Locus 146

Sequence ID Banth.0
Location 3,091,538 – 3,091,643
Length 105
Max. P 0.999763
window959 window960 window961 window962 window963 window964

overview

Window 9

Location 3,091,538 – 3,091,643
Length 105
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 65.45
Mean single sequence MFE -36.47
Consensus MFE -17.39
Energy contribution -17.45
Covariance contribution 0.06
Combinations/Pair 1.34
Mean z-score -4.07
Structure conservation index 0.48
SVM decision value 3.65
SVM RNA-class probability 0.999489
Prediction RNA

Download alignment: ClustalW | MAF

>Banth.0 3091538 105 + 5227293/0-120
AAAAAACCUCUCCGAUAAGAAGAAGUUACGUAUAUAUCUUCGUCUUAUCUCCCAGAACAAAUUUGUUCUGCUGGAAUUAGCACCUGCAUC-GC--------------GGUUGCUGGGUUU
...(((((..((((((((((.((((.((......)).)))).)))))))...(((((((....)))))))..)))..(((((.((((...-))--------------)).)))))))))) ( -34.30)
>Bcere.0 3108512 105 + 5224283/0-120
AAAAAACCUCUCCGAUAAGAAGAAGUUACGUAUAUAUCUUCGUCUUAUCUCCCAGAACAAAUAUGUUCUGCUGGAAUUAGCACCUGCAUC-GC--------------GGUUGCUGGGUUU
...(((((..((((((((((.((((.((......)).)))).)))))))...(((((((....)))))))..)))..(((((.((((...-))--------------)).)))))))))) ( -34.30)
>Bhalo.0 2853388 114 - 4202352/0-120
AAAAAACCUUUCCGAUAAGGAAAGGUU-----UUCGCCUUCG-CUUAUCUUCCAGAAUGAAAUCAUUCUGCUGAAAUUAGCACCUUCGUUUGCUUGGCUAACAAACGGGUUGCCGGGCAU
..(((((((((((.....)))))))))-----)).......(-((..((...(((((((....)))))))..))....))).........((((((((.(((......))))))))))). ( -40.00)
>Bclau.0 3352324 104 - 4303871/0-120
AAAGAAGCU-----GCGAAAAUCCGUU---UCCGUUUUUCCGGCUUAUCUUUCAGAAUGAUCCCAUUCUGCAGGAAUUGGCACCUUCCCC-GU-------AACGGGAGGUUGCUGGACGU
....(((((-----(.(((((..((..---..)).))))))))))).((((.(((((((....))))))).)))).(..(((.((((((.-..-------...)))))).)))..).... ( -37.30)
>consensus
AAAAAACCUCUCCGAUAAGAAGAAGUU___UAUAUAUCUUCGUCUUAUCUCCCAGAACAAAUUCAUUCUGCUGGAAUUAGCACCUGCAUC_GC______________GGUUGCUGGGCUU
.............(((((((.((((............)))).)))))))((((((((((....)))))))..))).((((((((.......................)).)))))).... (-17.39 = -17.45 +   0.06)

alignment

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secondary structure

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Window 0

Location 3,091,538 – 3,091,643
Length 105
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 65.45
Mean single sequence MFE -36.42
Consensus MFE -16.38
Energy contribution -17.00
Covariance contribution 0.62
Combinations/Pair 1.27
Mean z-score -3.66
Structure conservation index 0.45
SVM decision value 3.26
SVM RNA-class probability 0.998879
Prediction RNA

Download alignment: ClustalW | MAF

>Banth.0 3091538 105 + 5227293/0-120
AAACCCAGCAACC--------------GC-GAUGCAGGUGCUAAUUCCAGCAGAACAAAUUUGUUCUGGGAGAUAAGACGAAGAUAUAUACGUAACUUCUUCUUAUCGGAGAGGUUUUUU
(((((.((((.((--------------..-......))))))..((((..(((((((....)))))))...(((((((.((((.(((....))).)))).))))))))))).)))))... ( -34.70)
>Bcere.0 3108512 105 + 5224283/0-120
AAACCCAGCAACC--------------GC-GAUGCAGGUGCUAAUUCCAGCAGAACAUAUUUGUUCUGGGAGAUAAGACGAAGAUAUAUACGUAACUUCUUCUUAUCGGAGAGGUUUUUU
(((((.((((.((--------------..-......))))))..((((..(((((((....)))))))...(((((((.((((.(((....))).)))).))))))))))).)))))... ( -35.50)
>Bhalo.0 2853388 114 - 4202352/0-120
AUGCCCGGCAACCCGUUUGUUAGCCAAGCAAACGAAGGUGCUAAUUUCAGCAGAAUGAUUUCAUUCUGGAAGAUAAG-CGAAGGCGAA-----AACCUUUCCUUAUCGGAAAGGUUUUUU
..(((.....(((((((((((.....))))))))..)))(((.((((...(((((((....)))))))..)))).))-)...)))(((-----(((((((((.....)))))))))))). ( -42.00)
>Bclau.0 3352324 104 - 4303871/0-120
ACGUCCAGCAACCUCCCGUU-------AC-GGGGAAGGUGCCAAUUCCUGCAGAAUGGGAUCAUUCUGAAAGAUAAGCCGGAAAAACGGA---AACGGAUUUUCGC-----AGCUUCUUU
.......(((.((((((...-------..-.))).)))))).........(((((((....)))))))(((((..(((((((((..((..---..))..)))))).-----.)))))))) ( -33.50)
>consensus
AAACCCAGCAACC______________GC_GAUGAAGGUGCUAAUUCCAGCAGAACAAAUUCAUUCUGGAAGAUAAGACGAAGAUAUAUA___AACUUCUUCUUAUCGGAGAGGUUUUUU
......((((.((.......................))))))..((((..(((((((....))))))))))).....................(((((((((.....))))))))).... (-16.38 = -17.00 +   0.62)

alignment

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secondary structure

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dotplot

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Window 1

Location 3,091,538 – 3,091,642
Length 104
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 71.57
Mean single sequence MFE -34.33
Consensus MFE -25.38
Energy contribution -23.00
Covariance contribution -2.38
Combinations/Pair 1.30
Mean z-score -2.52
Structure conservation index 0.74
SVM decision value 4.03
SVM RNA-class probability 0.999763
Prediction RNA

Download alignment: ClustalW | MAF

>Banth.0 3091538 104 + 5227293/40-160
CGUCUUAUCUCCCAGAACAAAUUUGUUCUGCUGGAAUUAGCACCUGCAUC-GC--------------GGUUGCUGGGUUUCAUCGGGCC-AGUCCCUCCACCUCUCUGGAUAAGAAAAUA
..((((((((..(((((((....))))))).((((.((((((.((((...-))--------------)).))))))........(((..-...))))))).......))))))))..... ( -31.70)
>Bcere.0 3108512 104 + 5224283/40-160
CGUCUUAUCUCCCAGAACAAAUAUGUUCUGCUGGAAUUAGCACCUGCAUC-GC--------------GGUUGCUGGGUUUCAUCGGGCC-AGUCCCUCCACCUCUCUGGAUAAGAAAAUA
..((((((((..(((((((....))))))).((((.((((((.((((...-))--------------)).))))))........(((..-...))))))).......))))))))..... ( -31.70)
>Bhalo.0 2853388 116 - 4202352/40-160
CG-CUUAUCUUCCAGAAUGAAAUCAUUCUGCUGAAAUUAGCACCUUCGUUUGCUUGGCUAACAAACGGGUUGCCGGGCAUCAUCGGGUC-AGUCCCUCUGCCUCUCUCGAUAAGUC--UU
.(-((((((((((((((((....)))))))..)))....(((........((((((((.(((......))))))))))).....(((..-...)))..))).......))))))).--.. ( -35.10)
>Bclau.0 3352324 112 - 4303871/40-160
CGGCUUAUCUUUCAGAAUGAUCCCAUUCUGCAGGAAUUGGCACCUUCCCC-GU-------AACGGGAGGUUGCUGGACGUCAUUGGGCCUAAUCCCUCAGUCGCUCUUGAUAAGUCCUUU
.((((((((...(((((((....))))))).((((.(..(((.((((((.-..-------...)))))).)))..)..((.((((((........)))))).)))))))))))))).... ( -38.80)
>consensus
CGUCUUAUCUCCCAGAACAAAUUCAUUCUGCUGGAAUUAGCACCUGCAUC_GC______________GGUUGCUGGGCUUCAUCGGGCC_AGUCCCUCCACCUCUCUGGAUAAGAAAAUA
..(((((((((((((((((....)))))))..)))..(((((((.......................)).)))))(((......(((......)))...)))......)))))))..... (-25.38 = -23.00 +  -2.38)

alignment

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secondary structure

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dotplot

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Window 2

Location 3,091,538 – 3,091,642
Length 104
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 71.57
Mean single sequence MFE -34.88
Consensus MFE -24.08
Energy contribution -22.32
Covariance contribution -1.75
Combinations/Pair 1.19
Mean z-score -1.87
Structure conservation index 0.69
SVM decision value 2.02
SVM RNA-class probability 0.985691
Prediction RNA

Download alignment: ClustalW | MAF

>Banth.0 3091538 104 + 5227293/40-160
UAUUUUCUUAUCCAGAGAGGUGGAGGGACU-GGCCCGAUGAAACCCAGCAACC--------------GC-GAUGCAGGUGCUAAUUCCAGCAGAACAAAUUUGUUCUGGGAGAUAAGACG
.....((((((((.......(((((((...-..)))..........((((.((--------------..-......))))))...)))).(((((((....))))))).).))))))).. ( -29.80)
>Bcere.0 3108512 104 + 5224283/40-160
UAUUUUCUUAUCCAGAGAGGUGGAGGGACU-GGCCCGAUGAAACCCAGCAACC--------------GC-GAUGCAGGUGCUAAUUCCAGCAGAACAUAUUUGUUCUGGGAGAUAAGACG
.....((((((((.......(((((((...-..)))..........((((.((--------------..-......))))))...)))).(((((((....))))))).).))))))).. ( -30.60)
>Bhalo.0 2853388 116 - 4202352/40-160
AA--GACUUAUCGAGAGAGGCAGAGGGACU-GACCCGAUGAUGCCCGGCAACCCGUUUGUUAGCCAAGCAAACGAAGGUGCUAAUUUCAGCAGAAUGAUUUCAUUCUGGAAGAUAAG-CG
..--(.(((((((((((.((((..(((...-..))).....)))))((((.((((((((((.....))))))))..))))))..))))..(((((((....)))))))...))))))-). ( -41.20)
>Bclau.0 3352324 112 - 4303871/40-160
AAAGGACUUAUCAAGAGCGACUGAGGGAUUAGGCCCAAUGACGUCCAGCAACCUCCCGUU-------AC-GGGGAAGGUGCCAAUUCCUGCAGAAUGGGAUCAUUCUGAAAGAUAAGCCG
...((.((((((...........(((((((.(((((..((.(.....)))...((((...-------..-.)))).)).)))))))))).(((((((....)))))))...)))))))). ( -37.90)
>consensus
AAUUGACUUAUCCAGAGAGGCGGAGGGACU_GGCCCGAUGAAACCCAGCAACC______________GC_GAUGAAGGUGCUAAUUCCAGCAGAACAAAUUCAUUCUGGAAGAUAAGACG
......((((((....(.(((...(((......)))......))))((((.((.......................))))))........(((((((....)))))))...))))))... (-24.08 = -22.32 +  -1.75)

alignment

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secondary structure

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dotplot

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Window 3

Location 3,091,538 – 3,091,642
Length 104
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 71.72
Mean single sequence MFE -30.53
Consensus MFE -21.62
Energy contribution -19.25
Covariance contribution -2.38
Combinations/Pair 1.29
Mean z-score -2.00
Structure conservation index 0.71
SVM decision value 2.47
SVM RNA-class probability 0.994341
Prediction RNA

Download alignment: ClustalW | MAF

>Banth.0 3091538 104 + 5227293/44-164
UUAUCUCCCAGAACAAAUUUGUUCUGCUGGAAUUAGCACCUGCAUC-GC--------------GGUUGCUGGGUUUCAUCGGGCC-AGUCCCUCCACCUCUCUGGAUAAGAAAAUAUUCA
...(((..(((((((....)))))))..))).((((((.((((...-))--------------)).)))))).((((...(((..-...)))((((......))))...))))....... ( -27.60)
>Bcere.0 3108512 104 + 5224283/44-164
UUAUCUCCCAGAACAAAUAUGUUCUGCUGGAAUUAGCACCUGCAUC-GC--------------GGUUGCUGGGUUUCAUCGGGCC-AGUCCCUCCACCUCUCUGGAUAAGAAAAUAUUCA
...(((..(((((((....)))))))..))).((((((.((((...-))--------------)).)))))).((((...(((..-...)))((((......))))...))))....... ( -27.60)
>Bhalo.0 2853388 117 - 4202352/44-164
UUAUCUUCCAGAAUGAAAUCAUUCUGCUGAAAUUAGCACCUUCGUUUGCUUGGCUAACAAACGGGUUGCCGGGCAUCAUCGGGUC-AGUCCCUCUGCCUCUCUCGAUAAGUC--UUUUUA
(((((((((((((((....)))))))..)))....(((........((((((((.(((......))))))))))).....(((..-...)))..))).......)))))...--...... ( -30.90)
>Bclau.0 3352324 112 - 4303871/44-164
UUAUCUUUCAGAAUGAUCCCAUUCUGCAGGAAUUGGCACCUUCCCC-GU-------AACGGGAGGUUGCUGGACGUCAUUGGGCCUAAUCCCUCAGUCGCUCUUGAUAAGUCCUUUUUUA
...((((.(((((((....))))))).))))...((((.((((((.-..-------...)))))).))))((((((((..((((..............)))).))))..))))....... ( -36.04)
>consensus
UUAUCUCCCAGAACAAAUUCAUUCUGCUGGAAUUAGCACCUGCAUC_GC______________GGUUGCUGGGCUUCAUCGGGCC_AGUCCCUCCACCUCUCUGGAUAAGAAAAUAUUCA
(((((((((((((((....)))))))..)))..(((((((.......................)).)))))(((......(((......)))...)))......)))))........... (-21.62 = -19.25 +  -2.38)

alignment

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secondary structure

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dotplot

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Window 4

Location 3,091,538 – 3,091,642
Length 104
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 71.72
Mean single sequence MFE -31.42
Consensus MFE -20.62
Energy contribution -18.88
Covariance contribution -1.75
Combinations/Pair 1.21
Mean z-score -1.50
Structure conservation index 0.66
SVM decision value 0.57
SVM RNA-class probability 0.786899
Prediction RNA

Download alignment: ClustalW | MAF

>Banth.0 3091538 104 + 5227293/44-164
UGAAUAUUUUCUUAUCCAGAGAGGUGGAGGGACU-GGCCCGAUGAAACCCAGCAACC--------------GC-GAUGCAGGUGCUAAUUCCAGCAGAACAAAUUUGUUCUGGGAGAUAA
....(((((((...((((......))))((((.(-(((((..((.....))(((...--------------..-..))).)).)))).))))..(((((((....)))))))))))))). ( -28.40)
>Bcere.0 3108512 104 + 5224283/44-164
UGAAUAUUUUCUUAUCCAGAGAGGUGGAGGGACU-GGCCCGAUGAAACCCAGCAACC--------------GC-GAUGCAGGUGCUAAUUCCAGCAGAACAUAUUUGUUCUGGGAGAUAA
....(((((((...((((......))))((((.(-(((((..((.....))(((...--------------..-..))).)).)))).))))..(((((((....)))))))))))))). ( -29.20)
>Bhalo.0 2853388 117 - 4202352/44-164
UAAAAA--GACUUAUCGAGAGAGGCAGAGGGACU-GACCCGAUGAUGCCCGGCAACCCGUUUGUUAGCCAAGCAAACGAAGGUGCUAAUUUCAGCAGAAUGAUUUCAUUCUGGAAGAUAA
......--....(((((((((.((((..(((...-..))).....)))))((((.((((((((((.....))))))))..))))))..))))..(((((((....)))))))...)))). ( -37.20)
>Bclau.0 3352324 112 - 4303871/44-164
UAAAAAAGGACUUAUCAAGAGCGACUGAGGGAUUAGGCCCAAUGACGUCCAGCAACCUCCCGUU-------AC-GGGGAAGGUGCCAAUUCCUGCAGAAUGGGAUCAUUCUGAAAGAUAA
.......((((...(((........)))(((......)))......)))).(((.((((((...-------..-.))).))))))....((...(((((((....)))))))...))... ( -30.90)
>consensus
UAAAAAUUGACUUAUCCAGAGAGGCGGAGGGACU_GGCCCGAUGAAACCCAGCAACC______________GC_GAUGAAGGUGCUAAUUCCAGCAGAACAAAUUCAUUCUGGAAGAUAA
............((((....(.(((...(((......)))......))))((((.((.......................))))))........(((((((....)))))))...)))). (-20.62 = -18.88 +  -1.75)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz $RNAz::rnazVersion) on Thu Apr 6 17:28:08 2006