Locus 1904

Sequence ID 3R_DroMel_CAF1
Location 5,429,365 – 5,429,467
Length 102
Max. P 0.990480
window3131 window3132

overview

Window 1

Location 5,429,365 – 5,429,467
Length 102
Sequences 5
Columns 108
Reading direction forward
Mean pairwise identity 92.19
Mean single sequence MFE -35.60
Consensus MFE -29.76
Energy contribution -30.28
Covariance contribution 0.52
Combinations/Pair 1.07
Mean z-score -2.21
Structure conservation index 0.84
SVM decision value 2.22
SVM RNA-class probability 0.990480
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5429365 102 + 27905053
AAUCACAUGCAACAAUUGAUGUCGAUUGUUGCCGCU------GCCGCUGGCGUGUCAUGCAACGUUUUGUGCUCGCCCUUUUGUGGCUGCACUCGUGCACAUUGUUUG
...(((..((((((((((....)))))))))).((.------(((((.((((.((...((((....)))))).)))).....))))).))....)))........... ( -35.00)
>DroSec_CAF1 16109 108 + 1
AAUCACAUGCAACAAUUGAUGUCGAUUGUUGCCGCUGCCGCUGCCGCUGGCGUGUCAUGCAACGUUUUGUGCUCGCCCUUUUGUGGCUGCACUCGUGCACUUUGUUUG
...(((..((((((((((....))))))))))....(((((....)).))))))...((((.((....((((..((((....).))).)))).))))))......... ( -36.70)
>DroSim_CAF1 11096 108 + 1
AAUCACAUGCAACAAUUGAUGUCGAUUGUUGCCGCUGCCGCUGCCGCUGGCGUGUCAUGCAACGUUUUGUGUUCGCCCUUUUGUGGCUGCACUCGUGCACUUUGUUUG
...(((..((((((((((....))))))))))....(((((....)).))))))...((((.((....((((..((((....).))).)))).))))))......... ( -35.00)
>DroEre_CAF1 16583 100 + 1
AAUCACAUGCAACAAUUGAUGUCGAUUGUUGCCACAGCCG------CUGGCGUGUCAUGCAACGUUUUGUGCUCGCCCUUUUGUGGCUGCACUCGUGC--UUUGUUUG
...(((..((((((((((....))))))))))..((((((------(.((((.((...((((....)))))).)))).....))))))).....))).--........ ( -35.10)
>DroYak_CAF1 16876 106 + 1
AAUCACAUGCAACAAUUGAUGUCGAUUGUUGCCGCAGUCGCUGCCACUGGCGUGUCAUGCUACGUUUUGUGCUCGCCCUUUUGUGGCUGCACUCGUGC--UUUGUUUG
...(((..((((((((((....)))))))))).((((((((.......((((.(.((((........))))).)))).....))))))))....))).--........ ( -36.20)
>consensus
AAUCACAUGCAACAAUUGAUGUCGAUUGUUGCCGCUGCCGCUGCCGCUGGCGUGUCAUGCAACGUUUUGUGCUCGCCCUUUUGUGGCUGCACUCGUGCACUUUGUUUG
...(((..((((((((((....))))))))))....((((.......)))))))....((.(((....((((..((((....).))).)))).))))).......... (-29.76 = -30.28 +   0.52)

alignment

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secondary structure

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dotplot

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Window 2

Location 5,429,365 – 5,429,467
Length 102
Sequences 5
Columns 108
Reading direction reverse
Mean pairwise identity 92.19
Mean single sequence MFE -33.54
Consensus MFE -26.50
Energy contribution -27.38
Covariance contribution 0.88
Combinations/Pair 1.11
Mean z-score -2.66
Structure conservation index 0.79
SVM decision value 2.04
SVM RNA-class probability 0.986392
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5429365 102 - 27905053
CAAACAAUGUGCACGAGUGCAGCCACAAAAGGGCGAGCACAAAACGUUGCAUGACACGCCAGCGGC------AGCGGCAACAAUCGACAUCAAUUGUUGCAUGUGAUU
...........((((.((((.(((.......)))..))))....((((((.((......))...))------))))((((((((.(....).)))))))).))))... ( -33.00)
>DroSec_CAF1 16109 108 - 1
CAAACAAAGUGCACGAGUGCAGCCACAAAAGGGCGAGCACAAAACGUUGCAUGACACGCCAGCGGCAGCGGCAGCGGCAACAAUCGACAUCAAUUGUUGCAUGUGAUU
........(((((((.((((.(((.......)))..))))....)).)))))..((((((.((....)))))....((((((((.(....).))))))))..)))... ( -36.00)
>DroSim_CAF1 11096 108 - 1
CAAACAAAGUGCACGAGUGCAGCCACAAAAGGGCGAACACAAAACGUUGCAUGACACGCCAGCGGCAGCGGCAGCGGCAACAAUCGACAUCAAUUGUUGCAUGUGAUU
.........((((....))))(((.......)))...((((...((((((.((...((....)).))...))))))((((((((.(....).)))))))).))))... ( -34.30)
>DroEre_CAF1 16583 100 - 1
CAAACAAA--GCACGAGUGCAGCCACAAAAGGGCGAGCACAAAACGUUGCAUGACACGCCAG------CGGCUGUGGCAACAAUCGACAUCAAUUGUUGCAUGUGAUU
........--......((((.(((.......)))..)))).....((..(((..((((((..------.))).)))((((((((.(....).)))))))))))..)). ( -30.60)
>DroYak_CAF1 16876 106 - 1
CAAACAAA--GCACGAGUGCAGCCACAAAAGGGCGAGCACAAAACGUAGCAUGACACGCCAGUGGCAGCGACUGCGGCAACAAUCGACAUCAAUUGUUGCAUGUGAUU
........--.((((.((((.(((.......)))..))))....((((((.((.(((....))).))..).)))))((((((((.(....).)))))))).))))... ( -33.80)
>consensus
CAAACAAAGUGCACGAGUGCAGCCACAAAAGGGCGAGCACAAAACGUUGCAUGACACGCCAGCGGCAGCGGCAGCGGCAACAAUCGACAUCAAUUGUUGCAUGUGAUU
...........((((.((((.(((.......)))..))))....((((((......((....))......))))))((((((((.(....).)))))))).))))... (-26.50 = -27.38 +   0.88)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:22:28 2006