNA-class probability 0.967107
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13981838 102 - 27905053
GGGCCGCGCUGACCGCCGGCCAUUUUGCAAAAGCGCAUUCUGCUGAUCGCCACAUGCAUAUGUAUGUAAUAUAUAUAUAUCGGCAAAUAUCGGCAUAUAAUG
.(((((.((.....)))))))....(((......)))...(((((((.(((((((((....)))))).((((....)))).)))....)))))))....... ( -31.40)
>DroEre_CAF1 243535 101 - 1
GGGCCGCGCUGACCGCCGGCCAUUUUGCAAAAGCGCAUUCUGCUGAUCGCCACAUACAUAUACUCGU-AUGUAUAUACAUAGGUAUAUGUAGGCAUAUAAUG
.(((((.((.....))))))).....((....))((.....)).....(((...((((((((((..(-((((....))))))))))))))))))........ ( -32.40)
>DroYak_CAF1 264936 81 - 1
GGGCCGCGCUGACCGCCGGCCAUUUUGCAAAAGCGCAUUCUGCUGAUCGCCACAUAGUU------GU-------------AGGUAUA--UCGGCAUAUAAUG
.(((((.((.....)))))))....(((......)))...(((((((.((((((....)------))-------------.)))..)--))))))....... ( -27.60)
>consensus
GGGCCGCGCUGACCGCCGGCCAUUUUGCAAAAGCGCAUUCUGCUGAUCGCCACAUACAUAU____GU_AU_UAUAUA_AUAGGUAUAU_UCGGCAUAUAAUG
.(((((.((.....)))))))....(((......)))...(((((((.(((......((((((.......)))))).....)))....)))))))....... (-21.79 = -22.80 +   1.01)

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 11:52:14 2006