Locus 5097

Sequence ID	3L_DroMel_CAF1
Location	13,977,950 – 13,978,132
Length	182
Max. P	0.847525

overview

Window 3

Location	13,977,950 – 13,978,062
Length	112
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	79.57
Mean single sequence MFE	-29.86
Consensus MFE	-19.84
Energy contribution	-18.90
Covariance contribution	-0.94
Combinations/Pair	1.42
Mean z-score	-1.29
Structure conservation index	0.66
SVM decision value	0.07
SVM RNA-class probability	0.570114
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13977950 112 + 23771897
CUACACGAUUCCGGUAUUUGCACUUCGUCCUCUUCGCCGUCGGUGUCCAUUCCCUCACCGACACCCACCCAGAUGCAGUCGCCGACCUUACAACAGCAUCCGCAA---CAGAUAC-----
...........((((..(((((((.((.......))..(((((((..........)))))))........)).)))))..))))...........((....))..---.......----- ( -23.20)
>DroPse_CAF1 16667 120 + 1
CUGCACGACUCGGGCAUCUGCACGUCGUCCUCGUCGCCAUCGGUGUCUAUUCCCUCGCCGACGCCCAUCCAGCUGCAGUCGCCCACAUUGCAGCAGCAGCAGCAGUCGCAGAUACAAAUU
((((..(((((((((....(((((.......))).))..((((((..........)))))).)))).....(((((.((.((.......)).)).))))).).))))))))......... ( -39.40)
>DroSec_CAF1 15160 112 + 1
CUACACGAUUCUGGUAUCUGCACUUCGUCCUCUUCGCCGUCGGUGUCCAUUCCCUCACCGACACCCACCCAGAUGCAGUCGCCGACCUUACAGCAGCAUCCGCAA---CAGAUAC-----
.........(((((((((((.....((.......))..(((((((..........))))))).......))))))).((.((.(......).)).))........---))))...----- ( -25.20)
>DroYak_CAF1 15658 112 + 1
CUGCACGAUUCUGGUAUUUGCACUUCGUCCUCUUCGCCGUCGGUGUCCAUUCCGUCACCGACACCAACCCAGAUGCAGUCACCAACACCACAGCAGCAUCCGCAA---CCGAUAC-----
((((.......((((..(((((((.((.......))..(((((((.(......).)))))))........)).)))))..))))........)))).........---.......----- ( -25.06)
>DroAna_CAF1 16125 103 + 1
CUGCACGACUCGGGCAUCUGUACGUCCUCCUCGUCCCCCUCGGUGUCCAUACCCUCGCCCACGCCCGCUCAGCUGCAGUCGCCCACCCUGCAGCACCACCAGC-----------------
(((...((..(((((......(((.......))).......((((..........))))...))))).)).(((((((.........))))))).....))).----------------- ( -26.90)
>DroPer_CAF1 23248 120 + 1
CUGCACGACUCGGGCAUCUGCACGUCGUCCUCGUCGCCAUCGGUGUCUAUUCCCUCGCCGACGCCCAUCCAGCUGCAGUCGCCCACAUUGCAGCAGCAGCAGCAGUCGCAGAUACAAAUU
((((..(((((((((....(((((.......))).))..((((((..........)))))).)))).....(((((.((.((.......)).)).))))).).))))))))......... ( -39.40)
>consensus
CUGCACGACUCGGGCAUCUGCACGUCGUCCUCGUCGCCGUCGGUGUCCAUUCCCUCACCGACACCCACCCAGAUGCAGUCGCCCACAUUACAGCAGCAUCAGCAA___CAGAUAC_____
...........((((..(((((...((.......)).....((((((............))))))........)))))..))))...........((....))................. (-19.84 = -18.90 +  -0.94)

alignment

secondary structure

dotplot

Window 4

Location	13,978,030 – 13,978,132
Length	102
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	83.12
Mean single sequence MFE	-44.18
Consensus MFE	-28.50
Energy contribution	-28.87
Covariance contribution	0.37
Combinations/Pair	1.28
Mean z-score	-3.23
Structure conservation index	0.65
SVM decision value	0.77
SVM RNA-class probability	0.847525
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13978030 102 - 23771897
AGCGCAGCUAGGAUCUGUUGCUGAUGCUGUUGCGUUGGACUGCGCUGCAAAAGCGACAAUUGUU---GCUGCG---------GUAUCUG---UUGCGGAUGCUGUUGUAAGGUCGGC
...(((((.((.((((((.((.((((((((.((((......))))......((((((....)))---))))))---------))))).)---).)))))).)))))))......... ( -39.70)
>DroSec_CAF1 15240 102 - 1
AACGCAGCAAGGAUCUGUUGCUGAUGUUGUUGCGUUGGACUGCGCUGCAAAAGCGACAAUUGUU---GCUGCG---------GUAUCUG---UUGCGGAUGCUGCUGUAAGGUCGGC
..((((((((.(((.(((((((....((((.((((......)))).)))).)))))))))).))---))))))---------(((((((---...))))))).((((......)))) ( -45.20)
>DroSim_CAF1 14457 102 - 1
AACGCAGCAAGGAUCUGUUGCUGAUGCUGUUGCGUUGGACUGCGCUGCAAGAGCGACAAUUGUU---GCUGUG---------GUAUCUG---UUGCGGAUGCUGCUGUAAGGUCGGC
..((((((((.(((.(((((((..(((....((((......)))).)))..)))))))))).))---))))))---------(((((((---...))))))).((((......)))) ( -42.90)
>DroEre_CAF1 15795 102 - 1
AGCGCAGCAAGGAUCUGUUGCUGAUGCUGUUGCGUUGGACUGCGUUGCAAAAGCGACAAUUGUU---GCUGCG---------GUAUCUG---UUGCGGAUGCUGCUGUAAGGUCGGG
(((((((((.(.(((.......))).))))))))))...((((.(((((..((((((....)))---)))(((---------(((((((---...))))))))))))))).).))). ( -43.50)
>DroYak_CAF1 15738 102 - 1
AGCGCAGCAAGGAUCUGCUGCUGAUGUUGUUGCGUUGGACUGCGCUGCAAAAGCGACAAUUGUU---GCGGCG---------GUAUCGG---UUGCGGAUGCUGCUGUGGUGUUGGU
..(((((((.(.((((((.(((((((..((((((...((.((((((.....)))).)).))..)---))))).---------.))))))---).)))))).))))))))........ ( -47.00)
>DroPer_CAF1 23328 114 - 1
AGAGAGGCCAGGAUCUGUUGCUGCUGCU---GUGUGGGACUCCGUUGCAGCAGCGACAGCUGUGCAGGCUGUGCUCCAAUUUGUAUCUGCGACUGCUGCUGCUGCUGCAAUGUGGGC
......(((.(((((..(.((....)).---..)..))..)))((((((((((((.((((..(((((...((((........)))))))))...)))).))))))))))))...))) ( -46.80)
>consensus
AGCGCAGCAAGGAUCUGUUGCUGAUGCUGUUGCGUUGGACUGCGCUGCAAAAGCGACAAUUGUU___GCUGCG_________GUAUCUG___UUGCGGAUGCUGCUGUAAGGUCGGC
..((((((((.(((.(((((((..(((....((((......)))).)))..)))))))))).))...)))))).........(((((((......))))))).((((......)))) (-28.50 = -28.87 +   0.37)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:41:53 2006