Locus 5780

Sequence ID	2R_DroMel_CAF1
Location	18,312,808 – 18,312,908
Length	100
Max. P	0.687949

overview

Window 9

Location	18,312,808 – 18,312,908
Length	100
Sequences	6
Columns	110
Reading direction	forward
Mean pairwise identity	81.74
Mean single sequence MFE	-38.43
Consensus MFE	-25.35
Energy contribution	-25.69
Covariance contribution	0.34
Combinations/Pair	1.32
Mean z-score	-1.67
Structure conservation index	0.66
SVM decision value	0.16
SVM RNA-class probability	0.613772
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18312808 100 + 20766785
AAUGUCCUCGAUUCCAGCCAAGCGCUUGCUGGAAAGGGACAUGGUGGUGGGCAUCGUAGAUGUGGUCGUAGUGACUGCA--CUGUUGCCCCUAAUAAGG-----GGC---
.(((((((...(((((((.((....))))))))).)))))))((((.....)))).(((.((..(((.....)))..))--)))..((((((....)))-----)))--- ( -39.80)
>DroSec_CAF1 6078 100 + 1
GAUAUCCUCGAUUCCAGCCAAGCGCUUGCUGGAAAGGGACAUGGUGGUGGGCAUCGUGGAUGUGGUCGUAGUGACCGCA--CUGUUGCCCCUAAUAAGG-----GGC---
...((((.((((.((.((((.....((.((....)).)).....)))).)).)))).))))((((((.....)))))).--.....((((((....)))-----)))--- ( -40.60)
>DroSim_CAF1 5459 100 + 1
GAUAUCCUCGAUUCCAGCCAAGCGCUUGCUGGAAAGGGACAUGGUGGUGGGCAUCGUGGAUGUGGUCGUAGUGACCGCA--CUGUUGCCCCUAAUAAGG-----GGC---
...((((.((((.((.((((.....((.((....)).)).....)))).)).)))).))))((((((.....)))))).--.....((((((....)))-----)))--- ( -40.60)
>DroEre_CAF1 6084 100 + 1
GAUGUCCUCGAUUCCAGCCAAGCGCUUGCUGGAAAGGGACAUGGUGGUGGGCAUGGUGGAUGUGGUUGUAGUGACUGCA--CUGUUGCCCCUAAUAAGG-----GGC---
.(((((((...(((((((.((....))))))))).)))))))..(((.(((((..(..(.((..(((.....)))..))--)..)))))))))......-----...--- ( -36.70)
>DroWil_CAF1 33614 103 + 1
AAUGUCCUCAAUGUUGGCCAAACGCUUGCUGGACAAGGACAGAGCGGCUGA-------GAUGGAGUUGCAGCUGCUGCUGCCUGUGGCCUGAGCUGAGGAUAGCUGCGGC
..((((((((.....(((((...(((....)).).(((.(((((((((((.-------.((...))..)))))))).)))))).))))).....))))))))........ ( -40.10)
>DroYak_CAF1 5988 100 + 1
GAUAUCCUCGAUUCCAGCCAAUCGCUUGCUGGAAAGGGACAUGGUGGUGGGCAUGGUGGAUGUGGUUGUAGUGACUGCA--CUGUUGCCCCUAAUAAGA-----GGC---
.....((((..(((((((.........)))))))..........(((.(((((..(..(.((..(((.....)))..))--)..)))))))))....))-----)).--- ( -32.80)
>consensus
GAUAUCCUCGAUUCCAGCCAAGCGCUUGCUGGAAAGGGACAUGGUGGUGGGCAUCGUGGAUGUGGUCGUAGUGACUGCA__CUGUUGCCCCUAAUAAGG_____GGC___
....((((...(((((((.((....))))))))).)))).....(((.(((((.......(((((((.....)))))))......))))))))................. (-25.35 = -25.69 +   0.34)

alignment

secondary structure

dotplot

Window 0

Location	18,312,808 – 18,312,908
Length	100
Sequences	6
Columns	110
Reading direction	reverse
Mean pairwise identity	81.74
Mean single sequence MFE	-32.90
Consensus MFE	-17.42
Energy contribution	-18.25
Covariance contribution	0.83
Combinations/Pair	1.14
Mean z-score	-2.59
Structure conservation index	0.53
SVM decision value	0.32
SVM RNA-class probability	0.687949
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18312808 100 - 20766785
---GCC-----CCUUAUUAGGGGCAACAG--UGCAGUCACUACGACCACAUCUACGAUGCCCACCACCAUGUCCCUUUCCAGCAAGCGCUUGGCUGGAAUCGAGGACAUU
---(((-----(((....))))))....(--((..(((.....))))))...................(((((((.(((((((.........)))))))..).)))))). ( -33.40)
>DroSec_CAF1 6078 100 - 1
---GCC-----CCUUAUUAGGGGCAACAG--UGCGGUCACUACGACCACAUCCACGAUGCCCACCACCAUGUCCCUUUCCAGCAAGCGCUUGGCUGGAAUCGAGGAUAUC
---(((-----(((....))))))....(--((.((((.....)))).((((...))))..)))....(((((((.(((((((.........)))))))..).)))))). ( -35.60)
>DroSim_CAF1 5459 100 - 1
---GCC-----CCUUAUUAGGGGCAACAG--UGCGGUCACUACGACCACAUCCACGAUGCCCACCACCAUGUCCCUUUCCAGCAAGCGCUUGGCUGGAAUCGAGGAUAUC
---(((-----(((....))))))....(--((.((((.....)))).((((...))))..)))....(((((((.(((((((.........)))))))..).)))))). ( -35.60)
>DroEre_CAF1 6084 100 - 1
---GCC-----CCUUAUUAGGGGCAACAG--UGCAGUCACUACAACCACAUCCACCAUGCCCACCACCAUGUCCCUUUCCAGCAAGCGCUUGGCUGGAAUCGAGGACAUC
---(((-----(((....))))))...((--((....))))...........................(((((((.(((((((.........)))))))..).)))))). ( -31.30)
>DroWil_CAF1 33614 103 - 1
GCCGCAGCUAUCCUCAGCUCAGGCCACAGGCAGCAGCAGCUGCAACUCCAUC-------UCAGCCGCUCUGUCCUUGUCCAGCAAGCGUUUGGCCAACAUUGAGGACAUU
..........(((((((....(((((..(((((.(((.((((..........-------.)))).))))))))((((.....))))....)))))....))))))).... ( -34.70)
>DroYak_CAF1 5988 100 - 1
---GCC-----UCUUAUUAGGGGCAACAG--UGCAGUCACUACAACCACAUCCACCAUGCCCACCACCAUGUCCCUUUCCAGCAAGCGAUUGGCUGGAAUCGAGGAUAUC
---(((-----(((....))))))...((--((....))))........((((..((((........))))((...(((((((.........)))))))..))))))... ( -26.80)
>consensus
___GCC_____CCUUAUUAGGGGCAACAG__UGCAGUCACUACAACCACAUCCACGAUGCCCACCACCAUGUCCCUUUCCAGCAAGCGCUUGGCUGGAAUCGAGGACAUC
...................((((((......))).((....))................)))......((((((..(((((((.........)))))))....)))))). (-17.42 = -18.25 +   0.83)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:54:14 2006