Locus 4855

Sequence ID	2R_DroMel_CAF1
Location	15,915,537 – 15,915,682
Length	145
Max. P	0.915890

overview

Window 6

Location	15,915,537 – 15,915,648
Length	111
Sequences	5
Columns	114
Reading direction	reverse
Mean pairwise identity	93.86
Mean single sequence MFE	-24.82
Consensus MFE	-21.04
Energy contribution	-21.32
Covariance contribution	0.28
Combinations/Pair	1.08
Mean z-score	-1.35
Structure conservation index	0.85
SVM decision value	0.28
SVM RNA-class probability	0.666705
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15915537 111 - 20766785
---AUUGCCUUUCCAACUGGUUGUCCCGCGAGUACUCGCAGUUCUAAUUAAGAUCCUAGGCUAAACAACCGCAGCCUAAUCACGCUCCACCUGCCAUCUAUGCACCUUUCCACU
---..(((..........((((((.((((((....))))...(((.....))).....))....))))))((((................)))).......))).......... ( -18.79)
>DroSec_CAF1 43283 114 - 1
CAGAUUGCCUUGCCAACUGGCUGUCCCGCGAGUACUCGCACUUCUAAUUAACAUCCUGGGCCAAACAACCGCAGCCUAAUCACGCUGCACCUGCCAUCUUUGCACCUUUCCACU
(((...((((.(((....)))......((((....))))..................)))).........(((((........)))))..)))..................... ( -24.40)
>DroSim_CAF1 40713 114 - 1
CAGAUUGCCUUGCCAACUGGCUGUCCCGCGAGUACUCGCACUUCUAAUUAAGAUCCUGGGCCAAACAACCGCAGCCUAAUCACGCUGCACCUGCCAUCUUUGCACCUUUCCACU
.((((.((...(((....)))((.(((((((....))))...(((.....)))....))).)).......(((((........)))))....)).))))............... ( -27.30)
>DroEre_CAF1 41464 114 - 1
UUGAUUGCUUUGCCAACUGGCUGUCCCGCGAGUACUCGCACUUCUAAUUAAGAUGCUGGGCCAAACAACCGCAGCCUAAUCACGCUGCACCUGCCAUCUUUGCACCUUUCCACU
..........(((.((.((((((.(((((((....))))...(((.....)))....))).)).......(((((........)))))....))))..)).))).......... ( -27.10)
>DroYak_CAF1 44699 114 - 1
CCGAUUGCUUCGCCAACUGGCUGUCCCGCGAGUAGUCGCACUUCUAAUUAAGAUCCUGGGCCAAACAACCGCAGCCUAAUCACGCUGCACCUGCCAUCUUUGCACCUUUCCACU
..(((.((...(((....)))((.(((((((....))))...(((.....)))....))).)).......(((((........)))))....)).)))................ ( -26.50)
>consensus
CAGAUUGCCUUGCCAACUGGCUGUCCCGCGAGUACUCGCACUUCUAAUUAAGAUCCUGGGCCAAACAACCGCAGCCUAAUCACGCUGCACCUGCCAUCUUUGCACCUUUCCACU
.....(((.........((((((.(((((((....))))...(((.....)))....))).)).......(((((........)))))....)))).....))).......... (-21.04 = -21.32 +   0.28)

alignment

secondary structure

dotplot

Window 7

Location	15,915,572 – 15,915,682
Length	110
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	84.92
Mean single sequence MFE	-39.36
Consensus MFE	-29.16
Energy contribution	-29.36
Covariance contribution	0.20
Combinations/Pair	1.19
Mean z-score	-2.24
Structure conservation index	0.74
SVM decision value	1.10
SVM RNA-class probability	0.915890
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15915572 110 - 20766785
AUGUAGGU--UGUGGUGGGCGUAGUAAAGCAUUAAG-------AUUGCCUUUCCAACUGGUUGUCCCGCGAGUACUCGCAGUUCUAAUUAAGAUCCUAGGCUAAACAACCGCAGCCUAA
...(((((--((((((.(((.(((...........(-------((.(((.........))).)))..((((....))))................))).))).....))))))))))). ( -35.10)
>DroSec_CAF1 43318 117 - 1
AUGUAGGU--UGUGGUGGGCGUAGUAAAGCAUUCAGAUCGCAGAUUGCCUUGCCAACUGGCUGUCCCGCGAGUACUCGCACUUCUAAUUAACAUCCUGGGCCAAACAACCGCAGCCUAA
...(((((--((((((.(((.(((....(((..(((...((((......))))...)))..)))...((((....))))................))).))).....))))))))))). ( -40.00)
>DroSim_CAF1 40748 117 - 1
AUGUAGGU--UGUGGUGGGCGUAGUAAAGCAUUCAGAUCGCAGAUUGCCUUGCCAACUGGCUGUCCCGCGAGUACUCGCACUUCUAAUUAAGAUCCUGGGCCAAACAACCGCAGCCUAA
...(((((--((((((.(((.(((...........((((...(((.(((.........))).)))..((((....))))............))))))).))).....))))))))))). ( -40.10)
>DroEre_CAF1 41499 110 - 1
UUGUAGGU--UGUGGUGGGCACAGUAAGGCAUU-------UUGAUUGCUUUGCCAACUGGCUGUCCCGCGAGUACUCGCACUUCUAAUUAAGAUGCUGGGCCAAACAACCGCAGCCUAA
...(((((--((((((.(((.(.....((((((-------(((((((....(((....)))......((((....)))).....))))))))))))).)))).....))))))))))). ( -45.20)
>DroYak_CAF1 44734 105 - 1
AUGCAGGUGGUGUGGUGGGCA----------UUCG----CCCGAUUGCUUCGCCAACUGGCUGUCCCGCGAGUAGUCGCACUUCUAAUUAAGAUCCUGGGCCAAACAACCGCAGCCUAA
.....(((((.(..((((((.----------...)----))).))..).)))))....(((((((((((((....))))...(((.....)))....)))..........))))))... ( -36.40)
>consensus
AUGUAGGU__UGUGGUGGGCGUAGUAAAGCAUUCAG____CAGAUUGCCUUGCCAACUGGCUGUCCCGCGAGUACUCGCACUUCUAAUUAAGAUCCUGGGCCAAACAACCGCAGCCUAA
...(((((..((((((.(((.(((..................(((.(((.........))).)))..((((....))))................))).))).....))))))))))). (-29.16 = -29.36 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:30:52 2006