Locus 3889

Sequence ID	2R_DroMel_CAF1
Location	12,862,662 – 12,862,763
Length	101
Max. P	0.989797

overview

Window 9

Location	12,862,662 – 12,862,763
Length	101
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	80.64
Mean single sequence MFE	-44.65
Consensus MFE	-28.76
Energy contribution	-29.20
Covariance contribution	0.44
Combinations/Pair	1.09
Mean z-score	-2.76
Structure conservation index	0.64
SVM decision value	2.18
SVM RNA-class probability	0.989797
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12862662 101 + 20766785
--------------GCUCCAAGCAUCCAGCUCCUAGUAGCUGAUGGCCAACAGCUGCGUACCCAAAAGGG-GGUUUAACUU--GGGGCAAGGAUG--ACGAUGGAGCUGGGAUCCCAAGA
--------------((((((.((((((.(((((..(((((((........)))))))..((((......)-))).......--)))))..)))))--.)..))))))(((....)))... ( -44.00)
>DroSim_CAF1 217971 101 + 1
--------------GCUCCAAGCAUCCAGCUCCUAGUCGCUGAUGGCCAACAGCUGCGUACCCAAAAGGG-GGUUUAAGUU--GGGGCAAGGAUG--ACGAUGGAGCUGGGAUCCCAAGA
--------------((.....)).(((((((((..((((((....(((..(((((....((((......)-)))...))))--).)))..)).))--))...)))))))))......... ( -41.60)
>DroEre_CAF1 210156 110 + 1
GCUUGCAGCUC-------CCAGCACCCAGCUCCCAGUAGCUGAUGGCCAACAGCUGCGUACCCAGAAGAG-GGUUUAACUGGCGGGGCAAGGAUG--GCCAAGGAGCUGGGCUCCCAAGA
.((((..((..-------...)).((((((((((((...))).((((((.(.(((.(((((((......)-))).......))).)))...).))--)))).)))))))))....)))). ( -45.91)
>DroYak_CAF1 216022 119 + 1
UCUUCCAGCUCCAAGCUCCAAGCAUCCAGCUCCUAGUGGCUGAUGGCCAACAGCUGCGUACCCAAAAGGGGGGCUUAACUGG-GGGGCAAGGAAGGAGCGAAGUAGCUGGGAUCCCAAGA
..(((((((((...(((((.....(((.((((((.(..((((........))))..)(..(((.....)))..).......)-)))))..))).)))))...).))))))))........ ( -47.10)
>consensus
______________GCUCCAAGCAUCCAGCUCCUAGUAGCUGAUGGCCAACAGCUGCGUACCCAAAAGGG_GGUUUAACUG__GGGGCAAGGAUG__ACGAAGGAGCUGGGAUCCCAAGA
........................(((((((((..(((((((........)))))))((.(((...((..........))...)))))..............)))))))))......... (-28.76 = -29.20 +   0.44)

alignment

secondary structure

dotplot

Window 0

Location	12,862,662 – 12,862,763
Length	101
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	80.64
Mean single sequence MFE	-40.30
Consensus MFE	-25.95
Energy contribution	-26.95
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-1.86
Structure conservation index	0.64
SVM decision value	0.40
SVM RNA-class probability	0.720249
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12862662 101 - 20766785
UCUUGGGAUCCCAGCUCCAUCGU--CAUCCUUGCCCC--AAGUUAAACC-CCCUUUUGGGUACGCAGCUGUUGGCCAUCAGCUACUAGGAGCUGGAUGCUUGGAGC--------------
...(((....)))((((((..(.--(((((..((.((--.(((...(((-(......))))....(((((........)))))))).)).)).)))))).))))))-------------- ( -37.10)
>DroSim_CAF1 217971 101 - 1
UCUUGGGAUCCCAGCUCCAUCGU--CAUCCUUGCCCC--AACUUAAACC-CCCUUUUGGGUACGCAGCUGUUGGCCAUCAGCGACUAGGAGCUGGAUGCUUGGAGC--------------
(((.((.((((.((((((...((--(.....((((((--((........-.....)))))...)))((((........)))))))..)))))))))).)).)))..-------------- ( -35.52)
>DroEre_CAF1 210156 110 - 1
UCUUGGGAGCCCAGCUCCUUGGC--CAUCCUUGCCCCGCCAGUUAAACC-CUCUUCUGGGUACGCAGCUGUUGGCCAUCAGCUACUGGGAGCUGGGUGCUGG-------GAGCUGCAAGC
(((..(..((((((((((.((((--((.....((...))(((((..(((-(......))))....))))).)))))).(((...))))))))))))).)..)-------))......... ( -45.60)
>DroYak_CAF1 216022 119 - 1
UCUUGGGAUCCCAGCUACUUCGCUCCUUCCUUGCCCC-CCAGUUAAGCCCCCCUUUUGGGUACGCAGCUGUUGGCCAUCAGCCACUAGGAGCUGGAUGCUUGGAGCUUGGAGCUGGAAGA
..........((((((.((..(((((......((...-((((((..((..(((....)))...))..(((.((((.....)))).))).))))))..))..)))))..)))))))).... ( -43.00)
>consensus
UCUUGGGAUCCCAGCUCCAUCGC__CAUCCUUGCCCC__AAGUUAAACC_CCCUUUUGGGUACGCAGCUGUUGGCCAUCAGCUACUAGGAGCUGGAUGCUUGGAGC______________
(((..(.((((.((((((.............(((((.....................)))))....((((........)))).....)))))))))).)..)))................ (-25.95 = -26.95 +   1.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:06:31 2006