Locus 6497

Sequence ID	2R_DroMel_CAF1
Location	20,304,828 – 20,304,922
Length	94
Max. P	0.990914

overview

Window 0

Location	20,304,828 – 20,304,922
Length	94
Sequences	6
Columns	94
Reading direction	forward
Mean pairwise identity	70.42
Mean single sequence MFE	-26.20
Consensus MFE	-20.32
Energy contribution	-20.85
Covariance contribution	0.53
Combinations/Pair	1.24
Mean z-score	-2.04
Structure conservation index	0.78
SVM decision value	2.24
SVM RNA-class probability	0.990914
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20304828 94 + 20766785
CUCGCUGGAGGCGCUCCUUCAGGAAGCGCCUGAUGCUGACCAGCUCCCUAUCCGCCUCCGGCAUUUUCGCUCUCGGAUCGGAACUCCUUUAUUC
...((((((((((((((....)).)))))))........)))))......((((..((((((......))...)))).))))............ ( -32.00)
>DroVir_CAF1 25760 78 + 1
CGCGCUGCAGUCGCUCCUUUAGAAAACGACGCGUUUUAAUUAACUCCUGCACCGAAUCAUGCAUAAUUCAA------UUAAAAU----------
......((.((((.((.....))...))))))(((((((((......((((........))))......))------)))))))---------- ( -11.20)
>DroSec_CAF1 21721 74 + 1
CUCGCUGGAGGCGCUCCUUUAGGAAGCGCCUGAUGCUGACCAGCUCCCUAUCCGCCUCCGGCAUUUUCGCUCCU--------------------
...((((((((((((((....)).)))....((.(((....))))).......)))))))))............-------------------- ( -28.90)
>DroSim_CAF1 23417 74 + 1
CUCGCUGGAGGCGCUCCUUCAGGAAGCGCCUGAUGUUGACCAGCUCUCUAUCCGCCUCCGGCAUUUUCGCUCCU--------------------
...((((((((((.....(((((.....))))).(((....)))........))))))))))............-------------------- ( -27.70)
>DroEre_CAF1 22095 88 + 1
CUCGCUGGAGGCGCUCCUUAAGGAAGCGCCUGAUGCUGACCAGUUCCUUAUCCGCCUCCGGCAUUUGCGCUCUCGGUUUACAGUUCCU------
...((((((((((.....(((((((....(((........))))))))))..))))))))))..........................------ ( -29.00)
>DroYak_CAF1 21818 88 + 1
CCCGCUGCAGGCGCUCCUUUAGGAAGCGCCUGAUGCUGACCAGUUCCUUAUCCGCCUCCGGCAUUUGCGCUCUCAAAUUGGAAUUCCU------
...((..((((((((((....)).))))))))..)).....((((((......(((...)))(((((......))))).))))))...------ ( -28.40)
>consensus
CUCGCUGGAGGCGCUCCUUUAGGAAGCGCCUGAUGCUGACCAGCUCCCUAUCCGCCUCCGGCAUUUUCGCUCUC___UU__AAU__________
...((((((((((((((....)).))).......(((....))).........)))))))))................................ (-20.32 = -20.85 +   0.53)

alignment

secondary structure

dotplot

Window 1

Location	20,304,828 – 20,304,922
Length	94
Sequences	6
Columns	94
Reading direction	reverse
Mean pairwise identity	70.42
Mean single sequence MFE	-27.70
Consensus MFE	-20.14
Energy contribution	-20.62
Covariance contribution	0.48
Combinations/Pair	1.21
Mean z-score	-1.42
Structure conservation index	0.73
SVM decision value	1.55
SVM RNA-class probability	0.963251
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20304828 94 - 20766785
GAAUAAAGGAGUUCCGAUCCGAGAGCGAAAAUGCCGGAGGCGGAUAGGGAGCUGGUCAGCAUCAGGCGCUUCCUGAAGGAGCGCCUCCAGCGAG
...........((((.(((((.(.((......))).....))))).))))(((((........(((((((((.....))))))))))))))... ( -34.00)
>DroVir_CAF1 25760 78 - 1
----------AUUUUAA------UUGAAUUAUGCAUGAUUCGGUGCAGGAGUUAAUUAAAACGCGUCGUUUUCUAAAGGAGCGACUGCAGCGCG
----------.((((((------((((....(((((......)))))....)))))))))).((((((((((.....)))))))).))...... ( -22.40)
>DroSec_CAF1 21721 74 - 1
--------------------AGGAGCGAAAAUGCCGGAGGCGGAUAGGGAGCUGGUCAGCAUCAGGCGCUUCCUAAAGGAGCGCCUCCAGCGAG
--------------------...........(((.(((((((..((((((((..(((.......)))))))))))......))))))).))).. ( -28.70)
>DroSim_CAF1 23417 74 - 1
--------------------AGGAGCGAAAAUGCCGGAGGCGGAUAGAGAGCUGGUCAACAUCAGGCGCUUCCUGAAGGAGCGCCUCCAGCGAG
--------------------...........(((.((((((..........(((((....)))))..(((((.....))))))))))).))).. ( -25.70)
>DroEre_CAF1 22095 88 - 1
------AGGAACUGUAAACCGAGAGCGCAAAUGCCGGAGGCGGAUAAGGAACUGGUCAGCAUCAGGCGCUUCCUUAAGGAGCGCCUCCAGCGAG
------..................((((....)).((((((..........(((((....)))))..(((((.....))))))))))).))... ( -26.30)
>DroYak_CAF1 21818 88 - 1
------AGGAAUUCCAAUUUGAGAGCGCAAAUGCCGGAGGCGGAUAAGGAACUGGUCAGCAUCAGGCGCUUCCUAAAGGAGCGCCUGCAGCGGG
------..((.((((.(((((......))))).(((....)))....))))....)).((..((((((((((.....))))))))))..))... ( -29.10)
>consensus
__________AUU__AA___GAGAGCGAAAAUGCCGGAGGCGGAUAAGGAGCUGGUCAGCAUCAGGCGCUUCCUAAAGGAGCGCCUCCAGCGAG
...............................(((.((((((..........(((((....)))))..(((((.....))))))))))).))).. (-20.14 = -20.62 +   0.48)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:12:19 2006