Locus 2600

Sequence ID	3L_DroMel_CAF1
Location	7,210,795 – 7,210,995
Length	200
Max. P	0.950666

overview

Window 7

Location	7,210,795 – 7,210,915
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	96.53
Mean single sequence MFE	-44.25
Consensus MFE	-38.39
Energy contribution	-39.08
Covariance contribution	0.69
Combinations/Pair	1.08
Mean z-score	-2.48
Structure conservation index	0.87
SVM decision value	0.91
SVM RNA-class probability	0.880685
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7210795 120 + 23771897
CCCAUUCCAUCCGCUUGGCACCGUCUGCGAGCCUAAUGUGCCACUUAAGACGCAUUUAUUGUCUUUCGUUGCUGCUGCCGGCGUUCUUGCCGCGCGGCGGCUGUUGGUGGUGCCGCAUUU
............((..((((((..(.((.((((......((.((..((((((.......))))))..)).)).((((((((((....))))).))))))))))).)..)))))))).... ( -50.00)
>DroSec_CAF1 3927 120 + 1
CCCAUUCCAUCCGCUUGGCACCGUCUGCGAGCCUAAUGUGCCACUUAAGACGCAUUUAUUGUCUUUCGUUGCUGCUGCCGGCGUUCUUGCCGCACGGCGGCUGUUGUUGGUGCCGCAUUU
............((..(((((((...((.((((......((.((..((((((.......))))))..)).)).((((.(((((....)))))..))))))))))...))))))))).... ( -43.00)
>DroSim_CAF1 3953 120 + 1
CCCAUUCCAUCCGCUUGGCACCGUCUGCGAGCCUAAUGUGCCACUUAAGACGCAUUUAUUGUCUUUCGUUCCUGCUGCCGGCGUUCUUGCCGCACGGCGGCUGUUGUUGGUGCCGCAUUU
............((..(((((((...((.((((...(((((.((..((((((.......))))))..))..........((((....)))))))))..))))))...))))))))).... ( -39.40)
>DroEre_CAF1 500 120 + 1
CCCAUUCCAUCCGCUUGGCACCGUCUGCGAGCCUAAUGUGCCACUUAAGACGCAUUUAUUGUCUUUCGUUGUUGCUGCUGCUGUUCUUGCAGCACGGCGGCUGUUGGUGGUGCCGCAUUU
............((..((((((..(.((.((((......((.((..((((((.......))))))..)).)).((((.((((((....)))))))))))))))).)..)))))))).... ( -44.60)
>consensus
CCCAUUCCAUCCGCUUGGCACCGUCUGCGAGCCUAAUGUGCCACUUAAGACGCAUUUAUUGUCUUUCGUUGCUGCUGCCGGCGUUCUUGCCGCACGGCGGCUGUUGGUGGUGCCGCAUUU
............((..(((((((((.((.((((......((.((..((((((.......))))))..)).)).((((.(((((....)))))..)))))))))).))))))))))).... (-38.39 = -39.08 +   0.69)

alignment

secondary structure

dotplot

Window 8

Location	7,210,875 – 7,210,995
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	92.36
Mean single sequence MFE	-41.03
Consensus MFE	-33.96
Energy contribution	-35.52
Covariance contribution	1.56
Combinations/Pair	1.00
Mean z-score	-2.59
Structure conservation index	0.83
SVM decision value	1.40
SVM RNA-class probability	0.950666
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7210875 120 - 23771897
GCAAGUUGGGCUUGGAAAGCGGUGCAGCGAAAGCCAACACACGACCGCCAUUUUGUCAACAAUGGCGUCAAUUAAAUGGAAAAUGCGGCACCACCAACAGCCGCCGCGCGGCAAGAACGC
((..((((((((.....)))(((((.(((....(((......(((.((((((........))))))))).......)))....))).))))).))))).(((((...)))))......)) ( -44.42)
>DroSec_CAF1 4007 120 - 1
GCAAGUUGGGCUUGGAAAGCGGUGCAGCGUAAGCCAACACACGACCGCCAUUUUGUCAACAAUGGCGUCAAUUAAAUGGAAAAUGCGGCACCAACAACAGCCGCCGUGCGGCAAGAACGC
((..((((.(((.....)))(((((.((((...(((......(((.((((((........))))))))).......)))...)))).)))))..)))).(((((...)))))......)) ( -42.82)
>DroSim_CAF1 4033 120 - 1
GCAAGUUGGGCUUGGAAAGCGGUGCAGCGAAAGCCAACACACGACCGCCAUUUUGUCAACAAUGGCGUCAAUUAAAUGGAAAAUGCGGCACCAACAACAGCCGCCGUGCGGCAAGAACGC
((..((((.(((.....)))(((((.(((....(((......(((.((((((........))))))))).......)))....))).)))))..)))).(((((...)))))......)) ( -41.12)
>DroEre_CAF1 580 112 - 1
GCAACUUGGGU--------GGGUGCAGCGAAAGCCAACACACAACCGCCAUUUUGUCAACAAUGGCGUCAAUUAAAUGGAAAAUGCGGCACCACCAACAGCCGCCGUGCUGCAAGAACAG
....(((((((--------((.(((.(((....(((.........(((((((........))))))).........)))....))).))))))))..((((......))))))))..... ( -35.77)
>consensus
GCAAGUUGGGCUUGGAAAGCGGUGCAGCGAAAGCCAACACACGACCGCCAUUUUGUCAACAAUGGCGUCAAUUAAAUGGAAAAUGCGGCACCAACAACAGCCGCCGUGCGGCAAGAACGC
....((((((((.....)))(((((.(((....(((.........(((((((........))))))).........)))....))).))))).))))).(((((...)))))........ (-33.96 = -35.52 +   1.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:37:08 2006