Locus 695

Sequence ID 2R_DroMel_CAF1
Location 3,413,827 – 3,413,955
Length 128
Max. P 0.947144
window1225 window1226

overview

Window 5

Location 3,413,827 – 3,413,921
Length 94
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 78.96
Mean single sequence MFE -24.27
Consensus MFE -16.55
Energy contribution -16.95
Covariance contribution 0.40
Combinations/Pair 1.06
Mean z-score -1.17
Structure conservation index 0.68
SVM decision value 0.06
SVM RNA-class probability 0.561554
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3413827 94 - 20766785
AUGUGUACA--------------UACAAUCA-GAAAAAGAGGUGAAGGCUGACAACAGGCGCCAAAAACCGCAUUGCUCGAUGCAGCAGCAGCCA-CACUGCAGCGGCAA
.((((....--------------))))....-..............(.(((....))).)(((.......(((((....))))).((.((((...-..)))).))))).. ( -23.20)
>DroSec_CAF1 44005 89 - 1
AUAUGUACA--------------UACAAUCA-GAAAAAGAGGUGAAGGCUGACAACAGGCGCCAAAAACCGCAUUGCUCGAUGCAGCAGC------CACUGCAGCGGCAA
.........--------------........-........((((....(((....))).)))).....((((..(((.....)))((((.------..)))).))))... ( -20.10)
>DroSim_CAF1 44209 89 - 1
AUAUGUACA--------------UACAAUCA-GAAAAAGAGGUGAAGGCUGACAACAGGCGCCAAAAACCGCAUUGCUCGAUGCAGCAGC------CACUGCAGCGGCAA
.........--------------........-........((((....(((....))).)))).....((((..(((.....)))((((.------..)))).))))... ( -20.10)
>DroEre_CAF1 44823 106 - 1
AUAUCUACAUUCAUGCGCGAGCGUACGAAGA-GAAAAAGAGGUGAAGGCUGACGACAGGCGCCAAAAACCGCAUUGCUCGAUGCUGCAGC---CAUAACUGCAGCGGCAA
...(((...(((((((....))))..))).)-)).............(((..(((((((((........))).))).)))..(((((((.---.....)))))))))).. ( -30.90)
>DroYak_CAF1 47319 103 - 1
AUAUCUACACUCAUGCGCAAGCGUACGAAGA-GAAAAAGAGGUGAAGGCUGACGACAGGCGCCAAAAACCGCAUUGUUCGAUGCAGCAGC------AACUGCAGCGGCAA
.....(((.(((((((....)))).(.....-).....))))))..(.(((....))).)(((.......(((((....))))).((((.------..))))...))).. ( -28.50)
>DroPer_CAF1 44966 83 - 1
----CCACAU----------GCAUUCGGAGAGGAAAAAGAGGUGAAGGCUGACAACAGGCGCCAAAAACCGCAUUGCU-GCUGCUGCA------------GCAGCAACCA
----.....(----------((.(((......))).....((((....(((....))).)))).......)))(((((-((((...))------------)))))))... ( -22.80)
>consensus
AUAUCUACA______________UACAAACA_GAAAAAGAGGUGAAGGCUGACAACAGGCGCCAAAAACCGCAUUGCUCGAUGCAGCAGC______CACUGCAGCGGCAA
........................................((((....(((....))).)))).....((((...((.....)).((((.........)))).))))... (-16.55 = -16.95 +   0.40)

alignment

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secondary structure

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dotplot

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Window 6

Location 3,413,865 – 3,413,955
Length 90
Sequences 5
Columns 108
Reading direction reverse
Mean pairwise identity 81.15
Mean single sequence MFE -24.74
Consensus MFE -11.09
Energy contribution -10.61
Covariance contribution -0.48
Combinations/Pair 1.07
Mean z-score -2.85
Structure conservation index 0.45
SVM decision value 1.37
SVM RNA-class probability 0.947144
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3413865 90 - 20766785
AAAGGCAACGAGAUAUGUAUGUAUGUGCACUU----AUAUGUGUACA--------------UACAAUCAGAAAAAGAGGUGAAGGCUGACAACAGGCGCCAAAAACCG
...(((.............(((((((((((..----....)))))))--------------))))..................(.(((....))).))))........ ( -25.70)
>DroSec_CAF1 44038 86 - 1
AAAGGCAACGAGAUAUGU----AUGUGCACUU----GUAUAUGUACA--------------UACAAUCAGAAAAAGAGGUGAAGGCUGACAACAGGCGCCAAAAACCG
...(((.....(((.(((----(((((((...----.....))))))--------------)))))))...............(.(((....))).))))........ ( -23.30)
>DroSim_CAF1 44242 88 - 1
AAAGGCAACGAGAUAUGU--GCAUGUGCACUU----GUAUAUGUACA--------------UACAAUCAGAAAAAGAGGUGAAGGCUGACAACAGGCGCCAAAAACCG
...(((...((..(((((--((((((((....----)))))))))))--------------))...))...............(.(((....))).))))........ ( -27.00)
>DroEre_CAF1 44859 96 - 1
AAAGGCAACGAGAUAUG--------UGCACUU----AUAUAUCUACAUUCAUGCGCGAGCGUACGAAGAGAAAAAGAGGUGAAGGCUGACGACAGGCGCCAAAAACCG
...(((..(((((((((--------((....)----))))))))......((((....)))).))..................(.(((....))).))))........ ( -23.10)
>DroYak_CAF1 47352 100 - 1
AAAGGCAACGAGAUAUG--------UGCACUUACAUAUAUAUCUACACUCAUGCGCAAGCGUACGAAGAGAAAAAGAGGUGAAGGCUGACGACAGGCGCCAAAAACCG
...(((...((.(((((--------((......))))))).))(((.(((((((....)))).(.....).....))))))..(.(((....))).))))........ ( -24.60)
>consensus
AAAGGCAACGAGAUAUGU____AUGUGCACUU____AUAUAUGUACA______________UACAAUCAGAAAAAGAGGUGAAGGCUGACAACAGGCGCCAAAAACCG
...(((.....................(((((.........((........................)).......)))))..(.(((....))).))))........ (-11.09 = -10.61 +  -0.48)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:44:52 2006