Locus 3016

Sequence ID 3R_DroMel_CAF1
Location 8,065,771 – 8,065,941
Length 170
Max. P 0.839416
window4850 window4851 window4852

overview

Window 0

Location 8,065,771 – 8,065,867
Length 96
Sequences 5
Columns 98
Reading direction forward
Mean pairwise identity 82.74
Mean single sequence MFE -38.20
Consensus MFE -27.71
Energy contribution -28.19
Covariance contribution 0.48
Combinations/Pair 1.07
Mean z-score -1.88
Structure conservation index 0.73
SVM decision value 0.57
SVM RNA-class probability 0.785105
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8065771 96 + 27905053
CCAGCCUGGAGCCCAGAGGAGC--GUAGUGGAGCUGAACAUGGAGCUACAGCCCGGAGGAGGACGAAAUCGUCGUUGUGCUCCAGCCAGGUCGGAACU
((.((((((((((((.......--....))).))).....((((((.(((((((...))..((((....))))))))))))))).)))))).)).... ( -38.20)
>DroSec_CAF1 11930 86 + 1
CCAGCCUGGAGCACAGGGGAG------------CUGAACAUGGAGCUGCAGCCCGGAGGAGGACGACAUCGUCGUUGUGCUCCAGCCAGGUCGGAACU
((.((((((......(((.((------------((........))))....)))((((.(.((((((...)))))).).))))..)))))).)).... ( -36.50)
>DroSim_CAF1 11921 98 + 1
CCAGCCUGGAGCACAGGGGAGCUGGAGUUGGAGCUGAACAUGGAGCUGCUGCCCGGAGGAGGACGACAUCGUCGUUGUGCUCCAGCCAGGUCGGAACU
((.((((((......(((.(((.........((((........))))))).)))((((.(.((((((...)))))).).))))..)))))).)).... ( -41.70)
>DroEre_CAF1 10351 78 + 1
CCAGCCUGGAGCCCAGAGGAGC------UGGAGCUGAAGAUGGAGCUGCAGC-CGGAGGAG-------------CUGUGCUCCAGCCAGGUCGGAACU
((.(((((((((((((.....)------))).))).....((((((.(((((-(....).)-------------)))))))))).)))))).)).... ( -39.20)
>DroYak_CAF1 10572 86 + 1
CCAGCCUGGAGCCCAGAGGAG------------CUGAAGAUGGAGCUGCAGCCCGGAGGAGGACGACAUCGUCGUGGUGCUCCAGCCAGGUCGGAACU
((.((((((........((.(------------(((.((......)).))))))((((.(..(((((...)))))..).))))..)))))).)).... ( -35.40)
>consensus
CCAGCCUGGAGCCCAGAGGAGC______UGGAGCUGAACAUGGAGCUGCAGCCCGGAGGAGGACGACAUCGUCGUUGUGCUCCAGCCAGGUCGGAACU
((.((((((....(((.................)))....((((((.(((((.(......)((((....))))))))))))))).)))))).)).... (-27.71 = -28.19 +   0.48)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 8,065,771 – 8,065,867
Length 96
Sequences 5
Columns 98
Reading direction reverse
Mean pairwise identity 82.74
Mean single sequence MFE -35.34
Consensus MFE -23.50
Energy contribution -23.90
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -2.12
Structure conservation index 0.66
SVM decision value 0.74
SVM RNA-class probability 0.839416
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8065771 96 - 27905053
AGUUCCGACCUGGCUGGAGCACAACGACGAUUUCGUCCUCCUCCGGGCUGUAGCUCCAUGUUCAGCUCCACUAC--GCUCCUCUGGGCUCCAGGCUGG
((((..((((..(..(((((.....((((....)))).......((((((.(((.....))))))).)).....--))))).)..)).))..)))).. ( -34.00)
>DroSec_CAF1 11930 86 - 1
AGUUCCGACCUGGCUGGAGCACAACGACGAUGUCGUCCUCCUCCGGGCUGCAGCUCCAUGUUCAG------------CUCCCCUGUGCUCCAGGCUGG
........((.(.((((((((((..((((....)))).......((((((.(((.....))))))------------)))...)))))))))).).)) ( -38.10)
>DroSim_CAF1 11921 98 - 1
AGUUCCGACCUGGCUGGAGCACAACGACGAUGUCGUCCUCCUCCGGGCAGCAGCUCCAUGUUCAGCUCCAACUCCAGCUCCCCUGUGCUCCAGGCUGG
........((.(.((((((((((..((((....)))).......(((.(((((((........)))).........))).))))))))))))).).)) ( -37.00)
>DroEre_CAF1 10351 78 - 1
AGUUCCGACCUGGCUGGAGCACAG-------------CUCCUCCG-GCUGCAGCUCCAUCUUCAGCUCCA------GCUCCUCUGGGCUCCAGGCUGG
....(((.(((((.((((((.(((-------------((.....)-))))..)))))).....(((.(((------(.....)))))))))))).))) ( -33.30)
>DroYak_CAF1 10572 86 - 1
AGUUCCGACCUGGCUGGAGCACCACGACGAUGUCGUCCUCCUCCGGGCUGCAGCUCCAUCUUCAG------------CUCCUCUGGGCUCCAGGCUGG
........((.(.(((((((.(((.((((....)))).......((((((.((......)).)))------------)))...)))))))))).).)) ( -34.30)
>consensus
AGUUCCGACCUGGCUGGAGCACAACGACGAUGUCGUCCUCCUCCGGGCUGCAGCUCCAUGUUCAGCUCCA______GCUCCUCUGGGCUCCAGGCUGG
........((.(.(((((((.....((((....)))).......((((....))))..............................))))))).).)) (-23.50 = -23.90 +   0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 8,065,827 – 8,065,941
Length 114
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 82.01
Mean single sequence MFE -37.18
Consensus MFE -27.38
Energy contribution -28.43
Covariance contribution 1.06
Combinations/Pair 1.12
Mean z-score -1.68
Structure conservation index 0.74
SVM decision value 0.36
SVM RNA-class probability 0.704311
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8065827 114 + 27905053
GAGGACGAAAUCGUCGUUGUGCUCCAGCCAGGUCGGAACUGAUCUAUGGUAGCCGUUAGUGUCGUCGGCAGUGAAAAGUUGUCGACCUGCACUGGCAAAAU------AUAGUAAAUAGCG
...((((....))))(((((((((((...((((((....)))))).))).))).((((((((.(((((((((....).))))))))..)))))))).....------.......))))). ( -40.70)
>DroSec_CAF1 11976 113 + 1
GAGGACGACAUCGUCGUUGUGCUCCAGCCAGGUCGGAACUGAUCUAUGGUAGCCGUUAGUGUCGUCGGCAGUGAAAAGUUGUCGACCUGCACUGGCAG-GU------AUAGUAAAUAGCG
...((((....))))(((((((((((...((((((....)))))).))).))).((((((((.(((((((((....).))))))))..))))))))..-..------.......))))). ( -40.70)
>DroSim_CAF1 11979 114 + 1
GAGGACGACAUCGUCGUUGUGCUCCAGCCAGGUCGGAACUGAUCUAUGGUAGCCGUUAGUGUCGUCGGCAGUGAAAAGUUGUCGACCUGCACUGGCAAAAU------AUAGUAAAUAGCG
...((((....))))(((((((((((...((((((....)))))).))).))).((((((((.(((((((((....).))))))))..)))))))).....------.......))))). ( -40.70)
>DroEre_CAF1 10402 107 + 1
GAG-------------CUGUGCUCCAGCCAGGUCGGAACUGAUCUAUGGUAGCCGUUAGUGUCGUCGGCAGUGAAAAGUUGUCGACCUGCACUGGCAAAAUACGAGUAUAGUAAAUAGAG
..(-------------((((((((..(((((((((....)))))..))))....((((((((.(((((((((....).))))))))..)))))))).......)))))))))........ ( -39.80)
>DroYak_CAF1 10618 114 + 1
GAGGACGACAUCGUCGUGGUGCUCCAGCCAGGUCGGAACUGAUCCAUGGUAGCCGUUAGUGUCGUCGGCAGUGAAAAGUUGUCGACCUGCACUGGCAAAAU------AUAGUAAAUAGAG
...((((....))))..(((...(((....(((((....)))))..)))..)))((((((((.(((((((((....).))))))))..)))))))).....------............. ( -37.00)
>DroAna_CAF1 17555 91 + 1
-----CCACUGA------GU-CCUCGGCCAGGUUGAAUCUGAUCUAUGGUGGCCGUUAGUGUCUUCGGCAGUGAAAAGUUGGCGACCUGCUCGUGCAAAAU------AU-----------
-----.(((.((------((-....(..(((((...)))))..)...(((.(((((((.((.(....))).))).....)))).))).)))))))......------..----------- ( -24.20)
>consensus
GAGGACGACAUCGUCGUUGUGCUCCAGCCAGGUCGGAACUGAUCUAUGGUAGCCGUUAGUGUCGUCGGCAGUGAAAAGUUGUCGACCUGCACUGGCAAAAU______AUAGUAAAUAGCG
...((((....))))...(.((((((...((((((....)))))).))).))))((((((((.((((((((.......))))))))..))))))))........................ (-27.38 = -28.43 +   1.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:50:14 2006