Locus 8310

Sequence ID	X_DroMel_CAF1
Location	20,660,403 – 20,660,553
Length	150
Max. P	0.980992

overview

Window 6

Location	20,660,403 – 20,660,513
Length	110
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	87.36
Mean single sequence MFE	-29.14
Consensus MFE	-22.20
Energy contribution	-22.20
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.04
Structure conservation index	0.76
SVM decision value	0.87
SVM RNA-class probability	0.870547
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20660403 110 - 22224390
AAAACAAGACUGGUCGCAGAACGCAUCAAUCAACGGACAGAGAUUGAUGUGUGUCCACAGGCGGGUUAACAAAAUCCACCCCCACCUCC------UCCUACACC--AGACAC--GCCUCC
.........(((((.(.((.(((((((((((..........))))))))))).......((.((((...........))))))......------..)).))))--))....--...... ( -28.10)
>DroSec_CAF1 62173 116 - 1
AAAACAAGACUGGUCGCAGAACGCAUCAAUCAACGGACAGAGAUUGAUGUGUGUCCACAGGCGGGUUAACAAAAUCCACCUCCACCUCCUCCUCCUCCCACACC--AGCCAC--GCCCCC
.......(.(((((......(((((((((((..........)))))))))))......(((.(((((.....))))).)))....................)))--)).)..--...... ( -27.90)
>DroSim_CAF1 39580 113 - 1
AAAACAAGACUGGUCGCAGAACGCAUCAAUCAACGGACAGAGAUUGAUGUGUGUCCACAGGCGGGUUAACAAAAUCCACCUCCACCUCC---UCCUCCCACACC--AGCCAC--GCCCCC
.......(.(((((......(((((((((((..........)))))))))))......(((.(((((.....))))).)))........---.........)))--)).)..--...... ( -27.90)
>DroEre_CAF1 57691 112 - 1
AAAACAAGACUGGUCGCAGAACGCAUCAAUCAACGGACAGAGAUUGAUGUGUGUCCACAGGCGGGUUAACAUAAGCCACCUCCACCUCC------CC--CUGCCCCUGCCCCUGCCCCCC
...........((..((((.(((((((((((..........))))))))))).....((((.(((......................))------))--))).........))))..)). ( -30.55)
>DroYak_CAF1 59001 105 - 1
AAAACAAGACUGGUCGCAGAACGCAUCAAUCAACGGACAGAGAUUGAUGUGUGUCCACAGGCGGGUUAACAAA---CUCCUCCACCGCC------CU--CCGCC--AGCCAC--GCCCAU
.......(.((((.((.((.(((((((((((..........))))))))))).......(((((.........---........)))))------))--.))))--)).)..--...... ( -31.23)
>consensus
AAAACAAGACUGGUCGCAGAACGCAUCAAUCAACGGACAGAGAUUGAUGUGUGUCCACAGGCGGGUUAACAAAAUCCACCUCCACCUCC______UCC_ACACC__AGCCAC__GCCCCC
.......((((.(((...(((((((((((((..........))))))))))).))....))).))))..................................................... (-22.20 = -22.20 +  -0.00)

alignment

secondary structure

dotplot

Window 7

Location	20,660,433 – 20,660,553
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.25
Mean single sequence MFE	-33.44
Consensus MFE	-32.16
Energy contribution	-32.24
Covariance contribution	0.08
Combinations/Pair	1.06
Mean z-score	-1.44
Structure conservation index	0.96
SVM decision value	1.50
SVM RNA-class probability	0.959118
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20660433 120 + 22224390
GGUGGAUUUUGUUAACCCGCCUGUGGACACACAUCAAUCUCUGUCCGUUGAUUGAUGCGUUCUGCGACCAGUCUUGUUUUUGAAAGCAAAAAUUAAACUCGCACACGAGUAGACGAAAAA
(((((.((.....)).)))))((..((.((.((((((((..........)))))))).))))..))....((((.(((((((....)))))))...(((((....)))))))))...... ( -34.10)
>DroSec_CAF1 62209 120 + 1
GGUGGAUUUUGUUAACCCGCCUGUGGACACACAUCAAUCUCUGUCCGUUGAUUGAUGCGUUCUGCGACCAGUCUUGUUUUUGAAAGCAAAAAUUAAACUCGCAUACGAGUGGACGAAAAA
(((((.((.....)).)))))((..((.((.((((((((..........)))))))).))))..))....((((.(((((((....)))))))...(((((....)))))))))...... ( -34.10)
>DroSim_CAF1 39613 120 + 1
GGUGGAUUUUGUUAACCCGCCUGUGGACACACAUCAAUCUCUGUCCGUUGAUUGAUGCGUUCUGCGACCAGUCUUGUUUUUGAAAGCAAAAAUUAAACUCGCAUACGAGUGGACGAAAAA
(((((.((.....)).)))))((..((.((.((((((((..........)))))))).))))..))....((((.(((((((....)))))))...(((((....)))))))))...... ( -34.10)
>DroEre_CAF1 57723 120 + 1
GGUGGCUUAUGUUAACCCGCCUGUGGACACACAUCAAUCUCUGUCCGUUGAUUGAUGCGUUCUGCGACCAGUCUUGUUUUUGAAAGCAAAAAUUAAACUCGCAUGCGAGUGGACGAAAAA
(((((.(((...))).)))))((..((.((.((((((((..........)))))))).))))..))....((((.(((((((....)))))))...(((((....)))))))))...... ( -35.30)
>DroYak_CAF1 59029 117 + 1
GGAG---UUUGUUAACCCGCCUGUGGACACACAUCAAUCUCUGUCCGUUGAUUGAUGCGUUCUGCGACCAGUCUUGUUUUUGAAAGCAAAAAUUAAACUCGCAUGUGAGUGGACGAAAGA
((.(---((....)))))...((..((.((.((((((((..........)))))))).))))..))....((((.(((((((....)))))))...(((((....)))))))))...... ( -29.60)
>consensus
GGUGGAUUUUGUUAACCCGCCUGUGGACACACAUCAAUCUCUGUCCGUUGAUUGAUGCGUUCUGCGACCAGUCUUGUUUUUGAAAGCAAAAAUUAAACUCGCAUACGAGUGGACGAAAAA
(((((...........)))))((..((.((.((((((((..........)))))))).))))..))....((((.(((((((....)))))))...(((((....)))))))))...... (-32.16 = -32.24 +   0.08)

alignment

secondary structure

dotplot

Window 8

Location	20,660,433 – 20,660,553
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.25
Mean single sequence MFE	-31.94
Consensus MFE	-31.52
Energy contribution	-31.48
Covariance contribution	-0.04
Combinations/Pair	1.03
Mean z-score	-1.50
Structure conservation index	0.99
SVM decision value	1.88
SVM RNA-class probability	0.980992
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 20660433 120 - 22224390
UUUUUCGUCUACUCGUGUGCGAGUUUAAUUUUUGCUUUCAAAAACAAGACUGGUCGCAGAACGCAUCAAUCAACGGACAGAGAUUGAUGUGUGUCCACAGGCGGGUUAACAAAAUCCACC
......((((..((.(((((.(((((..((((((....))))))..))))).).))))))(((((((((((..........)))))))))))......))))(((((.....)))))... ( -33.70)
>DroSec_CAF1 62209 120 - 1
UUUUUCGUCCACUCGUAUGCGAGUUUAAUUUUUGCUUUCAAAAACAAGACUGGUCGCAGAACGCAUCAAUCAACGGACAGAGAUUGAUGUGUGUCCACAGGCGGGUUAACAAAAUCCACC
......((..((((((.(((((((((..((((((....))))))..))))...)))))..(((((((((((..........)))))))))))........))))))..)).......... ( -31.70)
>DroSim_CAF1 39613 120 - 1
UUUUUCGUCCACUCGUAUGCGAGUUUAAUUUUUGCUUUCAAAAACAAGACUGGUCGCAGAACGCAUCAAUCAACGGACAGAGAUUGAUGUGUGUCCACAGGCGGGUUAACAAAAUCCACC
......((..((((((.(((((((((..((((((....))))))..))))...)))))..(((((((((((..........)))))))))))........))))))..)).......... ( -31.70)
>DroEre_CAF1 57723 120 - 1
UUUUUCGUCCACUCGCAUGCGAGUUUAAUUUUUGCUUUCAAAAACAAGACUGGUCGCAGAACGCAUCAAUCAACGGACAGAGAUUGAUGUGUGUCCACAGGCGGGUUAACAUAAGCCACC
......((..((((((.(((((((((..((((((....))))))..))))...)))))..(((((((((((..........)))))))))))........))))))..)).......... ( -33.70)
>DroYak_CAF1 59029 117 - 1
UCUUUCGUCCACUCACAUGCGAGUUUAAUUUUUGCUUUCAAAAACAAGACUGGUCGCAGAACGCAUCAAUCAACGGACAGAGAUUGAUGUGUGUCCACAGGCGGGUUAACAAA---CUCC
......((..((((...(((((((((..((((((....))))))..))))...)))))..(((((((((((..........)))))))))))(((....)))))))..))...---.... ( -28.90)
>consensus
UUUUUCGUCCACUCGUAUGCGAGUUUAAUUUUUGCUUUCAAAAACAAGACUGGUCGCAGAACGCAUCAAUCAACGGACAGAGAUUGAUGUGUGUCCACAGGCGGGUUAACAAAAUCCACC
......((..((((((.(((((((((..((((((....))))))..))))...)))))..(((((((((((..........)))))))))))........))))))..)).......... (-31.52 = -31.48 +  -0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:00:50 2006