Locus 107

Sequence ID Eco_1
Location 4,177,798 – 4,178,019
Length 221
Max. P 0.993284
window373 window374 window375 window376 window377 window378 window379 window380

overview

Window 3

Location 4,177,798 – 4,177,918
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 95.56
Mean single sequence MFE -41.33
Consensus MFE -41.65
Energy contribution -41.10
Covariance contribution -0.55
Combinations/Pair 1.09
Mean z-score -2.80
Structure conservation index 1.01
SVM decision value 2.39
SVM RNA-class probability 0.993284
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 4177798 120 + 1
AAAGAUUUGUUCGUUGGAGCCUGGCCUAUCCAGGCCUCCGUCGAAGACCGCAGGAGUUUCGCAAGAAACUUAAUCCCCUGCGUAGACGGUGACAGAACGCUAAGAUUAUUCUUUUAUAUU
........((((...(((((((((.....))))).))))((((..(..((((((((((((....))))))......))))))....)..)))).))))...((((....))))....... ( -41.70)
>Sfl_1 1 120 + 1
AAAGAUUUGUUCGUUGGAGCCUGGCCUAUCCAGGCCUCCGUCGAAGACCGCAGGAGUUUCGCAAGAAACUUAAUCCCCUGCGUAGACGGUGACAGAACGCUAAGAUUAUUCUUUUAUAUU
........((((...(((((((((.....))))).))))((((..(..((((((((((((....))))))......))))))....)..)))).))))...((((....))))....... ( -41.70)
>Sty_1 1 119 + 1
AAGAAUUUGUUCGUUGGAGCCUGGCCUAUCCAGGCCUCCGUCGAAGACCGCAGGCGUCUCGCAAGAGGCUUAAUCCCCUGCGUAGACGGUGACAGAACGCUAAGAUUAUU-UUUUAUACU
........((((...(((((((((.....))))).))))((((..(..((((((.(((((....))))).......))))))....)..)))).))))............-......... ( -40.60)
>consensus
AAAGAUUUGUUCGUUGGAGCCUGGCCUAUCCAGGCCUCCGUCGAAGACCGCAGGAGUUUCGCAAGAAACUUAAUCCCCUGCGUAGACGGUGACAGAACGCUAAGAUUAUUCUUUUAUAUU
...(((((...(((((((((((((.....))))).))))((((..(..((((((((((((....))))))......))))))....)..))))..))))...)))))............. (-41.65 = -41.10 +  -0.55)

alignment

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secondary structure

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Window 4

Location 4,177,798 – 4,177,918
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 95.56
Mean single sequence MFE -39.43
Consensus MFE -37.24
Energy contribution -37.13
Covariance contribution -0.11
Combinations/Pair 1.07
Mean z-score -2.38
Structure conservation index 0.94
SVM decision value 1.32
SVM RNA-class probability 0.941455
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 4177798 120 - 1
AAUAUAAAAGAAUAAUCUUAGCGUUCUGUCACCGUCUACGCAGGGGAUUAAGUUUCUUGCGAAACUCCUGCGGUCUUCGACGGAGGCCUGGAUAGGCCAGGCUCCAACGAACAAAUCUUU
.......((((....))))...((((.....(((((..((((((((.((..((.....))..))))))))))......))))).(((((((.....))))))).....))))........ ( -38.50)
>Sfl_1 1 120 - 1
AAUAUAAAAGAAUAAUCUUAGCGUUCUGUCACCGUCUACGCAGGGGAUUAAGUUUCUUGCGAAACUCCUGCGGUCUUCGACGGAGGCCUGGAUAGGCCAGGCUCCAACGAACAAAUCUUU
.......((((....))))...((((.....(((((..((((((((.((..((.....))..))))))))))......))))).(((((((.....))))))).....))))........ ( -38.50)
>Sty_1 1 119 - 1
AGUAUAAAA-AAUAAUCUUAGCGUUCUGUCACCGUCUACGCAGGGGAUUAAGCCUCUUGCGAGACGCCUGCGGUCUUCGACGGAGGCCUGGAUAGGCCAGGCUCCAACGAACAAAUUCUU
.........-............((((.((((((((((.((((((((.......))))))))))))(....))))....)))((((.(((((.....)))))))))...))))........ ( -41.30)
>consensus
AAUAUAAAAGAAUAAUCUUAGCGUUCUGUCACCGUCUACGCAGGGGAUUAAGUUUCUUGCGAAACUCCUGCGGUCUUCGACGGAGGCCUGGAUAGGCCAGGCUCCAACGAACAAAUCUUU
......................((((.....(((((..((((((((.((..((.....))..))))))))))......))))).(((((((.....))))))).....))))........ (-37.24 = -37.13 +  -0.11)

alignment

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secondary structure

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Window 5

Location 4,177,838 – 4,177,958
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 94.44
Mean single sequence MFE -39.93
Consensus MFE -38.46
Energy contribution -38.13
Covariance contribution -0.33
Combinations/Pair 1.06
Mean z-score -3.65
Structure conservation index 0.96
SVM decision value 2.35
SVM RNA-class probability 0.992779
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 4177838 120 + 1
UCGAAGACCGCAGGAGUUUCGCAAGAAACUUAAUCCCCUGCGUAGACGGUGACAGAACGCUAAGAUUAUUCUUUUAUAUUCUGGCUUGUUUCUGCUCACCGUAAUUAAGACGCUCUCUCC
..(((((.((((((((((((....))))))......))))))...((((((((((((.((((.((.(((......))).))))))....))))).)))))))...........))).)). ( -38.90)
>Sfl_1 41 120 + 1
UCGAAGACCGCAGGAGUUUCGCAAGAAACUUAAUCCCCUGCGUAGACGGUGACAGAACGCUAAGAUUAUUCUUUUAUAUUCUGGCUUGUUUCUGCUCACCGUAAUUAAGACGCUCUCUCC
..(((((.((((((((((((....))))))......))))))...((((((((((((.((((.((.(((......))).))))))....))))).)))))))...........))).)). ( -38.90)
>Sty_1 41 118 + 1
UCGAAGACCGCAGGCGUCUCGCAAGAGGCUUAAUCCCCUGCGUAGACGGUGACAGAACGCUAAGAUUAUU-UUUUAUACUCUGGCUUGUUUCUGCUCACCGUA-UUAAGACGCUCUUCUC
..(((((.((((((.(((((....))))).......))))))...((((((((((((.((((.((.(((.-....))).))))))....))))).))))))).-.........))))).. ( -42.00)
>consensus
UCGAAGACCGCAGGAGUUUCGCAAGAAACUUAAUCCCCUGCGUAGACGGUGACAGAACGCUAAGAUUAUUCUUUUAUAUUCUGGCUUGUUUCUGCUCACCGUAAUUAAGACGCUCUCUCC
........((((((((((((....))))))......))))))...((((((((((((.((((.((.(((......))).))))))....))))).))))))).................. (-38.46 = -38.13 +  -0.33)

alignment

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secondary structure

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Window 6

Location 4,177,838 – 4,177,958
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 94.44
Mean single sequence MFE -40.73
Consensus MFE -37.06
Energy contribution -37.07
Covariance contribution 0.01
Combinations/Pair 1.08
Mean z-score -3.08
Structure conservation index 0.91
SVM decision value 1.69
SVM RNA-class probability 0.972238
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 4177838 120 - 1
GGAGAGAGCGUCUUAAUUACGGUGAGCAGAAACAAGCCAGAAUAUAAAAGAAUAAUCUUAGCGUUCUGUCACCGUCUACGCAGGGGAUUAAGUUUCUUGCGAAACUCCUGCGGUCUUCGA
(((((..((.........(((((((.(((((....((.(((.(((......))).)))..)).))))))))))))...((((((..((...))..))))))........))..))))).. ( -39.00)
>Sfl_1 41 120 - 1
GGAGAGAGCGUCUUAAUUACGGUGAGCAGAAACAAGCCAGAAUAUAAAAGAAUAAUCUUAGCGUUCUGUCACCGUCUACGCAGGGGAUUAAGUUUCUUGCGAAACUCCUGCGGUCUUCGA
(((((..((.........(((((((.(((((....((.(((.(((......))).)))..)).))))))))))))...((((((..((...))..))))))........))..))))).. ( -39.00)
>Sty_1 41 118 - 1
GAGAAGAGCGUCUUAA-UACGGUGAGCAGAAACAAGCCAGAGUAUAAAA-AAUAAUCUUAGCGUUCUGUCACCGUCUACGCAGGGGAUUAAGCCUCUUGCGAGACGCCUGCGGUCUUCGA
..(((((.(((.....-...(((((.(((((....((.(((.(((....-.))).)))..)).))))))))))((((.((((((((.......))))))))))))....))).))))).. ( -44.20)
>consensus
GGAGAGAGCGUCUUAAUUACGGUGAGCAGAAACAAGCCAGAAUAUAAAAGAAUAAUCUUAGCGUUCUGUCACCGUCUACGCAGGGGAUUAAGUUUCUUGCGAAACUCCUGCGGUCUUCGA
(((((..((.........(((((((.(((((....((.(((.(((......))).)))..)).))))))))))))...(((((((((.....)))))))))........))..))))).. (-37.06 = -37.07 +   0.01)

alignment

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secondary structure

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Window 7

Location 4,177,878 – 4,177,997
Length 119
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 90.53
Mean single sequence MFE -41.80
Consensus MFE -36.87
Energy contribution -36.77
Covariance contribution -0.11
Combinations/Pair 1.08
Mean z-score -3.43
Structure conservation index 0.88
SVM decision value 1.77
SVM RNA-class probability 0.976234
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 4177878 119 + 1
CGUAGACGGUGACAGAACGCUAAGAUUAUUCUUUUAUAUUCUGGCUUGUUUCUGCUCACCGUAAUUAAGACGCUCUCUCCGUUUGGAGGAGUGAAGUGAGUUCCAGAG-AUUUUCUCUGG
.....((((((((((((.((((.((.(((......))).))))))....))))).)))))))........(((((.((((....))))))))).........((((((-.....)))))) ( -42.30)
>Sfl_1 81 119 + 1
CGUAGACGGUGACAGAACGCUAAGAUUAUUCUUUUAUAUUCUGGCUUGUUUCUGCUCACCGUAAUUAAGACGCUCUCUCCGUUUGGAGGAGUGAAGUGAGUUCCAGAG-AUUUUCUCUGG
.....((((((((((((.((((.((.(((......))).))))))....))))).)))))))........(((((.((((....))))))))).........((((((-.....)))))) ( -42.30)
>Sty_1 81 118 + 1
CGUAGACGGUGACAGAACGCUAAGAUUAUU-UUUUAUACUCUGGCUUGUUUCUGCUCACCGUA-UUAAGACGCUCUUCUCGUUGAGAUGAGUGAAGUGAGUUCCGGAACAUGAGUUCCGG
.....((((((((((((.((((.((.(((.-....))).))))))....))))).))))))).-......(((((.((((...)))).))))).........(((((((....))))))) ( -40.80)
>consensus
CGUAGACGGUGACAGAACGCUAAGAUUAUUCUUUUAUAUUCUGGCUUGUUUCUGCUCACCGUAAUUAAGACGCUCUCUCCGUUUGGAGGAGUGAAGUGAGUUCCAGAG_AUUUUCUCUGG
.....((((((((((((.((((.((.(((......))).))))))....))))).)))))))........(((((.((((....))))))))).........((((((......)))))) (-36.87 = -36.77 +  -0.11)

alignment

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secondary structure

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Window 8

Location 4,177,878 – 4,177,997
Length 119
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 90.53
Mean single sequence MFE -37.00
Consensus MFE -32.96
Energy contribution -32.30
Covariance contribution -0.66
Combinations/Pair 1.12
Mean z-score -4.04
Structure conservation index 0.89
SVM decision value 1.80
SVM RNA-class probability 0.977664
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 4177878 119 - 1
CCAGAGAAAAU-CUCUGGAACUCACUUCACUCCUCCAAACGGAGAGAGCGUCUUAAUUACGGUGAGCAGAAACAAGCCAGAAUAUAAAAGAAUAAUCUUAGCGUUCUGUCACCGUCUACG
((((((.....-)))))).........(.(((((((....)))).))).)........(((((((.(((((....((.(((.(((......))).)))..)).))))))))))))..... ( -37.30)
>Sfl_1 81 119 - 1
CCAGAGAAAAU-CUCUGGAACUCACUUCACUCCUCCAAACGGAGAGAGCGUCUUAAUUACGGUGAGCAGAAACAAGCCAGAAUAUAAAAGAAUAAUCUUAGCGUUCUGUCACCGUCUACG
((((((.....-)))))).........(.(((((((....)))).))).)........(((((((.(((((....((.(((.(((......))).)))..)).))))))))))))..... ( -37.30)
>Sty_1 81 118 - 1
CCGGAACUCAUGUUCCGGAACUCACUUCACUCAUCUCAACGAGAAGAGCGUCUUAA-UACGGUGAGCAGAAACAAGCCAGAGUAUAAAA-AAUAAUCUUAGCGUUCUGUCACCGUCUACG
(((((((....))))))).........(.(((.((((...)))).))).)......-.(((((((.(((((....((.(((.(((....-.))).)))..)).))))))))))))..... ( -36.40)
>consensus
CCAGAGAAAAU_CUCUGGAACUCACUUCACUCCUCCAAACGGAGAGAGCGUCUUAAUUACGGUGAGCAGAAACAAGCCAGAAUAUAAAAGAAUAAUCUUAGCGUUCUGUCACCGUCUACG
((((((......)))))).........(.(((((((....)))).))).)........(((((((.(((((....((.(((.(((......))).)))..)).))))))))))))..... (-32.96 = -32.30 +  -0.66)

alignment

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secondary structure

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dotplot

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Window 9

Location 4,177,900 – 4,178,019
Length 119
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 90.53
Mean single sequence MFE -39.90
Consensus MFE -35.07
Energy contribution -34.97
Covariance contribution -0.11
Combinations/Pair 1.08
Mean z-score -3.59
Structure conservation index 0.88
SVM decision value 1.77
SVM RNA-class probability 0.976221
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 4177900 119 + 1
AGAUUAUUCUUUUAUAUUCUGGCUUGUUUCUGCUCACCGUAAUUAAGACGCUCUCUCCGUUUGGAGGAGUGAAGUGAGUUCCAGAG-AUUUUCUCUGGCAAACAUCCAGGAGCAAAGCUA
(((.(((......))).)))((((((((((((((((((........).(((((.((((....)))))))))..)))))..((((((-.....))))))........))))))).))))). ( -40.50)
>Sfl_1 103 119 + 1
AGAUUAUUCUUUUAUAUUCUGGCUUGUUUCUGCUCACCGUAAUUAAGACGCUCUCUCCGUUUGGAGGAGUGAAGUGAGUUCCAGAG-AUUUUCUCUGGCAAACAUCCAGGAGCAAAGCUA
(((.(((......))).)))((((((((((((((((((........).(((((.((((....)))))))))..)))))..((((((-.....))))))........))))))).))))). ( -40.50)
>Sty_1 103 118 + 1
AGAUUAUU-UUUUAUACUCUGGCUUGUUUCUGCUCACCGUA-UUAAGACGCUCUUCUCGUUGAGAUGAGUGAAGUGAGUUCCGGAACAUGAGUUCCGGCAAACAUCCAGGAGCAAAGCUA
(((.(((.-....))).)))((((((((((((((((((...-....).(((((.((((...)))).)))))..)))))..(((((((....)))))))........))))))).))))). ( -38.70)
>consensus
AGAUUAUUCUUUUAUAUUCUGGCUUGUUUCUGCUCACCGUAAUUAAGACGCUCUCUCCGUUUGGAGGAGUGAAGUGAGUUCCAGAG_AUUUUCUCUGGCAAACAUCCAGGAGCAAAGCUA
(((.(((......))).)))((((((((((((((((((........).(((((.((((....)))))))))..)))))..((((((......))))))........))))))).))))). (-35.07 = -34.97 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 0

Location 4,177,900 – 4,178,019
Length 119
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 90.53
Mean single sequence MFE -34.93
Consensus MFE -29.16
Energy contribution -28.50
Covariance contribution -0.66
Combinations/Pair 1.13
Mean z-score -3.13
Structure conservation index 0.83
SVM decision value 1.27
SVM RNA-class probability 0.938591
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 4177900 119 - 1
UAGCUUUGCUCCUGGAUGUUUGCCAGAGAAAAU-CUCUGGAACUCACUUCACUCCUCCAAACGGAGAGAGCGUCUUAAUUACGGUGAGCAGAAACAAGCCAGAAUAUAAAAGAAUAAUCU
...((((....((((.(((((.((((((.....-))))))..(((((....(((((((....)))).)))(((.......))))))))...)))))..))))......))))........ ( -34.20)
>Sfl_1 103 119 - 1
UAGCUUUGCUCCUGGAUGUUUGCCAGAGAAAAU-CUCUGGAACUCACUUCACUCCUCCAAACGGAGAGAGCGUCUUAAUUACGGUGAGCAGAAACAAGCCAGAAUAUAAAAGAAUAAUCU
...((((....((((.(((((.((((((.....-))))))..(((((....(((((((....)))).)))(((.......))))))))...)))))..))))......))))........ ( -34.20)
>Sty_1 103 118 - 1
UAGCUUUGCUCCUGGAUGUUUGCCGGAACUCAUGUUCCGGAACUCACUUCACUCAUCUCAACGAGAAGAGCGUCUUAA-UACGGUGAGCAGAAACAAGCCAGAGUAUAAAA-AAUAAUCU
......(((((.(((.(((((.(((((((....)))))))..(((((....(((.((((...)))).)))(((.....-.))))))))...)))))..)))))))).....-........ ( -36.40)
>consensus
UAGCUUUGCUCCUGGAUGUUUGCCAGAGAAAAU_CUCUGGAACUCACUUCACUCCUCCAAACGGAGAGAGCGUCUUAAUUACGGUGAGCAGAAACAAGCCAGAAUAUAAAAGAAUAAUCU
...........((((.(((((.((((((......))))))..(((((....(((((((....)))).)))(((.......))))))))...)))))..)))).................. (-29.16 = -28.50 +  -0.66)

alignment

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secondary structure

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Generated by rnazCluster.pl (part of RNAz 1.0) on Fri Dec 1 11:07:31 2006