Locus 55

Sequence ID Eco_1
Location 2,940,691 – 2,940,916
Length 225
Max. P 0.993266
window176 window177 window178 window179 window180 window181

overview

Window 6

Location 2,940,691 – 2,940,811
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 97.78
Mean single sequence MFE -40.13
Consensus MFE -41.01
Energy contribution -40.13
Covariance contribution -0.88
Combinations/Pair 1.10
Mean z-score -2.44
Structure conservation index 1.02
SVM decision value 1.94
SVM RNA-class probability 0.983309
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 2940691 120 + 1
CUACCAGCAAAUACCUAUAGUGGCGGCACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGGUGAACUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAU
......((((((((.....(..(((.(((..(((((((((((......(((((.((((((((....)))))))))))))))))))))).))..))).)))..)......))))))))... ( -40.50)
>Sfl_1 81 120 + 1
CUACCAGCAAAUACCUAUAGUGGCGGCACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUAUUCUGGUGAACUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAU
......((((((((.....(..(((.(((..(((((((((((......(((((.((((((((....)))))))))))))))))))))).))..))).)))..)......))))))))... ( -39.70)
>Sty_1 81 120 + 1
CUACCAGCAAAUACCUAUAGUGGCGGCACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAU
......((((((((.....(..(((.(((..(((((((((((......(((((.((((((((....)))))))))))))))))))))).))..))).)))..)......))))))))... ( -40.20)
>consensus
CUACCAGCAAAUACCUAUAGUGGCGGCACUUCCUGAGCCGGAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGGUGAACUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAU
......((((((((.....(..(((.(((..(((((((((((......(((((.((((((((....)))))))))))))))))))))).))..))).)))..)......))))))))... (-41.01 = -40.13 +  -0.88)

alignment

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secondary structure

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Window 7

Location 2,940,731 – 2,940,851
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 95.00
Mean single sequence MFE -33.73
Consensus MFE -34.62
Energy contribution -33.30
Covariance contribution -1.32
Combinations/Pair 1.15
Mean z-score -1.36
Structure conservation index 1.03
SVM decision value 0.34
SVM RNA-class probability 0.697445
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 2940731 120 + 1
GAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGGUGAACUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCAUGGUAGCAAAGCUACCUUUUU
.((((((((((((.((((((((....))))))))))))))))(((((((....)))).))).))))(((((....)))))(((((((.....))))))).((((((...))))))..... ( -34.90)
>Sfl_1 121 120 + 1
GAACGAAAAGUUUUAUCGGAAUGCGUAUUCUGGUGAACUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCAUGGUAGCAAAGCUACCUUUUU
.((((((((((((.((((((((....))))))))))))))))(((((((....)))).))).))))(((((....)))))(((((((.....))))))).((((((...))))))..... ( -34.10)
>Sty_1 121 120 + 1
GAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGAUGGGCUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUU
.((((((((((((.((((((((....))))))))))))))))(((((((....)))).))).))))(((((....)))))(((((((.....))))))).(((((.....)))))..... ( -32.20)
>consensus
GAACGAAAAGUUUUAUCGGAAUGCGUGUUCUGGUGAACUUUUGGCUUACGGUUGUGAUGUUGUGUUGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCAUGGUAGCAAAGCUACCUUUUU
...(.((((((((.((((((((....)))))))))))))))).).....(((.((..(((((....(((((....)))))(((((((.....)))))))...)))))..)).)))..... (-34.62 = -33.30 +  -1.32)

alignment

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secondary structure

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dotplot

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Window 8

Location 2,940,731 – 2,940,851
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 95.00
Mean single sequence MFE -23.77
Consensus MFE -21.84
Energy contribution -22.07
Covariance contribution 0.23
Combinations/Pair 1.08
Mean z-score -2.44
Structure conservation index 0.92
SVM decision value 1.18
SVM RNA-class probability 0.926981
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 2940731 120 - 1
AAAAAGGUAGCUUUGCUACCAUGGUCUGAAUCGCAGACCAAUUGCAAACACAACAACACAACAUCACAACCGUAAGCCAAAAGUUCACCAGAACACGCAUUCCGAUAAAACUUUUCGUUC
.....((((((...)))))).(((((((.....)))))))..(((.........................(....)......((((....))))..)))...(((.........)))... ( -25.20)
>Sfl_1 121 120 - 1
AAAAAGGUAGCUUUGCUACCAUGGUCUGAAUCGCAGACCAAUUGCAAACACAACAACACAACAUCACAACCGUAAGCCAAAAGUUCACCAGAAUACGCAUUCCGAUAAAACUUUUCGUUC
.....((((((...)))))).(((((((.....)))))))..................................(((.(((((((...(.((((....)))).)....))))))).))). ( -24.10)
>Sty_1 121 120 - 1
AAAAGGGUAGUCUCGCUACCGUGGUCUGAAUCGCAGACCAAUUGCAAACACAACAACACAACAUCACAACCGUAAGCCAAAAGCCCAUCAGAACACGCAUUCCGAUAAAACUUUUCGUUC
.....(((((.....))))).(((((((.....)))))))..................................(((.(((((...(((.(((......))).)))....))))).))). ( -22.00)
>consensus
AAAAAGGUAGCUUUGCUACCAUGGUCUGAAUCGCAGACCAAUUGCAAACACAACAACACAACAUCACAACCGUAAGCCAAAAGUUCACCAGAACACGCAUUCCGAUAAAACUUUUCGUUC
.....((((((...)))))).(((((((.....)))))))..(((.........................(....)......((((....))))..)))...(((.........)))... (-21.84 = -22.07 +   0.23)

alignment

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secondary structure

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Window 9

Location 2,940,771 – 2,940,891
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 97.22
Mean single sequence MFE -30.23
Consensus MFE -30.35
Energy contribution -30.13
Covariance contribution -0.22
Combinations/Pair 1.04
Mean z-score -3.02
Structure conservation index 1.00
SVM decision value 2.39
SVM RNA-class probability 0.993266
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 2940771 120 - 1
UAAUCACUAUGGACAGACAGGGUAAAUGUACAGGAAGUGAAAAAAGGUAGCUUUGCUACCAUGGUCUGAAUCGCAGACCAAUUGCAAACACAACAACACAACAUCACAACCGUAAGCCAA
.........(((....((...(((....))).((..((((.....((((((...)))))).(((((((.....))))))).......................))))..))))...))). ( -30.70)
>Sfl_1 161 120 - 1
UAAUCACUAUGGACAGACAGGGUAAAUGUACAGGAAGUGAAAAAAGGUAGCUUUGCUACCAUGGUCUGAAUCGCAGACCAAUUGCAAACACAACAACACAACAUCACAACCGUAAGCCAA
.........(((....((...(((....))).((..((((.....((((((...)))))).(((((((.....))))))).......................))))..))))...))). ( -30.70)
>Sty_1 161 120 - 1
UAAUCACUAUGGACAGACAGGGUAAAUGUACAGGAAGUGAAAAAGGGUAGUCUCGCUACCGUGGUCUGAAUCGCAGACCAAUUGCAAACACAACAACACAACAUCACAACCGUAAGCCAA
.........(((....((...(((....))).((..((((.....(((((.....))))).(((((((.....))))))).......................))))..))))...))). ( -29.30)
>consensus
UAAUCACUAUGGACAGACAGGGUAAAUGUACAGGAAGUGAAAAAAGGUAGCUUUGCUACCAUGGUCUGAAUCGCAGACCAAUUGCAAACACAACAACACAACAUCACAACCGUAAGCCAA
.........(((....((...(((....))).((..((((.....((((((...)))))).(((((((.....))))))).......................))))..))))...))). (-30.35 = -30.13 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 0

Location 2,940,796 – 2,940,916
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 96.11
Mean single sequence MFE -35.40
Consensus MFE -34.80
Energy contribution -34.80
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.44
Structure conservation index 0.98
SVM decision value 1.72
SVM RNA-class probability 0.974133
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 2940796 120 + 1
UGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCAUGGUAGCAAAGCUACCUUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCUAAUUGCGGUGC
.(((((....)))))(((((((.....))))))).((((((...)))))).((..(((((...((.(((...........))).)).)))))..))....(((((((......))))))) ( -36.20)
>Sfl_1 186 120 + 1
UGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCAUGGUAGCAAAGCUACCUUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCUAAUUGCGGUGC
.(((((....)))))(((((((.....))))))).((((((...)))))).((..(((((...((.(((...........))).)).)))))..))....(((((((......))))))) ( -36.20)
>Sty_1 186 120 + 1
UGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCACGGUAGCGAGACUACCCUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCAUAUUGCGGUGC
.(((((....)))))(((((((.....))))))).(((((.....)))))...............((((((...(((((......)))).)...))))))(((((((......))))))) ( -33.80)
>consensus
UGUUGUGUUUGCAAUUGGUCUGCGAUUCAGACCAUGGUAGCAAAGCUACCUUUUUUCACUUCCUGUACAUUUACCCUGUCUGUCCAUAGUGAUUAAUGUAGCACCGCCUAAUUGCGGUGC
.(((((....)))))(((((((.....))))))).(((((.....)))))...............((((((...(((((......)))).)...))))))(((((((......))))))) (-34.80 = -34.80 +   0.00)

alignment

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secondary structure

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dotplot

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Window 1

Location 2,940,796 – 2,940,916
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 96.11
Mean single sequence MFE -41.93
Consensus MFE -42.05
Energy contribution -41.83
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -4.56
Structure conservation index 1.00
SVM decision value 2.14
SVM RNA-class probability 0.988957
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 2940796 120 - 1
GCACCGCAAUUAGGCGGUGCUACAUUAAUCACUAUGGACAGACAGGGUAAAUGUACAGGAAGUGAAAAAAGGUAGCUUUGCUACCAUGGUCUGAAUCGCAGACCAAUUGCAAACACAACA
(((((((......)))))))((((((.(((....((......)).))).))))))......(((......((((((...)))))).(((((((.....)))))))........))).... ( -42.40)
>Sfl_1 186 120 - 1
GCACCGCAAUUAGGCGGUGCUACAUUAAUCACUAUGGACAGACAGGGUAAAUGUACAGGAAGUGAAAAAAGGUAGCUUUGCUACCAUGGUCUGAAUCGCAGACCAAUUGCAAACACAACA
(((((((......)))))))((((((.(((....((......)).))).))))))......(((......((((((...)))))).(((((((.....)))))))........))).... ( -42.40)
>Sty_1 186 120 - 1
GCACCGCAAUAUGGCGGUGCUACAUUAAUCACUAUGGACAGACAGGGUAAAUGUACAGGAAGUGAAAAAGGGUAGUCUCGCUACCGUGGUCUGAAUCGCAGACCAAUUGCAAACACAACA
(((((((......)))))))((((((.(((....((......)).))).))))))......(((......(((((.....))))).(((((((.....)))))))........))).... ( -41.00)
>consensus
GCACCGCAAUUAGGCGGUGCUACAUUAAUCACUAUGGACAGACAGGGUAAAUGUACAGGAAGUGAAAAAAGGUAGCUUUGCUACCAUGGUCUGAAUCGCAGACCAAUUGCAAACACAACA
(((((((......)))))))((((((.(((....((......)).))).))))))......(((......((((((...)))))).(((((((.....)))))))........))).... (-42.05 = -41.83 +  -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 11:04:37 2006