Locus 6135

Sequence ID	2R_DroMel_CAF1
Location	19,311,573 – 19,311,669
Length	96
Max. P	0.948716

overview

Window 1

Location	19,311,573 – 19,311,669
Length	96
Sequences	6
Columns	115
Reading direction	forward
Mean pairwise identity	79.85
Mean single sequence MFE	-29.80
Consensus MFE	-19.02
Energy contribution	-20.42
Covariance contribution	1.39
Combinations/Pair	1.42
Mean z-score	-2.64
Structure conservation index	0.64
SVM decision value	1.38
SVM RNA-class probability	0.948716
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19311573 96 + 20766785
GGCUCAUUGUGCGAAAGAAAUUUCGACCGAA--------------AACCGAUCUGAAUCAGAAGCCAAU---GCUCCUAACCUUGGAUUGGCCGAAAAUUAUCCGAAUGAGCC--
(((((((((..(((((....)))))..)...--------------..((((((..(...((.(((....---))).))....)..))))))..............))))))))-- ( -28.70)
>DroSec_CAF1 61256 110 + 1
GGCUCAUUGUGCGAAAGAAAUUUCGGCCGAAAACCGAAAGCUGAAAACCGAUCUGAAUCAGAAGCCAAU---GAUCCUAACCUUGGAUUGGCCGAAAAUUACCCGAAUGAGCC--
((((((((...(....)...((((((((((....(....).......((((...(.((((........)---))).).....)))).))))))))))........))))))))-- ( -32.70)
>DroSim_CAF1 50243 103 + 1
GGCUCAUUGUGCGAAAGAAAUUUCGGCCGAAAACCGA-------AAACCGAUCUGAAUCAGAAGCCAAU---GAUCCUAACCUUGGAUUGGCCGAAAAUUACCCGAAUGAGCC--
((((((((...(....)...((((((((.........-------.......((((...)))).......---(((((.......)))))))))))))........))))))))-- ( -32.60)
>DroEre_CAF1 54283 95 + 1
GGCUCUUUGUGCGAAAGAAAUUUCGACCGAA--------------AAUCGAUCUGAAUCAGAAGCCAAU---GAUCCUAACCUUGGGACGGCCGAAAAUUAC-CGAAUGAGCC--
(((((((((..(((((....)))))..))))--------------..(((.((((...)))).(((...---..(((((....))))).)))))).......-.....)))))-- ( -26.20)
>DroYak_CAF1 55470 96 + 1
GGCUCUUUGUGCGAAAGAAAUUUCGACCAAA--------------AAUCGAUCUGAAUCAGAAGCCAAU---GAUCCUAACCUUGGGUCGGUCGAAAAUCACCCGAAUGAGCC--
(((((((((..(....)...((((((((...--------------......((((...)))).......---(((((.......)))))))))))))......)))).)))))-- ( -30.70)
>DroAna_CAF1 59424 101 + 1
GGGUCUUUGUGUGAAAGAAAUUUUGGAUCGA--------------AAUCGAUCUAAAUCAGAAGCCUAUUGGGUUCCUAACCUUCAAUCUGUCAGCGAUUGACCUCAAGUGCUUU
(((((.((((.(((.(((...(((((((((.--------------...)))))))))...(((.((....)).)))...........))).)))))))..))))).......... ( -27.90)
>consensus
GGCUCAUUGUGCGAAAGAAAUUUCGACCGAA______________AACCGAUCUGAAUCAGAAGCCAAU___GAUCCUAACCUUGGAUCGGCCGAAAAUUACCCGAAUGAGCC__
((((((((...(....)...((((((((((.....................((((...))))............(((.......)))))))))))))........)))))))).. (-19.02 = -20.42 +   1.39)

alignment

secondary structure

dotplot

Window 2

Location	19,311,573 – 19,311,669
Length	96
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	79.85
Mean single sequence MFE	-31.62
Consensus MFE	-19.68
Energy contribution	-21.38
Covariance contribution	1.70
Combinations/Pair	1.20
Mean z-score	-2.57
Structure conservation index	0.62
SVM decision value	1.30
SVM RNA-class probability	0.939075
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 19311573 96 - 20766785
--GGCUCAUUCGGAUAAUUUUCGGCCAAUCCAAGGUUAGGAGC---AUUGGCUUCUGAUUCAGAUCGGUU--------------UUCGGUCGAAAUUUCUUUCGCACAAUGAGCC
--((((((((((((....((((((((.......((((((((((---....))))))))))..((......--------------.)))))))))).....))))...)))))))) ( -35.00)
>DroSec_CAF1 61256 110 - 1
--GGCUCAUUCGGGUAAUUUUCGGCCAAUCCAAGGUUAGGAUC---AUUGGCUUCUGAUUCAGAUCGGUUUUCAGCUUUCGGUUUUCGGCCGAAAUUUCUUUCGCACAAUGAGCC
--((((((((((((....((((((((((((.((((((.(((((---(........)))))).((.......)))))))).))))...)))))))).....))))...)))))))) ( -35.80)
>DroSim_CAF1 50243 103 - 1
--GGCUCAUUCGGGUAAUUUUCGGCCAAUCCAAGGUUAGGAUC---AUUGGCUUCUGAUUCAGAUCGGUUU-------UCGGUUUUCGGCCGAAAUUUCUUUCGCACAAUGAGCC
--((((((((((((....((((((((((((..(((((((....---.)))))))..)))).((((((....-------.))))))..)))))))).....))))...)))))))) ( -35.10)
>DroEre_CAF1 54283 95 - 1
--GGCUCAUUCG-GUAAUUUUCGGCCGUCCCAAGGUUAGGAUC---AUUGGCUUCUGAUUCAGAUCGAUU--------------UUCGGUCGAAAUUUCUUUCGCACAAAGAGCC
--(((((.((((-(....(((((((((......((((.(((((---(........)))))).))))....--------------..)))))))))......)))...)).))))) ( -29.30)
>DroYak_CAF1 55470 96 - 1
--GGCUCAUUCGGGUGAUUUUCGACCGACCCAAGGUUAGGAUC---AUUGGCUUCUGAUUCAGAUCGAUU--------------UUUGGUCGAAAUUUCUUUCGCACAAAGAGCC
--(((((......((((.((((((((((.....((((.(((((---(........)))))).))))....--------------.))))))))))......)))).....))))) ( -32.10)
>DroAna_CAF1 59424 101 - 1
AAAGCACUUGAGGUCAAUCGCUGACAGAUUGAAGGUUAGGAACCCAAUAGGCUUCUGAUUUAGAUCGAUU--------------UCGAUCCAAAAUUUCUUUCACACAAAGACCC
...........((((((((.......))))(((((((((((.((.....)).))))))(((.(((((...--------------.))))).)))....))))).......)))). ( -22.40)
>consensus
__GGCUCAUUCGGGUAAUUUUCGGCCAAUCCAAGGUUAGGAUC___AUUGGCUUCUGAUUCAGAUCGAUU______________UUCGGCCGAAAUUUCUUUCGCACAAAGAGCC
..((((((((((((....((((((((.......((((((........))))))((((...)))).......................)))))))).....))))...)))))))) (-19.68 = -21.38 +   1.70)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:03:36 2006