Locus 8892

Sequence ID 3R_DroMel_CAF1
Location 23,856,210 – 23,856,345
Length 135
Max. P 0.697482
window14267 window14268

overview

Window 7

Location 23,856,210 – 23,856,320
Length 110
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 79.83
Mean single sequence MFE -35.85
Consensus MFE -23.53
Energy contribution -23.12
Covariance contribution -0.41
Combinations/Pair 1.27
Mean z-score -1.26
Structure conservation index 0.66
SVM decision value -0.05
SVM RNA-class probability 0.506510
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23856210 110 - 27905053
GCAGGAUACCCACGAUUCCCAGUCCCGAGGCGGGACUGGUCGAUACUCCGGUCGACAGGUUCGCUAUUUUGGCCGCGACAGCAAGGUCAGCUUUAUUUAACUGCAAAUA-A
((((........(((..((((((((((...))))))))((((((......)))))).)).))).....((((((((....))..))))))..........)))).....-. ( -38.70)
>DroVir_CAF1 51983 106 - 1
GCAGGAUGCCCAUUAAGCGCAGUCCCACGGCGGGACUGGCAGGCUGUCCAGUUGCUAGGUUGUCUAUUUUGGCGGCGUCUUC----UCUG-CUUGUUCAACUGCAAAAUAA
((((((((((......((.(((((((.....))))))))).((((....))))((((((........))))))))))))...----.)))-)((((......))))..... ( -36.60)
>DroSec_CAF1 61757 110 - 1
GCAGGAUGCCCACGAUUCCCAGUCCCGAGGCGGGACUGGUCGAUACUCCGGUCGACAGGUUCGCUAUUUUGGCCGCGAGAAAAAGGUCAGCUAUAUUUAACUGAAAAUA-A
((.....))((.(((...(((((((((...))))))))))))...((((((((((..((....))...))))))).))).....))((((.((....)).)))).....-. ( -35.80)
>DroSim_CAF1 61186 110 - 1
GCAGGAUGCCCACGAUUCCCAGUCCCGAGGCGGGACUGGUCGAUACUCCGGUCGACAGGUUCGCUAUCUUGGCCUCGACAGAAAGGUCAGCUAUAUUUAACUGAAAAUA-A
((((((((....(((..((((((((((...))))))))((((((......)))))).)).))).))))))(((((........))))).))..................-. ( -35.20)
>DroEre_CAF1 65728 110 - 1
GCAGGAUGCCCACGAUACCCAGUCCCGCGGCGGGACUGGUCGAUACGCCGGUCGACAGGUUCGCUAUUUUGGCAGCGUCAGAUAGGUCAGCUAUAUUUAACUGAAAUUA-A
.((((((((....((.(((((((((((...))))))))((((((......)))))).)))))(((.....))).)))))..((((.....))))......)))......-. ( -37.50)
>DroYak_CAF1 63658 100 - 1
GCAGGAUGCCCACCAAUCCCAGUCCCGCGGCGGGACUGGUCGGUACUCCGGUCGACAGGUUCGCUAUUUUUGGCUCCUC----------UUUAUAUUUAGCUGAAAAUU-A
((.((....))(((....(((((((((...)))))))))((((....))))......)))..)).(((((..(((....----------.........)))..))))).-. ( -31.32)
>consensus
GCAGGAUGCCCACGAUUCCCAGUCCCGAGGCGGGACUGGUCGAUACUCCGGUCGACAGGUUCGCUAUUUUGGCCGCGACAGAAAGGUCAGCUAUAUUUAACUGAAAAUA_A
.(((((((((.........(((((((.....)))))))((((((......)))))).))).....))))))........................................ (-23.53 = -23.12 +  -0.41)

alignment

Postscript

secondary structure

Postscript

dotplot

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Window 8

Location 23,856,241 – 23,856,345
Length 104
Sequences 6
Columns 104
Reading direction reverse
Mean pairwise identity 86.22
Mean single sequence MFE -48.98
Consensus MFE -40.52
Energy contribution -41.97
Covariance contribution 1.45
Combinations/Pair 1.16
Mean z-score -1.91
Structure conservation index 0.83
SVM decision value 0.34
SVM RNA-class probability 0.697482
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23856241 104 - 27905053
GGCGGCUGCCAAUGGAGCGAGCAGGGCAGGAUACCCACGAUUCCCAGUCCCGAGGCGGGACUGGUCGAUACUCCGGUCGACAGGUUCGCUAUUUUGGCCGCGAC
....((.(((((...(((((((.(((.......)))........((((((((...))))))))((((((......))))))..)))))))...))))).))... ( -48.00)
>DroVir_CAF1 52010 104 - 1
GAUGGCUGCCACUGCAGUGCGCACGGCAGGAUGCCCAUUAAGCGCAGUCCCACGGCGGGACUGGCAGGCUGUCCAGUUGCUAGGUUGUCUAUUUUGGCGGCGUC
(((((((((((......(((((..(((.....)))......)))))(((((.....)))))))))).))))))..(((((((((........)))))))))... ( -42.80)
>DroSec_CAF1 61788 104 - 1
GGCGGCUGCCAAUGGAGCGAGCAGGGCAGGAUGCCCACGAUUCCCAGUCCCGAGGCGGGACUGGUCGAUACUCCGGUCGACAGGUUCGCUAUUUUGGCCGCGAG
....((.(((((...(((((((.((((.....))))........((((((((...))))))))((((((......))))))..)))))))...))))).))... ( -52.40)
>DroSim_CAF1 61217 104 - 1
GGCGGCUGCCAAUGGAGCGAGCAGGGCAGGAUGCCCACGAUUCCCAGUCCCGAGGCGGGACUGGUCGAUACUCCGGUCGACAGGUUCGCUAUCUUGGCCUCGAC
..(((..(((((...(((((((.((((.....))))........((((((((...))))))))((((((......))))))..)))))))...))))).))).. ( -49.20)
>DroEre_CAF1 65759 104 - 1
GGCGGCUGCCAAUGGAGUGAGCAGGGCAGGAUGCCCACGAUACCCAGUCCCGCGGCGGGACUGGUCGAUACGCCGGUCGACAGGUUCGCUAUUUUGGCAGCGUC
((((.(((((((...(((((((.((((.....))))........((((((((...))))))))((((((......))))))..)))))))...))))))))))) ( -56.00)
>DroYak_CAF1 63679 104 - 1
GGCGGCUGCCAAUGGAGGGAGCAGGGCAGGAUGCCCACCAAUCCCAGUCCCGCGGCGGGACUGGUCGGUACUCCGGUCGACAGGUUCGCUAUUUUUGGCUCCUC
...((..(((((...((.((((.((((.....))))(((....(((((((((...)))))))))..((....)))))......)))).))....))))).)).. ( -45.50)
>consensus
GGCGGCUGCCAAUGGAGCGAGCAGGGCAGGAUGCCCACGAUUCCCAGUCCCGAGGCGGGACUGGUCGAUACUCCGGUCGACAGGUUCGCUAUUUUGGCCGCGAC
....((.(((((...(((((((.((((.....))))........(((((((.....)))))))((((((......))))))..)))))))...))))).))... (-40.52 = -41.97 +   1.45)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:22:09 2006