Locus 78

Sequence ID Eco_1
Location 3,426,385 – 3,426,705
Length 320
Max. P 0.994367
window231 window232 window233 window234 window235 window236 window237 window238

overview

Window 1

Location 3,426,385 – 3,426,505
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 96.67
Mean single sequence MFE -50.07
Consensus MFE -51.17
Energy contribution -50.07
Covariance contribution -1.11
Combinations/Pair 1.08
Mean z-score -2.66
Structure conservation index 1.02
SVM decision value 2.29
SVM RNA-class probability 0.991840
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 3426385 120 - 1
GAUCCCUAGCUGGUCUGAGAGGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGC
..((((..(((((((.........)))))))(((.(((((.(((.....)))))))).((((....))))......)))))))...(((((...(((((....))))).)))))...... ( -51.20)
>Hin_1 41 120 - 1
GAUCUCUAGCUGGUCUGAGAGGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCGCAAUGGGGGGAACCCUGACGCAGCCAUGC
..((((..(((((((.........)))))))(((.(((((.(((.....)))))))).((((....))))......)))))))...(((((...(((((....))))).)))))...... ( -47.80)
>Sty_1 41 120 - 1
GAUCCCUAGCUGGUCUGAGAGGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGC
..((((..(((((((.........)))))))(((.(((((.(((.....)))))))).((((....))))......)))))))...(((((...(((((....))))).)))))...... ( -51.20)
>consensus
GAUCCCUAGCUGGUCUGAGAGGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGC
..((((..(((((((.........)))))))(((.(((((.(((.....)))))))).((((....))))......)))))))...(((((...(((((....))))).)))))...... (-51.17 = -50.07 +  -1.11)

alignment

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secondary structure

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dotplot

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Window 2

Location 3,426,425 – 3,426,545
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 93.89
Mean single sequence MFE -50.53
Consensus MFE -51.29
Energy contribution -49.97
Covariance contribution -1.33
Combinations/Pair 1.13
Mean z-score -2.67
Structure conservation index 1.02
SVM decision value 2.47
SVM RNA-class probability 0.994367
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 3426425 120 - 1
GGAUUAGCUUGUUGGUGGGGUAACGGCUCACCAAGGCGACGAUCCCUAGCUGGUCUGAGAGGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGG
(((((.(((..((((((((.......)))))))))))...)))))...(((((((.........)))))))(((.(((((.(((.....)))))))).((((....))))......))). ( -50.50)
>Hin_1 81 120 - 1
GGAUUAGGUAGUUGGUGGGGUAAAUGCCUACCAAGCCUGCGAUCUCUAGCUGGUCUGAGAGGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGG
(((((((((..((((((((.......))))))))))))..)))))...(((((((.........)))))))(((.(((((.(((.....)))))))).((((....))))......))). ( -49.70)
>Sty_1 81 120 - 1
GGAUUAGCUAGUUGGUGAGGUAACGGCUCACCAAGGCGACGAUCCCUAGCUGGUCUGAGAGGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGG
(((((.(((..((((((((.......)))))))))))...)))))...(((((((.........)))))))(((.(((((.(((.....)))))))).((((....))))......))). ( -51.40)
>consensus
GGAUUAGCUAGUUGGUGGGGUAACGGCUCACCAAGGCGACGAUCCCUAGCUGGUCUGAGAGGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGG
(((((.(((..((((((((.......)))))))))))...)))))...(((((((.........)))))))(((.(((((.(((.....)))))))).((((....))))......))). (-51.29 = -49.97 +  -1.33)

alignment

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secondary structure

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Window 3

Location 3,426,465 – 3,426,585
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 86.39
Mean single sequence MFE -43.70
Consensus MFE -36.70
Energy contribution -37.27
Covariance contribution 0.56
Combinations/Pair 1.11
Mean z-score -2.05
Structure conservation index 0.84
SVM decision value 0.59
SVM RNA-class probability 0.793593
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 3426465 120 + 1
UCCAGUGUGGCUGGUCAUCCUCUCAGACCAGCUAGGGAUCGUCGCCUUGGUGAGCCGUUACCCCACCAACAAGCUAAUCCCAUCUGGGCACAUCCGAUGGCAAGAGGCCCGAGGGUCCCC
.......(((((((((.........)))))))))((((((.(((((((((((...........))))............(((((.(((....))))))))...)))))..)).)))))). ( -45.40)
>Hin_1 121 120 + 1
UCCAGUGUGGCUGGUCAUCCUCUCAGACCAGCUAGAGAUCGCAGGCUUGGUAGGCAUUUACCCCACCAACUACCUAAUCCCACUUGGGCUCAUCCUAUGGCAUGCGGCCUCUCAGUCCCG
.......(((((((((.........)))))))))(((..((((.(((.(((((................)))))....(((....)))..........))).))))..)))......... ( -37.99)
>Sty_1 121 120 + 1
UCCAGUGUGGCUGGUCAUCCUCUCAGACCAGCUAGGGAUCGUCGCCUUGGUGAGCCGUUACCUCACCAACUAGCUAAUCCCAUCUGGGCACAUCUGAUGGCAAGAGGCCCGAAGGUCCCC
.......(((((((((.........)))))))))((((((.((((.((((((((.......))))))))...))...........((((...(((.......))).)))))).)))))). ( -47.70)
>consensus
UCCAGUGUGGCUGGUCAUCCUCUCAGACCAGCUAGGGAUCGUCGCCUUGGUGAGCCGUUACCCCACCAACUAGCUAAUCCCAUCUGGGCACAUCCGAUGGCAAGAGGCCCGAAGGUCCCC
(((((..(((((((((.........)))))))))(((((....((.((((((((.......))))))))...))..)))))..)))))...((((...(((.....)))...)))).... (-36.70 = -37.27 +   0.56)

alignment

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secondary structure

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dotplot

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Window 4

Location 3,426,465 – 3,426,585
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 86.39
Mean single sequence MFE -48.83
Consensus MFE -45.71
Energy contribution -45.17
Covariance contribution -0.55
Combinations/Pair 1.15
Mean z-score -1.75
Structure conservation index 0.94
SVM decision value 1.11
SVM RNA-class probability 0.917046
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 3426465 120 - 1
GGGGACCCUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUGGGAUUAGCUUGUUGGUGGGGUAACGGCUCACCAAGGCGACGAUCCCUAGCUGGUCUGAGAGGAUGACCAGCCACACUGGA
((((.((....))))))..(((((...))).))((((..((((((.(((..((((((((.......)))))))))))...))))))..(((((((.........)))))))....)))). ( -48.70)
>Hin_1 121 120 - 1
CGGGACUGAGAGGCCGCAUGCCAUAGGAUGAGCCCAAGUGGGAUUAGGUAGUUGGUGGGGUAAAUGCCUACCAAGCCUGCGAUCUCUAGCUGGUCUGAGAGGAUGACCAGCCACACUGGA
(((.....((((..(((((.((((.((......))..)))).)).((((..((((((((.......)))))))))))))))..)))).(((((((.........)))))))....))).. ( -45.70)
>Sty_1 121 120 - 1
GGGGACCUUCGGGCCUCUUGCCAUCAGAUGUGCCCAGAUGGGAUUAGCUAGUUGGUGAGGUAACGGCUCACCAAGGCGACGAUCCCUAGCUGGUCUGAGAGGAUGACCAGCCACACUGGA
((((.((....))))))......((((.((((.......((((((.(((..((((((((.......)))))))))))...))))))..(((((((.........))))))))))))))). ( -52.10)
>consensus
GGGGACCCUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUGGGAUUAGCUAGUUGGUGGGGUAACGGCUCACCAAGGCGACGAUCCCUAGCUGGUCUGAGAGGAUGACCAGCCACACUGGA
((((.((....))))))..(((((...))).))((((..((((((.(((..((((((((.......)))))))))))...))))))..(((((((.........)))))))....)))). (-45.71 = -45.17 +  -0.55)

alignment

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secondary structure

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dotplot

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Window 5

Location 3,426,505 – 3,426,625
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 81.11
Mean single sequence MFE -43.83
Consensus MFE -39.23
Energy contribution -36.47
Covariance contribution -2.77
Combinations/Pair 1.29
Mean z-score -1.66
Structure conservation index 0.90
SVM decision value 1.36
SVM RNA-class probability 0.946274
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 3426505 120 - 1
AACGGUAGCUAAUACCGCAUAACGUCGCAAGACCAAAGAGGGGGACCCUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUGGGAUUAGCUUGUUGGUGGGGUAACGGCUCACCAAGGCGAC
..((..(((((((..(((((..((..((((((((...(((((...))))).))..))))))...)).)))))(((....))))))))))(.((((((((.......)))))))).))).. ( -43.90)
>Hin_1 161 120 - 1
AACUGUCGCUAAUACCGCGUAUUAUCGGAAGAUGAAAGUGCGGGACUGAGAGGCCGCAUGCCAUAGGAUGAGCCCAAGUGGGAUUAGGUAGUUGGUGGGGUAAAUGCCUACCAAGCCUGC
..((((.((............(((((....)))))..((((((..((....)))))))))).))))......(((....)))..(((((..((((((((.......))))))))))))). ( -41.10)
>Sty_1 161 120 - 1
AACGGUGGCUAAUACCGCAUAACGUCGCAAGACCAAAGAGGGGGACCUUCGGGCCUCUUGCCAUCAGAUGUGCCCAGAUGGGAUUAGCUAGUUGGUGAGGUAACGGCUCACCAAGGCGAC
...(((((((..((((((.....(((....))).....((((((.((....))))))))))((((((..((.(((....)))....))...)))))).))))..))).))))........ ( -46.50)
>consensus
AACGGUAGCUAAUACCGCAUAACGUCGCAAGACCAAAGAGGGGGACCCUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUGGGAUUAGCUAGUUGGUGGGGUAACGGCUCACCAAGGCGAC
..((((.((..............(((....)))....((((((..((....)))))))))).))))......(((....)))....(((..((((((((.......)))))))))))... (-39.23 = -36.47 +  -2.77)

alignment

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secondary structure

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dotplot

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Window 6

Location 3,426,545 – 3,426,665
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 82.78
Mean single sequence MFE -36.40
Consensus MFE -27.86
Energy contribution -26.20
Covariance contribution -1.66
Combinations/Pair 1.22
Mean z-score -1.71
Structure conservation index 0.77
SVM decision value 0.24
SVM RNA-class probability 0.647085
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 3426545 120 + 1
CAUCUGGGCACAUCCGAUGGCAAGAGGCCCGAGGGUCCCCCUCUUUGGUCUUGCGACGUUAUGCGGUAUUAGCUACCGUUUCCAGUAGUUAUCCCCCUCCAUCAGGCAGUUUCCCAGACA
..((((((.((..(((((((...((((((.(((((...)))))...))))))((.((.....((((((.....)))))).....)).)).........))))).))..))..)))))).. ( -39.90)
>Hin_1 201 120 + 1
CACUUGGGCUCAUCCUAUGGCAUGCGGCCUCUCAGUCCCGCACUUUCAUCUUCCGAUAAUACGCGGUAUUAGCGACAGUUUCCCGUCGUUAUCCCCCUCCAUAAGCCAGAUUCCCAAGCA
..((((((...(((...((((.(((((..........)))))............(((((((((.((....(((....))).))))).))))))...........))))))).)))))).. ( -30.70)
>Sty_1 201 120 + 1
CAUCUGGGCACAUCUGAUGGCAAGAGGCCCGAAGGUCCCCCUCUUUGGUCUUGCGACGUUAUGCGGUAUUAGCCACCGUUUCCAGUAGUUAUCCCCCUCCAUCAGGCAGUUUCCCAGACA
..((((((.((.(((((((((((((...(((((((......))))))))))))).((.....(((((.......))))).....)).............)))))))..))..)))))).. ( -38.60)
>consensus
CAUCUGGGCACAUCCGAUGGCAAGAGGCCCGAAGGUCCCCCUCUUUGGUCUUGCGACGUUAUGCGGUAUUAGCCACCGUUUCCAGUAGUUAUCCCCCUCCAUCAGGCAGUUUCCCAGACA
..((((((.((..((((((((....((((....))))..........(((....))).....))((...(((((((........))))))).)).....)))).))..))..)))))).. (-27.86 = -26.20 +  -1.66)

alignment

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secondary structure

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dotplot

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Window 7

Location 3,426,545 – 3,426,665
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 82.78
Mean single sequence MFE -54.47
Consensus MFE -55.14
Energy contribution -50.60
Covariance contribution -4.54
Combinations/Pair 1.32
Mean z-score -4.94
Structure conservation index 1.01
SVM decision value 1.86
SVM RNA-class probability 0.980468
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 3426545 120 - 1
UGUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAUAACGUCGCAAGACCAAAGAGGGGGACCCUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUG
.(((((((..((...(((((((((((((....((((((....))))))......((.......(((....)))....(((((...))))))).)))))).)))))))..)).))))))). ( -55.30)
>Hin_1 201 120 - 1
UGCUUGGGAAUCUGGCUUAUGGAGGGGGAUAACGACGGGAAACUGUCGCUAAUACCGCGUAUUAUCGGAAGAUGAAAGUGCGGGACUGAGAGGCCGCAUGCCAUAGGAUGAGCCCAAGUG
.(((((((..((...(((((((.(.((..((.((((((....)))))).))...)).)...(((((....)))))..((((((..((....)))))))).)))))))..)).))))))). ( -52.40)
>Sty_1 201 120 - 1
UGUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUGGCUAAUACCGCAUAACGUCGCAAGACCAAAGAGGGGGACCUUCGGGCCUCUUGCCAUCAGAUGUGCCCAGAUG
.(((((((..((...(((((((((((((....((((((....))))))......(((......(((....)))....((((....))))))).)))))).)))))))..)).))))))). ( -55.70)
>consensus
UGUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAUAACGUCGCAAGACCAAAGAGGGGGACCCUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUG
.(((((((..((...(((((((.(.((..((.((((((....)))))).))...)).).....(((....)))....((((((..((....)))))))).)))))))..)).))))))). (-55.14 = -50.60 +  -4.54)

alignment

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secondary structure

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dotplot

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Window 8

Location 3,426,585 – 3,426,705
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 88.06
Mean single sequence MFE -38.17
Consensus MFE -35.80
Energy contribution -34.37
Covariance contribution -1.43
Combinations/Pair 1.23
Mean z-score -1.14
Structure conservation index 0.94
SVM decision value 0.03
SVM RNA-class probability 0.550710
Prediction RNA

Download alignment: ClustalW | MAF

>Eco_1 3426585 120 - 1
AGCUUGCUGUUUCGCUGACGAGUGGCGGACGGGUGAGUAAUGUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAUAACGUCGCAAGACCAAAGAG
..(((((.....((((.......))))((((.(((.(((.(((((((....)).(((......)))))))).((((((....))))))....))))))....)))))))))......... ( -39.20)
>Hin_1 241 120 - 1
AGCUUGCUUUCUUGCUGACGAGUGGCGGACGGGUGAGUAAUGCUUGGGAAUCUGGCUUAUGGAGGGGGAUAACGACGGGAAACUGUCGCUAAUACCGCGUAUUAUCGGAAGAUGAAAGUG
(((((((((.(((((((........))).)))).)))))).)))..........((((.....(.((..((.((((((....)))))).))...)).)...(((((....))))))))). ( -36.40)
>Sty_1 241 120 - 1
AGCUUGCUGCUUCGCUGACGAGUGGCGGACGGGUGAGUAAUGUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUGGCUAAUACCGCAUAACGUCGCAAGACCAAAGAG
..(((((.....((((.......))))((((.(((.(((.(((((((....)).(((......)))))))).((((((....))))))....))))))....)))))))))......... ( -38.90)
>consensus
AGCUUGCUGUUUCGCUGACGAGUGGCGGACGGGUGAGUAAUGUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAUAACGUCGCAAGACCAAAGAG
.(((..((..((((((.......))))))..))..))).((((..((....((.(((.....))).))....((((((....))))))......))))))...(((....)))....... (-35.80 = -34.37 +  -1.43)

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 11:05:27 2006