Locus 2540

Sequence ID 3L_DroMel_CAF1
Location 7,121,272 – 7,121,397
Length 125
Max. P 0.934313
window3945 window3946

overview

Window 5

Location 7,121,272 – 7,121,364
Length 92
Sequences 6
Columns 95
Reading direction forward
Mean pairwise identity 83.58
Mean single sequence MFE -42.47
Consensus MFE -32.16
Energy contribution -32.42
Covariance contribution 0.25
Combinations/Pair 1.32
Mean z-score -1.96
Structure conservation index 0.76
SVM decision value 0.33
SVM RNA-class probability 0.691657
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7121272 92 + 23771897
GGACGUCGAAAGGCGCGCCUUGUCCCUGU---GAGUUGAGGGUGUGCCAGGAGUUCCUGGUGCCGCACUAUUUCUAGGCAGACUCUCAGCUCUCU
((.((((....))))..))........(.---((((((((((((..(((((....)))))..).((.(((....)))))..))))))))))).). ( -42.40)
>DroSec_CAF1 36248 92 + 1
GGAGGUCGAAAGCCGCGCCUUGUCCCUGU---GAGUUGAGGGUGUGCCAGGAGUUCCUGGCGCCGCACUAUUUCUGGGCAGACUCUCCGCUCGCU
((.((.(....)))...))........((---((((.((((((((((((((....)))))))).((.(((....)))))..)))))).)))))). ( -41.90)
>DroSim_CAF1 36988 92 + 1
GGAGGUCGAAAGCCGCGCCUUGUCCCUGU---GAGUUGAGGGUGUGCCAGGAGUUCCUGGCGCCGCACUAUUUCUGGGCAGACUCUCCGCUCUCU
((.((.(....)))...))........(.---((((.((((((((((((((....)))))))).((.(((....)))))..)))))).)))).). ( -38.30)
>DroEre_CAF1 36269 92 + 1
GGAGGUCGAAAGGCGCGCCUUAUCCCUGU---GAGUGGAGGGUGUGCCAGGAGUGCCUGGUGCGGCACUGUUUCUGGGCAGGCUCUCCGCUCUCU
((.((((....))).).))........(.---(((((((((((.(((((((((((((......))))))...))).)))).))))))))))).). ( -47.50)
>DroYak_CAF1 37900 92 + 1
GGAGGUCGAAAGGCGCGACUUGUCCCUGU---GGGUGGAGGGUGUGCCAGGUGUUCCUGGUGCUGCACUGUUUCUGGGCAGGCUCUCCGCUCUCU
((((((((.......)))))..)))..(.---((((((((((((..(((((....)))))..)....(((((....)))))))))))))))).). ( -42.90)
>DroPer_CAF1 92426 95 + 1
GGAGGACGAGAGCCGUGCCUUUUCGCGGCUACCGGCUGACGGCGUGGCCGGGGACGGAGGUGCCGCACUGUUUCUGGGCAAGCUCACGGCCCGCU
(..((.((..(((((((......)))))))..)).))..)((((.(((((....).(((.((((.((.......))))))..)))..)))))))) ( -41.80)
>consensus
GGAGGUCGAAAGCCGCGCCUUGUCCCUGU___GAGUUGAGGGUGUGCCAGGAGUUCCUGGUGCCGCACUAUUUCUGGGCAGACUCUCCGCUCUCU
.(((((((.....)).)))))...........(((((((((((((((((((....)))))))).((.(((....)))))..)))))))))))... (-32.16 = -32.42 +   0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 7,121,300 – 7,121,397
Length 97
Sequences 6
Columns 100
Reading direction forward
Mean pairwise identity 79.22
Mean single sequence MFE -43.08
Consensus MFE -30.18
Energy contribution -30.88
Covariance contribution 0.70
Combinations/Pair 1.35
Mean z-score -2.11
Structure conservation index 0.70
SVM decision value 1.24
SVM RNA-class probability 0.934313
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7121300 97 + 23771897
U---GAGUUGAGGGUGUGCCAGGAGUUCCUGGUGCCGCACUAUUUCUAGGCAGACUCUCAGCUCUCUUUAAGUUGGCCACCCUGCCUCGUAAUUGAUCCU
.---((((((((((((..(((((....)))))..).((.(((....)))))..)))))))))))..........(((......))).............. ( -36.50)
>DroPse_CAF1 89551 100 + 1
CUACCGGCUGACGGCGUGGCCGGGGACGGAGGUGCCGCACUGUUUCUGGGCAAGCUCACGGCCCGCUUUAGGUUGGCCACUCGGCCACGCAGCUGCUCCA
....(((((....(((((((((((....(((.((((.((.......))))))..)))..((((.((.....)).)))).))))))))))))))))..... ( -47.80)
>DroSec_CAF1 36276 97 + 1
U---GAGUUGAGGGUGUGCCAGGAGUUCCUGGCGCCGCACUAUUUCUGGGCAGACUCUCCGCUCGCUUUAAGUUGGCCACCCUGCCUCGUAAUUGAUCCU
.---(((...((((((.((((((....))))))((((.(((.....(((((.(.....).))))).....)))))))))))))..)))............ ( -36.50)
>DroEre_CAF1 36297 97 + 1
U---GAGUGGAGGGUGUGCCAGGAGUGCCUGGUGCGGCACUGUUUCUGGGCAGGCUCUCCGCUCUCUUUAGGUUGGCCACCCGGCCACGCAAUUGAUCCU
.---(((((((((((.(((((((((((((......))))))...))).)))).))))))))))).......(((((((....))))).)).......... ( -48.50)
>DroYak_CAF1 37928 97 + 1
U---GGGUGGAGGGUGUGCCAGGUGUUCCUGGUGCUGCACUGUUUCUGGGCAGGCUCUCCGCUCUCUUCAGGUUGGCCACCCUGCCACGCAAUUGAUCCU
.---((((((((((((..(((((....)))))..)....(((((....))))))))))))))))...(((.((((((......)))).))...))).... ( -41.40)
>DroPer_CAF1 92454 100 + 1
CUACCGGCUGACGGCGUGGCCGGGGACGGAGGUGCCGCACUGUUUCUGGGCAAGCUCACGGCCCGCUUUAGGUUGGCCACUCGGCCACGCAGCUGCUCCA
....(((((....(((((((((((....(((.((((.((.......))))))..)))..((((.((.....)).)))).))))))))))))))))..... ( -47.80)
>consensus
U___GAGUUGAGGGUGUGCCAGGAGUUCCUGGUGCCGCACUGUUUCUGGGCAGGCUCUCCGCUCGCUUUAGGUUGGCCACCCGGCCACGCAAUUGAUCCU
....(((((((((((((((((((....)))))))).((.((......))))..)))))))))))..........(((......))).............. (-30.18 = -30.88 +   0.70)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:35:14 2006