Locus 79

Sequence ID Eco_1
Location 3,451,293 – 3,451,477
Length 184
Max. P 0.966998
window239 window240 window241 window242 window243

overview

Window 9

Location 3,451,293 – 3,451,413
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 98.33
Mean single sequence MFE -34.07
Consensus MFE -34.00
Energy contribution -34.00
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.80
Structure conservation index 1.00
SVM decision value 0.75
SVM RNA-class probability 0.840367
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 3451293 120 - 1
GGCUACCUAACAAUGCUCCCAAUCGGGGAGCUACGUAAGAACGGUUACACUCUCCCAUCAAUCGUAAUGGGUCUGAGGAGUAAUCAUUUUCGUUUAUAAAAUAAUUGGAGCUCUGGUCUC
((((.((.......((((((.....)))))).(((.((((..((((((.(((.(((((........)))))...)))..)))))).))))))).............))))))........ ( -34.10)
>Sfl_1 1 120 - 1
GGCUACCUAACAAUGCUCCCAAUCGGGGAGCUACGUAAGAACGGUUACACUCUCCCAUCAAUCGUAAUGGGUCUGAGGAGUAAUCAUUUUCGUUUAUAAAAUAAUUGGAGCUCUGGUCUC
((((.((.......((((((.....)))))).(((.((((..((((((.(((.(((((........)))))...)))..)))))).))))))).............))))))........ ( -34.10)
>Sty_1 1 120 - 1
GGCUAUUUAACAAUGCUCCCAAUCGGGGAGCUACGUAAGAACGGUUACACUCUCCCAUCAAUCGUAAUGGGUGUGAGGAGUAAUCAUUUUCGUUUAUAAAAUAAUUGGAGCUCUGGUCUC
(((((.....((((((((((.....)))))).(((.((((..((((((.(((.(((((........)))))...)))..)))))).)))))))..........))))......))))).. ( -34.00)
>consensus
GGCUACCUAACAAUGCUCCCAAUCGGGGAGCUACGUAAGAACGGUUACACUCUCCCAUCAAUCGUAAUGGGUCUGAGGAGUAAUCAUUUUCGUUUAUAAAAUAAUUGGAGCUCUGGUCUC
(((((.....((((((((((.....)))))).(((.((((..((((((.(((.(((((........)))))...)))..)))))).)))))))..........))))......))))).. (-34.00 = -34.00 +   0.00)

alignment

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secondary structure

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Window 0

Location 3,451,333 – 3,451,453
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 94.44
Mean single sequence MFE -38.50
Consensus MFE -37.34
Energy contribution -37.23
Covariance contribution -0.11
Combinations/Pair 1.03
Mean z-score -2.02
Structure conservation index 0.97
SVM decision value 1.09
SVM RNA-class probability 0.913444
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 3451333 120 + 1
CUCCUCAGACCCAUUACGAUUGAUGGGAGAGUGUAACCGUUCUUACGUAGCUCCCCGAUUGGGAGCAUUGUUAGGUAGCCAAAUUCGGCUAACUGAGGUUCAGAUUGAACCUGCUGUCAA
...(((...(((((((....))))))).))).((((......))))(((((((((.....))))))....((((.(((((......))))).))))(((((.....))))))))...... ( -38.70)
>Sfl_1 41 120 + 1
CUCCUCAGACCCAUUACGAUUGAUGGGAGAGUGUAACCGUUCUUACGUAGCUCCCCGAUUGGGAGCAUUGUUAGGUAGCCAAAUUCGGCUAACUGAGGUUCAGAUUGAACCUGCUGUCAA
...(((...(((((((....))))))).))).((((......))))(((((((((.....))))))....((((.(((((......))))).))))(((((.....))))))))...... ( -38.70)
>Sty_1 41 119 + 1
CUCCUCACACCCAUUACGAUUGAUGGGAGAGUGUAACCGUUCUUACGUAGCUCCCCGAUUGGGAGCAUUGUUAAAUAGCCAAAU-CGGCUAUUCGAGGUUCAAAUCGAACCUGCCGUCAA
...(((...(((((((....))))))).)))..(((((((....)))..((((((.....))))))...))))(((((((....-.)))))))..((((((.....))))))........ ( -38.10)
>consensus
CUCCUCAGACCCAUUACGAUUGAUGGGAGAGUGUAACCGUUCUUACGUAGCUCCCCGAUUGGGAGCAUUGUUAGGUAGCCAAAUUCGGCUAACUGAGGUUCAGAUUGAACCUGCUGUCAA
...(((...(((((((....))))))).))).((((......))))(((((((((.....))))))....((((.(((((......))))).))))(((((.....))))))))...... (-37.34 = -37.23 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 1

Location 3,451,333 – 3,451,453
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 94.44
Mean single sequence MFE -38.77
Consensus MFE -38.30
Energy contribution -37.63
Covariance contribution -0.66
Combinations/Pair 1.06
Mean z-score -2.16
Structure conservation index 0.99
SVM decision value 1.48
SVM RNA-class probability 0.958020
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 3451333 120 - 1
UUGACAGCAGGUUCAAUCUGAACCUCAGUUAGCCGAAUUUGGCUACCUAACAAUGCUCCCAAUCGGGGAGCUACGUAAGAACGGUUACACUCUCCCAUCAAUCGUAAUGGGUCUGAGGAG
.((((.(.((((((.....)))))))((.((((((....)))))).))......((((((.....))))))..(((....)))))))..(((.(((((........)))))...)))... ( -38.50)
>Sfl_1 41 120 - 1
UUGACAGCAGGUUCAAUCUGAACCUCAGUUAGCCGAAUUUGGCUACCUAACAAUGCUCCCAAUCGGGGAGCUACGUAAGAACGGUUACACUCUCCCAUCAAUCGUAAUGGGUCUGAGGAG
.((((.(.((((((.....)))))))((.((((((....)))))).))......((((((.....))))))..(((....)))))))..(((.(((((........)))))...)))... ( -38.50)
>Sty_1 41 119 - 1
UUGACGGCAGGUUCGAUUUGAACCUCGAAUAGCCG-AUUUGGCUAUUUAACAAUGCUCCCAAUCGGGGAGCUACGUAAGAACGGUUACACUCUCCCAUCAAUCGUAAUGGGUGUGAGGAG
.((((.(.((((((.....)))))))((((((((.-....))))))))......((((((.....))))))..(((....)))))))..(((.(((((........)))))...)))... ( -39.30)
>consensus
UUGACAGCAGGUUCAAUCUGAACCUCAGUUAGCCGAAUUUGGCUACCUAACAAUGCUCCCAAUCGGGGAGCUACGUAAGAACGGUUACACUCUCCCAUCAAUCGUAAUGGGUCUGAGGAG
.((((.(.((((((.....)))))))((.((((((....)))))).))......((((((.....))))))..(((....)))))))..(((.(((((........)))))...)))... (-38.30 = -37.63 +  -0.66)

alignment

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secondary structure

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dotplot

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Window 2

Location 3,451,357 – 3,451,477
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 94.44
Mean single sequence MFE -38.30
Consensus MFE -36.68
Energy contribution -36.90
Covariance contribution 0.22
Combinations/Pair 1.03
Mean z-score -1.57
Structure conservation index 0.96
SVM decision value 0.23
SVM RNA-class probability 0.642766
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 3451357 120 + 1
GGGAGAGUGUAACCGUUCUUACGUAGCUCCCCGAUUGGGAGCAUUGUUAGGUAGCCAAAUUCGGCUAACUGAGGUUCAGAUUGAACCUGCUGUCAACUACGACAAGCCCGCGCAUUAUAC
(((.((((.....(((....)))..)))))))(..((((((((...((((.(((((......))))).))))(((((.....)))))))))(((......)))...))))..)....... ( -39.20)
>Sfl_1 65 120 + 1
GGGAGAGUGUAACCGUUCUUACGUAGCUCCCCGAUUGGGAGCAUUGUUAGGUAGCCAAAUUCGGCUAACUGAGGUUCAGAUUGAACCUGCUGUCAACUACGACAAGCCCGCGCAUUAUAC
(((.((((.....(((....)))..)))))))(..((((((((...((((.(((((......))))).))))(((((.....)))))))))(((......)))...))))..)....... ( -39.20)
>Sty_1 65 119 + 1
GGGAGAGUGUAACCGUUCUUACGUAGCUCCCCGAUUGGGAGCAUUGUUAAAUAGCCAAAU-CGGCUAUUCGAGGUUCAAAUCGAACCUGCCGUCAAUUACGACAAGCCCGCGCAUUAUAC
(((.((((.....(((....)))..)))))))(..((((.(((...(..(((((((....-.)))))))..)(((((.....)))))))).(((......)))...))))..)....... ( -36.50)
>consensus
GGGAGAGUGUAACCGUUCUUACGUAGCUCCCCGAUUGGGAGCAUUGUUAGGUAGCCAAAUUCGGCUAACUGAGGUUCAGAUUGAACCUGCUGUCAACUACGACAAGCCCGCGCAUUAUAC
(((.((((.....(((....)))..)))))))(..((((((((...((((.(((((......))))).))))(((((.....)))))))))(((......)))...))))..)....... (-36.68 = -36.90 +   0.22)

alignment

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secondary structure

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dotplot

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Window 3

Location 3,451,357 – 3,451,477
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 94.44
Mean single sequence MFE -40.63
Consensus MFE -39.92
Energy contribution -39.03
Covariance contribution -0.88
Combinations/Pair 1.07
Mean z-score -2.28
Structure conservation index 0.98
SVM decision value 1.60
SVM RNA-class probability 0.966998
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 3451357 120 - 1
GUAUAAUGCGCGGGCUUGUCGUAGUUGACAGCAGGUUCAAUCUGAACCUCAGUUAGCCGAAUUUGGCUACCUAACAAUGCUCCCAAUCGGGGAGCUACGUAAGAACGGUUACACUCUCCC
(((....((.((..((((.((((((((...(.((((((.....)))))))((.((((((....)))))).))..))))((((((.....))))))))))))))..)))))))........ ( -40.00)
>Sfl_1 65 120 - 1
GUAUAAUGCGCGGGCUUGUCGUAGUUGACAGCAGGUUCAAUCUGAACCUCAGUUAGCCGAAUUUGGCUACCUAACAAUGCUCCCAAUCGGGGAGCUACGUAAGAACGGUUACACUCUCCC
(((....((.((..((((.((((((((...(.((((((.....)))))))((.((((((....)))))).))..))))((((((.....))))))))))))))..)))))))........ ( -40.00)
>Sty_1 65 119 - 1
GUAUAAUGCGCGGGCUUGUCGUAAUUGACGGCAGGUUCGAUUUGAACCUCGAAUAGCCG-AUUUGGCUAUUUAACAAUGCUCCCAAUCGGGGAGCUACGUAAGAACGGUUACACUCUCCC
..........((((((((((((.....))))))))))))...((((((..((((((((.-....)))))))).((...((((((.....))))))...))......)))).))....... ( -41.90)
>consensus
GUAUAAUGCGCGGGCUUGUCGUAGUUGACAGCAGGUUCAAUCUGAACCUCAGUUAGCCGAAUUUGGCUACCUAACAAUGCUCCCAAUCGGGGAGCUACGUAAGAACGGUUACACUCUCCC
(((....((.((..((((.((((((((...(.((((((.....)))))))((.((((((....)))))).))..))))((((((.....))))))))))))))..)))))))........ (-39.92 = -39.03 +  -0.88)

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 Fri Dec 1 11:05:31 2006