Locus 5195

Sequence ID X_DroMel_CAF1
Location 13,561,512 – 13,561,633
Length 121
Max. P 0.968933
window8423 window8424 window8425

overview

Window 3

Location 13,561,512 – 13,561,616
Length 104
Sequences 4
Columns 106
Reading direction reverse
Mean pairwise identity 86.59
Mean single sequence MFE -22.09
Consensus MFE -15.02
Energy contribution -16.52
Covariance contribution 1.50
Combinations/Pair 1.17
Mean z-score -1.72
Structure conservation index 0.68
SVM decision value 0.19
SVM RNA-class probability 0.624966
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13561512 104 - 22224390
CCAAUUGCGGCUUAAAACAUGAAG--AAAGCUGCAAAAAAUCGAAAAUGAAUAUGAGAAACAGAUCAACUGGCAACCAGAAUGCCAUGCGAUGCAGAUCGAUUCCU
....(((((((((...........--.)))))))))....................(((...((((...(((((.......)))))(((...)))))))..))).. ( -22.20)
>DroSec_CAF1 16435 106 - 1
CCAAUUGCGGCUUAAAACAUGAAGAGAAAGCUGCAAAGAAUCGGAAAUGAAUAUGAGAAAGAGAUCAACUGGCAAUCAGAAUGCCAUGCGAUGCAGAUCGAUUCCU
....(((((((((..............))))))))).(((((((...((....(((........)))..(((((.......))))).......))..))))))).. ( -24.54)
>DroSim_CAF1 8868 106 - 1
CCAAUUGCGGCUUAAAACAUGAAGAGAAAGCUGCAAAGAAUCGGAAAUGAAUUUGAGAAACAGAUCAACUGGCAAUCAGAAUGCCAUGCGAUGCAGAUCGAUUCCU
....(((((((((..............))))))))).(((((((...(((.((((.....)))))))..(((((.......)))))...........))))))).. ( -25.64)
>DroYak_CAF1 16246 101 - 1
CCAAUUGCGGCUUAAAACAUGAAG--AAAGCUACAAAAGG---UAAAGAAAUAUGCAAAAAUUAUCAACUGCAAAUCAGAAUCCAAUGCAAUGCAGUUCGAUUUCU
((..(((..((((...........--.))))..)))..))---....................((((((((((...((........))...))))))).))).... ( -16.00)
>consensus
CCAAUUGCGGCUUAAAACAUGAAG__AAAGCUGCAAAAAAUCGGAAAUGAAUAUGAGAAACAGAUCAACUGGCAAUCAGAAUGCCAUGCGAUGCAGAUCGAUUCCU
....(((((((((..............))))))))).(((((((.........................(((((.......)))))(((...)))..))))))).. (-15.02 = -16.52 +   1.50)

alignment

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secondary structure

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dotplot

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Window 4

Location 13,561,542 – 13,561,633
Length 91
Sequences 4
Columns 93
Reading direction forward
Mean pairwise identity 87.41
Mean single sequence MFE -19.45
Consensus MFE -16.17
Energy contribution -15.92
Covariance contribution -0.25
Combinations/Pair 1.18
Mean z-score -1.76
Structure conservation index 0.83
SVM decision value 0.65
SVM RNA-class probability 0.810076
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13561542 91 + 22224390
GUUGCCAGUUGAUCUGUUUCUCAUAUUCAUUUUCGAUUUUUUGCAGCUUU--CUUCAUGUUUUAAGCCGCAAUUGGCAGACUGGCGGCAUUUU
((((((((....((((((........((......))....((((.((((.--...........)))).))))..))))))))))))))..... ( -23.30)
>DroSec_CAF1 16465 93 + 1
AUUGCCAGUUGAUCUCUUUCUCAUAUUCAUUUCCGAUUCUUUGCAGCUUUCUCUUCAUGUUUUAAGCCGCAAUUGGCAGACUGGCGGCAUUUU
.(((((((((((......))............(((((....(((.((((...(.....)....)))).))))))))..)))))))))...... ( -20.70)
>DroSim_CAF1 8898 93 + 1
AUUGCCAGUUGAUCUGUUUCUCAAAUUCAUUUCCGAUUCUUUGCAGCUUUCUCUUCAUGUUUUAAGCCGCAAUUGGCAGACUGGCGGCAUUUU
.(((((((((((......))............(((((....(((.((((...(.....)....)))).))))))))..)))))))))...... ( -20.70)
>DroYak_CAF1 16276 88 + 1
AUUUGCAGUUGAUAAUUUUUGCAUAUUUCUUUA---CCUUUUGUAGCUUU--CUUCAUGUUUUAAGCCGCAAUUGGCAGACUGGCGGCAUUUU
...(((((..........)))))..........---..............--.............(((((....(.....)..)))))..... ( -13.10)
>consensus
AUUGCCAGUUGAUCUGUUUCUCAUAUUCAUUUCCGAUUCUUUGCAGCUUU__CUUCAUGUUUUAAGCCGCAAUUGGCAGACUGGCGGCAUUUU
.(((((((((((......))................((..((((.((((...(.....)....)))).))))..))..)))))))))...... (-16.17 = -15.92 +  -0.25)

alignment

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secondary structure

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dotplot

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Window 5

Location 13,561,542 – 13,561,633
Length 91
Sequences 4
Columns 93
Reading direction reverse
Mean pairwise identity 87.41
Mean single sequence MFE -20.29
Consensus MFE -16.14
Energy contribution -17.14
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.56
Structure conservation index 0.80
SVM decision value 1.63
SVM RNA-class probability 0.968933
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13561542 91 - 22224390
AAAAUGCCGCCAGUCUGCCAAUUGCGGCUUAAAACAUGAAG--AAAGCUGCAAAAAAUCGAAAAUGAAUAUGAGAAACAGAUCAACUGGCAAC
........((((((.......(((((((((...........--.))))))))).................(((........)))))))))... ( -21.70)
>DroSec_CAF1 16465 93 - 1
AAAAUGCCGCCAGUCUGCCAAUUGCGGCUUAAAACAUGAAGAGAAAGCUGCAAAGAAUCGGAAAUGAAUAUGAGAAAGAGAUCAACUGGCAAU
........(((((((((....(((((((((..............))))))))).....))))........(((........))).)))))... ( -22.74)
>DroSim_CAF1 8898 93 - 1
AAAAUGCCGCCAGUCUGCCAAUUGCGGCUUAAAACAUGAAGAGAAAGCUGCAAAGAAUCGGAAAUGAAUUUGAGAAACAGAUCAACUGGCAAU
........(((((((((....(((((((((..............))))))))).....))))..(((.((((.....))))))).)))))... ( -24.04)
>DroYak_CAF1 16276 88 - 1
AAAAUGCCGCCAGUCUGCCAAUUGCGGCUUAAAACAUGAAG--AAAGCUACAAAAGG---UAAAGAAAUAUGCAAAAAUUAUCAACUGCAAAU
....(((......((((((..(((..((((...........--.))))..)))..))---)..))).....)))................... ( -12.70)
>consensus
AAAAUGCCGCCAGUCUGCCAAUUGCGGCUUAAAACAUGAAG__AAAGCUGCAAAAAAUCGGAAAUGAAUAUGAGAAACAGAUCAACUGGCAAU
........((((((.......(((((((((..............))))))))).................(((........)))))))))... (-16.14 = -17.14 +   1.00)

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 11:42:03 2006