Locus 8766

Sequence ID	3R_DroMel_CAF1
Location	23,400,011 – 23,400,112
Length	101
Max. P	0.799662

overview

Window 3

Location	23,400,011 – 23,400,112
Length	101
Sequences	4
Columns	116
Reading direction	forward
Mean pairwise identity	81.10
Mean single sequence MFE	-30.02
Consensus MFE	-18.89
Energy contribution	-18.95
Covariance contribution	0.06
Combinations/Pair	1.09
Mean z-score	-1.83
Structure conservation index	0.63
SVM decision value	0.23
SVM RNA-class probability	0.645668
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23400011 101 + 27905053
GUGUGGUGGAGAUAAAACGGUGAGC---------------UUCAGUUCUGCAGAUGUCAGCUAAUAAAGCUCAACGAAAUAAAAUGCAUCCGUCGGAUGCAUCAGCAUGAAUGGCC
..(((.(((........((.(((((---------------((.....((((....).)))......))))))).))........(((((((...)))))))))).)))........ ( -25.70)
>DroSec_CAF1 14577 97 + 1
GCGUGGCGGAGAUAAAAGGGU-AGC---------------UGCAGUUCUGCAGUUGUCAGCUAAUAAAGCUCAACGAAAUAAAAUGCAUCCGUCGGAUGCAUCAGCAUGAAUA---
((((..((..((......(..-(((---------------((((....)))))))..).(((.....)))))..))..))...((((((((...))))))))..)).......--- ( -29.10)
>DroEre_CAF1 17687 113 + 1
GUGUGGCGGAGAUAAAAGAUG-AGCUUUGCCUAAAAUGGCUUCAGUUCUGCAGAUGUCAGCUAAUAAAGCUCGGCUAAAUAAAAUGCAUCCGUCGGAUGCAUCUGCAUGAAUUG--
....(((((((..........-..)))))))...........((((((((((((((((((((.....)))).)))..........((((((...))))))))))))).))))))-- ( -37.00)
>DroYak_CAF1 15540 112 + 1
GUGUGGCGGAGAUAA-AGAGA-AGCUUUGCCUAAAACGAUUUCAGUUCUGCAGAUGUCAGCUAAUAAAGCUCGGUGAAAUAAAAUGCAUCCGUCGGAUGCAUCAGCAUGAAUAG--
((..(((((((....-.....-..)))))))....)).......(((((((...(..(((((.....)))).)..).......((((((((...))))))))..))).))))..-- ( -28.30)
>consensus
GUGUGGCGGAGAUAAAAGAGU_AGC_______________UUCAGUUCUGCAGAUGUCAGCUAAUAAAGCUCAACGAAAUAAAAUGCAUCCGUCGGAUGCAUCAGCAUGAAUAG__
............................................(((((((....(((((((.....)))).)))........((((((((...))))))))..))).)))).... (-18.89 = -18.95 +   0.06)

alignment

secondary structure

dotplot

Window 4

Location	23,400,011 – 23,400,112
Length	101
Sequences	4
Columns	116
Reading direction	reverse
Mean pairwise identity	81.10
Mean single sequence MFE	-25.57
Consensus MFE	-18.45
Energy contribution	-18.45
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.82
Structure conservation index	0.72
SVM decision value	0.61
SVM RNA-class probability	0.799662
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23400011 101 - 27905053
GGCCAUUCAUGCUGAUGCAUCCGACGGAUGCAUUUUAUUUCGUUGAGCUUUAUUAGCUGACAUCUGCAGAACUGAA---------------GCUCACCGUUUUAUCUCCACCACAC
((...........(((((((((...)))))))))......((.(((((((((....(((.(....))))...))))---------------))))).))...........)).... ( -27.20)
>DroSec_CAF1 14577 97 - 1
---UAUUCAUGCUGAUGCAUCCGACGGAUGCAUUUUAUUUCGUUGAGCUUUAUUAGCUGACAACUGCAGAACUGCA---------------GCU-ACCCUUUUAUCUCCGCCACGC
---.......((.(((((((((...))))))))).......(((.((((.....)))))))..(((((....))))---------------)..-..............))..... ( -23.30)
>DroEre_CAF1 17687 113 - 1
--CAAUUCAUGCAGAUGCAUCCGACGGAUGCAUUUUAUUUAGCCGAGCUUUAUUAGCUGACAUCUGCAGAACUGAAGCCAUUUUAGGCAAAGCU-CAUCUUUUAUCUCCGCCACAC
--((.(((.(((((((((((((...)))))).......(((((..(......)..))))).)))))))))).))..(((......)))......-..................... ( -29.80)
>DroYak_CAF1 15540 112 - 1
--CUAUUCAUGCUGAUGCAUCCGACGGAUGCAUUUUAUUUCACCGAGCUUUAUUAGCUGACAUCUGCAGAACUGAAAUCGUUUUAGGCAAAGCU-UCUCU-UUAUCUCCGCCACAC
--........((.(((((((((...)))))))))..........(((((((....((........))....(((((.....)))))..))))))-)....-........))..... ( -22.00)
>consensus
__CUAUUCAUGCUGAUGCAUCCGACGGAUGCAUUUUAUUUCGCCGAGCUUUAUUAGCUGACAUCUGCAGAACUGAA_______________GCU_ACCCUUUUAUCUCCGCCACAC
.....(((.(((.(((((((((...)))))))))...........((((.....)))).......))))))............................................. (-18.45 = -18.45 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:19:17 2006