Locus 1299

Sequence ID 3R_DroMel_CAF1
Location 3,821,731 – 3,821,833
Length 102
Max. P 0.950470
window2129 window2130

overview

Window 9

Location 3,821,731 – 3,821,833
Length 102
Sequences 4
Columns 107
Reading direction forward
Mean pairwise identity 89.31
Mean single sequence MFE -45.82
Consensus MFE -42.45
Energy contribution -41.83
Covariance contribution -0.63
Combinations/Pair 1.18
Mean z-score -1.83
Structure conservation index 0.93
SVM decision value 1.23
SVM RNA-class probability 0.933462
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3821731 102 + 27905053
GUCGCUAGCCACAGGUUCUGAGCAACAGGUUGUCGAUGUGUGCUCUCGCUCUGACAGCCGAAGCGAUCGGGUCGGGCGUCAGGAUGCCAGAGCGAGAGCGAG-----
((((.(((((....((.....))....))))).))))...(((((((((((((((..((((.....))))))).(((((....)))))))))))))))))..----- ( -44.70)
>DroSec_CAF1 49474 102 + 1
GUCGCUAGCCACAGGUUCUGAGCAACAGGUUGUCGAUGUGUGCUCUCGCUCGGACAGCCGAAGCGAUCGGGUCGGGCGUCAGGAUGCCAGAGCGAGAGCGAG-----
((((.(((((....((.....))....))))).))))...(((((((((((.(((..((((.....))))))).(((((....))))).)))))))))))..----- ( -44.00)
>DroSim_CAF1 54038 102 + 1
GUCGCUAGCCACAGGUUCUGAGCAACAGGUUGUCGAUGUGUGCUCUCGCUCGGACAGCCGAAGCGAUCGGGUCGGGCGUCAGGAUGCCAGAGCGAGAGCGAG-----
((((.(((((....((.....))....))))).))))...(((((((((((.(((..((((.....))))))).(((((....))))).)))))))))))..----- ( -44.00)
>DroEre_CAF1 40759 105 + 1
GUCGCAAGCC--AGGUUCUGAGCAACAGGUUGGCGGCUCGUGCUCUCGCUCUGGCGGCUGAGGCGAUCGGGUCCGGCGUCAGGACGCCAGAGCGAUAGUGAGAGUGA
.......(((--((..((((.....))))))))).((((..(((.(((((((((((.((((.((...((....)))).))))..))))))))))).)))..)))).. ( -50.60)
>consensus
GUCGCUAGCCACAGGUUCUGAGCAACAGGUUGUCGAUGUGUGCUCUCGCUCGGACAGCCGAAGCGAUCGGGUCGGGCGUCAGGAUGCCAGAGCGAGAGCGAG_____
((((.(((((....((.....))....))))).))))...(((((((((((.(((..((((.....))))))).(((((....))))).)))))))))))....... (-42.45 = -41.83 +  -0.63)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 3,821,731 – 3,821,833
Length 102
Sequences 4
Columns 107
Reading direction reverse
Mean pairwise identity 89.31
Mean single sequence MFE -38.98
Consensus MFE -34.78
Energy contribution -35.27
Covariance contribution 0.50
Combinations/Pair 1.10
Mean z-score -2.03
Structure conservation index 0.89
SVM decision value 1.40
SVM RNA-class probability 0.950470
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3821731 102 - 27905053
-----CUCGCUCUCGCUCUGGCAUCCUGACGCCCGACCCGAUCGCUUCGGCUGUCAGAGCGAGAGCACACAUCGACAACCUGUUGCUCAGAACCUGUGGCUAGCGAC
-----.(((((((((((((((((.((.((.((...........)).)))).))))))))))))(((.(((((((((((....))).)).))...)))))))))))). ( -40.20)
>DroSec_CAF1 49474 102 - 1
-----CUCGCUCUCGCUCUGGCAUCCUGACGCCCGACCCGAUCGCUUCGGCUGUCCGAGCGAGAGCACACAUCGACAACCUGUUGCUCAGAACCUGUGGCUAGCGAC
-----.((((((((((((.(((........))).(((((((.....))))..))).)))))))(((.(((((((((((....))).)).))...)))))))))))). ( -36.90)
>DroSim_CAF1 54038 102 - 1
-----CUCGCUCUCGCUCUGGCAUCCUGACGCCCGACCCGAUCGCUUCGGCUGUCCGAGCGAGAGCACACAUCGACAACCUGUUGCUCAGAACCUGUGGCUAGCGAC
-----.((((((((((((.(((........))).(((((((.....))))..))).)))))))(((.(((((((((((....))).)).))...)))))))))))). ( -36.90)
>DroEre_CAF1 40759 105 - 1
UCACUCUCACUAUCGCUCUGGCGUCCUGACGCCGGACCCGAUCGCCUCAGCCGCCAGAGCGAGAGCACGAGCCGCCAACCUGUUGCUCAGAACCU--GGCUUGCGAC
.........((.(((((((((((..((((.((((....))...)).)))).))))))))))).))(.(((((((.....(((.....)))....)--)))))).).. ( -41.90)
>consensus
_____CUCGCUCUCGCUCUGGCAUCCUGACGCCCGACCCGAUCGCUUCGGCUGUCAGAGCGAGAGCACACAUCGACAACCUGUUGCUCAGAACCUGUGGCUAGCGAC
........(((((((((((((((..((((.((...........)).)))).)))))))))))))))...............((((((.((.........)))))))) (-34.78 = -35.27 +   0.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

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