Locus 3303

Sequence ID 3L_DroMel_CAF1
Location 9,682,716 – 9,682,880
Length 164
Max. P 0.983407
window5138 window5139 window5140

overview

Window 8

Location 9,682,716 – 9,682,821
Length 105
Sequences 6
Columns 105
Reading direction forward
Mean pairwise identity 93.59
Mean single sequence MFE -35.54
Consensus MFE -30.81
Energy contribution -30.62
Covariance contribution -0.19
Combinations/Pair 1.15
Mean z-score -2.45
Structure conservation index 0.87
SVM decision value 1.94
SVM RNA-class probability 0.983407
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9682716 105 + 23771897
AAUAGUAGCAAUAAAUUUUGUUAUCCAACGGCAGCGGCCAUGGAGAAUAUGUUCCAGAACAAUCAGAUGGCGGCCGCUGCCGCCGCACGCGAAUCCCUGCUGAAU
.....(((((......(((((.......(((((((((((.(((((......)))))((....)).......)))))))))))......)))))....)))))... ( -36.42)
>DroSec_CAF1 4419 105 + 1
AAUAGUAGCAAUAAAUUUUGUUAUCCAACGGCGGCGGCCAUGGAGAAUAUGUUCCAGAACAAUCACAUGGCAGCCGCUGCCGCCGCACGCGAAUCCCUGCUGAAU
..((((((....................(((((((.((((((((.....((((....)))).)).)))))).))))))).(((.....))).....))))))... ( -34.80)
>DroSim_CAF1 1661 105 + 1
AAUAGUAGCAAUAAAUUUUGUUAUCCAACGGCGGCGGCCAUGGAGAAUAUGUUCCAGAACAAUCAGAUGGCAGCCGCUGCCGCCGCACGCGAAUCCCUGCUGAAU
..((((((....................(((((((.(((((((((......)))).((....))..))))).))))))).(((.....))).....))))))... ( -32.20)
>DroEre_CAF1 4194 105 + 1
AAUAGUAGCAAUAAAUUUUGUUAUCCUACGGCGGCAGCCAUGGAGAAUAUGUUCCAAAACAAUCAGAUGGCGGCCGCUGCCGCCGCACGCGAAUCCCUGCUGAAU
....(((((((......)))))))....((((((((((..(((((......)))))............((...))))))))))))((.(((......)))))... ( -32.40)
>DroYak_CAF1 1671 105 + 1
AAUAGUAGCAAUAAAUUUUGUUAUCCUACGGCGGCGGCCAUGGAGAAUAUGUUCCAAAACAAUCAAAUGGCGGCCGCUGCCGCCGCACGCGAAUCCCUGCUAAAU
.....(((((......(((((.......(((((((((((.(((((......)))))...((......))..)))))))))))......)))))....)))))... ( -35.82)
>DroAna_CAF1 4150 105 + 1
AAUAGCAGCAACAAGUAUUGUUAUCCCACGGCGGCGGCCAUGGAGAACAUGUUCCAGAGCAAUCAGAUGGCAGCCGCCGCCGCCGCUCGCGAAUCGCUGCUCAAU
...((((((((((.....))))......(((((((.(((((((((......)))).((....))..))))).))))))).(((.....)))....)))))).... ( -41.60)
>consensus
AAUAGUAGCAAUAAAUUUUGUUAUCCAACGGCGGCGGCCAUGGAGAAUAUGUUCCAGAACAAUCAGAUGGCAGCCGCUGCCGCCGCACGCGAAUCCCUGCUGAAU
..((((((....................(((((((.(((((.((.....((((....)))).))..))))).))))))).(((.....))).....))))))... (-30.81 = -30.62 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 9

Location 9,682,716 – 9,682,821
Length 105
Sequences 6
Columns 105
Reading direction reverse
Mean pairwise identity 93.59
Mean single sequence MFE -36.70
Consensus MFE -30.93
Energy contribution -30.65
Covariance contribution -0.28
Combinations/Pair 1.08
Mean z-score -1.93
Structure conservation index 0.84
SVM decision value 0.54
SVM RNA-class probability 0.775387
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9682716 105 - 23771897
AUUCAGCAGGGAUUCGCGUGCGGCGGCAGCGGCCGCCAUCUGAUUGUUCUGGAACAUAUUCUCCAUGGCCGCUGCCGUUGGAUAACAAAAUUUAUUGCUACUAUU
....((((((((((...((.(((((((((((((((......((....))((((........))))))))))))))))))).)).....))))).)))))...... ( -39.50)
>DroSec_CAF1 4419 105 - 1
AUUCAGCAGGGAUUCGCGUGCGGCGGCAGCGGCUGCCAUGUGAUUGUUCUGGAACAUAUUCUCCAUGGCCGCCGCCGUUGGAUAACAAAAUUUAUUGCUACUAUU
....((((((((((...((.(((((((...(((.((((((.((.((((....))))...))..)))))).)))))))))).)).....))))).)))))...... ( -34.30)
>DroSim_CAF1 1661 105 - 1
AUUCAGCAGGGAUUCGCGUGCGGCGGCAGCGGCUGCCAUCUGAUUGUUCUGGAACAUAUUCUCCAUGGCCGCCGCCGUUGGAUAACAAAAUUUAUUGCUACUAUU
....((((((((((...((.(((((((.((((((.......((....))((((........)))).)))))).))))))).)).....))))).)))))...... ( -32.40)
>DroEre_CAF1 4194 105 - 1
AUUCAGCAGGGAUUCGCGUGCGGCGGCAGCGGCCGCCAUCUGAUUGUUUUGGAACAUAUUCUCCAUGGCUGCCGCCGUAGGAUAACAAAAUUUAUUGCUACUAUU
....((((((((((..(.((((((((((((((...))............((((........))))..)))))))))))).).......))))).)))))...... ( -34.70)
>DroYak_CAF1 1671 105 - 1
AUUUAGCAGGGAUUCGCGUGCGGCGGCAGCGGCCGCCAUUUGAUUGUUUUGGAACAUAUUCUCCAUGGCCGCCGCCGUAGGAUAACAAAAUUUAUUGCUACUAUU
...(((((((((((..(.(((((((((...(((((.((......))...((((........)))))))))))))))))).).......))))).))))))..... ( -34.00)
>DroAna_CAF1 4150 105 - 1
AUUGAGCAGCGAUUCGCGAGCGGCGGCGGCGGCUGCCAUCUGAUUGCUCUGGAACAUGUUCUCCAUGGCCGCCGCCGUGGGAUAACAAUACUUGUUGCUGCUAUU
....((((((..((((((.(((((((((((....)))............((((........))))..))))))))))))))..((((.....))))))))))... ( -45.30)
>consensus
AUUCAGCAGGGAUUCGCGUGCGGCGGCAGCGGCCGCCAUCUGAUUGUUCUGGAACAUAUUCUCCAUGGCCGCCGCCGUUGGAUAACAAAAUUUAUUGCUACUAUU
....(((((..(((((((.((((((((.((....)).............((((........))))..))))))))))).))))...........)))))...... (-30.93 = -30.65 +  -0.28)

alignment

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secondary structure

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dotplot

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Window 0

Location 9,682,781 – 9,682,880
Length 99
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 82.29
Mean single sequence MFE -35.90
Consensus MFE -24.70
Energy contribution -26.12
Covariance contribution 1.42
Combinations/Pair 1.19
Mean z-score -1.50
Structure conservation index 0.69
SVM decision value 0.02
SVM RNA-class probability 0.545916
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9682781 99 - 23771897
CAGUAGCUCUGCUCCGCCAUAUAAUUGCCGG---------CAUCGCUAUCCUUUUGAUAAAGAUAUGAAUUCAGCAGGGAUUCGCGUGCGGCGGCAGCGGCCGCCAUC
.....((.((((((((((.((....))...(---------((.(((.((((((((((.............)))).))))))..))))))))))).)))))..)).... ( -31.72)
>DroPse_CAF1 4740 108 - 1
CAGUAGCCUUGCUCAGACAUGUAGUUGGCGGCUGCCUCUGCGCCGCUCUCCUUCUGAUAGAGAUACGAAUUGAGCAGGGACUCGCGGGCGGCGGCGGCUGCCGCCAUC
..((((((((((((((...((((....(((((.((....)))))))((((.........))))))))..)))))))))).)).)).((((((((...))))))))... ( -47.10)
>DroSim_CAF1 1726 99 - 1
CAGUAGCUCUGCUCCGUCAUAUAAUUGCCGG---------CAUCGCUAUCCUUUUGAUAGAGAUAGGAAUUCAGCAGGGAUUCGCGUGCGGCGGCAGCGGCUGCCAUC
..((((((((((((((.(((...........---------.(((.(((((.....))))).)))..((((((.....))))))..)))))).))))).)))))).... ( -32.80)
>DroEre_CAF1 4259 99 - 1
CAAUAGCUCUGCUCCGACAUGUAAUUGCUGG---------CAUCGCUAUCUUUUUGAUAGAGAUAGGAAUUCAGCAGGGAUUCGCGUGCGGCGGCAGCGGCCGCCAUC
..........((.((((...((..(((((((---------..((.((((((((.....))))))))))..)))))))..))))).).))((((((....))))))... ( -36.70)
>DroYak_CAF1 1736 99 - 1
CAAUAGCUCUGCUCCGUCAUGUAGUUGCUGG---------CAUCGCUAUCUUUUUGAUAGAGAUAUGAAUUUAGCAGGGAUUCGCGUGCGGCGGCAGCGGCCGCCAUU
...((((.((((........))))..))))(---------((.((((((((((.....))))))).((((((.....))))))))))))((((((....))))))... ( -36.90)
>DroAna_CAF1 4215 90 - 1
CAGUAGCCCUGCUCCGACAUAUAA------------------UCUCCAUCCUUCUGAUACAGAUACGAAUUGAGCAGCGAUUCGCGAGCGGCGGCGGCGGCUGCCAUC
..((((((((((((((.(.....(------------------(((..(((.....)))..)))).(((((((.....)))))))...)))).))))).)))))).... ( -30.20)
>consensus
CAGUAGCUCUGCUCCGACAUAUAAUUGCCGG_________CAUCGCUAUCCUUUUGAUAGAGAUACGAAUUCAGCAGGGAUUCGCGUGCGGCGGCAGCGGCCGCCAUC
......((((((((((.((......)).)))..........(((.(((((.....))))).)))........)))))))..........((((((....))))))... (-24.70 = -26.12 +   1.42)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:54:24 2006