Locus 3458

Sequence ID	2L_DroMel_CAF1
Location	10,067,237 – 10,067,363
Length	126
Max. P	0.998112

overview

Window 7

Location	10,067,237 – 10,067,328
Length	91
Sequences	5
Columns	96
Reading direction	reverse
Mean pairwise identity	91.07
Mean single sequence MFE	-29.48
Consensus MFE	-24.36
Energy contribution	-23.68
Covariance contribution	-0.68
Combinations/Pair	1.23
Mean z-score	-1.42
Structure conservation index	0.83
SVM decision value	0.29
SVM RNA-class probability	0.672414
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10067237 91 - 22407834
GCAAGCCGGCAAGUGAGAGCGCGCUUGUGUGCACCGAUGUACCACUCGGCGUAUGCGUAAUGCGCACAUGGCACAUUCAAAUUCAAACACA-----
....((((....((....))((((.(((((((.((((........)))).)))))))....))))...))))...................----- ( -28.40)
>DroSec_CAF1 2421 89 - 1
GGAAGCCGGCAAGUGA--GCGCGCGUGUGUGCACCGAUGUACCACUCGGCGUAUGCGUAAUGCGCACAUGGCACAUUCAAAUUCAAACACA-----
....((((((......--))((((((((((((.((((........)))).))))))...))))))...))))...................----- ( -27.80)
>DroSim_CAF1 2437 87 - 1
GGAAGCCGGCAAGUGA--GCGCGCGUGUGUGCACCGAUGUACCACUCGGCGUAUGCGUAAUGCGCACAUGGCACAUUCAAAUUCAAACA-------
....((((((......--))((((((((((((.((((........)))).))))))...))))))...)))).................------- ( -27.80)
>DroEre_CAF1 2404 89 - 1
GCAAGCCGGCAAGUGA--GCGCGCGUGUGUGUACCGAUGUGCCACUCGGCGUAUGCGUAAUGCGCACAUGGCACAUUCAAAUUCAAACACA-----
((..((((.....)).--))..))((((.((....(((((((((....((((((.....))))))...)))))))))......)).)))).----- ( -30.40)
>DroYak_CAF1 2373 94 - 1
GCCAGCCGGCAAGUGU--GUGUGUGUGUGUAUACCGAUGUGCCACUCGGCGUAUGCGUAAUGCGCACAUGGCACAUUCAAAUUCAAACACAAAGAC
(((....)))....((--.(.(((((.((......(((((((((....((((((.....))))))...)))))))))......)).))))).).)) ( -33.00)
>consensus
GCAAGCCGGCAAGUGA__GCGCGCGUGUGUGCACCGAUGUACCACUCGGCGUAUGCGUAAUGCGCACAUGGCACAUUCAAAUUCAAACACA_____
....((((((........))((((((((((((.((((........)))).))))))...))))))...))))........................ (-24.36 = -23.68 +  -0.68)

alignment

secondary structure

dotplot

Window 8

Location	10,067,269 – 10,067,363
Length	94
Sequences	5
Columns	96
Reading direction	forward
Mean pairwise identity	93.38
Mean single sequence MFE	-33.74
Consensus MFE	-28.76
Energy contribution	-29.24
Covariance contribution	0.48
Combinations/Pair	1.07
Mean z-score	-2.51
Structure conservation index	0.85
SVM decision value	3.01
SVM RNA-class probability	0.998112
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10067269 94 + 22407834
UACGCAUACGCCGAGUGGUACAUCGGUGCACACAAGCGCGCUCUCACUUGCCGGCUUGCCACAUCAAAGUGU--GUGCGUGUAAUUAUGUGAUUAG
(((((((((((.((((((((..(((((((......))))((........)))))..)))))).))...))))--)))))))............... ( -33.50)
>DroSec_CAF1 2453 92 + 1
UACGCAUACGCCGAGUGGUACAUCGGUGCACACACGCGCGC--UCACUUGCCGGCUUCCCACAUCAAAGUGU--GUGCGUGUAAUUAUGUGAUUAG
..((((((((((((........)))))).....((((((((--.(((((...((....))......))))).--))))))))...))))))..... ( -32.80)
>DroSim_CAF1 2467 92 + 1
UACGCAUACGCCGAGUGGUACAUCGGUGCACACACGCGCGC--UCACUUGCCGGCUUCCCACAUCAAAGUGU--GUGCGUGUAAUUAUGUGAUUAG
..((((((((((((........)))))).....((((((((--.(((((...((....))......))))).--))))))))...))))))..... ( -32.80)
>DroEre_CAF1 2436 92 + 1
UACGCAUACGCCGAGUGGCACAUCGGUACACACACGCGCGC--UCACUUGCCGGCUUGCCACAUCAAAGUGU--GUGCGUGUAAUUAUGUGAUUAG
..((((((.(((((........)))))......((((((((--.(((((...((....))......))))).--))))))))...))))))..... ( -32.70)
>DroYak_CAF1 2410 94 + 1
UACGCAUACGCCGAGUGGCACAUCGGUAUACACACACACAC--ACACUUGCCGGCUGGCCACAUCAAAGUGUGUGUGCGUGUAAUUAUGUGAUUAG
..((((((.(((((........)))))....((((.(((((--(((((((((....))).......))))))))))).))))...))))))..... ( -36.91)
>consensus
UACGCAUACGCCGAGUGGUACAUCGGUGCACACACGCGCGC__UCACUUGCCGGCUUGCCACAUCAAAGUGU__GUGCGUGUAAUUAUGUGAUUAG
..((((((((((((........)))))).....((((((((...(((((...((....))......)))))...))))))))...))))))..... (-28.76 = -29.24 +   0.48)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:52:57 2006