Locus 3858

Sequence ID	2R_DroMel_CAF1
Location	12,758,377 – 12,758,473
Length	96
Max. P	0.998201

overview

Window 6

Location	12,758,377 – 12,758,473
Length	96
Sequences	5
Columns	98
Reading direction	forward
Mean pairwise identity	93.83
Mean single sequence MFE	-28.70
Consensus MFE	-26.18
Energy contribution	-26.18
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.04
Structure conservation index	0.91
SVM decision value	3.03
SVM RNA-class probability	0.998201
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12758377 96 + 20766785
UUCGCAGCCCGAGUGCAACUGUAUUCCGCUGUUUGCCAGCCCACUCGCAUGUUGCAUCCGCUGGCGCAUUGACUUUCAUGUUGCGCC--CCCCCGCCA
...(((((..(..(((((((((.....((((.....))))......))).))))))..))))((((((.((.....))...))))))--.....)).. ( -29.80)
>DroSec_CAF1 99705 98 + 1
UUCGCAGCCCGACUGCAACUGUAUUCCGCUGUUUGCCAGCCCACUCGCAUGUUGCAUCCGCUGGCGCAUUGACUUUCAUGUUGCGCCUCCCCCCGCCA
...(((((..((.(((((((((.....((((.....))))......))).)))))))).)))((((((.((.....))...)))))).......)).. ( -29.60)
>DroSim_CAF1 107296 98 + 1
UUCGCAGCCCGACUGCAACUGUAUUCCGCUGUUUGCCAGCCCACUCGCAUGUUGCAUCCGCUGGCGCAUUGACUUUCAUGUUGCGCCUCCCCCCGCCA
...(((((..((.(((((((((.....((((.....))))......))).)))))))).)))((((((.((.....))...)))))).......)).. ( -29.60)
>DroEre_CAF1 100707 94 + 1
UCCCCAUCCCGACUGCAACUGUAUUCCGCUGUUUGCCAGCCCACUCGCAUGUUGCAUCCGCUGGCGCAUUGACUUUCAUGUUGCGCC---C-CUGCCA
..........((.(((((((((.....((((.....))))......))).)))))))).((.((((((.((.....))...))))))---.-..)).. ( -26.60)
>DroYak_CAF1 107819 95 + 1
UCCCCAUCCCGACUGCAACUGUAUUCCGCUGGUUUCCAGCACACUCGCAUGUUGCAUCCGCUGGCGCAUUGACUUUCAUGUUGCGCC---CCCCGCCA
.........((..(((((((((.....(((((...)))))......))).))))))..))..((((((.((.....))...))))))---........ ( -27.90)
>consensus
UUCGCAGCCCGACUGCAACUGUAUUCCGCUGUUUGCCAGCCCACUCGCAUGUUGCAUCCGCUGGCGCAUUGACUUUCAUGUUGCGCC__CCCCCGCCA
.........((..(((((((((.....((((.....))))......))).))))))..))..((((((.((.....))...))))))........... (-26.18 = -26.18 +  -0.00)

alignment

secondary structure

dotplot

Window 7

Location	12,758,377 – 12,758,473
Length	96
Sequences	5
Columns	98
Reading direction	reverse
Mean pairwise identity	93.83
Mean single sequence MFE	-32.30
Consensus MFE	-29.56
Energy contribution	-30.20
Covariance contribution	0.64
Combinations/Pair	1.04
Mean z-score	-1.12
Structure conservation index	0.92
SVM decision value	0.09
SVM RNA-class probability	0.580620
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12758377 96 - 20766785
UGGCGGGGG--GGCGCAACAUGAAAGUCAAUGCGCCAGCGGAUGCAACAUGCGAGUGGGCUGGCAAACAGCGGAAUACAGUUGCACUCGGGCUGCGAA
..((((...--((((((..((....))...))))))..((..((((((..........((((.....))))(.....).))))))..))..))))... ( -34.40)
>DroSec_CAF1 99705 98 - 1
UGGCGGGGGGAGGCGCAACAUGAAAGUCAAUGCGCCAGCGGAUGCAACAUGCGAGUGGGCUGGCAAACAGCGGAAUACAGUUGCAGUCGGGCUGCGAA
..((((.....((((((..((....))...))))))..((..((((((..........((((.....))))(.....).))))))..))..))))... ( -33.80)
>DroSim_CAF1 107296 98 - 1
UGGCGGGGGGAGGCGCAACAUGAAAGUCAAUGCGCCAGCGGAUGCAACAUGCGAGUGGGCUGGCAAACAGCGGAAUACAGUUGCAGUCGGGCUGCGAA
..((((.....((((((..((....))...))))))..((..((((((..........((((.....))))(.....).))))))..))..))))... ( -33.80)
>DroEre_CAF1 100707 94 - 1
UGGCAG-G---GGCGCAACAUGAAAGUCAAUGCGCCAGCGGAUGCAACAUGCGAGUGGGCUGGCAAACAGCGGAAUACAGUUGCAGUCGGGAUGGGGA
......-.---((((((..((....))...))))))..((..((((((..........((((.....))))(.....).))))))..))......... ( -28.10)
>DroYak_CAF1 107819 95 - 1
UGGCGGGG---GGCGCAACAUGAAAGUCAAUGCGCCAGCGGAUGCAACAUGCGAGUGUGCUGGAAACCAGCGGAAUACAGUUGCAGUCGGGAUGGGGA
..((....---((((((..((....))...)))))).))(..((((((.((....(.((((((...)))))).)...))))))))..).......... ( -31.40)
>consensus
UGGCGGGGG__GGCGCAACAUGAAAGUCAAUGCGCCAGCGGAUGCAACAUGCGAGUGGGCUGGCAAACAGCGGAAUACAGUUGCAGUCGGGCUGCGAA
..((((.....((((((..((....))...))))))..((..((((((..........((((.....))))(.....).))))))..))..))))... (-29.56 = -30.20 +   0.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:05:49 2006