Locus 88

Sequence ID Eco_1
Location 3,999,200 – 3,999,398
Length 198
Max. P 0.993205
window285 window286 window287 window288 window289 window290

overview

Window 5

Location 3,999,200 – 3,999,320
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 97.78
Mean single sequence MFE -33.80
Consensus MFE -32.69
Energy contribution -32.47
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -1.99
Structure conservation index 0.97
SVM decision value 0.85
SVM RNA-class probability 0.866690
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 3999200 120 + 1
GCGUAACAUGCGCGCACGAUCACUCUAAGAGGACAUUCGCCUUGGACACACCCAGUAGAUACUGGCUCACUAUCCUGUCAUCCAGGAUCAACUCCUAAGGCUAUCCCUUUUUGCUGAUAG
((((.....)))).....((((....((((((......(((((((......(((((....)))))......((((((.....))))))......)))))))....))))))...)))).. ( -33.50)
>Sfl_1 121 120 + 1
GCGUAACAUGCGCGCACGAUCACUCUAAGAGGACAUUCGCCUUGGACACACCCAGUAGAUACUGGCUCACUAUCCUGUCAUCCAGGAUCAACUCCUAAGGCUAUCCCUUUUUGCUGAUAG
((((.....)))).....((((....((((((......(((((((......(((((....)))))......((((((.....))))))......)))))))....))))))...)))).. ( -33.50)
>Sty_1 29 120 + 1
GCGUAACAUGCGCCCACGAUUACGCUAAGAGGACAUUCGCCUUGGACACACCCAGUAGAUACUGGCUCAUUAUCCUGUCAUCCAGGAUCAACUCCUAAGGCUAUCCCUUUUUGCUGAUAG
((((.....)))).....((((.((.((((((......(((((((......(((((....)))))......((((((.....))))))......)))))))....)))))).)))))).. ( -34.40)
>consensus
GCGUAACAUGCGCGCACGAUCACUCUAAGAGGACAUUCGCCUUGGACACACCCAGUAGAUACUGGCUCACUAUCCUGUCAUCCAGGAUCAACUCCUAAGGCUAUCCCUUUUUGCUGAUAG
((((.....)))).....((((....((((((......(((((((......(((((....)))))......((((((.....))))))......)))))))....))))))...)))).. (-32.69 = -32.47 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 6

Location 3,999,200 – 3,999,320
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 97.78
Mean single sequence MFE -39.77
Consensus MFE -38.99
Energy contribution -38.77
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -1.50
Structure conservation index 0.98
SVM decision value 0.14
SVM RNA-class probability 0.604901
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 3999200 120 - 1
CUAUCAGCAAAAAGGGAUAGCCUUAGGAGUUGAUCCUGGAUGACAGGAUAGUGAGCCAGUAUCUACUGGGUGUGUCCAAGGCGAAUGUCCUCUUAGAGUGAUCGUGCGCGCAUGUUACGC
......((...(((((((((((((.(((....((((((.....))))))....(.(((((....))))).)...))))))))...))))).)))...((((.((((....)))))))))) ( -39.10)
>Sfl_1 121 120 - 1
CUAUCAGCAAAAAGGGAUAGCCUUAGGAGUUGAUCCUGGAUGACAGGAUAGUGAGCCAGUAUCUACUGGGUGUGUCCAAGGCGAAUGUCCUCUUAGAGUGAUCGUGCGCGCAUGUUACGC
......((...(((((((((((((.(((....((((((.....))))))....(.(((((....))))).)...))))))))...))))).)))...((((.((((....)))))))))) ( -39.10)
>Sty_1 29 120 - 1
CUAUCAGCAAAAAGGGAUAGCCUUAGGAGUUGAUCCUGGAUGACAGGAUAAUGAGCCAGUAUCUACUGGGUGUGUCCAAGGCGAAUGUCCUCUUAGCGUAAUCGUGGGCGCAUGUUACGC
...........(((((((((((((.(((....((((((.....))))))....(.(((((....))))).)...))))))))...))))).))).((((((.((((....)))))))))) ( -41.10)
>consensus
CUAUCAGCAAAAAGGGAUAGCCUUAGGAGUUGAUCCUGGAUGACAGGAUAGUGAGCCAGUAUCUACUGGGUGUGUCCAAGGCGAAUGUCCUCUUAGAGUGAUCGUGCGCGCAUGUUACGC
......((...(((((((((((((.(((....((((((.....))))))....(.(((((....))))).)...))))))))...))))).)))...((((.((((....)))))))))) (-38.99 = -38.77 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 7

Location 3,999,240 – 3,999,358
Length 118
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 97.77
Mean single sequence MFE -38.07
Consensus MFE -37.96
Energy contribution -37.96
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -4.31
Structure conservation index 1.00
SVM decision value 2.15
SVM RNA-class probability 0.989202
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 3999240 118 + 1
CUUGGACACACCCAGUAGAUACUGGCUCACUAUCCUGUCAUCCAGGAUCAACUCCUAAGGCUAUCCCUUUUUGCUGAUAGCCUUAGCGGUUGUCAGCGACCU--CAAUUUUUCCCGUCGC
....(((....(((((....)))))......((((((.....)))))).((((.(((((((((((..........))))))))))).))))))).(((((..--...........))))) ( -38.12)
>Sfl_1 161 118 + 1
CUUGGACACACCCAGUAGAUACUGGCUCACUAUCCUGUCAUCCAGGAUCAACUCCUAAGGCUAUCCCUUUUUGCUGAUAGCCUUAGCGGUUGUCAGCGACCU--CAAUUUUUCCCGUCGC
....(((....(((((....)))))......((((((.....)))))).((((.(((((((((((..........))))))))))).))))))).(((((..--...........))))) ( -38.12)
>Sty_1 69 120 + 1
CUUGGACACACCCAGUAGAUACUGGCUCAUUAUCCUGUCAUCCAGGAUCAACUCCUAAGGCUAUCCCUUUUUGCUGAUAGCCUUAGCGGUUGUCAGCGACCUUUCAUUUUUUCCCGUCGC
....(((....(((((....)))))......((((((.....)))))).((((.(((((((((((..........))))))))))).))))))).(((((...............))))) ( -37.96)
>consensus
CUUGGACACACCCAGUAGAUACUGGCUCACUAUCCUGUCAUCCAGGAUCAACUCCUAAGGCUAUCCCUUUUUGCUGAUAGCCUUAGCGGUUGUCAGCGACCU__CAAUUUUUCCCGUCGC
....(((....(((((....)))))......((((((.....)))))).((((.(((((((((((..........))))))))))).))))))).(((((...............))))) (-37.96 = -37.96 +   0.00)

alignment

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secondary structure

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dotplot

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Window 8

Location 3,999,240 – 3,999,358
Length 118
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 97.77
Mean single sequence MFE -43.09
Consensus MFE -41.86
Energy contribution -41.86
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -3.70
Structure conservation index 0.97
SVM decision value 2.18
SVM RNA-class probability 0.989826
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 3999240 118 - 1
GCGACGGGAAAAAUUG--AGGUCGCUGACAACCGCUAAGGCUAUCAGCAAAAAGGGAUAGCCUUAGGAGUUGAUCCUGGAUGACAGGAUAGUGAGCCAGUAUCUACUGGGUGUGUCCAAG
(.((((.(........--...(((((..((((..(((((((((((..(.....).)))))))))))..))))((((((.....))))))))))).(((((....))))).).)))))... ( -43.70)
>Sfl_1 161 118 - 1
GCGACGGGAAAAAUUG--AGGUCGCUGACAACCGCUAAGGCUAUCAGCAAAAAGGGAUAGCCUUAGGAGUUGAUCCUGGAUGACAGGAUAGUGAGCCAGUAUCUACUGGGUGUGUCCAAG
(.((((.(........--...(((((..((((..(((((((((((..(.....).)))))))))))..))))((((((.....))))))))))).(((((....))))).).)))))... ( -43.70)
>Sty_1 69 120 - 1
GCGACGGGAAAAAAUGAAAGGUCGCUGACAACCGCUAAGGCUAUCAGCAAAAAGGGAUAGCCUUAGGAGUUGAUCCUGGAUGACAGGAUAAUGAGCCAGUAUCUACUGGGUGUGUCCAAG
(((((...............)))))...((((..(((((((((((..(.....).)))))))))))..))))((((((.....))))))....(.(((((....))))).)......... ( -41.86)
>consensus
GCGACGGGAAAAAUUG__AGGUCGCUGACAACCGCUAAGGCUAUCAGCAAAAAGGGAUAGCCUUAGGAGUUGAUCCUGGAUGACAGGAUAGUGAGCCAGUAUCUACUGGGUGUGUCCAAG
(((((...............)))))...((((..(((((((((((..(.....).)))))))))))..))))((((((.....))))))....(.(((((....))))).)......... (-41.86 = -41.86 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 9

Location 3,999,280 – 3,999,398
Length 118
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 97.77
Mean single sequence MFE -39.53
Consensus MFE -39.25
Energy contribution -39.03
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -3.63
Structure conservation index 0.99
SVM decision value 2.38
SVM RNA-class probability 0.993205
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 3999280 118 + 1
UCCAGGAUCAACUCCUAAGGCUAUCCCUUUUUGCUGAUAGCCUUAGCGGUUGUCAGCGACCU--CAAUUUUUCCCGUCGCGCUGAGUCAGGCUGUUUAAUGGUCUGAAACCCAAUUUGUU
..(((((.(((((.(((((((((((..........))))))))))).))))))).(((((..--...........))))).)))..(((((((((...)))))))))............. ( -40.02)
>Sfl_1 201 118 + 1
UCCAGGAUCAACUCCUAAGGCUAUCCCUUUUUGCUGAUAGCCUUAGCGGUUGUCAGCGACCU--CAAUUUUUCCCGUCGCGCUGAGUCAGGCUGUUUAAUGGUCUGAAACCCAAUUUGUU
..(((((.(((((.(((((((((((..........))))))))))).))))))).(((((..--...........))))).)))..(((((((((...)))))))))............. ( -40.02)
>Sty_1 109 120 + 1
UCCAGGAUCAACUCCUAAGGCUAUCCCUUUUUGCUGAUAGCCUUAGCGGUUGUCAGCGACCUUUCAUUUUUUCCCGUCGCGUUGAGUCAGGCUGUUUAAUGGUCUGAAACCCAAUUUGUU
.....((.(((((.(((((((((((..........))))))))))).))))))).(((((...............)))))((((..(((((((((...)))))))))....))))..... ( -38.56)
>consensus
UCCAGGAUCAACUCCUAAGGCUAUCCCUUUUUGCUGAUAGCCUUAGCGGUUGUCAGCGACCU__CAAUUUUUCCCGUCGCGCUGAGUCAGGCUGUUUAAUGGUCUGAAACCCAAUUUGUU
..(((((.(((((.(((((((((((..........))))))))))).))))))).(((((...............))))).)))..(((((((((...)))))))))............. (-39.25 = -39.03 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 0

Location 3,999,280 – 3,999,398
Length 118
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 97.77
Mean single sequence MFE -34.59
Consensus MFE -33.78
Energy contribution -33.56
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -2.01
Structure conservation index 0.98
SVM decision value 0.95
SVM RNA-class probability 0.888673
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 3999280 118 - 1
AACAAAUUGGGUUUCAGACCAUUAAACAGCCUGACUCAGCGCGACGGGAAAAAUUG--AGGUCGCUGACAACCGCUAAGGCUAUCAGCAAAAAGGGAUAGCCUUAGGAGUUGAUCCUGGA
......(..((.....((((.((((....((((..((.....)))))).....)))--))))).....((((..(((((((((((..(.....).)))))))))))..))))..))..). ( -35.10)
>Sfl_1 201 118 - 1
AACAAAUUGGGUUUCAGACCAUUAAACAGCCUGACUCAGCGCGACGGGAAAAAUUG--AGGUCGCUGACAACCGCUAAGGCUAUCAGCAAAAAGGGAUAGCCUUAGGAGUUGAUCCUGGA
......(..((.....((((.((((....((((..((.....)))))).....)))--))))).....((((..(((((((((((..(.....).)))))))))))..))))..))..). ( -35.10)
>Sty_1 109 120 - 1
AACAAAUUGGGUUUCAGACCAUUAAACAGCCUGACUCAACGCGACGGGAAAAAAUGAAAGGUCGCUGACAACCGCUAAGGCUAUCAGCAAAAAGGGAUAGCCUUAGGAGUUGAUCCUGGA
.......(((........)))........((.((.((((((((((...............))))).........(((((((((((..(.....).)))))))))))..)))))))..)). ( -33.56)
>consensus
AACAAAUUGGGUUUCAGACCAUUAAACAGCCUGACUCAGCGCGACGGGAAAAAUUG__AGGUCGCUGACAACCGCUAAGGCUAUCAGCAAAAAGGGAUAGCCUUAGGAGUUGAUCCUGGA
.......(((........)))........((.((.((((((((((...............))))).........(((((((((((..(.....).)))))))))))..)))))))..)). (-33.78 = -33.56 +  -0.22)

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 11:06:12 2006