Locus 2597

Sequence ID X_DroMel_CAF1
Location 6,940,523 – 6,940,672
Length 149
Max. P 0.972579
window4242 window4243 window4244

overview

Window 2

Location 6,940,523 – 6,940,632
Length 109
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 85.23
Mean single sequence MFE -28.47
Consensus MFE -17.69
Energy contribution -18.47
Covariance contribution 0.78
Combinations/Pair 1.04
Mean z-score -2.61
Structure conservation index 0.62
SVM decision value 0.26
SVM RNA-class probability 0.657342
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6940523 109 - 22224390
UGCA------UCUUC---UAUAUGUAUAU--AUGUAUACAUUAGCUCAUGUACUUAAAUGGGCUUUUAUCAGCUGUUUAGAACACACAUUCACUCAAGCACUGCAUAAUAGUGCUGCUCU
.((.------..(((---((.(((((((.--...))))))).(((((((........))))))).............)))))..............(((((((.....)))))))))... ( -23.90)
>DroSec_CAF1 25524 112 - 1
UGCG------UCUUUAGAUAUAUGUAUGU--AUGUAUAUAUUAGCUCAUGUACUUAAAUGGGCUUUUAUCAGCUGUUUAGCACACACAUUCACUCAAGCACUGCAUAAUAGUGCUGCUCU
.(((------((....)))...((.((((--.(((..(((..(((((((........)))))))..)))..(((....)))))).)))).))....(((((((.....)))))))))... ( -26.30)
>DroEre_CAF1 34110 120 - 1
UGCAUACAUAUCUUUGGAUAUACGUAUCUAGAUGUACAUAUUAGCUCAUGUACUUAAAUGGGCUUAUAUCAGCUGUUUCGCACACACGUUCAAGCGAGCAGUGCAUAAUAGUGCUGCUCU
.......((((((..(((((....)))))))))))..((((.(((((((........))))))).))))..(((....((......))....)))((((((..(......)..)))))). ( -35.20)
>consensus
UGCA______UCUUU_GAUAUAUGUAUAU__AUGUAUAUAUUAGCUCAUGUACUUAAAUGGGCUUUUAUCAGCUGUUUAGCACACACAUUCACUCAAGCACUGCAUAAUAGUGCUGCUCU
.((................((((((((......)))))))).(((((((........))))))).......)).......................(((((((.....)))))))..... (-17.69 = -18.47 +   0.78)

alignment

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secondary structure

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dotplot

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Window 3

Location 6,940,563 – 6,940,672
Length 109
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 85.80
Mean single sequence MFE -26.63
Consensus MFE -17.59
Energy contribution -17.37
Covariance contribution -0.22
Combinations/Pair 1.06
Mean z-score -2.86
Structure conservation index 0.66
SVM decision value 0.71
SVM RNA-class probability 0.828178
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6940563 109 + 22224390
CUAAACAGCUGAUAAAAGCCCAUUUAAGUACAUGAGCUAAUGUAUACAU--AUAUACAUAUA---GAAGA------UGCAUGUACACAUCUGUGCAUCUAACAAUCGCUCAGCUGGGAAA
.....(((((((....(((.(((........))).))).(((((((...--.)))))))...---..(((------((((((........))))))))).........)))))))..... ( -28.20)
>DroSec_CAF1 25564 112 + 1
CUAAACAGCUGAUAAAAGCCCAUUUAAGUACAUGAGCUAAUAUAUACAU--ACAUACAUAUAUCUAAAGA------CGCAUGUACACAUCUCUGCAUCUAACAAUCGCUCAGCUGGGAAA
.....(((((((...............(((((((..((.((((((....--......))))))....)).------..)))))))........((...........)))))))))..... ( -21.00)
>DroEre_CAF1 34150 120 + 1
CGAAACAGCUGAUAUAAGCCCAUUUAAGUACAUGAGCUAAUAUGUACAUCUAGAUACGUAUAUCCAAAGAUAUGUAUGCAUGUGCACAUCUCUGCGUCUAACAGUCGCUCAGCUGGGUAA
.....((((((((((.(((.(((........))).))).)))(((((((....((((((((........))))))))..))))))).......(((.(.....).))))))))))..... ( -30.70)
>consensus
CUAAACAGCUGAUAAAAGCCCAUUUAAGUACAUGAGCUAAUAUAUACAU__ACAUACAUAUAUC_AAAGA______UGCAUGUACACAUCUCUGCAUCUAACAAUCGCUCAGCUGGGAAA
.....(((((((...............(((((((............................................)))))))........((...........)))))))))..... (-17.59 = -17.37 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 4

Location 6,940,563 – 6,940,672
Length 109
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 85.80
Mean single sequence MFE -33.57
Consensus MFE -27.19
Energy contribution -26.64
Covariance contribution -0.55
Combinations/Pair 1.14
Mean z-score -3.25
Structure conservation index 0.81
SVM decision value 1.70
SVM RNA-class probability 0.972579
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6940563 109 - 22224390
UUUCCCAGCUGAGCGAUUGUUAGAUGCACAGAUGUGUACAUGCA------UCUUC---UAUAUGUAUAU--AUGUAUACAUUAGCUCAUGUACUUAAAUGGGCUUUUAUCAGCUGUUUAG
.....(((((((((.(((....)))))...((((((((((((.(------((...---.....).)).)--)))))))))))(((((((........)))))))....)))))))..... ( -31.50)
>DroSec_CAF1 25564 112 - 1
UUUCCCAGCUGAGCGAUUGUUAGAUGCAGAGAUGUGUACAUGCG------UCUUUAGAUAUAUGUAUGU--AUGUAUAUAUUAGCUCAUGUACUUAAAUGGGCUUUUAUCAGCUGUUUAG
.....(((((((((.(((....)))))...((((((((((((((------(...((....))...))))--)))))))))))(((((((........)))))))....)))))))..... ( -34.60)
>DroEre_CAF1 34150 120 - 1
UUACCCAGCUGAGCGACUGUUAGACGCAGAGAUGUGCACAUGCAUACAUAUCUUUGGAUAUACGUAUCUAGAUGUACAUAUUAGCUCAUGUACUUAAAUGGGCUUAUAUCAGCUGUUUCG
.....((((((((((.(.....).)))....(((((((..((.(((((((((....)))))..)))).))..)))))))...(((((((........)))))))....)))))))..... ( -34.60)
>consensus
UUUCCCAGCUGAGCGAUUGUUAGAUGCAGAGAUGUGUACAUGCA______UCUUU_GAUAUAUGUAUAU__AUGUAUAUAUUAGCUCAUGUACUUAAAUGGGCUUUUAUCAGCUGUUUAG
.....((((((((((.(.....).)))...(((((((((((..............................)))))))))))(((((((........)))))))....)))))))..... (-27.19 = -26.64 +  -0.55)

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 10:38:39 2006