Locus 4120

Sequence ID 2L_DroMel_CAF1
Location 11,829,371 – 11,829,501
Length 130
Max. P 0.977388
window6504 window6505

overview

Window 4

Location 11,829,371 – 11,829,484
Length 113
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 78.32
Mean single sequence MFE -38.40
Consensus MFE -27.05
Energy contribution -28.58
Covariance contribution 1.53
Combinations/Pair 1.29
Mean z-score -1.17
Structure conservation index 0.70
SVM decision value 0.23
SVM RNA-class probability 0.644206
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11829371 113 + 22407834
GUGACCCCAGUCACGGAUCGCGUAAAAUACCCAGGCAUUG--CAGGCAGUACGGUCUUACCAUUGCGCAGCGUGGCCACCUGGUCA-----CGAUCGGCUGGCCAGUGUUGGUAAACAUU
(((((....))))).((((((((((.........(.((((--....)))).)((.....)).))))))...((((((....)))))-----)))))((....))((((((....)))))) ( -37.00)
>DroPse_CAF1 20252 102 + 1
GUGGCCGCAGCUGGAGAUCGCGA-AAAUACUCAGCUAUCGAUCAGGGCGUGUGGUCACACUUUUCGAUAG-GCGGUCGACCACACACAAAUCGAUCGGCGCGC----G------------
(((((((.((((((..((.....-..))..))))))((((((....(.((((((((((.(((......))-)..)).)))))))).)..)))))))))).)))----.------------ ( -36.10)
>DroSec_CAF1 52572 113 + 1
GUGACCCCAGUCACAGAUCGCGAAAAAUACCCAGACAUUG--CAGGCAGUACGGUCCUACCAUUGCGCAGCGUGGCCACCUGGUCA-----CGAUCAGCUGGCCAGUGUUGGCAAACAUU
(((((....))))).......................(((--(..(((((..((.....))))))).(((((((((((.(((((..-----..))))).)))))).)))))))))..... ( -37.10)
>DroSim_CAF1 18139 113 + 1
GUGACCCCAGUCACAGAUCGCGAAAAAUACCCAGGCAUUA--CAGGCAGUACGGUCUUACCAUUGCGCAGCGUGGCCACCUGGUCA-----CGAUCAGCUGGCCAGUGUUGGCAAACAUU
(((((....)))))((((((.......(((....((....--...)).))))))))).....((((.(((((((((((.(((((..-----..))))).)))))).)))))))))..... ( -37.31)
>DroEre_CAF1 18379 113 + 1
GUGACCCCAGUCACGGAUCGCGUAAAAUAUCGAGACAUUG--CGGGCAGUACGGUCUUACCAUUGCGUAGCGUGGCCACCUGGUCA-----CGAUCAGCUGGCCAGUGUUGGCAAAAAUU
(((((....))))).((((((((((......(((((..((--(.....)))..)))))....))))))...((((((....)))))-----))))).((..((....))..))....... ( -38.60)
>DroYak_CAF1 19372 113 + 1
GUGACCCCAGUCACAGAUCGCGUAAAAUGCCAAGGCAUUG--CAGGCAGUACGGUCUUACCAGUGCGUAGCGUGGCCACCUGGUCA-----CGAUCAGUUGGCCAGUGUUGGCAAACGUU
(((((....))))).....((((....((((((.((...(--(..((.((((((.....)).)))))).)).((((((.(((((..-----..))))).)))))))).)))))).)))). ( -44.30)
>consensus
GUGACCCCAGUCACAGAUCGCGAAAAAUACCCAGGCAUUG__CAGGCAGUACGGUCUUACCAUUGCGCAGCGUGGCCACCUGGUCA_____CGAUCAGCUGGCCAGUGUUGGCAAACAUU
(((((....))))).(((((...............................)))))......((((.(((((((((((.((((((.......)))))).)))))).)))))))))..... (-27.05 = -28.58 +   1.53)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 11,829,411 – 11,829,501
Length 90
Sequences 6
Columns 94
Reading direction forward
Mean pairwise identity 72.62
Mean single sequence MFE -27.13
Consensus MFE -19.77
Energy contribution -20.83
Covariance contribution 1.06
Combinations/Pair 1.26
Mean z-score -1.66
Structure conservation index 0.73
SVM decision value 1.79
SVM RNA-class probability 0.977388
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11829411 90 + 22407834
CAGGCAGUACGGUCUUACCAUUGCGCAGCGUGGCCACCUGGUCACGAUCGGCUGGCCAGUGUUGGUAAACAUUAA-ACGG-UAUUUA--ACACA
..((((((.(((((........((...))((((((....)))))))))))))).))).(((((((...((.....-...)-)..)))--)))). ( -28.80)
>DroSec_CAF1 52612 80 + 1
CAGGCAGUACGGUCCUACCAUUGCGCAGCGUGGCCACCUGGUCACGAUCAGCUGGCCAGUGUUGGCAAACAUUAA--------------ACACA
..........((.....)).((((.(((((((((((.(((((....))))).)))))).))))))))).......--------------..... ( -28.10)
>DroSim_CAF1 18179 80 + 1
CAGGCAGUACGGUCUUACCAUUGCGCAGCGUGGCCACCUGGUCACGAUCAGCUGGCCAGUGUUGGCAAACAUUAA--------------ACACA
.((((......)))).....((((.(((((((((((.(((((....))))).)))))).))))))))).......--------------..... ( -28.50)
>DroEre_CAF1 18419 81 + 1
CGGGCAGUACGGUCUUACCAUUGCGUAGCGUGGCCACCUGGUCACGAUCAGCUGGCCAGUGUUGGCAAAAAUUAG-U--------UU----ACA
.((((.....((.....)).((((.(((((((((((.(((((....))))).)))))).)))))))))......)-)--------))----... ( -27.10)
>DroYak_CAF1 19412 92 + 1
CAGGCAGUACGGUCUUACCAGUGCGUAGCGUGGCCACCUGGUCACGAUCAGUUGGCCAGUGUUGGCAAACGUUAA-UCGG-UAUUUUAUACACA
......(((..(...((((.(....((((((.(((((((((((((.....).))))))).).))))..)))))).-.)))-))..)..)))... ( -28.70)
>DroAna_CAF1 28625 73 + 1
---GGCGGACGGUCUUACUUGGCCACAGUGUAGCCACAUGGUUACGAUCACCAAU--------------CGAUAAGUCGAUUAUUUU----GAA
---((.((.(((((......)))).....((((((....))))))).)).))(((--------------(((....)))))).....----... ( -21.60)
>consensus
CAGGCAGUACGGUCUUACCAUUGCGCAGCGUGGCCACCUGGUCACGAUCAGCUGGCCAGUGUUGGCAAACAUUAA_U________UU__ACACA
...(((((..((.....))))))).(((((((((((.(((((....))))).)))))).))))).............................. (-19.77 = -20.83 +   1.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:10:06 2006