Locus 5819

Sequence ID 3L_DroMel_CAF1
Location 15,748,481 – 15,748,631
Length 150
Max. P 0.939304
window9243 window9244 window9245

overview

Window 3

Location 15,748,481 – 15,748,591
Length 110
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 90.29
Mean single sequence MFE -25.45
Consensus MFE -21.89
Energy contribution -22.95
Covariance contribution 1.06
Combinations/Pair 1.03
Mean z-score -1.46
Structure conservation index 0.86
SVM decision value 0.19
SVM RNA-class probability 0.626869
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15748481 110 + 23771897
AUGGCCCAAAUGGCAUUUUGUCAUAAACGUUGUACUCGUUUUUGCCCUCUU----------UUUUUGCCACUCUUGUGUUGCCGACACUAGUGGCAUAUUUUCGUGCAAAAUUUCAUGUU
((((((.....)))(((((((((.(((((.......))))).)).......----------....(((((((...(((((...))))).))))))).........)))))))..)))... ( -24.80)
>DroSec_CAF1 256 110 + 1
AUGGCCCAAAUGGAAUUUUGUCAUAAACGUUGUAGUCGUUGUUGGCCUCUU----------UUUUUGCCACUCUUGUGUUGCCGACACUAGUGGCAUAUUUUCGUGCAAAAUUUCACGUU
..........((((((((((.(((.......(..((((....))))..)..----------....(((((((...(((((...))))).))))))).......))))))))))))).... ( -27.70)
>DroSim_CAF1 311 110 + 1
AUGGCCCAAAUGGAAUUUUGUCAUAAACGUUGUACUUGUUUUUGCCCUCUU----------UUUUUGCCACUCUUGUGUUGCCGACACUAGUGGCAUAUUUUCGUGCAAAAUUUCACGUU
..........(((((((((((((.(((((.......))))).)).......----------....(((((((...(((((...))))).))))))).........))))))))))).... ( -25.80)
>DroEre_CAF1 252 119 + 1
AUGGCCCAAAUGGAAUUUUGUCAUAAACGUUGUAGUCGGUUUU-CCCUCUUUUUACUUUAUUUUUUGCCUCUGUUGAGUGGCCGACACUAGUGGCAUAUUUUCGUGCAAAAUUUCACGUU
..........((((((((((.(((....((...((..((....-))..))....)).........((((.((....((((.....)))))).)))).......))))))))))))).... ( -23.50)
>consensus
AUGGCCCAAAUGGAAUUUUGUCAUAAACGUUGUACUCGUUUUUGCCCUCUU__________UUUUUGCCACUCUUGUGUUGCCGACACUAGUGGCAUAUUUUCGUGCAAAAUUUCACGUU
..........((((((((((.((((((((.......)))))........................(((((((...((((.....)))).))))))).......))))))))))))).... (-21.89 = -22.95 +   1.06)

alignment

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secondary structure

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dotplot

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Window 4

Location 15,748,481 – 15,748,591
Length 110
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 90.29
Mean single sequence MFE -26.73
Consensus MFE -20.04
Energy contribution -20.60
Covariance contribution 0.56
Combinations/Pair 1.04
Mean z-score -2.56
Structure conservation index 0.75
SVM decision value 0.94
SVM RNA-class probability 0.885877
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15748481 110 - 23771897
AACAUGAAAUUUUGCACGAAAAUAUGCCACUAGUGUCGGCAACACAAGAGUGGCAAAAA----------AAGAGGGCAAAAACGAGUACAACGUUUAUGACAAAAUGCCAUUUGGGCCAU
..(((((..((((((.........(((((((..(((.(....))))..)))))))....----------......))))))(((.......)))))))).......(((.....)))... ( -28.11)
>DroSec_CAF1 256 110 - 1
AACGUGAAAUUUUGCACGAAAAUAUGCCACUAGUGUCGGCAACACAAGAGUGGCAAAAA----------AAGAGGCCAACAACGACUACAACGUUUAUGACAAAAUUCCAUUUGGGCCAU
..((((........))))......(((((((..(((.(....))))..)))))))....----------....((((...((((.......)))).....((((......)))))))).. ( -31.40)
>DroSim_CAF1 311 110 - 1
AACGUGAAAUUUUGCACGAAAAUAUGCCACUAGUGUCGGCAACACAAGAGUGGCAAAAA----------AAGAGGGCAAAAACAAGUACAACGUUUAUGACAAAAUUCCAUUUGGGCCAU
..((((........))))......(((((((..(((.(....))))..)))))))....----------.....(((..((((.........))))...........((....))))).. ( -27.20)
>DroEre_CAF1 252 119 - 1
AACGUGAAAUUUUGCACGAAAAUAUGCCACUAGUGUCGGCCACUCAACAGAGGCAAAAAAUAAAGUAAAAAGAGGG-AAAACCGACUACAACGUUUAUGACAAAAUUCCAUUUGGGCCAU
..((((........)))).......(((....(((((.(((.((....)).)))...................((.-....))))).))...........((((......)))))))... ( -20.20)
>consensus
AACGUGAAAUUUUGCACGAAAAUAUGCCACUAGUGUCGGCAACACAAGAGUGGCAAAAA__________AAGAGGGCAAAAACGACUACAACGUUUAUGACAAAAUUCCAUUUGGGCCAU
...(((.(((((((((..((....(((((((..(((.(....))))..)))))))..................(........)..........))..)).))))))).)))......... (-20.04 = -20.60 +   0.56)

alignment

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secondary structure

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dotplot

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Window 5

Location 15,748,521 – 15,748,631
Length 110
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 88.70
Mean single sequence MFE -26.60
Consensus MFE -20.48
Energy contribution -21.73
Covariance contribution 1.25
Combinations/Pair 1.00
Mean z-score -2.50
Structure conservation index 0.77
SVM decision value 1.28
SVM RNA-class probability 0.939304
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15748521 110 - 23771897
UGUGAUUUUUCCCCAAAAACUCUCUCUUUAAAUAUGCAUGAACAUGAAAUUUUGCACGAAAAUAUGCCACUAGUGUCGGCAACACAAGAGUGGCAAAAA----------AAGAGGGCAAA
.....................((((((((.....((((.((........)).))))........(((((((..(((.(....))))..)))))))...)----------))))))).... ( -27.80)
>DroSec_CAF1 296 110 - 1
UGUGAUUUUUCCCCAAAAACUCUCUCUUUAAAUAUGCAUGAACGUGAAAUUUUGCACGAAAAUAUGCCACUAGUGUCGGCAACACAAGAGUGGCAAAAA----------AAGAGGCCAAC
......................(((((((.............((((........))))......(((((((..(((.(....))))..)))))))...)----------))))))..... ( -27.10)
>DroSim_CAF1 351 110 - 1
UGUGAUUUUUCCCCAAAAACUCUCUCUUUAAAUAUGCAUGAACGUGAAAUUUUGCACGAAAAUAUGCCACUAGUGUCGGCAACACAAGAGUGGCAAAAA----------AAGAGGGCAAA
.....................((((((((.............((((........))))......(((((((..(((.(....))))..)))))))...)----------))))))).... ( -29.60)
>DroEre_CAF1 292 119 - 1
CGUGAUUCUGCUCCAAAAACGCUCCCUUUAAAUAUGCAAUAACGUGAAAUUUUGCACGAAAAUAUGCCACUAGUGUCGGCCACUCAACAGAGGCAAAAAAUAAAGUAAAAAGAGGG-AAA
......................(((((((...((((......))))...((((((..........(((((....)).)))..(((....)))))))))............))))))-).. ( -21.90)
>consensus
UGUGAUUUUUCCCCAAAAACUCUCUCUUUAAAUAUGCAUGAACGUGAAAUUUUGCACGAAAAUAUGCCACUAGUGUCGGCAACACAAGAGUGGCAAAAA__________AAGAGGGCAAA
.....................(((((((..............((((........))))......(((((((..(((.(....))))..)))))))..............))))))).... (-20.48 = -21.73 +   1.25)

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 12:00:43 2006